Mon, 25 Jan 2021

Package boot updated to version 1.3-26 with previous version 1.3-25 dated 2020-04-26

Title: Bootstrap Functions (Originally by Angelo Canty for S)
Description: Functions and datasets for bootstrapping from the book "Bootstrap Methods and Their Application" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.
Author: Angelo Canty [aut], Brian Ripley [aut, trl, cre] (author of parallel support)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between boot versions 1.3-25 dated 2020-04-26 and 1.3-26 dated 2021-01-25

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Package rdacca.hp updated to version 0.3.0 with previous version 0.2.0 dated 2021-01-18

Title: Hierarchical Partitioning for Canonical Analysis
Description: This function calculates the independent contribution of each explanatory variable to explained variation (R-squared) on RDA,CCA and db-RDA, applying the hierarchy algorithm of Chevan, A. and Sutherland, M. 1991 Hierarchical Partitioning.The American Statistician, 90-96 <DOI:10.1080/00031305.1991.10475776>.
Author: Jiangshan Lai,Pedro Peres-neto
Maintainer: Jiangshan Lai <lai@ibcas.ac.cn>

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Package mixSPE updated to version 0.9.1 with previous version 0.1.1 dated 2019-06-19

Title: Mixtures of Power Exponential and Skew Power Exponential Distributions for Use in Model-Based Clustering and Classification
Description: Mixtures of skewed and elliptical distributions are implemented using mixtures of multivariate skew power exponential and power exponential distributions, respectively. A generalized expectation-maximization framework is used for parameter estimation. Methodology for mixtures of power exponential distributions is from Dang et al. (2015) <doi: 10.1111/biom.12351>.
Author: Ryan P. Browne[aut, cre], Utkarsh J. Dang[aut, cre], Michael P. B. Gallaugher[ctb], and Paul D. McNicholas[aut]
Maintainer: Utkarsh J. Dang <udang@binghamton.edu>

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Package liger updated to version 2.0.1 with previous version 1.1.2 dated 2020-07-16

Title: Lightweight Iterative Geneset Enrichment
Description: Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states. The original algorithm is detailed in Subramanian et al. with 'Java' implementations available through the Broad Institute (Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>). The 'liger' package provides a lightweight R implementation of this enrichment test on a list of values (Fan et al., 2017 <doi:10.5281/zenodo.887386>). Given a list of values, such as p-values or log-fold changes derived from differential expression analysis or other analyses comparing biological states, this package enables you to test a priori defined set of genes for enrichment to enable interpretability of highly significant or high fold-change genes.
Author: Jean Fan [aut, cre] (<https://orcid.org/0000-0002-0212-5451>), Peter Kharchenko [aut]
Maintainer: Jean Fan <jeanfan@jhu.edu>

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Package ggpmisc updated to version 0.3.8 with previous version 0.3.7 dated 2020-11-09

Title: Miscellaneous Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Specialization of method ggplot(): accept and convert on the fly time series data. Geom: "table", "plot" and "grob" add insets to plots using native data coordinates, while "table_npc", "plot_npc" and "grob_npc" do the same using "npc" coordinates through new aesthetics "npcx" and "npcy". Statistics: locate and tag peaks and valleys; count observations in different quadrants of a plot; select observations based on 2D density; label with the equation of a polynomial fitted with lm() or other types of models; labels with P-value, R^2 or adjusted R^2 or information criteria for fitted models; label with ANOVA table for fitted models; label with summary for fitted models. Model fit classes for which suitable methods are provided by package 'broom' are supported. Scales and stats to build volcano and quadrant plots based on outcomes, fold changes, p-values and false discovery rates.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>), Kamil Slowikowski [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

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Package assertr updated to version 2.8 with previous version 2.7 dated 2020-02-05

Title: Assertive Programming for R Analysis Pipelines
Description: Provides functionality to assert conditions that have to be met so that errors in data used in analysis pipelines can fail quickly. Similar to 'stopifnot()' but more powerful, friendly, and easier for use in pipelines.
Author: Tony Fischetti [aut, cre]
Maintainer: Tony Fischetti <tony.fischetti@gmail.com>

Diff between assertr versions 2.7 dated 2020-02-05 and 2.8 dated 2021-01-25

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Sun, 24 Jan 2021

Package GenomeAdmixR updated to version 1.1.3 with previous version 1.1.2 dated 2021-01-21

Title: Simulate Admixture of Genomes
Description: Individual-based simulations forward in time, simulating how patterns in ancestry along the genome change after admixture. Full description can be found in Janzen (2020) <doi:10.1101/2020.10.19.343491>.
Author: Thijs Janzen [aut, cre], Fernando Diaz G. [ctb], Richèl J.C. Bilderbeek [ctb]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>

Diff between GenomeAdmixR versions 1.1.2 dated 2021-01-21 and 1.1.3 dated 2021-01-24

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Package forestmangr updated to version 0.9.3 with previous version 0.9.2 dated 2020-04-07

Title: Forest Mensuration and Management
Description: Processing forest inventory data with methods such as simple random sampling, stratified random sampling and systematic sampling. There are also functions for yield and growth predictions and model fitting, linear and nonlinear grouped data fitting, and statistical tests. References: Kershaw Jr., Ducey, Beers and Husch (2016). <doi:10.1002/9781118902028>.
Author: Sollano Rabelo Braga [aut, cre, cph], Marcio Leles Romarco de Oliveira [aut], Eric Bastos Gorgens [aut]
Maintainer: Sollano Rabelo Braga <sollanorb@gmail.com>

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Package econet updated to version 0.1.93 with previous version 0.1.92 dated 2020-09-02

Title: Estimation of Parameter-Dependent Network Centrality Measures
Description: Provides methods for estimating parameter-dependent network centrality measures with linear-in-means models. Both non linear least squares and maximum likelihood estimators are implemented. The methods allow for both link and node heterogeneity in network effects, endogenous network formation and the presence of unconnected nodes. The routines also compare the explanatory power of parameter-dependent network centrality measures with those of standard measures of network centrality. Benefits and features of the 'econet' package are illustrated using data from Battaglini and Patacchini (2018) and Battaglini, Patacchini, and Leone Sciabolazza (2020). For additional details, see the vignette.
Author: Marco Battaglini [aut] (<https://orcid.org/0000-0001-9690-0721>), Valerio Leone Sciabolazza [aut, cre] (<https://orcid.org/0000-0003-2537-3084>), Eleonora Patacchini [aut] (<https://orcid.org/0000-0002-3510-2969>), Sida Peng [aut] (<https://orcid.org/0000-0002-2151-0523>)
Maintainer: Valerio Leone Sciabolazza <valerio.leonesciabolazza@uniparthenope.it>

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Package assertive.base updated to version 0.0-8 with previous version 0.0-7 dated 2016-12-29

Title: A Lightweight Core of the 'assertive' Package
Description: A minimal set of predicates and assertions used by the assertive package. This is mainly for use by other package developers who want to include run-time testing features in their own packages. End-users will usually want to use assertive directly.
Author: Richard Cotton [aut, cre], Sunkyu Choi [trl], Ivanka Skakun [trl], Gergely Dar<c3><b3>czi [trl], Anton Antonov [trl], Hisham Ben Hamidane [trl], Anja Billing [trl], Aditya Bhagwat [trl], Rasmus B<c3><a5><c3><a5>th [trl], Mine Cetinkaya-Rundel [trl], Aspasia Chatziefthymiou [trl]
Maintainer: Richard Cotton <richierocks@gmail.com>

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Package faq updated to version 0.1.1 with previous version 0.1.0 dated 2020-07-30

Title: Create FAQ Page
Description: Create Frequently Asked Questions page for Shiny application.
Author: Jiena McLellan [aut, cre] (<https://orcid.org/0000-0002-5578-088X>), Michael Condouris [ctb] (<https://orcid.org/0000-0002-8862-4250>), Alex Lais [ctb], Jason Forrest [ctb], Gunvansh Khanna [ctb]
Maintainer: Jiena McLellan <jienagu90@gmail.com>

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Package censo2017 updated to version 0.3 with previous version 0.2 dated 2020-12-16

Title: Base de Datos de Facil Acceso del Censo 2017 de Chile (2017 Chilean Census Easy Access Database)
Description: Provee un acceso conveniente a mas de 17 millones de registros de la base de datos del Censo 2017. Los datos fueron importados desde el DVD oficial del INE usando el Convertidor REDATAM creado por Pablo De Grande y ademas se proporcionan los mapas que acompanian a estos datos. Esta paquete esta documentado intencionalmente en castellano asciificado para que funcione sin problema en diferentes plataformas. (Provides convenient access to more than 17 million records from the Chilean Census 2017 database. The datasets were imported from the official DVD provided by the Chilean National Bureau of Statistics by using the REDATAM converter created by Pablo De Grande and in addition it includes the maps accompanying these datasets.)
Author: Mauricio Vargas [aut, cre] (<https://orcid.org/0000-0003-1017-7574>), Juan Correa [ctb], Instituto Nacional de Estadisticas (INE) [dtc]
Maintainer: Mauricio Vargas <mvargas@dcc.uchile.cl>

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Package cchsflow updated to version 1.8.0 with previous version 1.6.0 dated 2020-03-30

Title: Transforming and Harmonizing CCHS Variables
Description: Supporting the use of the Canadian Community Health Survey (CCHS) by transforming variables from each cycle into harmonized, consistent versions that span survey cycles (currently, 2001 to 2014). CCHS data used in this library is accessed and adapted in accordance to the Statistics Canada Open Licence Agreement. This package uses rec_with_table(), which was developed from 'sjmisc' rec(). Lüdecke D (2018). "sjmisc: Data and Variable Transformation Functions". Journal of Open Source Software, 3(26), 754. <doi:10.21105/joss.00754>.
Author: Doug Manuel [aut, cph] (<https://orcid.org/0000-0003-0912-0845>), Warsame Yusuf [aut, cre], Rostyslav Vyuha [aut], Carol Bennett [aut], Yulric Sequeira [ctb], The Ottawa Hospital [cph]
Maintainer: Warsame Yusuf <waryusuf@ohri.ca>

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Package TSEtools updated to version 0.2.0 with previous version 0.1.4 dated 2020-01-07

Title: Manage Data from Stock Exchange Markets
Description: Tools to perform some descriptive data analysis for assets. Manage the portfolio and capital of assets. It also downloads and organizes data from the Tehran Stock Exchange (TSE).
Author: Ali Saeb
Maintainer: Ali Saeb <ali.saeb@gmail.com>

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Package sass updated to version 0.3.1 with previous version 0.3.0 dated 2021-01-13

Title: Syntactically Awesome Style Sheets ('Sass')
Description: An 'SCSS' compiler, powered by the 'LibSass' library. With this, R developers can use variables, inheritance, and functions to generate dynamic style sheets. The package uses the 'Sass CSS' extension language, which is stable, powerful, and CSS compatible.
Author: Joe Cheng [aut], Timothy Mastny [aut], Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>), Barret Schloerke [aut] (<https://orcid.org/0000-0001-9986-114X>), Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>), RStudio [cph, fnd], Sass Open Source Foundation [ctb, cph] (LibSass library), Greter Marcel [ctb, cph] (LibSass library), Mifsud Michael [ctb, cph] (LibSass library), Hampton Catlin [ctb, cph] (LibSass library), Natalie Weizenbaum [ctb, cph] (LibSass library), Chris Eppstein [ctb, cph] (LibSass library), Adams Joseph [ctb, cph] (json.cpp), Trifunovic Nemanja [ctb, cph] (utf8.h)
Maintainer: Carson Sievert <carson@rstudio.com>

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Package nhanesA updated to version 0.6.5.2 with previous version 0.6.5 dated 2018-10-17

Title: NHANES Data Retrieval
Description: Utility to retrieve data from the National Health and Nutrition Examination Survey (NHANES) website <https://www.cdc.gov/nchs/nhanes/index.htm>.
Author: Christopher J. Endres
Maintainer: Christopher J. Endres <cjendres1@gmail.com>

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Package sglg updated to version 0.1.9 with previous version 0.1.8 dated 2020-11-30

Title: Fitting Semi-Parametric Generalized log-Gamma Regression Models
Description: Set of tools to fit a linear multiple or semi-parametric regression models with the possibility of non-informative random right-censoring. Under this setup, the localization parameter of the response variable distribution is modeled by using linear multiple regression or semi-parametric functions, whose non-parametric components may be approximated by natural cubic spline or P-splines. The supported distribution for the model error is a generalized log-gamma distribution which includes the generalized extreme value and standard normal distributions as important special cases. Also, some numerical and graphical devices for diagnostic of the fitted models are offered.
Author: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com> and G. Paula and L. Vanegas
Maintainer: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com>

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Package RstoxData updated to version 1.0.24 with previous version 1.0.23 dated 2021-01-13

Title: Tools to Read and Manipulate Fisheries Data
Description: Set of tools to read and manipulate various data formats for fisheries. Mainly catered towards scientific trawl survey sampling ('biotic') data, acoustic trawl data, and commercial fishing catch ('landings') data. Among the supported data formats are the data products from the Norwegian Institute Marine Research ('IMR') and the International Council for the Exploration of the Sea (ICES).
Author: Ibrahim Umar [cre, aut], Sindre Vatnehol [aut], Arne Johannes Holmin [aut], Edvin Fuglebakk [aut], Espen Johnsen [aut], Norwegian Institute of Marine Research [cph, fnd]
Maintainer: Ibrahim Umar <ibrahim.umar@hi.no>

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Package reportfactory updated to version 0.1.2 with previous version 0.1.1 dated 2021-01-21

Title: Lightweight Infrastructure for Handling Multiple R Markdown Documents
Description: Provides an infrastructure for handling multiple R Markdown reports, including automated curation and time-stamping of outputs, parameterisation and provision of helper functions to manage dependencies.
Author: Thibaut Jombart [aut], Amy Gimma [ctb], Tim Taylor [aut, cre] (<https://orcid.org/0000-0002-8587-7113>)
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>

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Package nVennR updated to version 0.2.3 with previous version 0.2.2 dated 2020-05-04

Title: Create n-Dimensional, Quasi-Proportional Venn Diagrams
Description: Provides an interface for the "nVenn"" algorithm (Perez-Silva, Araujo-Voces and Quesada (2018), <doi:10.1093/bioinformatics/bty109>). This algorithm works for any number of sets, and usually yields pleasing and informative Venn diagrams with proportionality information. However, representing more than six sets takes a long time and is hard to interpret, unless many of the regions are empty. If you cannot make sense of the result, you may want to consider 'UpSetR'.
Author: Victor Quesada [aut, cre, cph]
Maintainer: Victor Quesada <quesadavictor@uniovi.es>

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Package squashinformr updated to version 0.2.0 with previous version 0.1.5 dated 2020-11-18

Title: Politely Web Scrape Data from SquashInfo
Description: Scrape SquashInfo <http://www.squashinfo.com/> for data on the Professional Squash Association World Tour and other squash events. 'squashinformr' functions scrape, parse, and clean data associated with players, tournaments, and rankings.
Author: Hayden MacDonald [aut, cre]
Maintainer: Hayden MacDonald <hayden.macdonald.8778@gmail.com>

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Package mlr3tuning updated to version 0.6.0 with previous version 0.5.0 dated 2020-12-07

Title: Tuning for 'mlr3'
Description: Implements methods for hyperparameter tuning with 'mlr3', e.g. Grid Search, Random Search, or Simulated Annealing. Various termination criteria can be set and combined. The class 'AutoTuner' provides a convenient way to perform nested resampling in combination with 'mlr3'.
Author: Marc Becker [cre, aut] (<https://orcid.org/0000-0002-8115-0400>), Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>), Jakob Richter [aut] (<https://orcid.org/0000-0003-4481-5554>), Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>), Daniel Schalk [aut] (<https://orcid.org/0000-0003-0950-1947>)
Maintainer: Marc Becker <marcbecker@posteo.de>

Diff between mlr3tuning versions 0.5.0 dated 2020-12-07 and 0.6.0 dated 2021-01-24

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Package mlr3fselect updated to version 0.5.0 with previous version 0.4.1 dated 2020-10-30

Title: Feature Selection for 'mlr3'
Description: Implements methods for feature selection with 'mlr3', e.g. random search and sequential selection. Various termination criteria can be set and combined. The class 'AutoFSelector' provides a convenient way to perform nested resampling in combination with 'mlr3'.
Author: Marc Becker [aut, cre] (<https://orcid.org/0000-0002-8115-0400>), Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>), Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>), Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>)
Maintainer: Marc Becker <marcbecker@posteo.de>

Diff between mlr3fselect versions 0.4.1 dated 2020-10-30 and 0.5.0 dated 2021-01-24

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Package umx updated to version 4.3.0 with previous version 4.2.5 dated 2020-12-12

Title: Structural Equation and Twin Modeling in R
Description: Quickly create, run, and report structural equation and twin models. See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS. Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R. Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.
Author: Timothy C. Bates [aut, cre] (<https://orcid.org/0000-0002-1153-9007>), Gillespie Nathan [ctb], Brenton Wiernik [ctb], Joshua N. Pritikin [ctb], Michael C. Neale [ctb], Hermine Maes [ctb]
Maintainer: Timothy C. Bates <timothy.c.bates@gmail.com>

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Package spatial updated to version 7.3-13 with previous version 7.3-12 dated 2020-04-26

Title: Functions for Kriging and Point Pattern Analysis
Description: Functions for kriging and point pattern analysis.
Author: Brian Ripley [aut, cre, cph], Roger Bivand [ctb], William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

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Package nnet updated to version 7.3-15 with previous version 7.3-14 dated 2020-04-26

Title: Feed-Forward Neural Networks and Multinomial Log-Linear Models
Description: Software for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models.
Author: Brian Ripley [aut, cre, cph], William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

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Package class updated to version 7.3-18 with previous version 7.3-17 dated 2020-04-26

Title: Functions for Classification
Description: Various functions for classification, including k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.
Author: Brian Ripley [aut, cre, cph], William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

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Package do updated to version 1.7.0.0 with previous version 1.6.0.0 dated 2020-12-03

Title: Data Operator
Description: Flexibly convert data between long and wide format using just two functions: reshape_toLong() and reshape_toWide().
Author: Jing Zhang, Zhi Jin
Maintainer: Jing Zhang<zj391120@163.com>

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Package RSQLite updated to version 2.2.3 with previous version 2.2.2 dated 2021-01-08

Title: 'SQLite' Interface for R
Description: Embeds the 'SQLite' database engine in R and provides an interface compliant with the 'DBI' package. The source for the 'SQLite' engine is included.
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>), Hadley Wickham [aut], David A. James [aut], Seth Falcon [aut], SQLite Authors [ctb] (for the included SQLite sources), Liam Healy [ctb] (for the included SQLite sources), R Consortium [fnd], RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>

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

Title: PC Algorithm with the Principle of Mendelian Randomization
Description: A PC Algorithm with the Principle of Mendelian Randomization. This package implements the MRPC (PC with the principle of Mendelian randomization) algorithm to infer causal graphs. It also contains functions to simulate data under a certain topology, to visualize a graph in different ways, and to compare graphs and quantify the differences. See Badsha and Fu (2019) <doi:10.3389/fgene.2019.00460>,Badsha, Martin and Fu (2018) <arXiv:1806.01899>.
Author: Md Bahadur Badsha [aut,cre],Evan A Martin [ctb] and Audrey Qiuyan Fu [aut]
Maintainer: Md Bahadur Badsha <mbbadshar@gmail.com>

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Package spatstat.utils updated to version 2.0-0 with previous version 1.20-2 dated 2021-01-07

Title: Utility Functions for 'spatstat'
Description: Contains utility functions for the 'spatstat' package which may also be useful for other purposes.
Author: Adrian Baddeley [aut, cre] (<https://orcid.org/0000-0001-9499-8382>), Rolf Turner [aut] (<https://orcid.org/0000-0001-5521-5218>), Ege Rubak [aut] (<https://orcid.org/0000-0002-6675-533X>)
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

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Package spatstat.local updated to version 4.0-0 with previous version 3.6-0 dated 2019-04-13

Title: Extension to 'spatstat' for Local Composite Likelihood
Description: Extension to the 'spatstat' package, enabling the user to fit point process models to point pattern data by local composite likelihood ('geographically weighted regression').
Author: Adrian Baddeley [aut, cre]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

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Package GSODR updated to version 3.0.0 with previous version 2.1.2 dated 2020-09-20

Title: Global Surface Summary of the Day ('GSOD') Weather Data Client
Description: Provides automated downloading, parsing, cleaning, unit conversion and formatting of Global Surface Summary of the Day ('GSOD') weather data from the from the USA National Centers for Environmental Information ('NCEI'). Units are converted from from United States Customary System ('USCS') units to International System of Units ('SI'). Stations may be individually checked for number of missing days defined by the user, where stations with too many missing observations are omitted. Only stations with valid reported latitude and longitude values are permitted in the final data. Additional useful elements, saturation vapour pressure ('es'), actual vapour pressure ('ea') and relative humidity ('RH') are calculated from the original data using the improved August-Roche-Magnus approximation (Alduchov & Eskridge 1996) and included in the final data set. The resulting metadata include station identification information, country, state, latitude, longitude, elevation, weather observations and associated flags. For information on the 'GSOD' data from 'NCEI', please see the 'GSOD' 'readme.txt' file available from, <https://www1.ncdc.noaa.gov/pub/data/gsod/readme.txt>.
Author: Adam Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>), Tomislav Hengl [aut] (<https://orcid.org/0000-0002-9921-5129>), Andrew Nelson [aut] (<https://orcid.org/0000-0002-7249-3778>), Hugh Parsonage [cph, ctb] (<https://orcid.org/0000-0003-4055-0835>), Taras Kaduk [ctb] (Suggestion for handling bulk station downloads more efficiently), Gwenael Giboire [ctb] (Several bug reports in early versions and testing feedback), Łukasz Pawlik [ctb] (Reported bug in windspeed conversion calculation), Ross Darnell [ctb] (Reported bug in 'Windows OS' versions causing 'GSOD' data untarring to fail, <https://orcid.org/0000-0002-7973-6322>), Tyler Widdison [ctb] (Reported bug where `nearest_stations()` did not return stations in order of nearest to farthest.)
Maintainer: Adam Sparks <adamhsparks@gmail.com>

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Package bqror updated to version 0.1.4 with previous version 0.1.3 dated 2020-11-10

Title: Bayesian Quantile Regression for Ordinal Models
Description: Provides an estimation technique for Bayesian quantile regression in ordinal models. Two algorithms are considered - one for an ordinal model with three outcomes and the other for an ordinal model with more than 3 outcomes. It further provides model performance criteria and trace plots for Markov chain Monte Carlo (MCMC) draws. Rahman, M. A. (2016) <doi:10.1214/15-BA939>. Greenberg, E. (2012) <doi:10.1017/CBO9781139058414>. Spiegelhalter, D. J., Best, N. G., Carlin B. P. and Linde A. (2002) <doi:10.1111/1467-9868.00353>.
Author: Dr. Mohammad Arshad Rahman Developer [aut], Prajual Maheshwari [cre]
Maintainer: Prajual Maheshwari <prajual1391@gmail.com>

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Sat, 23 Jan 2021

Package statswalesr updated to version 0.1.2 with previous version 0.1.1 dated 2020-11-29

Title: Easily Extract Data from 'StatsWales'
Description: Download data from 'StatsWales' into R. Removes the need for the user to write their own loops when parsing data from the 'StatsWales' API. Provides functions for datasets (<http://open.statswales.gov.wales/en-gb/dataset>) and metadata (<http://open.statswales.gov.wales/en-gb/discover/metadata>) endpoints.
Author: Jamie Ralph [aut, cre]
Maintainer: Jamie Ralph <jamesryanralph@outlook.com>

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Package gratia updated to version 0.5.1 with previous version 0.5.0 dated 2021-01-10

Title: Graceful 'ggplot'-Based Graphics and Other Functions for GAMs Fitted Using 'mgcv'
Description: Graceful 'ggplot'-based graphics and utility functions for working with generalized additive models (GAMs) fitted using the 'mgcv' package. Provides a reimplementation of the plot() method for GAMs that 'mgcv' provides, as well as 'tidyverse' compatible representations of estimated smooths.
Author: Gavin L. Simpson [aut, cre] (<https://orcid.org/0000-0002-9084-8413>), Henrik Singmann [ctb] (<https://orcid.org/0000-0002-4842-3657>)
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>

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Package clubSandwich updated to version 0.5.3 with previous version 0.5.2 dated 2020-11-14

Title: Cluster-Robust (Sandwich) Variance Estimators with Small-Sample Corrections
Description: Provides several cluster-robust variance estimators (i.e., sandwich estimators) for ordinary and weighted least squares linear regression models, including the bias-reduced linearization estimator introduced by Bell and McCaffrey (2002) <https://www150.statcan.gc.ca/n1/pub/12-001-x/2002002/article/9058-eng.pdf> and developed further by Pustejovsky and Tipton (2017) <DOI:10.1080/07350015.2016.1247004>. The package includes functions for estimating the variance- covariance matrix and for testing single- and multiple- contrast hypotheses based on Wald test statistics. Tests of single regression coefficients use Satterthwaite or saddle-point corrections. Tests of multiple- contrast hypotheses use an approximation to Hotelling's T-squared distribution. Methods are provided for a variety of fitted models, including lm() and mlm objects, glm(), ivreg() (from package 'AER'), plm() (from package 'plm'), gls() and lme() (from 'nlme'), lmer() (from `lme4`), robu() (from 'robumeta'), and rma.uni() and rma.mv() (from 'metafor').
Author: James Pustejovsky [aut, cre] (<https://orcid.org/0000-0003-0591-9465>)
Maintainer: James Pustejovsky <jepusto@gmail.com>

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Package bbotk updated to version 0.3.0 with previous version 0.2.2 dated 2020-10-08

Title: Black-Box Optimization Toolkit
Description: Provides a common framework for optimization of black-box functions for other packages, e.g. 'mlr3tuning' or 'mlr3fselect'. It offers various optimization methods e.g. grid search, random search and generalized simulated annealing.
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>

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Package intsvy updated to version 2.5 with previous version 2.4 dated 2019-05-10

Title: International Assessment Data Manager
Description: Provides tools for importing, merging, and analysing data from international assessment studies (TIMSS, PIRLS, PISA, ICILS, and PIAAC).
Author: Daniel Caro <dcarov@gmail.com>, Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Maintainer: Daniel Caro <dcarov@gmail.com>

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Package coronavirus updated to version 0.3.2 with previous version 0.3.1 dated 2021-01-10

Title: The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Dataset
Description: Provides a daily summary of the Coronavirus (COVID-19) cases by state/province. Data source: Johns Hopkins University Center for Systems Science and Engineering (JHU CCSE) Coronavirus <https://systems.jhu.edu/research/public-health/ncov/>.
Author: Rami Krispin [aut, cre], Jarrett Byrnes [aut] (<https://orcid.org/0000-0002-9791-9472>)
Maintainer: Rami Krispin <rami.krispin@gmail.com>

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Package rsmatrix updated to version 0.1.2 with previous version 0.1.1 dated 2020-10-31

Title: Matrices for Repeat-Sales Price Indexes
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.
Author: Steve Martin [aut, cre, cph]
Maintainer: Steve Martin <stevemartin041@gmail.com>

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Package prrd updated to version 0.0.4 with previous version 0.0.3 dated 2020-04-19

Title: Parallel Runs of Reverse Depends
Description: Reverse depends for a given package are queued such that multiple workers can run the tests in parallel.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package clam updated to version 2.3.8 with previous version 2.3.7 dated 2020-11-24

Title: Classical Age-Depth Modelling of Cores from Deposits
Description: Performs 'classical' age-depth modelling of dated sediment deposits - prior to applying more sophisticated techniques such as Bayesian age-depth modelling. Any radiocarbon dated depths are calibrated. Age-depth models are constructed by sampling repeatedly from the dated levels, each time drawing age-depth curves. Model types include linear interpolation, linear or polynomial regression, and a range of splines. See Blaauw (2010). <doi:10.1016/j.quageo.2010.01.002>.
Author: Maarten Blaauw [aut, cre], J. Andres Christen [ctb], Judith Esquivel Vazquez [ctb], Simon Goring [ctb]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>

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Package nomisr updated to version 0.4.4 with previous version 0.4.3 dated 2020-03-02

Title: Access 'Nomis' UK Labour Market Data
Description: Access UK official statistics from the 'Nomis' database. 'Nomis' includes data from the Census, the Labour Force Survey, DWP benefit statistics and other economic and demographic data from the Office for National Statistics, based around statistical geographies. See <https://www.nomisweb.co.uk/api/v01/help> for full API documentation.
Author: Evan Odell [aut, cre] (<https://orcid.org/0000-0003-1845-808X>), Paul Egeler [rev, ctb], Christophe Dervieux [rev] (<https://orcid.org/0000-0003-4474-2498>), Nina Robery [ctb] (Work and Health Indicators with nomisr vignette)
Maintainer: Evan Odell <evanodell91@gmail.com>

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Package NonlinearTSA updated to version 0.5.0 with previous version 0.4.0 dated 2020-06-08

Title: Nonlinear Time Series Analysis
Description: Function and data sets in the book entitled "Nonlinear Time Series Analysis with R Applications" B.Guris (2020). The book will be published in Turkish and the original name of this book will be "R Uygulamali Dogrusal Olmayan Zaman Serileri Analizi". It is possible to perform nonlinearity tests, nonlinear unit root tests, nonlinear cointegration tests and estimate nonlinear error correction models by using the functions written in this package. The Momentum Threshold Autoregressive (MTAR), the Smooth Threshold Autoregressive (STAR) and the Self Exciting Threshold Autoregressive (SETAR) type unit root tests can be performed using the functions written. In addition, cointegration tests using the Momentum Threshold Autoregressive (MTAR), the Smooth Threshold Autoregressive (STAR) and the Self Exciting Threshold Autoregressive (SETAR) models can be applied. It is possible to estimate nonlinear error correction models. The Granger causality test performed using nonlinear models can also be applied.
Author: Burak Guris <bguris@istanbul.edu.tr>
Maintainer: Burak Guris <bguris@istanbul.edu.tr>

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Package garchx updated to version 1.2 with previous version 1.1 dated 2020-05-10

Title: Flexible and Robust GARCH-X Modelling
Description: Flexible and robust estimation and inference of generalised autoregressive conditional heteroscedasticity (GARCH) models with covariates ('X') based on the results by Francq and Thieu (2018) <doi:10.1017/S0266466617000512>. Coefficients can straightforwardly be set to zero by omission, and quasi maximum likelihood methods ensure estimates are generally consistent and inference valid, even when the standardised innovations are non-normal and/or dependent over time.
Author: Genaro Sucarrat [aut, cre]
Maintainer: Genaro Sucarrat <gsucarrat@gmail.com>

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Package UniprotR updated to version 2.0.3 with previous version 2.0.2 dated 2021-01-12

Title: Retrieving Information of Proteins from Uniprot
Description: Connect to Uniprot <https://www.uniprot.org/> to retrieve information about proteins using their accession number such information could be name or taxonomy information, For detailed information kindly read the publication <https://www.sciencedirect.com/science/article/pii/S1874391919303859>.
Author: Mohamed Soudy [aut, cre], Ali Mostafa [aut]
Maintainer: Mohamed Soudy <MohmedSoudy2009@gmail.com>

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Package pracma updated to version 2.3.3 with previous version 2.2.9 dated 2019-12-15

Title: Practical Numerical Math Functions
Description: Provides a large number of functions from numerical analysis and linear algebra, numerical optimization, differential equations, time series, plus some well-known special mathematical functions. Uses 'MATLAB' function names where appropriate to simplify porting.
Author: Hans W. Borchers [aut, cre]
Maintainer: Hans W. Borchers <hwborchers@googlemail.com>

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Package BeSS updated to version 2.0.2 with previous version 2.0.0 dated 2021-01-13

Title: Best Subset Selection /Ridge Regression in Linear, Logistic, Poisson and CoxPH Models
Description: An implementation of best subset selection in generalized linear model and Cox proportional hazard model via the primal dual active set algorithm proposed by Wen, C., Zhang, A., Quan, S. and Wang, X. (2020) <doi:10.18637/jss.v094.i04>. The algorithm formulates coefficient parameters and residuals as primal and dual variables and utilizes efficient active set selection strategies based on the complementarity of the primal and dual variables.
Author: Canhong Wen [aut, cre], Aijun Zhang [aut], Shijie Quan [aut], Liyuan Hu [aut], Kangkang Jiang [aut], Yanhang Zhang [aut], Jin Zhu [aut], Xueqin Wang [aut]
Maintainer: Canhong Wen <wencanhong@gmail.com>

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Package plm updated to version 2.4-0 with previous version 2.2-5 dated 2020-10-13

Title: Linear Models for Panel Data
Description: A set of estimators and tests for panel data econometrics, as described in Baltagi (2013) Econometric Analysis of Panel Data, ISBN-13:978-1-118-67232-7, Hsiao (2014) Analysis of Panel Data <doi:10.1017/CBO9781139839327> and Croissant and Millo (2018), Panel Data Econometrics with R, ISBN:978-1-118-94918-4.
Author: Yves Croissant [aut, cre], Giovanni Millo [aut], Kevin Tappe [aut], Ott Toomet [ctb], Christian Kleiber [ctb], Achim Zeileis [ctb], Arne Henningsen [ctb], Liviu Andronic [ctb], Nina Schoenfelder [ctb]
Maintainer: Yves Croissant <yves.croissant@univ-reunion.fr>

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Package paradox updated to version 0.7.0 with previous version 0.6.0 dated 2020-12-04

Title: Define and Work with Parameter Spaces for Complex Algorithms
Description: Define parameter spaces, constraints and dependencies for arbitrary algorithms, to program on such spaces. Also includes statistical designs and random samplers. Objects are implemented as 'R6' classes.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>), Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>), Jakob Richter [aut] (<https://orcid.org/0000-0003-4481-5554>), Xudong Sun [aut] (<https://orcid.org/0000-0003-3269-2307>), Martin Binder [aut], Marc Becker [ctb] (<https://orcid.org/0000-0002-8115-0400>)
Maintainer: Michel Lang <michellang@gmail.com>

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

Title: Producing and Reproducing Results
Description: A system for embedded scientific computing and reproducible research with R. The OpenCPU server exposes a simple but powerful HTTP api for RPC and data interchange with R. This provides a reliable and scalable foundation for statistical services or building R web applications. The OpenCPU server runs either as a single-user development server within the interactive R session, or as a multi-user Linux stack based on Apache2. The entire system is fully open source and permissively licensed. The OpenCPU website has detailed documentation and example apps.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package batata updated to version 0.2.0 with previous version 0.1.1 dated 2020-06-16

Title: Managing Packages Removal and Installation
Description: Allows the user to manage easily R packages removal and installation. It offers many functions to display installed packages according to specific dates and removes them if needed. The user is always prompted when running the removal functions in order to confirm the required action. It also provides functions that will install 'Github' starred R packages whether available on 'CRAN' or not.
Author: Mohamed El Fodil Ihaddaden
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>

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Fri, 22 Jan 2021

Package TestDesign updated to version 1.2.0 with previous version 1.1.3 dated 2020-10-01

Title: Optimal Test Design Approach to Fixed and Adaptive Test Construction
Description: Use the optimal test design approach by Birnbaum (1968, ISBN:9781593119348) and van der Linden (2018) <doi:10.1201/9781315117430> in constructing fixed and adaptive tests. Supports the following mixed-integer programming (MIP) solver packages: 'lpsymphony', 'Rsymphony', 'gurobi', 'lpSolve', and 'Rglpk'. The 'gurobi' package is not available from CRAN; see <https://www.gurobi.com/downloads/>. See vignette for installing 'Rsymphony' package on Mac systems.
Author: Seung W. Choi [aut, cre] (<https://orcid.org/0000-0003-4777-5420>), Sangdon Lim [aut] (<https://orcid.org/0000-0002-2988-014X>)
Maintainer: Seung W. Choi <schoi@austin.utexas.edu>

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Package StrathE2E2 updated to version 3.3.0 with previous version 3.2.0 dated 2020-09-02

Title: End-to-End Marine Food Web Model
Description: A dynamic model of the big-picture, whole ecosystem effects of hydrodynamics, temperature, nutrients, and fishing on continental shelf marine food webs. The package is described in: Heath, M.R., Speirs, D.C., Thurlbeck, I. and Wilson, R.J. (2020) <doi:10.1111/2041-210X.13510> StrathE2E2: An R package for modelling the dynamics of marine food webs and fisheries. 8pp.
Author: Michael Heath [aut], Ian Thurlbeck [ctb]
Maintainer: Michael Heath <m.heath@strath.ac.uk>

Diff between StrathE2E2 versions 3.2.0 dated 2020-09-02 and 3.3.0 dated 2021-01-22

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 StrathE2E2-3.3.0/StrathE2E2/DESCRIPTION                                                                            |   20 
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 StrathE2E2-3.3.0/StrathE2E2/NAMESPACE                                                                              |    1 
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 StrathE2E2-3.3.0/StrathE2E2/R/StrathE2E2.R                                                                         |   21 
 StrathE2E2-3.3.0/StrathE2E2/R/derive_annual_results_inshore.R                                                      |    2 
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 StrathE2E2-3.3.0/StrathE2E2/R/e2e_run_ycurve.R                                                                     |    2 
 StrathE2E2-3.3.0/StrathE2E2/R/generate_df_yield_curve_data.R                                                       |    2 
 StrathE2E2-3.3.0/StrathE2E2/R/generate_pf_yield_curve_data.R                                                       |    2 
 StrathE2E2-3.3.0/StrathE2E2/R/internal.R                                                                           |    2 
 StrathE2E2-3.3.0/StrathE2E2/R/perturb_parameters.R                                                                 |    2 
 StrathE2E2-3.3.0/StrathE2E2/R/perturb_parameters_all.R                                                             |    6 
 StrathE2E2-3.3.0/StrathE2E2/R/plot_act_hr_optimization_diagnostics.R                                               |    2 
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 StrathE2E2-3.3.0/StrathE2E2/R/plot_inshore_vs_offshore_anavmass.R                                                  |    6 
 StrathE2E2-3.3.0/StrathE2E2/R/plot_sensitivity_results.R                                                           |   23 
 StrathE2E2-3.3.0/StrathE2E2/R/process_sensitivity_analysis_results.R                                               |   20 
 StrathE2E2-3.3.0/StrathE2E2/README.md                                                                              |    8 
 StrathE2E2-3.3.0/StrathE2E2/inst/CITATION                                                                          |    8 
 StrathE2E2-3.3.0/StrathE2E2/inst/doc/StrathE2E2_CheatSheet.pdf                                                     |binary
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Package RZooRoH updated to version 0.3.0 with previous version 0.2.4 dated 2021-01-20

Title: Partitioning of Individual Autozygosity into Multiple Homozygous-by-Descent Classes
Description: Functions to identify Homozygous-by-Descent (HBD) segments associated with runs of homozygosity (ROH) and to estimate individual autozygosity (or inbreeding coefficient). HBD segments and autozygosity are assigned to multiple HBD classes with a model-based approach relying on a mixture of exponential distributions. The rate of the exponential distribution is distinct for each HBD class and defines the expected length of the HBD segments. These HBD classes are therefore related to the age of the segments (longer segments and smaller rates for recent autozygosity / recent common ancestor). The functions allow to estimate the parameters of the model (rates of the exponential distributions, mixing proportions), to estimate global and local autozygosity probabilities and to identify HBD segments with the Viterbi decoding. The method is fully described in Druet and Gautier (2017) <doi:10.1111/mec.14324>.
Author: Tom Druet, Naveen Kumar Kadri, Amandine Bertrand and Mathieu Gautier
Maintainer: Tom Druet <tom.druet@uliege.be>

Diff between RZooRoH versions 0.2.4 dated 2021-01-20 and 0.3.0 dated 2021-01-22

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Package PhysicalActivity updated to version 0.2-4 with previous version 0.2-2 dated 2018-05-18

Title: Process Accelerometer Data for Physical Activity Measurement
Description: It provides a function "wearingMarking" for classification of monitor wear and nonwear time intervals in accelerometer data collected to assess physical activity. The package also contains functions for making plot for accelerometer data and obtaining the summary of various information including daily monitor wear time and the mean monitor wear time during valid days. "deliveryPred" and "markDelivery" can classify days for ActiGraph delivery by mail; "deliveryPreprocess" can process accelerometry data for analysis by zeropadding incomplete days and removing low activity days; "markPAI" can categorize physical activity intensity level based on user-defined cut-points of accelerometer counts. It also supports importing ActiGraph AGD files with "readActigraph" and "queryActigraph" functions.
Author: Leena Choi [aut, cre] (<https://orcid.org/0000-0002-2544-7090>), Cole Beck [aut] (<https://orcid.org/0000-0002-6849-6255>), Zhouwen Liu [aut], Ryan Moore [aut], Charles E. Matthews [aut], Maciej S. Buchowski [aut]
Maintainer: Leena Choi <leena.choi@Vanderbilt.Edu>

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Package htmltools updated to version 0.5.1.1 with previous version 0.5.1 dated 2021-01-12

Title: Tools for HTML
Description: Tools for HTML generation and output.
Author: Joe Cheng [aut], Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>), Winston Chang [aut], Yihui Xie [aut], Jeff Allen [aut], RStudio [cph]
Maintainer: Carson Sievert <carson@rstudio.com>

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Package HBV.IANIGLA updated to version 0.2.1 with previous version 0.2.0 dated 2021-01-21

Title: Modular Hydrological Model
Description: The HBV hydrological model (Bergström, S. and Lindström, G., (2015) <doi:10.1002/hyp.10510>) has been split in modules to allow the user to build his/her own model. This version was developed by the author in IANIGLA-CONICET (Instituto Argentino de Nivologia, Glaciologia y Ciencias Ambientales - Consejo Nacional de Investigaciones Cientificas y Tecnicas) for hydroclimatic studies in the Andes. HBV.IANIGLA incorporates routines for clean and debris covered glacier melt simulations.
Author: Ezequiel Toum <etoum@mendoza-conicet.gob.ar>
Maintainer: Ezequiel Toum <etoum@mendoza-conicet.gob.ar>

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Package eList updated to version 0.2.0 with previous version 0.0.1.0 dated 2021-01-11

Title: List Comprehension and Tools
Description: Create list comprehensions (and other types of comprehension) similar to those in 'python', 'haskell', and other languages. List comprehension in 'R' converts a regular for() loop into a vectorized lapply() function. Support for looping with multiple variables, parallelization, and across non-standard objects included. Package also contains a variety of functions to help with list comprehension.
Author: Chris Mann <cmann3@unl.edu>
Maintainer: Chris Mann <cmann3@unl.edu>

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Package BAT updated to version 2.4.2 with previous version 2.4.1 dated 2020-12-17

Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta diversity in all their dimensions (taxonomic, phylogenetic and functional). It allows performing a number of analyses based on species identities/abundances, phylogenetic/functional trees, convex-hulls or kernel density n-dimensional hypervolumes depicting species relationships.
Author: Pedro Cardoso, Stefano Mammola, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>

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Package MiRKAT updated to version 1.1.2 with previous version 1.1.1 dated 2020-08-27

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>

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Package statsr updated to version 0.3.0 with previous version 0.2.0 dated 2020-05-05

Title: Companion Software for the Coursera Statistics with R Specialization
Description: Data and functions to support Bayesian and frequentist inference and decision making for the Coursera Specialization "Statistics with R". See <https://github.com/StatsWithR/statsr> for more information.
Author: Colin Rundel [aut], Mine Cetinkaya-Rundel [aut], Merlise Clyde [aut, cre], David Banks [aut]
Maintainer: Merlise Clyde <clyde@duke.edu>

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Package discoveR updated to version 2.1.6 with previous version 1.2.9 dated 2020-08-03

Title: Exploratory Data Analysis System
Description: Performs an exploratory data analysis through a 'shiny' interface. It includes basic methods such as the mean, median, mode, normality test, among others. It also includes clustering techniques such as Principal Components Analysis, Hierarchical Clustering and the K-Means Method.
Author: Oldemar Rodriguez [aut, cre], Diego Jiménez [ctb]
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>

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Package scTenifoldKnk updated to version 1.0.1 with previous version 1.0.0 dated 2020-11-23

Title: In-Silico Knockout Experiments from Single-Cell Gene Regulatory Networks
Description: A workflow based on 'scTenifoldNet' to perform in-silico knockout experiments using single-cell RNA sequencing (scRNA-seq) data from wild-type (WT) control samples as input. First, the package constructs a single-cell gene regulatory network (scGRN) and knocks out a target gene from the adjacency matrix of the WT scGRN by setting the gene’s outdegree edges to zero. Then, it compares the knocked out scGRN with the WT scGRN to identify differentially regulated genes, called virtual-knockout perturbed genes, which are used to assess the impact of the gene knockout and reveal the gene’s function in the analyzed cells.
Author: Daniel Osorio [aut, cre] (<https://orcid.org/0000-0003-4424-8422>), Yan Zhong [aut, ctb], Guanxun Li [aut, ctb], Qian Xu [aut, ctb], Andrew Hillhouse [aut, ctb], Jingshu Chen [aut, ctb], Laurie Davidson [aut, ctb], Yanan Tian [aut, ctb], Robert Chapkin [aut, ctb], Jianhua Huang [aut, ctb], James Cai [aut, ctb, ths] (<https://orcid.org/0000-0002-8081-6725>)
Maintainer: Daniel Osorio <dcosorioh@tamu.edu>

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Package KnockoffScreen updated to version 0.2.0 with previous version 0.1.0 dated 2020-08-11

Title: Whole-Genome Sequencing Data Analysis via Knockoff Statistics
Description: Functions for identification of putative causal loci in whole-genome sequencing data. The functions allow genome-wide association scan. It also includes an efficient knockoff generator for genetic data.
Author: Zihuai He <zihuai@stanford.edu>
Maintainer: Zihuai He <zihuai@stanford.edu>

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Package candisc updated to version 0.8-5 with previous version 0.8-3 dated 2020-04-22

Title: Visualizing Generalized Canonical Discriminant and Canonical Correlation Analysis
Description: Functions for computing and visualizing generalized canonical discriminant analyses and canonical correlation analysis for a multivariate linear model. Traditional canonical discriminant analysis is restricted to a one-way 'MANOVA' design and is equivalent to canonical correlation analysis between a set of quantitative response variables and a set of dummy variables coded from the factor variable. The 'candisc' package generalizes this to higher-way 'MANOVA' designs for all factors in a multivariate linear model, computing canonical scores and vectors for each term. The graphic functions provide low-rank (1D, 2D, 3D) visualizations of terms in an 'mlm' via the 'plot.candisc' and 'heplot.candisc' methods. Related plots are now provided for canonical correlation analysis when all predictors are quantitative.
Author: Michael Friendly [aut, cre], John Fox [aut]
Maintainer: Michael Friendly <friendly@yorku.ca>

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Package asymmetry updated to version 2.0.3 with previous version 2.0.2 dated 2019-07-10

Title: Multidimensional Scaling of Asymmetric Data
Description: Multidimensional scaling models and methods for the visualization for asymmetric data <doi:10.1111/j.2044-8317.1996.tb01078.x>. An asymmetric matrix has the same number of rows and columns, and these rows and columns refer to the same set of objects. At least some elements in the upper-triangle are different from the corresponding elements in the lower triangle. An example is a student migration table, where the rows correspond to the countries of origin of the students and the columns to the destination countries. This package provides the slide-vector model <doi:10.1007/BF02294474>, a scaling model with unique dimensions and the asymscal model for asymmetric multidimensional scaling. Furthermore, a heat map for skew-symmetric data, and the decomposition of asymmetry are provided for the analysis of asymmetric tables.
Author: Berrie Zielman
Maintainer: Berrie Zielman <berrie.zielman@gmail.com>

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Package riverplot updated to version 0.10 with previous version 0.6 dated 2017-02-17

Title: Sankey or Ribbon Plots
Description: Sankey plots are a type of diagram that is convenient to illustrate how flow of information, resources etc. separates and joins, much like observing how rivers split and merge. For example, they can be used to compare different clusterings.
Author: January Weiner <january.weiner@gmail.com>
Maintainer: January Weiner <january.weiner@gmail.com>

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Package PRIMME updated to version 3.1-4 with previous version 3.1-3 dated 2020-10-25

Title: Eigenvalues and Singular Values and Vectors from Large Matrices
Description: R interface to 'PRIMME' <http://www.cs.wm.edu/~andreas/software/>, a C library for computing a few eigenvalues and their corresponding eigenvectors of a real symmetric or complex Hermitian matrix, or generalized Hermitian eigenproblem. It can also compute singular values and vectors of a square or rectangular matrix. 'PRIMME' finds largest, smallest, or interior singular/eigenvalues and can use preconditioning to accelerate convergence. General description of the methods are provided in the papers Stathopoulos (2010, <doi:10.1145/1731022.1731031>) and Wu (2017, <doi:10.1137/16M1082214>). See 'citation("PRIMME")' for details.
Author: Eloy Romero [aut, cre], Andreas Stathopoulos [aut], Lingfei Wu [aut], College of William & Mary [cph]
Maintainer: Eloy Romero <eloy@cs.wm.edu>

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Package brglm2 updated to version 0.7.1 with previous version 0.7.0 dated 2020-10-19

Title: Bias Reduction in Generalized Linear Models
Description: Estimation and inference from generalized linear models based on various methods for bias reduction and maximum penalized likelihood with powers of the Jeffreys prior as penalty. The 'brglmFit' fitting method can achieve reduction of estimation bias by solving either the mean bias-reducing adjusted score equations in Firth (1993) <doi:10.1093/biomet/80.1.27> and Kosmidis and Firth (2009) <doi:10.1093/biomet/asp055>, or the median bias-reduction adjusted score equations in Kenne et al. (2017) <doi:10.1093/biomet/asx046>, or through the direct subtraction of an estimate of the bias of the maximum likelihood estimator from the maximum likelihood estimates as in Cordeiro and McCullagh (1991) <https://www.jstor.org/stable/2345592>. See Kosmidis et al (2020) <doi:10.1007/s11222-019-09860-6> for more details. Estimation in all cases takes place via a quasi Fisher scoring algorithm, and S3 methods for the construction of of confidence intervals for the reduced-bias estimates are provided. In the special case of generalized linear models for binomial and multinomial responses (both ordinal and nominal), the adjusted score approaches to mean and media bias reduction have been found to return estimates with improved frequentist properties, that are also always finite, even in cases where the maximum likelihood estimates are infinite (e.g. complete and quasi-complete separation; see Kosmidis and Firth, 2020 <doi:10.1093/biomet/asaa052>, for a proof for mean bias reduction in logistic regression). 'brglm2' also provides pre-fit and post-fit methods for detecting separation and infinite maximum likelihood estimates in binomial response generalized linear models.
Author: Ioannis Kosmidis [aut, cre] (<https://orcid.org/0000-0003-1556-0302>), Kjell Konis [ctb], Euloge Clovis Kenne Pagui [ctb], Nicola Sartori [ctb]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>

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Package rminizinc updated to version 0.0.4 with previous version 0.0.3 dated 2021-01-05

Title: R Interface to Use 'MiniZinc'
Description: Constraint optimization, or constraint programming, is the name given to identifying feasible solutions out of a very large set of candidates, where the problem can be modeled in terms of arbitrary constraints. 'MiniZinc' is a free and open-source constraint modeling language. Constraint satisfaction and discrete optimization problems can be formulated in a high-level modeling language. Models are compiled into an intermediate representation that is understood by a wide range of solvers. 'MiniZinc' itself provides several solvers, for instance 'GeCode'. R users can use the package to solve constraint programming problems without using 'MiniZinc' directly, modify existing 'MiniZinc' models and also create their own models.
Author: Akshit Achara, Lars Kotthoff, Hans W. Borchers, Guido Tack
Maintainer: Akshit Achara <acharaakshit@gmail.com>

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Package airGR updated to version 1.6.9.27 with previous version 1.4.3.65 dated 2020-02-28

Title: Suite of GR Hydrological Models for Precipitation-Runoff Modelling
Description: Hydrological modelling tools developed at INRAE-Antony (HYCAR Research Unit, France). The package includes several conceptual rainfall-runoff models (GR4H, GR5H, GR4J, GR5J, GR6J, GR2M, GR1A), a snow accumulation and melt model (CemaNeige) and the associated functions for their calibration and evaluation. Use help(airGR) for package description and references.
Author: Laurent Coron [aut, trl] (<https://orcid.org/0000-0002-1503-6204>), Olivier Delaigue [aut, cre] (<https://orcid.org/0000-0002-7668-8468>), Guillaume Thirel [aut] (<https://orcid.org/0000-0002-1444-1830>), David Dorchies [aut] (<https://orcid.org/0000-0002-6595-7984>), Charles Perrin [aut, ths] (<https://orcid.org/0000-0001-8552-1881>), Claude Michel [aut, ths], Vazken Andréassian [ctb, ths] (<https://orcid.org/0000-0001-7124-9303>), François Bourgin [ctb] (<https://orcid.org/0000-0002-2820-7260>), Pierre Brigode [ctb] (<https://orcid.org/0000-0001-8257-0741>), Nicolas Le Moine [ctb], Thibaut Mathevet [ctb] (<https://orcid.org/0000-0002-4142-4454>), Safouane Mouelhi [ctb], Ludovic Oudin [ctb] (<https://orcid.org/0000-0002-3712-0933>), Raji Pushpalatha [ctb], Audrey Valéry [ctb]
Maintainer: Olivier Delaigue <airGR@inrae.fr>

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Package mdatools updated to version 0.11.3 with previous version 0.11.2 dated 2020-10-22

Title: Multivariate Data Analysis for Chemometrics
Description: Projection based methods for preprocessing, exploring and analysis of multivariate data used in chemometrics. S. Kucheryavskiy (2020) <doi: 10.1016/j.chemolab.2020.103937>.
Author: Sergey Kucheryavskiy (<https://orcid.org/0000-0002-3145-7244>)
Maintainer: Sergey Kucheryavskiy <svkucheryavski@gmail.com>

Diff between mdatools versions 0.11.2 dated 2020-10-22 and 0.11.3 dated 2021-01-22

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Package islasso updated to version 1.2.2 with previous version 1.2.0 dated 2021-01-21

Title: The Induced Smoothed Lasso
Description: An implementation of the induced smoothing (IS) idea to lasso regularization models to allow estimation and inference on the model coefficients (currently hypothesis testing only). Linear, logistic, Poisson and gamma regressions with several link functions are implemented. The algorithm is described in the original paper: Cilluffo, G., Sottile, G., La Grutta, S. and Muggeo, V. (2019) The Induced Smoothed lasso: A practical framework for hypothesis testing in high dimensional regression. <doi:10.1177/0962280219842890>, and discussed in a tutorial: Sottile, G., Cilluffo, G., and Muggeo, V. (2019) The R package islasso: estimation and hypothesis testing in lasso regression. <doi:10.13140/RG.2.2.16360.11521>.
Author: Gianluca Sottile [aut, cre], Giovanna Cilluffo [aut, ctb], Vito MR Muggeo [aut, cre]
Maintainer: Gianluca Sottile <gianluca.sottile@unipa.it>

Diff between islasso versions 1.2.0 dated 2021-01-21 and 1.2.2 dated 2021-01-22

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Package terra updated to version 1.0-10 with previous version 1.0-7 dated 2021-01-04

Title: Spatial Data Analysis
Description: Methods for spatial data analysis, especially raster data. Methods allow for low-level data manipulation as well as high-level global, local, zonal, and focal computation. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/terra/> to get started. 'terra' is very similar to the 'raster' package; but 'terra' is simpler, better, and faster.
Author: Robert J. Hijmans [cre, aut] (<https://orcid.org/0000-0001-5872-2872>), Roger Bivand [ctb] (<https://orcid.org/0000-0003-2392-6140>), Karl Forner [ctb], Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>), Edzer Pebesma [ctb] (<https://orcid.org/0000-0001-8049-7069>)
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>

Diff between terra versions 1.0-7 dated 2021-01-04 and 1.0-10 dated 2021-01-22

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Package SubtypeDrug updated to version 0.1.4 with previous version 0.1.3 dated 2020-11-24

Title: Prioritization of Candidate Cancer Subtype Specific Drugs
Description: A systematic biology tool was developed to prioritize cancer subtype-specific drugs by integrating genetic perturbation, drug action, biological pathway, and cancer subtype. The capabilities of this tool include inferring patient-specific subpathway activity profiles in the context of gene expression profiles with subtype labels, calculating differentially expressed subpathways based on cultured human cells treated with drugs in the 'cMap' (connectivity map) database, prioritizing cancer subtype specific drugs according to drug-disease reverse association score based on subpathway, and visualization of results (Castelo (2013) <doi:10.1186/1471-2105-14-7>; Han et al (2019) <doi:10.1093/bioinformatics/btz894>; Lamb and Justin (2006) <doi:10.1126/science.1132939>). Please cite using <doi:10.1093/bioinformatics/btab011>.
Author: Xudong Han, Junwei Han, Chonghui Liu
Maintainer: Junwei Han <hanjunwei1981@163.com>

Diff between SubtypeDrug versions 0.1.3 dated 2020-11-24 and 0.1.4 dated 2021-01-22

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Package Numero updated to version 1.7.4 with previous version 1.7.3 dated 2021-01-11

Title: Statistical Framework to Define Subgroups in Complex Datasets
Description: High-dimensional datasets that do not exhibit a clear intrinsic clustered structure pose a challenge to conventional clustering algorithms. For this reason, we developed an unsupervised framework that helps scientists to better subgroup their datasets based on visual cues, please see Gao S, Mutter S, Casey A, Makinen V-P (2019) Numero: a statistical framework to define multivariable subgroups in complex population-based datasets, Int J Epidemiology, 48:369-37, <doi:10.1093/ije/dyy113>. The framework includes the necessary functions to construct a self-organizing map of the data, to evaluate the statistical significance of the observed data patterns, and to visualize the results.
Author: Song Gao [aut], Stefan Mutter [aut], Aaron E. Casey [aut], Ville-Petteri Makinen [aut, cre]
Maintainer: Ville-Petteri Makinen <vpmakine@gmail.com>

Diff between Numero versions 1.7.3 dated 2021-01-11 and 1.7.4 dated 2021-01-22

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Package alfred updated to version 0.1.11 with previous version 0.1.10 dated 2021-01-07

Title: Downloading Time Series from ALFRED Database for Various Vintages
Description: Provides direct access to the ALFRED (<https://alfred.stlouisfed.org>) and FRED (<https://fred.stlouisfed.org>) databases. Its functions return tidy data frames for different releases of the specified time series. Note that this product uses the FRED© API but is not endorsed or certified by the Federal Reserve Bank of St. Louis.
Author: Onno Kleen [aut, cre] (<https://orcid.org/0000-0003-4731-4640>)
Maintainer: Onno Kleen <r@onnokleen.de>

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Package sisireg updated to version 0.8.0 with previous version 0.7.0 dated 2021-01-14

Title: Sign-Simplicity-Regression-Solver
Description: Implementation of the SSR-Algorithm. The Sign-Simplicity-Regression model is a nonparametric statistical model which is based on residual signs and simplicity assumptions on the regression function. Goal is to calculate the most parsimonious regression function satisfying the statistical adequacy requirements. Theory and functions are specified in Metzner (2020, ISBN: 9798682394203, "Trendbasierte Prognostik") and Metzner (2021, ISBN: 9798593470270, "Adäquates Maschinelles Lernen").
Author: Lars Metzner [aut, cre]
Maintainer: Lars Metzner <lars.metzner@ppi.de>

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Package r2dii.analysis updated to version 0.1.5 with previous version 0.1.4 dated 2021-01-05

Title: Tools to Calculate Climate Targets for Financial Portfolios
Description: These tools help you to assess if a financial portfolio aligns with climate goals. They summarize key metrics attributed to the portfolio (e.g. production, emission factors), and calculate targets based on climate scenarios. They implement in R the last step of the free software 'PACTA' (Paris Agreement Capital Transition Assessment; <https://2degrees-investing.org/>). Financial institutions use 'PACTA' to study how their capital allocation impacts the climate.
Author: Jackson Hoffart [aut, cre] (<https://orcid.org/0000-0002-8600-5042>), Mauro Lepore [aut, ctr] (<https://orcid.org/0000-0002-1986-7988>), Klaus Hogedorn [aut], 2 Degrees Investing Initiative [cph, fnd]
Maintainer: Jackson Hoffart <jackson.hoffart@gmail.com>

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Package WDI updated to version 2.7.2 with previous version 2.7.1 dated 2020-07-05

Title: World Development Indicators and Other World Bank Data
Description: Search and download data from over 40 databases hosted by the World Bank, including the World Development Indicators ('WDI'), International Debt Statistics, Doing Business, Human Capital Index, and Sub-national Poverty indicators.
Author: Vincent Arel-Bundock [aut, cre] (<https://orcid.org/0000-0003-2042-7063>), Etienne Bacher [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>

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Package sbtools updated to version 1.1.13 with previous version 1.1.12 dated 2020-08-30

Title: USGS ScienceBase Tools
Description: Tools for interacting with U.S. Geological Survey ScienceBase <https://www.sciencebase.gov> interfaces. ScienceBase is a data cataloging and collaborative data management platform. Functions included for querying ScienceBase, and creating and fetching datasets.
Author: David Blodgett [cre], Luke Winslow [aut], Scott Chamberlain [ctb], Alison Appling [ctb], Jordan Read [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>

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Package RSmallTelescopes updated to version 1.0.3 with previous version 1.0.2 dated 2020-09-23

Title: Empirical Small Telescopes Analysis
Description: We provide functions to perform an empirical small telescopes analysis. This package contains 2 functions, SimulatePower() and EstimatePower(). Users only need to call SimulatePower() to conduct the analysis. For more information on small telescopes analysis see Uri Simonsohn (2015) <doi:10.1177/0956797614567341>.
Author: John Ruscio [aut, cre], Samantha Costigan [ctb]
Maintainer: John Ruscio <ruscio@tcnj.edu>

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Package quantreg updated to version 5.83 with previous version 5.82 dated 2021-01-10

Title: Quantile Regression
Description: Estimation and inference methods for models of conditional quantiles: Linear and nonlinear parametric and non-parametric (total variation penalized) models for conditional quantiles of a univariate response and several methods for handling censored survival data. Portfolio selection methods based on expected shortfall risk are also now included.
Author: Roger Koenker [cre, aut], Stephen Portnoy [ctb] (Contributions to Censored QR code), Pin Tian Ng [ctb] (Contributions to Sparse QR code), Blaise Melly [ctb] (Contributions to preprocessing code), Achim Zeileis [ctb] (Contributions to dynrq code essentially identical to his dynlm code), Philip Grosjean [ctb] (Contributions to nlrq code), Cleve Moler [ctb] (author of several linpack routines), Yousef Saad [ctb] (author of sparskit2), Victor Chernozhukov [ctb] (contributions to extreme value inference code), Ivan Fernandez-Val [ctb] (contributions to extreme value inference code), Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my everlasting shame -- how could I have been so slow to adopt R!) and for numerous other suggestions and useful advice)
Maintainer: Roger Koenker <rkoenker@illinois.edu>

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Package hal9001 updated to version 0.2.7 with previous version 0.2.6 dated 2020-06-27

Title: The Scalable Highly Adaptive Lasso
Description: A scalable implementation of the highly adaptive lasso algorithm, including routines for constructing sparse matrices of basis functions of the observed data, as well as a custom implementation of Lasso regression tailored to enhance efficiency when the matrix of predictors is composed exclusively of indicator functions. For ease of use and increased flexibility, the Lasso fitting routines invoke code from the 'glmnet' package by default. The highly adaptive lasso was first formulated and described by MJ van der Laan (2017) <doi:10.1515/ijb-2015-0097>, with practical demonstrations of its performance given by Benkeser and van der Laan (2016) <doi:10.1109/DSAA.2016.93>.
Author: Jeremy Coyle [aut, cre] (<https://orcid.org/0000-0002-9874-6649>), Nima Hejazi [aut] (<https://orcid.org/0000-0002-7127-2789>), David Benkeser [ctb] (<https://orcid.org/0000-0002-1019-8343>), Oleg Sofrygin [ctb], Rachael Phillips [ctb] (<https://orcid.org/0000-0002-8474-591X>), Weixin Cai [ctb] (<https://orcid.org/0000-0003-2680-3066>), Mark van der Laan [aut, cph, ths] (<https://orcid.org/0000-0003-1432-5511>)
Maintainer: Jeremy Coyle <jeremyrcoyle@gmail.com>

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Package GNRS updated to version 0.1.1 with previous version 0.1.0 dated 2020-04-28

Title: Access the 'Geographic Name Resolution Service'
Description: Provides tools for interacting with the 'geographic name resolution service' ('GNRS') API <https://github.com/ojalaquellueva/gnrs> and associated functionality. The 'GNRS' is a batch application for resolving & standardizing political division names against standard name in the geonames database <http://www.geonames.org/>. The 'GNRS' resolves political division names at three levels: country, state/province and county/parish. Resolution is performed in a series of steps, beginning with direct matching to standard names, followed by direct matching to alternate names in different languages, followed by direct matching to standard codes (such as ISO and FIPS codes). If direct matching fails, the 'GNRS' attempts to match to standard and then alternate names using fuzzy matching, but does not perform fuzzing matching of political division codes. The 'GNRS' works down the political division hierarchy, stopping at the current level if all matches fail. In other words, if a country cannot be matched, the 'GNRS' does not attempt to match state or county.
Author: Brad Boyle [aut], Brian Maitner [aut, cre]
Maintainer: Brian Maitner <bmaitner@gmail.com>

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Thu, 21 Jan 2021

Package yamlet updated to version 0.5.3 with previous version 0.5.2 dated 2020-11-25

Title: Versatile Curation of Table Metadata
Description: A YAML-based mechanism for working with table metadata. It supports compact syntax for creating, modifying, exporting, importing, displaying, and plotting metadata coded as column attributes. The 'yamlet' dialect is valid 'YAML' with defaults and conventions chosen to improve readability. See ?yamlet, ?decorate.data.frame and ?modify.default. See ?read_yamlet ?write_yamlet, ?io_csv, and ?ggplot.decorated.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>

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Package spNetwork updated to version 0.1.1 with previous version 0.1.0 dated 2021-01-18

Title: Spatial Analysis on Network
Description: Perform spatial analysis on network. Allow to calculate Network Kernel Density Estimate, and to build spatial matrices ('listw' objects like in 'spdep' package) to conduct any kind of traditional spatial analysis with spatial weights based on reticular distances. K functions on network are also available but still experimental. References: Okabe et al (2019) <doi:10.1080/13658810802475491>; Okabe et al (2012, ISBN:978-0470770818);Baddeley el al (2015, ISBN:9781482210200).
Author: Jeremy Gelb [aut, cre], Philippe Apparicio [ctb]
Maintainer: Jeremy Gelb <jeremy.gelb@ucs.inrs.ca>

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Package RcppXsimd updated to version 7.1.6 with previous version 7.1.5 dated 2021-01-07

Title: Xsimd C++ Header-Only Library Files
Description: This header-only library provides modern, portable C++ wrappers for SIMD intrinsics and parallelized, optimized math implementations (SSE, AVX, NEON, AVX512). By placing this library in this package, we offer an efficient distribution system for Xsimd <https://github.com/xtensor-stack/xsimd> for R packages using CRAN.
Author: Marc A. Suchard [aut, cre], Andrew J. Holbrook [aut], Observational Health Data Sciences and Informatics [cph], Johan Mabille [cph, ctb] (author and copyright holder of Xsimd library under a BSD-3 license), Sylvain Corlay [cph, ctb] (author and copyright holder of Xsimd library under a BSD-3 license), Alexander J. Lee [cph, ctb] (author and copyright holder of FeatureDetector library under a CC0 1.0 license)
Maintainer: Marc A. Suchard <msuchard@ucla.edu>

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Package pmd updated to version 0.2.1 with previous version 0.1.9 dated 2020-06-04

Title: Paired Mass Distance Analysis for GC/LC-MS Based Non-Targeted Analysis and Reactomics Analysis
Description: Paired mass distance (PMD) analysis proposed in Yu, Olkowicz and Pawliszyn (2018) <doi:10.1016/j.aca.2018.10.062> for gas/liquid chromatography–mass spectrometry (GC/LC-MS) based non-targeted analysis. PMD analysis including GlobalStd algorithm and structure/reaction directed analysis. GlobalStd algorithm could found independent peaks in m/z-retention time profiles based on retention time hierarchical cluster analysis and frequency analysis of paired mass distances within retention time groups. Structure directed analysis could be used to find potential relationship among those independent peaks in different retention time groups based on frequency of paired mass distances. Reactomics analysis could also be performed to build PMD network, assign sources and make biomarker reaction discovery. GUIs for PMD analysis is also included as 'shiny' applications.
Author: Miao YU [aut, cre] (<https://orcid.org/0000-0002-2804-6014>)
Maintainer: Miao YU <yufreecas@gmail.com>

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Package pdqr updated to version 0.3.0 with previous version 0.2.1 dated 2019-12-15

Title: Work with Custom Distribution Functions
Description: Create, transform, and summarize custom random variables with distribution functions (analogues of 'p*()', 'd*()', 'q*()', and 'r*()' functions from base R). Two types of distributions are supported: "discrete" (random variable has finite number of output values) and "continuous" (infinite number of values in the form of continuous random variable). Functions for distribution transformations and summaries are available. Implemented approaches often emphasize approximate and numerical solutions: all distributions assume finite support and finite values of density function; some methods implemented with simulation techniques.
Author: Evgeni Chasnovski [aut, cre] (<https://orcid.org/0000-0002-1617-4019>)
Maintainer: Evgeni Chasnovski <evgeni.chasnovski@gmail.com>

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Package MDFS updated to version 1.1.1 with previous version 1.1.0 dated 2021-01-06

Title: MultiDimensional Feature Selection
Description: Functions for MultiDimensional Feature Selection (MDFS): calculating multidimensional information gains, scoring variables, finding important variables, plotting selection results. This package includes an optional CUDA implementation that speeds up information gain calculation using NVIDIA GPGPUs.
Author: Radosław Piliszek [aut, cre], Krzysztof Mnich [aut], Paweł Tabaszewski [aut], Szymon Migacz [aut], Andrzej Sułecki [aut], Witold Remigiusz Rudnicki [aut]
Maintainer: Radosław Piliszek <r.piliszek@uwb.edu.pl>

Diff between MDFS versions 1.1.0 dated 2021-01-06 and 1.1.1 dated 2021-01-21

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Package islasso updated to version 1.2.1 with previous version 1.2.0 dated 2021-01-21

Title: The Induced Smoothed Lasso
Description: An implementation of the induced smoothing (IS) idea to lasso regularization models to allow estimation and inference on the model coefficients (currently hypothesis testing only). Linear, logistic, Poisson and gamma regressions with several link functions are implemented. The algorithm is described in the original paper: Cilluffo, G., Sottile, G., La Grutta, S. and Muggeo, V. (2019) The Induced Smoothed lasso: A practical framework for hypothesis testing in high dimensional regression. <doi:10.1177/0962280219842890>, and discussed in a tutorial: Sottile, G., Cilluffo, G., and Muggeo, V. (2019) The R package islasso: estimation and hypothesis testing in lasso regression. <doi:10.13140/RG.2.2.16360.11521>.
Author: Gianluca Sottile [aut, cre], Giovanna Cilluffo [aut, ctb], Vito MR Muggeo [aut, cre]
Maintainer: Gianluca Sottile <gianluca.sottile@unipa.it>

Diff between islasso versions 1.2.0 dated 2021-01-21 and 1.2.1 dated 2021-01-21

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Package multiApply updated to version 2.1.2 with previous version 2.1.1 dated 2019-09-03

Title: Apply Functions to Multiple Multidimensional Arrays or Vectors
Description: The base apply function and its variants, as well as the related functions in the 'plyr' package, typically apply user-defined functions to a single argument (or a list of vectorized arguments in the case of mapply). The 'multiApply' package extends this paradigm with its only function, Apply, which efficiently applies functions taking one or a list of multiple unidimensional or multidimensional arrays (or combinations thereof) as input. The input arrays can have different numbers of dimensions as well as different dimension lengths, and the applied function can return one or a list of unidimensional or multidimensional arrays as output. This saves development time by preventing the R user from writing often error-prone and memory-inefficient loops dealing with multiple complex arrays. Also, a remarkable feature of Apply is the transparent use of multi-core through its parameter 'ncores'. In contrast to the base apply function, this package suggests the use of 'target dimensions' as opposite to the 'margins' for specifying the dimensions relevant to the function to be applied.
Author: BSC-CNS [aut, cph], Nicolau Manubens [aut], Alasdair Hunter [aut], Nuria Perez [cre]
Maintainer: Nuria Perez <nuria.perez@bsc.es>

Diff between multiApply versions 2.1.1 dated 2019-09-03 and 2.1.2 dated 2021-01-21

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Package iccde updated to version 0.3.0 with previous version 0.2.0 dated 2020-12-04

Title: Computation of the Double-Entry Intraclass Correlation
Description: The function computes the profile similarity measure double-entry intraclass correlation. It is a more precise index of the agreement of two empirically observed profiles than the often used intraclass correlation or profile correlation. Profiles comprising correlations are transformed according to the Fisher z transformation before the index is calculated. In the case of score data with different scale formats (e.g., if the profile contains different IQ or a variety of personality tests), it is recommended to z-standardize the scores before entering into the function. For details, see Furr (2010) <doi:10.1080/00223890903379134> or McCrae (2008) <doi:10.1080/00223890701845104>.
Author: Christian Blötner, Michael Paul Grosz
Maintainer: Christian Blötner <c.bloetner@gmail.com>

Diff between iccde versions 0.2.0 dated 2020-12-04 and 0.3.0 dated 2021-01-21

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Package KFAS updated to version 1.4.4 with previous version 1.4.2 dated 2021-01-14

Title: Kalman Filter and Smoother for Exponential Family State Space Models
Description: State space modelling is an efficient and flexible framework for statistical inference of a broad class of time series and other data. KFAS includes computationally efficient functions for Kalman filtering, smoothing, forecasting, and simulation of multivariate exponential family state space models, with observations from Gaussian, Poisson, binomial, negative binomial, and gamma distributions. See the paper by Helske (2017) <doi:10.18637/jss.v078.i10> for details.
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>

Diff between KFAS versions 1.4.2 dated 2021-01-14 and 1.4.4 dated 2021-01-21

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Package httpgd updated to version 1.0.1 with previous version 1.0.0 dated 2021-01-19

Title: A 'HTTP' Server Graphics Device
Description: A graphics device for R that is accessible via network protocols. This package was created to make it easier to embed live R graphics in integrated development environments and other applications. The included 'HTML/JavaScript' client (plot viewer) aims to provide a better overall user experience when dealing with R graphics. The device asynchronously serves 'SVG' graphics via 'HTTP' and 'WebSockets'.
Author: Florian Rupprecht [aut, cre] (<https://orcid.org/0000-0002-1795-8624>), Kun Ren [ctb], Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>), Hadley Wickham [cph] (Author of included svglite code), Lionel Henry [cph] (Author of included svglite code), Thomas Lin Pedersen [cph] (Author and creator of included svglite code), T Jake Luciani [cph] (Author of included svglite code), Matthieu Decorde [cph] (Author of included svglite code), Vaudor Lise [cph] (Author of included svglite code), Tony Plate [cph] (Contributor to included svglite code), David Gohel [cph] (Contributor to included svglite code), Yixuan Qiu [cph] (Contributor to included svglite code), Håkon Malmedal [cph] (Contributor to included svglite code), RStudio [cph] (Copyright holder of included svglite code), Brett Robinson [cph] (Author of included belle library), Google [cph] (Copyright holder of included material design icons), Victor Zverovich [cph] (Author of included fmt library)
Maintainer: Florian Rupprecht <floruppr@gmail.com>

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Package GetBCBData updated to version 0.6 with previous version 0.5 dated 2019-04-23

Title: Imports Datasets from BCB (Central Bank of Brazil) using Its Official API
Description: Downloads and organizes datasets using BCB's API <https://www.bcb.gov.br/>. Offers options for caching with the 'memoise' package and , multicore/multisession with 'furrr' and format of output data (long/wide).
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

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Package cglasso updated to version 2.0.2 with previous version 2.0.1 dated 2021-01-11

Title: Conditional Graphical LASSO for Gaussian Graphical Models with Censored and Missing Values
Description: Conditional graphical lasso estimator is an extension of the graphical lasso proposed to estimate the conditional dependence structure of a set of p response variables given q predictors. This package provides suitable extensions developed to study datasets with censored and/or missing values. Standard conditional graphical lasso is available as a special case. Furthermore, the package provides an integrated set of core routines for visualization, analysis, and simulation of datasets with censored and/or missing values drawn from a Gaussian graphical model. Details about the implemented models can be found in Augugliaro et al. (2020b) <doi: 10.1007/s11222-020-09945-7>, Augugliaro et al. (2020a) <doi: 10.1093/biostatistics/kxy043>, Yin et al. (2001) <doi: 10.1214/11-AOAS494> and Stadler et al. (2012) <doi: 10.1007/s11222-010-9219-7>.
Author: Luigi Augugliaro [aut, cre] (<https://orcid.org/0000-0002-4603-7541>), Gianluca Sottile [aut] (<https://orcid.org/0000-0001-9347-7251>), Ernst C. Wit [aut] (<https://orcid.org/0000-0002-3671-9610>), Veronica Vinciotti [aut] (<https://orcid.org/0000-0002-2625-7977>)
Maintainer: Luigi Augugliaro <luigi.augugliaro@unipa.it>

Diff between cglasso versions 2.0.1 dated 2021-01-11 and 2.0.2 dated 2021-01-21

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Package cachem updated to version 1.0.1 with previous version 1.0.0 dated 2021-01-18

Title: Cache R Objects with Automatic Pruning
Description: Key-value stores with automatic pruning. Caches can limit either their total size or the age of the oldest object (or both), automatically pruning objects to maintain the constraints.
Author: Winston Chang [aut, cre], RStudio [cph, fnd]
Maintainer: Winston Chang <winston@rstudio.com>

Diff between cachem versions 1.0.0 dated 2021-01-18 and 1.0.1 dated 2021-01-21

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Package bmabasket updated to version 0.1.1 with previous version 0.1.0 dated 2021-01-15

Title: Bayesian Model Averaging for Basket Trials
Description: An implementation of the Bayesian model averaging method of Psioda and others (2019) <doi:10.1093/biostatistics/kxz014> for basket trials. Contains a user-friendly wrapper for simulating basket trials under conditions and analyzing them with a Bayesian model averaging approach.
Author: Matt Psioda [cre], Ethan Alt [aut]
Maintainer: Matt Psioda <matt_psioda@unc.edu>

Diff between bmabasket versions 0.1.0 dated 2021-01-15 and 0.1.1 dated 2021-01-21

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Package attachment updated to version 0.2.1 with previous version 0.2.0 dated 2021-01-19

Title: Deal with Dependencies
Description: Tools to help manage dependencies during package development. This can retrieve all dependencies that are used in R files in the "R" directory, in Rmd files in "vignettes" directory and in 'roxygen2' documentation of functions. There is a function to update the Description file of your package and a function to create a file with the R commands to install all dependencies of your package. All functions to retrieve dependencies of R scripts and Rmd files can be used independently of a package development.
Author: Sébastien Rochette [cre, aut] (<https://orcid.org/0000-0002-1565-9313>), Vincent Guyader [aut] (<https://orcid.org/0000-0003-0671-9270>, previous maintainer), ThinkR [cph, fnd]
Maintainer: Sébastien Rochette <sebastien@thinkr.fr>

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Package RegSDC updated to version 0.5.0 with previous version 0.4.0 dated 2020-05-08

Title: Information Preserving Regression-Based Tools for Statistical Disclosure Control
Description: Implementation of the methods described in the paper with the above title: Langsrud, Ø. (2019) <doi:10.1007/s11222-018-9848-9>. The package can be used to generate synthetic or hybrid continuous microdata, and the relationship to the original data can be controlled in several ways. A function for replacing suppressed tabular cell frequencies with decimal numbers is included.
Author: Øyvind Langsrud [aut, cre]
Maintainer: Øyvind Langsrud <oyl@ssb.no>

Diff between RegSDC versions 0.4.0 dated 2020-05-08 and 0.5.0 dated 2021-01-21

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Package explore updated to version 0.7.0 with previous version 0.6.2 dated 2020-10-14

Title: Simplifies Exploratory Data Analysis
Description: Interactive data exploration with one line of code or use an easy to remember set of tidy functions for exploratory data analysis. Introduces three main verbs. explore() to graphically explore a variable or table, describe() to describe a variable or table and report() to create an automated report.
Author: Roland Krasser
Maintainer: Roland Krasser <roland.krasser@gmail.com>

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Package elevatr updated to version 0.3.4 with previous version 0.3.3 dated 2021-01-08

Title: Access Elevation Data from Various APIs
Description: Several web services are available that provide access to elevation data. This package provides access to several of those services and returns elevation data either as a SpatialPointsDataFrame from point elevation services or as a raster object from raster elevation services. Currently, the package supports access to the Amazon Web Services Terrain Tiles <https://registry.opendata.aws/terrain-tiles/>, the Open Topography Global Datasets API <https://opentopography.org/developers/>, and the USGS Elevation Point Query Service <https://nationalmap.gov/epqs/>.
Author: Jeffrey Hollister [aut, cre] (<https://orcid.org/0000-0002-9254-9740>), Tarak Shah [ctb], Alec L. Robitaille [ctb] (<https://orcid.org/0000-0002-4706-1762>), Marcus W. Beck [rev] (<https://orcid.org/0000-0002-4996-0059>), Mike Johnson [ctb] (<https://orcid.org/0000-0002-5288-8350>)
Maintainer: Jeffrey Hollister <hollister.jeff@epa.gov>

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Package anomaly updated to version 4.0.1 with previous version 4.0.0 dated 2020-09-29

Title: Detecting Anomalies in Data
Description: Implements Collective And Point Anomaly (CAPA) <arXiv:1806.01947>, Multi-Variate Collective And Point Anomaly (MVCAPA) <arXiv:1909.01691>, Proportion Adaptive Segment Selection (PASS) <doi:10.1093/biomet/ass059>, and Bayesian Abnormal Region Detector (BARD) <doi:10.1214/16-BA998> methods for the detection of anomalies in time series data. Also includes sequential versions of CAPA and MVCAPA <arXiv:2009.06670>.
Author: Alex Fisch [aut], Daniel Grose [aut, cre], Lawrence Bardwell [aut, ctb], Idris Eckley [aut, ths], Paul Fearnhead [aut, ths]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>

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Package SoyNAM updated to version 1.6.1 with previous version 1.6 dated 2019-02-13

Title: Soybean Nested Association Mapping Dataset
Description: Genomic and multi-environmental soybean data. Soybean Nested Association Mapping (SoyNAM) project dataset funded by the United Soybean Board (USB). BLUP function formats data for genome-wide prediction and association analysis.
Author: Alencar Xavier, William Beavis, James Specht, Brian Diers, Rouf Mian, Reka Howard, George Graef, Randall Nelson, William Schapaugh, Dechun Wang, Grover Shannon, Leah McHale, Perry Cregan, Qijian Song, Miguel Lopez, William Muir, Katy Rainey.
Maintainer: Alencar Xavier <alenxav@gmail.com>

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Package simstandard updated to version 0.6.2 with previous version 0.6.0 dated 2020-11-25

Title: Generate Standardized Data
Description: Creates simulated data from structural equation models with standardized loading. Data generation methods are described in Schneider (2013) <doi:10.1177/0734282913478046>.
Author: W. Joel Schneider [aut, cre] (<https://orcid.org/0000-0002-8393-5316>)
Maintainer: W. Joel Schneider <w.joel.schneider@gmail.com>

Diff between simstandard versions 0.6.0 dated 2020-11-25 and 0.6.2 dated 2021-01-21

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Package RoBMA updated to version 1.2.0 with previous version 1.1.2 dated 2020-12-10

Title: Robust Bayesian Meta-Analyses
Description: A framework for estimating ensembles of meta-analytic models (assuming either presence or absence of the effect, heterogeneity, and publication bias) and using Bayesian model averaging to combine them. The ensembles use Bayes factors to test for the presence or absence of the individual components (e.g., effect vs. no effect) and model-averages parameter estimates based on posterior model probabilities (Maier, Bartoš & Wagenmakers, 2020, <doi:10.31234/osf.io/u4cns>). The user can define a wide range of non-informative or informative priors for the effect size, heterogeneity, and weight functions. The package provides convenient functions for summary, visualizations, and fit diagnostics.
Author: František Bartoš [aut, cre] (<https://orcid.org/0000-0002-0018-5573>), Maximilian Maier [aut] (<https://orcid.org/0000-0002-9873-6096>), Eric-Jan Wagenmakers [ths] (<https://orcid.org/0000-0003-1596-1034>), Joris Goosen [ctb]
Maintainer: František Bartoš <f.bartos96@gmail.com>

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Package mdmb updated to version 1.5-8 with previous version 1.4-12 dated 2020-05-12

Title: Model Based Treatment of Missing Data
Description: Contains model-based treatment of missing data for regression models with missing values in covariates or the dependent variable using maximum likelihood or Bayesian estimation (Ibrahim et al., 2005; <doi:10.1198/016214504000001844>; Luedtke, Robitzsch, & West, 2020a, 2020b; <doi:10.1080/00273171.2019.1640104><doi:10.1037/met0000233>). The regression model can be nonlinear (e.g., interaction effects, quadratic effects or B-spline functions). Multilevel models with missing data in predictors are available for Bayesian estimation. Substantive-model compatible multiple imputation can be also conducted.
Author: Alexander Robitzsch [aut, cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@leibniz-ipn.de>

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Package islasso updated to version 1.2.0 with previous version 1.1.1 dated 2020-02-25

Title: The Induced Smoothed Lasso
Description: An implementation of the induced smoothing (IS) idea to lasso regularization models to allow estimation and inference on the model coefficients (currently hypothesis testing only). Linear, logistic, Poisson and gamma regressions with several link functions are implemented. The algorithm is described in the original paper: Cilluffo, G., Sottile, G., La Grutta, S. and Muggeo, V. (2019) The Induced Smoothed lasso: A practical framework for hypothesis testing in high dimensional regression. <doi:10.1177/0962280219842890>, and discussed in a tutorial: Sottile, G., Cilluffo, G., and Muggeo, V. (2019) The R package islasso: estimation and hypothesis testing in lasso regression. <doi:10.13140/RG.2.2.16360.11521>.
Author: Gianluca Sottile [aut, cre], Giovanna Cilluffo [aut, ctb], Vito MR Muggeo [aut, cre]
Maintainer: Gianluca Sottile <gianluca.sottile@unipa.it>

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Package HBV.IANIGLA updated to version 0.2.0 with previous version 0.1.1 dated 2019-08-29

Title: Modular Hydrological Model
Description: The HBV hydrological model (Bergström, S. and Lindström, G., (2015) <doi:10.1002/hyp.10510>) has been split in modules to allow the user to build his/her own model. This version was developed by the author in IANIGLA-CONICET (Instituto Argentino de Nivologia, Glaciologia y Ciencias Ambientales - Consejo Nacional de Investigaciones Cientificas y Tecnicas) for hydroclimatic studies in the Andes. HBV.IANIGLA incorporates routines for clean and debris covered glacier melt simulations.
Author: Ezequiel Toum <etoum@mendoza-conicet.gob.ar>
Maintainer: Ezequiel Toum <etoum@mendoza-conicet.gob.ar>

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Package ELISAtools updated to version 0.1.5 with previous version 0.1.0 dated 2019-03-08

Title: ELISA Data Analysis with Batch Correction
Description: To run data analysis for enzyme-link immunosorbent assays (ELISAs). Either the five- or four-parameter logistic model will be fitted for data of single ELISA. Moreover, the batch effect correction/normalization will be carried out, when there are more than one batches of ELISAs. Feng (2018) <doi:10.1101/483800>.
Author: Feng Feng [aut, cre]
Maintainer: Feng Feng <ffeng@BU.edu>

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Package heplots updated to version 1.3-8 with previous version 1.3-7 dated 2020-10-28

Title: Visualizing Hypothesis Tests in Multivariate Linear Models
Description: Provides HE plot and other functions for visualizing hypothesis tests in multivariate linear models. HE plots represent sums-of-squares-and- products matrices for linear hypotheses and for error using ellipses (in two dimensions) and ellipsoids (in three dimensions). The related 'candisc' package provides visualizations in a reduced-rank canonical discriminant space when there are more than a few response variables.
Author: John Fox [aut], Michael Friendly [aut, cre], Georges Monette [ctb], Phil Chalmers [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>

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Package QCA updated to version 3.11 with previous version 3.10 dated 2020-10-21

Title: Qualitative Comparative Analysis
Description: An extensive set of functions to perform Qualitative Comparative Analysis: crisp sets ('csQCA'), temporal ('tQCA'), multi-value ('mvQCA') and fuzzy sets ('fsQCA'), using a GUI - graphical user interface. 'QCA' is a methodology that bridges the qualitative and quantitative divide in social science research. It uses a Boolean algorithm, resulting in a minimal causal configuration that explains a given phenomenon.
Author: Adrian Dusa [aut, cre, cph] (<https://orcid.org/0000-0002-3525-9253>), Ciprian Paduraru [ctb] (<https://orcid.org/0000-0002-4518-374X>), jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/gui/www/lib/jquery-AUTHORS.txt), lp_solve [cph] (http://lpsolve.sourceforge.net), Vasil Dinkov [ctb, cph] (jquery.smartmenus.js library), Dmitry Baranovskiy [ctb, cph] (raphael.js library), Emmanuel Quentin [ctb, cph] (raphael.inline_text_editing.js library), Jimmy Breck-McKye [ctb, cph] (raphael-paragraph.js library), Alrik Thiem [aut] (from version 1.0-0 up to version 1.1-3)
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>

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Package packager updated to version 1.9.0 with previous version 1.8.0 dated 2020-12-02

Title: Create, Build and Maintain Packages
Description: Helper functions for package creation, building and maintenance. Designed to work with a build system such as 'GNU make' or package 'fakemake' to help you to conditionally work through the stages of package development (such as spell checking, linting, testing, before building and checking a package).
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>

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Package MoMPCA updated to version 1.0.1 with previous version 1.0.0 dated 2020-07-01

Title: Inference and Clustering for Mixture of Multinomial Principal Component Analysis
Description: Cluster any count data matrix with a fixed number of variables, such as document/term matrices. It integrates the dimension reduction aspect of topic models in the mixture models framework. Inference is done by means of a greedy Classification Variational Expectation Maximisation (C-VEM) algorithm. An Integrated Classication Likelihood (ICL) model selection is designed for selecting the latent dimension (number of topics) and the number of clusters. For more details, see the article of Jouvin et. al. (2020) <arxiv:1909.00721>.
Author: Nicolas Jouvin
Maintainer: Nicolas Jouvin <nicolas.jouvin@ec-lyon.fr>

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Package TSPred updated to version 5.1 with previous version 5.0 dated 2021-01-09

Title: Functions for Benchmarking Time Series Prediction
Description: Functions for defining and conducting a time series prediction process including pre(post)processing, decomposition, modelling, prediction and accuracy assessment. The generated models and its yielded prediction errors can be used for benchmarking other time series prediction methods and for creating a demand for the refinement of such methods. For this purpose, benchmark data from prediction competitions may be used.
Author: Rebecca Pontes Salles [aut, cre, cph] (CEFET/RJ), Eduardo Ogasawara [ths] (CEFET/RJ)
Maintainer: Rebecca Pontes Salles <rebeccapsalles@acm.org>

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Package opalr updated to version 1.5.2 with previous version 1.5.1 dated 2020-12-16

Title: 'Opal' Data Repository Client and 'DataSHIELD' Utils
Description: Data integration Web application for biobanks by 'OBiBa'. 'Opal' is the core database application for biobanks. Participant data, once collected from any data source, must be integrated and stored in a central data repository under a uniform model. 'Opal' is such a central repository. It can import, process, validate, query, analyze, report, and export data. 'Opal' is typically used in a research center to analyze the data acquired at assessment centres. Its ultimate purpose is to achieve seamless data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal' web services and to perform operations on the R server side. 'DataSHIELD' administration tools are also provided.
Author: Yannick Marcon [aut, cre] (<https://orcid.org/0000-0003-0138-2023>), Amadou Gaye [ctb] (<https://orcid.org/0000-0002-1180-2792>), OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>

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Package miceadds updated to version 3.11-6 with previous version 3.10-28 dated 2020-07-30

Title: Some Additional Multiple Imputation Functions, Especially for 'mice'
Description: Contains functions for multiple imputation which complements existing functionality in R. In particular, several imputation methods for the mice package (van Buuren & Groothuis-Oudshoorn, 2011, <doi:10.18637/jss.v045.i03>) are included. Main features of the miceadds package include plausible value imputation (Mislevy, 1991, <doi:10.1007/BF02294457>), multilevel imputation for variables at any level or with any number of hierarchical and non-hierarchical levels (Grund, Luedtke & Robitzsch, 2018, <doi:10.1177/1094428117703686>; van Buuren, 2018, Ch.7, <doi:10.1201/9780429492259>), imputation using partial least squares (PLS) for high dimensional predictors (Robitzsch, Pham & Yanagida, 2016), nested multiple imputation (Rubin, 2003, <doi:10.1111/1467-9574.00217>), substantive model compatible imputation (Bartlett et al., 2015, <doi:10.1177/0962280214521348>), and features for the generation of synthetic datasets (Reiter, 2005, <doi:10.1111/j.1467-985X.2004.00343.x>; Nowok, Raab, & Dibben, 2016, <doi:10.18637/jss.v074.i11>).
Author: Alexander Robitzsch [aut,cre] (<https://orcid.org/0000-0002-8226-3132>), Simon Grund [aut] (<https://orcid.org/0000-0002-1290-8986>), Thorsten Henke [ctb]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

Diff between miceadds versions 3.10-28 dated 2020-07-30 and 3.11-6 dated 2021-01-21

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Package bama updated to version 1.2 with previous version 1.0.1 dated 2020-05-02

Title: High Dimensional Bayesian Mediation Analysis
Description: Perform mediation analysis in the presence of high-dimensional mediators based on the potential outcome framework. Bayesian Mediation Analysis (BAMA), developed by Song et al (2019) <doi:10.1111/biom.13189> and Song et al (2020) <arXiv:2009.11409>, relies on two Bayesian sparse linear mixed models to simultaneously analyze a relatively large number of mediators for a continuous exposure and outcome assuming a small number of mediators are truly active. This sparsity assumption also allows the extension of univariate mediator analysis by casting the identification of active mediators as a variable selection problem and applying Bayesian methods with continuous shrinkage priors on the effects.
Author: Alexander Rix [aut], Mike Kleinsasser [aut, cre], Yanyi Song [aut]
Maintainer: Mike Kleinsasser <mkleinsa@umich.edu>

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Package Rthingsboard updated to version 0.2.4 with previous version 0.2.2 dated 2021-01-15

Title: 'ThingsBoard' API
Description: The goal of 'Rthingsboard' is to provide interaction with the API of 'ThingsBoard' (<https://thingsboard.io/>), an open-source IoT platform for device management, data collection, processing and visualization.
Author: David Dorchies [aut, cre] (<https://orcid.org/0000-0002-6595-7984>)
Maintainer: David Dorchies <david.dorchies@inrae.fr>

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Package rivr updated to version 1.2-3 with previous version 1.2-2 dated 2020-02-27

Title: Steady and Unsteady Open-Channel Flow Computation
Description: A tool for undergraduate and graduate courses in open-channel hydraulics. Provides functions for computing normal and critical depths, steady-state water surface profiles (e.g. backwater curves) and unsteady flow computations (e.g. flood wave routing) as described in Koohafkan MC, Younis BA (2015). "Open-channel computation with R." The R Journal, 7(2), 249–262. <doi: 10.32614/RJ-2015-034>.
Author: Michael C Koohafkan [aut, cre]
Maintainer: Michael C Koohafkan <michael.koohafkan@gmail.com>

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Package noaastormevents updated to version 0.2.0 with previous version 0.1.1 dated 2019-04-09

Title: Explore NOAA Storm Events Database
Description: Allows users to explore and plot data from the National Oceanic and Atmospheric Administration (NOAA) Storm Events database through R for United States counties. Functionality includes matching storm event listings by time and location to hurricane best tracks data. This work was supported by grants from the Colorado Water Center, the National Institute of Environmental Health Sciences (R00ES022631) and the National Science Foundation (1331399).
Author: Brooke Anderson [aut, cre], Ziyu Chen [aut], Therese Kondash [aut]
Maintainer: Brooke Anderson <brooke.anderson@colostate.edu>

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Package miWQS updated to version 0.4.2 with previous version 0.2.0 dated 2019-12-12

Title: Multiple Imputation Using Weighted Quantile Sum Regression
Description: The `miWQS` package handles the uncertainty due to below the detection limit in a correlated component mixture problem. Researchers want to determine if a set/mixture of continuous and correlated components/chemicals is associated with an outcome and if so, which components are important in that mixture. These components share a common outcome but are interval-censored between zero and low thresholds, or detection limits, that may be different across the components. The `miWQS` package applies the multiple imputation (MI) procedure to the weighted quantile sum regression (WQS) methodology for continuous, binary, or count outcomes (Hargarten & Wheeler (2020) <doi:10.1016/j.envres.2020.109466>). The imputation models are: bootstrapping imputation (Lubin et.al (2004) <doi:10.1289/ehp.7199>), univariate Bayesian imputation (Hargarten & Wheeler (2020) <doi:10.1016/j.envres.2020.109466>), and multivariate Bayesian regression imputation.
Author: Paul M. Hargarten [aut, cre], David C. Wheeler [aut, rev, ths]
Maintainer: Paul M. Hargarten <hargartenp@vcu.edu>

Diff between miWQS versions 0.2.0 dated 2019-12-12 and 0.4.2 dated 2021-01-21

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Package Lahman updated to version 8.0-1 with previous version 8.0-0 dated 2020-06-08

Title: Sean 'Lahman' Baseball Database
Description: Provides the tables from the 'Sean Lahman Baseball Database' as a set of R data.frames. It uses the data on pitching, hitting and fielding performance and other tables from 1871 through 2019, as recorded in the 2020 version of the database. Documentation examples show how many baseball questions can be investigated.
Author: Michael Friendly [aut], Chris Dalzell [cre, aut], Martin Monkman [aut], Dennis Murphy [aut], Vanessa Foot [ctb], Justeena Zaki-Azat [ctb]
Maintainer: Chris Dalzell <cdalzell@gmail.com>

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Package IndexNumR updated to version 0.2.0 with previous version 0.1.3 dated 2020-03-04

Title: Index Number Calculation
Description: Computes bilateral and multilateral index numbers. It has support for many standard bilateral indexes as well as multilateral index number methods such as GEKS, GEKS-Tornqvist (or CCDI), Geary-Khamis and the weighted time product dummy (for details on these methods see Diewert and Fox (2020) <doi:10.1080/07350015.2020.1816176>). It also supports updating of multilateral indexes using several splicing methods.
Author: Graham White
Maintainer: Graham White <g.white@unswalumni.com>

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Package git2rdata updated to version 0.3.1 with previous version 0.2.1 dated 2020-03-02

Title: Store and Retrieve Data.frames in a Git Repository
Description: The git2rdata package is an R package for writing and reading dataframes as plain text files. A metadata file stores important information. 1) Storing metadata allows to maintain the classes of variables. By default, git2rdata optimizes the data for file storage. The optimization is most effective on data containing factors. The optimization makes the data less human readable. The user can turn this off when they prefer a human readable format over smaller files. Details on the implementation are available in vignette("plain_text", package = "git2rdata"). 2) Storing metadata also allows smaller row based diffs between two consecutive commits. This is a useful feature when storing data as plain text files under version control. Details on this part of the implementation are available in vignette("version_control", package = "git2rdata"). Although we envisioned git2rdata with a git workflow in mind, you can use it in combination with other version control systems like subversion or mercurial. 3) git2rdata is a useful tool in a reproducible and traceable workflow. vignette("workflow", package = "git2rdata") gives a toy example. 4) vignette("efficiency", package = "git2rdata") provides some insight into the efficiency of file storage, git repository size and speed for writing and reading. Please cite using <doi:10.5281/zenodo.1485309>.
Author: Thierry Onkelinx [aut, cre] (<https://orcid.org/0000-0001-8804-4216>), Floris Vanderhaeghe [ctb] (<https://orcid.org/0000-0002-6378-6229>), Peter Desmet [ctb] (<https://orcid.org/0000-0002-8442-8025>), Els Lommelen [ctb] (<https://orcid.org/0000-0002-3481-5684>), Research Institute for Nature and Forest [cph, fnd]
Maintainer: Thierry Onkelinx <thierry.onkelinx@inbo.be>

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Package excursions updated to version 2.5.1 with previous version 2.4.5 dated 2020-02-26

Title: Excursion Sets and Contour Credibility Regions for Random Fields
Description: Functions that compute probabilistic excursion sets, contour credibility regions, contour avoiding regions, and simultaneous confidence bands for latent Gaussian random processes and fields. The package also contains functions that calculate these quantities for models estimated with the INLA package. The main references for excursions are Bolin and Lindgren (2015) <doi:10.1111/rssb.12055>, Bolin and Lindgren (2017) <doi:10.1080/10618600.2016.1228537>, and Bolin and Lindgren (2018) <doi:10.18637/jss.v086.i05>. These can be generated by the citation function in R.
Author: David Bolin [cre, aut], Finn Lindgren [aut]
Maintainer: David Bolin <davidbolin@gmail.com>

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Package repr updated to version 1.1.3 with previous version 1.1.0 dated 2020-01-28

Title: Serializable Representations
Description: String and binary representations of objects for several formats / mime types.
Author: Philipp Angerer [aut, cre] (<https://orcid.org/0000-0002-0369-2888>), Thomas Kluyver [aut], Jan Schulz [aut], abielr [ctb], Denilson Figueiredo de Sa [ctb], Jim Hester [ctb], karldw [ctb], Dave Foster [ctb], Carson Sievert [ctb]
Maintainer: Philipp Angerer <phil.angerer@gmail.com>

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Package RatingScaleReduction updated to version 1.4 with previous version 1.2.2 dated 2018-05-29

Title: Rating Scale Reduction Procedure
Description: Describes a new procedure of reducing items in a rating scale called Rating Scale Reduction (RSR). The new stop criterion in RSR procedure is added (stop global max). The function order is replaced by sort.list.
Author: Waldemar W. Koczkodaj, Feng Li, Alicja Wolny-Dominiak
Maintainer: Alicja Wolny-Dominiak <alicja.wolny-dominiak@ue.katowice.pl>

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Package dagitty updated to version 0.3-1 with previous version 0.3-0 dated 2020-07-21

Title: Graphical Analysis of Structural Causal Models
Description: A port of the web-based software 'DAGitty', available at <http://dagitty.net>, for analyzing structural causal models (also known as directed acyclic graphs or DAGs). This package computes covariate adjustment sets for estimating causal effects, enumerates instrumental variables, derives testable implications (d-separation and vanishing tetrads), generates equivalent models, and includes a simple facility for data simulation.
Author: Johannes Textor, Benito van der Zander, Ankur Ankan
Maintainer: Johannes Textor <johannes.textor@gmx.de>

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Package worcs updated to version 0.1.7 with previous version 0.1.6 dated 2020-12-16

Title: Workflow for Open Reproducible Code in Science
Description: Create reproducible and transparent research projects in 'R'. This package is based on the Workflow for Open Reproducible Code in Science (WORCS), a step-by-step procedure based on best practices for Open Science. It includes an 'RStudio' project template, several convenience functions, and all dependencies required to make your project reproducible and transparent. WORCS is explained in the tutorial paper by Van Lissa, Brandmaier, Brinkman, Lamprecht, Struiksma, & Vreede (2020). <doi:10.17605/OSF.IO/ZCVBS>.
Author: Caspar J. van Lissa [aut, cre] (<https://orcid.org/0000-0002-0808-5024>), Aaron Peikert [aut] (<https://orcid.org/0000-0001-7813-818X>), Andreas M. Brandmaier [aut] (<https://orcid.org/0000-0001-8765-6982>)
Maintainer: Caspar J. van Lissa <c.j.vanlissa@uu.nl>

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Package mlr3 updated to version 0.10.0 with previous version 0.9.0 dated 2020-12-06

Title: Machine Learning in R - Next Generation
Description: Efficient, object-oriented programming on the building blocks of machine learning. Provides 'R6' objects for tasks, learners, resamplings, and measures. The package is geared towards scalability and larger datasets by supporting parallelization and out-of-memory data-backends like databases. While 'mlr3' focuses on the core computational operations, add-on packages provide additional functionality.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>), Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>), Jakob Richter [aut] (<https://orcid.org/0000-0003-4481-5554>), Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>), Giuseppe Casalicchio [ctb] (<https://orcid.org/0000-0001-5324-5966>), Stefan Coors [ctb] (<https://orcid.org/0000-0002-7465-2146>), Quay Au [ctb] (<https://orcid.org/0000-0002-5252-8902>), Martin Binder [aut], Marc Becker [ctb] (<https://orcid.org/0000-0002-8115-0400>)
Maintainer: Michel Lang <michellang@gmail.com>

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Package tinytex updated to version 0.29 with previous version 0.28 dated 2020-12-14

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>

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Package plotrix updated to version 3.8-1 with previous version 3.7-8 dated 2020-04-16

Title: Various Plotting Functions
Description: Lots of plots, various labeling, axis and color scaling functions.
Author: Jim Lemon, Ben Bolker, Sander Oom, Eduardo Klein, Barry Rowlingson, Hadley Wickham, Anupam Tyagi, Olivier Eterradossi, Gabor Grothendieck, Michael Toews, John Kane, Rolf Turner, Carl Witthoft, Julian Stander, Thomas Petzoldt, Remko Duursma, Elisa Biancotto, Ofir Levy, Christophe Dutang, Peter Solymos, Robby Engelmann, Michael Hecker, Felix Steinbeck, Hans Borchers, Henrik Singmann, Ted Toal, Derek Ogle, Darshan Baral, Ulrike Groemping, Bill Venables
Maintainer: Jim Lemon <drjimlemon@gmail.com>

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Package Omisc updated to version 0.1.4 with previous version 0.1.3 dated 2020-08-11

Title: Univariate Bootstrapping and Other Things
Description: Primarily devoted to implementing the Univariate Bootstrap (as well as the Traditional Bootstrap). In addition there are multiple functions for DeFries-Fulker behavioral genetics models. The univariate bootstrapping functions, DeFries-Fulker functions, regression and traditional bootstrapping functions form the original core. Additional features may come online later, however this software is a work in progress. For more information about univariate bootstrapping see: Lee and Rodgers (1998) and Beasley et al (2007) <doi:10.1037/1082-989X.12.4.414>.
Author: Patrick O'Keefe
Maintainer: Patrick O'Keefe <patrick.okeefe@vanderbilt.edu>

Diff between Omisc versions 0.1.3 dated 2020-08-11 and 0.1.4 dated 2021-01-21

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Package iCellR updated to version 1.5.9 with previous version 1.5.8 dated 2020-10-09

Title: Analyzing High-Throughput Single Cell Sequencing Data
Description: A toolkit that allows scientists to work with data from single cell sequencing technologies such as scRNA-seq, scVDJ-seq and CITE-Seq. Single (i) Cell R package ('iCellR') provides unprecedented flexibility at every step of the analysis pipeline, including normalization, clustering, dimensionality reduction, imputation, visualization, and so on. Users can design both unsupervised and supervised models to best suit their research. In addition, the toolkit provides 2D and 3D interactive visualizations, differential expression analysis, filters based on cells, genes and clusters, data merging, normalizing for dropouts, data imputation methods, correcting for batch differences, pathway analysis, tools to find marker genes for clusters and conditions, predict cell types and pseudotime analysis. See Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.05.05.078550> and Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.03.31.019109> for more details.
Author: Alireza Khodadadi-Jamayran [aut, cre] (<https://orcid.org/0000-0003-2495-7504>), Joseph Pucella [aut, ctb] (<https://orcid.org/0000-0003-0875-8046>), Hua Zhou [aut, ctb] (<https://orcid.org/0000-0003-1822-1306>), Nicole Doudican [aut, ctb] (<https://orcid.org/0000-0003-3827-9644>), John Carucci [aut, ctb] (<https://orcid.org/0000-0001-6817-9439>), Adriana Heguy [aut, ctb], Boris Reizis [aut, ctb] (<https://orcid.org/0000-0003-1140-7853>), Aristotelis Tsirigos [aut, ctb] (<https://orcid.org/0000-0002-7512-8477>)
Maintainer: Alireza Khodadadi-Jamayran <alireza.khodadadi.j@gmail.com>

Diff between iCellR versions 1.5.8 dated 2020-10-09 and 1.5.9 dated 2021-01-21

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Package fastmatrix updated to version 0.3-8 with previous version 0.3 dated 2020-11-24

Title: Fast Computation of some Matrices Useful in Statistics
Description: Small set of functions to fast computation of some matrices and operations useful in statistics.
Author: Felipe Osorio [aut, cre] (<https://orcid.org/0000-0002-4675-5201>), Alonso Ogueda [aut]
Maintainer: Felipe Osorio <felipe.osorios@usm.cl>

Diff between fastmatrix versions 0.3 dated 2020-11-24 and 0.3-8 dated 2021-01-21

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Package ennet updated to version 0.2.0 with previous version 0.1.0 dated 2020-11-24

Title: Utilities to Extract and Analyse Text Data from the Emergency Nutrition Network Forum
Description: The Emergency Nutrition Network or en-net forum is the go to online forum for field practitioners requiring prompt technical advice for operational challenges for which answers are not readily accessible in current guidelines. The questions and the corresponding answers raised within en-net can provide insight into what the key topics of discussion are within the nutrition sector. This package provides utility functions for the extraction, processing and analysis of text data from the online forum.
Author: Ernest Guevarra [aut, cre] (<https://orcid.org/0000-0002-4887-4415>)
Maintainer: Ernest Guevarra <ernest@guevarra.io>

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Wed, 20 Jan 2021

Package IRdisplay updated to version 1.0 with previous version 0.7.0 dated 2018-11-29

Title: 'Jupyter' Display Machinery
Description: An interface to the rich display capabilities of 'Jupyter' front-ends (e.g. 'Jupyter Notebook') <https://jupyter.org>. Designed to be used from a running 'IRkernel' session <https://irkernel.github.io>.
Author: Thomas Kluyver [aut, cph], Philipp Angerer [aut, cph, cre] (<https://orcid.org/0000-0002-0369-2888>), Jan Schulz [aut, cph]
Maintainer: Philipp Angerer <phil.angerer@gmail.com>

Diff between IRdisplay versions 0.7.0 dated 2018-11-29 and 1.0 dated 2021-01-20

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Package changepoint.np updated to version 1.0.3 with previous version 1.0.2 dated 2020-05-15

Title: Methods for Nonparametric Changepoint Detection
Description: Implements the multiple changepoint algorithm PELT with a nonparametric cost function based on the empirical distribution of the data. This package extends the changepoint package (see Killick, R and Eckley, I (2014) <doi:10.18637/jss.v058.i03> ).
Author: Kaylea Haynes [aut], Rebecca Killick [aut], Paul Fearnhead [ths, ctb], Idris Eckley [ths], Daniel Grose [ctb, cre]
Maintainer: Daniel Grose <changepoints@lancaster.ac.uk>

Diff between changepoint.np versions 1.0.2 dated 2020-05-15 and 1.0.3 dated 2021-01-20

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Package roadoi updated to version 0.7 with previous version 0.6 dated 2019-09-15

Title: Find Free Versions of Scholarly Publications via Unpaywall
Description: This web client interfaces Unpaywall <https://unpaywall.org/products/api>, formerly oaDOI, a service finding free full-texts of academic papers by linking DOIs with open access journals and repositories. It provides unified access to various data sources for open access full-text links including Crossref and the Directory of Open Access Journals (DOAJ). API usage is free and no registration is required.
Author: Najko Jahn [aut, cre], Tuija Sonkkila [rev] (Tuija Sonkkila reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/115, <https://orcid.org/0000-0002-6892-9305>), Ross Mounce [rev] (Ross Mounce reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/115, <https://orcid.org/0000-0002-3520-2046>), Anne Hobert [ctb] (<https://orcid.org/0000-0003-2429-2995>), Delwen Franzen [ctb]
Maintainer: Najko Jahn <najko.jahn@gmail.com>

Diff between roadoi versions 0.6 dated 2019-09-15 and 0.7 dated 2021-01-20

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Package rorcid updated to version 0.7.0 with previous version 0.6.4 dated 2020-02-06

Title: Interface to the 'Orcid.org' API
Description: Client for the 'Orcid.org' API (<https://orcid.org/>). Functions included for searching for people, searching by 'DOI', and searching by 'Orcid' 'ID'.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), rOpenSci [fnd] (https://ropensci.org/)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package iIneq updated to version 1.0.2 with previous version 1.0.1 dated 2020-03-20

Title: Computing Individual Components of the Gini and the Theil Indices
Description: Computes individual contributions to the overall Gini and Theil's T and Theil's L measures and their decompositions by groups such as race, gender, national origin, with the three functions of iGini(), iTheiT(), and iTheilL(). For details, see Tim F. Liao (2019) <doi:10.1177/0049124119875961>.
Author: Tim Liao
Maintainer: Tim Liao <tfliao@illinois.edu>

Diff between iIneq versions 1.0.1 dated 2020-03-20 and 1.0.2 dated 2021-01-20

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Package tsiR updated to version 0.4.3 with previous version 0.4.2 dated 2019-07-09

Title: An Implementation of the TSIR Model
Description: An implementation of the time-series Susceptible-Infected-Recovered (TSIR) model using a number of different fitting options for infectious disease time series data. The manuscript based on this package can be found here <doi:10.1371/journal.pone.0185528>. The method implemented here is described by Finkenstadt and Grenfell (2000) <doi:10.1111/1467-9876.00187>.
Author: Alexander D. Becker [aut, cre], Sinead E. Morris [ctb], Ottar N. Bjornstad [ctb]
Maintainer: Alexander D. Becker <adbecker@princeton.edu>

Diff between tsiR versions 0.4.2 dated 2019-07-09 and 0.4.3 dated 2021-01-20

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Package RZooRoH updated to version 0.2.4 with previous version 0.2.3 dated 2019-03-22

Title: Partitioning of Individual Autozygosity into Multiple Homozygous-by-Descent Classes
Description: Functions to identify Homozygous-by-Descent (HBD) segments associated with runs of homozygosity (ROH) and to estimate individual autozygosity (or inbreeding coefficient). HBD segments and autozygosity are assigned to multiple HBD classes with a model-based approach relying on a mixture of exponential distributions. The rate of the exponential distribution is distinct for each HBD class and defines the expected length of the HBD segments. These HBD classes are therefore related to the age of the segments (longer segments and smaller rates for recent autozygosity / recent common ancestor). The functions allow to estimate the parameters of the model (rates of the exponential distributions, mixing proportions), to estimate global and local autozygosity probabilities and to identify HBD segments with the Viterbi decoding. The method is fully described in Druet and Gautier (2017) <doi:10.1111/mec.14324>.
Author: Tom Druet, Naveen Kumar Kadri, Amandine Bertrand and Mathieu Gautier
Maintainer: Tom Druet <tom.druet@uliege.be>

Diff between RZooRoH versions 0.2.3 dated 2019-03-22 and 0.2.4 dated 2021-01-20

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Package nlsmsn updated to version 0.0-6 with previous version 0.0-5 dated 2019-11-14

Title: Fitting Nonlinear Models with Scale Mixture of Skew-Normal Distributions
Description: Fit univariate non-linear scale mixture of skew-normal(NL-SMSN) regression, details in Garay, Lachos and Abanto-Valle (2011) <doi:10.1016/j.jkss.2010.08.003> and Lachos, Bandyopadhyay and Garay (2011) <doi:10.1016/j.spl.2011.03.019>.
Author: Marcos Prates [aut, cre, trl], Victor Lachos [aut], Aldo Garay [aut]
Maintainer: Marcos Prates <marcosop@est.ufmg.br>

Diff between nlsmsn versions 0.0-5 dated 2019-11-14 and 0.0-6 dated 2021-01-20

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Package brio updated to version 1.1.1 with previous version 1.1.0 dated 2020-08-31

Title: Basic R Input Output
Description: Functions to handle basic input output, these functions always read and write UTF-8 (8-bit Unicode Transformation Format) files and provide more explicit control over line endings.
Author: Jim Hester [aut, cre] (<https://orcid.org/0000-0002-2739-7082>), RStudio [cph, fnd]
Maintainer: Jim Hester <jim.hester@rstudio.com>

Diff between brio versions 1.1.0 dated 2020-08-31 and 1.1.1 dated 2021-01-20

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Package multinet updated to version 3.3.2 with previous version 3.3.1 dated 2020-06-02

Title: Analysis and Mining of Multilayer Social Networks
Description: Functions for the creation/generation and analysis of multilayer social networks.
Author: Matteo Magnani, Luca Rossi (API design), Obaida Hanteer (mdlpa, flat_ec, flat_nw, some community eval. functions), Davide Vega (API and code design), Mikael Dubik (glouvain). The package uses functions from eclat (www.borgelt.net/eclat.html), for association rule mining, Eigen (eigen.tuxfamily.org) and spectra (https://spectralib.org), for matrix manipulation, Infomap (www.mapequation.org), for the Infomap community detection method, and Howard Hinnant's date and time library (https://github.com/HowardHinnant/date). The code from these libraries has been included in our source package.
Maintainer: Matteo Magnani <matteo.magnani@it.uu.se>

Diff between multinet versions 3.3.1 dated 2020-06-02 and 3.3.2 dated 2021-01-20

 multinet-3.3.1/multinet/src/src/community/VertexCommunity.hpp                                        |only
 multinet-3.3.1/multinet/src/src/community/VertexLayerCommunity.hpp                                   |only
 multinet-3.3.1/multinet/src/src/core/olap/datastructures/CCube.hpp                                   |only
 multinet-3.3.1/multinet/src/src/networks/_impl/olap                                                  |only
 multinet-3.3.2/multinet/DESCRIPTION                                                                  |   12 
 multinet-3.3.2/multinet/MD5                                                                          |  268 +++++-----
 multinet-3.3.2/multinet/NEWS                                                                         |   11 
 multinet-3.3.2/multinet/man/Communities.Rd                                                           |   44 +
 multinet-3.3.2/multinet/man/CommunityGeneration.Rd                                                   |only
 multinet-3.3.2/multinet/man/Generation.Rd                                                            |    4 
 multinet-3.3.2/multinet/src/Makevars                                                                 |    4 
 multinet-3.3.2/multinet/src/Makevars.win                                                             |    4 
 multinet-3.3.2/multinet/src/eclat/eclat/src/eclat.c                                                  |   14 
 multinet-3.3.2/multinet/src/eclat/eclat/src/eclat.h                                                  |    1 
 multinet-3.3.2/multinet/src/eclat/tract/src/report.c                                                 |    4 
 multinet-3.3.2/multinet/src/r_functions.cpp                                                          |  163 +++++-
 multinet-3.3.2/multinet/src/r_functions.h                                                            |   55 +-
 multinet-3.3.2/multinet/src/rcpp_module_definition.cpp                                               |   56 +-
 multinet-3.3.2/multinet/src/rcpp_utils.cpp                                                           |   18 
 multinet-3.3.2/multinet/src/rcpp_utils.h                                                             |   14 
 multinet-3.3.2/multinet/src/src/CMakeLists.txt                                                       |only
 multinet-3.3.2/multinet/src/src/algorithms/BFS.hpp                                                   |   79 ++
 multinet-3.3.2/multinet/src/src/algorithms/BFS.ipp                                                   |  101 +++
 multinet-3.3.2/multinet/src/src/algorithms/DFS.hpp                                                   |   78 ++
 multinet-3.3.2/multinet/src/src/algorithms/DFS.ipp                                                   |  105 +++
 multinet-3.3.2/multinet/src/src/algorithms/components.ipp                                            |    3 
 multinet-3.3.2/multinet/src/src/algorithms/sssp.ipp                                                  |    4 
 multinet-3.3.2/multinet/src/src/community/Community.hpp                                              |    4 
 multinet-3.3.2/multinet/src/src/community/CommunityStructure.hpp                                     |    7 
 multinet-3.3.2/multinet/src/src/community/MLCPMCommunity.hpp                                         |   24 
 multinet-3.3.2/multinet/src/src/community/PillarCommunity.hpp                                        |   83 +--
 multinet-3.3.2/multinet/src/src/community/_impl/abacus_utils.hpp                                     |   20 
 multinet-3.3.2/multinet/src/src/community/_impl/abacus_utils.ipp                                     |  112 +++-
 multinet-3.3.2/multinet/src/src/community/_impl/common.hpp                                           |   26 
 multinet-3.3.2/multinet/src/src/community/_impl/cutils.cpp                                           |   12 
 multinet-3.3.2/multinet/src/src/community/_impl/cutils.hpp                                           |   44 -
 multinet-3.3.2/multinet/src/src/community/_impl/glouvain2_utils.cpp                                  |  106 +--
 multinet-3.3.2/multinet/src/src/community/_impl/glouvain2_utils.hpp                                  |   12 
 multinet-3.3.2/multinet/src/src/community/_impl/infomap_utils.hpp                                    |   47 -
 multinet-3.3.2/multinet/src/src/community/_impl/louvain_utils.cpp                                    |   14 
 multinet-3.3.2/multinet/src/src/community/_impl/louvain_utils.hpp                                    |   10 
 multinet-3.3.2/multinet/src/src/community/abacus.hpp                                                 |   15 
 multinet-3.3.2/multinet/src/src/community/abacus.ipp                                                 |   25 
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 multinet-3.3.2/multinet/src/src/community/community_stats.ipp                                        |only
 multinet-3.3.2/multinet/src/src/community/flat.hpp                                                   |only
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 multinet-3.3.2/multinet/src/src/community/glouvain.hpp                                               |   15 
 multinet-3.3.2/multinet/src/src/community/glouvain.ipp                                               |   30 -
 multinet-3.3.2/multinet/src/src/community/glouvain2.hpp                                              |   11 
 multinet-3.3.2/multinet/src/src/community/glouvain2.ipp                                              |   15 
 multinet-3.3.2/multinet/src/src/community/infomap.hpp                                                |   13 
 multinet-3.3.2/multinet/src/src/community/infomap.ipp                                                |   12 
 multinet-3.3.2/multinet/src/src/community/label_propagation.hpp                                      |    8 
 multinet-3.3.2/multinet/src/src/community/label_propagation.ipp                                      |    8 
 multinet-3.3.2/multinet/src/src/community/louvain.hpp                                                |   10 
 multinet-3.3.2/multinet/src/src/community/louvain.ipp                                                |    8 
 multinet-3.3.2/multinet/src/src/community/ml-cpm.hpp                                                 |   12 
 multinet-3.3.2/multinet/src/src/community/ml-cpm.ipp                                                 |   16 
 multinet-3.3.2/multinet/src/src/community/mlp.hpp                                                    |only
 multinet-3.3.2/multinet/src/src/community/modularity.hpp                                             |   26 
 multinet-3.3.2/multinet/src/src/community/omega_index.hpp                                            |only
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 multinet-3.3.2/multinet/src/src/core/attributes/AttributeValueMap.hpp                                |    3 
 multinet-3.3.2/multinet/src/src/core/attributes/MainMemoryAttributeValueMap.hpp                      |    3 
 multinet-3.3.2/multinet/src/src/core/datastructures/containers/PtrSortedRandomSet.hpp                |    1 
 multinet-3.3.2/multinet/src/src/core/datastructures/containers/SortedRandomSet.hpp                   |   47 +
 multinet-3.3.2/multinet/src/src/core/datastructures/observers/ObserverStore.hpp                      |    6 
 multinet-3.3.2/multinet/src/src/core/datastructures/observers/UnionObserver.hpp                      |only
 multinet-3.3.2/multinet/src/src/core/olap/datastructures/Cube.hpp                                    |    1 
 multinet-3.3.2/multinet/src/src/core/olap/datastructures/NCube.hpp                                   |   17 
 multinet-3.3.2/multinet/src/src/core/olap/operators/rollup.hpp                                       |only
 multinet-3.3.2/multinet/src/src/core/olap/operators/slice.hpp                                        |   89 ---
 multinet-3.3.2/multinet/src/src/core/olap/operators/slice.ipp                                        |only
 multinet-3.3.2/multinet/src/src/core/olap/selection/All.cpp                                          |    2 
 multinet-3.3.2/multinet/src/src/core/olap/selection/All.hpp                                          |    2 
 multinet-3.3.2/multinet/src/src/core/olap/selection/EntryIterator.hpp                                |    2 
 multinet-3.3.2/multinet/src/src/core/olap/selection/IndexIterator.cpp                                |    2 
 multinet-3.3.2/multinet/src/src/core/olap/selection/IndexIterator.hpp                                |    2 
 multinet-3.3.2/multinet/src/src/core/olap/selection/Indexes.cpp                                      |    2 
 multinet-3.3.2/multinet/src/src/core/olap/selection/Indexes.hpp                                      |    2 
 multinet-3.3.2/multinet/src/src/core/olap/selection/Range.cpp                                        |    2 
 multinet-3.3.2/multinet/src/src/core/olap/selection/Range.hpp                                        |    2 
 multinet-3.3.2/multinet/src/src/core/olap/selection/Set.cpp                                          |    2 
 multinet-3.3.2/multinet/src/src/core/olap/selection/Set.hpp                                          |    2 
 multinet-3.3.2/multinet/src/src/core/stores/ObjectStore.hpp                                          |    3 
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 multinet-3.3.2/multinet/src/src/generation/communities.cpp                                           |only
 multinet-3.3.2/multinet/src/src/generation/communities.hpp                                           |only
 multinet-3.3.2/multinet/src/src/generation/sample.hpp                                                |only
 multinet-3.3.2/multinet/src/src/generation/standard_graphs.cpp                                       |   61 ++
 multinet-3.3.2/multinet/src/src/generation/standard_graphs.hpp                                       |   21 
 multinet-3.3.2/multinet/src/src/io/_impl/MultilayerIOFileSection.hpp                                 |    2 
 multinet-3.3.2/multinet/src/src/io/_impl/read_common.cpp                                             |    5 
 multinet-3.3.2/multinet/src/src/io/_impl/read_ml_common.cpp                                          |   15 
 multinet-3.3.2/multinet/src/src/io/_impl/read_ml_common.hpp                                          |   19 
 multinet-3.3.2/multinet/src/src/io/read_multilayer_communities.hpp                                   |only
 multinet-3.3.2/multinet/src/src/io/read_multilayer_communities.ipp                                   |only
 multinet-3.3.2/multinet/src/src/io/read_multilayer_network.cpp                                       |    1 
 multinet-3.3.2/multinet/src/src/io/write_multilayer_communities.hpp                                  |only
 multinet-3.3.2/multinet/src/src/io/write_multilayer_communities.ipp                                  |only
 multinet-3.3.2/multinet/src/src/io/write_multilayer_network.cpp                                      |only
 multinet-3.3.2/multinet/src/src/io/write_multilayer_network.hpp                                      |   12 
 multinet-3.3.2/multinet/src/src/io/write_multilayer_network.ipp                                      |    2 
 multinet-3.3.2/multinet/src/src/networks/MultiNetwork.hpp                                            |    3 
 multinet-3.3.2/multinet/src/src/networks/MultilayerNetwork.hpp                                       |    2 
 multinet-3.3.2/multinet/src/src/networks/Network.hpp                                                 |    7 
 multinet-3.3.2/multinet/src/src/networks/OrderedMultiplexNetwork.hpp                                 |    2 
 multinet-3.3.2/multinet/src/src/networks/_impl/Graph.hpp                                             |    4 
 multinet-3.3.2/multinet/src/src/networks/_impl/stores/AttrMultiEdgeStore.hpp                         |    2 
 multinet-3.3.2/multinet/src/src/networks/_impl/stores/AttrSimpleEdgeStore.hpp                        |    2 
 multinet-3.3.2/multinet/src/src/networks/_impl/stores/AttrVertexStore.hpp                            |    2 
 multinet-3.3.2/multinet/src/src/networks/_impl/stores/AttributedDynamicInterlayerSimpleEdgeStore.hpp |    2 
 multinet-3.3.2/multinet/src/src/networks/_impl/stores/DynamicInterlayerSimpleEdgeStore.hpp           |    5 
 multinet-3.3.2/multinet/src/src/networks/_impl/stores/MDEdgeStore.hpp                                |    2 
 multinet-3.3.2/multinet/src/src/networks/_impl/stores/MDSimpleEdgeStore.hpp                          |    2 
 multinet-3.3.2/multinet/src/src/networks/_impl/stores/MultiEdgeStore.hpp                             |    2 
 multinet-3.3.2/multinet/src/src/networks/_impl/stores/SimpleEdgeStore.hpp                            |    3 
 multinet-3.3.2/multinet/src/src/networks/_impl/stores/VertexOverlappingLayerStore.hpp                |    2 
 multinet-3.3.2/multinet/src/src/networks/_impl/stores/VertexOverlappingOrderedLayerStore.hpp         |    2 
 multinet-3.3.2/multinet/src/src/networks/_impl/stores/VertexStore.hpp                                |   17 
 multinet-3.3.2/multinet/src/src/objects/MLVertex.hpp                                                 |only
 multinet-3.3.2/multinet/src/src/olap                                                                 |only
 multinet-3.3.2/multinet/src/src/operations/_impl/add_predefined_subgraphs.ipp                        |    5 
 multinet-3.3.2/multinet/src/src/operations/flatten.ipp                                               |   24 
 multinet-3.3.2/multinet/src/src/operations/union.ipp                                                 |   14 
 multinet-3.3.2/multinet/src/src/utils/summary.ipp                                                    |    2 
 130 files changed, 1507 insertions(+), 716 deletions(-)

More information about multinet at CRAN
Permanent link

Package TreeDist updated to version 2.0.0 with previous version 1.2.1 dated 2020-09-17

Title: Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including information-based generalized Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information Distance, Matching Split Information Distance; Smith, 2020) <doi:10.1093/bioinformatics/btaa614>; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) <doi:10.1007/978-3-642-40453-5_13>, including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>; the Matching Split Distance (Bogdanowicz & Giaro 2012) <doi:10.1109/TCBB.2011.48>; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) <doi:10.1007/3-540-61332-3_168>. Includes tools for visualizing the landscape of a tree space, and for calculating the median of a set of trees under any distance metric.
Author: Martin R. Smith [aut, cre, cph, prg] (<https://orcid.org/0000-0001-5660-1727>), Roy Jonker [prg, cph], Yong Yang [ctb, cph], Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>

Diff between TreeDist versions 1.2.1 dated 2020-09-17 and 2.0.0 dated 2021-01-20

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 TreeDist-2.0.0/TreeDist/NAMESPACE                                            |   13 
 TreeDist-2.0.0/TreeDist/NEWS.md                                              |   21 
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 TreeDist-2.0.0/TreeDist/src/ints.h                                           |    3 
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 94 files changed, 1845 insertions(+), 1071 deletions(-)

More information about TreeDist at CRAN
Permanent link

Package simplePHENOTYPES updated to version 1.3.0 with previous version 1.2.4 dated 2020-05-06

Title: Simulation of Pleiotropic, Linked and Epistatic Phenotypes
Description: The number of studies involving correlated traits and the availability of tools to handle this type of data has increased considerably in the last decade. With such a demand, we need tools for testing hypotheses related to single and multi-trait (correlated) phenotypes based on many genetic settings. Thus, we implemented various options for simulation of pleiotropy and Linkage Disequilibrium under additive, dominance and epistatic models. The simulation currently takes a marker data set as an input and then uses it for simulating multiple traits as described in Fernandes and Lipka (2020) <doi:10.1186/s12859-020-03804-y>.
Author: Samuel Fernandes [aut, cre] (<https://orcid.org/0000-0001-8269-535X>), Alexander Lipka [aut] (<https://orcid.org/0000-0003-1571-8528>)
Maintainer: Samuel Fernandes <samuelf@illinois.edu>

Diff between simplePHENOTYPES versions 1.2.4 dated 2020-05-06 and 1.3.0 dated 2021-01-20

 simplePHENOTYPES-1.2.4/simplePHENOTYPES/R/QTN_linkage.R                  |only
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Package model4you updated to version 0.9-7 with previous version 0.9-6 dated 2020-11-25

Title: Stratified and Personalised Models Based on Model-Based Trees and Forests
Description: Model-based trees for subgroup analyses in clinical trials and model-based forests for the estimation and prediction of personalised treatment effects (personalised models). Currently partitioning of linear models, lm(), generalised linear models, glm(), and Weibull models, survreg(), is supported. Advanced plotting functionality is supported for the trees and a test for parameter heterogeneity is provided for the personalised models. For details on model-based trees for subgroup analyses see Seibold, Zeileis and Hothorn (2016) <doi:10.1515/ijb-2015-0032>; for details on model-based forests for estimation of individual treatment effects see Seibold, Zeileis and Hothorn (2017) <doi:10.1177/0962280217693034>.
Author: Heidi Seibold [aut, cre], Achim Zeileis [aut], Torsten Hothorn [aut]
Maintainer: Heidi Seibold <heidi@seibold.co>

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Package ggthemes updated to version 4.2.4 with previous version 4.2.0 dated 2019-05-13

Title: Extra Themes, Scales and Geoms for 'ggplot2'
Description: Some extra themes, geoms, and scales for 'ggplot2'. Provides 'ggplot2' themes and scales that replicate the look of plots by Edward Tufte, Stephen Few, 'Fivethirtyeight', 'The Economist', 'Stata', 'Excel', and 'The Wall Street Journal', among others. Provides 'geoms' for Tufte's box plot and range frame.
Author: Jeffrey B. Arnold [aut, cre] (<https://orcid.org/0000-0001-9953-3904>), Gergely Daroczi [ctb], Bo Werth [ctb], Brian Weitzner [ctb], Joshua Kunst [ctb], Baptise Auguie [ctb], Bob Rudis [ctb], Hadley Wickham [ctb] (Code from the ggplot2 package.), Justin Talbot [ctb] (Code from the labeling package), Joshua London [ctb]
Maintainer: Jeffrey B. Arnold <jeffrey.arnold@gmail.com>

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Package fmpcloudr updated to version 0.1.2 with previous version 0.1.1 dated 2020-11-03

Title: R Access to the 'FMP Cloud' and 'Financial Modeling Prep' API
Description: Use R to access to the 'FMP Cloud' API <https://fmpcloud.io/> and 'Financial Modeling Prep' API <https://financialmodelingprep.com/developer/docs/>. Data available includes stock prices, market indexes, company fundamentals, 13F holdings data, and much more. A valid API token must be set to enable functions.
Author: Tony Trevisan [aut, cre]
Maintainer: Tony Trevisan <anthonytrevisan@gmail.com>

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Package apollo updated to version 0.2.3 with previous version 0.2.2 dated 2020-12-05

Title: Tools for Choice Model Estimation and Application
Description: The Choice Modelling Centre (CMC) at the University of Leeds has developed flexible code for the estimation and application of choice models in R. Users are able to write their own model functions or use a mix of already available ones. Random heterogeneity, both continuous and discrete and at the level of individuals and choices, can be incorporated for all models. There is support for both standalone models and hybrid model structures. Both classical and Bayesian estimation is available, and multiple discrete continuous models are covered in addition to discrete choice. Multi-threading processing is supported for estimation and a large number of pre and post-estimation routines, including for computing posterior (individual-level) distributions are available. For examples, a manual, and a support forum, visit <http://www.ApolloChoiceModelling.com>. For more information on choice models see Train, K. (2009) <isbn:978-0-521-74738-7> and Hess, S. & Daly, A.J. (2014) <isbn:978-1-781-00314-5> for an overview of the field.
Author: Stephane Hess [aut], David Palma [aut, cre]
Maintainer: David Palma <D.Palma@leeds.ac.uk>

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Package gamboostLSS updated to version 2.0-5 with previous version 2.0-1.1 dated 2020-04-02

Title: Boosting Methods for 'GAMLSS'
Description: Boosting models for fitting generalized additive models for location, shape and scale ('GAMLSS') to potentially high dimensional data.
Author: Benjamin Hofner [aut, cre] (<https://orcid.org/0000-0003-2810-3186>), Andreas Mayr [aut], Nora Fenske [aut], Janek Thomas [aut], Matthias Schmid [aut]
Maintainer: Benjamin Hofner <benjamin.hofner@pei.de>

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Package tidycensus updated to version 0.11.4 with previous version 0.11 dated 2020-12-14

Title: Load US Census Boundary and Attribute Data as 'tidyverse' and 'sf'-Ready Data Frames
Description: An integrated R interface to the decennial US Census and American Community Survey APIs and the US Census Bureau's geographic boundary files. Allows R users to return Census and ACS data as tidyverse-ready data frames, and optionally returns a list-column with feature geometry for all Census geographies.
Author: Kyle Walker [aut, cre], Matt Herman [aut], Kris Eberwein [ctb]
Maintainer: Kyle Walker <kyle@walker-data.com>

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Package simmr updated to version 0.4.4 with previous version 0.4.2 dated 2020-06-11

Title: A Stable Isotope Mixing Model
Description: Fits Stable Isotope Mixing Models (SIMMs) and is meant as a longer term replacement to the previous widely-used package SIAR. SIMMs are used to infer dietary proportions of organisms consuming various food sources from observations on the stable isotope values taken from the organisms' tissue samples. However SIMMs can also be used in other scenarios, such as in sediment mixing or the composition of fatty acids. The main functions are simmr_load and simmr_mcmc. The two vignettes contain a quick start and a full listing of all the features. The methods used are detailed in the papers Parnell et al 2010 <doi:10.1371/journal.pone.0009672>, and Parnell et al 2013 <doi:10.1002/env.2221>.
Author: Andrew Parnell
Maintainer: Andrew Parnell <andrew.parnell@mu.ie>

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Package MTA updated to version 0.3.0 with previous version 0.2.0 dated 2019-10-16

Title: Multiscalar Territorial Analysis
Description: Build multiscalar territorial analysis based on various contexts.
Author: Ronan Ysebaert [aut], Nicolas Lambert [aut], Timothée Giraud [aut, cre]
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>

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Package extendedFamily updated to version 0.2.0 with previous version 0.1.1 dated 2020-06-21

Title: Additional Families for Generalized Linear Models
Description: Creates family objects identical to stats family but for new links.
Author: Greg McMahan
Maintainer: Greg McMahan <gmcmacran@gmail.com>

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Package TraMineRextras updated to version 0.6.1 with previous version 0.6.0 dated 2020-04-24

Title: TraMineR Extension
Description: Collection of ancillary functions and utilities to be used in conjunction with the 'TraMineR' package for sequence data exploration. Most of the functions are in test phase, lack systematic consistency check of the arguments and are subject to changes. Once fully checked, some of the functions of this collection could be included in a next release of 'TraMineR'.
Author: Gilbert Ritschard [aut, cre, ths, cph] (<https://orcid.org/0000-0001-7776-0903>), Matthias Studer [aut] (<https://orcid.org/0000-0002-6269-1412>), Reto Buergin [aut], Tim Liao [ctb], Alexis Gabadinho [ctb], Pierre-Alexandre Fonta [ctb], Nicolas Muller [ctb], Patrick Rousset [ctb]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>

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Package fsbrain updated to version 0.4.1 with previous version 0.4.0 dated 2020-09-10

Title: Managing and Visualizing Brain Surface Data
Description: Provides high-level access to neuroimaging data from standard software packages like 'FreeSurfer' <http://freesurfer.net/> on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize data and statistical results directly in 'R'.
Author: Tim Schäfer [aut, cre] (<https://orcid.org/0000-0002-3683-8070>)
Maintainer: Tim Schäfer <ts+code@rcmd.org>

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Package fakemake updated to version 1.10.1 with previous version 1.10.0 dated 2021-01-07

Title: Mock the Unix Make Utility
Description: Use R as a minimal build system. This might come in handy if you are developing R packages and can not use a proper build system. Stay away if you can (use a proper build system).
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>

Diff between fakemake versions 1.10.0 dated 2021-01-07 and 1.10.1 dated 2021-01-20

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Package RAthena updated to version 1.12.0 with previous version 1.11.1 dated 2020-11-17

Title: Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Description: Designed to be compatible with the R package 'DBI' (Database Interface) when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>. To do this 'Python' 'Boto3' Software Development Kit ('SDK') <https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>

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Package rainette updated to version 0.1.2 with previous version 0.1.1 dated 2020-05-09

Title: The Reinert Method for Textual Data Clustering
Description: An R implementation of the Reinert text clustering method. For more details about the algorithm see the included vignettes or Reinert (1990) <doi:10.1177/075910639002600103>.
Author: Julien Barnier [aut, cre], Florian Privé [ctb]
Maintainer: Julien Barnier <julien.barnier@cnrs.fr>

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Package noctua updated to version 1.10.0 with previous version 1.9.1 dated 2020-11-17

Title: Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI' Interface)
Description: Designed to be compatible with the 'R' package 'DBI' (Database Interface) when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>. To do this the 'R' 'AWS' Software Development Kit ('SDK') 'paws' <https://github.com/paws-r/paws> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>

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Package breakDown updated to version 0.2.1 with previous version 0.2.0 dated 2020-04-05

Title: Model Agnostic Explainers for Individual Predictions
Description: Model agnostic tool for decomposition of predictions from black boxes. Break Down Table shows contributions of every variable to a final prediction. Break Down Plot presents variable contributions in a concise graphical way. This package work for binary classifiers and general regression models.
Author: Przemyslaw Biecek [aut, cre], Aleksandra Grudziaz [ctb]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>

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Package barsurf updated to version 0.7.0 with previous version 0.6.1 dated 2020-08-28

Title: Contour Plots, 3D Plots, Vector Fields and Heatmaps
Description: Combined contour/heatmap plots, 3d bar/surface plots, 2d/3d triangular plots, isosurface plots and 2d/3d vector fields. By default, uses vector graphics, but it's possible to use raster graphics for regular heatmaps. Builds on the colorspace package (Zeileis, et al., 2020 <doi:10.18637/jss.v096.i01>), by supporting smooth multiband color interpolation, in sRGB, HSV and HCL color spaces.
Author: Abby Spurdle
Maintainer: Abby Spurdle <spurdle.a@gmail.com>

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Package tweedie updated to version 2.3.3 with previous version 2.3.2 dated 2017-12-14

Title: Evaluation of Tweedie Exponential Family Models
Description: Maximum likelihood computations for Tweedie families, including the series expansion (Dunn and Smyth, 2005; <doi:10.1007/s11222-005-4070-y>) and the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>), and related methods.
Author: Peter K. Dunn [cre, aut]
Maintainer: Peter K. Dunn <pdunn2@usc.edu.au>

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Package shiny.router updated to version 0.2.2 with previous version 0.2.1 dated 2021-01-15

Title: Basic Routing for Shiny Web Applications
Description: It is a simple router for your Shiny apps. The router allows you to create dynamic web applications with real-time User Interface and easily share url to pages within your Shiny apps.
Author: Filip Stachura [aut], Dominik Krzemiński [cre, aut], Krystian Igras [aut], Appsilon [cph]
Maintainer: Dominik Krzemiński <dominik@appsilon.com>

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Package MCMCpack updated to version 1.5-0 with previous version 1.4-9 dated 2020-08-02

Title: Markov Chain Monte Carlo (MCMC) Package
Description: Contains functions to perform Bayesian inference using posterior simulation for a number of statistical models. Most simulation is done in compiled C++ written in the Scythe Statistical Library Version 1.0.3. All models return 'coda' mcmc objects that can then be summarized using the 'coda' package. Some useful utility functions such as density functions, pseudo-random number generators for statistical distributions, a general purpose Metropolis sampling algorithm, and tools for visualization are provided.
Author: Andrew D. Martin [aut], Kevin M. Quinn [aut], Jong Hee Park [aut,cre], Ghislain Vieilledent [ctb], Michael Malecki[ctb], Matthew Blackwell [ctb], Keith Poole [ctb], Craig Reed [ctb], Ben Goodrich [ctb], Ross Ihaka [cph], The R Development Core Team [cph], The R Foundation [cph], Pierre L'Ecuyer [cph], Makoto Matsumoto [cph], Takuji Nishimura [cph]
Maintainer: Jong Hee Park <jongheepark@snu.ac.kr>

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Package fritools updated to version 1.1.0 with previous version 1.0.0 dated 2021-01-11

Title: Utilities for the Forest Research Institute of the State Baden-Wuerttemberg
Description: Miscellaneous utilities, tools and helper functions for finding and searching files on disk, searching for and removing R objects from the workspace. These are utilities for packages <https://CRAN.R-project.org/package=cleanr>, <https://CRAN.R-project.org/package=document>, <https://CRAN.R-project.org/package=fakemake>, <https://CRAN.R-project.org/package=packager> and <https://CRAN.R-project.org/package=rasciidoc>. Does not import or depend on any third party party package, but on core R only.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>

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Package bssm updated to version 1.1.0 with previous version 1.0.1-1 dated 2020-11-12

Title: Bayesian Inference of Non-Linear and Non-Gaussian State Space Models
Description: Efficient methods for Bayesian inference of state space models via particle Markov chain Monte Carlo (MCMC) and MCMC based on parallel importance sampling type weighted estimators (Vihola, Helske, and Franks, 2020, <doi:10.1111/sjos.12492>). Gaussian, Poisson, binomial, negative binomial, and Gamma observation densities and basic stochastic volatility models with linear-Gaussian state dynamics, as well as general non-linear Gaussian models and discretised diffusion models are supported.
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>), Matti Vihola [aut] (<https://orcid.org/0000-0002-8041-7222>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>

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Package llama updated to version 0.10 with previous version 0.9.4 dated 2021-01-07

Title: Leveraging Learning to Automatically Manage Algorithms
Description: Provides functionality to train and evaluate algorithm selection models for portfolios.
Author: Lars Kotthoff [aut,cre], Bernd Bischl [aut], Barry Hurley [ctb], Talal Rahwan [ctb], Damir Pulatov [ctb]
Maintainer: Lars Kotthoff <larsko@uwyo.edu>

Diff between llama versions 0.9.4 dated 2021-01-07 and 0.10 dated 2021-01-20

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Package ITGM updated to version 0.42 with previous version 0.41 dated 2018-11-19

Title: Individual Tree Growth Modeling
Description: Individual tree model is an instrument to support the decision with regard to forest management. This package provides functions that let you work with data for this model. Also other support functions and extension related to this model are available.
Author: Clayton Vieira Fraga Filho, Gilson Fernandes da Silva, Miqueias Fernandes
Maintainer: Clayton Vieira Fraga Filho <forestgrowthsoftware@gmail.com>

Diff between ITGM versions 0.41 dated 2018-11-19 and 0.42 dated 2021-01-20

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Package allestimates updated to version 0.2.1 with previous version 0.1.9 dated 2020-09-29

Title: Effect Estimates from All Models
Description: Estimates and plots effect estimates from models with all possible combinations of a list of variables. It can be used for assessing treatment effects in clinical trials or risk factors in bio-medical and epidemiological research. Like Stata command 'confall' (Wang Z (2007) <doi:10.1177/1536867X0700700203> ), 'allestimates' calculates and stores all effect estimates, and plots them against p values or Akaike information criterion (AIC) values. It currently has functions for linear regression: all_lm(), logistic and Poisson regression: all_glm() and all_speedglm(), and Cox proportional hazards regression: all_cox().
Author: Zhiqiang Wang [aut, cre]
Maintainer: Zhiqiang Wang <zhiqiang.wang@menzies.edu.au>

Diff between allestimates versions 0.1.9 dated 2020-09-29 and 0.2.1 dated 2021-01-20

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Package mcmcsae updated to version 0.6.0 with previous version 0.5.0 dated 2020-09-01

Title: Markov Chain Monte Carlo Small Area Estimation
Description: Fit multi-level models with possibly correlated random effects using Markov Chain Monte Carlo simulation. Such models allow smoothing over space and time and are useful in, for example, small area estimation.
Author: Harm Jan Boonstra [aut, cre], Grzegorz Baltissen [ctb]
Maintainer: Harm Jan Boonstra <hjboonstra@gmail.com>

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Package seacarb updated to version 3.2.15 with previous version 3.2.14 dated 2020-10-30

Title: Seawater Carbonate Chemistry
Description: Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Author: Jean-Pierre Gattuso [aut, cre, cph], Jean-Marie Epitalon [aut], Heloise Lavigne [aut], James Orr [aut], Bernard Gentili [ctb], Mathilde Hagens [ctb], Andreas Hofmann [ctb], Jens-Daniel Mueller [ctb], Aurélien Proye [ctb], James Rae [ctb], Karline Soetaert [ctb]
Maintainer: Jean-Pierre Gattuso <gattuso@obs-vlfr.fr>

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 seacarb-3.2.15/seacarb/R/fCO2insi.R    |only
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 7 files changed, 14 insertions(+), 9 deletions(-)

More information about seacarb at CRAN
Permanent link

Package shinyWidgets updated to version 0.5.6 with previous version 0.5.5 dated 2021-01-13

Title: Custom Inputs Widgets for Shiny
Description: Collection of custom input controls and user interface components for 'Shiny' applications. Give your applications a unique and colorful style !
Author: Victor Perrier [aut, cre, cph], Fanny Meyer [aut], David Granjon [aut], Ian Fellows [ctb] (Methods for mutating vertical tabs & updateMultiInput), Wil Davis [ctb] (numericRangeInput function), Spencer Matthews [ctb] (autoNumeric methods)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

Diff between shinyWidgets versions 0.5.5 dated 2021-01-13 and 0.5.6 dated 2021-01-20

 DESCRIPTION                                                                  |    6 
 MD5                                                                          |  514 -
 NAMESPACE                                                                    |  336 
 NEWS.md                                                                      |    7 
 R/actionBttn.R                                                               |  360 -
 R/addSpinner.R                                                               |  504 -
 R/bootstrap-utils.R                                                          |  200 
 R/chooseSliderSkin.R                                                         |  408 -
 R/demos.R                                                                    |  136 
 R/dependencies.R                                                             |  656 -
 R/drop-menu.R                                                                |  482 -
 R/execute_safely.R                                                           |  112 
 R/input-actiongroupbuttons.R                                                 |  192 
 R/input-airDatepicker.R                                                      |  762 +-
 R/input-autonumeric.R                                                        | 1218 +--
 R/input-awesomecheckbox.R                                                    |  690 -
 R/input-awesomeradio.R                                                       |  510 -
 R/input-checkboxgroupbuttons.R                                               |  674 -
 R/input-circlebutton.R                                                       |  152 
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 R/input-dropdown.R                                                           |  486 -
 R/input-favbutton.R                                                          |  180 
 R/input-icon.R                                                               |  592 -
 R/input-knob.R                                                               |  430 -
 R/input-materialswitch.R                                                     |  182 
 R/input-multi.R                                                              |  438 -
 R/input-noUiSlider.R                                                         |  556 -
 R/input-numericRange.R                                                       |  212 
 R/input-pretty.R                                                             | 1472 ++--
 R/input-radiogroupbuttons.R                                                  |  606 -
 R/input-search.R                                                             |  336 
 R/input-selectpicker.R                                                       |  618 -
 R/input-sliderText.R                                                         |  444 -
 R/input-spectrum.R                                                           |  340 
 R/input-switch.R                                                             |  636 -
 R/input-textaddon.R                                                          |  100 
 R/module-pickerGroup.R                                                       |  602 -
 R/module-selectizeGroup.R                                                    |  524 -
 R/module-utils.R                                                             |  108 
 R/onLoad.R                                                                   |   80 
 R/pickerOptions.R                                                            |  236 
 R/progressBars.R                                                             |  366 -
 R/set-background.R                                                           |  422 -
 R/setShadow.R                                                                |  238 
 R/setSliderColor.R                                                           |  164 
 R/shinyWidgets.R                                                             |   24 
 R/shinyWidgetsGallery.R                                                      |   44 
 R/stati-card.R                                                               |  168 
 R/sw-dropdown.R                                                              |  484 -
 R/sweetalert.R                                                               | 1306 +--
 R/useArgonDash.R                                                             |  336 
 R/useBs4Dash.R                                                               |  266 
 R/useShinydashboard.R                                                        |  220 
 R/useShinydashboardPlus.R                                                    |  402 -
 R/useTablerDash.R                                                            |   50 
 R/utils.R                                                                    |  386 -
 R/vertical-tab.R                                                             |  670 -
 README.md                                                                    |  478 -
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 inst/assets/animate/LICENSE                                                  |   42 
 inst/assets/animate/animate-config.json                                      |  242 
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 inst/assets/autonumeric/autoNumeric.min.js                                   |   12 
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 inst/assets/awesome-bootstrap-checkbox/LICENSE                               |   40 
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 inst/assets/bootstrap-switch/LICENSE.txt                                     |   42 
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 inst/assets/bootstrap-switch/switch-bindings.js                              |  132 
 inst/assets/bounty/bounty-wrapper.js                                         |  186 
 inst/assets/bttn/bttn.min.css                                                |   24 
 inst/assets/buttons-group/checkboxGroupButtons-bindings.js                   |  320 
 inst/assets/buttons-group/checkboxGroupButtons.css                           |   94 
 inst/assets/buttons-group/radioGroupButtons-bindings.js                      |  266 
 inst/assets/buttons-group/radioGroupButtons.css                              |  200 
 inst/assets/circleButton/circle-button.css                                   |  168 
 inst/assets/colorSelector/sw-color-selector.css                              |   70 
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 inst/assets/numeric/text-icon-bindings.js                                    |  150 
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 inst/assets/popper/popper.min.js                                             |   10 
 inst/assets/search-input/search-bindings.js                                  |  156 
 inst/assets/shinyWidgets-bindings.min.js                                     |    2 
 inst/assets/shinyWidgets.css                                                 |  594 -
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 inst/assets/spectrum/spectrum-bindings.js                                    |  150 
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 inst/assets/spectrum/sw-spectrum.css                                         |   96 
 inst/assets/spinner/spin.css                                                 | 1464 ++--
 inst/assets/stati/stati.css                                                  |  136 
 inst/assets/sw-dropdown/sw-dropdown.css                                      |  112 
 inst/assets/sw-dropdown/sw-dropdown.js                                       |  288 
 inst/assets/sweetalert2/LICENSE.txt                                          |   44 
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 inst/assets/tippy/dist/animations.min.css                                    |    2 
 inst/assets/tippy/dist/themes.min.css                                        |    2 
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 inst/assets/uglify.R                                                         |  128 
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 inst/examples/airDatepicker/datepicker/app.R                                 |  254 
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 inst/examples/airDatepicker/years/app.R                                      |  176 
 inst/examples/bookmarking/test-sw.R                                          |   96 
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 inst/examples/bootstrapSwitch/ui.R                                           |  214 
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 inst/examples/colorSelector/example.R                                        |  210 
 inst/examples/dropdown/ex-color-dropdown.R                                   |  126 
 inst/examples/dropdown/ex-renderUI.R                                         |   92 
 inst/examples/dropdown/ex-sw-dropdown.R                                      |   78 
 inst/examples/examples-spin.R                                                |   98 
 inst/examples/jQueryKnob/app.R                                               |  154 
 inst/examples/multi/test-update.R                                            |  130 
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 inst/examples/numericRange/app.R                                             |   42 
 inst/examples/pretty/pretty_readme.R                                         |  136 
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 inst/examples/shinyWidgets/code_dropdown.R                                   |  124 
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 inst/examples/shinyWidgets/code_sa.R                                         |  116 
 inst/examples/shinyWidgets/global.R                                          |  270 
 inst/examples/shinyWidgets/server.R                                          |  732 +-
 inst/examples/shinyWidgets/ui.R                                              | 3466 +++++-----
 inst/examples/update_switchInput.R                                           |  298 
 man/airDatepicker.Rd                                                         |  400 -
 man/autonumericInput.Rd                                                      |  574 -
 man/formaNumericInputUpdate.Rd                                               |  188 
 man/formatNumericInput.Rd                                                    |  252 
 man/numericInputIcon.Rd                                                      |  230 
 man/numericRangeInput.Rd                                                     |  130 
 man/stati-card.Rd                                                            |    2 
 man/textInputIcon.Rd                                                         |  202 
 man/updateAutonumericInput.Rd                                                |  218 
 tests/testthat.R                                                             |    8 
 tests/testthat/helper.R                                                      |   42 
 tests/testthat/test-SweetAlert.R                                             |  338 
 tests/testthat/test-airdatepicker.R                                          |  176 
 tests/testthat/test-autonumeric.R                                            |  234 
 tests/testthat/test-bsplus.R                                                 |  144 
 tests/testthat/test-checkboxGroupButtons.R                                   |  358 -
 tests/testthat/test-chooseSliderSkin.R                                       |   86 
 tests/testthat/test-colorSelector.R                                          |   62 
 tests/testthat/test-drop-menu.R                                              |  104 
 tests/testthat/test-dropdown.R                                               |   60 
 tests/testthat/test-dropdownButton.R                                         |   52 
 tests/testthat/test-input-icon.R                                             |  122 
 tests/testthat/test-knob.R                                                   |  106 
 tests/testthat/test-modules.R                                                |  158 
 tests/testthat/test-multi.R                                                  |  106 
 tests/testthat/test-noUiSlider.R                                             |   38 
 tests/testthat/test-numericRange.R                                           |  140 
 tests/testthat/test-panel.R                                                  |   76 
 tests/testthat/test-pickerOptions.R                                          |   40 
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 tests/testthat/test-set-background.R                                         |   60 
 tests/testthat/test-setShadow.R                                              |   30 
 tests/testthat/test-shinyWidgetsGallery.R                                    |   34 
 tests/testthat/test-sliderText.R                                             |  144 
 tests/testthat/test-spectrum.R                                               |   48 
 tests/testthat/test-spinners.R                                               |  188 
 tests/testthat/test-textInputAddon.R                                         |   32 
 tests/testthat/test-updateAwesomeCheckbox.R                                  |   40 
 tests/testthat/test-updateAwesomeCheckboxGroup.R                             |   40 
 tests/testthat/test-updateAwesomeRadio.R                                     |   40 
 tests/testthat/test-updateCheckboxGroupButtons.R                             |   86 
 tests/testthat/test-updateMaterialSwitch.R                                   |   38 
 tests/testthat/test-updateRadioGroupButtons.R                                |   86 
 tests/testthat/test-updateSwitchInput.R                                      |   42 
 tests/testthat/test-utilityinputs.R                                          |  100 
 tests/testthat/test-vertical-tab.R                                           |  100 
 258 files changed, 27972 insertions(+), 27965 deletions(-)

More information about shinyWidgets at CRAN
Permanent link

Package blavaan updated to version 0.3-14 with previous version 0.3-13 dated 2021-01-18

Title: Bayesian Latent Variable Analysis
Description: Fit a variety of Bayesian latent variable models, including confirmatory factor analysis, structural equation models, and latent growth curve models.
Author: Edgar Merkle [aut, cre] (<https://orcid.org/0000-0001-7158-0653>), Yves Rosseel [aut], Ben Goodrich [aut], Mauricio Garnier-Villarreal [ctb] (<https://orcid.org/0000-0002-2951-6647>, R/blav_compare.R, R/ctr_bayes_fit.R), Terrence D. Jorgensen [ctb] (<https://orcid.org/0000-0001-5111-6773>, R/ctr_bayes_fit.R, R/ctr_ppmc.R), Huub Hoofs [ctb] (R/ctr_bayes_fit.R), Rens van de Schoot [ctb] (R/ctr_bayes_fit.R)
Maintainer: Edgar Merkle <merklee@missouri.edu>

Diff between blavaan versions 0.3-13 dated 2021-01-18 and 0.3-14 dated 2021-01-20

 DESCRIPTION               |    6 +++---
 MD5                       |    6 ++++--
 inst/testdata/sysdata.rda |binary
 tests/lavExport           |only
 4 files changed, 7 insertions(+), 5 deletions(-)

More information about blavaan at CRAN
Permanent link

Tue, 19 Jan 2021

Package shotGroups updated to version 0.8 with previous version 0.7.5.2 dated 2020-11-27

Title: Analyze Shot Group Data
Description: Analyzes shooting data with respect to group shape, precision, and accuracy. This includes graphical methods, descriptive statistics, and inference tests using standard, but also non-parametric and robust statistical methods. Implements distributions for radial error in bivariate normal variables. Works with files exported by 'OnTarget PC/TDS', 'Silver Mountain' e-target, 'ShotMarker' e-target, or 'Taran', as well as with custom data files in text format. Supports inference from range statistics like extreme spread. Includes a set of web-based graphical user interfaces.
Author: Daniel Wollschlaeger
Maintainer: Daniel Wollschlaeger <dwoll@kuci.org>

Diff between shotGroups versions 0.7.5.2 dated 2020-11-27 and 0.8 dated 2021-01-19

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 shotGroups-0.8/shotGroups/R/hoyt.R                                                   |    2 
 shotGroups-0.8/shotGroups/R/maxwell.R                                                |    2 
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Package ggvoronoi updated to version 0.8.4 with previous version 0.8.3 dated 2019-02-19

Title: Voronoi Diagrams and Heatmaps with 'ggplot2'
Description: Easy creation and manipulation of Voronoi diagrams using 'deldir' with visualization in 'ggplot2'.
Author: Robert C. Garrett [aut, cre], Austin Nar [aut], Thomas J. Fisher [aut], Karsten Maurer [ctb]
Maintainer: Robert C. Garrett <garretrc@miamioh.edu>

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Package autostsm updated to version 1.1 with previous version 1.0 dated 2021-01-15

Title: Automatic Structural Time Series Models
Description: Automatic model selection for structural time series decomposition into trend, cycle, and seasonal components using the Kalman filter. See Koopman, Siem Jan and Marius Ooms (2012) "Forecasting Economic Time Series Using Unobserved Components Time Series Models <doi:10.1093/oxfordhb/9780195398649.013.0006>.
Author: Alex Hubbard
Maintainer: Alex Hubbard <hubbard.alex@gmail.com>

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Package lazytrade updated to version 0.4.4 with previous version 0.4.3 dated 2020-12-16

Title: Learn Computer and Data Science using Algorithmic Trading
Description: Provide sets of functions and methods to learn and practice data science using idea of algorithmic trading. Main goal is to process information within "Decision Support System" to come up with analysis or predictions. There are several utilities such as dynamic and adaptive risk management using reinforcement learning and even functions to generate predictions of price changes using pattern recognition deep regression learning. Summary of Methods used: Awesome H2O tutorials: <https://github.com/h2oai/awesome-h2o>, Market Type research of Van Tharp Institute: <https://www.vantharp.com/>, Reinforcement Learning R package: <https://CRAN.R-project.org/package=ReinforcementLearning>.
Author: Vladimir Zhbanko
Maintainer: Vladimir Zhbanko <vladimir.zhbanko@gmail.com>

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Package parsnip updated to version 0.1.5 with previous version 0.1.4 dated 2020-10-27

Title: A Common API to Modeling and Analysis Functions
Description: A common interface is provided to allow users to specify a model without having to remember the different argument names across different functions or computational engines (e.g. 'R', 'Spark', 'Stan', etc).
Author: Max Kuhn [aut, cre], Davis Vaughan [aut], RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>

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Package tmaptools updated to version 3.1-1 with previous version 3.1 dated 2020-07-01

Title: Thematic Map Tools
Description: Set of tools for reading and processing spatial data. The aim is to supply the workflow to create thematic maps. This package also facilitates 'tmap', the package for visualizing thematic maps.
Author: Martijn Tennekes [aut, cre]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>

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Package bcmaps updated to version 1.0.1 with previous version 1.0.0 dated 2021-01-10

Title: Map Layers and Spatial Utilities for British Columbia
Description: Provides access to various spatial layers for B.C., such as administrative boundaries, natural resource management boundaries, etc. Most layers are imported from the 'bcdata' package as 'sf' or 'Spatial' objects through function calls in this package.
Author: Andy Teucher [aut, cre], Stephanie Hazlitt [aut], Sam Albers [aut], Province of British Columbia [cph]
Maintainer: Andy Teucher <andy.teucher@gov.bc.ca>

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Package MachineShop updated to version 2.6.0 with previous version 2.5.0 dated 2020-08-05

Title: Machine Learning Models and Tools
Description: Meta-package for statistical and machine learning with a unified interface for model fitting, prediction, performance assessment, and presentation of results. Approaches for model fitting and prediction of numerical, categorical, or censored time-to-event outcomes include traditional regression models, regularization methods, tree-based methods, support vector machines, neural networks, ensembles, data preprocessing, filtering, and model tuning and selection. Performance metrics are provided for model assessment and can be estimated with independent test sets, split sampling, cross-validation, or bootstrap resampling. Resample estimation can be executed in parallel for faster processing and nested in cases of model tuning and selection. Modeling results can be summarized with descriptive statistics; calibration curves; variable importance; partial dependence plots; confusion matrices; and ROC, lift, and other performance curves.
Author: Brian J Smith [aut, cre]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>

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Package tmap updated to version 3.3 with previous version 3.2 dated 2020-09-15

Title: Thematic Maps
Description: Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, and easy to use approach to create thematic maps, such as choropleths and bubble maps.
Author: Martijn Tennekes [aut, cre], Jakub Nowosad [ctb], Joel Gombin [ctb], Sebastian Jeworutzki [ctb], Kent Russell [ctb], Richard Zijdeman [ctb], John Clouse [ctb], Robin Lovelace [ctb], Jannes Muenchow [ctb]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>

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Package R.devices updated to version 2.17.0 with previous version 2.16.1 dated 2019-10-24

Title: Unified Handling of Graphics Devices
Description: Functions for creating plots and image files in a unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). Default device options as well as scales and aspect ratios are controlled in a uniform way across all device types. Switching output format requires minimal changes in code. This package is ideal for large-scale batch processing, because it will never leave open graphics devices or incomplete image files behind, even on errors or user interrupts.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

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More information about R.devices at CRAN
Permanent link

Package LNIRT updated to version 0.5.1 with previous version 0.5.0 dated 2020-11-16

Title: LogNormal Response Time Item Response Theory Models
Description: Allows the simultaneous analysis of responses and response times in an Item Response Theory (IRT) modelling framework. Supports variable person speed functions (intercept, trend, quadratic), and covariates for item and person (random) parameters. Data missing-by-design can be specified. Parameter estimation is done with a MCMC algorithm. LNIRT replaces the package CIRT, which was written by Rinke Klein Entink. For reference, see the paper by Fox, Klein Entink and Van der Linden (2007), "Modeling of Responses and Response Times with the Package cirt", Journal of Statistical Software, <doi:10.18637/jss.v020.i07>.
Author: Jean-Paul Fox, Konrad Klotzke, Rinke Klein Entink
Maintainer: Konrad Klotzke <omd.bms.utwente.stats@gmail.com>

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More information about LNIRT at CRAN
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Package blogdown updated to version 1.1 with previous version 1.0 dated 2021-01-09

Title: Create Blogs and Websites with R Markdown
Description: Write blog posts and web pages in R Markdown. This package supports the static site generator 'Hugo' (<https://gohugo.io>) best, and it also supports 'Jekyll' (<https://jekyllrb.com>) and 'Hexo' (<https://hexo.io>).
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Christophe Dervieux [aut] (<https://orcid.org/0000-0003-4474-2498>), Alison Presmanes Hill [aut] (<https://orcid.org/0000-0002-8082-1890>), Amber Thomas [ctb], Beilei Bian [ctb], Brandon Greenwell [ctb], Brian Barkley [ctb], Deependra Dhakal [ctb], Eric Nantz [ctb], Forest Fang [ctb], Garrick Aden-Buie [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], Jake Barlow [ctb], James Balamuta [ctb], JJ Allaire [ctb], Jon Calder [ctb], Jozef Hajnala [ctb], Juan Manuel Vazquez [ctb], Kevin Ushey [ctb], Leonardo Collado-Torres [ctb], Maëlle Salmon [ctb], Maria Paula Caldas [ctb], Nicolas Roelandt [ctb], Oliver Madsen [ctb], Raniere Silva [ctb], TC Zhang [ctb], Xianying Tan [ctb], RStudio, PBC [cph]
Maintainer: Yihui Xie <xie@yihui.name>

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Package tidyBF updated to version 0.4.3 with previous version 0.4.2 dated 2020-12-08

Title: Tidy Wrapper for 'BayesFactor' Package
Description: Provides helper functions that make it easy to run 'BayesFactor' package tests on a data which is in a tidy format. Additionally, it provides a more consistent syntax and by default returns a dataframe with rich details. These functions can also return expressions containing results from Bayes Factor tests that can then be displayed on custom plots. Posterior estimation is carried out using the 'bayestestR' package.
Author: Indrajeet Patil [aut, cre, cph] (<https://orcid.org/0000-0003-1995-6531>, @patilindrajeets)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

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Package mongolite updated to version 2.3.0 with previous version 2.2.1 dated 2020-11-21

Title: Fast and Simple 'MongoDB' Client for R
Description: High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'. Includes support for aggregation, indexing, map-reduce, streaming, encryption, enterprise authentication, and GridFS. The online user manual provides an overview of the available methods in the package: <https://jeroen.github.io/mongolite/>.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>), MongoDB, Inc [cph] (Bundled mongo-c-driver, see AUTHORS file)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package ggstatsplot updated to version 0.6.8 with previous version 0.6.6 dated 2020-12-03

Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates graphics with details from statistical tests included in the plots themselves. It provides an easier API to generate information-rich plots for statistical analysis of continuous (violin plots, scatterplots, histograms, dot plots, dot-and-whisker plots) or categorical (pie and bar charts) data. Currently, it supports the most common types of statistical tests: parametric, nonparametric, robust, and Bayesian versions of t-test/ANOVA, correlation analyses, contingency table analysis, meta-analysis, and regression analyses.
Author: Indrajeet Patil [cre, aut, cph] (<https://orcid.org/0000-0003-1995-6531>, @patilindrajeets)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

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More information about ggstatsplot at CRAN
Permanent link

Package BOIN updated to version 2.7.2 with previous version 2.7.1 dated 2020-11-19

Title: Bayesian Optimal INterval (BOIN) Design for Single-Agent and Drug- Combination Phase I Clinical Trials
Description: The Bayesian optimal interval (BOIN) design is a novel phase I clinical trial design for finding the maximum tolerated dose (MTD). It can be used to design both single-agent and drug-combination trials. The BOIN design is motivated by the top priority and concern of clinicians when testing a new drug, which is to effectively treat patients and minimize the chance of exposing them to subtherapeutic or overly toxic doses. The prominent advantage of the BOIN design is that it achieves simplicity and superior performance at the same time. The BOIN design is algorithm-based and can be implemented in a simple way similar to the traditional 3+3 design. The BOIN design yields an average performance that is comparable to that of the continual reassessment method (CRM, one of the best model-based designs) in terms of selecting the MTD, but has a substantially lower risk of assigning patients to subtherapeutic or overly toxic doses. For tutorial, please check Yan et al. (2020) <doi:10.18637/jss.v094.i13>.
Author: Ying Yuan and Suyu Liu
Maintainer: Ying Yuan <yyuan@mdanderson.org>

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More information about BOIN at CRAN
Permanent link

Package VIM updated to version 6.1.0 with previous version 6.0.0 dated 2020-05-08

Title: Visualization and Imputation of Missing Values
Description: New tools for the visualization of missing and/or imputed values are introduced, which can be used for exploring the data and the structure of the missing and/or imputed values. Depending on this structure of the missing values, the corresponding methods may help to identify the mechanism generating the missing values and allows to explore the data including missing values. In addition, the quality of imputation can be visually explored using various univariate, bivariate, multiple and multivariate plot methods. A graphical user interface available in the separate package VIMGUI allows an easy handling of the implemented plot methods.
Author: Matthias Templ [aut, cre], Alexander Kowarik [aut] (<https://orcid.org/0000-0001-8598-4130>), Andreas Alfons [aut], Gregor de Cillia [aut], Bernd Prantner [ctb], Wolfgang Rannetbauer [aut]
Maintainer: Matthias Templ <matthias.templ@gmail.com>

Diff between VIM versions 6.0.0 dated 2020-05-08 and 6.1.0 dated 2021-01-19

 DESCRIPTION                         |   16 
 MD5                                 |   94 -
 NAMESPACE                           |    1 
 NEWS.md                             |   16 
 R/barMiss.R                         |   24 
 R/histMiss.R                        |   22 
 R/hotdeck.R                         |  263 ++--
 R/kNN.R                             |    4 
 R/matrixplot.R                      |    3 
 R/regressionImp.R                   |    4 
 R/scattMiss.R                       |   24 
 R/tableMiss.R                       |only
 build/vignette.rds                  |binary
 data/SBS5242.rda                    |binary
 data/bcancer.rda                    |binary
 data/brittleness.rda                |binary
 data/chorizonDL.rda                 |binary
 data/colic.rda                      |binary
 data/diabetes.rda                   |binary
 data/food.rda                       |binary
 data/kola.background.rda            |binary
 data/pulplignin.rda                 |binary
 data/sleep.rda                      |binary
 data/tao.rda                        |binary
 data/testdata.RData                 |binary
 data/toydataMiss.rda                |binary
 data/wine.rda                       |binary
 inst/doc/VIM.Rmd                    |   18 
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 inst/doc/modelImp.R                 |   53 
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 man/colSequence.Rd                  |    2 
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 man/matchImpute.Rd                  |    2 
 man/rugNA.Rd                        |    2 
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 tests/testthat/Rplots.pdf           |only
 tests/testthat/test_hotdeck.R       |   27 
 tests/testthat/test_kNN.R           |   12 
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 vignettes/VIM.Rmd                   |   18 
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 vignettes/donorImp.Rmd              |only
 vignettes/irmi.Rmd                  |only
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 56 files changed, 3030 insertions(+), 688 deletions(-)

More information about VIM at CRAN
Permanent link

Package UCSCXenaTools updated to version 1.4.0 with previous version 1.3.6 dated 2020-11-23

Title: Download and Explore Datasets from UCSC Xena Data Hubs
Description: Download and explore datasets from UCSC Xena data hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>), Xue-Song Liu [aut] (<https://orcid.org/0000-0002-7736-0077>), Martin Morgan [ctb], Christine Stawitz [rev] (Christine reviewed the package for ropensci, see <https://github.com/ropensci/software-review/issues/315>), Carl Ganz [rev] (Carl reviewed the package for ropensci, see <https://github.com/ropensci/software-review/issues/315>)
Maintainer: Shixiang Wang <w_shixiang@163.com>

Diff between UCSCXenaTools versions 1.3.6 dated 2020-11-23 and 1.4.0 dated 2021-01-19

 DESCRIPTION                 |    6 -
 MD5                         |   20 +--
 NEWS.md                     |    4 
 R/XenaHub-class.R           |   23 ++++
 R/XenaQuery.R               |   11 +-
 R/fetch.R                   |    3 
 README.md                   |   79 +++++++++------
 inst/doc/USCSXenaTools.R    |    6 +
 inst/doc/USCSXenaTools.Rmd  |   34 ++++--
 inst/doc/USCSXenaTools.html |  227 ++++++++++++++++----------------------------
 vignettes/USCSXenaTools.Rmd |   34 ++++--
 11 files changed, 235 insertions(+), 212 deletions(-)

More information about UCSCXenaTools at CRAN
Permanent link


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