Tue, 27 Sep 2022

Package bootCT updated to version 1.1.1 with previous version 1.1 dated 2022-07-18

Title: Bootstrapping the ARDL Tests for Cointegration
Description: The bootstrap ARDL tests for cointegration is the main functionality of this package. It also acts as a wrapper of the most commond ARDL testing procedures for cointegration: the bound tests of Pesaran, Shin and Smith (PSS; 2001 - <doi:10.1002/jae.616>) and the asymptotic test on the independent variables of Sam, McNown and Goh (SMG: 2019 - <doi:10.1016/j.econmod.2018.11.001>). Bootstrap and bound tests are performed under both the conditional and unconditional ARDL models.
Author: Gianmarco Vacca, Stefano Bertelli
Maintainer: Gianmarco Vacca <gianmarco.vacca@unicatt.it>

Diff between bootCT versions 1.1 dated 2022-07-18 and 1.1.1 dated 2022-09-27

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Package tinytex updated to version 0.42 with previous version 0.41 dated 2022-08-16

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] , RStudio, PBC [cph], Christophe Dervieux [ctb] , Devon Ryan [ctb] , Ethan Heinzen [ctb], Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

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More information about tinytex at CRAN
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Package RPresto updated to version 1.4.0 with previous version 1.3.7 dated 2021-09-04

Title: DBI Connector to Presto
Description: Implements a 'DBI' compliant interface to Presto. Presto is an open source distributed SQL query engine for running interactive analytic queries against data sources of all sizes ranging from gigabytes to petabytes: <https://prestodb.io/>.
Author: Onur Ismail Filiz [aut], Sergey Goder [aut], Jarod G.R. Meng [aut, cre], Thomas J. Leeper [ctb], John Myles White [ctb]
Maintainer: Jarod G.R. Meng <jarodm@fb.com>

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More information about RPresto at CRAN
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Package rocbc updated to version 0.1.1 with previous version 0.1.0 dated 2022-09-20

Title: Statistical Inference for Box-Cox Based Receiver Operating Characteristic Curves
Description: Generation of Box-Cox based ROC curves and several aspects of inferences and hypothesis testing. Can be used when inferences for one biomarker (Bantis LE, Nakas CT, Reiser B. (2018) <doi:10.1002/bimj.201700107>) are of interest or when comparisons of two correlated biomarkers (Bantis LE, Nakas CT, Reiser B. (2021) <doi:10.1002/bimj.202000128>) are of interest. Provides inferences and comparisons around the AUC, the Youden index, the sensitivity at a given specificity level (and vice versa), the optimal operating point of the ROC curve (in the Youden sense), and the Youden based cutoff.
Author: Leonidas Bantis [aut], Benjamin Brewer [cre, ctb], Christos Nakas [ctb], Benjamin Reiser [ctb]
Maintainer: Benjamin Brewer <tennisbenj@gmail.com>

Diff between rocbc versions 0.1.0 dated 2022-09-20 and 0.1.1 dated 2022-09-27

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Package migraph updated to version 0.12.0 with previous version 0.11.3 dated 2022-09-13

Title: Tools for Multimodal Network Analysis
Description: A set of tools for analysing multimodal networks. All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects, and on one-mode, two-mode (bipartite), and sometimes three-mode networks. It includes functions for measuring centrality, centralization, cohesion, closure, and constraint, as well as for network block-modelling and regression. The package is released as a complement to 'Multimodal Political Networks' (2021, ISBN:9781108985000), and includes various datasets used in the book in addition to other network data.
Author: James Hollway [cre, aut, ctb] , Jael Tan [ctb] , Bernhard Bieri [ctb] , Henrique Sposito [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>

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Package iheiddown updated to version 0.9.5 with previous version 0.9.3 dated 2022-05-13

Title: For Writing Geneva Graduate Institute Documents
Description: A set of tools for writing documents according to Geneva Graduate Institute conventions and regulations. The most common use is for writing and compiling theses or thesis chapters, as drafts or for examination with correct preamble formatting. However, the package also offers users to create HTML presentation slides with 'xaringan', complete problem sets, format posters, and, for course instructors, prepare a syllabus. The package includes additional functions for institutional color palettes, an institutional 'ggplot' theme, a function for counting manuscript words, and a bibliographical analysis toolkit.
Author: James Hollway [aut, cre, cph] , Bernhard Bieri [ctb] , Henrique Sposito [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>

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Package IDSL.MXP updated to version 1.6 with previous version 1.5 dated 2022-07-07

Title: Parser for mzML, mzXML, and netCDF Files (Mass Spectrometry Data)
Description: A tiny parser to extract mass spectra data and metadata table of MS acquisition properties from mzML, mzXML and netCDF mass spectrometry files.
Author: Sadjad Fakouri-Baygi [cre, aut] , Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>

Diff between IDSL.MXP versions 1.5 dated 2022-07-07 and 1.6 dated 2022-09-27

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Package IDSL.IPA updated to version 2.3 with previous version 2.2 dated 2022-09-09

Title: Intrinsic Peak Analysis (IPA) for HRMS Data
Description: A sophisticated pipeline for processing LC/HRMS data to extract signals of organic compounds. The package performs isotope pairing, peak detection, alignment, RT correction, gap filling, peak annotation and visualization of extracted ion chromatograms (EIC) and total ion chromatograms (TIC).
Author: Sadjad Fakouri-Baygi [cre, aut] , Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>

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Package EFAtools updated to version 0.4.2 with previous version 0.4.1 dated 2022-04-24

Title: Fast and Flexible Implementations of Exploratory Factor Analysis Tools
Description: Provides functions to perform exploratory factor analysis (EFA) procedures and compare their solutions. The goal is to provide state-of-the-art factor retention methods and a high degree of flexibility in the EFA procedures. This way, for example, implementations from R 'psych' and 'SPSS' can be compared. Moreover, functions for Schmid-Leiman transformation and the computation of omegas are provided. To speed up the analyses, some of the iterative procedures, like principal axis factoring (PAF), are implemented in C++.
Author: Markus Steiner [aut, cre], Silvia Grieder [aut], William Revelle [ctb], Max Auerswald [ctb], Morten Moshagen [ctb], John Ruscio [ctb], Brendan Roche [ctb], Urbano Lorenzo-Seva [ctb], David Navarro-Gonzalez [ctb]
Maintainer: Markus Steiner <markus.d.steiner@gmail.com>

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Package shinymanager updated to version 1.0.410 with previous version 1.0.400 dated 2021-06-16

Title: Authentication Management for 'Shiny' Applications
Description: Simple and secure authentification mechanism for single 'Shiny' applications. Credentials are stored in an encrypted 'SQLite' database. Source code of main application is protected until authentication is successful.
Author: Benoit Thieurmel [aut, cre], Victor Perrier [aut]
Maintainer: Benoit Thieurmel <bthieurmel@gmail.com>

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Package rsprite2 updated to version 0.2.0 with previous version 0.1.0 dated 2021-09-22

Title: Identify Distributions that Match Reported Sample Parameters (SPRITE)
Description: The SPRITE algorithm creates possible distributions of discrete responses based on reported sample parameters, such as mean, standard deviation and range (Heathers et al., 2018, <doi:10.7287/peerj.preprints.26968v1>). This package implements it, drawing heavily on the code for Nick Brown's 'rSPRITE' Shiny app <https://shiny.ieis.tue.nl/sprite/>. In addition, it supports the modeling of distributions based on multi-item (Likert-type) scales and the use of restrictions on the frequency of particular responses.
Author: Lukas Wallrich [aut, cre] , Aurelien Allard [ctb]
Maintainer: Lukas Wallrich <lukas.wallrich@gmail.com>

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Package chameleon updated to version 0.2-3 with previous version 0.2-1 dated 2022-07-13

Title: Automatic Colors for Multi-Dimensional Data
Description: Assign distinct colors to arbitrary multi-dimensional data, considering its structure.
Author: Oren Ben-Kiki [aut, cre], Weizmann Institute of Science [cph]
Maintainer: Oren Ben-Kiki <oren@ben-kiki.org>

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Mon, 26 Sep 2022

Package rsurveycto updated to version 0.1.0 with previous version 0.0.5 dated 2022-09-08

Title: Interact with Data on 'SurveyCTO'
Description: 'SurveyCTO' is a platform for mobile data collection in offline settings. The 'rsurveycto' R package uses the 'SurveyCTO' REST API <https://docs.surveycto.com/05-exporting-and-publishing-data/05-api-access/01.api-access.html> to read datasets and forms from a 'SurveyCTO' server into R as 'data.table's and to download file attachments. The package also has limited support to write datasets to a server.
Author: Jake Hughey [aut, cre], Robert On [aut]
Maintainer: Jake Hughey <jakejhughey@gmail.com>

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Package roger updated to version 1.1-0 with previous version 1.0-0 dated 2022-08-25

Title: Automated Grading of R Scripts
Description: Tools for grading the coding style and documentation of R scripts. This is the R component of Roger the Omni Grader, an automated grading system for computer programming projects based on Unix shell scripts; see <https://gitlab.com/roger-project>. The package also provides an R interface to the shell scripts. Inspired by the lintr package.
Author: Vincent Goulet [aut, cre], Samuel Frechette [aut], Jean-Christophe Langlois [aut], Jim Hester [ctb]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>

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Package ggcorrplot updated to version 0.1.4 with previous version 0.1.3 dated 2019-05-19

Title: Visualization of a Correlation Matrix using 'ggplot2'
Description: The 'ggcorrplot' package can be used to visualize easily a correlation matrix using 'ggplot2'. It provides a solution for reordering the correlation matrix and displays the significance level on the plot. It also includes a function for computing a matrix of correlation p-values.
Author: Alboukadel Kassambara [aut, cre], Indrajeet Patil [ctb]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>

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Package relSim updated to version 0.3-4 with previous version 0.3-3 dated 2022-09-15

Title: Relative Simulator
Description: A set of tools to explore the behaviour statistics used for forensic DNA interpretation when close relatives are involved. The package also offers some useful tools for exploring other forensic DNA situations.
Author: James M. Curran
Maintainer: James M. Curran <j.curran@auckland.ac.nz>

Diff between relSim versions 0.3-3 dated 2022-09-15 and 0.3-4 dated 2022-09-26

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Package pagedown updated to version 0.19 with previous version 0.18 dated 2022-04-26

Title: Paginate the HTML Output of R Markdown with CSS for Print
Description: Use the paged media properties in CSS and the JavaScript library 'paged.js' to split the content of an HTML document into discrete pages. Each page can have its page size, page numbers, margin boxes, and running headers, etc. Applications of this package include books, letters, reports, papers, business cards, resumes, and posters.
Author: Yihui Xie [aut, cre] , Romain Lesur [aut, cph] , Brent Thorne [aut] , Xianying Tan [aut] , Christophe Dervieux [ctb] , Atsushi Yasumoto [ctb] , RStudio, PBC [cph], Adam Hyde [ctb] , Min-Zhong Lu [ctb] , Zulko [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

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Package flextable updated to version 0.8.2 with previous version 0.8.1 dated 2022-09-19

Title: Functions for Tabular Reporting
Description: Create pretty tables for 'HTML', 'PDF', 'Microsoft Word', 'Microsoft PowerPoint' documents from 'R Markdown' and as 'Grid Graphics' objects. Functions are provided to let users create tables, modify and format their content. It also extends package 'officer' that does not contain any feature for customized tabular reporting.
Author: David Gohel [aut, cre], Clementine Jager [ctb], Panagiotis Skintzos [aut], Quentin Fazilleau [ctb], Maxim Nazarov [ctb] , Titouan Robert [ctb], Michael Barrowman [ctb] , Atsushi Yasumoto [ctb] , Paul Julian [ctb] , Sean Browning [ctb] , Remi Theriaul [...truncated...]
Maintainer: David Gohel <david.gohel@ardata.fr>

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Package extrafrail updated to version 1.2 with previous version 1.1 dated 2022-08-06

Title: Estimation and Additional Tools for Alternative Shared Frailty Models
Description: Provide estimation and data generation tools for some new multivariate frailty models. This version includes the gamma, inverse Gaussian and weighted Lindley as the distribution for the frailty terms. For the basal model, it is considered a parametric approach based on the Weibull distribution and a semiparametric approach. For details, see Gallardo and Bourguignon (2022) <arXiv:2206.12973>.
Author: Diego Gallardo [aut, cre], Marcelo Bourguignon [aut]
Maintainer: Diego Gallardo <diego.gallardo@uda.cl>

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Package netrankr updated to version 1.2.0 with previous version 1.1.1 dated 2021-12-21

Title: Analyzing Partial Rankings in Networks
Description: Implements methods for centrality related analyses of networks. While the package includes the possibility to build more than 20 indices, its main focus lies on index-free assessment of centrality via partial rankings obtained by neighborhood-inclusion or positional dominance. These partial rankings can be analyzed with different methods, including probabilistic methods like computing expected node ranks and relative rank probabilities (how likely is it that a node is more central than another?). The methodology is described in depth in the vignettes and in Schoch (2018) <doi:10.1016/j.socnet.2017.12.003>.
Author: David Schoch [aut, cre] , Julian Mueller [ctb]
Maintainer: David Schoch <david@schochastics.net>

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Package dttr2 updated to version 0.4.2 with previous version 0.4.1 dated 2022-08-26

Title: Manipulate Date, POSIXct and hms Vectors
Description: Manipulates date ('Date'), date time ('POSIXct') and time ('hms') vectors. Date/times are considered discrete and are floored whenever encountered. Times are wrapped and time zones are maintained unless explicitly altered by the user.
Author: Joe Thorley [aut] , Ayla Pearson [aut, cre] , Poisson Consulting [cph, fnd]
Maintainer: Ayla Pearson <ayla@poissonconsulting.ca>

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Package RCALI updated to version 0.3.4 with previous version 0.3.3 dated 2022-08-12

Title: Calculation of the Integrated Flow of Particles Between Polygons
Description: Calculate the flow of particles between polygons by two integration methods: integration by a cubature method and integration on a grid of points. Annie Bouvier, Kien Kieu, Kasia Adamczyk and Herve Monod (2009) <doi:10.1016/j.envsoft.2008.11.006>.
Author: Annie Bouvier [aut, cph], Kien Kieu [aut, cph], Kasia Adamczyk [aut, cph], Herve Monod [aut, cph], Jean-Francois Rey [cre]
Maintainer: Jean-Francois Rey <jean-francois.rey@inrae.fr>

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Package multidplyr updated to version 0.1.2 with previous version 0.1.1 dated 2021-12-01

Title: A Multi-Process 'dplyr' Backend
Description: Partition a data frame across multiple worker processes to provide simple multicore parallelism.
Author: Hadley Wickham [aut, cre], RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package eatATA updated to version 1.1.0 with previous version 1.0.0 dated 2021-07-06

Title: Create Constraints for Small Test Assembly Problems
Description: Provides simple functions to create constraints for small test assembly problems (e.g. van der Linden (2005, ISBN: 978-0-387-29054-6)) using sparse matrices. Currently, 'GLPK', 'lpSolve', 'Symphony', and 'Gurobi' are supported as solvers. The 'gurobi' package is not available from any mainstream repository; see <https://www.gurobi.com/downloads/>.
Author: Benjamin Becker [aut, cre], Dries Debeer [aut]
Maintainer: Benjamin Becker <b.becker@iqb.hu-berlin.de>

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Package climatrends updated to version 0.4 with previous version 0.2 dated 2022-02-24

Title: Climate Variability Indices for Ecological Modelling
Description: Supports analysis of trends in climate change, ecological and crop modelling.
Author: Kaue de Sousa [aut, cre] , Jacob van Etten [ctb, ths] , Svein O. Solberg [ctb, ths]
Maintainer: Kaue de Sousa <desousa.kaue@gmail.com>

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Package basemaps updated to version 0.0.5 with previous version 0.0.4 dated 2022-09-08

Title: Accessing Spatial Basemaps in R
Description: A lightweight package to access spatial basemaps from open sources such as 'OpenStreetMap', 'Carto', 'Mapbox' and others in R.
Author: Jakob Schwalb-Willmann [aut, cre]
Maintainer: Jakob Schwalb-Willmann <dev@schwalb-willmann.de>

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Package webshot updated to version 0.5.4 with previous version 0.5.3 dated 2022-04-14

Title: Take Screenshots of Web Pages
Description: Takes screenshots of web pages, including Shiny applications and R Markdown documents.
Author: Winston Chang [aut, cre], Yihui Xie [ctb], Francois Guillem [ctb], Barret Schloerke [ctb], Nicolas Perriault [ctb]
Maintainer: Winston Chang <winston@rstudio.com>

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Package targets updated to version 0.13.5 with previous version 0.13.4 dated 2022-09-15

Title: Dynamic Function-Oriented 'Make'-Like Declarative Workflows
Description: As a pipeline toolkit for Statistics and data science in R, the 'targets' package brings together function-oriented programming and 'Make'-like declarative workflows. It analyzes the dependency relationships among the tasks of a workflow, skips steps that are already up to date, runs the necessary computation with optional parallel workers, abstracts files as R objects, and provides tangible evidence that the results match the underlying code and data. The methodology in this package borrows from GNU 'Make' (2015, ISBN:978-9881443519) and 'drake' (2018, <doi:10.21105/joss.00550>).
Author: William Michael Landau [aut, cre] , Matthew T. Warkentin [ctb], Mark Edmondson [ctb] , Samantha Oliver [rev] , Tristan Mahr [rev] , Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>

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Package survSpearman updated to version 1.0.1 with previous version 1.0.0 dated 2021-01-29

Title: Nonparametric Spearman's Correlation for Survival Data
Description: Nonparametric estimation of Spearman's rank correlation with bivariate survival (right-censored) data as described in Eden, S.K., Li, C., Shepherd B.E. (2021), Nonparametric Estimation of Spearman's Rank Correlation with Bivariate Survival Data, Biometrics (under revision). The package also provides functions that visualize bivariate survival data and bivariate probability mass function.
Author: Svetlana Eden [aut, cre], Chun Li [aut, anl], Bryan Shepherd [aut, anl]
Maintainer: Svetlana Eden <svetlana.k.eden.1@vumc.org>

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Package SIHR updated to version 1.1.0 with previous version 1.0.1 dated 2022-08-10

Title: Statistical Inference in High Dimensional Regression
Description: Inference procedures in the high-dimensional setting for (1) linear functionals in generalized linear regression ('Cai et al.' (2019) <arXiv:1904.12891>, 'Guo et al.' (2020) <arXiv:2012.07133>, 'Cai et al.' (2021)), (2) individual treatment effects in generalized linear regression, (3) quadratic functionals in generalized linear regression ('Guo et al.' (2019) <arXiv:1909.01503>).
Author: Prabrisha Rakshit, Zhenyu Wang, Tony Cai, Zijian Guo
Maintainer: Zijian Guo <zijguo@stat.rutgers.edu>

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Package shinytest2 updated to version 0.2.0 with previous version 0.1.1 dated 2022-09-06

Title: Testing for Shiny Applications
Description: Automated unit testing of Shiny applications through a headless 'Chromium' browser.
Author: Barret Schloerke [cre, aut] , RStudio [cph, fnd], Winston Chang [ctb] , Gabor Csardi [ctb] , Hadley Wickham [ctb] , Mango Solutions [cph, ccp]
Maintainer: Barret Schloerke <barret@rstudio.com>

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Package reactlog updated to version 1.1.1 with previous version 1.1.0 dated 2020-09-12

Title: Reactivity Visualizer for 'shiny'
Description: Building interactive web applications with R is incredibly easy with 'shiny'. Behind the scenes, 'shiny' builds a reactive graph that can quickly become intertwined and difficult to debug. 'reactlog' (Schloerke 2019) <doi:10.5281/zenodo.2591517> provides a visual insight into that black box of 'shiny' reactivity by constructing a directed dependency graph of the application's reactive state at any time point in a reactive recording.
Author: Barret Schloerke [aut, cre] , Joe Cheng [ctb], RStudio [cph, fnd]
Maintainer: Barret Schloerke <barret@rstudio.com>

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Package micromapST updated to version 2.0.1 with previous version 2.0.0 dated 2022-08-20

Title: Linked Micromap Plots for U. S. and Other Geographic Areas
Description: Provides the users with the ability to quickly create linked micromap plots for a collection of geographic areas. Linked micromap plots are visualizations of geo-referenced data that link statistical graphics to an organized series of small maps or graphic images. The Help description contains examples of how to use the 'micromapST' function. Contained in this package are border group datasets to support creating linked micromap plots for the 50 U.S. states and District of Columbia (51 areas), the U. S. 20 Seer Registries, the 105 counties in the state of Kansas, the 62 counties of New York, the 24 counties of Maryland, the 29 counties of Utah, the 32 administrative areas in China, the 218 administrative areas in the UK and Ireland (for testing only), the 25 districts in the city of Seoul South Korea, and the 52 counties on the Africa continent. A border group dataset contains the boundaries related to the data level areas, a second layer boundaries, a top or third layer boundary, a pa [...truncated...]
Author: Jim Pearson [aut, cre, cph], Dan Carr [aut, cph], Linda Pickle [ctb, cph]
Maintainer: Jim Pearson <jbpearson353@gmail.com>

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Package rdecision updated to version 1.1.3 with previous version 1.1.2 dated 2022-09-07

Title: Decision Analytic Modelling in Health Economics
Description: Classes and functions for modelling health care interventions using decision trees and semi-Markov models. Mechanisms are provided for associating an uncertainty distribution with each source variable and for ensuring transparency of the mathematical relationships between variables. The package terminology follows Briggs "Decision Modelling for Health Economic Evaluation" (2006, ISBN:978-0-19-852662-9).
Author: Andrew Sims [aut, cre] , Kim Fairbairn [aut] , Paola Cognigni [aut]
Maintainer: Andrew Sims <andrew.sims@newcastle.ac.uk>

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Package MCM updated to version 0.1.7 with previous version 0.1.6 dated 2022-09-25

Title: Estimating and Testing Intergenerational Social Mobility Effect
Description: Estimate and test inter-generational social mobility effect on an outcome with cross-sectional or longitudinal data.
Author: Jiahui Xu [aut, cre], Liying Luo [aut]
Maintainer: Jiahui Xu <jpx5053@psu.edu>

Diff between MCM versions 0.1.6 dated 2022-09-25 and 0.1.7 dated 2022-09-26

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Package fso updated to version 2.1-2 with previous version 2.1-1 dated 2018-06-01

Title: Fuzzy Set Ordination
Description: Fuzzy set ordination is a multivariate analysis used in ecology to relate the composition of samples to possible explanatory variables. While differing in theory and method, in practice, the use is similar to 'constrained ordination.' The package contains plotting and summary functions as well as the analyses.
Author: David W. Roberts <droberts@montana.edu>
Maintainer: David W. Roberts <droberts@montana.edu>

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Package comorbidity updated to version 1.0.5 with previous version 1.0.3 dated 2022-07-12

Title: Computing Comorbidity Scores
Description: Computing comorbidity indices and scores such as the weighted Charlson score (Charlson, 1987 <doi:10.1016/0021-9681(87)90171-8>) and the Elixhauser comorbidity score (Elixhauser, 1998 <doi:10.1097/00005650-199801000-00004>) using ICD-9-CM or ICD-10 codes (Quan, 2005 <doi:10.1097/01.mlr.0000182534.19832.83>). Australian and Swedish modifications of the Charlson Comorbidity Index are available as well (Sundararajan, 2004 <doi:10.1016/j.jclinepi.2004.03.012> and Ludvigsson, 2021 <doi:10.2147/CLEP.S282475>).
Author: Alessandro Gasparini [aut, cre] , Hojjat Salmasian [ctb] , Jonathan Williman [ctb] , Sing Yi Chia [ctb] , Edmund Teo [ctb]
Maintainer: Alessandro Gasparini <alessandro@ellessenne.xyz>

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Package shorts updated to version 2.1.0 with previous version 2.0.0 dated 2022-07-07

Title: Short Sprints
Description: Create short sprint (<6sec) profiles using the split times or the radar gun data. Mono-exponential equation is used to estimate maximal sprinting speed (MSS), relative acceleration (TAU), and other parameters such us maximal acceleration (MAC) and maximal relative power (PMAX). These parameters can be used to predict kinematic and kinetics variables and to compare individuals. The modeling method utilized in this package is based on the works of Chelly SM, Denis C. (2001) <doi: 10.1097/00005768-200102000-00024>, Clark KP, Rieger RH, Bruno RF, Stearne DJ. (2017) <doi: 10.1519/JSC.0000000000002081>, Furusawa K, Hill AV, Parkinson JL (1927) <doi: 10.1098/rspb.1927.0035>, Greene PR. (1986) <doi: 10.1016/0025-5564(86)90063-5>, and Samozino P. (2018) <doi: 10.1007/978-3-319-05633-3_11>.
Author: Mladen Jovanović [aut, cre], Jason D. Vescovi [dtc]
Maintainer: Mladen Jovanović <coach.mladen.jovanovic@gmail.com>

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Package colorDF updated to version 0.1.7 with previous version 0.1.5 dated 2022-09-25

Title: Colorful Data Frames in R Terminal
Description: Colorful Data Frames in the terminal. The new class does change the behaviour of any of the objects, but adds a style definition and a print method. Using ANSI escape codes, it colors the terminal output of data frames. Some column types (such as p-values and identifiers) are automatically recognized.
Author: January Weiner [aut, cre]
Maintainer: January Weiner <january.weiner@gmail.com>

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Package ACEt updated to version 1.8.2 with previous version 1.8.1 dated 2020-10-21

Title: Estimating Dynamic Heritability and Twin Model Comparison
Description: Twin models that are able to estimate the dynamic behaviour of the variance components in the classical twin models with respect to age using B-splines and P-splines.
Author: Liang He
Maintainer: Liang He <lianghe@health.sdu.dk>

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Package rgl updated to version 0.110.2 with previous version 0.109.6 dated 2022-07-08

Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Duncan Murdoch [aut, cre], Daniel Adler [aut], Oleg Nenadic [ctb], Simon Urbanek [ctb], Ming Chen [ctb], Albrecht Gebhardt [ctb], Ben Bolker [ctb], Gabor Csardi [ctb], Adam Strzelecki [ctb], Alexander Senger [ctb], The R Core Team [ctb, cph], Dirk Ed [...truncated...]
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>

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Package dsfa updated to version 1.0.0 with previous version 0.0.3 dated 2022-09-07

Title: Distributional Stochastic Frontier Analysis
Description: Framework to fit distributional stochastic frontier models. Casts the stochastic frontier model into the flexible framework of distributional regression or otherwise known as General Additive Models of Location, Scale and Shape (GAMLSS). Allows for linear, non-linear, random and spatial effects on all the parameters of the distribution of the output, e.g. effects on the production or cost function, heterogeneity of the noise and inefficiency. Available distributions are the normal-halfnormal and normal-exponential distribution. Estimation via the fast and reliable routines of the 'mgcv' package. For more details see Schmidt R, Kneib T (2022) <doi:10.48550/arXiv.2208.10294>.
Author: Rouven Schmidt [aut, cre]
Maintainer: Rouven Schmidt <rouven.schmidt@tu-clausthal.de>

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Package IDSL.UFAx updated to version 1.6 with previous version 1.5 dated 2022-09-09

Title: Exhaustive Chemical Enumeration for United Formula Annotation
Description: A pipeline to annotate a number of peaks from the IDSL.IPA peaklists using an exhaustive chemical enumeration-based approach. This package can perform elemental composition calculations using the following 15 elements : C, B, Br, Cl, K, S, Se, Si, N, H, As, F, I, Na, O, and P.
Author: Sadjad Fakouri-Baygi [cre, aut] , Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>

Diff between IDSL.UFAx versions 1.5 dated 2022-09-09 and 1.6 dated 2022-09-26

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Package ggOceanMaps updated to version 1.3.4 with previous version 1.3.0 dated 2022-09-20

Title: Plot Data on Oceanographic Maps using 'ggplot2'
Description: Allows plotting data on bathymetric maps using 'ggplot2'. Plotting oceanographic spatial data is made as simple as feasible, but also flexible for custom modifications. Data that contain geographic information from anywhere around the globe can be plotted on maps generated by the basemap() or qmap() functions using 'ggplot2' layers separated by the '+' operator. The package uses spatial shapefiles stored in the 'ggOceanMapsData' package, geospatial packages for R to manipulate, and the 'ggspatial' package to help to plot these shapefiles. High-resolution shapefiles for detailed maps are stored on GitHub and downloaded automatically when needed.
Author: Mikko Vihtakari [aut, cre] , Yves Reecht [ctb] , Hadley Wickham [ctb], Simon O'Hanlon [ctb], Roger Bivand [ctb]
Maintainer: Mikko Vihtakari <mikko.vihtakari@hi.no>

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Package calculus updated to version 1.0.0 with previous version 0.3.4 dated 2022-08-20

Title: High Dimensional Numerical and Symbolic Calculus
Description: Efficient C++ optimized functions for numerical and symbolic calculus as described in Guidotti (2022) <doi:10.18637/jss.v104.i05>. It includes basic arithmetic, tensor calculus, Einstein summing convention, fast computation of the Levi-Civita symbol and generalized Kronecker delta, Taylor series expansion, multivariate Hermite polynomials, high-order derivatives, ordinary differential equations, differential operators (Gradient, Jacobian, Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, parabolic or user defined by custom scale factors.
Author: Emanuele Guidotti [aut, cre]
Maintainer: Emanuele Guidotti <emanuele.guidotti@unine.ch>

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Package tidytree updated to version 0.4.1 with previous version 0.4.0 dated 2022-08-13

Title: A Tidy Tool for Phylogenetic Tree Data Manipulation
Description: Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.
Author: Guangchuang Yu [aut, cre, cph] , Bradley Jones [ctb], Zebulun Arendsee [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between tidytree versions 0.4.0 dated 2022-08-13 and 0.4.1 dated 2022-09-26

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Package Rogue updated to version 2.1.3 with previous version 2.1.2 dated 2022-08-16

Title: Identify Rogue Taxa in Sets of Phylogenetic Trees
Description: Rogue ("wildcard") taxa are leaves with uncertain phylogenetic position. Their position may vary from tree to tree under inference methods that yield a tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony). The presence of rogue taxa in a tree set can potentially remove all information from a consensus tree. The information content of a consensus tree - a function of its resolution and branch support values - can often be increased by removing rogue taxa. 'Rogue' provides an explicitly information-theoretic approach to rogue detection (Smith 2022) <doi:10.1093/sysbio/syab099>, and an interface to 'RogueNaRok' (Aberer et al. 2013) <doi:10.1093/sysbio/sys078>.
Author: Martin R. Smith [aut, cre, cph] , Andre J. Aberer [aut, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>

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Package mnormt updated to version 2.1.1 with previous version 2.1.0 dated 2022-06-07

Title: The Multivariate Normal and t Distributions, and Their Truncated Versions
Description: Functions are provided for computing the density and the distribution function of d-dimensional normal and "t" random variables, possibly truncated (on one side or two sides), and for generating random vectors sampled from these distributions, except sampling from the truncated "t". Moments of arbitrary order of a multivariate truncated normal are computed, and converted to cumulants up to order 4. Probabilities are computed via non-Monte Carlo methods; different routines are used in the case d=1, d=2, d=3, d>3, if d denotes the dimensionality.
Author: Adelchi Azzalini [aut, cre], Alan Genz [aut] , Alan Miller [ctb] , Michael J. Wichura [ctb] , G. W. Hill [ctb] , Yihong Ge [ctb] .
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>

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Package intensitynet updated to version 1.3.1 with previous version 1.3.0 dated 2022-05-16

Title: Intensity Analysis of Spatial Point Patterns on Complex Networks
Description: Tools to analyze point patterns in space occurring over planar network structures derived from graph-related intensity measures for undirected, directed, and mixed networks. This package is based on the following research: Eckardt and Mateu (2018) <doi:10.1080/10618600.2017.1391695>. Eckardt and Mateu (2021) <doi:10.1007/s11749-020-00720-4>.
Author: Pol Llagostera [aut, cre], Matthias Eckardt [aut]
Maintainer: Pol Llagostera <pol.llagostera@udl.cat>

Diff between intensitynet versions 1.3.0 dated 2022-05-16 and 1.3.1 dated 2022-09-26

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Package rcdk updated to version 3.7.0 with previous version 3.6.0 dated 2021-10-17

Title: Interface to the 'CDK' Libraries
Description: Allows the user to access functionality in the 'CDK', a Java framework for chemoinformatics. This allows the user to load molecules, evaluate fingerprints, calculate molecular descriptors and so on. In addition, the 'CDK' API allows the user to view structures in 2D.
Author: Rajarshi Guha [aut, cph], Zachary Charlop-Powers [cre], Emma Schymanski [ctb]
Maintainer: Zachary Charlop-Powers <zach.charlop.powers@gmail.com>

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Package hmm.discnp updated to version 3.0-9 with previous version 3.0-7 dated 2022-02-08

Title: Hidden Markov Models with Discrete Non-Parametric Observation Distributions
Description: Fits hidden Markov models with discrete non-parametric observation distributions to data sets. The observations may be univariate or bivariate. Simulates data from such models. Finds most probable underlying hidden states, the most probable sequences of such states, and the log likelihood of a collection of observations given the parameters of the model. Auxiliary predictors are accommodated in the univariate setting.
Author: Rolf Turner
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>

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Package HistDAWass updated to version 1.0.7 with previous version 1.0.6 dated 2021-06-22

Title: Histogram-Valued Data Analysis
Description: In the framework of Symbolic Data Analysis, a relatively new approach to the statistical analysis of multi-valued data, we consider histogram-valued data, i.e., data described by univariate histograms. The methods and the basic statistics for histogram-valued data are mainly based on the L2 Wasserstein metric between distributions, i.e., the Euclidean metric between quantile functions. The package contains unsupervised classification techniques, least square regression and tools for histogram-valued data and for histogram time series. An introducing paper is Irpino A. Verde R. (2015) <doi: 10.1007/s11634-014-0176-4>.
Author: Antonio Irpino [aut, cre]
Maintainer: Antonio Irpino <antonio.irpino@unicampania.it>

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Package Bergm updated to version 5.0.5 with previous version 5.0.4 dated 2022-08-15

Title: Bayesian Exponential Random Graph Models
Description: Bayesian analysis for exponential random graph models using advanced computational algorithms. More information can be found at: <https://acaimo.github.io/Bergm/>.
Author: Alberto Caimo [aut, cre], Lampros Bouranis [aut], Robert Krause [aut] Nial Friel [ctb]
Maintainer: Alberto Caimo <alberto.caimo@tudublin.ie>

Diff between Bergm versions 5.0.4 dated 2022-08-15 and 5.0.5 dated 2022-09-26

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Package mlim updated to version 0.2.0 with previous version 0.0.9 dated 2022-09-07

Title: Multiple Imputation with Automated Machine Learning
Description: Machine learning algorithms have been used for performing single missing data imputation and most recently, multiple imputations. However, this is the first attempt for using automated machine learning algorithms for performing both single and multiple imputation. Automated machine learning is a procedure for fine-tuning the model automatic, performing a random search for a model that results in less error, without overfitting the data. The main idea is to allow the model to set its own parameters for imputing each variable seperately instead of setting fixed predefined parameters to impute all variables of the dataset. Using automated machine learning, the package fine-tunes an Elastic Net (default) or Gradient Boosting, Random Forest, Deep Learning, Extreme Gradient Boosting, or Stacked Ensemble machine learning model (from one or a combination of other supported algorithms) for imputing the missing observations. This procedure has been implemented for the first time by this package [...truncated...]
Author: E. F. Haghish [aut, cre, cph]
Maintainer: E. F. Haghish <haghish@uio.no>

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Package actilifecounts updated to version 1.1.0 with previous version 1.0.0 dated 2022-05-30

Title: Generate Activity Counts from Raw Accelerometer Data
Description: A tool to obtain activity counts, originally a translation of the 'python' package 'agcounts' <https://github.com/actigraph/agcounts>. This tool allows the processing of data from any accelerometer brand, with a more flexible approach to handle different sampling frequencies.
Author: Jairo Hidalgo Migueles
Maintainer: Jairo Hidalgo Migueles <jairo.hidalgo.migueles@gmail.com>

Diff between actilifecounts versions 1.0.0 dated 2022-05-30 and 1.1.0 dated 2022-09-26

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Package workflows updated to version 1.1.0 with previous version 1.0.0 dated 2022-07-05

Title: Modeling Workflows
Description: Managing both a 'parsnip' model and a preprocessor, such as a model formula or recipe from 'recipes', can often be challenging. The goal of 'workflows' is to streamline this process by bundling the model alongside the preprocessor, all within the same object.
Author: Davis Vaughan [aut], Simon Couch [aut, cre] , RStudio [cph, fnd]
Maintainer: Simon Couch <simonpatrickcouch@gmail.com>

Diff between workflows versions 1.0.0 dated 2022-07-05 and 1.1.0 dated 2022-09-26

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Package riskRegression updated to version 2022.09.23 with previous version 2022.09.13 dated 2022-09-17

Title: Risk Regression Models and Prediction Scores for Survival Analysis with Competing Risks
Description: Implementation of the following methods for event history analysis. Risk regression models for survival endpoints also in the presence of competing risks are fitted using binomial regression based on a time sequence of binary event status variables. A formula interface for the Fine-Gray regression model and an interface for the combination of cause-specific Cox regression models. A toolbox for assessing and comparing performance of risk predictions (risk markers and risk prediction models). Prediction performance is measured by the Brier score and the area under the ROC curve for binary possibly time-dependent outcome. Inverse probability of censoring weighting and pseudo values are used to deal with right censored data. Lists of risk markers and lists of risk models are assessed simultaneously. Cross-validation repeatedly splits the data, trains the risk prediction models on one part of each split and then summarizes and compares the performance across splits.
Author: Thomas Alexander Gerds [aut, cre], Johan Sebastian Ohlendorff [aut], Paul Blanche [ctb], Rikke Mortensen [ctb], Marvin Wright [ctb], Nikolaj Tollenaar [ctb], John Muschelli [ctb], Ulla Brasch Mogensen [ctb], Brice Ozenne [aut]
Maintainer: Thomas Alexander Gerds <tag@biostat.ku.dk>

Diff between riskRegression versions 2022.09.13 dated 2022-09-17 and 2022.09.23 dated 2022-09-26

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Package RGBM updated to version 1.0-10 with previous version 1.0-9 dated 2022-08-11

Title: LS-TreeBoost and LAD-TreeBoost for Gene Regulatory Network Reconstruction
Description: Provides an implementation of Regularized LS-TreeBoost & LAD-TreeBoost algorithm for Regulatory Network inference from any type of expression data (Microarray/RNA-seq etc).
Author: Raghvendra Mall [aut, cre], Khalid Kunji [aut], Melissa O'Neill [ctb]
Maintainer: Raghvendra Mall <raghvendra5688@gmail.com>

Diff between RGBM versions 1.0-9 dated 2022-08-11 and 1.0-10 dated 2022-09-26

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Package golem updated to version 0.3.4 with previous version 0.3.3 dated 2022-07-13

Title: A Framework for Robust Shiny Applications
Description: An opinionated framework for building a production-ready 'Shiny' application. This package contains a series of tools for building a robust 'Shiny' application from start to finish.
Author: Colin Fay [cre, aut] , Vincent Guyader [aut] , Sebastien Rochette [aut] , Cervan Girard [aut] , Novica Nakov [ctb], David Granjon [ctb], Arthur Breant [ctb], Antoine Languillaume [ctb], ThinkR [cph]
Maintainer: Colin Fay <contact@colinfay.me>

Diff between golem versions 0.3.3 dated 2022-07-13 and 0.3.4 dated 2022-09-26

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Package ggridges updated to version 0.5.4 with previous version 0.5.3 dated 2021-01-08

Title: Ridgeline Plots in 'ggplot2'
Description: Ridgeline plots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in 'ggplot2'.
Author: Claus O. Wilke [aut, cre]
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>

Diff between ggridges versions 0.5.3 dated 2021-01-08 and 0.5.4 dated 2022-09-26

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Package conos updated to version 1.4.8 with previous version 1.4.7 dated 2022-09-04

Title: Clustering on Network of Samples
Description: Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.
Author: Viktor Petukhov [aut], Nikolas Barkas [aut], Peter Kharchenko [aut], Weiliang Qiu [ctb], Evan Biederstedt [aut, cre]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>

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Sun, 25 Sep 2022

Package leidenAlg updated to version 1.0.4 with previous version 1.0.3 dated 2022-04-11

Title: Implements the Leiden Algorithm via an R Interface
Description: An R interface to the Leiden algorithm, an iterative community detection algorithm on networks. The algorithm is designed to converge to a partition in which all subsets of all communities are locally optimally assigned, yielding communities guaranteed to be connected. The implementation proves to be fast, scales well, and can be run on graphs of millions of nodes (as long as they can fit in memory). The original implementation was constructed as a python interface "leidenalg" found here: <https://github.com/vtraag/leidenalg>. The algorithm was originally described in Traag, V.A., Waltman, L. & van Eck, N.J. "From Louvain to Leiden: guaranteeing well-connected communities". Sci Rep 9, 5233 (2019) <doi:10.1038/s41598-019-41695-z>.
Author: Peter Kharchenko [aut], Viktor Petukhov [aut], V.A. Traag [ctb], Gabor Csardi [ctb], Tamas Nepusz [ctb], Minh Van Nguyen [ctb], Evan Biederstedt [cre, aut]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>

Diff between leidenAlg versions 1.0.3 dated 2022-04-11 and 1.0.4 dated 2022-09-25

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Package MCM updated to version 0.1.6 with previous version 0.1.5 dated 2022-01-04

Title: Estimating and Testing Intergenerational Social Mobility Effect
Description: Estimate and test inter-generational social mobility effect on an outcome with cross-sectional or longitudinal data.
Author: Jiahui Xu [aut, cre], Liying Luo [aut]
Maintainer: Jiahui Xu <jpx5053@psu.edu>

Diff between MCM versions 0.1.5 dated 2022-01-04 and 0.1.6 dated 2022-09-25

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Package Exact updated to version 3.2 with previous version 3.1 dated 2021-11-26

Title: Unconditional Exact Test
Description: Performs unconditional exact tests and power calculations for 2x2 contingency tables. For comparing two independent proportions, performs Barnard's test (1945) <doi:10.1038/156177a0> using the original CSM test (Barnard, 1947 <doi:10.1093/biomet/34.1-2.123>), using Fisher's p-value referred to as Boschloo's test (1970) <doi:10.1111/j.1467-9574.1970.tb00104.x>, or using a Z-statistic (Suissa and Shuster, 1985, <doi:10.2307/2981892>). For comparing two binary proportions, performs unconditional exact test using McNemar's Z-statistic (Berger and Sidik, 2003, <doi:10.1191/0962280203sm312ra>), using McNemar's conditional p-value, using McNemar's Z-statistic with continuity correction, or using CSM test. Calculates confidence intervals for the difference in proportion. This package interacts with pre-computed data available through the ExactData R package, which is available in a 'drat' repository. Install the ExactData R package from GitHub at <https://pcal [...truncated...]
Author: Peter Calhoun [aut, cre]
Maintainer: Peter Calhoun <calhoun.peter@gmail.com>

Diff between Exact versions 3.1 dated 2021-11-26 and 3.2 dated 2022-09-25

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Package rcdklibs updated to version 2.8 with previous version 2.3 dated 2020-03-08

Title: The CDK Libraries Packaged for R
Description: An R interface to the Chemistry Development Kit, a Java library for chemoinformatics. Given the size of the library itself, this package is not expected to change very frequently. To make use of the CDK within R, it is suggested that you use the 'rcdk' package. Note that it is possible to directly interact with the CDK using 'rJava'. However 'rcdk' exposes functionality in a more idiomatic way. The CDK library itself is released as LGPL and the sources can be obtained from <https://github.com/cdk/cdk>.
Author: Rajarshi Guha [aut], Zachary Charlop-Powers [cre], CDK Project [ctb, cph]
Maintainer: Zachary Charlop-Powers <zach.charlop.powers@gmail.com>

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Package osfr updated to version 0.2.9 with previous version 0.2.8 dated 2020-02-17

Title: Interface to the 'Open Science Framework' ('OSF')
Description: An interface for interacting with 'OSF' (<https://osf.io>). 'osfr' enables you to access open research materials and data, or create and manage your own private or public projects.
Author: Aaron Wolen [aut, cre] , Chris Hartgerink [aut] , Timothy York [ctb] , Ryan Hafen [ctb], Brian Richards [ctb], Courtney Soderberg [ctb] , Carl Boettiger [rev] , Heidi Seibold [rev]
Maintainer: Aaron Wolen <aaron@wolen.com>

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Package graphql updated to version 1.5.1 with previous version 1.5 dated 2018-12-01

Title: A GraphQL Query Parser
Description: Bindings to the 'libgraphqlparser' C++ library. Parses GraphQL syntax and exports the AST in JSON format.
Author: Jeroen Ooms [cre, aut], Barret Schloerke [ctb], Scott Wolchok [ctb], Facebook, Inc [aut, cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package bibtex updated to version 0.5.0 with previous version 0.4.2.3 dated 2020-09-19

Title: Bibtex Parser
Description: Utility to parse a bibtex file.
Author: Romain Francois [aut, cph] , James Joseph Balamuta [ctb, cre] , Diego Hernangomez [aut] , Scott Chamberlain [ctb] , Kurt Hornik [ctb] , Brian Ripley [ctb] , Michael Koohafkan [ctb], Mathew W. McLean [ctb]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>

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Package unittest updated to version 1.5-3 with previous version 1.5-1 dated 2022-09-07

Title: TAP-Compliant Unit Testing
Description: Concise TAP <http://testanything.org/> compliant unit testing package. Authored tests can be run using CMD check with minimal implementation overhead.
Author: Jamie Lentin [aut, cre], Anthony Hennessey [aut]
Maintainer: Jamie Lentin <jm@ravingmantis.com>

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Package ichimoku updated to version 1.4.1 with previous version 1.4.0 dated 2022-09-08

Title: Visualization and Tools for Ichimoku Kinko Hyo Strategies
Description: An implementation of 'Ichimoku Kinko Hyo', also commonly known as 'cloud charts'. Static and interactive visualizations with tools for creating, backtesting and development of quantitative 'ichimoku' strategies. As described in Sasaki (1996, ISBN:4925152009), the technique is a refinement on candlestick charting, originating from Japan and now in widespread use in technical analysis worldwide. Translating as 'one-glance equilibrium chart', it allows the price action and market structure of financial securities to be determined 'at-a-glance'. Incorporates an interface with the OANDA fxTrade API <https://developer.oanda.com/> for retrieving historical and live streaming price data for major currencies, metals, commodities, government bonds and stock indices.
Author: Charlie Gao [aut, cre] , Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>

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Package psychTools updated to version 2.2.9 with previous version 2.2.5 dated 2022-05-10

Title: Tools to Accompany the 'psych' Package for Psychological Research
Description: Support functions, data sets, and vignettes for the 'psych' package. Contains several of the biggest data sets for the 'psych' package as well as one vignette. A few helper functions for file manipulation are included as well. For more information, see the <https://personality-project.org/r/> web page.
Author: William Revelle [aut, cre]
Maintainer: William Revelle <revelle@northwestern.edu>

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Package lvplot updated to version 0.2.1 with previous version 0.2.0 dated 2016-05-01

Title: Letter Value 'Boxplots'
Description: Implements the letter value 'boxplot' which extends the standard 'boxplot' to deal with both larger and smaller number of data points by dynamically selecting the appropriate number of letter values to display.
Author: Hadley Wickham [aut, cre], Heike Hofmann [aut]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package httr2 updated to version 0.2.2 with previous version 0.2.1 dated 2022-05-10

Title: Perform HTTP Requests and Process the Responses
Description: Tools for creating and modifying HTTP requests, then performing them and processing the results. 'httr2' is a modern re-imagining of 'httr' that uses a pipe-based interface and solves more of the problems that API wrapping packages face.
Author: Hadley Wickham [aut, cre], RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package fastGLCM updated to version 1.0.2 with previous version 1.0.1 dated 2022-09-04

Title: 'GLCM' Texture Features
Description: Two 'Gray Level Co-occurrence Matrix' ('GLCM') implementations are included: The first is a fast 'GLCM' feature texture computation based on 'Python' 'Numpy' arrays ('Github' Repository, <https://github.com/tzm030329/GLCM>). The second is a fast 'GLCM' 'RcppArmadillo' implementation which is parallelized (using 'OpenMP') with the option to return all 'GLCM' features at once. For more information, see "Artifact-Free Thin Cloud Removal Using Gans" by Toizumi Takahiro, Zini Simone, Sagi Kazutoshi, Kaneko Eiji, Tsukada Masato, Schettini Raimondo (2019), IEEE International Conference on Image Processing (ICIP), pp. 3596-3600, <doi:10.1109/ICIP.2019.8803652>.
Author: Lampros Mouselimis [aut, cre] , Takahiro Toizumi [cph]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>

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Package onmaRg updated to version 0.1.2 with previous version 0.1.1 dated 2022-09-18

Title: Import Public Health Ontario's Ontario Marginalization Index
Description: The Ontario Marginalization Index is a socioeconomic model that is built on Statistics Canada census data. The model consists of four dimensions: Residential Instability, Material Deprivation, Dependency and Ethnic Concentration. Each of these dimensions are imported for a variety of geographic levels (DA, CD, etc.) for both the 2011 and 2016 administrations of the census (2021 pending). These data sets contribute to community analysis of equity with respect to Ontario's Anti-Racism Act. The Ontario Marginalization Index data is retrieved from the Public Health Ontario website: <https://www.publichealthontario.ca/en/data-and-analysis/health-equity/ontario-marginalization-index>. The shapefile data is retrieved from the Statistics Canada website: <https://www12.statcan.gc.ca/census-recensement/2011/geo/bound-limit/bound-limit-eng.cfm>.
Author: William Conley [aut, cre]
Maintainer: William Conley <william@cconley.ca>

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Package nflreadr updated to version 1.3.1 with previous version 1.3.0 dated 2022-08-06

Title: Download 'nflverse' Data
Description: A minimal package for downloading data from 'GitHub' repositories of the 'nflverse' project.
Author: Tan Ho [aut, cre, cph] , Sebastian Carl [aut], John Edwards [ctb], Ben Baldwin [ctb], Thomas Mock [ctb], Lee Sharpe [ctb], Pranav Rajaram [ctb]
Maintainer: Tan Ho <tan@tanho.ca>

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Package ngramr updated to version 1.8.3 with previous version 1.8.2 dated 2022-09-20

Title: Retrieve and Plot Google n-Gram Data
Description: Retrieve and plot word frequencies through time from the "Google Ngram Viewer" <https://books.google.com/ngrams>.
Author: Sean Carmody [aut, cre, cph]
Maintainer: Sean Carmody <seancarmody@gmail.com>

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Package GENEAclassify updated to version 1.5.3 with previous version 1.5.2 dated 2021-01-05

Title: Segmentation and Classification of Accelerometer Data
Description: Segmentation and classification procedures for data from the 'Activinsights GENEActiv' <https://activinsights.com/technology/geneactiv/> accelerometer that provides the user with a model to guess behaviour from test data where behaviour is missing. Includes a step counting algorithm, a function to create segmented data with custom features and a function to use recursive partitioning provided in the function rpart() of the 'rpart' package to create classification models.
Author: Chris Campbell [aut], Aimee Gott [aut], Joss Langford [aut], Charles Sweetland [aut, cre], Activinsights Ltd [cph]
Maintainer: Charles Sweetland <charles@springhead-data.com>

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Package epiR updated to version 2.0.52 with previous version 2.0.50 dated 2022-07-01

Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> and Evan Sergeant <evansergeant@gmail.com> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>

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Package edecob updated to version 1.2.0 with previous version 1.1.0 dated 2022-05-27

Title: Event Detection Using Confidence Bounds
Description: Detects sustained change in digital bio-marker data using simultaneous confidence bands. Accounts for noise using an auto-regressive model. Based on Buehlmann (1998) "Sieve bootstrap for smoothing in nonstationary time series" <doi:10.1214/aos/1030563978>.
Author: Zheng Chen Man [aut, cre]
Maintainer: Zheng Chen Man <zheng.chen.man@alumni.ethz.ch>

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Package cld2 updated to version 1.2.2 with previous version 1.2.1 dated 2020-12-15

Title: Google's Compact Language Detector 2
Description: Bindings to Google's C++ library Compact Language Detector 2 (see <https://github.com/cld2owners/cld2#readme> for more information). Probabilistically detects over 80 languages in plain text or HTML. For mixed-language input it returns the top three detected languages and their approximate proportion of the total classified text bytes (e.g. 80% English and 20% French out of 1000 bytes). There is also a 'cld3' package on CRAN which uses a neural network model instead.
Author: Jeroen Ooms [aut, cre] , Dirk Sites [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between cld2 versions 1.2.1 dated 2020-12-15 and 1.2.2 dated 2022-09-25

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Package phase updated to version 1.2.2 with previous version 1.2.1 dated 2021-08-16

Title: Analyse Biological Time-Series Data
Description: Compiles functions to trim, bin, visualise, and analyse activity/sleep time-series data collected from the Drosophila Activity Monitor (DAM) system (Trikinetics, USA). The following methods were used to compute periodograms - Chi-square periodogram: Sokolove and Bushell (1978) <doi:10.1016/0022-5193(78)90022-X>, Lomb-Scargle periodogram: Lomb (1976) <doi:10.1007/BF00648343>, Scargle (1982) <doi:10.1086/160554> and Ruf (1999) <doi:10.1076/brhm.30.2.178.1422>, and Autocorrelation: Eijzenbach et al. (1986) <doi:10.1111/j.1440-1681.1986.tb00943.x>. Identification of activity peaks is done after using a Savitzky-Golay filter (Savitzky and Golay (1964) <doi:10.1021/ac60214a047>) to smooth raw activity data. Three methods to estimate anticipation of activity are used based on the following papers - Slope method: Fernandez et al. (2020) <doi:10.1016/j.cub.2020.04.025>, Harrisingh method: Harrisingh et al. (2007) <doi:10.1523/JNEUROSCI.3680-07.2007&g [...truncated...]
Author: Lakshman Abhilash [aut, cre]
Maintainer: Lakshman Abhilash <labhilash@gc.cuny.edu>

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Package openair updated to version 2.11 with previous version 2.10-0 dated 2022-06-21

Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air pollution data. Data are typically regular time series and air quality measurement, meteorological data and dispersion model output can be analysed. The package is described in Carslaw and Ropkins (2012, <doi:10.1016/j.envsoft.2011.09.008>) and subsequent papers.
Author: David Carslaw [aut, cre], Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>

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Package datawizard updated to version 0.6.1 with previous version 0.6.0 dated 2022-09-15

Title: Easy Data Wrangling and Statistical Transformations
Description: A lightweight package to easily manipulate, clean, transform, and prepare your data for analysis. It also forms the data wrangling backend for the packages in the 'easystats' ecosystem.
Author: Indrajeet Patil [aut, cre] , Dominique Makowski [aut] , Daniel Luedecke [aut] , Mattan S. Ben-Shachar [aut] , Brenton M. Wiernik [aut] , Etienne Bacher [aut] , Remi Theriault [ctb]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

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Package metamisc updated to version 0.4.0 with previous version 0.2.5 dated 2021-09-20

Title: Meta-Analysis of Diagnosis and Prognosis Research Studies
Description: Facilitate frequentist and Bayesian meta-analysis of diagnosis and prognosis research studies. It includes functions to summarize multiple estimates of prediction model discrimination and calibration performance (Debray et al., 2019) <doi:10.1177/0962280218785504>. It also includes functions to evaluate funnel plot asymmetry (Debray et al., 2018) <doi:10.1002/jrsm.1266>. Finally, the package provides functions for developing multivariable prediction models from datasets with clustering (de Jong et al., 2021) <doi:10.1002/sim.8981>.
Author: Thomas Debray [aut, cre] , Valentijn de Jong [aut]
Maintainer: Thomas Debray <thomas.debray@gmail.com>

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Package WDI updated to version 2.7.8 with previous version 2.7.7 dated 2022-07-16

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] , Etienne Bacher [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>

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Package owidR updated to version 1.4.0 with previous version 1.3.1 dated 2022-08-07

Title: Import Data from Our World in Data
Description: Search and download the data used in over 3,000 Our World in Data charts.
Author: Piers York
Maintainer: Piers York <piersyork@gmail.com>

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Package marginaleffects updated to version 0.7.1 with previous version 0.7.0 dated 2022-08-06

Title: Marginal Effects, Marginal Means, Predictions, and Contrasts
Description: Compute and plot adjusted predictions, contrasts, marginal effects, and marginal means for over 65 classes of statistical models in R. Conduct linear and non-linear hypothesis tests using the delta method.
Author: Vincent Arel-Bundock [aut, cre, cph] , Marcio Augusto Diniz [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>

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Package cat2cat updated to version 0.4.5 with previous version 0.4.4 dated 2022-08-31

Title: Handling an Inconsistently Coded Categorical Variable in a Panel Dataset
Description: Unifying of an inconsistently coded categorical variable between two different time points in accordance with a mapping table. The main rule is to replicate the observation if it could be assign to a few categories. Then using simple frequencies or statistical methods to approximate probabilities of being assign to each of them. This procedure was invented and implemented in the paper by (Nasinski, Majchrowska and Broniatowska (2020) <doi:10.24425/cejeme.2020.134747>).
Author: Maciej Nasinski [aut, cre]
Maintainer: Maciej Nasinski <nasinski.maciej@gmail.com>

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Package survivoR updated to version 2.0.1 with previous version 2.0 dated 2022-09-21

Title: Data from all Seasons of Survivor (US) TV Series in Tidy Format
Description: Several datasets which detail the results and events of each season of Survivor. This includes details on the cast, voting history, immunity and reward challenges, jury votes and viewers. This data is useful for practicing data wrangling, graph analytics and analysing how each season of Survivor played out. Includes 'ggplot2' scales and colour palettes for visualisation.
Author: Daniel Oehm [aut, cre], Carly Levitz [ctb], Dario Mavec [ctb]
Maintainer: Daniel Oehm <danieloehm@gmail.com>

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Package openCR updated to version 2.2.5 with previous version 2.2.4 dated 2022-07-01

Title: Open Population Capture-Recapture
Description: Non-spatial and spatial open-population capture-recapture analysis.
Author: Murray Efford [aut, cre]
Maintainer: Murray Efford <murray.efford@otago.ac.nz>

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Sat, 24 Sep 2022

Package TidyMultiqc updated to version 1.0.3 with previous version 1.0.2 dated 2022-02-10

Title: Converts 'MultiQC' Reports into Tidy Data Frames
Description: Provides the means to convert 'multiqc_data.json' files, produced by the wonderful 'MultiQC' tool, into tidy data frames for downstream analysis in R. This analysis might involve cohort analysis, quality control visualisation, change-point detection, statistical process control, clustering, or any other type of quality analysis.
Author: Michael Milton
Maintainer: Michael Milton <michael.r.milton@gmail.com>

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Package BayesianMediationA updated to version 1.0.1 with previous version 1.0 dated 2022-08-18

Title: Bayesian Mediation Analysis
Description: We perform general mediation analysis in the Bayesian setting using the methods described in Yu and Li (2022, ISBN:9780367365479). With the package, the mediation analysis can be performed on different types of outcomes (e.g., continuous, binary, categorical, or time-to-event), with default or user-defined priors and predictive models. The Bayesian estimates and credible sets of mediation effects are reported as analytic results.
Author: Qingzhao Yu [aut, cre, cph], Bin Li [aut]
Maintainer: Qingzhao Yu <qyu@lsuhsc.edu>

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Package ssh updated to version 0.8.1 with previous version 0.8.0 dated 2021-05-03

Title: Secure Shell (SSH) Client for R
Description: Connect to a remote server over SSH to transfer files via SCP, setup a secure tunnel, or run a command or script on the host while streaming stdout and stderr directly to the client.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package clickR updated to version 0.8.3 with previous version 0.8.0 dated 2021-08-10

Title: Semi-Automatic Preprocessing of Messy Data with Change Tracking for Dataset Cleaning
Description: Tools for assessing data quality, performing exploratory analysis, and semi-automatic preprocessing of messy data with change tracking for integral dataset cleaning.
Author: David Hervas Marin
Maintainer: David Hervas Marin <ddhervas@yahoo.es>

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Package reclin2 updated to version 0.2.0 with previous version 0.1.1 dated 2022-01-07

Title: Record Linkage Toolkit
Description: Functions to assist in performing probabilistic record linkage and deduplication: generating pairs, comparing records, em-algorithm for estimating m- and u-probabilities (I. Fellegi & A. Sunter (1969) <doi:10.1080/01621459.1969.10501049>, T.N. Herzog, F.J. Scheuren, & W.E. Winkler (2007), "Data Quality and Record Linkage Techniques", ISBN:978-0-387-69502-0), forcing one-to-one matching. Can also be used for pre- and post-processing for machine learning methods for record linkage. Focus is on memory, CPU performance and flexibility.
Author: Jan van der Laan [aut, cre]
Maintainer: Jan van der Laan <r@eoos.dds.nl>

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Package mbRes updated to version 0.1.5 with previous version 0.1.4 dated 2022-08-24

Title: Exploration of Multiple Biomarker Responses using Effect Size
Description: Summarize multiple biomarker responses of aquatic organisms to contaminants using Cliff’s delta, as described in Pham & Sokolova (2022) <doi:10.1002/ieam.4676>.
Author: Duy Nghia Pham [aut, cre] , Inna M. Sokolova [ths]
Maintainer: Duy Nghia Pham <nghiapham@yandex.com>

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Package sportyR updated to version 2.0.1 with previous version 2.0.0 dated 2022-08-15

Title: Plot Scaled 'ggplot' Representations of Sports Playing Surfaces
Description: Create scaled 'ggplot' representations of playing surfaces. Playing surfaces are drawn pursuant to rule-book specifications. This package should be used as a baseline plot for displaying any type of tracking data.
Author: Ross Drucker [aut, cre]
Maintainer: Ross Drucker <ross.a.drucker@gmail.com>

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Package robis updated to version 2.11.3 with previous version 2.8.2 dated 2021-10-13

Title: Ocean Biodiversity Information System (OBIS) Client
Description: Client for the Ocean Biodiversity Information System (<https://obis.org>).
Author: Pieter Provoost [cre, aut], Samuel Bosch [aut], Ward Appeltans [ctb], OBIS [cph]
Maintainer: Pieter Provoost <pieterprovoost@gmail.com>

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Package dtwclust updated to version 5.5.11 with previous version 5.5.10 dated 2022-04-14

Title: Time Series Clustering Along with Optimizations for the Dynamic Time Warping Distance
Description: Time series clustering along with optimized techniques related to the Dynamic Time Warping distance and its corresponding lower bounds. Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole clustering are available. Functionality can be easily extended with custom distance measures and centroid definitions. Implementations of DTW barycenter averaging, a distance based on global alignment kernels, and the soft-DTW distance and centroid routines are also provided. All included distance functions have custom loops optimized for the calculation of cross-distance matrices, including parallelization support. Several cluster validity indices are included.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>

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Package PLSiMCpp updated to version 1.0.4 with previous version 1.0.3 dated 2022-08-20

Title: Methods for Partial Linear Single Index Model
Description: Estimation, hypothesis tests, and variable selection in partially linear single-index models. Please see H. (2010) at <doi:10.1214/10-AOS835> for more details.
Author: Shunyao Wu, Qi Zhang, Zhiruo Li, Hua Liang
Maintainer: Shunyao Wu <wushunyao@qdu.edu.cn>

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Package iotables updated to version 0.9.1 with previous version 0.9 dated 2022-02-10

Title: Reproducible Input-Output Economics Analysis, Economic and Environmental Impact Assessment with Empirical Data
Description: Pre-processing and basic analytical tasks related to working with Eurostat's symmetric input-output tables and provide basic input-output economics calculations. The package is part of rOpenGov <http://ropengov.github.io/> to open source open government initiatives.
Author: Daniel Antal [aut, cre] , Kasia Kulma [ctb] , Pyry Kantanen [ctb]
Maintainer: Daniel Antal <daniel.antal@dataobservatory.eu>

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Package rlang updated to version 1.0.6 with previous version 1.0.5 dated 2022-08-31

Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.
Author: Lionel Henry [aut, cre], Hadley Wickham [aut], mikefc [cph] , Yann Collet [cph] , RStudio [cph, fnd]
Maintainer: Lionel Henry <lionel@rstudio.com>

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Package pins updated to version 1.0.3 with previous version 1.0.2 dated 2022-08-23

Title: Pin, Discover and Share Resources
Description: Publish data sets, models, and other R objects, making it easy to share them across projects and with your colleagues. You can pin objects to a variety of "boards", including local folders (to share on a networked drive or with 'DropBox'), 'RStudio' connect, Amazon S3, and more.
Author: Julia Silge [cre, aut] , Hadley Wickham [aut] , Javier Luraschi [aut], RStudio [cph, fnd]
Maintainer: Julia Silge <julia.silge@rstudio.com>

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Package adw updated to version 0.2.1 with previous version 0.2.0 dated 2022-09-22

Title: Angular Distance Weighting Interpolation
Description: The irregularly-spaced data are interpolated onto regular latitude-longitude grids by weighting each station according to its distance and angle from the center of a search radius.
Author: Panfeng Zhang [aut, cre]
Maintainer: Panfeng Zhang <zhangpanfeng@cug.edu.cn>

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Package blogdown updated to version 1.13 with previous version 1.12 dated 2022-09-15

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] , Christophe Dervieux [aut] , Alison Presmanes Hill [aut] , 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] [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>

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Fri, 23 Sep 2022

Package rmoo updated to version 0.2.0 with previous version 0.1.8 dated 2022-08-11

Title: Multi-Objective Optimization in R
Description: The 'rmoo' package is a framework for multi- and many-objective optimization, which allows researchers and users versatility in parameter configuration, as well as tools for analysis, replication and visualization of results. The 'rmoo' package was built as a fork of the 'GA' package by Luca Scrucca(2017) <DOI:10.32614/RJ-2017-008> and implementing the Non-Dominated Sorting Genetic Algorithms proposed by K. Deb's.
Author: Francisco Benitez [aut, cre], Diego Pinto Roa [aut]
Maintainer: Francisco Benitez <benitezfj94@gmail.com>

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Package extras updated to version 0.4.0 with previous version 0.3.0 dated 2022-06-08

Title: Helper Functions for Bayesian Analyses
Description: Functions to 'numericise' 'R' objects (coerce to numeric objects), summarise 'MCMC' (Monte Carlo Markov Chain) samples and calculate deviance residuals as well as 'R' translations of some 'BUGS' (Bayesian Using Gibbs Sampling), 'JAGS' (Just Another Gibbs Sampler), 'STAN' and 'TMB' (Template Model Builder) functions.
Author: Joe Thorley [aut, cre] , Kirill Mueller [ctb] , Nadine Hussein [ctb] , Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

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Package mixture updated to version 2.0.5 with previous version 2.0.4 dated 2021-04-19

Title: Mixture Models for Clustering and Classification
Description: An implementation of 14 parsimonious mixture models for model-based clustering or model-based classification. Gaussian, Student's t, generalized hyperbolic, variance-gamma or skew-t mixtures are available. All approaches work with missing data. Celeux and Govaert (1995) <doi:10.1016/0031-3203(94)00125-6>, Browne and McNicholas (2014) <doi:10.1007/s11634-013-0139-1>, Browne and McNicholas (2015) <doi:10.1002/cjs.11246>.
Author: Nik Pocuca [aut] , Ryan P. Browne [aut] , Paul D. McNicholas [aut, cre]
Maintainer: Paul D. McNicholas <mcnicholas@math.mcmaster.ca>

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More information about mixture at CRAN
Permanent link

Package tokenizers updated to version 0.2.3 with previous version 0.2.1 dated 2018-03-29

Title: Fast, Consistent Tokenization of Natural Language Text
Description: Convert natural language text into tokens. Includes tokenizers for shingled n-grams, skip n-grams, words, word stems, sentences, paragraphs, characters, shingled characters, lines, tweets, Penn Treebank, regular expressions, as well as functions for counting characters, words, and sentences, and a function for splitting longer texts into separate documents, each with the same number of words. The tokenizers have a consistent interface, and the package is built on the 'stringi' and 'Rcpp' packages for fast yet correct tokenization in 'UTF-8'.
Author: Lincoln Mullen [aut, cre] , Os Keyes [ctb] , Dmitriy Selivanov [ctb], Jeffrey Arnold [ctb] , Kenneth Benoit [ctb]
Maintainer: Lincoln Mullen <lincoln@lincolnmullen.com>

Diff between tokenizers versions 0.2.1 dated 2018-03-29 and 0.2.3 dated 2022-09-23

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Package NNS updated to version 0.9.2 with previous version 0.9.1 dated 2022-08-22

Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre], Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>

Diff between NNS versions 0.9.1 dated 2022-08-22 and 0.9.2 dated 2022-09-23

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Package broom.helpers updated to version 1.9.0 with previous version 1.8.0 dated 2022-07-05

Title: Helpers for Model Coefficients Tibbles
Description: Provides suite of functions to work with regression model 'broom::tidy()' tibbles. The suite includes functions to group regression model terms by variable, insert reference and header rows for categorical variables, add variable labels, and more.
Author: Joseph Larmarange [aut, cre] , Daniel D. Sjoberg [aut]
Maintainer: Joseph Larmarange <joseph@larmarange.net>

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Package WeMix updated to version 3.2.2 with previous version 3.2.1 dated 2021-12-07

Title: Weighted Mixed-Effects Models Using Multilevel Pseudo Maximum Likelihood Estimation
Description: Run mixed-effects models that include weights at every level. The WeMix package fits a weighted mixed model, also known as a multilevel, mixed, or hierarchical linear model (HLM). The weights could be inverse selection probabilities, such as those developed for an education survey where schools are sampled probabilistically, and then students inside of those schools are sampled probabilistically. Although mixed-effects models are already available in R, WeMix is unique in implementing methods for mixed models using weights at multiple levels. Both linear and logit models are supported. Models may have up to three levels.
Author: Emmanuel Sikali [pdr], Paul Bailey [aut, cre], Claire Kelley [aut], Trang Nguyen [aut], Huade Huo [aut], Eric Buehler [ctb], Christian Kjeldsen [ctb]
Maintainer: Paul Bailey <pbailey@air.org>

Diff between WeMix versions 3.2.1 dated 2021-12-07 and 3.2.2 dated 2022-09-23

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Package tidytable updated to version 0.9.0 with previous version 0.8.1 dated 2022-08-17

Title: Tidy Interface to 'data.table'
Description: A tidy interface to 'data.table', giving users the speed of 'data.table' while using tidyverse-like syntax.
Author: Mark Fairbanks [aut, cre], Abdessabour Moutik [ctb], Matt Carlson [ctb], Ivan Leung [ctb], Ross Kennedy [ctb], Robert On [ctb], Alexander Sevostianov [ctb]
Maintainer: Mark Fairbanks <mark.t.fairbanks@gmail.com>

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Package sgo updated to version 0.9.2 with previous version 0.9.1 dated 2021-12-11

Title: Simple Geographical Operations (with OSGB36)
Description: Methods focused in performing the OSGB36/ETRS89 transformation (Great Britain and the Isle of Man only) by using the Ordnance Survey's OSTN15/OSGM15 transformation model. Calculation of distances and areas from sets of points defined in any of the supported Coordinated Systems is also available.
Author: Carlos Lozano Ruiz [aut, cre]
Maintainer: Carlos Lozano Ruiz <carloslozanoruiz@outlook.com>

Diff between sgo versions 0.9.1 dated 2021-12-11 and 0.9.2 dated 2022-09-23

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Package gosset updated to version 0.5 with previous version 0.4 dated 2022-06-28

Title: Tools for Data Analysis in Experimental Agriculture
Description: Toolkit for a workflow to analyse experimental agriculture data, from data synthesis to model selection and visualisation. The package is named after W.S. Gosset aka ‘Student’, a pioneer of modern statistics in small sample experimental design and analysis.
Author: Kaue de Sousa [aut, cre] , Jacob van Etten [aut] , David Brown [aut] , Jonathan Steinke [aut]
Maintainer: Kaue de Sousa <desousa.kaue@gmail.com>

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Package EnrichIntersect updated to version 0.4 with previous version 0.3 dated 2022-09-14

Title: Enrichment Analysis and Intersecting Sankey Diagram
Description: A flexible tool for enrichment analysis based on user-defined sets. It allows users to perform over-representation analysis of the custom sets among any specified ranked feature list, hence making enrichment analysis applicable to various types of data from different scientific fields. 'EnrichIntersect' also enables an interactive means to visualize identified associations based on, for example, the mix-lasso model (Zhao et al. (2022) <doi:10.1016/j.isci.2022.104767>) or similar methods.
Author: Zhi Zhao [aut, cre], Manuela Zucknick [aut], Tero Aittokallio [ctb]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>

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Package EdSurvey updated to version 3.0.0 with previous version 2.7.1 dated 2021-10-05

Title: Analysis of NCES Education Survey and Assessment Data
Description: Read in and analyze functions for education survey and assessment data from the National Center for Education Statistics (NCES) <https://nces.ed.gov/>, including National Assessment of Educational Progress (NAEP) data <https://nces.ed.gov/nationsreportcard/> and data from the International Assessment Database: Organisation for Economic Co-operation and Development (OECD) <https://www.oecd.org/>, including Programme for International Student Assessment (PISA), Teaching and Learning International Survey (TALIS), Programme for the International Assessment of Adult Competencies (PIAAC), and International Association for the Evaluation of Educational Achievement (IEA) <https://www.iea.nl/>, including Trends in International Mathematics and Science Study (TIMSS), TIMSS Advanced, Progress in International Reading Literacy Study (PIRLS), International Civic and Citizenship Study (ICCS), International Computer and Information Literacy Study (ICILS), and Civic Education S [...truncated...]
Author: Paul Bailey [aut, cre], Ahmad Emad [aut], Huade Huo [aut], Michael Lee [aut], Yuqi Liao [aut], Alex Lishinski [aut], Trang Nguyen [aut], Qingshu Xie [aut], Jiao Yu [aut], Ting Zhang [aut], Eric Buehler [aut], person, person), Jeppe Bundsgaard [ctb], [...truncated...]
Maintainer: Paul Bailey <pbailey@air.org>

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Package funrar updated to version 1.5.0 with previous version 1.4.1 dated 2020-04-20

Title: Functional Rarity Indices Computation
Description: Computes functional rarity indices as proposed by Violle et al. (2017) <doi:10.1016/j.tree.2017.02.002>. Various indices can be computed using both regional and local information. Functional Rarity combines both the functional aspect of rarity as well as the extent aspect of rarity. 'funrar' is presented in Grenié et al. (2017) <doi:10.1111/ddi.12629>.
Author: Matthias Grenie [aut, cre] , Pierre Denelle [aut] , Caroline Tucker [aut] , Francois Munoz [ths] , Cyrille Violle [ths]
Maintainer: Matthias Grenie <matthias.grenie@gmail.com>

Diff between funrar versions 1.4.1 dated 2020-04-20 and 1.5.0 dated 2022-09-23

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Package DrDimont updated to version 0.1.4 with previous version 0.1.3 dated 2022-05-17

Title: Drug Response Prediction from Differential Multi-Omics Networks
Description: While it has been well established that drugs affect and help patients differently, personalized drug response predictions remain challenging. Solutions based on single omics measurements have been proposed, and networks provide means to incorporate molecular interactions into reasoning. However, how to integrate the wealth of information contained in multiple omics layers still poses a complex problem. We present a novel network analysis pipeline, DrDimont, Drug response prediction from Differential analysis of multi-omics networks. It allows for comparative conclusions between two conditions and translates them into differential drug response predictions. DrDimont focuses on molecular interactions. It establishes condition-specific networks from correlation within an omics layer that are then reduced and combined into heterogeneous, multi-omics molecular networks. A novel semi-local, path-based integration step ensures integrative conclusions. Differential predictions are derived fro [...truncated...]
Author: Katharina Baum [cre] , Pauline Hiort [aut] , Julian Hugo [aut] , Spoorthi Kashyap [aut] , Nataniel Mueller [aut] , Justus Zeinert [aut]
Maintainer: Katharina Baum <katharina.baum@hpi.de>

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Package wdnr.gis updated to version 0.1.4 with previous version 0.1.3 dated 2022-03-17

Title: Pull Spatial Layers from 'WDNR ArcGIS REST API'
Description: Functions for finding and pulling data from the 'Wisconsin Department of Natural Resources ArcGIS REST APIs' <https://dnrmaps.wi.gov/arcgis/rest/services> and <https://dnrmaps.wi.gov/arcgis2/rest/services>.
Author: Paul Frater [aut, cre] , Zac Driscoll [aut]
Maintainer: Paul Frater <paul.frater@wisconsin.gov>

Diff between wdnr.gis versions 0.1.3 dated 2022-03-17 and 0.1.4 dated 2022-09-23

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Package memoiR updated to version 1.2-2 with previous version 1.2-1 dated 2022-08-14

Title: R Markdown and Bookdown Templates to Publish Documents
Description: Producing high-quality documents suitable for publication directly from R is made possible by the R Markdown ecosystem. 'memoiR' makes it easy. It provides templates to knit memoirs, articles and slideshows with helpers to publish the documents on GitHub Pages and activate continuous integration.
Author: Eric Marcon [aut, cre]
Maintainer: Eric Marcon <eric.marcon@agroparistech.fr>

Diff between memoiR versions 1.2-1 dated 2022-08-14 and 1.2-2 dated 2022-09-23

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Package desla updated to version 0.2.0 with previous version 0.1.0 dated 2021-11-11

Title: Desparsified Lasso Inference for Time Series
Description: Calculates the desparsified lasso as originally introduced in van de Geer et al. (2014) <doi:10.1214/14-AOS1221>, and provides inference suitable for high-dimensional time series, based on the long run covariance estimator in Adamek et al. (2020) <arXiv:2007.10952>. Also estimates high-dimensional local projections by the desparsified lasso, as described in Adamek et al. (2022) <arXiv:2209.03218>.
Author: Robert Adamek [cre, aut], Stephan Smeekes [aut], Ines Wilms [aut]
Maintainer: Robert Adamek <robertadamek94@gmail.com>

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Package volcano3D updated to version 2.0.8 with previous version 2.0.0 dated 2022-07-05

Title: 3D Volcano Plots and Polar Plots for Three-Class Data
Description: Generates interactive plots for analysing and visualising three-class high dimensional data. It is particularly suited to visualising differences in continuous attributes such as gene/protein/biomarker expression levels between three groups. Differential gene/biomarker expression analysis between two classes is typically shown as a volcano plot. However, with three groups this type of visualisation is particularly difficult to interpret. This package generates 3D volcano plots and 3-way polar plots for easier interpretation of three-class data.
Author: Katriona Goldmann [aut, cre] , Myles Lewis [aut]
Maintainer: Katriona Goldmann <k.goldmann@qmul.ac.uk>

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Package cffr updated to version 0.3.0 with previous version 0.2.3 dated 2022-08-15

Title: Generate Citation File Format ('cff') Metadata for R Packages
Description: The Citation File Format version 1.2.0 <doi:10.5281/zenodo.5171937> is a human and machine readable file format which provides citation metadata for software. This package provides core utilities to generate and validate this metadata.
Author: Diego Hernangomez [aut, cre, cph] , Joao Martins [rev] , Scott Chamberlain [rev]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>

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Package tidyterra updated to version 0.2.1 with previous version 0.2.0 dated 2022-06-21

Title: 'tidyverse' Methods and 'ggplot2' Utils for 'terra' Objects
Description: Extension of the 'tidyverse' for 'SpatRaster' and 'SpatVector' objects of the 'terra' package. It includes also new 'geom_' functions that provide a convenient way of visualizing 'terra' objects with 'ggplot2'.
Author: Diego Hernangomez [aut, cre, cph] , Dewey Dunnington [ctb] , ggplot2 authors [cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>

Diff between tidyterra versions 0.2.0 dated 2022-06-21 and 0.2.1 dated 2022-09-23

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Package this.path updated to version 1.0.1 with previous version 1.0.0 dated 2022-09-21

Title: Get Executing Script's Path, from 'RStudio', 'Rgui', 'VSCode', 'Rscript' (Shells Including Windows Command-Line / / Unix Terminal), and 'source'
Description: Determine the full path of the executing script. Works when running a line or selection from a script in 'RStudio', 'Rgui', and 'VSCode', when using 'source', 'sys.source', 'debugSource' in 'RStudio', and 'testthat::source_file', and when running from a shell.
Author: Andrew Simmons
Maintainer: Andrew Simmons <akwsimmo@gmail.com>

Diff between this.path versions 1.0.0 dated 2022-09-21 and 1.0.1 dated 2022-09-23

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Package Require updated to version 0.1.2 with previous version 0.0.13 dated 2021-05-31

Title: Installing and Loading R Packages for Reproducible Workflows
Description: A single key function, 'Require' that makes rerun-tolerant versions of 'install.packages' and `require` for CRAN packages, packages no longer on CRAN (i.e., archived), specific versions of packages, and GitHub packages. This approach is developed to create reproducible workflows that are flexible and fast enough to use while in development stages, while able to build snapshots once a stable package collection is found. As with other functions in a reproducible workflow, this package emphasizes functions that return the same result whether it is the first or subsequent times running the function, with subsequent times being sufficiently fast that they can be run every time without undue waiting burden on the user or developer.
Author: Eliot J B McIntire [aut, cre] , Her Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>

Diff between Require versions 0.0.13 dated 2021-05-31 and 0.1.2 dated 2022-09-23

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Package h2o updated to version 3.38.0.1 with previous version 3.36.1.2 dated 2022-05-27

Title: R Interface for the 'H2O' Scalable Machine Learning Platform
Description: R interface for 'H2O', the scalable open source machine learning platform that offers parallelized implementations of many supervised and unsupervised machine learning algorithms such as Generalized Linear Models (GLM), Gradient Boosting Machines (including XGBoost), Random Forests, Deep Neural Networks (Deep Learning), Stacked Ensembles, Naive Bayes, Generalized Additive Models (GAM), ANOVA GLM, Cox Proportional Hazards, K-Means, PCA, ModelSelection, Word2Vec, as well as a fully automatic machine learning algorithm (H2O AutoML).
Author: Erin LeDell [aut, cre], Navdeep Gill [aut], Spencer Aiello [aut], Anqi Fu [aut], Arno Candel [aut], Cliff Click [aut], Tom Kraljevic [aut], Tomas Nykodym [aut], Patrick Aboyoun [aut], Michal Kurka [aut], Michal Malohlava [aut], Ludi Rehak [ctb], Eric [...truncated...]
Maintainer: Erin LeDell <erin@h2o.ai>

Diff between h2o versions 3.36.1.2 dated 2022-05-27 and 3.38.0.1 dated 2022-09-23

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Package DatabaseConnector updated to version 5.1.0 with previous version 5.0.4 dated 2022-06-28

Title: Connecting to Various Database Platforms
Description: An R 'DataBase Interface' ('DBI') compatible interface to various database platforms ('PostgreSQL', 'Oracle', 'Microsoft SQL Server', 'Amazon Redshift', 'Microsoft Parallel Database Warehouse', 'IBM Netezza', 'Apache Impala', 'Google BigQuery', 'Snowflake', 'Spark', and 'SQLite'). Also includes support for fetching data as 'Andromeda' objects. Uses 'Java Database Connectivity' ('JDBC') to connect to databases (except SQLite).
Author: Martijn Schuemie [aut, cre], Marc Suchard [aut], Observational Health Data Science and Informatics [cph], Microsoft Inc. [cph] , PostgreSQL Global Development Group [cph] , Oracle Inc. [cph] , Amazon Inc. [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>

Diff between DatabaseConnector versions 5.0.4 dated 2022-06-28 and 5.1.0 dated 2022-09-23

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Package cli updated to version 3.4.1 with previous version 3.4.0 dated 2022-09-08

Title: Helpers for Developing Command Line Interfaces
Description: A suite of tools to build attractive command line interfaces ('CLIs'), from semantic elements: headings, lists, alerts, paragraphs, etc. Supports custom themes via a 'CSS'-like language. It also contains a number of lower level 'CLI' elements: rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and text styles as well.
Author: Gabor Csardi [aut, cre], Hadley Wickham [ctb], Kirill Mueller [ctb], RStudio [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>

Diff between cli versions 3.4.0 dated 2022-09-08 and 3.4.1 dated 2022-09-23

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Package vglmer updated to version 1.0.2 with previous version 1.0.1 dated 2022-09-17

Title: Variational Inference for Hierarchical Generalized Linear Models
Description: Estimates hierarchical models using mean-field variational Bayes. At present, it can estimate logistic, linear, and negative binomial models. It can accommodate models with an arbitrary number of random effects and requires no integration to estimate. It also provides the ability to improve the quality of the approximation using marginal augmentation. Goplerud (2022) <doi:10.1214/21-BA1266> provides details on the variational algorithms.
Author: Max Goplerud [aut, cre]
Maintainer: Max Goplerud <mgoplerud@pitt.edu>

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Package Rgff updated to version 0.1.5 with previous version 0.1.4 dated 2022-09-19

Title: R Utilities for GFF Files
Description: R utilities for gff files, either general feature format (GFF3) or gene transfer format (GTF) formatted files. This package includes functions for producing summary stats, check for consistency and sorting errors, conversion from GTF to GFF3 format, file sorting, visualization and plotting of feature hierarchy, and exporting user defined feature subsets to SAF format. This tool was developed by the BioinfoGP core facility at CNB-CSIC.
Author: Juan Antonio Garcia-Martin [cre, aut] , Juan Carlos Oliveros [aut, ctb] , Rafael Torres-Perez [aut, ctb]
Maintainer: Juan Antonio Garcia-Martin <ja.garcia@cnb.csic.es>

Diff between Rgff versions 0.1.4 dated 2022-09-19 and 0.1.5 dated 2022-09-23

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Package fbst updated to version 1.9 with previous version 1.7 dated 2022-03-08

Title: The Full Bayesian Evidence Test, Full Bayesian Significance Test and the e-Value
Description: Provides access to a range of functions for computing and visualizing the Full Bayesian Significance Test (FBST) and the e-value for testing a sharp hypothesis against its alternative, and the Full Bayesian Evidence Test (FBET) and the (generalized) Bayesian evidence value for testing a composite (or interval) hypothesis against its alternative. The methods are widely applicable as long as a posterior MCMC sample is available.
Author: Riko Kelter
Maintainer: Riko Kelter <riko.kelter@uni-siegen.de>

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Package cvCovEst updated to version 1.1.1 with previous version 1.1.0 dated 2022-05-04

Title: Cross-Validated Covariance Matrix Estimation
Description: An efficient cross-validated approach for covariance matrix estimation, particularly useful in high-dimensional settings. This method relies upon the theory of loss-based estimator selection to identify the optimal estimator of the covariance matrix from among a prespecified set of candidates.
Author: Philippe Boileau [aut, cre, cph] , Nima Hejazi [aut] , Brian Collica [aut] , Jamarcus Liu [ctb], Mark van der Laan [ctb, ths] , Sandrine Dudoit [ctb, ths]
Maintainer: Philippe Boileau <philippe_boileau@berkeley.edu>

Diff between cvCovEst versions 1.1.0 dated 2022-05-04 and 1.1.1 dated 2022-09-23

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Package CommKern updated to version 1.0.1 with previous version 1.0.0 dated 2022-09-20

Title: Network-Based Communities and Kernel Machine Methods
Description: Analysis of network community objects with applications to neuroimaging data. There are two main components to this package. The first is the hierarchical multimodal spinglass (HMS) algorithm, which is a novel community detection algorithm specifically tailored to the unique issues within brain connectivity. The other is a suite of semiparametric kernel machine methods that allow for statistical inference to be performed to test for potential associations between these community structures and an outcome of interest (binary or continuous).
Author: Alexandria Jensen [aut, cre] , Peter DeWitt [ctb] , Debashis Ghosh [ths]
Maintainer: Alexandria Jensen <alexandria.jensen@cuanschutz.edu>

Diff between CommKern versions 1.0.0 dated 2022-09-20 and 1.0.1 dated 2022-09-23

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Package autostsm updated to version 3.0.3 with previous version 3.0.2 dated 2022-09-02

Title: Automatic Structural Time Series Models
Description: Automatic model selection for structural time series decomposition into trend, cycle, and seasonal components, plus optionality for structural interpolation, using the Kalman filter. Koopman, Siem Jan and Marius Ooms (2012) "Forecasting Economic Time Series Using Unobserved Components Time Series Models" <doi:10.1093/oxfordhb/9780195398649.013.0006>. Kim, Chang-Jin and Charles R. Nelson (1999) "State-Space Models with Regime Switching: Classical and Gibbs-Sampling Approaches with Applications" <doi:10.7551/mitpress/6444.001.0001><http://econ.korea.ac.kr/~cjkim/>.
Author: Alex Hubbard [aut, cre]
Maintainer: Alex Hubbard <hubbard.alex@gmail.com>

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Package strvalidator updated to version 2.4.0 with previous version 2.3.0 dated 2020-07-10

Title: Process Control and Validation of Forensic STR Kits
Description: An open source platform for validation and process control. Tools to analyze data from internal validation of forensic short tandem repeat (STR) kits are provided. The tools are developed to provide the necessary data to conform with guidelines for internal validation issued by the European Network of Forensic Science Institutes (ENFSI) DNA Working Group, and the Scientific Working Group on DNA Analysis Methods (SWGDAM). A front-end graphical user interface is provided. More information about each function can be found in the respective help documentation.
Author: Oskar Hansson
Maintainer: Oskar Hansson <oskhan@ous-hf.no>

Diff between strvalidator versions 2.3.0 dated 2020-07-10 and 2.4.0 dated 2022-09-23

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Package hBayesDM updated to version 1.2.1 with previous version 1.2.0 dated 2022-09-10

Title: Hierarchical Bayesian Modeling of Decision-Making Tasks
Description: Fit an array of decision-making tasks with computational models in a hierarchical Bayesian framework. Can perform hierarchical Bayesian analysis of various computational models with a single line of coding (Ahn et al., 2017) <doi:10.1162/CPSY_a_00002>.
Author: Woo-Young Ahn [aut, cre], Nate Haines [aut], Lei Zhang [aut], Harhim Park [ctb], Jaeyeong Yang [ctb], Jethro Lee [ctb]
Maintainer: Woo-Young Ahn <wooyoung.ahn@gmail.com>

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Package umbridge updated to version 1.0 with previous version 0.9 dated 2022-09-12

Title: Integration for the UM-Bridge Protocol
Description: A convenient wrapper for the UM-Bridge protocol. UM-Bridge is a protocol designed for coupling uncertainty quantification (or statistical / optimization) software to numerical models. A model is represented as a mathematical function with optional support for derivatives via Jacobian actions etc.
Author: Linus Seelinger [aut, cre]
Maintainer: Linus Seelinger <mail@linusseelinger.de>

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Package anndata updated to version 0.7.5.5 with previous version 0.7.5.4 dated 2022-08-23

Title: 'anndata' for R
Description: A 'reticulate' wrapper for the Python package 'anndata'. Provides a scalable way of keeping track of data and learned annotations. Used to read from and write to the h5ad file format.
Author: Philipp Angerer [ccp] , Alex Wolf [ccp] , Isaac Virshup [ccp] , Sergei Rybakov [ccp] , Robrecht Cannoodt [aut, cre, cph]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>

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Package AlphaPart updated to version 0.9.7 with previous version 0.9.5 dated 2022-07-07

Title: Partition/Decomposition of Breeding Values by Paths of Information
Description: A software that implements a method for partitioning genetic trends to quantify the sources of genetic gain in breeding programmes. The partitioning method is described in Garcia-Cortes et al. (2008) <doi:10.1017/S175173110800205X>. The package includes the main function AlphaPart for partitioning breeding values and auxiliary functions for manipulating data and summarizing, visualizing, and saving results.
Author: Gregor Gorjanc [aut, cre] , Jana Obsteter [aut] , Thiago de Paula Oliveira [aut]
Maintainer: Gregor Gorjanc <highlander.research.lab@gmail.com>

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Package GillespieSSA2 updated to version 0.2.10 with previous version 0.2.8 dated 2021-05-18

Title: Gillespie's Stochastic Simulation Algorithm for Impatient People
Description: A fast, scalable, and versatile framework for simulating large systems with Gillespie's Stochastic Simulation Algorithm ('SSA'). This package is the spiritual successor to the 'GillespieSSA' package originally written by Mario Pineda-Krch. Benefits of this package include major speed improvements (>100x), easier to understand documentation, and many unit tests that try to ensure the package works as intended. Cannoodt and Saelens et al. (2020) <doi:10.1101/2020.02.06.936971>.
Author: Robrecht Cannoodt [aut, cre] , Wouter Saelens [aut]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>

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Package RVIpkg updated to version 0.3.1 with previous version 0.3.0 dated 2022-03-10

Title: Regional Vulnerability Index
Description: The Regional Vulnerability Index (RVI), a statistical measure of brain structural abnormality, quantifies an individual's similarity to the expected pattern (effect size) of deficits in schizophrenia (Kochunov P, Fan F, Ryan MC, et al. (2020) <doi:10.1002/hbm.25045>).
Author: Si Gao [aut, cre, dtc] , Peter Kochunov [aut, dtc, cph, fnd] , Kathryn Hatch [ctb, dtc] , Yizhou Ma [ctb, dtc] , Fatima Talib [ctb]
Maintainer: Si Gao <sgao@som.umaryland.edu>

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Package dynutils updated to version 1.0.10 with previous version 1.0.9 dated 2021-10-08

Title: Common Functionality for the 'dynverse' Packages
Description: Provides common functionality for the 'dynverse' packages. 'dynverse' is created to support the development, execution, and benchmarking of trajectory inference methods. For more information, check out <https://dynverse.org>.
Author: Robrecht Cannoodt [aut, cre] , Wouter Saelens [aut]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>

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Thu, 22 Sep 2022

Package rxode2 updated to version 2.0.8 with previous version 2.0.7 dated 2022-05-17

Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary differential equation ('ODE') models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual. Also the code is mostly released under GPL. The 'VODE' and 'LSODA' are in the public domain. The information is available in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] , Melissa Hallow [aut], Wenping Wang [aut], Zufar Mulyukov [ctb], Alan Hindmarsh [ctb], Awad H. Al-Mohy [ctb], Matt Dowle [ctb], Cleve Moler [ctb], David Cooley [ctb], Drew Schmidt [ctb], Arun Srinivasan [ctb], Ernst Hair [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>

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Package GeoTcgaData updated to version 1.1.1.992 with previous version 1.1.1 dated 2022-08-12

Title: Processing various types of data on GEO and TCGA
Description: Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP and Copy number variation data. It's easy to download data from TCGA using the gdc tool, but processing these data into a format suitable for bioinformatics analysis requires more work. This R package was developed to handle these data.
Author: Erqiang Hu [aut, cre]
Maintainer: Erqiang Hu <13766876214@163.com>

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Package bbknnR updated to version 1.0.2 with previous version 1.0.1 dated 2022-08-23

Title: Perform Batch Balanced KNN in R
Description: A fast and intuitive batch effect removal tool for single-cell data. BBKNN is originally used in the 'scanpy' python package, and now can be used with 'Seurat' seamlessly.
Author: Yuchen Li [aut, cre]
Maintainer: Yuchen Li <liyuchen_1995@outlook.com>

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Package IsoriX updated to version 0.9.0 with previous version 0.8.3 dated 2022-09-12

Title: Isoscape Computation and Inference of Spatial Origins using Mixed Models
Description: Building isoscapes using mixed models and inferring the geographic origin of samples based on their isotopic ratios. This package is essentially a simplified interface to several other packages which implements a new statistical framework based on mixed models. It uses 'spaMM' for fitting and predicting isoscapes, and assigning an organism's origin depending on its isotopic ratio. 'IsoriX' also relies heavily on the package 'rasterVis' for plotting the maps produced with 'raster' using 'lattice'.
Author: Alexandre Courtiol [aut, cre] , Francois Rousset [aut] , Marie-Sophie Rohwaeder [aut], Stephanie Kramer-Schadt [aut]
Maintainer: Alexandre Courtiol <alexandre.courtiol@gmail.com>

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Package ClimMobTools updated to version 0.5 with previous version 0.4.6 dated 2022-08-10

Title: API Client for the 'ClimMob' Platform
Description: API client for 'ClimMob', an open source software for decentralized large-N trials with the 'tricot' approach <https://climmob.net/>. Developed by van Etten et al. (2016) <doi:10.1017/S0014479716000739>, it turns the research paradigm on its head; instead of a few researchers designing complicated trials to compare several technologies in search of the best solutions for the target environment, it enables many participants to carry out reasonably simple experiments that taken together can offer even more information. 'ClimMobTools' enables project managers to deep explore and analyse their 'ClimMob' data in R.
Author: Kaue de Sousa [aut, cre] , Jacob van Etten [aut] , Brandon Madriz [aut]
Maintainer: Kaue de Sousa <desousa.kaue@gmail.com>

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Package satin updated to version 1.1.0 with previous version 1.0 dated 2020-10-07

Title: Visualisation and Analysis of Ocean Data Derived from Satellites
Description: With 'satin' functions, visualisation, data extraction and further analysis like producing climatologies from several images, and anomalies of satellite derived ocean data can be easily done. Reading functions can import a user defined geographical extent of data stored in netCDF files. Currently supported ocean data sources include NASA's Oceancolor web page <https://oceancolor.gsfc.nasa.gov/>, sensors VIIRS-SNPP; MODIS-Terra; MODIS-Aqua; and SeaWiFS. Available variables from this source includes chlorophyll concentration, sea surface temperature (SST), and several others. Data sources specific for SST that can be imported too includes Pathfinder AVHRR <https://www.ncei.noaa.gov/products/avhrr-pathfinder-sst> and GHRSST <https://www.ghrsst.org/>. In addition, ocean productivity data produced by Oregon State University <http://sites.science.oregonstate.edu/ocean.productivity/> can also be handled previous conversion from HDF4 to HDF5 format. Many other oce [...truncated...]
Author: Hector Villalobos and Eduardo Gonzalez-Rodriguez <egonzale@cicese.mx>
Maintainer: Hector Villalobos <hvillalo@ipn.mx>

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Package Rdimtools updated to version 1.1.0 with previous version 1.0.9 dated 2022-02-04

Title: Dimension Reduction and Estimation Methods
Description: We provide linear and nonlinear dimension reduction techniques. Intrinsic dimension estimation methods for exploratory analysis are also provided. For more details on the package, see the paper by You (2020) <arXiv:2005.11107>.
Author: Kisung You [aut, cre] , Changhee Suh [ctb], Dennis Shung [ctb]
Maintainer: Kisung You <kisungyou@outlook.com>

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Package NEONiso updated to version 0.6.1 with previous version 0.6.0 dated 2022-08-08

Title: Tools to Calibrate and Work with NEON Atmospheric Isotope Data
Description: Functions for downloading, calibrating, and analyzing atmospheric isotope data bundled into the eddy covariance data products of the National Ecological Observatory Network (NEON) <https://www.neonscience.org>. Calibration tools are provided for carbon and water isotope products. Carbon isotope calibration details are found in Fiorella et al. (2021) <doi:10.1029/2020JG005862>, and the readme file at <https://github.com/lanl/NEONiso>. Tools for calibrating water isotope products have been added as of 0.6.0, but have known deficiencies and should be considered very experimental currently.
Author: Rich Fiorella [aut, cre]
Maintainer: Rich Fiorella <rfiorella@lanl.gov>

Diff between NEONiso versions 0.6.0 dated 2022-08-08 and 0.6.1 dated 2022-09-22

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Package sglasso updated to version 1.2.5 with previous version 1.2.4 dated 2019-12-05

Title: Lasso Method for RCON(V,E) Models
Description: RCON(V, E) models are a kind of restriction of the Gaussian Graphical Models defined by a set of equality constraints on the entries of the concentration matrix. 'sglasso' package implements the structured graphical lasso (sglasso) estimator proposed in Abbruzzo et al. (2014) for the weighted l1-penalized RCON(V, E) model. Two cyclic coordinate algorithms are implemented to compute the sglasso estimator, i.e. a cyclic coordinate minimization (CCM) and a cyclic coordinate descent (CCD) algorithm.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro <luigi.augugliaro@unipa.it>

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Package scoper updated to version 1.2.1 with previous version 1.2.0 dated 2021-11-02

Title: Spectral Clustering-Based Method for Identifying B Cell Clones
Description: Provides a computational framework for identification of B cell clones from Adaptive Immune Receptor Repertoire sequencing (AIRR-Seq) data. Three main functions are included (identicalClones, hierarchicalClones, and spectralClones) that perform clustering among sequences of BCRs/IGs (B cell receptors/immunoglobulins) which share the same V gene, J gene and junction length. Nouri N and Kleinstein SH (2018) <doi: 10.1093/bioinformatics/bty235>. Nouri N and Kleinstein SH (2019) <doi: 10.1101/788620>. Gupta NT, et al. (2017) <doi: 10.4049/jimmunol.1601850>.
Author: Nima Nouri [aut], Edel Aron [ctb], Susanna Marquez [ctb, cre], Jason Vander Heiden [aut], Steven Kleinstein [aut, cph]
Maintainer: Susanna Marquez <susanna.marquez@yale.edu>

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Package refdb updated to version 0.1.1 with previous version 0.1.0 dated 2022-09-19

Title: A DNA Reference Library Manager
Description: Reference database manager offering a set of functions to import, organize, clean, filter, audit and export reference genetic data. Provide functions to download sequence data from Bold Systems (<https://www.boldsystems.org/>) and NCBI GenBank <https://www.ncbi.nlm.nih.gov/genbank/>. Designed as an environment for semi-automatic and assisted construction of reference databases and to improve standardization and repeatability in barcoding and metabarcoding studies.
Author: Francois Keck [aut, cre, cph]
Maintainer: Francois Keck <francois.keck@gmail.com>

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Package adw updated to version 0.2.0 with previous version 0.1.0 dated 2022-03-01

Title: Angular Distance Weighting Interpolation
Description: The irregularly-spaced data are interpolated onto regular latitude-longitude grids by weighting each station according to its distance and angle from the center of a search radius.
Author: Panfeng Zhang [aut, cre]
Maintainer: Panfeng Zhang <zhangpanfeng@cug.edu.cn>

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Package rabhit updated to version 0.2.4 with previous version 0.2.1 dated 2022-02-16

Title: Inference Tool for Antibody Haplotype
Description: Infers V-D-J haplotypes and gene deletions from AIRR-seq data for Ig and TR chains, based on J, D, or V genes as anchor, by adapting a Bayesian framework. It also calculates a Bayes factor, a number that indicates the certainty level of the inference, for each haplotyped gene. Citation: Gidoni, et al (2019) <doi:10.1038/s41467-019-08489-3>. Peres and Gidoni, et al (2019) <doi:10.1093/bioinformatics/btz481>.
Author: Ayelet Peres [aut, cre], Moriah Gidoni [aut], Gur Yaari [aut, cph]
Maintainer: Ayelet Peres <peresay@biu.ac.il>

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Package universals updated to version 0.0.5 with previous version 0.0.4 dated 2020-09-24

Title: S3 Generics for Bayesian Analyses
Description: Provides S3 generic methods and some default implementations for Bayesian analyses that generate Markov Chain Monte Carlo (MCMC) samples. The purpose of 'universals' is to reduce package dependencies and conflicts. The 'nlist' package implements many of the methods for its 'nlist' class.
Author: Joe Thorley [aut, cre] , Kirill Mueller [ctb] , Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

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Package sen2r updated to version 1.5.3 with previous version 1.5.1 dated 2022-04-12

Title: Find, Download and Process Sentinel-2 Data
Description: Functions to download Sentinel-2 optical images and perform preliminary processing operations. 'sen2r' provides the instruments required to easily perform (and eventually automate) the steps necessary to build a complete Sentinel-2 processing chain. A Graphical User Interface to facilitate data processing is also provided. For additional documentation refer to the following article: Ranghetti et al. (2020) <doi:10.1016/j.cageo.2020.104473>.
Author: Luigi Ranghetti [aut, cre] , Lorenzo Busetto [aut] , Marina Ranghetti [ctb]
Maintainer: Luigi Ranghetti <sen2r@ranghetti.info>

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Package pracma updated to version 2.4.2 with previous version 2.3.8 dated 2022-03-04

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 envir updated to version 0.2.2 with previous version 0.2.1 dated 2021-09-20

Title: Manage R Environments Better
Description: Provides a small set of functions for managing R environments, with defaults designed to encourage usage patterns that scale well to larger code bases. It provides: import_from(), a flexible way to assign bindings that defaults to the current environment; include(), a vectorized alternative to base::source() that also default to the current environment; and attach_eval() and attach_source(), a way to evaluate expressions in attached environments. Together, these (and other) functions pair to provide a robust alternative to base::library() and base::source().
Author: Tomasz Kalinowski [aut, cre]
Maintainer: Tomasz Kalinowski <kalinowskit@gmail.com>

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Package DiceView updated to version 2.0-2 with previous version 2.0-1 dated 2020-11-27

Title: Methods for Visualization of Computer Experiments Design and Surrogate
Description: View 2D/3D sections, contour plots, mesh of excursion sets for computer experiments designs, surrogates or test functions.
Author: Yann Richet [aut, cre] , Yves Deville [aut], Clement Chevalier [ctb]
Maintainer: Yann Richet <yann.richet@irsn.fr>

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Package datefixR updated to version 1.2.0 with previous version 1.1.0 dated 2022-08-12

Title: Standardize Dates in Different Formats or with Missing Data
Description: There are many different formats dates are commonly represented with: the order of day, month, or year can differ, different separators ("-", "/", or whitespace) can be used, months can be numerical, names, or abbreviations and year given as two digits or four. 'datefixR' takes dates in all these different formats and converts them to R's built-in date class. If 'datefixR' cannot standardize a date, such as because it is too malformed, then the user is told which date cannot be standardized and the corresponding ID for the row. 'datefixR' also allows the imputation of missing days and months with user-controlled behavior.
Author: Nathan Constantine-Cooke [aut, cre] , Jonathan Kitt [ctb, trl], Antonio J. Perez-Luque [ctb, trl] , Kaique dos S. Alves [rev] , Al-Ahmadgaid B. Asaad [rev]
Maintainer: Nathan Constantine-Cooke <nathan.constantine-cooke@ed.ac.uk>

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Package rAmCharts4 updated to version 1.6.0 with previous version 1.5.0 dated 2021-10-10

Title: Interface to the JavaScript Library 'amCharts 4'
Description: Creates JavaScript charts. The charts can be included in 'Shiny' apps and R markdown documents, or viewed from the R console and 'RStudio' viewer. Based on the JavaScript library 'amCharts 4' and the R packages 'htmlwidgets' and 'reactR'. Currently available types of chart are: vertical and horizontal bar chart, radial bar chart, stacked bar chart, vertical and horizontal Dumbbell chart, line chart, scatter chart, range area chart, gauge chart, boxplot chart, pie chart, and 100% stacked bar chart.
Author: Stephane Laurent [aut, cre], Antanas Marcelionis [ctb, cph] ), Terence Eden [ctb, cph] ), Tom Alexander [ctb, cph] )
Maintainer: Stephane Laurent <laurent_step@outlook.fr>

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Package SCORPION updated to version 1.0.1 with previous version 1.0.0 dated 2022-09-21

Title: Single Cell Oriented Reconstruction of PANDA Individual Optimized Networks
Description: Constructs gene regulatory networks from single-cell gene expression data using the PANDA (Passing Attributes between Networks for Data Assimilation) algorithm.
Author: Daniel Osorio [aut, cre] , Marieke L. Kuijjer [aut]
Maintainer: Daniel Osorio <daniecos@uio.no>

Diff between SCORPION versions 1.0.0 dated 2022-09-21 and 1.0.1 dated 2022-09-22

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Package LambertW updated to version 0.6.7-1 with previous version 0.6.7 dated 2022-02-28

Title: Probabilistic Models to Analyze and Gaussianize Heavy-Tailed, Skewed Data
Description: Lambert W x F distributions are a generalized framework to analyze skewed, heavy-tailed data. It is based on an input/output system, where the output random variable (RV) Y is a non-linearly transformed version of an input RV X ~ F with similar properties as X, but slightly skewed (heavy-tailed). The transformed RV Y has a Lambert W x F distribution. This package contains functions to model and analyze skewed, heavy-tailed data the Lambert Way: simulate random samples, estimate parameters, compute quantiles, and plot/ print results nicely. The most useful function is 'Gaussianize', which works similarly to 'scale', but actually makes the data Gaussian. A do-it-yourself toolkit allows users to define their own Lambert W x 'MyFavoriteDistribution' and use it in their analysis right away.
Author: Georg M. Goerg [aut, cre]
Maintainer: Georg M. Goerg <im@gmge.org>

Diff between LambertW versions 0.6.7 dated 2022-02-28 and 0.6.7-1 dated 2022-09-22

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Package sparsegl updated to version 0.5.0 with previous version 0.4.0 dated 2022-09-05

Title: Sparse Group Lasso
Description: Efficient implementation of sparse group lasso with optional bound constraints on the coefficients. It supports the use of a sparse design matrix as well as returning coefficient estimates in a sparse matrix. Furthermore, it correctly calculates the degrees of freedom to allow for information criteria rather than cross-validation with very large data. Finally, the interface to compiled code avoids unnecessary copies and allows for the use of long integers.
Author: Daniel J. McDonald [aut, cre], Xiaoxuan Liang [aut], Aaron Cohen [aut]
Maintainer: Daniel J. McDonald <daniel@stat.ubc.ca>

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Package mosaicCore updated to version 0.9.2.1 with previous version 0.9.2 dated 2022-08-26

Title: Common Utilities for Other MOSAIC-Family Packages
Description: Common utilities used in other MOSAIC-family packages are collected here.
Author: Randall Pruim <rpruim@calvin.edu>, Daniel T. Kaplan <kaplan@macalester.edu>, Nicholas J. Horton <nhorton@amherst.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>

Diff between mosaicCore versions 0.9.2 dated 2022-08-26 and 0.9.2.1 dated 2022-09-22

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Package miceadds updated to version 3.15-21 with previous version 3.14-3 dated 2022-08-25

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 implemented. 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. [...truncated...]
Author: Alexander Robitzsch [aut,cre] , Simon Grund [aut] , Thorsten Henke [ctb]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

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Package Directional updated to version 5.6 with previous version 5.5 dated 2022-05-24

Title: A Collection of Functions for Directional Data Analysis
Description: A collection of functions for directional data (including massive data, with millions of observations) analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000). Other references include a) Phillip J. Paine, Simon P. Preston Michail Tsagris and Andrew T. A. Wood (2018). An elliptically symmetric angular Gaussian distribution. Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>. b) Tsagris M. and Alenazi A. (2019). Comparison of discriminant analysis methods on the sphere. Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>. c) P. J. Paine, S. P. Preston, M. Tsagris and Andrew T. A. Wood (2020). Spherical regression models with general covariates and anisotropic errors. Statistics and Computing 30(1): 153--165. <doi:10. [...truncated...]
Author: Michail Tsagris, Giorgos Athineou, Christos Adam, Anamul Sajib, Eli Amson, Micah J. Waldstein
Maintainer: Michail Tsagris <mtsagris@uoc.gr>

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Package sdcTable updated to version 0.32.4 with previous version 0.32.3 dated 2022-07-16

Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in tabular data such as primary and secondary cell suppression as described for example in Hundepol et al. (2012) <doi:10.1002/9781118348239> are covered in this package.
Author: Bernhard Meindl [aut, cre]
Maintainer: Bernhard Meindl <bernhard.meindl@gmail.com>

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Package mlr3misc updated to version 0.11.0 with previous version 0.10.0 dated 2022-01-11

Title: Helper Functions for 'mlr3'
Description: Frequently used helper functions and assertions used in 'mlr3' and its companion packages. Comes with helper functions for functional programming, for printing, to work with 'data.table', as well as some generally useful 'R6' classes. This package also supersedes the package 'BBmisc'.
Author: Michel Lang [cre, aut] , Patrick Schratz [aut]
Maintainer: Michel Lang <michellang@gmail.com>

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Package igraph updated to version 1.3.5 with previous version 1.3.4 dated 2022-07-19

Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.
Author: See AUTHORS file.
Maintainer: Tamas Nepusz <ntamas@gmail.com>

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Package shinyHugePlot updated to version 0.1.0 with previous version 0.0.1 dated 2022-08-22

Title: Efficient Plotting of Large-Sized Data
Description: A tool to plot data with large sample size using 'shiny' and 'plotly'. Relatively small samples are chosen from the data using an appropriate algorithm according to a user-defined x range. Jonas Van Der Donckt, Jeroen Van Der Donckt, Emiel Deprost (2022) <https://github.com/predict-idlab/plotly-resampler>.
Author: Junta Tagusari [aut, cre, cph], Jonas Van Der Donckt [cph], Jeroen Van Der Donckt [cph], Emiel Deprost [cph]
Maintainer: Junta Tagusari <j.tagusari@eng.hokudai.ac.jp>

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Wed, 21 Sep 2022

Package this.path updated to version 1.0.0 with previous version 0.11.0 dated 2022-09-03

Title: Get Executing Script's Path, from 'RStudio', 'Rgui', 'VSCode', 'Rscript' (Shells Including Windows Command-Line / / Unix Terminal), and 'source'
Description: Determine the full path of the executing script. Works when running a line or selection from a script in 'RStudio', 'Rgui', and 'VSCode', when using 'source', 'sys.source', 'debugSource' in 'RStudio', and 'testthat::source_file', and when running from a shell.
Author: Andrew Simmons
Maintainer: Andrew Simmons <akwsimmo@gmail.com>

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Package survivoR updated to version 2.0 with previous version 1.0.1 dated 2022-05-31

Title: Data from all Seasons of Survivor (US) TV Series in Tidy Format
Description: Several datasets which detail the results and events of each season of Survivor. This includes details on the cast, voting history, immunity and reward challenges, jury votes and viewers. This data is useful for practicing data wrangling, graph analytics and analysing how each season of Survivor played out. Includes 'ggplot2' scales and colour palettes for visualisation.
Author: Daniel Oehm [aut, cre], Carly Levitz [ctb], Dario Mavec [ctb]
Maintainer: Daniel Oehm <danieloehm@gmail.com>

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Package shar updated to version 2.0.0 with previous version 1.3.2 dated 2022-03-08

Title: Species-Habitat Associations
Description: Analyse species-habitat associations in R. Therefore, information about the location of the species (as a point pattern) is needed together with environmental conditions (as a categorical raster). To test for significance habitat associations, one of the two components is randomized. Methods are mainly based on Plotkin et al. (2000) <doi:10.1006/jtbi.2000.2158> and Harms et al. (2001) <doi:10.1111/j.1365-2745.2001.00615.x>.
Author: Maximillian H.K. Hesselbarth [aut, cre] , Marco Sciaini [aut] , Zeke Marshall [ctb] , Thomas Etherington [ctb]
Maintainer: Maximillian H.K. Hesselbarth <mhk.hesselbarth@gmail.com>

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Package Seurat updated to version 4.2.0 with previous version 4.1.1 dated 2022-05-02

Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Author: Andrew Butler [ctb] , Saket Choudhary [ctb] , Charlotte Darby [ctb] , Jeff Farrell [ctb], Christoph Hafemeister [ctb] , Yuhan Hao [ctb] , Paul Hoffman [aut, cre] , Jaison Jain [ctb] , Efthymia Papalexi [ctb] , Patrick Roelli [ctb], Rahul Satija [ctb] [...truncated...]
Maintainer: Paul Hoffman <seurat@nygenome.org>

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Package sageR updated to version 0.6.0 with previous version 0.3.0 dated 2021-07-20

Title: Applied Statistics for Economics and Management with R
Description: Datasets and functions for the book "Statistiques pour l’économie et la gestion", "Théorie et applications en entreprise", F. Bertrand, Ch. Derquenne, G. Dufrénot, F. Jawadi and M. Maumy, C. Borsenberger editor, (2021, ISBN:9782807319448, De Boeck Supérieur, Louvain-la-Neuve). The first chapter of the book is dedicated to an introduction to statistics and their world. The second chapter deals with univariate exploratory statistics and graphics. The third chapter deals with bivariate and multivariate exploratory statistics and graphics. The fourth chapter is dedicated to data exploration with Principal Component Analysis. The fifth chapter is dedicated to data exploration with Correspondance Analysis. The sixth chapter is dedicated to data exploration with Multiple Correspondance Analysis. The seventh chapter is dedicated to data exploration with automatic clustering. The eighth chapter is dedicated to an introduction to probability theory and classical probability distributions. The ni [...truncated...]
Author: Frederic Bertrand [cre, aut] , Claire Borsenberger [ctb], Christian Derquenne [ctb], Gilles Dufrenot [ctb], Fredj Jawadi [ctb], Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>

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Package mMARCH.AC updated to version 2.4.0.1 with previous version 2.4.0.0 dated 2022-08-22

Title: Processing of Accelerometry Data with 'GGIR' in mMARCH
Description: Mobile Motor Activity Research Consortium for Health (mMARCH) is a collaborative network of studies of clinical and community samples that employ common clinical, biological, and digital mobile measures across involved studies. One of the main scientific goals of mMARCH sites is developing a better understanding of the inter-relationships between accelerometry-measured physical activity (PA), sleep (SL), and circadian rhythmicity (CR) and mental and physical health in children, adolescents, and adults. Currently, there is no consensus on a standard procedure for a data processing pipeline of raw accelerometry data, and few open-source tools to facilitate their development. The R package 'GGIR' is the most prominent open-source software package that offers great functionality and tremendous user flexibility to process raw accelerometry data. However, even with 'GGIR', processing done in a harmonized and reproducible fashion requires a non-trivial amount of expertise combined with a care [...truncated...]
Author: Wei Guo [aut, cre], Andrew Leroux [aut], Vadim Zipunnikov [aut], Kathleen Merikangas [aut]
Maintainer: Wei Guo <wei.guo3@nih.gov>

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Package geoknife updated to version 1.6.8 with previous version 1.6.7 dated 2022-07-20

Title: Web-Processing of Large Gridded Datasets
Description: Processes gridded datasets found on the U.S. Geological Survey Geo Data Portal web application or elsewhere, using a web-enabled workflow that eliminates the need to download and store large datasets that are reliably hosted on the Internet. The package provides access to several data subset and summarization algorithms that are available on remote web processing servers (Read et al. (2015) <doi:10.1111/ecog.01880>).
Author: Jordan Read [aut], Jordan Walker [aut], Alison Appling [aut], David Blodgett [aut, cre], Emily Read [aut], Luke Winslow [aut], Lindsay Carr [aut], David Watkins [aut]
Maintainer: David Blodgett <dblodgett@usgs.gov>

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Package Correlplot updated to version 1.0.4 with previous version 1.0.3 dated 2022-09-20

Title: A Collection of Functions for Graphing Correlation Matrices
Description: Routines for the graphical representation of correlation matrices by means of correlograms, biplots and MDS maps.
Author: Jan Graffelman
Maintainer: Jan Graffelman <jan.graffelman@upc.edu>

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Package bnlearn updated to version 4.8.1 with previous version 4.8 dated 2022-09-19

Title: Bayesian Network Structure Learning, Parameter Learning and Inference
Description: Bayesian network structure learning, parameter learning and inference. This package implements constraint-based (PC, GS, IAMB, Inter-IAMB, Fast-IAMB, MMPC, Hiton-PC, HPC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing and Tabu Search) and hybrid (MMHC, RSMAX2, H2PC) structure learning algorithms for discrete, Gaussian and conditional Gaussian networks, along with many score functions and conditional independence tests. The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also implemented. Some utility functions (model comparison and manipulation, random data generation, arc orientation testing, simple and advanced plots) are included, as well as support for parameter estimation (maximum likelihood and Bayesian) and inference, conditional probability queries, cross-validation, bootstrap and model averaging. Development snapshots with the latest bugfixes are available from <https://www.bnlearn.com/>.
Author: Marco Scutari [aut, cre], Tomi Silander [ctb], Robert Ness [ctb]
Maintainer: Marco Scutari <scutari@bnlearn.com>

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Package toolbox updated to version 0.1.1 with previous version 0.1.0 dated 2022-06-23

Title: List, String, and Meta Programming Utility Functions
Description: Includes functions for mapping named lists to function arguments, random strings, pasting and combining rows together across columns, etc.
Author: Timothy Conwell
Maintainer: Timothy Conwell <timconwell@gmail.com>

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Package Rlabkey updated to version 2.9.0 with previous version 2.8.4 dated 2022-04-01

Title: Data Exchange Between R and 'LabKey' Server
Description: The 'LabKey' client library for R makes it easy for R users to load live data from a 'LabKey' Server, <https://www.labkey.com/>, into the R environment for analysis, provided users have permissions to read the data. It also enables R users to insert, update, and delete records stored on a 'LabKey' Server, provided they have appropriate permissions to do so.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>

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Package catmaply updated to version 0.9.2 with previous version 0.9.0 dated 2020-09-07

Title: Heatmap for Categorical Data using 'plotly'
Description: Methods and plotting functions for displaying categorical data on an interactive heatmap using 'plotly'. Provides functionality for strictly categorical heatmaps, heatmaps illustrating categorized continuous data and annotated heatmaps. Also, there are various options to interact with the x-axis to prevent overlapping axis labels, e.g. via simple sliders or range sliders. Besides the viewer pane, resulting plots can be saved as a standalone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app.
Author: Yves Mauron [aut, cre], Trivadis AG [cph]
Maintainer: Yves Mauron <ypmauron@gmail.com>

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Package snahelper updated to version 1.4.1 with previous version 1.4.0 dated 2021-12-17

Title: 'RStudio' Addin for Network Analysis and Visualization
Description: 'RStudio' addin which provides a GUI to visualize and analyse networks. After finishing a session, the code to produce the plot is inserted in the current script. Alternatively, the function SNAhelperGadget() can be used directly from the console. Additional addins include the Netreader() for reading network files, Netbuilder() to create small networks via point and click, and the Componentlayouter() to layout networks with many components manually.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david@schochastics.net>

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Package calidad updated to version 0.2.0 with previous version 0.1.0 dated 2022-08-23

Title: Assesses the Quality of Estimates Made by Complex Sample Designs
Description: Assesses the quality of estimates made by complex sample designs, following the methodology developed by the National Institute of Statistics Chile (2020, <https://www.ine.cl/docs/default-source/institucionalidad/buenas-pr%C3%A1cticas/clasificaciones-y-estandares/est%C3%A1ndar-evaluaci%C3%B3n-de-calidad-de-estimaciones-publicaci%C3%B3n-27022020.pdf>) and by Economic Commission for Latin America and Caribbean (2020, <https://repositorio.cepal.org/bitstream/handle/11362/45681/1/S2000293_es.pdf>).
Author: Klaus Lehmann [aut, cre], Ricardo Pizarro [aut], Ignacio Agloni [ctb]
Maintainer: Klaus Lehmann <klehmann@fen.uchile.cl>

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Package Signac updated to version 1.8.0 with previous version 1.7.0 dated 2022-06-01

Title: Analysis of Single-Cell Chromatin Data
Description: A framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis. Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.
Author: Tim Stuart [aut, cre] , Avi Srivastava [aut] , Paul Hoffman [ctb] , Rahul Satija [ctb]
Maintainer: Tim Stuart <tstuart@nygenome.org>

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Package pksensi updated to version 1.2.3 with previous version 1.2.2 dated 2021-07-04

Title: Global Sensitivity Analysis in Physiologically Based Kinetic Modeling
Description: Applying the global sensitivity analysis workflow to investigate the parameter uncertainty and sensitivity in physiologically based kinetic (PK) models, especially the physiologically based pharmacokinetic/toxicokinetic model with multivariate outputs. The package also provides some functions to check the convergence and sensitivity of model parameters. The workflow was first mentioned in Hsieh et al., (2018) <doi:10.3389/fphar.2018.00588>, then further refined (Hsieh et al., 2020 <doi:10.1016/j.softx.2020.100609>).
Author: Nan-Hung Hsieh [aut, cre] , Brad Reisfeld [ctb] , Weihsueh A. Chiu [ctb]
Maintainer: Nan-Hung Hsieh <d99622005@ntu.edu.tw>

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Package stdmod updated to version 0.2.0.0 with previous version 0.1.7.4 dated 2022-08-07

Title: Standardized Moderation Effect and Its Confidence Interval
Description: Functions for computing a standardized moderation effect in moderated regression and forming its confidence interval by nonparametric bootstrapping as proposed in Cheung, Cheung, Lau, Hui, and Vong (2022) <doi:10.1037/hea0001188>. Also includes simple-to-use functions for computing conditional effects (unstandardized or standardized) and plotting moderation effects.
Author: Shu Fai Cheung [aut, cre] , David Weng Ngai Vong [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>

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Package sctransform updated to version 0.3.5 with previous version 0.3.4 dated 2022-08-20

Title: Variance Stabilizing Transformations for Single Cell UMI Data
Description: A normalization method for single-cell UMI count data using a variance stabilizing transformation. The transformation is based on a negative binomial regression model with regularized parameters. As part of the same regression framework, this package also provides functions for batch correction, and data correction. See Hafemeister and Satija (2019) <doi:10.1186/s13059-019-1874-1>, and Choudhary and Satija (2022) <doi:10.1186/s13059-021-02584-9> for more details.
Author: Christoph Hafemeister [aut] , Saket Choudhary [aut, cre] , Rahul Satija [ctb]
Maintainer: Saket Choudhary <schoudhary@nygenome.org>

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Package kalmanfilter updated to version 2.0.0 with previous version 1.0.0 dated 2022-09-02

Title: Kalman Filter
Description: 'Rcpp' implementation of the multivariate Kalman filter for state space models that can handle missing values and exogenous data in the observation and state equations. Kim, Chang-Jin and Charles R. Nelson (1999) "State-Space Models with Regime Switching: Classical and Gibbs-Sampling Approaches with Applications" <doi:10.7551/mitpress/6444.001.0001><http://econ.korea.ac.kr/~cjkim/>.
Author: Alex Hubbard [aut, cre]
Maintainer: Alex Hubbard <hubbard.alex@gmail.com>

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Package envalysis updated to version 0.5.3 with previous version 0.5.1 dated 2021-03-05

Title: Miscellaneous Functions for Environmental Analyses
Description: Small toolbox for data analyses in environmental chemistry and ecotoxicology. Provides, for example, calibration() to calculate calibration curves and corresponding limits of detection (LODs) and limits of quantification (LOQs) according to German DIN 32645 (2008). texture() makes it easy to estimate soil particle size distributions from hydrometer measurements (ASTM D422-63, 2007).
Author: Zacharias Steinmetz [aut, cre] , Julius Albert [ctb] , Kilian Kenngott [ctb]
Maintainer: Zacharias Steinmetz <steinmetz-z@uni-landau.de>

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Package r2redux updated to version 1.0.11 with previous version 1.0.10 dated 2022-08-08

Title: R2 Statistic
Description: R2 statistic for significance test. Variance and covariance of R2 values used to assess the 95% CI and p-value of the R2 difference.
Author: Hong Lee [aut, cph], Moksedul Momin [aut, cre, cph]
Maintainer: Moksedul Momin <cvasu.momin@gmail.com>

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Package deepregression updated to version 0.2 with previous version 0.1 dated 2021-10-04

Title: Fitting Deep Distributional Regression
Description: Allows for the specification of semi-structured deep distributional regression models which are fitted in a neural network as proposed by Ruegamer et al. (2021) <arXiv:2104.02705>. Predictors can be modeled using structured (penalized) linear effects, structured non-linear effects or using an unstructured deep network model.
Author: David Ruegamer [aut, cre], Florian Pfisterer [ctb], Philipp Baumann [ctb], Chris Kolb [ctb], Lucas Kook [ctb]
Maintainer: David Ruegamer <david.ruegamer@gmail.com>

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Package pRecipe updated to version 0.3.0 with previous version 0.2.0 dated 2022-04-22

Title: Precipitation R Recipe
Description: An open-access tool/framework to download, validate, visualize, and analyze multi-source precipitation data across various spatio-temporal scales. Ultimately providing the hydrology science community with the tools for consistent and reproducible analysis regarding precipitation.
Author: Mijael Rodrigo Vargas Godoy [aut, cre], Yannis Markonis [aut, ths]
Maintainer: Mijael Rodrigo Vargas Godoy <mirovago@gmail.com>

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More information about pRecipe at CRAN
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Package circletyper updated to version 1.0.2 with previous version 1.0.1 dated 2021-07-17

Title: Curve Text Elements in 'Shiny' Using 'CircleType.js'
Description: Enables curving text elements in 'Shiny' apps.
Author: Etienne Bacher [aut, cre, cph]
Maintainer: Etienne Bacher <etienne.bacher@protonmail.com>

Diff between circletyper versions 1.0.1 dated 2021-07-17 and 1.0.2 dated 2022-09-21

 DESCRIPTION                          |    6 -
 LICENSE                              |    4 
 MD5                                  |   38 ++++-----
 NAMESPACE                            |    2 
 NEWS.md                              |   18 ++--
 R/circletype.R                       |  144 +++++++++++++++++------------------
 R/remove_circletype.R                |   86 ++++++++++----------
 R/use_circletype.R                   |   64 +++++++--------
 R/zzz.R                              |   20 ++--
 README.md                            |  122 ++++++++++++++---------------
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 inst/custom/destroy.js               |    8 -
 man/circletype.Rd                    |   70 ++++++++---------
 man/remove_circletype.Rd             |   94 +++++++++++-----------
 man/use_circletype.Rd                |   56 ++++++-------
 tests/spelling.R                     |    6 -
 tests/testthat.R                     |    8 -
 tests/testthat/test-circletype.R     |  114 +++++++++++++--------------
 tests/testthat/test-use_circletype.R |    6 -
 20 files changed, 446 insertions(+), 442 deletions(-)

More information about circletyper at CRAN
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Package saeMSPE updated to version 1.1 with previous version 1.0 dated 2022-03-29

Title: Compute MSPE Estimates for the Fay Herriot Model and Nested Error Regression Model
Description: We describe a new R package entitled 'saeMSPE' for the well-known Fay Herriot model and nested error regression model in small area estimation. Based on this package, it is possible to easily compute various common mean squared predictive error (MSPE) estimators, as well as several existing variance component predictors as a byproduct, for these two models.
Author: Peiwen Xiao [aut, cre], Xiaohui Liu [aut], Yuzi Liu [aut], Shaochu Liu [aut], Jiming Jiang [ths]
Maintainer: Peiwen Xiao <2569613200@qq.com>

Diff between saeMSPE versions 1.0 dated 2022-03-29 and 1.1 dated 2022-09-21

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 29 files changed, 269 insertions(+), 247 deletions(-)

More information about saeMSPE at CRAN
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