Sat, 06 Aug 2022

Package FIESTAutils updated to version 1.1.3 with previous version 1.1.2 dated 2022-06-14

Title: Utility Functions for Forest Inventory Estimation and Analysis
Description: A set of tools for data wrangling, spatial data analysis, statistical modeling (including direct, model-assisted, photo-based, and small area tools), and USDA Forest Service data base tools. These tools are aimed to help Foresters, Analysts, and Scientists extract and perform analyses on USDA Forest Service data.
Author: Tracey Frescino [aut], Chris Toney [aut], Grayson White [aut, cre]
Maintainer: Grayson White <graysonwhite13@gmail.com>

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Package DLPCA updated to version 0.0.5 with previous version 0.0.2 dated 2022-05-18

Title: The Distributed Local PCA Algorithm
Description: Algorithm to handle with optimal subset selection for distributed local principal component analysis. The philosophy of the package is described in Guo G. (2020) <doi:10.1080/02331888.2020.1823979>.
Author: Guangbao Guo [aut, cre] , Guoqi Qian [aut], Yixiao Liu [aut], Haoyue Song [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>

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Package ravetools updated to version 0.0.5 with previous version 0.0.4 dated 2022-05-29

Title: Signal Processing Toolbox for Analyzing 'Electrophysiology' Data
Description: Implemented fast and memory-efficient 'Notch'-filter, 'Welch-periodogram', and discrete wavelet transform algorithm for hours of high-resolution signals; providing fundamental toolbox for 'iEEG' preprocess pipelines. Documentation and examples about 'RAVE' project are provided at <https://openwetware.org/wiki/RAVE>, and the paper by John F. Magnotti, Zhengjia Wang, Michael S. Beauchamp (2020) <doi:10.1016/j.neuroimage.2020.117341>; see 'citation("ravetools")' for details.
Author: Zhengjia Wang [aut, cre, cph], Beauchamp lab [cph], Karim Rahim [cph] , Prerau Lab [cph] , RcppParallel Authors [cph] , Marcus Geelnard [cph]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>

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Package hdtg updated to version 0.2.0 with previous version 0.1.0 dated 2022-06-28

Title: Generate Samples from Multivariate Truncated Normal Distributions
Description: Efficient sampling from high-dimensional truncated Gaussian distributions, or multivariate truncated normal (MTN). Techniques include zigzag Hamiltonian Monte Carlo as in Akihiko Nishimura, Zhenyu Zhang and Marc A. Suchard (2021) <arXiv:2104.07694>, and harmonic Monte in Ari Pakman and Liam Paninski (2014) <doi:10.1080/10618600.2013.788448>.
Author: Zhenyu Zhang [aut, cre], Andrew Chin [aut], Akihiko Nishimura [aut], Marc A. Suchard [aut], John W. Ratcliff et al. [cph, ctb]
Maintainer: Zhenyu Zhang <zhangzhenyusa@gmail.com>

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Package nparLD updated to version 2.2 with previous version 2.1-1 dated 2022-06-27

Title: Nonparametric Analysis of Longitudinal Data in Factorial Experiments
Description: Performs nonparametric analysis of longitudinal data in factorial experiments. Longitudinal data are those which are collected from the same subjects over time, and they frequently arise in biological sciences. Nonparametric methods do not require distributional assumptions, and are applicable to a variety of data types (continuous, discrete, purely ordinal, and dichotomous). Such methods are also robust with respect to outliers and for small sample sizes.
Author: Kimihiro Noguchi <noguchk@wwu.edu>, Mahbub Latif <mlatif@isrt.ac.bd>, Karthinathan Thangavelu, Frank Konietschke <frank.konietschke@charite.de>, Yulia R. Gel <yxg142030@utdallas.edu>, Edgar Brunner <ebrunne1@gwdg.de>
Maintainer: Frank Konietschke <frank.konietschke@charite.de>

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Package mark updated to version 0.5.1 with previous version 0.5.0 dated 2022-03-09

Title: Miscellaneous, Analytic R Kernels
Description: Miscellaneous functions and wrappers for development in other packages created, maintained by Jordan Mark Barbone.
Author: Jordan Mark Barbone [aut, cph, cre]
Maintainer: Jordan Mark Barbone <jmbarbone@gmail.com>

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Package MAd updated to version 0.8-3 with previous version 0.8-2.1 dated 2018-08-31

Title: Meta-Analysis with Mean Differences
Description: A collection of functions for conducting a meta-analysis with mean differences data. It uses recommended procedures as described in The Handbook of Research Synthesis and Meta-Analysis (Cooper, Hedges, & Valentine, 2009).
Author: AC Del Re [aut, cre] , William Hoyt [aut]
Maintainer: AC Del Re <acdelre@gmail.com>

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Package nflfastR updated to version 4.4.0 with previous version 4.3.0 dated 2021-10-06

Title: Functions to Efficiently Access NFL Play by Play Data
Description: A set of functions to access National Football League play-by-play data from <https://www.nfl.com/>.
Author: Sebastian Carl [aut], Ben Baldwin [cre, aut], Lee Sharpe [ctb], Maksim Horowitz [ctb], Ron Yurko [ctb], Samuel Ventura [ctb], Tan Ho [ctb], John Edwards [ctb]
Maintainer: Ben Baldwin <bbaldwin206@gmail.com>

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Package nflreadr updated to version 1.3.0 with previous version 1.2.0 dated 2022-03-17

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 DBR updated to version 1.4.0 with previous version 1.3.0 dated 2022-07-18

Title: Discrete Beta Regression
Description: Bayesian Beta Regression, adapted for bounded discrete responses, commonly seen in survey responses. Estimation is done via Markov Chain Monte Carlo sampling, using a Gibbs wrapper around univariate slice sampler (Neal (2003) <DOI:10.1214/aos/1056562461>), as implemented in the R package MfUSampler (Mahani and Sharabiani (2017) <DOI: 10.18637/jss.v078.c01>).
Author: Alireza Mahani [cre, aut], Mansour Sharabiani [aut], Alex Bottle [aut], Cathy Price [aut]
Maintainer: Alireza Mahani <alireza.s.mahani@gmail.com>

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Package tipr updated to version 1.0.0 with previous version 0.4.1 dated 2022-05-05

Title: Tipping Point Analyses
Description: The strength of evidence provided by epidemiological and observational studies is inherently limited by the potential for unmeasured confounding. We focus on three key quantities: the observed bound of the confidence interval closest to the null, a plausible residual effect size for an unmeasured continuous or binary confounder, and a realistic mean difference or prevalence difference for this hypothetical confounder. Building on the methods put forth by Lin, Psaty, & Kronmal (1998) <doi:10.2307/2533848>, we can use these quantities to assess how an unmeasured confounder may tip our result to insignificance, rendering the study inconclusive.
Author: Lucy D'Agostino McGowan [aut, cre]
Maintainer: Lucy D'Agostino McGowan <lucydagostino@gmail.com>

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Package recometrics updated to version 0.1.6-1 with previous version 0.1.6 dated 2022-01-20

Title: Evaluation Metrics for Implicit-Feedback Recommender Systems
Description: Calculates evaluation metrics for implicit-feedback recommender systems that are based on low-rank matrix factorization models, given the fitted model matrices and data, thus allowing to compare models from a variety of libraries. Metrics include P@K (precision-at-k, for top-K recommendations), R@K (recall at k), AP@K (average precision at k), NDCG@K (normalized discounted cumulative gain at k), Hit@K (from which the 'Hit Rate' is calculated), RR@K (reciprocal rank at k, from which the 'MRR' or 'mean reciprocal rank' is calculated), ROC-AUC (area under the receiver-operating characteristic curve), and PR-AUC (area under the precision-recall curve). These are calculated on a per-user basis according to the ranking of items induced by the model, using efficient multi-threaded routines. Also provides functions for creating train-test splits for model fitting and evaluation.
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>

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Package readsparse updated to version 0.1.5-2 with previous version 0.1.5-1 dated 2021-10-14

Title: Read and Write Sparse Matrices in 'SVMLight' and 'LibSVM' Formats
Description: Read and write labelled sparse matrices in text format as used by software such as 'SVMLight', 'LibSVM', 'ThunderSVM', 'LibFM', 'xLearn', 'XGBoost', 'LightGBM', and others. Supports labelled data for regression, classification (binary, multi-class, multi-label), and ranking (with 'qid' field), and can handle header metadata and comments in files.
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>

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Package outliertree updated to version 1.8.1-1 with previous version 1.8.1 dated 2022-02-17

Title: Explainable Outlier Detection Through Decision Tree Conditioning
Description: Outlier detection method that flags suspicious values within observations, constrasting them against the normal values in a user-readable format, potentially describing conditions within the data that make a given outlier more rare. Full procedure is described in Cortes (2020) <arXiv:2001.00636>. Loosely based on the 'GritBot' <https://www.rulequest.com/gritbot-info.html> software.
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>

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Package MatrixExtra updated to version 0.1.11 with previous version 0.1.10 dated 2022-05-15

Title: Extra Methods for Sparse Matrices
Description: Extends sparse matrix and vector classes from the 'Matrix' package by providing: (a) Methods and operators that work natively on CSR formats (compressed sparse row, a.k.a. 'RsparseMatrix') such as slicing/sub-setting, assignment, rbind(), mathematical operators for CSR and COO such as addition ("+") or sqrt(), and methods such as diag(); (b) Multi-threaded matrix multiplication and cross-product for many <sparse, dense> types, including the 'float32' type from 'float'; (c) Coercion methods between pairs of classes which are not present in 'Matrix', such as 'dgCMatrix' -> 'ngRMatrix', as well as convenience conversion functions; (d) Utility functions for sparse matrices such as sorting the indices or removing zero-valued entries; (e) Fast transposes that work by outputting in the opposite storage format; (f) Faster replacements for many 'Matrix' methods for all sparse types, such as slicing and elementwise multiplication. (g) Convenience functions for sparse objects, such as 'mapSparse' or a shorter 'show' method.
Author: David Cortes [aut, cre, cph], Dmitry Selivanov [cph], Thibaut Goetghebuer-Planchon [cph] , Martin Maechler [cph] , Robert Gentleman [cph] , Ross Ihaka [cph]
Maintainer: David Cortes <david.cortes.rivera@gmail.com>

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Package isotree updated to version 0.5.16 with previous version 0.5.15 dated 2022-03-31

Title: Isolation-Based Outlier Detection
Description: Fast and multi-threaded implementation of isolation forest (Liu, Ting, Zhou (2008) <doi:10.1109/ICDM.2008.17>), extended isolation forest (Hariri, Kind, Brunner (2018) <arXiv:1811.02141>), SCiForest (Liu, Ting, Zhou (2010) <doi:10.1007/978-3-642-15883-4_18>), fair-cut forest (Cortes (2021) <arXiv:2110:13402>), robust random-cut forest (Guha, Mishra, Roy, Schrijvers (2016) <http://proceedings.mlr.press/v48/guha16.html>), and customizable variations of them, for isolation-based outlier detection, clustered outlier detection, distance or similarity approximation (Cortes (2019) <arXiv:1910.12362>), isolation kernel calculation (Ting, Zhu, Zhou (2018) <doi:10.1145/3219819.3219990>), and imputation of missing values (Cortes (2019) <arXiv:1911.06646>), based on random or guided decision tree splitting, and providing different metrics for scoring anomalies based on isolation depth or density (Cortes (2021) <arXiv:2111.11639>). Provides simple heuristics for fitting the model to categorical columns and handling missing data, and offers options for varying between random and guided splits, and for using different splitting criteria.
Author: David Cortes [aut, cre, cph], Thibaut Goetghebuer-Planchon [cph] , David Blackman [cph] , Sebastiano Vigna [cph] , NumPy Developers [cph]
Maintainer: David Cortes <david.cortes.rivera@gmail.com>

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Package climextRemes updated to version 0.3.0 with previous version 0.2.2 dated 2020-08-26

Title: Tools for Analyzing Climate Extremes
Description: Functions for fitting GEV and POT (via point process fitting) models for extremes in climate data, providing return values, return probabilities, and return periods for stationary and nonstationary models. Also provides differences in return values and differences in log return probabilities for contrasts of covariate values. Functions for estimating risk ratios for event attribution analyses, including uncertainty. Under the hood, many of the functions use functions from 'extRemes', including for fitting the statistical models. Details are given in Paciorek, Stone, and Wehner (2018) <doi:10.1016/j.wace.2018.01.002>.
Author: Christopher Paciorek [aut, cre], Harinarayan Krishnan [ctb]
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>

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Package rpymat updated to version 0.1.3 with previous version 0.1.2 dated 2022-02-19

Title: Easy to Configure an Isolated 'Python' Environment
Description: Aims to create a single isolated 'Miniconda' and 'Python' environment for reproducible pipeline scripts. The package provides utilities to run system command within the 'conda' environment, making it easy to install, launch, manage, and stop 'Jupyter-lab'.
Author: Zhengjia Wang [cph, aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>

Diff between rpymat versions 0.1.2 dated 2022-02-19 and 0.1.3 dated 2022-08-06

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Package rockchalk updated to version 1.8.157 with previous version 1.8.152 dated 2022-05-20

Title: Regression Estimation and Presentation
Description: A collection of functions for interpretation and presentation of regression analysis. These functions are used to produce the statistics lectures in <https://pj.freefaculty.org/guides/>. Includes regression diagnostics, regression tables, and plots of interactions and "moderator" variables. The emphasis is on "mean-centered" and "residual-centered" predictors. The vignette 'rockchalk' offers a fairly comprehensive overview. The vignette 'Rstyle' has advice about coding in R. The package title 'rockchalk' refers to our school motto, 'Rock Chalk Jayhawk, Go K.U.'.
Author: Paul E. Johnson [aut, cre], Gabor Grothendieck [ctb], Dimitri Papadopoulos OrfanosGabor [ctb]
Maintainer: Paul E. Johnson <pauljohn@ku.edu>

Diff between rockchalk versions 1.8.152 dated 2022-05-20 and 1.8.157 dated 2022-08-06

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Package dipsaus updated to version 0.2.3 with previous version 0.2.2 dated 2022-06-18

Title: A Dipping Sauce for Data Analysis and Visualizations
Description: Works as an "add-on" to packages like 'shiny', 'future', as well as 'rlang', and provides utility functions. Just like dipping sauce adding flavors to potato chips or pita bread, 'dipsaus' for data analysis and visualizations adds handy functions and enhancements to popular packages. The goal is to provide simple solutions that are frequently asked for online, such as how to synchronize 'shiny' inputs without freezing the app, or how to get memory size on 'Linux' or 'MacOS' system. The enhancements roughly fall into these four categories: 1. 'shiny' input widgets; 2. high-performance computing using 'RcppParallel' and 'future' package; 3. modify R calls and convert among numbers, strings, and other objects. 4. utility functions to get system information such like CPU chip-set, memory limit, etc.
Author: Zhengjia Wang [aut, cre], John Magnotti [ctb] , Xiang Zhang [ctb]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>

Diff between dipsaus versions 0.2.2 dated 2022-06-18 and 0.2.3 dated 2022-08-06

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Package rcompanion updated to version 2.4.18 with previous version 2.4.16 dated 2022-07-04

Title: Functions to Support Extension Education Program Evaluation
Description: Functions and datasets to support "Summary and Analysis of Extension Program Evaluation in R" and "An R Companion for the Handbook of Biological Statistics". Vignettes are available at <http://rcompanion.org>.
Author: Salvatore Mangiafico [aut, cre]
Maintainer: Salvatore Mangiafico <mangiafico@njaes.rutgers.edu>

Diff between rcompanion versions 2.4.16 dated 2022-07-04 and 2.4.18 dated 2022-08-06

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Package shidashi updated to version 0.1.3 with previous version 0.1.2 dated 2022-06-21

Title: A Shiny Dashboard Template System
Description: A template system based on 'AdminLTE3' (<https://adminlte.io/themes/v3/>) theme. Comes with default theme that can be easily customized. Developers can upload modified templates on 'Github', and users can easily download templates with 'RStudio' project wizard. The key features of the default template include light and dark theme switcher, resizing graphs, synchronizing inputs across sessions, new notification system, fancy progress bars, and card-like flip panels with back sides, as well as various of 'HTML' tool widgets.
Author: Zhengjia Wang [cph, aut, cre] , ColorlibHQ [cph] , Bootstrap contributors [ctb] , Twitter, Inc [cph] , Ivan Sagalaev [ctb, cph] , Rene Haas [ctb, cph] , Zeno Rocha [ctb, cph]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>

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Package RcppCCTZ updated to version 0.2.11 with previous version 0.2.10 dated 2021-12-14

Title: 'Rcpp' Bindings for the 'CCTZ' Library
Description: 'Rcpp' Access to the 'CCTZ' timezone library is provided. 'CCTZ' is a C++ library for translating between absolute and civil times using the rules of a time zone. The 'CCTZ' source code, released under the Apache 2.0 License, is included in this package. See <https://github.com/google/cctz> for more details.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package marginaleffects updated to version 0.7.0 with previous version 0.6.0 dated 2022-06-20

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]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>

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Package HDiR updated to version 1.1.2 with previous version 1.1.1 dated 2021-03-31

Title: Directional Highest Density Regions
Description: We provide an R tool for computation and nonparametric plug-in estimation of Highest Density Regions (HDRs) and general level sets in the directional setting. Concretely, circular and spherical HDRs can be reconstructed from a data sample following Saavedra-Nieves and Crujeiras (2021) <doi:10.1007/s11634-021-00457-4>. This library also contains two real datasets in the circular and spherical settings. The first one concerns a problem from animal orientation studies and the second one is related to earthquakes occurrences.
Author: Paula Saavedra-Nieves [aut, cre], Rosa M Crujeiras [aut], Andres Prieto [ctb], Felicita Scapini [dtc]
Maintainer: Paula Saavedra-Nieves <paula.saavedra@usc.es>

Diff between HDiR versions 1.1.1 dated 2021-03-31 and 1.1.2 dated 2022-08-06

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Package filearray updated to version 0.1.4 with previous version 0.1.3 dated 2022-01-27

Title: File-Backed Array for Out-of-Memory Computation
Description: Stores large arrays in files to avoid occupying large memories. Implemented with super fast gigabyte-level multi-threaded reading/writing via 'OpenMP'. Supports multiple non-character data types (double, float, complex, integer, logical, and raw).
Author: Zhengjia Wang [aut, cre, cph]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>

Diff between filearray versions 0.1.3 dated 2022-01-27 and 0.1.4 dated 2022-08-06

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Package fGarch updated to version 4021.87 with previous version 4021.86 dated 2022-07-16

Title: Rmetrics - Autoregressive Conditional Heteroskedastic Modelling
Description: Analyze and model heteroskedastic behavior in financial time series.
Author: Diethelm Wuertz [aut] , Yohan Chalabi [aut], Tobias Setz [aut], Martin Maechler [aut] , Chris Boudt [ctb], Pierre Chausse [ctb], Michal Miklovac [ctb], Georgi N. Boshnakov [cre, ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>

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Package fExtremes updated to version 4021.83 with previous version 3042.82 dated 2017-11-17

Title: Rmetrics - Modelling Extreme Events in Finance
Description: Provides functions for analysing and modelling extreme events in financial time Series. The topics include: (i) data pre-processing, (ii) explorative data analysis, (iii) peak over threshold modelling, (iv) block maxima modelling, (v) estimation of VaR and CVaR, and (vi) the computation of the extreme index.
Author: Diethelm Wuertz [aut], Tobias Setz [aut], Yohan Chalabi [aut], Paul J. Northrop [cre, ctb]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>

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Package BiodiversityR updated to version 2.14-3 with previous version 2.14-2.1 dated 2022-07-04

Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt [cre, aut]
Maintainer: Roeland Kindt <RoelandCEKindt@gmail.com>

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Package tidywikidatar updated to version 0.5.4 with previous version 0.5.3 dated 2022-06-07

Title: Explore 'Wikidata' Through Tidy Data Frames
Description: Query 'Wikidata' API <https://www.wikidata.org/wiki/Wikidata:Main_Page> with ease, get tidy data frames in response, and cache data in a local 'SQLite' database.
Author: Giorgio Comai [aut, cre, cph] , EDJNet [fnd]
Maintainer: Giorgio Comai <giorgio.comai@cci.tn.it>

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Package riverconn updated to version 0.3.22 with previous version 0.3.18 dated 2022-07-05

Title: Common Fragmentation and Connectivity Indices for Riverscapes
Description: Indices for assessing riverscape fragmentation, including the Dendritic Connectivity Index, the Population Connectivity Index, the River Fragmentation Index, the Probability of Connectivity, and the Integral Index of connectivity. For a review, see Jumani et al. (2020) <doi:10.1088/1748-9326/abcb37> and Baldan et al. (2022) <doi:10.1016/j.envsoft.2022.105470> Functions to calculate temporal indices improvement when fragmentation due to barriers is reduced are also included.
Author: Damiano Baldan [aut, cre] , David Cunillera-Montcusi [ctb] , Andrea Funk [ctb]
Maintainer: Damiano Baldan <damiano.baldan91@gmail.com>

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Package rhype updated to version 0.3.0 with previous version 0.2.0 dated 2022-02-16

Title: Work with Hypergraphs in R
Description: Create and manipulate hypergraph objects. This early version of rhype allows for the output of matrices associated with the hypergraphs themselves. It also uses these matrices to calculate hypergraph spectra and perform spectral comparison. Functionality coming soon includes calculation of hyperpaths and hypergraph centrality measures.
Author: Hugh Warden [aut, cre]
Maintainer: Hugh Warden <hugh.warden@outlook.com>

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Package metaconfoundr updated to version 0.1.1 with previous version 0.1.0 dated 2021-10-12

Title: Visualize 'Confounder' Control in Meta-Analyses
Description: Visualize 'confounder' control in meta-analysis. 'metaconfoundr' is an approach to evaluating bias in studies used in meta-analyses based on the causal inference framework. Study groups create a causal diagram displaying their assumptions about the scientific question. From this, they develop a list of important 'confounders'. Then, they evaluate whether studies controlled for these variables well. 'metaconfoundr' is a toolkit to facilitate this process and visualize the results as heat maps, traffic light plots, and more.
Author: Malcolm Barrett [aut, cre] , Julie M. Petersen [aut] , Ludovic Trinquart [aut]
Maintainer: Malcolm Barrett <malcolmbarrett@gmail.com>

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Package intsvy updated to version 2.6 with previous version 2.5 dated 2021-01-23

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

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Package fUnitRoots updated to version 4021.80 with previous version 3042.79 dated 2017-11-16

Title: Rmetrics - Modelling Trends and Unit Roots
Description: Provides four addons for analyzing trends and unit roots in financial time series: (i) functions for the density and probability of the augmented Dickey-Fuller Test, (ii) functions for the density and probability of MacKinnon's unit root test statistics, (iii) reimplementations for the ADF and MacKinnon Test, and (iv) an 'urca' Unit Root Test Interface for Pfaff's unit root test suite.
Author: Diethelm Wuertz [aut] , Tobias Setz [aut], Yohan Chalabi [aut], Georgi N. Boshnakov [cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>

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Package ferrn updated to version 0.0.2 with previous version 0.0.1 dated 2021-03-17

Title: Facilitate Exploration of touRR optimisatioN
Description: Diagnostic plots for optimisation, with a focus on projection pursuit. These show paths the optimiser takes in the high-dimensional space in multiple ways: by reducing the dimension using principal component analysis, and also using the tour to show the path on the high-dimensional space. Several botanical colour palettes are included, reflecting the name of the package. A paper describing the methodology can be found at <https://journal.r-project.org/archive/2021/RJ-2021-105/index.html>.
Author: H. Sherry Zhang [aut, cre] , Dianne Cook [aut] , Ursula Laa [aut] , Nicolas Langrene [aut] , Patricia Menendez [aut]
Maintainer: H. Sherry Zhang <huize.zhang@monash.edu>

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Package BayesSUR updated to version 2.1-1 with previous version 2.1-0 dated 2022-06-30

Title: Bayesian Seemingly Unrelated Regression
Description: Bayesian seemingly unrelated regression with general variable selection and dense/sparse covariance matrix. The sparse seemingly unrelated regression is described in Bottolo et al. (2021) <doi:10.1111/rssc.12490>, the software paper is in Zhao et al. (2021) <doi:10.18637/jss.v100.i11>, and the model with random effects is described in Zhao et al. (2021) <arXiv:2101.05899>.
Author: Marco Banterle [aut], Zhi Zhao [aut, cre], Leonardo Bottolo [ctb], Sylvia Richardson [ctb], Waldir Leoncio [ctb], Alex Lewin [aut], Manuela Zucknick [aut]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>

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Package BayesGPfit updated to version 1.1.0 with previous version 0.1.0 dated 2020-02-20

Title: Fast Bayesian Gaussian Process Regression Fitting
Description: Bayesian inferences on nonparametric regression via Gaussian Processes with a modified exponential square kernel using a basis expansion approach.
Author: Jian Kang [aut, cre], John Burkardt [ctb]
Maintainer: Jian Kang <jiankang@umich.edu>

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Package SSDforR updated to version 1.5.25 with previous version 1.5.24 dated 2022-04-24

Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre], Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>

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Package splm updated to version 1.6-2 with previous version 1.5-3 dated 2022-01-12

Title: Econometric Models for Spatial Panel Data
Description: ML and GM estimation and diagnostic testing of econometric models for spatial panel data.
Author: Giovanni Millo [aut, cre], Gianfranco Piras [aut], Roger Bivand [ctb]
Maintainer: Giovanni Millo <giovanni.millo@deams.units.it>

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Package reveneraR updated to version 0.1.2 with previous version 0.1.1 dated 2022-02-03

Title: Connect to Your 'Revenera' (Formerly 'Revulytics') Data
Description: Facilitates making a connection to the 'Revenera' API and executing various queries. You can use it to get event data and metadata. The 'Revenera' documentation is available at <https://docs.revenera.com/ui560/report/>. This package is not supported by 'Flexera' (owner of the software).
Author: Chris Umphlett [aut, cre], Avinash Panigrahi [aut]
Maintainer: Chris Umphlett <christopher.umphlett@gmail.com>

Diff between reveneraR versions 0.1.1 dated 2022-02-03 and 0.1.2 dated 2022-08-06

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Package ngboostForecast updated to version 0.1.1 with previous version 0.1.0 dated 2022-05-03

Title: Probabilistic Time Series Forecasting
Description: Probabilistic time series forecasting via Natural Gradient Boosting for Probabilistic Prediction.
Author: Resul Akay [aut, cre]
Maintainer: Resul Akay <resulakay1@gmail.com>

Diff between ngboostForecast versions 0.1.0 dated 2022-05-03 and 0.1.1 dated 2022-08-06

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Package roptim updated to version 0.1.6 with previous version 0.1.5 dated 2020-06-29

Title: General Purpose Optimization in R using C++
Description: Perform general purpose optimization in R using C++. A unified wrapper interface is provided to call C functions of the five optimization algorithms ('Nelder-Mead', 'BFGS', 'CG', 'L-BFGS-B' and 'SANN') underlying optim().
Author: Yi Pan [aut, cre]
Maintainer: Yi Pan <ypan1988@gmail.com>

Diff between roptim versions 0.1.5 dated 2020-06-29 and 0.1.6 dated 2022-08-06

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Package rEDM updated to version 1.13.1 with previous version 1.13.0 dated 2022-06-22

Title: Empirical Dynamic Modeling ('EDM')
Description: An implementation of 'EDM' algorithms based on research software developed for internal use at the Sugihara Lab ('UCSD/SIO'). The package is implemented with 'Rcpp' wrappers around the 'cppEDM' library. It implements the 'simplex' projection method from Sugihara & May (1990) <doi:10.1038/344734a0>, the 'S-map' algorithm from Sugihara (1994) <doi:10.1098/rsta.1994.0106>, convergent cross mapping described in Sugihara et al. (2012) <doi:10.1126/science.1227079>, and, 'multiview embedding' described in Ye & Sugihara (2016) <doi:10.1126/science.aag0863>.
Author: Joseph Park [aut, cre] , Cameron Smith [aut] , George Sugihara [aut, ccp] , Ethan Deyle [aut] , Erik Saberski [ctb] , Hao Ye [ctb] , The Regents of the University of California [cph]
Maintainer: Joseph Park <JosephPark@IEEE.org>

Diff between rEDM versions 1.13.0 dated 2022-06-22 and 1.13.1 dated 2022-08-06

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Package GeoTcgaData updated to version 1.1.0 with previous version 1.0.2 dated 2021-10-24

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>

Diff between GeoTcgaData versions 1.0.2 dated 2021-10-24 and 1.1.0 dated 2022-08-06

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Package tidyfst updated to version 1.7.0 with previous version 1.6.5 dated 2022-04-28

Title: Tidy Verbs for Fast Data Manipulation
Description: A toolkit of tidy data manipulation verbs with 'data.table' as the backend. Combining the merits of syntax elegance from 'dplyr' and computing performance from 'data.table', 'tidyfst' intends to provide users with state-of-the-art data manipulation tools with least pain. This package is an extension of 'data.table'. While enjoying a tidy syntax, it also wraps combinations of efficient functions to facilitate frequently-used data operations.
Author: Tian-Yuan Huang [aut, cre]
Maintainer: Tian-Yuan Huang <huang.tian-yuan@qq.com>

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Package R6causal updated to version 0.6.1 with previous version 0.6.0 dated 2021-08-06

Title: R6 Class for Structural Causal Models
Description: The implemented R6 class 'SCM' aims to simplify working with structural causal models. The missing data mechanism can be defined as a part of the structural model. The class contains methods for 1) defining a structural causal model via functions, text or conditional probability tables, 2) printing basic information on the model, 3) plotting the graph for the model using packages 'igraph' or 'qgraph', 4) simulating data from the model, 5) applying an intervention, 6) checking the identifiability of a query using the R packages 'causaleffect' and 'dosearch', 7) defining the missing data mechanism, 8) simulating incomplete data from the model according to the specified missing data mechanism and 9) checking the identifiability in a missing data problem using the R package 'dosearch'. In addition, there are functions for running experiments and doing counterfactual inference using simulation.
Author: Juha Karvanen [aut, cre]
Maintainer: Juha Karvanen <juha.karvanen@iki.fi>

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Package overviewR updated to version 0.0.11 with previous version 0.0.10 dated 2022-04-15

Title: Easily Extracting Information About Your Data
Description: Makes it easy to display descriptive information on a data set. Getting an easy overview of a data set by displaying and visualizing sample information in different tables (e.g., time and scope conditions). The package also provides publishable 'LaTeX' code to present the sample information.
Author: Cosima Meyer [cre, aut], Dennis Hammerschmidt [aut]
Maintainer: Cosima Meyer <cosima.meyer@gmail.com>

Diff between overviewR versions 0.0.10 dated 2022-04-15 and 0.0.11 dated 2022-08-06

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Package grf updated to version 2.2.0 with previous version 2.1.0 dated 2022-03-17

Title: Generalized Random Forests
Description: Forest-based statistical estimation and inference. GRF provides non-parametric methods for heterogeneous treatment effects estimation (optionally using right-censored outcomes, multiple treatment arms or outcomes, or instrumental variables), as well as least-squares regression, quantile regression, and survival regression, all with support for missing covariates.
Author: Julie Tibshirani [aut, cre], Susan Athey [aut], Rina Friedberg [ctb], Vitor Hadad [ctb], David Hirshberg [ctb], Luke Miner [ctb], Erik Sverdrup [aut], Stefan Wager [aut], Marvin Wright [ctb]
Maintainer: Julie Tibshirani <jtibs@cs.stanford.edu>

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Package sasLM updated to version 0.9.0 with previous version 0.8.1 dated 2022-05-10

Title: 'SAS' Linear Model
Description: This is a core implementation of 'SAS' procedures for linear models - GLM, REG, ANOVA, FREQ, and UNIVARIATE. Some R packages provide type II and type III SS. However, the results of nested and complex designs are often different from those of 'SAS.' Different results does not necessarily mean incorrectness. However, many wants the same results to SAS. This package aims to achieve that. Reference: Littell RC, Stroup WW, Freund RJ (2002, ISBN:0-471-22174-0).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>

Diff between sasLM versions 0.8.1 dated 2022-05-10 and 0.9.0 dated 2022-08-06

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Package NNS updated to version 0.9.0 with previous version 0.8.70 dated 2022-04-24

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 0.8.70 dated 2022-04-24 and 0.9.0 dated 2022-08-06

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Package influential updated to version 2.2.6 with previous version 2.2.5 dated 2022-04-14

Title: Identification and Classification of the Most Influential Nodes
Description: Contains functions for the classification and ranking of top candidate features, reconstruction of networks from adjacency matrices and data frames, analysis of the topology of the network and calculation of centrality measures, and identification of the most influential nodes. Also, a function is provided for running SIRIR model, which is the combination of leave-one-out cross validation technique and the conventional SIR model, on a network to unsupervisedly rank the true influence of vertices. Additionally, some functions have been provided for the assessment of dependence and correlation of two network centrality measures as well as the conditional probability of deviation from their corresponding means in opposite direction. Fred Viole and David Nawrocki (2013, ISBN:1490523995). Csardi G, Nepusz T (2006). "The igraph software package for complex network research." InterJournal, Complex Systems, 1695. Adopted algorithms and sources are referenced in function document.
Author: Abbas Salavaty [aut, cre], Mirana Ramialison [ths], Peter D. Currie [ths]
Maintainer: Adrian Salavaty <abbas.salavaty@gmail.com>

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Package IDSL.IPA updated to version 2.0 with previous version 1.9 dated 2022-07-07

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 and total ion chromatograms.
Author: Sadjad Fakouri-Baygi [cre, aut] , Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>

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Package groundhog updated to version 2.0.1 with previous version 2.0.0 dated 2022-07-12

Title: Version-Control for CRAN, GitHub, and GitLab Packages
Description: Make R scripts reproducible, by ensuring that every time a given script is run, the same version of the used packages are loaded (instead of whichever version the user running the script happens to have installed). This is achieved by using the command groundhog.library() instead of the base command library(), and including a date in the call. The date is used to call on the same version of the package every time (the most recent version available at that date). Load packages from CRAN, GitHub, or Gitlab.
Author: Uri Simonsohn [aut, cre] , Hugo Gruson [ctb, aut]
Maintainer: Uri Simonsohn <urisohn@gmail.com>

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Package dm updated to version 1.0.1 with previous version 1.0.0 dated 2022-07-21

Title: Relational Data Models
Description: Provides tools for working with multiple related tables, stored as data frames or in a relational database. Multiple tables (data and metadata) are stored in a compound object, which can then be manipulated with a pipe-friendly syntax.
Author: Tobias Schieferdecker [aut], Kirill Mueller [aut, cre] , Antoine Fabri [ctb], Darko Bergant [aut], Katharina Brunner [ctb], James Wondrasek [ctb], Indrajeet Patil [ctb] , Maelle Salmon [ctb] , energie360° AG [fnd], cynkra GmbH [fnd, cph]
Maintainer: Kirill Mueller <krlmlr+r@mailbox.org>

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Package dcifer updated to version 1.1.0 with previous version 1.0.1 dated 2022-07-15

Title: Genetic Relatedness Between Polyclonal Infections
Description: An implementation of Dcifer (Distance for complex infections: fast estimation of relatedness), an identity by descent (IBD) based method to calculate genetic relatedness between polyclonal infections from biallelic and multiallelic data. The package includes functions that format and preprocess the data, implement the method, and visualize the results. Gerlovina et al. (2022) <doi:10.1101/2022.04.14.488406>.
Author: Inna Gerlovina [aut, cre]
Maintainer: Inna Gerlovina <innager@berkeley.edu>

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Package CNAIM updated to version 2.1.2 with previous version 2.1.1 dated 2022-07-14

Title: Common Network Asset Indices Methodology (CNAIM)
Description: Implementation of the CNAIM standard in R. Contains a series of algorithms which determine the probability of failure, consequences of failure and monetary risk associated with electricity distribution companies' assets such as transformers and cables. Results are visualized in an easy-to-understand risk matrix.
Author: Emil Larsen [aut], Kalle Hansen [aut], Peter Larsen [aut], Mohsin Vindhani [aut, cre]
Maintainer: Mohsin Vindhani <mohsin@utiligize.com>

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Package BayesSenMC updated to version 0.1.5 with previous version 0.1.4 dated 2021-10-05

Title: Different Models of Posterior Distributions of Adjusted Odds Ratio
Description: Generates different posterior distributions of adjusted odds ratio under different priors of sensitivity and specificity, and plots the models for comparison. It also provides estimations for the specifications of the models using diagnostics of exposure status with a non-linear mixed effects model. It implements the methods that are first proposed in <doi:10.1016/j.annepidem.2006.04.001> and <doi:10.1177/0272989X09353452>.
Author: Jinhui Yang, Haitao Chu, and Lifeng Lin
Maintainer: Jinhui Yang <james.yangjinhui@gmail.com>

Diff between BayesSenMC versions 0.1.4 dated 2021-10-05 and 0.1.5 dated 2022-08-06

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Package bartcs updated to version 0.1.2 with previous version 0.1.1 dated 2022-07-19

Title: Bayesian Additive Regression Trees for Confounder Selection
Description: Fit Bayesian Regression Additive Trees (BART) models to select relevant confounders among a large set of potential confounders and to estimate average treatment effect. For more information, see Kim et al. (2022) <doi:10.48550/arXiv.2203.11798>.
Author: Yeonghoon Yoo [aut, cre]
Maintainer: Yeonghoon Yoo <yooyh.stat@gmail.com>

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Package string2path updated to version 0.1.1 with previous version 0.1.0 dated 2022-07-17

Title: Rendering Font into 'data.frame'
Description: Extract glyph information from font data, and translate the outline curves to flattened paths or tessellated polygons. The converted data is returned as a 'data.frame' in easy-to-plot format.
Author: Hiroaki Yutani [aut, cre] , The authors of the dependency Rust crates [ctb]
Maintainer: Hiroaki Yutani <yutani.ini@gmail.com>

Diff between string2path versions 0.1.0 dated 2022-07-17 and 0.1.1 dated 2022-08-06

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Package itsmr updated to version 1.10 with previous version 1.9 dated 2018-09-10

Title: Time Series Analysis Using the Innovations Algorithm
Description: Provides functions for modeling and forecasting time series data. Forecasting is based on the innovations algorithm. A description of the innovations algorithm can be found in the textbook "Introduction to Time Series and Forecasting" by Peter J. Brockwell and Richard A. Davis. <https://link.springer.com/book/10.1007/b97391>.
Author: George Weigt
Maintainer: George Weigt <g808391@icloud.com>

Diff between itsmr versions 1.9 dated 2018-09-10 and 1.10 dated 2022-08-06

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Package FastJM updated to version 1.2.0 with previous version 1.1.3 dated 2022-06-01

Title: Semi-Parametric Joint Modeling of Longitudinal and Survival Data
Description: Maximum likelihood estimation for the semi-parametric joint modeling of competing risks and longitudinal data applying customized linear scan algorithms, proposed by Li and colleagues (2022) <doi:10.1155/2022/1362913>. The time-to-event data is modelled using a (cause-specific) Cox proportional hazards regression model with time-fixed covariates. The longitudinal outcome is modelled using a linear mixed effects model. The association is captured by shared random effects. The model is estimated using an Expectation Maximization algorithm.
Author: Shanpeng Li [aut, cre], Ning Li [ctb], Hong Wang [ctb], Jin Zhou [ctb], Hua Zhou [ctb], Gang Li [ctb]
Maintainer: Shanpeng Li <lishanpeng0913@ucla.edu>

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Package extrafrail updated to version 1.1 with previous version 1.0 dated 2022-06-30

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 GPBayes updated to version 0.1.0-4 with previous version 0.1.0-3 dated 2021-12-03

Title: Tools for Gaussian Process Modeling in Uncertainty Quantification
Description: Gaussian processes (GPs) have been widely used to model spatial data, spatio-temporal data, and computer experiments in diverse areas of statistics including spatial statistics, spatio-temporal statistics, uncertainty quantification, and machine learning. This package creates basic tools for fitting and prediction based on GPs with spatial data, spatio-temporal data, and computer experiments. Key characteristics for this GP tool include: (1) the comprehensive implementation of various covariance functions including the Matérn family and the Confluent Hypergeometric family with isotropic form, tensor form, and automatic relevance determination form, where the isotropic form is widely used in spatial statistics, the tensor form is widely used in design and analysis of computer experiments and uncertainty quantification, and the automatic relevance determination form is widely used in machine learning; (2) implementations via Markov chain Monte Carlo (MCMC) algorithms and optimization algorithms for GP models with all the implemented covariance functions. The methods for fitting and prediction are mainly implemented in a Bayesian framework; (3) model evaluation via Fisher information and predictive metrics such as predictive scores; (4) built-in functionality for simulating GPs with all the implemented covariance functions; (5) unified implementation to allow easy specification of various GPs.
Author: Pulong Ma [aut, cre]
Maintainer: Pulong Ma <mpulong@gmail.com>

Diff between GPBayes versions 0.1.0-3 dated 2021-12-03 and 0.1.0-4 dated 2022-08-06

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

Title: Bioequivalence Study Data Analysis
Description: Analyze bioequivalence study data with industrial strength. Sample size could be determined for various crossover designs, such as 2x2 design, 2x4 design, 4x4 design, Balaam design, Two-sequence dual design, and William design. Reference: Chow SC, Liu JP. Design and Analysis of Bioavailability and Bioequivalence Studies. 3rd ed. (2009, ISBN:978-1-58488-668-6).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>

Diff between BE versions 0.2.1 dated 2022-05-10 and 0.2.2 dated 2022-08-06

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