Mon, 13 Sep 2021

Package faux updated to version 1.1.0 with previous version 1.0.0 dated 2021-03-26

Title: Simulation for Factorial Designs
Description: Create datasets with factorial structure through simulation by specifying variable parameters. Extended documentation at <https://debruine.github.io/faux/>. Described in DeBruine (2020) <doi:10.5281/zenodo.2669586>.
Author: Lisa DeBruine [aut, cre] (<https://orcid.org/0000-0002-7523-5539>), Anna Krystalli [ctb] (<https://orcid.org/0000-0002-2378-4915>), Andrew Heiss [ctb] (<https://orcid.org/0000-0002-3948-3914>)
Maintainer: Lisa DeBruine <debruine@gmail.com>

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Package spaMM updated to version 3.9.0 with previous version 3.8.23 dated 2021-08-05

Title: Mixed-Effect Models, with or without Spatial Random Effects
Description: Inference based on models with or without spatially-correlated random effects, multivariate responses, or non-Gaussian random effects (e.g., Beta). Variation in residual variance (heteroscedasticity) can itself be represented by a mixed-effect model. Both classical geostatistical models, and Markov random field models on irregular grids (as considered in the 'INLA' package, <https://www.r-inla.org>), can be fitted, with distinct computational procedures exploiting the sparse matrix representations for the latter case and other autoregressive models. Laplace approximations are used for likelihood or restricted likelihood. Penalized quasi-likelihood and other variants discussed in the h-likelihood literature (Lee and Nelder 2001 <doi:10.1093/biomet/88.4.987>) are also implemented.
Author: François Rousset [aut, cre, cph] (<https://orcid.org/0000-0003-4670-0371>), Jean-Baptiste Ferdy [aut, cph], Alexandre Courtiol [aut] (<https://orcid.org/0000-0003-0637-2959>), GSL authors [ctb] (src/gsl_bessel.*)
Maintainer: François Rousset <francois.rousset@umontpellier.fr>

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Package mlbstatsR updated to version 0.1.0.3 with previous version 0.1.0.2 dated 2021-09-05

Title: Stats, Photos, Logos, and Colors of M.L.B. (Major League Baseball)
Description: Main use case is to gives users the ability to work with Major League Baseball data in a clean and detailed way. Which provides users with a variety of ways to improve visualizations.
Author: Ivan Villanueva
Maintainer: Ivan Villanueva <ivan.v23@yahoo.com>

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Package pacs updated to version 0.3.5 with previous version 0.3.4 dated 2021-09-06

Title: Supplementary Tools for R Packages Developers
Description: Supplementary utils for CRAN maintainers and R packages developers. Validating the library or packages. Exploring a complexity of a specific package like evaluating sizes in bytes of all its dependencies. Assessing the life duration of a specific package version. Checking a CRAN package check page status for any errors and warnings. Retrieving a DESCRIPTION or NAMESPACE file for any package version. Comparing DESCRIPTION or NAMESPACE files between different package versions. Getting a list of all releases for a specific package. The Bioconductor is partly supported.
Author: Maciej Nasinski [aut, cre]
Maintainer: Maciej Nasinski <nasinski.maciej@gmail.com>

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Package mlr3fselect updated to version 0.6.0 with previous version 0.5.1 dated 2021-03-09

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

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Package shinytest updated to version 1.5.1 with previous version 1.5.0 dated 2021-01-13

Title: Test Shiny Apps
Description: For automated testing of Shiny applications, using a headless browser, driven through 'WebDriver'.
Author: Winston Chang [aut, cre], Gábor Csárdi [aut], Hadley Wickham [aut], RStudio [cph, fnd], Mango Solutions [cph, ccp]
Maintainer: Winston Chang <winston@rstudio.com>

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Package rATTAINS updated to version 0.1.2 with previous version 0.1.1 dated 2021-09-02

Title: Access EPA 'ATTAINS' Data
Description: An R interface to United States Environmental Protection Agency (EPA) Assessment, Total Maximum Daily Load (TMDL) Tracking and Implementation System ('ATTAINS') data. 'ATTAINS' is the EPA database used to track information provided by states about water quality assessments conducted under federal Clean Water Act requirements. ATTAINS information and API information is available at <https://www.epa.gov/waterdata/attains>.
Author: Michael Schramm [aut, cre, cph] (<https://orcid.org/0000-0003-1876-6592>)
Maintainer: Michael Schramm <mpschramm@gmail.com>

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Package esaps updated to version 0.2.2 with previous version 0.1.0 dated 2018-03-15

Title: Indicators of Electoral Systems and Party Systems
Description: It allows structuring electoral data of different size and structure to calculate various indicators frequently used in the studies of electoral systems and party systems. Indicators of electoral volatility, electoral disproportionality, party nationalization and the effective number of parties are included.
Author: Nicolas Schmidt [aut, cre] (<https://orcid.org/0000-0001-5083-5792>)
Maintainer: Nicolas Schmidt <nschmidt@cienciassociales.edu.uy>

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Package permimp updated to version 1.0-2 with previous version 1.0-1 dated 2021-02-11

Title: Conditional Permutation Importance
Description: An add-on to the 'party' package, with a faster implementation of the partial-conditional permutation importance for random forests. The standard permutation importance is implemented exactly the same as in the 'party' package. The conditional permutation importance can be computed faster, with an option to be backward compatible to the 'party' implementation. The package is compatible with random forests fit using the 'party' and the 'randomForest' package. The methods are described in Strobl et al. (2007) <doi:10.1186/1471-2105-8-25> and Debeer and Strobl (2020) <doi:10.1186/s12859-020-03622-2>.
Author: Dries Debeer [aut, cre], Torsten Hothorn [aut], Carolin Strobl [aut]
Maintainer: Dries Debeer <debeer.dries@gmail.com>

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Package netgsa updated to version 4.0.1 with previous version 4.0.0 dated 2021-05-15

Title: Network-Based Gene Set Analysis
Description: Carry out network-based gene set analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data. Implements methods described in Shojaie A, Michailidis G (2010) <doi:10.1093/biomet/asq038>, Shojaie A, Michailidis G (2009) <doi:10.1089/cmb.2008.0081>, and Ma J, Shojaie A, Michailidis G (2016) <doi:10.1093/bioinformatics/btw410>.
Author: Michael Hellstern [aut, cre], Ali Shojaie [aut], Jing Ma [aut], Kun Yue [aut]
Maintainer: Michael Hellstern <mikeh1@uw.edu>

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Package frailtySurv updated to version 1.3.7 with previous version 1.3.6 dated 2019-04-19

Title: General Semiparametric Shared Frailty Model
Description: Simulates and fits semiparametric shared frailty models under a wide range of frailty distributions using a consistent and asymptotically-normal estimator. Currently supports: gamma, power variance function, log-normal, and inverse Gaussian frailty models.
Author: Vinnie Monaco [aut, cre], Malka Gorfine [aut], Li Hsu [aut]
Maintainer: Vinnie Monaco <contact@vmonaco.com>

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Package strawr updated to version 0.0.9 with previous version 0.0.8 dated 2021-06-25

Title: Fast Implementation of Reading/Dump for .hic Files
Description: API for fast data extraction for .hic files that provides programmatic access to the matrices. It doesn't store the pointer data for all the matrices, only the one queried, and currently we are only supporting matrices (not vectors).
Author: Neva Cherniavsky Durand [aut, cre], Muhammad Saad Shamim [aut], Aiden Lab [cph]
Maintainer: Neva Cherniavsky Durand <neva@broadinstitute.org>

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Package VIC5 updated to version 0.2.3 with previous version 0.2.2 dated 2021-09-13

Title: The Variable Infiltration Capacity (VIC) Hydrological Model
Description: The Variable Infiltration Capacity (VIC) model is a macroscale hydrologic model that solves full water and energy balances, originally developed by Xu Liang at the University of Washington (UW). The version of VIC source code used is of 5.0.1 on <https://github.com/UW-Hydro/VIC/>, see Hamman et al. (2018). Development and maintenance of the current official version of the VIC model at present is led by the UW Hydro (Computational Hydrology group) in the Department of Civil and Environmental Engineering at UW. VIC is a research model and in its various forms it has been applied to most of the major river basins around the world, as well as globally <http://vic.readthedocs.io/en/master/Documentation/References/>. References: "Liang, X., D. P. Lettenmaier, E. F. Wood, and S. J. Burges (1994), A simple hydrologically based model of land surface water and energy fluxes for general circulation models, J. Geophys. Res., 99(D7), 14415-14428, <doi:10.1029/94JD00483>"; "Hamman, J. J., Nijssen, B., Bohn, T. J., Gergel, D. R., and Mao, Y. (2018), The Variable Infiltration Capacity model version 5 (VIC-5): infrastructure improvements for new applications and reproducibility, Geosci. Model Dev., 11, 3481-3496, <doi:10.5194/gmd-11-3481-2018>".
Author: Ruida Zhong [aut, ctb], Dongdong Kong [aut, cre] (<https://orcid.org/0000-0003-1836-8172>), Xiaohong Chen [aut, ctb], Zhaoli Wang [aut, ctb], Chengguang Lai [aut, ctb], Joseph J Hamman [ctb] (Contributor and maintainer of VIC source code), Keith Cherkauer [ctb]
Maintainer: Dongdong Kong <kongdd.sysu@gmail.com>

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Package TreeDist updated to version 2.2.0 with previous version 2.1.1 dated 2021-07-13

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

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Package suppdata updated to version 1.1-7 with previous version 1.1-6 dated 2020-12-17

Title: Downloading Supplementary Data from Published Manuscripts
Description: Downloads data supplementary materials from manuscripts, using papers' DOIs as references. Facilitates open, reproducible research workflows: scientists re-analyzing published datasets can work with them as easily as if they were stored on their own computer, and others can track their analysis workflow painlessly. The main function suppdata() returns a (temporary) location on the user's computer where the file is stored, making it simple to use suppdata() with standard functions like read.csv().
Author: William D. Pearse [aut, cre] (<https://orcid.org/0000-0002-6241-3164>), Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>), Daniel Nuest [aut] (<https://orcid.org/0000-0002-0024-5046>), Ross Mounce [rev] (Ross Mounce reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/195), Sarah Supp [rev] (Sarah Supp reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/195)
Maintainer: William D. Pearse <will.pearse@gmail.com>

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Package starvars updated to version 1.1.5 with previous version 1.1.2 dated 2021-01-11

Title: Vector Logistic Smooth Transition Models / Realized Covariances Construction
Description: Allows the user to estimate a vector logistic smooth transition autoregressive model via maximum log-likelihood or nonlinear least squares. It further permits to test for linearity in the multivariate framework against a vector logistic smooth transition autoregressive model with a single transition variable. The estimation method is discussed in Terasvirta and Yang (2014, <doi:10.1108/S0731-9053(2013)0000031008>). Also, realized covariances can be constructed from stock market prices or returns, as explained in Andersen et al. (2001, <doi:10.1016/S0304-405X(01)00055-1>).
Author: Andrea Bucci [aut, cre, cph], Giulio Palomba [aut], Eduardo Rossi [aut], Andrea Faragalli [ctb]
Maintainer: Andrea Bucci <andrea.bucci@unich.it>

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Package Rogue updated to version 2.0.0 with previous version 1.0.0 dated 2021-07-01

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, forthcoming), and an interface to 'RogueNaRok' (Aberer et al. 2013) <doi:10.1093/sysbio/sys078>.
Author: Martin R. Smith [aut, cre, cph] (<https://orcid.org/0000-0001-5660-1727>), Andre J. Aberer [aut, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>

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Package nser updated to version 1.3.1 with previous version 1.3.0 dated 2021-08-22

Title: Bhavcopy and Live Market Data from National Stock Exchange (NSE) India for Equities and Equity Derivatives (F&O)
Description: Download Historical Bhavcopy and get Live Market data from NSE India of Equities and Derivatives(F&O) segment. Data source <https://www.nseindia.com/>.
Author: Nandan Patil [cre, aut]
Maintainer: Nandan Patil <tryanother609@gmail.com>

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Package NNS updated to version 0.8.0 with previous version 0.7.2 dated 2021-08-06

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
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>

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Package nCal updated to version 2021.9-12 with previous version 2020.9-10 dated 2020-09-11

Title: Nonlinear Calibration
Description: Performs nonlinear calibration and curve fitting for data from Luminex, RT-PCR, ELISA, RPPA etc. Its precursor is Ruminex. This package is described in Fong et al. (2013) <DOI:10.1093/bioinformatics/btt456>.
Author: Youyi Fong <youyifong@gmail.com>, Krisztian Sebestyen <ksebestyen@gmail.com>, Xuesong Yu <xyu@scharp.org>
Maintainer: Youyi Fong <youyifong@gmail.com>

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Package MBNMAtime updated to version 0.2.1 with previous version 0.2.0 dated 2021-04-26

Title: Run Time-Course Model-Based Network Meta-Analysis (MBNMA) Models
Description: Fits Bayesian time-course models for model-based network meta-analysis (MBNMA) that allows inclusion of multiple time-points from studies. Repeated measures over time are accounted for within studies by applying different time-course functions, following the method of Pedder et al. (2019) <doi:10.1002/jrsm.1351>. The method allows synthesis of studies with multiple follow-up measurements that can account for time-course for a single or multiple treatment comparisons. Several general time-course functions are provided; others may be added by the user. Various characteristics can be flexibly added to the models, such as correlation between time points and shared class effects. The consistency of direct and indirect evidence in the network can be assessed using unrelated mean effects models and/or by node-splitting.
Author: Hugo Pedder [aut, cre], Nicky Welton [ctb, rev], Sofia Dias [ctb, rev], Meg Bennetts [ctb, rev], Martin Boucher [ctb, rev]
Maintainer: Hugo Pedder <hugopedder@gmail.com>

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Package flexsurv updated to version 2.1 with previous version 2.0 dated 2021-02-22

Title: Flexible Parametric Survival and Multi-State Models
Description: Flexible parametric models for time-to-event data, including the Royston-Parmar spline model, generalized gamma and generalized F distributions. Any user-defined parametric distribution can be fitted, given at least an R function defining the probability density or hazard. There are also tools for fitting and predicting from fully parametric multi-state models, based on either cause-specific hazards or mixture models.
Author: Christopher Jackson [aut, cre], Paul Metcalfe [ctb], Jordan Amdahl [ctb], Matthew T. Warkentin [ctb], Kevin Kunzmann [ctb]
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>

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Package bbotk updated to version 0.4.0 with previous version 0.3.2 dated 2021-03-18

Title: Black-Box Optimization Toolkit
Description: Provides a common framework for optimization of black-box functions for other packages, e.g. 'mlr3tuning' or 'mlr3fselect'. It offers various optimization methods e.g. grid search, random search, generalized simulated annealing and iterated racing.
Author: Marc Becker [cre, aut] (<https://orcid.org/0000-0002-8115-0400>), Jakob Richter [aut] (<https://orcid.org/0000-0003-4481-5554>), Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>), Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>), Martin Binder [aut], Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>

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Package Bayesrel updated to version 0.7.1 with previous version 0.7.0.7 dated 2021-03-29

Title: Bayesian Reliability Estimation
Description: Functionality for reliability estimates. For unidimensional tests: Coefficient alpha, 'Guttman's' lambda-2/-4/-6, the Greatest lower bound and coefficient omega in a Bayesian and a frequentist version. For multidimensional tests: omega-total and omega-hierarchical. The results include confidence and credible intervals, the probability of a coefficient being larger than a cutoff, and a check for the factor models, necessary for the omega coefficients. The method for the Bayesian unidimensional estimates, except for omega, is sampling from the posterior inverse 'Wishart' for the covariance matrix based measures (see 'Murphy', 2007, <https://groups.seas.harvard.edu/courses/cs281/papers/murphy-2007.pdf>. The Bayesian omegas (unidimensional, hierarchical, and total) are obtained by 'Gibbs' Sampling from the conditional posterior distributions of (1) the single factor model and (2) the higher order factor model ('Lee', 2007, <doi:10.1002/9780470024737>).
Author: Julius M. Pfadt [aut, cre], Don van den Bergh [aut], Joris Goosen [aut]
Maintainer: Julius M. Pfadt <julius.pfadt@gmail.com>

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Package ARpLMEC updated to version 2.1 with previous version 1.1 dated 2020-06-26

Title: Censored Mixed-Effects Models with Different Correlation Structures
Description: Left, right or interval censored mixed-effects linear model with autoregressive errors of order p or DEC correlation structure using the type-EM algorithm. The error distribution can be Normal or t-Student. It provides the parameter estimates, the standard errors and prediction of future observations (available only for the normal case). Olivari et all (2021) <doi:10.1080/10543406.2020.1852246>.
Author: Rommy C. Olivari, Kelin Zhong, Aldo M. Garay and Victor H. Lachos
Maintainer: Rommy C. Olivari <rco1@de.ufpe.br>

Diff between ARpLMEC versions 1.1 dated 2020-06-26 and 2.1 dated 2021-09-13

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Package mlr3hyperband updated to version 0.2.0 with previous version 0.1.2 dated 2021-01-29

Title: Hyperband for 'mlr3'
Description: Implements hyperband method for hyperparameter tuning. Various termination criteria can be set and combined. The class 'AutoTuner' provides a convenient way to perform nested resampling in combination with 'mlr3'. The hyperband algorithm was proposed by Lisha Li, Kevin Jamieson, Giulia DeSalvo, Afshin Rostamizadeh and Ameet Talwalkar (2018) <arXiv:1603.06560>.
Author: Marc Becker [aut, cre] (<https://orcid.org/0000-0002-8115-0400>), Sebastian Gruber [aut] (<https://orcid.org/0000-0002-8544-3470>), Jakob Richter [aut] (<https://orcid.org/0000-0003-4481-5554>), Julia Moosbauer [aut] (<https://orcid.org/0000-0002-0000-9297>), Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>)
Maintainer: Marc Becker <marcbecker@posteo.de>

Diff between mlr3hyperband versions 0.1.2 dated 2021-01-29 and 0.2.0 dated 2021-09-13

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New package SplitKnockoff with initial version 0.8
Package: SplitKnockoff
Title: Split Knockoffs for Structural Sparsity
Version: 0.8
Date: 2021-09-01
Author: Haoxue Wang [aut, cre] (Development of the whole packages), Yang Cao [aut] (Revison of this package), Xinwei Sun [aut] (Original ideas about the package), Yuan Yao [aut] (Testing for the package and management of the development)
Maintainer: Haoxue Wang <haoxwang@student.ethz.ch>
Description: A novel method for controlling the false discovery rate (FDR) in structural sparsity setting. This proposed scheme relaxes the linear subspace constraint to its neighborhood, often known as variable splitting in optimization. Simulation experiments can be reproduced following the Vignette. 'Split Knockoffs' is defined in Cao et al. (2021) <arXiv:2103.16159>.
URL: https://github.com/wanghaoxue0/SplitKnockoff
BugReports: https://github.com/wanghaoxue0/SplitKnockoff/issues
Depends: R (>= 3.5.0)
Imports: glmnet, MASS, latex2exp, RSpectra, ggplot2, Matrix, stats, mvtnorm
Suggests: knitr, rmarkdown
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
License: MIT + file LICENSE
Packaged: 2021-09-12 11:26:31 UTC; wang
Repository: CRAN
Date/Publication: 2021-09-13 12:40:02 UTC

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Package sm updated to version 2.2-5.7 with previous version 2.2-5.6 dated 2018-09-27

Title: Smoothing Methods for Nonparametric Regression and Density Estimation
Description: This is software linked to the book 'Applied Smoothing Techniques for Data Analysis - The Kernel Approach with S-Plus Illustrations' Oxford University Press.
Author: Adrian Bowman and Adelchi Azzalini. Ported to R by B. D. Ripley <ripley@stats.ox.ac.uk> up to version 2.0, version 2.1 by Adrian Bowman and Adelchi Azzalini, version 2.2 by Adrian Bowman.
Maintainer: Adrian Bowman <adrian.bowman@glasgow.ac.uk>

Diff between sm versions 2.2-5.6 dated 2018-09-27 and 2.2-5.7 dated 2021-09-13

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New package rscc with initial version 0.1.0
Package: rscc
Title: R Source Code Similarity Evaluation by Similarity Coefficients
Version: 0.1.0
Date: 2021-09-11
Description: Evaluates R source codes by variable and/or functions names. Similar source codes should deliver similarity coefficients near one. Since neither the frequency nor the order of the used names is considered, a manual inspection of the R source code is required to check for similarity. Possible use cases include detection of code clones for improving software quality and of plagiarism amongst students' assignments.
License: GPL-3
URL: https://github.com/sigbertklinke/rscc (development version)
Imports: crayon, formatR, highlight, igraph
Encoding: UTF-8
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-09-11 07:51:40 UTC; sk
Author: Sigbert Klinke [aut, cre]
Maintainer: Sigbert Klinke <sigbert@hu-berlin.de>
Repository: CRAN
Date/Publication: 2021-09-13 12:20:02 UTC

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Package hyperSpec updated to version 0.100.0 with previous version 0.99-20201127 dated 2020-11-29

Title: Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)
Description: Comfortable ways to work with hyperspectral data sets. I.e. spatially or time-resolved spectra, or spectra with any other kind of information associated with each of the spectra. The spectra can be data as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS, etc. More generally, any data that is recorded over a discretized variable, e.g. absorbance = f(wavelength), stored as a vector of absorbance values for discrete wavelengths is suitable.
Author: Claudia Beleites [aut, cre, dtc] (<https://orcid.org/0000-0003-1626-154X>), Valter Sergo [aut], Alois Bonifacio [ctb, dtc], Marcel Dahms [ctb], Björn Egert [ctb], Simon Fuller [ctb], Vilmantas Gegzna [ctb], Rustam Guliev [ctb], Bryan A. Hanson [ctb], Michael Hermes [ctb], Martin Kammer [dtc], Roman Kiselev [ctb], Sebastian Mellor [ctb]
Maintainer: Claudia Beleites <Claudia.Beleites@chemometrix.gmbh>

Diff between hyperSpec versions 0.99-20201127 dated 2020-11-29 and 0.100.0 dated 2021-09-13

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New package GreyModel with initial version 0.1.0
Package: GreyModel
Title: Fitting and Forecasting of Grey Model
Version: 0.1.0
Maintainer: Mrinmoy Ray <mrinmoy4848@gmail.com>
Description: Testing, Implementation and Forecasting of Grey Model (GM(1, 1)). For method details see Hsu, L. and Wang, C. (2007). <doi:10.1016/j.techfore.2006.02.005>.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2021-09-12 08:03:59 UTC; Rajeev-PC
Author: Mrinmoy Ray [aut, cre], Rajeev Ranjan kumar [aut, ctb], K.N. Singh [ctb], Ramasubramanian V. [ctb], Kanchan Sinha [ctb]
Repository: CRAN
Date/Publication: 2021-09-13 12:30:02 UTC

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New package RevGadgets with initial version 1.0.0
Package: RevGadgets
Title: Visualization and Post-Processing of 'RevBayes' Analyses
Version: 1.0.0
Maintainer: Carrie Tribble <ctribble09@gmail.com>
Description: Processes and visualizes the output of complex phylogenetic analyses from the 'RevBayes' phylogenetic graphical modeling software.
URL: https://github.com/cmt2/RevGadgets, https://revbayes.github.io/tutorials/intro/revgadgets
BugReports: https://github.com/cmt2/RevGadgets/issues
License: GPL-3
Encoding: UTF-8
Depends: R (>= 4.0.0)
biocViews:
Imports: ape (>= 5.4), phytools (>= 0.7-70), dplyr (>= 1.0.0), ggtree (>= 3.0.2), treeio (>= 1.12.0), tidytree (>= 0.3.4), ggplot2 (>= 3.0.0), reshape (>= 0.8.8), ggthemes (>= 4.2.0), tidyr (>= 1.1.0), tibble (>= 3.0.1), gginnards (>= 0.0.3), ggplotify (>= 0.0.5), ggimage, ggpp, png (>= 0.1-7), stats (>= 4.0.1), utils (>= 4.0.1), grDevices (>= 4.0.1), deeptime (>= 0.1.0)
Suggests: testthat, knitr, rmarkdown
NeedsCompilation: no
Packaged: 2021-09-11 07:04:25 UTC; carrietribble
Author: Carrie Tribble [aut, cre] (<https://orcid.org/0000-0001-7263-7885>), Michael R. May [aut], William A. Freyman [aut], Michael J. Landis [aut], Lim Jun Ying [aut], Joelle Barido-Sottani [aut], Andrew Magee [aut], Bjorn Tore Kopperud [aut], Sebastian Hohna [aut], Nagashima Kengo [ctb], Schliep Klaus [ctb]
Repository: CRAN
Date/Publication: 2021-09-13 11:40:04 UTC

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New package GPBayes with initial version 0.1.0-2
Package: GPBayes
Title: Tools for Gaussian Process Modeling in Uncertainty Quantification
Version: 0.1.0-2
Date: 2021-08-25
Maintainer: Pulong Ma <mpulong@gmail.com>
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.
License: GPL (>= 3)
Encoding: UTF-8
URL: https://github.com/pulongma/GPBayes/issues
Imports: Rcpp (>= 1.0.1), stats, methods
LinkingTo: Rcpp, RcppEigen, RcppProgress
SystemRequirements: GNU Scientific Library version >= 2.5
NeedsCompilation: yes
Packaged: 2021-09-10 19:28:10 UTC; mapulong
Author: Pulong Ma [aut, cre]
Repository: CRAN
Date/Publication: 2021-09-13 11:20:02 UTC

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New package gcTensor with initial version 0.99.0
Package: gcTensor
Title: Generalized Coupled Tensor Factorization
Version: 0.99.0
Date: 2021-08-24
Suggests: testthat
Depends: R (>= 4.1.0)
Imports: rTensor, einsum
Description: Multiple matrices/tensors can be specified and decomposed simultaneously by Probabilistic Latent Tensor Factorisation (PLTF). See the reference section of GitHub README.md <https://github.com/rikenbit/gcTensor>, for details of the method.
License: Artistic-2.0
URL: https://github.com/rikenbit/gcTensor
NeedsCompilation: no
Packaged: 2021-09-11 04:01:25 UTC; root
Author: Koki Tsuyuzaki [aut, cre]
Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>
Repository: CRAN
Date/Publication: 2021-09-13 11:30:02 UTC

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New package FixedPoint with initial version 0.6.2
Package: FixedPoint
Title: Algorithms for Finding Fixed Point Vectors of Functions
Version: 0.6.2
Author: Stuart Baumann & Margaryta Klymak
Maintainer: Stuart Baumann <Stuart@StuartBaumann.com>
Description: For functions that take and return vectors (or scalars), this package provides 8 algorithms for finding fixed point vectors (vectors for which the inputs and outputs to the function are the same vector). These algorithms include Anderson (1965) acceleration <doi:10.1145/321296.321305>, epsilon extrapolation methods (Wynn 1962 <doi:10.2307/2004051>) and minimal polynomial methods (Cabay and Jackson 1976 <doi:10.1137/0713060>).
License: MIT + file LICENSE
Depends: MASS
Suggests: testthat, schumaker, cubature, knitr, foreach, doParallel, SQUAREM, rmarkdown, qpdf
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-09-10 15:24:54 UTC; dr
Repository: CRAN
Date/Publication: 2021-09-13 11:10:02 UTC

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New package causal.decomp with initial version 0.0.1
Package: causal.decomp
Title: Causal Decomposition Analysis
Version: 0.0.1
Date: 2021-9-7
Depends: R (>= 2.10)
Imports: stats, parallel, MASS, nnet, SuppDists, CBPS, PSweight, spelling, utils
Description: We implement causal decomposition analysis using the methods proposed by Park, Lee, and Qin (2020) <arXiv:2008.12812> and Park, Kang, and Lee (2021+). This package allows researchers to use the multiple-mediator-imputation, single-mediator-imputation, and product-of-coefficients regression methods to estimate the initial disparity, disparity reduction, and disparity remaining. It also allows to make the inference conditional on baseline covariates.
License: GPL-2
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2021-09-11 05:14:28 UTC; Suyeon Kang
Author: Suyeon Kang [aut, cre], Soojin Park [aut]
Maintainer: Suyeon Kang <skang062@ucr.edu>
Repository: CRAN
Date/Publication: 2021-09-13 11:40:02 UTC

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New package TiPS with initial version 1.0
Package: TiPS
Title: Trajectories and Phylogenies Simulator
Version: 1.0
Date: 2021-08-17
Maintainer: Gonche Danesh <gonche.danesh@gmail.com>
Description: Generates stochastic time series and genealogies associated with a population dynamics model. Times series are simulated using the Gillespie exact and approximate algorithms and a new algorithm we introduce that uses both approaches to optimize the time execution of the simulations. Genealogies are simulated from a trajectory using a backwards-in-time based approach. Methods are described in Danesh G et al (2020) <doi:10.1101/2020.11.09.373795>.
License: GPL (>= 2)
SystemRequirements: C++11
Depends: R (>= 3.2.0)
Imports: graphics, grDevices, gtools, inline, methods, Rcpp (>= 0.12.14), stats, stringr, utils
Suggests: knitr, rmarkdown, ape
LinkingTo: Rcpp
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2021-09-10 13:01:39 UTC; danech
Encoding: UTF-8
Author: Gonche Danesh [aut, cre, cph], Emma Saulnier [aut, cph], Marc Choisy [aut, cph, ths], Samuel Alizon [aut, cph, ths]
Repository: CRAN
Date/Publication: 2021-09-13 10:40:02 UTC

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New package MAnorm2 with initial version 1.2.0
Package: MAnorm2
Title: Tools for Normalizing and Comparing ChIP-seq Samples
Version: 1.2.0
Description: Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is the premier technology for profiling genome-wide localization of chromatin-binding proteins, including transcription factors and histones with various modifications. This package provides a robust method for normalizing ChIP-seq signals across individual samples or groups of samples. It also designs a self-contained system of statistical models for calling differential ChIP-seq signals between two or more biological conditions as well as for calling hypervariable ChIP-seq signals across samples. Refer to Tu et al. (2021) <doi:10.1101/gr.262675.120> and Chen et al. (2021) <doi:10.1101/2021.07.27.453915> for associated statistical details.
URL: https://github.com/tushiqi/MAnorm2
BugReports: https://github.com/tushiqi/MAnorm2/issues
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Imports: stats, graphics, methods, locfit (>= 1.5.9), scales (>= 0.3.0), statmod (>= 1.4.34)
Suggests: gplots (>= 3.0.1), DescTools (>= 0.99.24), knitr, rmarkdown
Date: 2021-09-10
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-09-10 11:31:42 UTC; Administrator
Author: Shiqi Tu [aut, cre] (<https://orcid.org/0000-0003-3534-5714>)
Maintainer: Shiqi Tu <tushiqi@picb.ac.cn>
Repository: CRAN
Date/Publication: 2021-09-13 10:30:05 UTC

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New package Gini with initial version 0.1.0
Package: Gini
Title: Gini Coefficient
Version: 0.1.0
Description: Providing various equations to calculate Gini coefficients. The methods used in this package can be referenced from Brown MC (1994) <doi: 10.1016/0277-9536(94)90189-9>.
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2021-09-10 13:03:54 UTC; dgdzc
Author: Zhicheng Du [aut, cre, cph], Zebing Chen [aut], Yuantao Hao [aut]
Maintainer: Zhicheng Du <dgdzc@hotmail.com>
Repository: CRAN
Date/Publication: 2021-09-13 10:30:10 UTC

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Package box updated to version 1.1.0 with previous version 1.0.2 dated 2021-04-22

Title: Write Reusable, Composable and Modular R Code
Description: A modern module system for R. Organise code into hierarchical, composable, reusable modules, and use it effortlessly across projects via a flexible, declarative dependency loading syntax.
Author: Konrad Rudolph [aut, cre] (<https://orcid.org/0000-0002-9866-7051>), Michael Schubert [ctb] (<https://orcid.org/0000-0002-6862-5221>)
Maintainer: Konrad Rudolph <konrad.rudolph@gmail.com>

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New package blaise with initial version 1.3.8
Package: blaise
Title: Read and Write FWF Files in the 'Blaise' Format
Version: 1.3.8
Description: Can be used to read and write a fwf with an accompanying 'Blaise' datamodel. Blaise is the software suite built by Statistics Netherlands (CBS). It is essentially a way to write and collect surveys and perform statistical analysis on the data. It stores its data in fixed width format with an accompanying metadata file, this is the Blaise format. The package automatically interprets this metadata and reads the file into an R dataframe. When supplying a datamodel for writing, the dataframe will be automatically converted to that format and checked for compatibility. Supports dataframes, tibbles and LaF objects. For more information about 'Blaise', see <https://blaise.com/products/general-information>.
License: GPL-3
Encoding: UTF-8
Imports: dplyr (>= 0.7.2), readr (>= 1.1.1), stringr (>= 1.2.0), utils (>= 3.4.1), tibble (>= 1.3.3), tools (>= 3.4.1), methods (>= 3.4.1), stats (>= 3.4.1)
Suggests: testthat, LaF (>= 0.6.3), knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-09-10 14:06:10 UTC; kingmob
Author: Sjoerd Ophof [aut, cre]
Maintainer: Sjoerd Ophof <sjoerd.ophof@gmail.com>
Repository: CRAN
Date/Publication: 2021-09-13 11:00:02 UTC

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Package convertid updated to version 0.1.3 with previous version 0.1.2 dated 2021-09-02

Title: Convert Gene IDs Between Each Other and Fetch Annotations from Biomart
Description: Gene Symbols or Ensembl Gene IDs are converted using the Bimap interface in 'AnnotationDbi' in convertId2() but that function is only provided as fallback mechanism for the most common use cases in data analysis. The main function in the package is convert.bm() which queries BioMart using the full capacity of the API provided through the 'biomaRt' package. Presets and defaults are provided for convenience but all "marts", "filters" and "attributes" can be set by the user. Function convert.alias() converts Gene Symbols to Aliases and vice versa and function likely_symbol() attempts to determine the most likely current Gene Symbol.
Author: Vidal Fey [aut, cre], Henrik Edgren [aut]
Maintainer: Vidal Fey <vidal.fey@gmail.com>

Diff between convertid versions 0.1.2 dated 2021-09-02 and 0.1.3 dated 2021-09-13

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Package AzureAuth updated to version 1.3.3 with previous version 1.3.2 dated 2021-05-19

Title: Authentication Services for Azure Active Directory
Description: Provides Azure Active Directory (AAD) authentication functionality for R users of Microsoft's 'Azure' cloud <https://azure.microsoft.com/>. Use this package to obtain 'OAuth' 2.0 tokens for services including Azure Resource Manager, Azure Storage and others. It supports both AAD v1.0 and v2.0, as well as multiple authentication methods, including device code and resource owner grant. Tokens are cached in a user-specific directory obtained using the 'rappdirs' package. The interface is based on the 'OAuth' framework in the 'httr' package, but customised and streamlined for Azure. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre], Tyler Littlefield [ctb], httr development team [ctb] (Original OAuth listener code), Scott Holden [ctb] (Advice on AAD authentication), Chris Stone [ctb] (Advice on AAD authentication), Microsoft [cph]
Maintainer: Hong Ooi <hongooi73@gmail.com>

Diff between AzureAuth versions 1.3.2 dated 2021-05-19 and 1.3.3 dated 2021-09-13

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Package spmoran updated to version 0.2.2 with previous version 0.2.1 dated 2021-01-10

Title: Moran Eigenvector-Based Spatial Additive Mixed Models
Description: Functions for estimating spatial additive mixed models and other spatial regression models for Gaussian and non-Gaussian data. Moran eigenvectors are used to an approximate Gaussian process modeling which is interpretable in terms of the Moran coefficient. The GP is used for modeling the spatial processes in residuals and regression coefficients. For details see Murakami (2021) <arXiv:1703.04467v10>.
Author: Daisuke Murakami <dmuraka@ism.ac.jp>
Maintainer: Daisuke Murakami <dmuraka@ism.ac.jp>

Diff between spmoran versions 0.2.1 dated 2021-01-10 and 0.2.2 dated 2021-09-13

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New package SPLICE with initial version 1.0.0
Package: SPLICE
Title: Synthetic Paid Loss and Incurred Cost Experience (SPLICE) Simulator
Version: 1.0.0
Author: Benjamin Avanzi [aut], Greg Taylor [aut], Melantha Wang [aut, cre], William Ho [rev]
Maintainer: Melantha Wang <wang.melantha@gmail.com>
Imports: stats, methods, zoo
Description: An extension to the individual claim simulator called 'SynthETIC' (on CRAN), to simulate the evolution of case estimates of incurred losses through the lifetime of an insurance claim. The transactional simulation output now comprises key dates, and both claim payments and revisions of estimated incurred losses. An initial set of test parameters, designed to mirror the experience of a real insurance portfolio, were set up and applied by default to generate a realistic test data set of incurred histories (see vignette). However, the distributional assumptions used to generate this data set can be easily modified by users to match their experiences. Reference: Avanzi B, Taylor G, Wang M (2021) "SPLICE: A Synthetic Paid Loss and Incurred Cost Experience Simulator" <arXiv:2109.04058>.
License: GPL-3
Encoding: UTF-8
URL: https://github.com/agi-lab/SPLICE
BugReports: https://github.com/agi-lab/SPLICE/issues
LazyData: true
Suggests: knitr, rmarkdown, dplyr, RColorBrewer, actuar, poisson, ChainLadder
VignetteBuilder: knitr
Depends: R (>= 2.10), SynthETIC (>= 1.0.0)
NeedsCompilation: no
Packaged: 2021-09-10 02:45:50 UTC; melantha
Repository: CRAN
Date/Publication: 2021-09-13 08:40:06 UTC

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New package rdaemon with initial version 1.0.5
Package: rdaemon
Title: Run an R Daemon Process in the Background
Version: 1.0.5
Date: 2021-09-10
Description: Run an independent R daemon process in the background. The process will keep running even after its terminal quits. The other R sessions can connect with the existing daemon using the same daemon name and send the task via daemonSetTask().
License: GPL (>= 2)
Imports: Rcpp (>= 1.0.6), futile.logger, base64enc, utils
LinkingTo: Rcpp
Encoding: UTF-8
Suggests: rmarkdown, markdown, knitr, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2021-09-10 09:48:30 UTC; lenovo
Author: Jiefei Wang [aut, cre]
Maintainer: Jiefei Wang <szwjf08@gmail.com>
Repository: CRAN
Date/Publication: 2021-09-13 08:50:01 UTC

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New package PH1XBAR with initial version 0.9.4
Package: PH1XBAR
Title: Phase I Shewhart X-Bar Chart
Version: 0.9.4
Maintainer: Yuhui Yao <yyao17@cba.ua.edu>
Description: The purpose of 'PH1XBAR' is to build a Phase I Shewhart X-Bar control chart with variance components model in R. More details can be found: Yao and Chakraborti (2020) <doi: 10.1002/qre.2793>, and Yao and Chakraborti (2021) <doi: 10.1080/08982112.2021.1878220>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0), mvtnorm
URL: https://github.com/bolus123/PH1XBAR
NeedsCompilation: no
Packaged: 2021-09-09 13:28:16 UTC; yyao17
Author: Yuhui Yao [aut, cre], Subha Chakraborti [ctb], Tyler Thomas [ctb]
Repository: CRAN
Date/Publication: 2021-09-13 08:10:02 UTC

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New package masscor with initial version 0.0.7.1
Package: masscor
Title: Mass Measurement Corrections
Version: 0.0.7.1
Date: 2021-09-09
Description: Mass measurement corrections and uncertainties using calibration data, as recommended by EURAMET's guideline No. 18 (2015) ISBN:978-3-942992-40-4 . The package provides classes, functions, and methods for storing information contained in calibration certificates and converting balance readings to both conventional mass and real mass. For the latter, the Magnitude of the Air Buoyancy Correction factor employs models (such as the CIMP-2007 formula revised by Picard, Davis, Gläser, and Fujii (2008) <doi:10.1088/0026-1394/45/2/004>) to estimate the local air density using measured environmental conditions.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
Imports: metRology
Depends: R (>= 3.5.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-09-09 15:43:26 UTC; cris
Author: Cristhian Paredes [aut, cre] (<https://orcid.org/0000-0001-7049-9597>)
Maintainer: Cristhian Paredes <craparedesca@unal.edu.co>
Repository: CRAN
Date/Publication: 2021-09-13 08:20:02 UTC

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New package iRoCoDe with initial version 1.0.0
Package: iRoCoDe
Title: Incomplete Row-Column Designs
Version: 1.0.0
Maintainer: Md. Ashraful Haque <ashrafulhaque664@gmail.com>
Description: The Row-column designs are widely recommended for experimental situations when there are two well-identified factors that are cross-classified representing known sources of variability. These designs are expected to result a gain in accuracy of estimating treatment comparisons in an experiment as they eliminate the effects of the row and column factors. However, these designs are not readily available when the number of treatments is more than the levels of row and column blocking factors. This package named 'iRoCoDe' generates row-column designs with incomplete rows and columns, by amalgamating two incomplete block designs (D1 and D2). The selection of D1 and D2 (the input designs) can be done from the available incomplete block designs, viz., balanced incomplete block designs/ partially balanced incomplete block designs/ t-designs. (Mcsorley, J.P., Phillips, N.C., Wallis, W.D. and Yucas, J.L. (2005).<doi:10.1007/s10623-003-6149-9>).
License: GPL (>= 2)
Encoding: UTF-8
Author: Sayantani Karmakar [aut], Md. Ashraful Haque [aut, cre], Cini Varghese [aut], Seema Jaggi [aut], Eldho Varghese [aut], Mohd. Harun [aut]
Repository: CRAN
NeedsCompilation: no
Packaged: 2021-09-09 14:20:57 UTC; ashraf
Date/Publication: 2021-09-13 08:20:05 UTC

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Package VTrack (with last version 1.21) was removed from CRAN

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

2018-02-22 1.21
2015-07-04 1.11
2015-07-02 1.10

Permanent link
Package multimark (with last version 2.1.2) was removed from CRAN

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

2020-02-06 2.1.2

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Package deisotoper (with last version 0.0.7) was removed from CRAN

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

2019-04-18 0.0.7
2017-12-19 0.0.3
2017-12-08 0.0.2
2017-11-26 0.0.1

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New package VIC5 with initial version 0.2.2
Package: VIC5
Title: The Variable Infiltration Capacity (VIC) Hydrological Model
Version: 0.2.2
Description: The Variable Infiltration Capacity (VIC) model is a macroscale hydrologic model that solves full water and energy balances, originally developed by Xu Liang at the University of Washington (UW). The version of VIC source code used is of 5.0.1 on <https://github.com/UW-Hydro/VIC/>, see Hamman et al. (2018). Development and maintenance of the current official version of the VIC model at present is led by the UW Hydro (Computational Hydrology group) in the Department of Civil and Environmental Engineering at UW. VIC is a research model and in its various forms it has been applied to most of the major river basins around the world, as well as globally. If you make use of this model, please acknowledge the appropriate references listed in the help page of this package or on the references page <http://vic.readthedocs.io/en/master/Documentation/References/> of the VIC official documentation website. These should include Liang et al. (1994) plus any references relevant to the features you are using Reference: "Liang, X., D. P. Lettenmaier, E. F. Wood, and S. J. Burges (1994), A simple hydrologically based model of land surface water and energy fluxes for general circulation models, J. Geophys. Res., 99(D7), 14415-14428, <doi:10.1029/94JD00483>". Hamman et al. (2018) about VIC 5.0.1 also can be considered: "Hamman, J. J., Nijssen, B., Bohn, T. J., Gergel, D. R., and Mao, Y. (2018), The Variable Infiltration Capacity model version 5 (VIC-5): infrastructure improvements for new applications and reproducibility, Geosci. Model Dev., 11, 3481-3496, <doi:10.5194/gmd-11-3481-2018>".
License: GPL-3
Copyright: file inst/COPYRIGHTS
URL: https://github.com/rpkgs/VIC5
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.6.0)
Imports: stats, utils, lubridate, Rcpp, foreach
Suggests: testthat (>= 3.0.0), doParallel
LinkingTo: RcppArmadillo, Rcpp
NeedsCompilation: yes
Packaged: 2021-09-09 10:37:00 UTC; kong
Author: Ruida Zhong [aut, ctb], Dongdong Kong [aut, cre] (<https://orcid.org/0000-0003-1836-8172>), Xiaohong Chen [aut, ctb], Zhaoli Wang [aut, ctb], Chengguang Lai [aut, ctb], Joseph J Hamman [ctb] (Contributor and maintainer of VIC source code), Keith Cherkauer [ctb]
Maintainer: Dongdong Kong <kongdd.sysu@gmail.com>
Repository: CRAN
Date/Publication: 2021-09-13 07:50:02 UTC

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New package prider with initial version 1.0.2
Package: prider
Title: Multiplexed Primer Design by Linear Set Coverage Approximation
Version: 1.0.2
Date: 2021-08-17
Maintainer: Manu Tamminen <mavatam@utu.fi>
Description: Implementation of an oligonucleotide primer and probe design algorithm using a linearly scaling approximation of set coverage. A detailed description available at Smolander and Tamminen, 2021; <doi:10.1101/2021.09.06.459073>.
License: BSD_3_clause + file LICENSE
Imports: Rcpp (>= 1.0.5), dplyr, tidyr, purrr, stringr, magrittr, tibble, blaster, gplots
LinkingTo: Rcpp
SystemRequirements: C++11
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2021-09-09 09:49:13 UTC; mavatam
Author: Manu Tamminen [aut, cre] (<https://orcid.org/0000-0001-5891-7653>), Niina Smolander [aut] (<https://orcid.org/0000-0003-4329-4785>)
Repository: CRAN
Date/Publication: 2021-09-13 07:30:02 UTC

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New package ntwk with initial version 1.0.0
Package: ntwk
Title: Statistical Inference for Network Time Series
Version: 1.0.0
Maintainer: Valentin Courgeau <val.courgeau@gmail.com>
Description: Statistical inference tools for network time series, including implementation of the Graph Ornstein-Uhlenbeck ('GrOU') model and sparse AR-like regression on irregularly-spaced data (Courgeau and Veraart (2020) <arXiv:2005.12720>; Courgeau and Veraart <arXiv:2008.10930>). It also handles jumps and Levy-type driving noises through Wiener-Poisson mixtures and Generalised Hyperbolic distributions.
License: MIT + file LICENSE
Imports: assertthat (>= 0.2.1), copCAR, ghyp, Matrix, mvtnorm, pracma, stats, zoo
Suggests: igraph, knitr, numDeriv, rmarkdown, spelling, testthat (>= 3.0.0)
Encoding: UTF-8
Language: en-GB
NeedsCompilation: no
Packaged: 2021-09-09 10:25:26 UTC; vcourgeau
Author: Valentin Courgeau [aut, cre, cph] (<https://orcid.org/0000-0002-7423-0090>)
Repository: CRAN
Date/Publication: 2021-09-13 07:30:05 UTC

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New package NIMAA with initial version 0.1.0
Package: NIMAA
Title: Nominal Data Mining Analysis
Version: 0.1.0
Description: Functions for nominal data mining based on bipartite graphs, which build a pipeline for analysis and missing values imputation. Methods are mainly from the paper: Jafari, Mohieddin, et al. (2021) <doi:10.1101/2021.03.18.436040>, some new ones are also included.
License: GPL (>= 3)
URL: https://github.com/jafarilab/NIMAA
BugReports: https://github.com/jafarilab/NIMAA/issues
Encoding: UTF-8
LazyData: true
Suggests: knitr, utils, rmarkdown, htmltools, testthat (>= 3.0.0)
Imports: plotly, tidyr, bipartite, crayon, dplyr, ggplot2, igraph, purrr, skimr, bnstruct, RColorBrewer, fpc, mice, missMDA, networkD3, scales, softImpute, tibble, tidytext, visNetwork, stats
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2021-09-09 11:46:38 UTC; cheng
Author: Mohieddin Jafari [aut], Cheng Chen [aut, cre]
Maintainer: Cheng Chen <cheng.chen@helsinki.fi>
Repository: CRAN
Date/Publication: 2021-09-13 08:00:05 UTC

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Package mdatools updated to version 0.12.0 with previous version 0.11.5 dated 2021-04-30

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

Diff between mdatools versions 0.11.5 dated 2021-04-30 and 0.12.0 dated 2021-09-13

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New package ggHoriPlot with initial version 1.0.0
Package: ggHoriPlot
Title: Horizon Plots for 'ggplot2'
Version: 1.0.0
Maintainer: Iker Rivas-González <ikerrivas96@gmail.com>
Description: A user-friendly, highly customizable R package for building horizon plots in the 'ggplot2' environment.
License: GPL-3
URL: https://rivasiker.github.io/ggHoriPlot/, https://github.com/rivasiker/ggHoriPlot
BugReports: https://github.com/rivasiker/ggHoriPlot/issues
Depends: ggplot2, R (>= 2.10)
Imports: dplyr, glue, magrittr, stringr, tidyr
Suggests: ggh4x, ggthemes, knitr, patchwork, rmarkdown, testthat (>= 3.0.0), tidyverse, utils
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2021-09-09 11:46:50 UTC; au595587
Author: Iker Rivas-González [aut, cre] (<https://orcid.org/0000-0002-0515-0628>)
Repository: CRAN
Date/Publication: 2021-09-13 08:00:02 UTC

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New package DOSPortfolio with initial version 0.1.0
Package: DOSPortfolio
Title: Dynamic Optimal Shrinkage Portfolio
Version: 0.1.0
Maintainer: Erik Thorsén <erik.thorsen@math.su.se>
Author: Taras Bodnar [aut] (<https://orcid.org/0000-0001-7855-8221>), Nestor Parolya [aut] (<https://orcid.org/0000-0003-2147-2288>), Erik Thorsén [aut, cre] (<https://orcid.org/0000-0001-5992-1216>)
Description: Constructs dynamic optimal shrinkage estimators for the weights of the global minimum variance portfolio which are reconstructed at given reallocation points as derived in Bodnar, Parolya, and Thorsén (2021) (<arXiv:2106.02131>). Two dynamic shrinkage estimators are available in this package. One using overlapping samples while the other use nonoverlapping samples.
License: GPL-3
URL: https://github.com/Statistics-In-Portfolio-Theory/DOSportfolio
Encoding: UTF-8
RdMacros: Rdpack
Depends: R (>= 3.5.0)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), HDShOP
Imports: Rdpack (>= 0.7)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-09-09 08:27:08 UTC; ethor
Repository: CRAN
Date/Publication: 2021-09-13 07:30:08 UTC

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Package MatchIt updated to version 4.3.0 with previous version 4.2.0 dated 2021-05-26

Title: Nonparametric Preprocessing for Parametric Causal Inference
Description: Selects matched samples of the original treated and control groups with similar covariate distributions -- can be used to match exactly on covariates, to match on propensity scores, or perform a variety of other matching procedures. The package also implements a series of recommendations offered in Ho, Imai, King, and Stuart (2007) <DOI:10.1093/pan/mpl013>. (The 'gurobi' package, which is not on CRAN, is optional and comes with an installation of the Gurobi Optimizer, available at <https://www.gurobi.com>.)
Author: Daniel Ho [aut] (<https://orcid.org/0000-0002-2195-5469>), Kosuke Imai [aut] (<https://orcid.org/0000-0002-2748-1022>), Gary King [aut] (<https://orcid.org/0000-0002-5327-7631>), Elizabeth Stuart [aut] (<https://orcid.org/0000-0002-9042-8611>), Alex Whitworth [ctb], Noah Greifer [ctb, cre, aut] (<https://orcid.org/0000-0003-3067-7154>)
Maintainer: Noah Greifer <noah.greifer@gmail.com>

Diff between MatchIt versions 4.2.0 dated 2021-05-26 and 4.3.0 dated 2021-09-13

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Package BayesSPsurv updated to version 0.1.4 with previous version 0.1.3 dated 2021-05-14

Title: Bayesian Spatial Split Population Survival Model
Description: Parametric spatial split-population (SP) survival models for clustered event processes. The models account for structural and spatial heterogeneity among “at risk” and “immune” populations, and incorporate time-varying covariates. This package currently implements Weibull, Exponential and Log-logistic forms for the duration component. It also includes functions for a series of diagnostic tests and plots to easily visualize spatial autocorrelation, convergence, and spatial effects. Users can create their own spatial weights matrix based on their units and adjacencies of interest, making the use of these models flexible and broadly applicable to a variety of research areas. Joo et al. (2020) <https://github.com/Nicolas-Schmidt/BayesSPsurv/blob/master/man/figures/SPcure.pdf> describe the estimators included in this package.
Author: Brandon L. Bolte [aut], Nicolas Schmidt [aut, cre], Sergio Bejar [aut], Minnie M. Joo [aut], Nguyen K. Huynh [aut], Bumba Mukherjee [aut]
Maintainer: Nicolas Schmidt <nschmidt@cienciassociales.edu.uy>

Diff between BayesSPsurv versions 0.1.3 dated 2021-05-14 and 0.1.4 dated 2021-09-13

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Package hhsmm updated to version 0.1.3 with previous version 0.1.2 dated 2021-06-16

Title: Hidden Hybrid Markov/Semi-Markov Model Fitting
Description: Develops algorithms for fitting, prediction, simulation and initialization of the hidden hybrid Markov/semi-Markov model, introduced by Guedon (2005) <doi:10.1016/j.csda.2004.05.033>.
Author: Morteza Amini [aut, cre, cph], Afarin Bayat [aut]
Maintainer: Morteza Amini <morteza.amini@ut.ac.ir>

Diff between hhsmm versions 0.1.2 dated 2021-06-16 and 0.1.3 dated 2021-09-13

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Package dictionar6 updated to version 0.1.3 with previous version 0.1.2 dated 2021-07-26

Title: R6 Dictionary Interface
Description: Efficient object-oriented R6 dictionary capable of holding objects of any class, including R6. Typed and untyped dictionaries are provided as well as the 'usual' dictionary methods that are available in other OOP languages, for example listing keys, items, values, and methods to get/set these.
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>)
Maintainer: Raphael Sonabend <raphaelsonabend@gmail.com>

Diff between dictionar6 versions 0.1.2 dated 2021-07-26 and 0.1.3 dated 2021-09-13

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