Sun, 10 Oct 2021

Package SUNGEO updated to version 0.2.27 with previous version 0.2.25 dated 2021-08-12

Title: Sub-National Geospatial Data Archive: Geoprocessing Toolkit
Description: Tools for integrating spatially-misaligned GIS datasets. Part of the Sub-National Geospatial Data Archive System.
Author: Jason Byers, Marty Davidson, Yuri M. Zhukov
Maintainer: Yuri M. Zhukov <zhukov@umich.edu>

Diff between SUNGEO versions 0.2.25 dated 2021-08-12 and 0.2.27 dated 2021-10-10

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Package Markovchart updated to version 2.1.3 with previous version 2.0.1 dated 2021-05-08

Title: Markov Chain-Based Cost-Optimal Control Charts
Description: Functions for cost-optimal control charts with a focus on health care applications. Compared to assumptions in traditional control chart theory, here, we allow random shift sizes, random repair and random sampling times. The package focuses on X-bar charts with a sample size of 1 (representing the monitoring of a single patient at a time). The methods are described in Zempleni et al. (2004) <doi:10.1002/asmb.521>, Dobi and Zempleni (2019) <doi:10.1002/qre.2518> and Dobi and Zempleni (2019) <http://ac.inf.elte.hu/Vol_049_2019/129_49.pdf>.
Author: Balazs Dobi & Andras Zempleni
Maintainer: Balazs Dobi <dobibalazs@inf.elte.hu>

Diff between Markovchart versions 2.0.1 dated 2021-05-08 and 2.1.3 dated 2021-10-10

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Package Rfast2 updated to version 0.1.1 with previous version 0.0.9 dated 2021-03-21

Title: A Collection of Efficient and Extremely Fast R Functions II
Description: A collection of fast statistical and utility functions for data analysis. Functions for regression, maximum likelihood, column-wise statistics and many more have been included. C++ has been utilized to speed up the functions.
Author: Manos Papadakis, Michail Tsagris, Stefanos Fafalios and Marios Dimitriadis.
Maintainer: Manos Papadakis <rfastofficial@gmail.com>

Diff between Rfast2 versions 0.0.9 dated 2021-03-21 and 0.1.1 dated 2021-10-10

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Package rAmCharts4 updated to version 1.5.0 with previous version 1.4.1 dated 2021-09-30

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

Diff between rAmCharts4 versions 1.4.1 dated 2021-09-30 and 1.5.0 dated 2021-10-10

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Package ggdag updated to version 0.2.4 with previous version 0.2.3 dated 2021-01-12

Title: Analyze and Create Elegant Directed Acyclic Graphs
Description: Tidy, analyze, and plot directed acyclic graphs (DAGs). 'ggdag' is built on top of 'dagitty', an R package that uses the 'DAGitty' web tool (<http://dagitty.net>) for creating and analyzing DAGs. 'ggdag' makes it easy to tidy and plot 'dagitty' objects using 'ggplot2' and 'ggraph', as well as common analytic and graphical functions, such as determining adjustment sets and node relationships.
Author: Malcolm Barrett [aut, cre] (<https://orcid.org/0000-0003-0299-5825>)
Maintainer: Malcolm Barrett <malcolmbarrett@gmail.com>

Diff between ggdag versions 0.2.3 dated 2021-01-12 and 0.2.4 dated 2021-10-10

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Package bgmm updated to version 1.8.5 with previous version 1.8.4 dated 2020-03-03

Title: Gaussian Mixture Modeling Algorithms and the Belief-Based Mixture Modeling
Description: Two partially supervised mixture modeling methods: soft-label and belief-based modeling are implemented. For completeness, we equipped the package also with the functionality of unsupervised, semi- and fully supervised mixture modeling. The package can be applied also to selection of the best-fitting from a set of models with different component numbers or constraints on their structures. For detailed introduction see: Przemyslaw Biecek, Ewa Szczurek, Martin Vingron, Jerzy Tiuryn (2012), The R Package bgmm: Mixture Modeling with Uncertain Knowledge, Journal of Statistical Software <doi:10.18637/jss.v047.i03>.
Author: Przemyslaw Biecek \& Ewa Szczurek
Maintainer: Przemyslaw Biecek <Przemyslaw.Biecek@gmail.com>

Diff between bgmm versions 1.8.4 dated 2020-03-03 and 1.8.5 dated 2021-10-10

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Package ChemoSpecUtils updated to version 1.0.0 with previous version 0.4.96 dated 2021-03-15

Title: Functions Supporting Packages ChemoSpec and ChemoSpec2D
Description: Functions supporting the common needs of packages 'ChemoSpec' and 'ChemoSpec2D'.
Author: Bryan A. Hanson [aut, cre] (<https://orcid.org/0000-0003-3536-8246>), Tejasvi Gupta [ctb] (author of ggplot2 graphics)
Maintainer: Bryan A. Hanson <hanson@depauw.edu>

Diff between ChemoSpecUtils versions 0.4.96 dated 2021-03-15 and 1.0.0 dated 2021-10-10

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Package pathwayTMB updated to version 0.1.1 with previous version 0.1.0 dated 2021-07-15

Title: Pathway Based Tumor Mutational Burden
Description: A systematic bioinformatics tool to develop a new pathway-based gene panel for tumor mutational burden (TMB) assessment (pathway-based tumor mutational burden, PTMB), using somatic mutations files in an efficient manner from either The Cancer Genome Atlas sources or any in-house studies as long as the data is in mutation annotation file (MAF) format. Besides, we develop a multiple machine learning method using the sample's PTMB profiles to identify cancer-specific dysfunction pathways, which can be a biomarker of prognostic and predictive for cancer immunotherapy.
Author: Junwei Han [aut, cre, cph], Xiangmei Li [aut]
Maintainer: Junwei Han <hanjunwei1981@163.com>

Diff between pathwayTMB versions 0.1.0 dated 2021-07-15 and 0.1.1 dated 2021-10-10

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Package GerminaR updated to version 2.1.3 with previous version 2.1.2 dated 2021-06-11

Title: Indices and Graphics for Assess Seed Germination Process
Description: A collection of different indices and visualization techniques for evaluate the seed germination process in ecophysiological studies (Lozano-Isla et al. 2019) <doi:10.1111/1440-1703.1275>.
Author: Flavio Lozano-Isla [aut, cre] (<https://orcid.org/0000-0002-0714-669X>), Omar Benites Alfaro [aut] (<https://orcid.org/0000-0002-6852-9598>), Denise Garcia de Santana [aut], Marli A. Ranal [aut], Marcelo F. Pompelli [aut, ths] (<https://orcid.org/0000-0002-4408-6374>), Federal University of Pernambuco [cph] (Register of application), Federal Rural University of Pernambuco [cph] (Post Graduate Program)
Maintainer: Flavio Lozano-Isla <flavjack@gmail.com>

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Package bestridge updated to version 1.0.7 with previous version 1.0.6 dated 2021-09-02

Title: A Comprehensive R Package for Best Subset Selection
Description: The bestridge package is designed to provide a one-stand service for users to successfully carry out best ridge regression in various complex situations via the primal dual active set algorithm proposed by Wen, C., Zhang, A., Quan, S. and Wang, X. (2020) <doi:10.18637/jss.v094.i04>. This package allows users to perform the regression, classification, count regression and censored regression for (ultra) high dimensional data, and it also supports advanced usages like group variable selection and nuisance variable selection.
Author: Liyuan Hu [aut, cre] (<https://orcid.org/0000-0003-2064-8990>), Jin Zhu [aut] (<https://orcid.org/0000-0001-8550-5822>), Junxian Zhu [aut], Kangkang Jiang [aut], Yanhang Zhang [aut], Xueqin Wang [aut] (<https://orcid.org/0000-0001-5205-9950>), Canhong Wen [aut]
Maintainer: Liyuan Hu <huly5@mail2.sysu.edu.cn>

Diff between bestridge versions 1.0.6 dated 2021-09-02 and 1.0.7 dated 2021-10-10

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Package yorkr updated to version 0.0.27 with previous version 0.0.26 dated 2021-09-20

Title: Analyze Cricket Performances Based on Data from Cricsheet
Description: Analyzing performances of cricketers and cricket teams based on 'yaml' match data from Cricsheet <https://cricsheet.org/>.
Author: Tinniam V Ganesh
Maintainer: Tinniam V Ganesh <tvganesh.85@gmail.com>

Diff between yorkr versions 0.0.26 dated 2021-09-20 and 0.0.27 dated 2021-10-10

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Package mcmcsae updated to version 0.7.0 with previous version 0.6.0 dated 2021-01-20

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

Diff between mcmcsae versions 0.6.0 dated 2021-01-20 and 0.7.0 dated 2021-10-10

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More information about mcmcsae at CRAN
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Package wsrf updated to version 1.7.22 with previous version 1.7.21 dated 2021-04-28

Title: Weighted Subspace Random Forest for Classification
Description: A parallel implementation of Weighted Subspace Random Forest. The Weighted Subspace Random Forest algorithm was proposed in the International Journal of Data Warehousing and Mining by Baoxun Xu, Joshua Zhexue Huang, Graham Williams, Qiang Wang, and Yunming Ye (2012) <DOI:10.4018/jdwm.2012040103>. The algorithm can classify very high-dimensional data with random forests built using small subspaces. A novel variable weighting method is used for variable subspace selection in place of the traditional random variable sampling.This new approach is particularly useful in building models from high-dimensional data.
Author: Qinghan Meng [aut], He Zhao [aut, cre] (<https://orcid.org/0000-0001-5763-9743>), Graham J. Williams [aut] (<https://orcid.org/0000-0001-7041-4127>), Junchao Lv [aut], Baoxun Xu [aut], Joshua Zhexue Huang [aut] (<https://orcid.org/0000-0002-6797-2571>)
Maintainer: He Zhao <Simon.Yansen.Zhao@gmail.com>

Diff between wsrf versions 1.7.21 dated 2021-04-28 and 1.7.22 dated 2021-10-10

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More information about wsrf at CRAN
Permanent link

Package stringfish updated to version 0.15.3 with previous version 0.15.2 dated 2021-07-24

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

Diff between stringfish versions 0.15.2 dated 2021-07-24 and 0.15.3 dated 2021-10-10

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More information about stringfish at CRAN
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Package tempR updated to version 0.9.9.18 with previous version 0.9.9.16 dated 2020-01-08

Title: Temporal Sensory Data Analysis
Description: Analysis and visualization of data from temporal sensory methods, including for temporal check-all-that-apply (TCATA) and temporal dominance of sensations (TDS).
Author: J.C. Castura [aut, cre, ctb] (<https://orcid.org/0000-0002-1640-833X>)
Maintainer: J.C. Castura <jcastura@compusense.com>

Diff between tempR versions 0.9.9.16 dated 2020-01-08 and 0.9.9.18 dated 2021-10-10

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Package rnpn (with last version 1.2.2) was removed from CRAN

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

2021-10-05 1.2.2

Permanent link
Package ridge updated to version 3.0 with previous version 2.9 dated 2021-02-04

Title: Ridge Regression with Automatic Selection of the Penalty Parameter
Description: Linear and logistic ridge regression functions. Additionally includes special functions for genome-wide single-nucleotide polymorphism (SNP) data. More details can be found in <doi: 10.1002/gepi.21750> and <doi: 10.1186/1471-2105-12-372>.
Author: Steffen Moritz [aut, cre] (<https://orcid.org/0000-0002-0085-1804>), Erika Cule [aut], Dan Frankowski [aut]
Maintainer: Steffen Moritz <steffen.moritz10@gmail.com>

Diff between ridge versions 2.9 dated 2021-02-04 and 3.0 dated 2021-10-10

 DESCRIPTION     |    8 
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Package reporter updated to version 1.2.0 with previous version 1.1.6 dated 2021-09-08

Title: Creates Statistical Reports
Description: Contains functions to create regulatory-style statistical reports. Originally designed to create tables, listings, and figures for the pharmaceutical, biotechnology, and medical device industries, these reports are generalized enough that they could be used in any industry. Generates text, rich-text, and PDF file formats. The package specializes in printing wide and long tables with automatic page wrapping and splitting. Reports can be produced with a minimum of function calls, and without relying on other table packages. The package supports titles, footnotes, page header, page footers, spanning headers, page by variables, and automatic page numbering.
Author: David Bosak [aut, cre], Kevin Kramer [ctb], Archytas Clinical Solutions [cph]
Maintainer: David Bosak <dbosak01@gmail.com>

Diff between reporter versions 1.1.6 dated 2021-09-08 and 1.2.0 dated 2021-10-10

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Package rayvertex updated to version 0.3.3 with previous version 0.2.3 dated 2021-06-17

Title: 3D Software Rasterizer
Description: Rasterize images using a 3D software renderer. 3D scenes are created either by importing external files, building scenes out of the included objects, or by constructing meshes manually. Supports point and directional lights, anti-aliased lines, shadow mapping, transparent objects, translucent objects, multiple materials types, reflection, refraction, environment maps, multicore rendering, bloom, tone-mapping, and screen-space ambient occlusion.
Author: Tyler Morgan-Wall [aut, cph, cre] (<https://orcid.org/0000-0002-3131-3814>), Syoyo Fujita [ctb, cph], Vilya Harvey [ctb, cph], G-Truc Creation [ctb, cph], Sean Barrett [ctb, cph]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>

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Package radiant.model updated to version 1.4.1 with previous version 1.4.0 dated 2021-05-13

Title: Model Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Model menu includes interfaces for linear and logistic regression, naive Bayes, neural networks, classification and regression trees, model evaluation, collaborative filtering, decision analysis, and simulation. The application extends the functionality in 'radiant.data'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>

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

Title: Estimate Sample Size Based on Precision Rather than Power
Description: Estimate sample size based on precision rather than power. 'precisely' is a study planning tool to calculate sample size based on precision. Power calculations are focused on whether or not an estimate will be statistically significant; calculations of precision are based on the same principles as power calculation but turn the focus to the width of the confidence interval. 'precisely' is based on the work of 'Rothman and Greenland' (2018).
Author: Malcolm Barrett [aut, cre] (<https://orcid.org/0000-0003-0299-5825>)
Maintainer: Malcolm Barrett <malcolmbarrett@gmail.com>

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Package geeCRT updated to version 0.1.1 with previous version 0.1.0 dated 2021-04-15

Title: Bias-Corrected GEE for Cluster Randomized Trials
Description: Population-averaged models have been increasingly used in the design and analysis of cluster randomized trials (CRTs). To facilitate the applications of population-averaged models in CRTs, the package implements the generalized estimating equations (GEE) and matrix-adjusted estimating equations (MAEE) approaches to jointly estimate the marginal mean models correlation models both for general CRTs and stepped wedge CRTs. Despite the general GEE/MAEE approach, the package also implements a fast cluster-period GEE method by Li et al. (2021) <doi:10.1093/biostatistics/kxaa056> specifically for stepped wedge CRTs with large and variable cluster-period sizes and gives a simple and efficient estimating equations approach based on the cluster-period means to estimate the intervention effects as well as correlation parameters. In addition, the package also provides functions for generating correlated binary data with specific mean vector and correlation matrix based on the multivariate probit method in Emrich and Piedmonte (1991) <doi:10.1080/00031305.1991.10475828> or the conditional linear family method in Qaqish (2003) <doi:10.1093/biomet/90.2.455>.
Author: Hengshi Yu [aut, cre], Fan Li [aut], Paul Rathouz [aut], Elizabeth L. Turner [aut], John Preisser [aut]
Maintainer: Hengshi Yu <hengshi@umich.edu>

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Package future.tests updated to version 0.3.0 with previous version 0.2.1 dated 2020-03-20

Title: Test Suite for 'Future API' Backends
Description: Backends implementing the 'Future' API, as defined by the 'future' package, should use the tests provided by this package to validate that they meet the minimal requirements of the 'Future' API. The tests can be performed easily from within R or from outside of R from the command line making it easy to include them package tests and in Continuous Integration (CI) pipelines.
Author: Henrik Bengtsson [aut, cre, cph], The R Consortium [fnd] (Project was awared an Infrastructure Steering Committee (ISC) grant in 2017)
Maintainer: Henrik Bengtsson <henrikb@braju.com>

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