Mon, 06 Feb 2023

Package geocmeans updated to version 0.3.3 with previous version 0.3.2 dated 2023-01-08

Title: Implementing Methods for Spatial Fuzzy Unsupervised Classification
Description: Provides functions to apply spatial fuzzy unsupervised classification, visualize and interpret results. This method is well suited when the user wants to analyze data with a fuzzy clustering algorithm and to account for the spatial dimension of the dataset. In addition, indexes for estimating the spatial consistency and classification quality are proposed. The methods were originally proposed in the field of brain imagery (seed Cai and al. 2007 <doi:10.1016/j.patcog.2006.07.011> and Zaho and al. 2013 <doi:10.1016/j.dsp.2012.09.016>) and recently applied in geography (see Gelb and Apparicio <doi:10.4000/cybergeo.36414>).
Author: Jeremy Gelb [aut, cre], Philippe Apparicio [ctb]
Maintainer: Jeremy Gelb <jeremy.gelb@ucs.inrs.ca>

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Package epiR updated to version 2.0.57 with previous version 2.0.56 dated 2023-01-15

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

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Package MassWateR updated to version 2.0.1 with previous version 2.0.0 dated 2023-01-20

Title: Quality Control and Analysis of Massachusetts Water Quality Data
Description: Methods for quality control and exploratory analysis of surface water quality data collected in Massachusetts, USA. Functions are developed to facilitate data formatting for the Water Quality Exchange Network <https://www.epa.gov/waterdata/water-quality-data-upload-wqx> and reporting of data quality objectives to state agencies. Quality control methods are from Massachusetts Department of Environmental Protection (2020) <https://www.mass.gov/orgs/massachusetts-department-of-environmental-protection>.
Author: Marcus Beck [aut, cre] , Jill Carr [aut], Ben Wetherill [aut] , Pam DiBona [aut]
Maintainer: Marcus Beck <mbeck@tbep.org>

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Package EMT updated to version 1.3 with previous version 1.2 dated 2021-11-02

Title: Exact Multinomial Test: Goodness-of-Fit Test for Discrete Multivariate Data
Description: Goodness-of-fit tests for discrete multivariate data. It is tested if a given observation is likely to have occurred under the assumption of an ab-initio model. Monte Carlo methods are provided to make the package capable of solving high-dimensional problems.
Author: Uwe Menzel
Maintainer: Uwe Menzel <uwemenzel@gmail.com>

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Package colourvalues updated to version 0.3.8 with previous version 0.3.7 dated 2020-12-07

Title: Assigns Colours to Values
Description: Maps one of the viridis colour palettes, or a user-specified palette to values. Viridis colour maps are created by Stéfan van der Walt and Nathaniel Smith, and were set as the default palette for the 'Python' 'Matplotlib' library <https://matplotlib.org/>. Other palettes available in this library have been derived from 'RColorBrewer' <https://CRAN.R-project.org/package=RColorBrewer> and 'colorspace' <https://CRAN.R-project.org/package=colorspace> packages.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <dcooley@symbolix.com.au>

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Package rlemon updated to version 0.2.1 with previous version 0.2.0 dated 2022-04-15

Title: R Access to LEMON Graph Algorithms
Description: Allows easy access to the LEMON Graph Library set of algorithms, written in C++. See the LEMON project page at <https://lemon.cs.elte.hu/trac/lemon>. Current LEMON version is 1.3.1.
Author: Arav Agarwal [aut], Aditya Tewari [aut], Josh Errickson [cre, aut]
Maintainer: Josh Errickson <jerrick@umich.edu>

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Package mBvs updated to version 1.6 with previous version 1.5 dated 2021-06-17

Title: Bayesian Variable Selection Methods for Multivariate Data
Description: Bayesian variable selection methods for data with multivariate responses and multiple covariates. The package contains implementations of multivariate Bayesian variable selection methods for continuous data (Lee et al., Biometrics, 2017 <doi:10.1111/biom.12557>) and zero-inflated count data (Lee et al., Biostatistics, 2020 <doi:10.1093/biostatistics/kxy067>).
Author: Kyu Ha Lee, Mahlet G. Tadesse, Brent A. Coull, Jacqueline R. Starr
Maintainer: Kyu Ha Lee <klee15239@gmail.com>

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Package fs updated to version 1.6.1 with previous version 1.6.0 dated 2023-01-23

Title: Cross-Platform File System Operations Based on 'libuv'
Description: A cross-platform interface to file system operations, built on top of the 'libuv' C library.
Author: Jim Hester [aut], Hadley Wickham [aut], Gabor Csardi [aut, cre], libuv project contributors [cph] , Joyent, Inc. and other Node contributors [cph] , RStudio [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>

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Package brglm2 updated to version 0.9 with previous version 0.8.2 dated 2021-11-21

Title: Bias Reduction in Generalized Linear Models
Description: Estimation and inference from generalized linear models based on various methods for bias reduction and maximum penalized likelihood with powers of the Jeffreys prior as penalty. The 'brglmFit' fitting method can achieve reduction of estimation bias by solving either the mean bias-reducing adjusted score equations in Firth (1993) <doi:10.1093/biomet/80.1.27> and Kosmidis and Firth (2009) <doi:10.1093/biomet/asp055>, or the median bias-reduction adjusted score equations in Kenne et al. (2017) <doi:10.1093/biomet/asx046>, or through the direct subtraction of an estimate of the bias of the maximum likelihood estimator from the maximum likelihood estimates as in Cordeiro and McCullagh (1991) <https://www.jstor.org/stable/2345592>. See Kosmidis et al (2020) <doi:10.1007/s11222-019-09860-6> for more details. Estimation in all cases takes place via a quasi Fisher scoring algorithm, and S3 methods for the construction of of confidence intervals for the reduced-bia [...truncated...]
Author: Ioannis Kosmidis [aut, cre] , Euloge Clovis Kenne Pagui [aut], Kjell Konis [ctb], Nicola Sartori [ctb]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>

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Package arf updated to version 0.1.3 with previous version 0.1.2 dated 2022-12-16

Title: Adversarial Random Forests
Description: Adversarial random forests (ARFs) recursively partition data into fully factorized leaves, where features are jointly independent. The procedure is iterative, with alternating rounds of generation and discrimination. Data becomes increasingly realistic at each round, until original and synthetic samples can no longer be reliably distinguished. This is useful for several unsupervised learning tasks, such as density estimation and data synthesis. Methods for both are implemented in this package. ARFs naturally handle unstructured data with mixed continuous and categorical covariates. They inherit many of the benefits of random forests, including speed, flexibility, and solid performance with default parameters. For details, see Watson et al. (2022) <arXiv:2205.09435>.
Author: Marvin N. Wright [aut, cre] , David S. Watson [aut]
Maintainer: Marvin N. Wright <cran@wrig.de>

Diff between arf versions 0.1.2 dated 2022-12-16 and 0.1.3 dated 2023-02-06

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Package accept updated to version 1.0.0 with previous version 0.9.1 dated 2022-07-15

Title: The Acute COPD Exacerbation Prediction Tool (ACCEPT)
Description: Allows clinicians to predict the rate and severity of future acute exacerbation in Chronic Obstructive Pulmonary Disease (COPD) patients, based on the clinical prediction models published in Adibi et al. (2020) <doi:10.1016/S2213-2600(19)30397-2> and Safari et al. (2022) <doi:10.1016/j.eclinm.2022.101574>.
Author: Amin Adibi [aut, cre], Mohsen Sadatsafavi [aut, cph], Abdollah Safari [aut], Ainsleigh Hill [aut]
Maintainer: Amin Adibi <adibi@alumni.ubc.ca>

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Package W3CMarkupValidator updated to version 0.1-7 with previous version 0.1-6 dated 2017-02-20

Title: R Interface to W3C Markup Validation Services
Description: R interface to a W3C Markup Validation service. See <https://validator.w3.org/> for more information.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

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Package PDE updated to version 1.4.3 with previous version 1.4.2 dated 2022-12-12

Title: Extract Tables and Sentences from PDFs with User Interface
Description: The PDE (Pdf Data Extractor) allows the extraction of information and tables optionally based on search words from PDF (Portable Document Format) files and enables the visualization of the results, both by providing a convenient user-interface.
Author: Erik Stricker [aut, cre]
Maintainer: Erik Stricker <erik.stricker@gmx.com>

Diff between PDE versions 1.4.2 dated 2022-12-12 and 1.4.3 dated 2023-02-06

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Package openxlsx updated to version 4.2.5.2 with previous version 4.2.5.1 dated 2022-10-24

Title: Read, Write and Edit xlsx Files
Description: Simplifies the creation of Excel .xlsx files by providing a high level interface to writing, styling and editing worksheets. Through the use of 'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect' packages with the added benefit of removing the dependency on Java.
Author: Philipp Schauberger [aut, cre], Alexander Walker [aut], Luca Braglia [ctb], Joshua Sturm [ctb], Jan Marvin Garbuszus [ctb], Jordan Mark Barbone [ctb]
Maintainer: Philipp Schauberger <philipp@schauberger.co.at>

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Package kml3d (with last version 2.4.2) was removed from CRAN

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

2017-08-08 2.4.2

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Package torchaudio updated to version 0.3.0 with previous version 0.2.2 dated 2023-01-23

Title: R Interface to 'pytorch''s 'torchaudio'
Description: Provides access to datasets, models and processing facilities for deep learning in audio.
Author: Sigrid Keydana [aut, cre], Athos Damiani [aut], Daniel Falbel [aut]
Maintainer: Sigrid Keydana <sigrid@posit.co>

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Package ade4 updated to version 1.7-22 with previous version 1.7-20 dated 2022-11-01

Title: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences
Description: Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.
Author: Stephane Dray <stephane.dray@univ-lyon1.fr>, Anne-Beatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sebastien Ollier, D [...truncated...]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>

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Package rabhit updated to version 0.2.5 with previous version 0.2.4 dated 2022-09-22

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

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Package protViz updated to version 0.7.7 with previous version 0.7.3 dated 2022-04-04

Title: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics
Description: Helps with quality checks, visualizations and analysis of mass spectrometry data, coming from proteomics experiments. The package is developed, tested and used at the Functional Genomics Center Zurich <https://fgcz.ch>. We use this package mainly for prototyping, teaching, and having fun with proteomics data. But it can also be used to do data analysis for small scale data sets.
Author: Christian Panse [aut, cre] , Jonas Grossmann [aut] , Simon Barkow-Oesterreicher [ctb]
Maintainer: Christian Panse <cp@fgcz.ethz.ch>

Diff between protViz versions 0.7.3 dated 2022-04-04 and 0.7.7 dated 2023-02-06

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Package NCA updated to version 3.3.0 with previous version 3.2.1 dated 2022-09-15

Title: Necessary Condition Analysis
Description: Performs a Necessary Condition Analysis (NCA). (Dul, J. 2016. Necessary Condition Analysis (NCA). ''Logic and Methodology of 'Necessary but not Sufficient' causality." Organizational Research Methods 19(1), 10-52, <https://journals.sagepub.com/doi/full/10.1177/1094428115584005>). NCA identifies necessary (but not sufficient) conditions in datasets, where x causes (e.g. precedes) y. Instead of drawing a regression line ''through the middle of the data'' in an xy-plot, NCA draws the ceiling line. The ceiling line y = f(x) separates the area with observations from the area without observations. (Nearly) all observations are below the ceiling line: y <= f(x). The empty zone is in the upper left hand corner of the xy-plot (with the convention that the x-axis is ''horizontal'' and the y-axis is ''vertical'' and that values increase ''upwards'' and ''to the right''). The ceiling line is a (piecewise) linear non-decreasing line: a linear step function or a straight line. It indicates [...truncated...]
Author: Jan Dul <jdul@rsm.nl>
Maintainer: Govert Buijs <buijs@rsm.nl>

Diff between NCA versions 3.2.1 dated 2022-09-15 and 3.3.0 dated 2023-02-06

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Package jsmodule updated to version 1.3.6 with previous version 1.3.4 dated 2022-12-14

Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] , Zarathu [cph, fnd], Hyunki Lee [aut], Changwoo Lim [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>

Diff between jsmodule versions 1.3.4 dated 2022-12-14 and 1.3.6 dated 2023-02-06

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New package synMicrodata with initial version 1.0.0
Package: synMicrodata
Title: Synthetic Microdata Generator
Version: 1.0.0
Date: 2023-02-04
Maintainer: Hang J. Kim <hangkim0@gmail.com>
Description: This tool fits a non-parametric Bayesian model called "hierarchically coupled mixture model (HCMM)" to the original microdata in order to generate synthetic microdata for privacy protection. The non-parametric feature of the adopted model is useful for catching the joint distribution of the original data in a highly flexible manner, leading to the generation of synthetic data very similar to the original data. Important reference papers on this method include Murray & Reiter (2016) <doi:10.1080/01621459.2016.1174132>.
License: GPL (>= 3)
Imports: methods, Rcpp
LinkingTo: Rcpp, RcppArmadillo
RcppModules: IO_module
NeedsCompilation: yes
Packaged: 2023-02-04 02:41:01 UTC; user
Author: Hang J. Kim [aut, cre], Juhee Lee [aut], Young-Min Kim [aut]
Repository: CRAN
Date/Publication: 2023-02-06 11:00:02 UTC

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New package sMTL with initial version 0.1.0
Package: sMTL
Title: Sparse Multi-Task Learning
Version: 0.1.0
Description: Implements L0-constrained Multi-Task Learning and domain generalization algorithms. The algorithms are coded in Julia allowing for fast implementations of the coordinate descent and local combinatorial search algorithms. For more details, see a preprint of the paper: Loewinger et al., (2022) <arXiv:2212.08697>.
URL: https://github.com/gloewing/sMTL, https://rpubs.com/gloewinger/996629
BugReports: https://github.com/gloewing/sMTL/issues
Maintainer: Gabriel Loewinger <gloewinger@gmail.com>
Depends: R (>= 3.5.0)
License: MIT + file LICENSE
Encoding: UTF-8
Imports: glmnet, JuliaCall, JuliaConnectoR, caret, dplyr
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2023-02-04 22:58:56 UTC; loewingergc
Author: Gabriel Loewinger [aut, cre] , Kayhan Behdin [aut], Giovanni Parmigiani [aut], Rahul Mazumder [aut], National Science Foundation Grant DMS1810829 [fnd], National Science Foundation Grant DMS2113707 [fnd], National Science Foundation Grant NSF-IIS1718 [...truncated...]
Repository: CRAN
Date/Publication: 2023-02-06 11:20:02 UTC

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New package oc with initial version 1.2.1
Package: oc
Version: 1.2.1
Date: 2023-02-03
Title: Optimal Classification Roll Call Analysis Software
Depends: R (>= 2.3.1), pscl (>= 0.59)
Description: Estimates optimal classification (Poole 2000) <doi:10.1093/oxfordjournals.pan.a029814> scores from roll call votes supplied though a 'rollcall' object from package 'pscl'.
License: GPL-2
URL: https://legacy.voteview.com/oc_in_R.htm, https://github.com/wmay/oc
BugReports: https://github.com/wmay/oc/issues
Repository: CRAN
NeedsCompilation: yes
Packaged: 2023-02-06 02:43:12 UTC; will
Author: Keith Poole [aut], Jeffrey Lewis [aut] , James Lo [aut], Royce Carroll [aut] , William May [aut, cre] , U.S. National Science Foundation [fnd]
Maintainer: William May <wmay@hey.com>
Date/Publication: 2023-02-06 11:32:31 UTC

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New package nblR with initial version 0.0.4
Package: nblR
Title: Data Extraction of Australian NBL Basketball Statistics
Version: 0.0.4
Description: Allow users to obtain basketball statistics for the Australian basketball league 'NBL'<https://nbl.com.au/>. Stats include play-by-play, shooting locations, results and box scores for teams and players.
License: GPL-3
URL: https://github.com/JaseZiv/nblR
BugReports: https://github.com/JaseZiv/nblR/issues
Depends: R (>= 4.0.0)
Imports: magrittr, cli
Suggests: dplyr, knitr, rmarkdown, testthat (>= 3.0.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-02-04 09:19:14 UTC; zivkovij
Author: Jason Zivkovic [aut, cre, cph]
Maintainer: Jason Zivkovic <jaseziv83@gmail.com>
Repository: CRAN
Date/Publication: 2023-02-06 11:02:33 UTC

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New package mmstat4 with initial version 0.1.2
Package: mmstat4
Title: Access to Teaching Materials from a ZIP File or GitHub
Version: 0.1.2
Description: Teaching materials, e.g. R programs, Shiny apps, data and PDF/HTML documents, which are stored on the Internet in a ZIP file (e.g. as a GitHub repository) can be downloaded. They can be displayed or run locally. The content of the ZIP file is temporarily (or permanently) stored. The GitHub repository 'sigbertklinke/mmstat4.data' is used as the default repository. In addition, some auxiliary functions are implemented.
License: GPL-3
Encoding: UTF-8
Imports: tcltk, rappdirs, rio, rstudioapi, shiny
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-02-04 13:55:33 UTC; sk
Author: Sigbert Klinke [aut, cre]
Maintainer: Sigbert Klinke <sigbert@hu-berlin.de>
Repository: CRAN
Date/Publication: 2023-02-06 11:02:36 UTC

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New package deFit with initial version 0.1.0
Package: deFit
Title: Fitting Differential Equations to Time Series Data
Version: 0.1.0
Description: Use numerical optimization to fit ordinary differential equations (ODEs) to time series data to examine the dynamic relationships between variables or the characteristics of a dynamical system. It can now be used to estimate the parameters of ODEs up to second order. See <https://github.com/yueqinhu/defit> for details.
License: GPL (>= 3)
URL: https://github.com/yueqinhu/defit
Encoding: UTF-8
LazyData: true
Suggests: testthat (>= 3.0.0)
Imports: deSolve, ggplot2, stats, R6
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2023-02-05 10:37:31 UTC; yueqinhu
Author: Yueqin Hu [aut, cre], Qingshan Liu [aut]
Maintainer: Yueqin Hu <yueqinhu@bnu.edu.cn>
Repository: CRAN
Date/Publication: 2023-02-06 11:22:34 UTC

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Package codename updated to version 0.5.0 with previous version 0.4.0 dated 2021-09-07

Title: Generation of Code Names for Organizations, People, Projects, and Whatever Else
Description: This creates code names that a user can consider for their organizations, their projects, themselves, people in their organizations or projects, or whatever else. The user can also supply a numeric seed (and even a character seed) for maximum reproducibility. Use is simple and the code names produced come in various types too, contingent on what the user may be desiring as a code name or nickname.
Author: Steve Miller [aut, cre]
Maintainer: Steve Miller <steven.v.miller@gmail.com>

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Package blockCV updated to version 3.0-0 with previous version 2.1.4 dated 2021-06-17

Title: Spatial and Environmental Blocking for K-Fold and LOO Cross-Validation
Description: Creating spatially or environmentally separated folds for cross-validation to provide a robust error estimation in spatially structured environments; Investigating and visualising the effective range of spatial autocorrelation in continuous raster covariates and point samples to find an initial realistic distance band to separate training and testing datasets spatially described in Valavi, R. et al. (2019) <doi:10.1111/2041-210X.13107>.
Author: Roozbeh Valavi [aut, cre], Jane Elith [aut], Jose Lahoz-Monfort [aut], Ian Flint [aut], Gurutzeta Guillera-Arroita [aut]
Maintainer: Roozbeh Valavi <valavi.r@gmail.com>

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New package svars with initial version 1.3.11
Package: svars
Title: Data-Driven Identification of SVAR Models
Version: 1.3.11
Date: 2023-01-29
Author: Alexander Lange [aut, cre], Bernhard Dalheimer [aut], Helmut Herwartz [aut], Simone Maxand [aut], Hannes Riebl [ctb]
Maintainer: Alexander Lange <alexander.lange@uni-goettingen.de>
Description: Implements data-driven identification methods for structural vector autoregressive (SVAR) models as described in Lange et al. (2021) <doi:10.18637/jss.v097.i05>. Based on an existing VAR model object (provided by e.g. VAR() from the 'vars' package), the structural impact matrix is obtained via data-driven identification techniques (i.e. changes in volatility (Rigobon, R. (2003) <doi:10.1162/003465303772815727>), patterns of GARCH (Normadin, M., Phaneuf, L. (2004) <doi:10.1016/j.jmoneco.2003.11.002>), independent component analysis (Matteson, D. S, Tsay, R. S., (2013) <doi:10.1080/01621459.2016.1150851>), least dependent innovations (Herwartz, H., Ploedt, M., (2016) <doi:10.1016/j.jimonfin.2015.11.001>), smooth transition in variances (Luetkepohl, H., Netsunajev, A. (2017) <doi:10.1016/j.jedc.2017.09.001>) or non-Gaussian maximum likelihood (Lanne, M., Meitz, M., Saikkonen, P. (2017) <doi:10.1016/j.jeconom.2016.06.002>)).
Depends: R (>= 2.10), vars (>= 1.5.3)
Imports: expm, reshape2, ggplot2, copula, clue, pbapply, steadyICA, DEoptim, zoo, strucchange, Rcpp, methods
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
License: MIT + file LICENSE
LazyData: TRUE
SystemRequirements: C++17
Suggests: testthat (>= 2.1.0), tsDyn
Packaged: 2023-01-30 19:51:32 UTC; alex
Repository: CRAN
Date/Publication: 2023-02-06 10:00:02 UTC

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Package openair updated to version 2.15 with previous version 2.14 dated 2023-01-25

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

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Package worldmet updated to version 0.9.7 with previous version 0.9.6 dated 2022-10-05

Title: Import Surface Meteorological Data from NOAA Integrated Surface Database (ISD)
Description: Functions to import data from more than 30,000 surface meteorological sites around the world managed by the National Oceanic and Atmospheric Administration (NOAA) Integrated Surface Database.
Author: David Carslaw [aut, cre]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>

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Package sivs updated to version 0.2.7 with previous version 0.2.6 dated 2023-02-02

Title: Stable Iterative Variable Selection
Description: An iterative feature selection method (manuscript submitted) that internally utilizes various Machine Learning methods that have embedded feature reduction in order to shrink down the feature space into a small and yet robust set.
Author: Mehrad Mahmoudian [aut, cre] , Mikko Venaelaeinen [aut, rev] , Riku Klen [aut, ths] , Laura Elo [aut, ths, fnd]
Maintainer: Mehrad Mahmoudian <mehrad.mahmoudian@utu.fi>

Diff between sivs versions 0.2.6 dated 2023-02-02 and 0.2.7 dated 2023-02-06

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New package rSRD with initial version 0.1.6
Package: rSRD
Title: Sum of Ranking Differences Statistical Test
Version: 0.1.6
Maintainer: Jochen Staudacher <jochen.staudacher@hs-kempten.de>
Description: We provide an implementation for Sum of Ranking Differences (SRD), a novel statistical test introduced by Héberger (2010) <doi:10.1016/j.trac.2009.09.009>. The test allows the comparison of different solutions through a reference by first performing a rank transformation on the input, then calculating and comparing the distances between the solutions and the reference - the latter is measured in the L1 norm. The reference can be an external benchmark (e.g. an established gold standard) or can be aggregated from the data. The calculated distances, called SRD scores, are validated in two ways, see Héberger and Kollár-Hunek (2011) <doi:10.1002/cem.1320>. A randomization test (also called permutation test) compares the SRD scores of the solutions to the SRD scores of randomly generated rankings. The second validation option is cross-validation that checks whether the rankings generated from the solutions come from the same distribution or not. For a detailed analysis about the [...truncated...]
License: GPL-3
Encoding: UTF-8
LinkingTo: Rcpp
Imports: Rcpp, dplyr, janitor, tibble, ggplot2, stringr, methods, rlang, ggrepel, gplots
SystemRequirements: C++20, Rtools (>= 4.2) for Windows
NeedsCompilation: yes
Packaged: 2023-02-04 08:46:36 UTC; Jochen
Author: Jochen Staudacher [aut, cph, cre], Balazs R. Sziklai [aut, cph], Linus Olsson [aut, cph], Dennis Horn [ctb], Alexander Pothmann [ctb], Ali Tugay Sen [ctb], Attila Gere [ctb], Karoly Hebeger [ctb]
Repository: CRAN
Date/Publication: 2023-02-06 08:22:32 UTC

More information about rSRD at CRAN
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Package rempsyc updated to version 0.1.1 with previous version 0.1.0 dated 2022-11-01

Title: Convenience Functions for Psychology
Description: Make your workflow faster and easier. Easily customizable plots (via 'ggplot2'), nice APA tables (following the style of the *American Psychological Association*) exportable to Word (via 'flextable'), easily run statistical tests or check assumptions, and automatize various other tasks.
Author: Remi Theriault [aut, cre]
Maintainer: Remi Theriault <remi.theriault@mail.mcgill.ca>

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Package RcppAlgos updated to version 2.7.1 with previous version 2.6.0 dated 2022-08-15

Title: High Performance Tools for Combinatorics and Computational Mathematics
Description: Provides optimized functions and flexible combinatorial iterators implemented in C++ for solving problems in combinatorics and computational mathematics. Utilizes the RMatrix class from 'RcppParallel' for thread safety. There are combination/permutation functions with constraint parameters that allow for generation of all results of a vector meeting specific criteria (e.g. generating integer partitions/compositions or finding all combinations such that the sum is between two bounds). Capable of generating specific combinations/permutations (e.g. retrieve only the nth lexicographical result) which sets up nicely for parallelization as well as random sampling. Gmp support permits exploration where the total number of results is large (e.g. comboSample(10000, 500, n = 4)). Additionally, there are several high performance number theoretic functions that are useful for problems common in computational mathematics. Some of these functions make use of the fast integer division library 'libdiv [...truncated...]
Author: Joseph Wood
Maintainer: Joseph Wood <jwood000@gmail.com>

Diff between RcppAlgos versions 2.6.0 dated 2022-08-15 and 2.7.1 dated 2023-02-06

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Permanent link

Package finbif updated to version 0.7.2 with previous version 0.7.1 dated 2022-11-24

Title: Interface for the 'Finnish Biodiversity Information Facility' API
Description: A programmatic interface to the 'Finnish Biodiversity Information Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates Finnish biodiversity data from multiple sources in a single open access portal for researchers, citizen scientists, industry and government. 'FinBIF' allows users of biodiversity information to find, access, combine and visualise data on Finnish plants, animals and microorganisms. The 'finbif' package makes the publicly available data in 'FinBIF' easily accessible to programmers. Biodiversity information is available on taxonomy and taxon occurrence. Occurrence data can be filtered by taxon, time, location and other variables. The data accessed are conveniently preformatted for subsequent analyses.
Author: Finnish Museum of Natural History - Luomus [cph], William K. Morris [aut, cre]
Maintainer: William K. Morris <willi@mmorris.email>

Diff between finbif versions 0.7.1 dated 2022-11-24 and 0.7.2 dated 2023-02-06

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Permanent link

Package faux updated to version 1.2.0 with previous version 1.1.0 dated 2021-09-13

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] , Anna Krystalli [ctb] , Andrew Heiss [ctb]
Maintainer: Lisa DeBruine <debruine@gmail.com>

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Package enviGCMS updated to version 0.7.1 with previous version 0.6.6 dated 2020-06-04

Title: GC/LC-MS Data Analysis for Environmental Science
Description: Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data Analysis for Environmental Science. This package covered topics such molecular isotope ratio, matrix effects and Short-Chain Chlorinated Paraffins analysis etc. in environmental analysis.
Author: Miao YU [aut, cre] , Thanh Wang [ctb]
Maintainer: Miao YU <yufreecas@gmail.com>

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Package doolkit updated to version 1.42.2 with previous version 1.42.1 dated 2022-05-14

Title: Exploration of Dental Surface Topography
Description: Tools for exploring the topography of 3d triangle meshes. The functions were developed with dental surfaces in mind, but could be applied to any triangle mesh of class 'mesh3d'. More specifically, 'doolkit' allows to isolate the border of a mesh, or a subpart of the mesh using the polygon networks method; crop a mesh; compute basic descriptors (elevation, orientation, footprint area); compute slope, angularity and relief index (Ungar and Williamson (2000) <https://palaeo-electronica.org/2000_1/gorilla/issue1_00.htm>; Boyer (2008) <doi:10.1016/j.jhevol.2008.08.002>), inclination and occlusal relief index or gamma (Guy et al. (2013) <doi:10.1371/journal.pone.0066142>), OPC (Evans et al. (2007) <doi:10.1038/nature05433>), OPCR (Wilson et al. (2012) <doi:10.1038/nature10880>), DNE (Bunn et al. (2011) <doi:10.1002/ajpa.21489>; Pampush et al. (2016) <doi:10.1007/s10914-016-9326-0>), form factor (Horton (1932) <doi:10.1029/TR013i001p00350>), bas [...truncated...]
Author: Ghislain Thiery [aut, cre], Franck Guy [aut], Vincent Lazzari [aut]
Maintainer: Ghislain Thiery <ghislain.thiery@ntymail.com>

Diff between doolkit versions 1.42.1 dated 2022-05-14 and 1.42.2 dated 2023-02-06

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New package blockTools with initial version 0.6.4
Package: blockTools
Title: Block, Assign, and Diagnose Potential Interference in Randomized Experiments
Version: 0.6.4
Date: 2023-02-03
Imports: dplyr, MASS, tibble
Suggests: nbpMatching, RItools, testthat (>= 3.0.0), xtable
Description: Blocks units into experimental blocks, with one unit per treatment condition, by creating a measure of multivariate distance between all possible pairs of units. Maximum, minimum, or an allowable range of differences between units on one variable can be set. Randomly assign units to treatment conditions. Diagnose potential interference between units assigned to different treatment conditions. Write outputs to .tex and .csv files.
License: GPL (>= 2) | file LICENSE
URL: https://www.ryantmoore.org/html/software.blockTools.html
NeedsCompilation: yes
Packaged: 2023-02-04 20:29:12 UTC; rtm
Author: Ryan T. Moore [aut, cre] , Keith Schnakenberg [aut]
Maintainer: Ryan T. Moore <rtm@american.edu>
Repository: CRAN
Date/Publication: 2023-02-06 08:22:38 UTC

More information about blockTools at CRAN
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Sun, 05 Feb 2023

Package interplex (with last version 0.1.0) was removed from CRAN

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

2022-06-21 0.1.0

Permanent link
Package conquer updated to version 1.3.2 with previous version 1.3.1 dated 2022-09-13

Title: Convolution-Type Smoothed Quantile Regression
Description: Estimation and inference for conditional linear quantile regression models using a convolution smoothed approach. In the low-dimensional setting, efficient gradient-based methods are employed for fitting both a single model and a regression process over a quantile range. Normal-based and (multiplier) bootstrap confidence intervals for all slope coefficients are constructed. In high dimensions, the conquer method is complemented with flexible types of penalties (Lasso, elastic-net, group lasso, sparse group lasso, scad and mcp) to deal with complex low-dimensional structures.
Author: Xuming He [aut], Xiaoou Pan [aut, cre], Kean Ming Tan [aut], Wen-Xin Zhou [aut]
Maintainer: Xiaoou Pan <xip024@ucsd.edu>

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Package sunburstR updated to version 2.1.8 with previous version 2.1.6 dated 2021-09-19

Title: Sunburst 'Htmlwidget'
Description: Make interactive 'd3.js' sequence sunburst diagrams in R with the convenience and infrastructure of an 'htmlwidget'.
Author: Mike Bostock [aut, cph] , Kerry Rodden [aut, cph] , Kevin Warne [aut, cph] , Kent Russell [aut, cre] , Florian Breitwieser [ctb] , CJ Yetman [ctb]
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>

Diff between sunburstR versions 2.1.6 dated 2021-09-19 and 2.1.8 dated 2023-02-05

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Package sasLM updated to version 0.9.5 with previous version 0.9.4 dated 2023-01-07

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 0.9.4 dated 2023-01-07 and 0.9.5 dated 2023-02-05

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Package rmatio updated to version 0.18.0 with previous version 0.17.0 dated 2023-01-25

Title: Read and Write 'Matlab' Files
Description: Read and write 'Matlab' MAT files from R. The 'rmatio' package supports reading MAT version 4, MAT version 5 and MAT compressed version 5. The 'rmatio' package can write version 5 MAT files and version 5 files with variable compression.
Author: Stefan Widgren [aut, cre] , Christopher Hulbert [aut]
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>

Diff between rmatio versions 0.17.0 dated 2023-01-25 and 0.18.0 dated 2023-02-05

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Package reproducer updated to version 0.5.1 with previous version 0.5.0 dated 2023-01-16

Title: Reproduce Statistical Analyses and Meta-Analyses
Description: Includes data analysis functions (e.g., to calculate effect sizes and 95% Confidence Intervals (CI) on Standardised Effect Sizes (d) for AB/BA cross-over repeated-measures experimental designs), data presentation functions (e.g., density curve overlaid on histogram), and the data sets analyzed in different research papers in software engineering (e.g., related to software defect prediction or multi-site experiment concerning the extent to which structured abstracts were clearer and more complete than conventional abstracts) to streamline reproducible research in software engineering.
Author: Lech Madeyski [cre, aut, ctb] , Barbara Kitchenham [ctb] , Tomasz Lewowski [ctb] , Marian Jureczko [ctb] , David Budgen [ctb] , Pearl Brereton [ctb] , Jacky Keung [ctb] , Stuart Charters [ctb] , Shirley Gibbs [ctb] , Amnart Pohthong [ctb] , Giuseppe [...truncated...]
Maintainer: Lech Madeyski <lech.madeyski@gmail.com>

Diff between reproducer versions 0.5.0 dated 2023-01-16 and 0.5.1 dated 2023-02-05

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Package disk.frame updated to version 0.8.0 with previous version 0.7.2 dated 2022-03-07

Title: Larger-than-RAM Disk-Based Data Manipulation Framework
Description: A disk-based data manipulation tool for working with large-than-RAM datasets. Aims to lower the barrier-to-entry for manipulating large datasets by adhering closely to popular and familiar data manipulation paradigms like 'dplyr' verbs and 'data.table' syntax.
Author: Dai ZJ [aut, cre], Jacky Poon [ctb]
Maintainer: Dai ZJ <zhuojia.dai@gmail.com>

Diff between disk.frame versions 0.7.2 dated 2022-03-07 and 0.8.0 dated 2023-02-05

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Package d3r updated to version 1.0.1 with previous version 1.0.0 dated 2021-08-15

Title: 'd3.js' Utilities for R
Description: Provides a suite of functions to help ease the use of 'd3.js' in R. These helpers include 'htmltools::htmlDependency' functions, hierarchy builders, and conversion tools for 'partykit', 'igraph,' 'table', and 'data.frame' R objects into the 'JSON' that 'd3.js' expects.
Author: Mike Bostock [aut, cph] , Kent Russell [aut, cre, cph] , Gregor Aisch [aut, cph] , Adam Pearce [aut] , Ben Ortiz [ctb]
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>

Diff between d3r versions 1.0.0 dated 2021-08-15 and 1.0.1 dated 2023-02-05

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Package av updated to version 0.8.3 with previous version 0.8.2 dated 2022-10-06

Title: Working with Audio and Video in R
Description: Bindings to 'FFmpeg' <http://www.ffmpeg.org/> AV library for working with audio and video in R. Generates high quality video from images or R graphics with custom audio. Also offers high performance tools for reading raw audio, creating 'spectrograms', and converting between countless audio / video formats. This package interfaces directly to the C API and does not require any command line utilities.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between av versions 0.8.2 dated 2022-10-06 and 0.8.3 dated 2023-02-05

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Package RedditExtractoR updated to version 3.0.7 with previous version 3.0.6 dated 2022-03-03

Title: Reddit Data Extraction Toolkit
Description: A collection of tools for extracting structured data from <https://www.reddit.com/>.
Author: Ivan Rivera <ivan.s.rivera@gmail.com>
Maintainer: Ivan Rivera <ivan.s.rivera@gmail.com>

Diff between RedditExtractoR versions 3.0.6 dated 2022-03-03 and 3.0.7 dated 2023-02-05

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Package JSmediation updated to version 0.2.1 with previous version 0.2.0 dated 2021-09-02

Title: Mediation Analysis Using Joint Significance
Description: A set of helper functions to conduct joint-significance tests for mediation analysis, as recommended by Yzerbyt, Muller, Batailler, & Judd. (2018) <doi:10.1037/pspa0000132>.
Author: Cedric Batailler [aut, cre] , Dominique Muller [aut] , Vincent Yzerbyt [aut], Charles Judd [aut], Yoann Julliard [ctb] , Arnold Ho [dtc], Nour Kteily [dtc], Jacqueline Chen [dtc], Simone Dohle [dtc], Michael Siegrist [dtc]
Maintainer: Cedric Batailler <cedric.batailler@gmail.com>

Diff between JSmediation versions 0.2.0 dated 2021-09-02 and 0.2.1 dated 2023-02-05

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 JSmediation-0.2.1/JSmediation/MD5                                                                            |  180 
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Package AirMonitor updated to version 0.3.9 with previous version 0.2.2 dated 2022-03-31

Title: Air Quality Data Analysis
Description: Utilities for working with hourly air quality monitoring data with a focus on small particulates (PM2.5). A compact data model is structured as a list with two dataframes. A 'meta' dataframe contains spatial and measuring device metadata associated with deployments at known locations. A 'data' dataframe contains a 'datetime' column followed by columns of measurements associated with each "device-deployment". Algorithms to calculate NowCast and the associated Air Quality Index (AQI) are defined at the US Environmental Projection Agency AirNow program: <https://www.airnow.gov/sites/default/files/2020-05/aqi-technical-assistance-document-sept2018.pdf>.
Author: Jonathan Callahan [aut, cre], Spencer Pease [ctb], Hans Martin [ctb], Rex Thompson [ctb]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>

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Package rdatacite updated to version 0.5.4 with previous version 0.5.2 dated 2020-03-04

Title: Client for the 'DataCite' API
Description: Client for the web service methods provided by 'DataCite' (<https://www.datacite.org/>), including functions to interface with their 'RESTful' search API. The API is backed by 'Elasticsearch', allowing expressive queries, including faceting.
Author: Scott Chamberlain [aut] , Bianca Kramer [cre]
Maintainer: Bianca Kramer <bianca.kramer@gmail.com>

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Package report updated to version 0.5.6 with previous version 0.5.5 dated 2022-08-22

Title: Automated Reporting of Results and Statistical Models
Description: The aim of the 'report' package is to bridge the gap between R’s output and the formatted results contained in your manuscript. This package converts statistical models and data frames into textual reports suited for publication, ensuring standardization and quality in results reporting.
Author: Dominique Makowski [aut] , Daniel Luedecke [aut] , Indrajeet Patil [aut] , Remi Theriault [aut, cre] , Mattan S. Ben-Shachar [aut] , Brenton M. Wiernik [aut] , Rudolf Siegel [ctb]
Maintainer: Remi Theriault <remi.theriault@mail.mcgill.ca>

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Package lillies updated to version 0.2.10 with previous version 0.2.9 dated 2021-02-16

Title: Estimation of Life Years Lost
Description: Estimation of life expectancy and Life Years Lost (LYL, or lillies for short) for a given population, for example those with a given disease or condition. In addition, the package can be used to compare estimates from different populations, or to estimate confidence intervals. Technical details of the method are available in Plana-Ripoll et al. (2020) <doi:10.1371/journal.pone.0228073> and Andersen (2017) <doi:10.1002/sim.7357>.
Author: Oleguer Plana-Ripoll [aut, cre]
Maintainer: Oleguer Plana-Ripoll <opr@clin.au.dk>

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Package howManyImputations updated to version 0.2.4 with previous version 0.2.3 dated 2022-05-31

Title: Calculate How many Imputations are Needed for Multiple Imputation
Description: When performing multiple imputations, while 5-10 imputations are sufficient for obtaining point estimates, a larger number of imputations are needed for proper standard error estimates. This package allows you to calculate how many imputations are needed, following the work of von Hippel (2020) <doi:10.1177/0049124117747303>.
Author: Josh Errickson [aut, cre]
Maintainer: Josh Errickson <jerrick@umich.edu>

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Package andrews updated to version 1.1.1 with previous version 1.1.0 dated 2023-01-08

Title: Various Andrews Curves
Description: Visualisation of multidimensional data through different Andrews curves: Andrews, D. F. (1972) Plots of High-Dimensional Data. Biometrics, 28(1), 125-136. <doi:10.2307/2528964>.
Author: Jaroslav Myslivec [aut], Sigbert Klinke [cre, ctb]
Maintainer: Sigbert Klinke <sigbert@hu-berlin.de>

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Package tm updated to version 0.7-11 with previous version 0.7-10 dated 2022-12-14

Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut, cre] , Kurt Hornik [aut] , Artifex Software, Inc. [ctb, cph]
Maintainer: Ingo Feinerer <feinerer@logic.at>

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Package RSiena updated to version 1.3.14.1 with previous version 1.3.14 dated 2022-11-04

Title: Siena - Simulation Investigation for Empirical Network Analysis
Description: The main purpose of this package is to perform simulation-based estimation of stochastic actor-oriented models for longitudinal network data collected as panel data. Dependent variables can be single or multivariate networks, which can be directed, non-directed, or two-mode; and associated actor variables. There are also functions for testing parameters and checking goodness of fit. An overview of these models is given in Tom A.B. Snijders (2017), Stochastic Actor-Oriented Models for Network Dynamics, Annual Review of Statistics and Its Application, 4, 343-363 <doi: 10.1146/annurev-statistics-060116-054035>. An extensive manual, scripts, and much further information is at the Siena website <http://www.stats.ox.ac.uk/~snijders/siena/>.
Author: Tom A.B. Snijders [cre, aut] , Ruth Ripley [aut], Krists Boitmanis [aut, ctb], Christian Steglich [aut, ctb] , Johan Koskinen [aut, ctb] , Nynke Niezink [aut, ctb] , Viviana Amati [aut, ctb] , Christoph Stadtfeld [ctb] , James Hollway [ctb] , Per Blo [...truncated...]
Maintainer: Tom A.B. Snijders <tom.snijders@nuffield.ox.ac.uk>

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Package elbird (with last version 0.2.5) was removed from CRAN

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

2022-08-12 0.2.5
2022-04-19 0.2.3
2022-04-17 0.2.2
2022-04-04 0.1.3
2022-03-31 0.1.1

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Package tree updated to version 1.0-43 with previous version 1.0-42 dated 2022-05-29

Title: Classification and Regression Trees
Description: Classification and regression trees.
Author: Brian Ripley [aut, cre]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

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Package shipunov updated to version 1.17.1 with previous version 1.17 dated 2022-02-26

Title: Miscellaneous Functions from Alexey Shipunov
Description: A collection of functions for data manipulation, plotting and statistical computing, to use separately or with the book "Visual Statistics. Use R!": Shipunov (2020) <http://ashipunov.info/shipunov/software/r/r-en.htm>. Dr Alexey Shipunov died in December 2022. Most useful functions: Bclust(), Jclust() and BootA() which bootstrap hierarchical clustering; Recode() which does multiple recoding in a fast, simple and flexible way; Misclass() which outputs confusion matrix even if classes are not concerted; Overlap() which measures group separation on any projection; Biarrows() which converts any scatterplot into biplot; and Pleiad() which is fast and flexible correlogram.
Author: Alexey Shipunov [aut, cre], Paul Murrell [ctb], Marcello D'Orazio [ctb], Stephen Turner [ctb], Eugeny Altshuler [ctb], Roland Rau [ctb], Marcus W Beck [ctb], Sebastian Gibb [ctb], Weiliang Qiu [ctb], Emmanuel Paradis [ctb], Roger Koenker [ctb], R Cor [...truncated...]
Maintainer: ORPHANED

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Sat, 04 Feb 2023

Package lavaanExtra updated to version 0.1.4 with previous version 0.1.3 dated 2022-10-04

Title: Convenience Functions for Package 'lavaan'
Description: Affords an alternative, vector-based syntax to 'lavaan', as well as other convenience functions such as naming paths and defining indirect links automatically, in addition to convenience formatting optimized for a publication and script sharing workflow.
Author: Remi Theriault [aut, cre]
Maintainer: Remi Theriault <remi.theriault@mail.mcgill.ca>

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Package dsmmR updated to version 1.0.1 with previous version 0.0.96 dated 2022-11-16

Title: Estimation and Simulation of Drifting Semi-Markov Models
Description: Performs parametric and non-parametric estimation and simulation of drifting semi-Markov processes. The definition of parametric and non-parametric model specifications is also possible. Furthermore, three different types of drifting semi-Markov models are considered. These models differ in the number of transition matrices and sojourn time distributions used for the computation of a number of semi-Markov kernels, which in turn characterize the drifting semi-Markov kernel. For the parametric model estimation and specification, several discrete distributions are considered for the sojourn times: Uniform, Poisson, Geometric, Discrete Weibull and Negative Binomial. The non-parametric model specification makes no assumptions about the shape of the sojourn time distributions. Semi-Markov models are described in: Barbu, V.S., Limnios, N. (2008) <doi:10.1007/978-0-387-73173-5>. Drifting Markov models are described in: Vergne, N. (2008) <doi:10.2202/1544-6115.1326>. Reliability ind [...truncated...]
Author: Vlad Stefan Barbu [aut] , Ioannis Mavrogiannis [aut, cre], Nicolas Vergne [aut]
Maintainer: Ioannis Mavrogiannis <mavrogiannis.ioa@gmail.com>

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Package BART updated to version 2.9.3 with previous version 2.9 dated 2021-01-05

Title: Bayesian Additive Regression Trees
Description: Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary, categorical and time-to-event outcomes. For more information see Sparapani, Spanbauer and McCulloch <doi:10.18637/jss.v097.i01>.
Author: Robert McCulloch [aut], Rodney Sparapani [aut, cre], Charles Spanbauer [aut], Robert Gramacy [aut], Matthew Pratola [aut], Martyn Plummer [ctb], Nicky Best [ctb], Kate Cowles [ctb], Karen Vines [ctb]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>

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Package IPEDSuploadables updated to version 2.7.5 with previous version 2.6.5 dated 2022-12-07

Title: Transforms Institutional Data into Text Files for IPEDS Automated Import/Upload
Description: Starting from user-supplied institutional data, these scripts transform, aggregate, and reshape the information to produce key-value pair data files that are able to be uploaded to IPEDS (Integrated Postsecondary Education Data System) through their submission portal <https://surveys.nces.ed.gov/ipeds/>. Starting data specifications can be found in the vignettes. Final files are saved locally to a location of the user's choice. User-friendly readable files can also be produced for purposes of data review and validation.
Author: Alison Lanski [aut, cre], Shiloh Fling [aut]
Maintainer: Alison Lanski <alanski@nd.edu>

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Package gaselect updated to version 1.0.21 with previous version 1.0.11 dated 2022-04-06

Title: Genetic Algorithm (GA) for Variable Selection from High-Dimensional Data
Description: Provides a genetic algorithm for finding variable subsets in high dimensional data with high prediction performance. The genetic algorithm can use ordinary least squares (OLS) regression models or partial least squares (PLS) regression models to evaluate the prediction power of variable subsets. By supporting different cross-validation schemes, the user can fine-tune the tradeoff between speed and quality of the solution.
Author: David Kepplinger
Maintainer: David Kepplinger <david.kepplinger@gmail.com>

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Package TDA updated to version 1.9 with previous version 1.8.8 dated 2022-10-30

Title: Statistical Tools for Topological Data Analysis
Description: Tools for the statistical analysis of persistent homology and for density clustering. For that, this package provides an R interface for the efficient algorithms of the C++ libraries 'GUDHI' <https://project.inria.fr/gudhi/software/>, 'Dionysus' <https://www.mrzv.org/software/dionysus/>, and 'PHAT' <https://bitbucket.org/phat-code/phat/>. This package also implements the methods in Fasy et al. (2014) <doi:10.1214/14-AOS1252> and Chazal et al. (2014) <doi:10.1145/2582112.2582128> for analyzing the statistical significance of persistent homology features.
Author: Brittany T. Fasy, Jisu Kim, Fabrizio Lecci, Clement Maria, David L. Millman, Vincent Rouvreau.
Maintainer: Jisu Kim <jisu.kim@inria.fr>

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Package nnlib2Rcpp updated to version 0.1.10 with previous version 0.1.9 dated 2022-05-26

Title: A Tool for Creating Custom Neural Networks in C++ and using Them in R
Description: Contains a module to define neural networks from custom components and versions of Autoencoder, BP, LVQ, MAM NN.
Author: Vasilis Nikolaidis [aut, cph, cre]
Maintainer: Vasilis Nikolaidis <vnikolaidis@us.uop.gr>

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Package mcmcsae updated to version 0.7.2 with previous version 0.7.1 dated 2022-09-02

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

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Package jds.rmd updated to version 0.3.2 with previous version 0.3.1 dated 2022-07-05

Title: R Markdown Templates for Journal of Data Science
Description: Customized R Markdown templates for authoring articles for Journal of Data Science.
Author: Wenjie Wang [aut, cre] , Jun Yan [aut]
Maintainer: Wenjie Wang <wang@wwenjie.org>

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Package coefa updated to version 1.0.3 with previous version 1.0.2 dated 2022-11-18

Title: Meta Analysis of Factor Analysis Based on CO-Occurrence Matrices
Description: Provide a series of functions to conduct a meta analysis of factor analysis based on co-occurrence matrices. The tool can be used to solve the factor structure (i.e. inner structure of a construct, or scale) debate in several disciplines, such as psychology, psychiatry, management, education so on. References: Shafer (2005) <doi:10.1037/1040-3590.17.3.324>; Shafer (2006) <doi:10.1002/jclp.20213>; Loeber and Schmaling (1985) <doi:10.1007/BF00910652>.
Author: Xijian Zheng [aut, cre], Huiyong Fan [aut]
Maintainer: Xijian Zheng <psydreammer@foxmail.com>

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Package validatedb (with last version 0.1.4) was removed from CRAN

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

2021-10-06 0.1.4
2021-03-18 0.1.3

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Package rcage (with last version 1.2) was removed from CRAN

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

2022-06-06 1.2
2021-06-14 1.1

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Package dcmodifydb (with last version 0.3.1) was removed from CRAN

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

2022-06-17 0.3.1
2022-01-21 0.2.0
2021-09-27 0.1.2

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Package CAST updated to version 0.7.1 with previous version 0.7.0 dated 2022-08-24

Title: 'caret' Applications for Spatial-Temporal Models
Description: Supporting functionality to run 'caret' with spatial or spatial-temporal data. 'caret' is a frequently used package for model training and prediction using machine learning. CAST includes functions to improve spatial or spatial-temporal modelling tasks using 'caret'. It includes the newly suggested 'Nearest neighbor distance matching' cross-validation to estimate the performance of spatial prediction models and allows for spatial variable selection to selects suitable predictor variables in view to their contribution to the spatial model performance. CAST further includes functionality to estimate the (spatial) area of applicability of prediction models. Methods are described in Meyer et al. (2018) <doi:10.1016/j.envsoft.2017.12.001>; Meyer et al. (2019) <doi:10.1016/j.ecolmodel.2019.108815>; Meyer and Pebesma (2021) <doi:10.1111/2041-210X.13650>; Milà et al. (2022) <doi:10.1111/2041-210X.13851>; Meyer and Pebesma (2022) <doi:10.1038/s41467-022-29838-9>.
Author: Hanna Meyer [cre, aut], Carles Mila [aut], Marvin Ludwig [aut], Philipp Otto [ctb], Jan Linnenbrink [ctb], Chris Reudenbach [ctb], Thomas Nauss [ctb], Edzer Pebesma [ctb]
Maintainer: Hanna Meyer <hanna.meyer@uni-muenster.de>

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Package tidybayes updated to version 3.0.3 with previous version 3.0.2 dated 2022-01-05

Title: Tidy Data and 'Geoms' for Bayesian Models
Description: Compose data for and extract, manipulate, and visualize posterior draws from Bayesian models ('JAGS', 'Stan', 'rstanarm', 'brms', 'MCMCglmm', 'coda', ...) in a tidy data format. Functions are provided to help extract tidy data frames of draws from Bayesian models and that generate point summaries and intervals in a tidy format. In addition, 'ggplot2' 'geoms' and 'stats' are provided for common visualization primitives like points with multiple uncertainty intervals, eye plots (intervals plus densities), and fit curves with multiple, arbitrary uncertainty bands.
Author: Matthew Kay [aut, cre], Timothy Mastny [ctb]
Maintainer: Matthew Kay <mjskay@northwestern.edu>

Diff between tidybayes versions 3.0.2 dated 2022-01-05 and 3.0.3 dated 2023-02-04

 tidybayes-3.0.2/tidybayes/tests/testthat/fontconfig-helper.R                                                  |only
 tidybayes-3.0.3/tidybayes/DESCRIPTION                                                                         |   13 
 tidybayes-3.0.3/tidybayes/MD5                                                                                 |  105 
 tidybayes-3.0.3/tidybayes/NAMESPACE                                                                           |    2 
 tidybayes-3.0.3/tidybayes/NEWS.md                                                                             |   10 
 tidybayes-3.0.3/tidybayes/R/compare_levels.R                                                                  |    2 
 tidybayes-3.0.3/tidybayes/R/deprecated.R                                                                      |   24 
 tidybayes-3.0.3/tidybayes/R/predicted_draws.R                                                                 |   55 
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 tidybayes-3.0.3/tidybayes/R/spread_rvars.R                                                                    |    2 
 tidybayes-3.0.3/tidybayes/R/tidy_draws.R                                                                      |    9 
 tidybayes-3.0.3/tidybayes/R/ungather_draws.R                                                                  |    2 
 tidybayes-3.0.3/tidybayes/R/unspread_draws.R                                                                  |    8 
 tidybayes-3.0.3/tidybayes/build/partial.rdb                                                                   |binary
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 tidybayes-3.0.3/tidybayes/inst/doc/tidy-posterior.R                                                           |   60 
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 tidybayes-3.0.3/tidybayes/inst/doc/tidy-rstanarm.R                                                            |    6 
 tidybayes-3.0.3/tidybayes/inst/doc/tidy-rstanarm.Rmd                                                          |    8 
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 tidybayes-3.0.3/tidybayes/inst/doc/tidybayes-residuals.R                                                      |   22 
 tidybayes-3.0.3/tidybayes/inst/doc/tidybayes-residuals.Rmd                                                    |   24 
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 tidybayes-3.0.3/tidybayes/inst/doc/tidybayes.R                                                                |    5 
 tidybayes-3.0.3/tidybayes/inst/doc/tidybayes.Rmd                                                              |    9 
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 tidybayes-3.0.3/tidybayes/man/add_predicted_draws.Rd                                                          |   72 
 tidybayes-3.0.3/tidybayes/man/add_predicted_rvars.Rd                                                          |   73 
 tidybayes-3.0.3/tidybayes/man/reexports.Rd                                                                    |    2 
 tidybayes-3.0.3/tidybayes/man/spread_draws.Rd                                                                 |    6 
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 tidybayes-3.0.3/tidybayes/tests/testthat/test.add_draws.R                                                     |    2 
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 tidybayes-3.0.3/tidybayes/tests/testthat/test.epred_draws.R                                                   |   23 
 tidybayes-3.0.3/tidybayes/tests/testthat/test.epred_rvars.R                                                   |    2 
 tidybayes-3.0.3/tidybayes/tests/testthat/test.gather_emmeans_draws.R                                          |    2 
 tidybayes-3.0.3/tidybayes/tests/testthat/test.linpred_draws.R                                                 |    8 
 tidybayes-3.0.3/tidybayes/tests/testthat/test.linpred_rvars.R                                                 |    2 
 tidybayes-3.0.3/tidybayes/tests/testthat/test.predicted_draws.R                                               |   12 
 tidybayes-3.0.3/tidybayes/tests/testthat/test.predicted_rvars.R                                               |    5 
 tidybayes-3.0.3/tidybayes/tests/testthat/test.residual_draws.R                                                |    2 
 tidybayes-3.0.3/tidybayes/tests/testthat/test.spread_draws.R                                                  |    8 
 tidybayes-3.0.3/tidybayes/vignettes/tidy-brms.Rmd                                                             |   35 
 tidybayes-3.0.3/tidybayes/vignettes/tidy-posterior.Rmd                                                        |   86 
 tidybayes-3.0.3/tidybayes/vignettes/tidy-rstanarm.Rmd                                                         |    8 
 tidybayes-3.0.3/tidybayes/vignettes/tidybayes-residuals.Rmd                                                   |   24 
 tidybayes-3.0.3/tidybayes/vignettes/tidybayes.Rmd                                                             |    9 
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Package Rfmtool updated to version 4.1.10 with previous version 4.1.9 dated 2022-11-30

Title: Fuzzy Measure Tools
Description: Various tools for handling fuzzy measures, calculating Shapley value and interaction index, Choquet and Sugeno integrals, as well as fitting fuzzy measures to empirical data are provided. Construction of fuzzy measures from empirical data is done by solving a linear programming problem by using 'lpsolve' package, whose source in C adapted to the R environment is included. The description of the basic theory of fuzzy measures is in the manual in the Doc folder in this package. Please refer to the following: [1] <https://personal-sites.deakin.edu.au/~gleb/fmtools.html> [2] G. Beliakov, H. Bustince, T. Calvo, 'A Practical Guide to Averaging', Springer, (2016, ISBN: 978-3-319-24753-3). [3] G. Beliakov, S. James, J-Z. Wu, 'Discrete Fuzzy Measures', Springer, (2020, ISBN: 978-3-030-15305-2).
Author: Gleb Beliakov [aut, cre], Quan Vu [ctb], Andrei Kelarev [ctb], Michel Berkelaar [ctb], Kjell Eikland [ctb], Samuel E. Buttrey [ctb], Stefan I. Larimore [ctb], Timothy A. Davis [ctb], John Gilbert [ctb], Esmond Ng [ctb], Peter Notebaert [ctb], Richard [...truncated...]
Maintainer: Gleb Beliakov <gleb@deakin.edu.au>

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Package evreg updated to version 1.0.1 with previous version 1.0.0 dated 2023-01-17

Title: Evidential Regression
Description: An implementation of the 'Evidential Neural Network for Regression' model recently introduced in Denoeux (2023) <doi:10.36227/techrxiv.21791831.v1>. In this model, prediction uncertainty is quantified by Gaussian random fuzzy numbers as introduced in Denoeux (2023) <doi:10.1016/j.fss.2022.06.004>. The package contains functions for training the network, tuning hyperparameters by cross-validation or the hold-out method, and making predictions. It also contains utilities for making calculations with Gaussian random fuzzy numbers (such as, e.g., computing the degrees of belief and plausibility of an interval, or combining Gaussian random fuzzy numbers).
Author: Thierry Denoeux [aut, cre]
Maintainer: Thierry Denoeux <tdenoeux@utc.fr>

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Package compositions updated to version 2.0-5 with previous version 2.0-4 dated 2022-01-05

Title: Compositional Data Analysis
Description: Provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations) in the way proposed by J. Aitchison and V. Pawlowsky-Glahn.
Author: K. Gerald van den Boogaart <boogaart@hzdr.de>, Raimon Tolosana-Delgado, Matevz Bren
Maintainer: K. Gerald van den Boogaart <support@boogaart.de>

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Package supernova updated to version 2.5.5 with previous version 2.5.3 dated 2022-07-11

Title: Judd, McClelland, & Ryan Formatting for ANOVA Output
Description: Produces ANOVA tables in the format used by Judd, McClelland, and Ryan (2017, ISBN: 978-1138819832) in their introductory textbook, Data Analysis. This includes proportional reduction in error and formatting to improve ease the transition between the book and R.
Author: Adam Blake [cre, aut] , Jeff Chrabaszcz [aut], Ji Son [aut] , Jim Stigler [aut]
Maintainer: Adam Blake <adamblake@g.ucla.edu>

Diff between supernova versions 2.5.3 dated 2022-07-11 and 2.5.5 dated 2023-02-04

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New package simulator with initial version 0.2.5
Package: simulator
Title: An Engine for Running Simulations
Version: 0.2.5
Date: 2023-02-02
Description: A framework for performing simulations such as those common in methodological statistics papers. The design principles of this package are described in greater depth in Bien, J. (2016) "The simulator: An Engine to Streamline Simulations," which is available at <arXiv:1607.00021>.
Depends: R (>= 3.5.0)
Imports: methods, graphics, grDevices, stats, utils, magrittr
Suggests: digest, ggplot2, knitr, rmarkdown, testthat, glmnet, mvtnorm
License: GPL-3
VignetteBuilder: knitr
URL: https://github.com/jacobbien/simulator
BugReports: https://github.com/jacobbien/simulator/issues
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-02-02 16:33:59 UTC; jacobbien
Author: Jacob Bien [aut, cre]
Maintainer: Jacob Bien <jbien@usc.edu>
Repository: CRAN
Date/Publication: 2023-02-04 07:50:02 UTC

More information about simulator at CRAN
Permanent link

New package mateable with initial version 0.3.2
Package: mateable
Title: Assess Mating Potential in Space and Time
Version: 0.3.2
Date: 2023-01-04
Maintainer: Stuart Wagenius <stuart.wagenius@gmail.com>
URL: https://github.com/stuartWagenius/mateable
BugReports: https://github.com/stuartWagenius/mateable/issues
Description: Simulate, manage, visualize, and analyze spatially and temporally explicit datasets of mating potential. Implements methods to calculate synchrony, proximity, and compatibility.Synchrony calculations are based on methods described in Augspurger (1983) <doi:10.2307/2387650>, Kempenaers (1993) <doi:10.2307/3676415>, Ison et al. (2014) <doi:10.3732/ajb.1300065>, and variations on these, as described.
License: GPL
LazyData: true
Imports: FNN, graphics, grDevices, Rcpp, sn, stats
Depends: R(>= 2.10.0)
Suggests: knitr, rmarkdown
LinkingTo: Rcpp
VignetteBuilder: knitr
Encoding: UTF-8
Biarch: true
NeedsCompilation: yes
Packaged: 2023-02-04 00:04:41 UTC; SWagenius
Author: Stuart Wagenius [cre, aut], Danny Hanson [aut], Amy Waananen [aut]
Repository: CRAN
Date/Publication: 2023-02-04 07:42:31 UTC

More information about mateable at CRAN
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Package echoice2 updated to version 0.2.1 with previous version 0.2.0 dated 2023-02-02

Title: Choice Models with Economic Foundation
Description: Implements choice models based on economic theory, including estimation using Markov chain Monte Carlo (MCMC), prediction, and more. Its usability is inspired by ideas from 'tidyverse'. Models include versions of the Hierarchical Multinomial Logit and Multiple Discrete-Continous (Volumetric) models with and without screening. The foundations of these models are described in Allenby, Hardt and Rossi (2019) <doi:10.1016/bs.hem.2019.04.002>. Models with conjunctive screening are described in Kim, Hardt, Kim and Allenby (2022) <doi:10.1016/j.ijresmar.2022.04.001>. Models with set-size variation are described in Hardt and Kurz (2020) <doi:10.2139/ssrn.3418383>.
Author: Nino Hardt [aut, cre]
Maintainer: Nino Hardt <me@ninohardt.com>

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Package QuantileGH updated to version 0.1.3 with previous version 0.1.2 dated 2022-05-05

Title: Quantile Least Mahalanobis Distance Estimator for Tukey g-&-h Mixture
Description: Functions for simulation, estimation, and model selection of finite mixtures of Tukey's g-and-h distributions.
Author: Tingting Zhan [aut, cre, cph], Inna Chervoneva [ctb]
Maintainer: Tingting Zhan <Tingting.Zhan@jefferson.edu>

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Package hisse (with last version 2.1.10) was removed from CRAN

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

2023-01-19 2.1.10
2022-06-15 2.1.9

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Fri, 03 Feb 2023

Package RItools updated to version 0.3-2 with previous version 0.3-1 dated 2022-08-10

Title: Randomization Inference Tools
Description: Tools for randomization-based inference. Current focus is on the d^2 omnibus test of differences of means following Hansen and Bowers (2008) <doi:10.1214/08-STS254> . This test is useful for assessing balance in matched observational studies or for analysis of outcomes in block-randomized experiments.
Author: Jake Bowers [aut, cre], Mark Fredrickson [aut], Ben Hansen [aut], Josh Errickson [ctb]
Maintainer: Jake Bowers <jwbowers@illinois.edu>

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Package UKFE updated to version 0.2.7 with previous version 0.2.6 dated 2023-01-23

Title: UK Flood Estimation
Description: Functions to implement the methods of the Flood Estimation Handbook (FEH), associated updates and the revitalised flood hydrograph model (ReFH). Currently the package uses NRFA peak flow dataset version 11. Aside from FEH functionality, further hydrological functions are available. Most of the methods implemented in this package are described in one or more of the following: "Flood Estimation Handbook", Centre for Ecology & Hydrology (1999, ISBN:0 948540 94 X). "Flood Estimation Handbook Supplementary Report No. 1", Kjeldsen (2007, ISBN:0 903741 15 7). "Regional Frequency Analysis - an approach based on L-moments", Hosking & Wallis (1997, ISBN: 978 0 521 01940 8). "Proposal of the extreme rank plot for extreme value analysis: with an emphasis on flood frequency studies", Hammond (2019, <doi:10.2166/nh.2019.157>). "Making better use of local data in flood frequency estimation", Environment Agency (2017, ISBN: 978 1 84911 387 8). "Sampling uncertainty of UK design flood est [...truncated...]
Author: Anthony Hammond
Maintainer: Anthony Hammond <agqhammond@gmail.com>

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Package pbatR updated to version 2.2-15 with previous version 2.2-13 dated 2018-04-19

Title: Pedigree/Family-Based Genetic Association Tests Analysis and Power
Description: This R package provides power calculations via internal simulation methods. The package also provides a frontend to the now abandoned PBAT program (developed by Christoph Lange), and reads in the corresponding output and displays results and figures when appropriate. The license of this R package itself is GPL. However, to have the program interact with the PBAT program for some functionality of the R package, users must additionally obtain the PBAT program from Christoph Lange, and accept his license. Both the data analysis and power calculations have command line and graphical interfaces using tcltk.
Author: Thomas Hoffmann <tjhoffm@gmail.com>, with contributions from Christoph Lange <clange@hsph.harvard.edu>
Maintainer: Thomas Hoffmann <tjhoffm@gmail.com>

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Package opa updated to version 0.7.1 with previous version 0.6 dated 2023-01-06

Title: An Implementation of Ordinal Pattern Analysis
Description: Quantifies hypothesis to data fit for repeated measures and longitudinal data, as described by Thorngate (1987) <doi:10.1016/S0166-4115(08)60083-7> and Grice et al., (2015) <doi:10.1177/2158244015604192>. Hypothesis and data are encoded as pairwise relative orderings which are then compared to determine the percentage of orderings in the data that are matched by the hypothesis.
Author: Timothy Beechey [aut, cre]
Maintainer: Timothy Beechey <tim.beechey@proton.me>

Diff between opa versions 0.6 dated 2023-01-06 and 0.7.1 dated 2023-02-03

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Package ggalluvial updated to version 0.12.4 with previous version 0.12.3 dated 2020-12-05

Title: Alluvial Plots in 'ggplot2'
Description: Alluvial plots use variable-width ribbons and stacked bar plots to represent multi-dimensional or repeated-measures data with categorical or ordinal variables; see Riehmann, Hanfler, and Froehlich (2005) <doi:10.1109/INFVIS.2005.1532152> and Rosvall and Bergstrom (2010) <doi:10.1371/journal.pone.0008694>. Alluvial plots are statistical graphics in the sense of Wilkinson (2006) <doi:10.1007/0-387-28695-0>; they share elements with Sankey diagrams and parallel sets plots but are uniquely determined from the data and a small set of parameters. This package extends Wickham's (2010) <doi:10.1198/jcgs.2009.07098> layered grammar of graphics to generate alluvial plots from tidy data.
Author: Jason Cory Brunson [aut, cre], Quentin D. Read [aut]
Maintainer: Jason Cory Brunson <cornelioid@gmail.com>

Diff between ggalluvial versions 0.12.3 dated 2020-12-05 and 0.12.4 dated 2023-02-03

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Package geometry updated to version 0.4.7 with previous version 0.4.6.1 dated 2022-07-04

Title: Mesh Generation and Surface Tessellation
Description: Makes the 'Qhull' library <http://www.qhull.org> available in R, in a similar manner as in Octave and MATLAB. Qhull computes convex hulls, Delaunay triangulations, halfspace intersections about a point, Voronoi diagrams, furthest-site Delaunay triangulations, and furthest-site Voronoi diagrams. It runs in 2D, 3D, 4D, and higher dimensions. It implements the Quickhull algorithm for computing the convex hull. Qhull does not support constrained Delaunay triangulations, or mesh generation of non-convex objects, but the package does include some R functions that allow for this.
Author: Jean-Romain Roussel [cph, ctb] , C. B. Barber [cph], Kai Habel [cph, aut], Raoul Grasman [cph, aut], Robert B. Gramacy [cph, aut], Pavlo Mozharovskyi [cph, aut], David C. Sterratt [cph, aut, cre]
Maintainer: David C. Sterratt <david.c.sterratt@ed.ac.uk>

Diff between geometry versions 0.4.6.1 dated 2022-07-04 and 0.4.7 dated 2023-02-03

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Package fbati updated to version 1.0-7 with previous version 1.0-5 dated 2022-02-12

Title: Gene by Environment Interaction and Conditional Gene Tests for Nuclear Families
Description: Does family-based gene by environment interaction tests, joint gene, gene-environment interaction test, and a test of a set of genes conditional on another set of genes.
Author: Thomas Hoffmann <tjhoffm@gmail.com>
Maintainer: Thomas Hoffmann <tjhoffm@gmail.com>

Diff between fbati versions 1.0-5 dated 2022-02-12 and 1.0-7 dated 2023-02-03

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Package bayesTFR updated to version 7.3-0 with previous version 7.2-2 dated 2022-12-12

Title: Bayesian Fertility Projection
Description: Making probabilistic projections of total fertility rate for all countries of the world, using a Bayesian hierarchical model <doi:10.1007/s13524-011-0040-5>. Subnational probabilistic projections are also supported.
Author: Hana Sevcikova , Leontine Alkema , Peiran Liu , Adrian Raftery , Bailey Fosdick , Patrick Gerland
Maintainer: Hana Sevcikova <hanas@uw.edu>

Diff between bayesTFR versions 7.2-2 dated 2022-12-12 and 7.3-0 dated 2023-02-03

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Package SASmarkdown updated to version 0.8.1 with previous version 0.8.0 dated 2022-09-20

Title: 'SAS' Markdown
Description: Settings and functions to extend the 'knitr' 'SAS' engine.
Author: Doug Hemken [aut, cre] , Chao Cheng [ctb]
Maintainer: Doug Hemken <dehemken@wisc.edu>

Diff between SASmarkdown versions 0.8.0 dated 2022-09-20 and 0.8.1 dated 2023-02-03

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New package whitewater with initial version 0.1.2
Package: whitewater
Title: Parallel Processing Options for Package 'dataRetrieval'
Version: 0.1.2
Description: Provides methods for retrieving United States Geological Survey (USGS) water data using sequential and parallel processing (Bengtsson, 2022 <doi:10.32614/RJ-2021-048>). In addition to parallel methods, data wrangling and additional statistical attributes are provided.
URL: https://github.com/joshualerickson/whitewater/, https://joshualerickson.github.io/whitewater/
BugReports: https://github.com/joshualerickson/whitewater/issues/
License: MIT + file LICENSE
Encoding: UTF-8
Imports: dataRetrieval, dplyr, cli, crayon, furrr, httr, plyr, purrr, stringr, usethis, lubridate, readr, tidyr, future
Suggests: ggplot2, covr, rmarkdown, knitr, ggfx, broom, patchwork, jsonlite, Kendall, testthat (>= 3.0.0)
Depends: R (>= 3.4.0)
LazyData: true
NeedsCompilation: no
Packaged: 2023-02-03 15:15:03 UTC; joshualerickson
Author: Josh Erickson [aut, cre, cph]
Maintainer: Josh Erickson <joshualerickson@gmail.com>
Repository: CRAN
Date/Publication: 2023-02-03 20:30:02 UTC

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Package shapes updated to version 1.2.7 with previous version 1.2.6 dated 2021-03-31

Title: Statistical Shape Analysis
Description: Routines for the statistical analysis of landmark shapes, including Procrustes analysis, graphical displays, principal components analysis, permutation and bootstrap tests, thin-plate spline transformation grids and comparing covariance matrices. See Dryden, I.L. and Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd Edition), John Wiley and Sons.
Author: Ian L. Dryden
Maintainer: Ian Dryden <ian.dryden@nottingham.ac.uk>

Diff between shapes versions 1.2.6 dated 2021-03-31 and 1.2.7 dated 2023-02-03

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New package formatBibtex with initial version 0.1.0
Package: formatBibtex
Title: Format BibTeX Entries and Files
Version: 0.1.0
Description: Format BibTeX entries and files in an opinionated way.
Depends: R (>= 4.0)
Imports: utils
Suggests: bibtex
License: GPL (>= 3)
Encoding: UTF-8
URL: https://github.com/wenjie2wang/formatBibtex
BugReports: https://github.com/wenjie2wang/formatBibtex/issues
NeedsCompilation: no
Packaged: 2023-02-03 01:20:11 UTC; wenjie
Author: Wenjie Wang [aut, cre]
Maintainer: Wenjie Wang <wang@wwenjie.org>
Repository: CRAN
Date/Publication: 2023-02-03 20:22:30 UTC

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New package climetrics with initial version 1.0-11
Package: climetrics
Title: Climate Change Metrics
Version: 1.0-11
Date: 2023-02-01
Depends: methods, sp (>= 1.2-0), R (>= 3.5.0), rts
Imports: raster, terra, zoo, yaImpute, xts
Suggests: R.rsp, dplyr, tidyr
VignetteBuilder: R.rsp
Description: A framework that facilitates spatio-temporal analysis of climate dynamics through exploring and measuring different dimensions of climate change in space and time.
License: GPL (>= 3)
Encoding: UTF-8
URL: https://r-gis.net/
BugReports: https://github.com/shirintaheri/climetrics/issues/
NeedsCompilation: no
Packaged: 2023-02-01 13:14:09 UTC; babak
Author: Shirin Taheri [cre, aut] , Babak Naimi [aut] , Miguel Araujo [aut]
Maintainer: Shirin Taheri <taheri.shi@gmail.com>
Repository: CRAN
Date/Publication: 2023-02-03 20:02:34 UTC

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New package bndesr with initial version 1.0
Package: bndesr
Title: Access Data from the Brazilian Development Bank (BNDES)
Version: 1.0
Description: Allows access to data on BNDES disbursements and contracts since 1995. The package makes it easy to import data from the bank into R.<https://www.bndes.gov.br/SiteBNDES/bndes/bndes_en>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: dplyr, janitor, lubridate, readr, readxl, stringr
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2023-02-03 16:59:35 UTC; igorl
Author: Igor Laltuf [aut, cre]
Maintainer: Igor Laltuf <igorlaltuf@gmail.com>
Repository: CRAN
Date/Publication: 2023-02-03 20:32:34 UTC

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Package sievePH updated to version 1.0.4 with previous version 1.0.3 dated 2022-08-16

Title: Sieve Analysis Methods for Proportional Hazards Models
Description: Implements semiparametric estimation and testing procedures for a continuous, possibly multivariate, mark-specific hazard ratio (treatment/placebo) of an event of interest in a randomized treatment efficacy trial with a time-to-event endpoint, as described in Juraska M and Gilbert PB (2013), Mark-specific hazard ratio model with multivariate continuous marks: an application to vaccine efficacy. Biometrics 69(2):328 337 <doi:10.1111/biom.12016>, and in Juraska M and Gilbert PB (2016), Mark-specific hazard ratio model with missing multivariate marks. Lifetime Data Analysis 22(4): 606-25 <doi:10.1007/s10985-015-9353-9>. The former considers continuous multivariate marks fully observed in all subjects who experience the event of interest, whereas the latter extends the previous work to allow multivariate marks that are subject to missingness-at-random. For models with missing marks, two estimators are implemented based on (i) inverse probability weighting (IPW) of complete case [...truncated...]
Author: Michal Juraska [aut, cre], Stephanie Wu [ctb], Li Li [ctb]
Maintainer: Michal Juraska <mjuraska@fredhutch.org>

Diff between sievePH versions 1.0.3 dated 2022-08-16 and 1.0.4 dated 2023-02-03

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Package PROsetta updated to version 0.4.1 with previous version 0.3.5 dated 2022-01-03

Title: Linking Patient-Reported Outcomes Measures
Description: Perform scale linking to establish relationships between instruments that measure similar constructs according to the PROsetta Stone methodology, as in Choi, Schalet, Cook, & Cella (2014) <doi:10.1037/a0035768>.
Author: Seung W. Choi [aut, cre] , Sangdon Lim [aut] , Benjamin D. Schalet [ctb], Aaron J. Kaat [ctb], David Cella [ctb]
Maintainer: Seung W. Choi <schoi@austin.utexas.edu>

Diff between PROsetta versions 0.3.5 dated 2022-01-03 and 0.4.1 dated 2023-02-03

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 PROsetta-0.4.1/PROsetta/MD5                                                                            |  200 
 PROsetta-0.4.1/PROsetta/NAMESPACE                                                                      |    6 
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 PROsetta-0.4.1/PROsetta/R/datasets.R                                                                   |   12 
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 PROsetta-0.4.1/PROsetta/R/import.R                                                                     |    3 
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More information about PROsetta at CRAN
Permanent link

Package lares updated to version 5.2.0 with previous version 5.1.4 dated 2022-09-08

Title: Analytics & Machine Learning Sidekick
Description: Auxiliary package for better/faster analytics, visualization, data mining, and machine learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling, Exploratory, API, and Scrapper, it helps the analyst or data scientist to get quick and robust results, without the need of repetitive coding or extensive R programming skills.
Author: Bernardo Lares [aut, cre]
Maintainer: Bernardo Lares <laresbernardo@gmail.com>

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Package VisitorCounts updated to version 1.0.2 with previous version 1.0.1 dated 2022-04-21

Title: Modeling and Forecasting Visitor Counts Using Social Media
Description: Performs modeling and forecasting of park visitor counts using social media data and (partial) on-site visitor counts. Specifically, the model is built based on an automatic decomposition of the trend and seasonal components of the social media-based park visitor counts, from which short-term forecasts of the visitor counts and percent changes in the visitor counts can be made. A reference for generating social media-based visitor counts can be found at Wood, Guerry, Silver, and Lacayo (2013) <doi:10.1038/srep02976>.
Author: Russell Goebel [aut], Robert Bowen [aut, cre], Beth Ann Brackett [ctb], Kimihiro Noguchi [aut], Dylan Way [aut]
Maintainer: Robert Bowen <robertbowen.bham@gmail.com>

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Package tidyCDISC updated to version 0.2.0 with previous version 0.1.0 dated 2022-08-30

Title: Quick Table Generation & Exploratory Analyses on ADaM-Ish Datasets
Description: Provides users a quick exploratory dive into common visualizations without writing a single line of code given the users data follows the Analysis Data Model (ADaM) standards put forth by the Clinical Data Interchange Standards Consortium (CDISC) <https://www.cdisc.org>. Prominent modules/ features of the application are the Table Generator, Population Explorer, and the Individual Explorer. The Table Generator allows users to drag and drop variables and desired statistics (frequencies, means, ANOVA, t-test, and other summary statistics) into bins that automagically create stunning tables with validated information. The Population Explorer offers various plots to visualize general trends in the population from various vantage points. Plot modules currently include scatter plot, spaghetti plot, box plot, histogram, means plot, and bar plot. Each plot type allows the user to plot uploaded variables against one another, and dissect the population by filtering out certain subjects. La [...truncated...]
Author: Aaron Clark [aut, cre] , Jeff Thompson [aut], Teresa Wilson [aut], Nate Mockler [ccp, led], Maya Gans [aut], Robert Krajcik [ctb], Marly Gotti [ctb], Biogen Inc [cph]
Maintainer: Aaron Clark <clark.aaronchris@gmail.com>

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Package logrx updated to version 0.2.1 with previous version 0.2.0 dated 2023-01-18

Title: A Logging Utility Focus on Clinical Trial Programming Workflows
Description: A utility to facilitate the logging and review of R programs in clinical trial programming workflows.
Author: Nathan Kosiba [aut, cre], Thomas Bermudez [aut], Ben Straub [aut], Michael Rimler [aut], Nicholas Masel [aut], GSK/Atorus JPT [cph, fnd]
Maintainer: Nathan Kosiba <nhkosiba@gmail.com>

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Package ggpp updated to version 0.5.1 with previous version 0.5.0 dated 2022-12-05

Title: Grammar Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Geometries: geom_table(), geom_plot() and geom_grob() add insets to plots using native data coordinates, while geom_table_npc(), geom_plot_npc() and geom_grob_npc() do the same using "npc" coordinates through new aesthetics "npcx" and "npcy". Statistics: select observations based on 2D density. Positions: radial nudging away from a center point and nudging away from a line or curve; combined stacking and nudging; combined dodging and nudging.
Author: Pedro J. Aphalo [aut, cre] , Kamil Slowikowski [ctb] , Michal Krassowski [ctb] , Daniel Sabanes Bove [ctb], Stella Banjo [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

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Package QCA updated to version 3.18 with previous version 3.17 dated 2022-10-03

Title: Qualitative Comparative Analysis
Description: An extensive set of functions to perform Qualitative Comparative Analysis: crisp sets ('csQCA'), temporal ('tQCA'), multi-value ('mvQCA') and fuzzy sets ('fsQCA'), using a GUI - graphical user interface. 'QCA' is a methodology that bridges the qualitative and quantitative divide in social science research. It uses a Boolean minimization algorithm, resulting in a minimal causal configuration associated with a given phenomenon.
Author: Adrian Dusa [aut, cre, cph] , Ciprian Paduraru [ctb] , jQuery Foundation [cph] , jQuery contributors [ctb, cph] , lp_solve [cph] , Vasil Dinkov [ctb, cph] , Dmitry Baranovskiy [ctb, cph] , Emmanuel Quentin [ctb, cph] , Jimmy Breck-McKye [ctb, cph] , [...truncated...]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>

Diff between QCA versions 3.17 dated 2022-10-03 and 3.18 dated 2023-02-03

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Package CSMES updated to version 1.0.1 with previous version 1.0.0 dated 2020-02-22

Title: Cost-Sensitive Multi-Criteria Ensemble Selection for Uncertain Cost Conditions
Description: Functions for cost-sensitive multi-criteria ensemble selection (CSMES) (as described in De bock et al. (2020) <doi:10.1016/j.ejor.2020.01.052>) for cost-sensitive learning under unknown cost conditions.
Author: Koen W. De Bock, Kristof Coussement and Stefan Lessmann
Maintainer: Koen W. De Bock <kdebock@audencia.com>

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Package chronicler updated to version 0.2.1 with previous version 0.2.0 dated 2022-05-17

Title: Add Logging to Functions
Description: Decorate functions to make them return enhanced output. The enhanced output consists in an object of type 'chronicle' containing the result of the function applied to its arguments, as well as a log detailing when the function was run, what were its inputs, what were the errors (if the function failed to run) and other useful information. Tools to handle decorated functions are included, such as a forward pipe operator that makes chaining decorated functions possible.
Author: Bruno Rodrigues [aut, cre, cph]
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>

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Package stan4bart updated to version 0.0-6 with previous version 0.0-5 dated 2023-01-23

Title: Bayesian Additive Regression Trees with Stan-Sampled Parametric Extensions
Description: Fits semiparametric linear and multilevel models with non-parametric additive Bayesian additive regression tree (BART; Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>) components and Stan (Stan Development Team (2021) <https://mc-stan.org/>) sampled parametric ones. Multilevel models can be expressed using 'lme4' syntax (Bates, Maechler, Bolker, and Walker (2015) <doi:10.18637/jss.v067.i01>).
Author: Vincent Dorie [aut, cre] , Ben Goodrich [ctb] , Jonah Gabry [ctb] , Imad Ali [ctb] , Sam Brilleman [ctb] , Paul-Christian Burkner [ctb] , Joshua Pritikin [ctb] , Andrew Gelman [ctb] , Bob Carpenter [ctb] , Matt Hoffman [ctb] , Daniel Lee [ctb] , Mich [...truncated...]
Maintainer: Vincent Dorie <vdorie@gmail.com>

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Package readxlsb updated to version 0.1.5 with previous version 0.1.4 dated 2020-09-29

Title: Read 'Excel' Binary (.xlsb) Workbooks
Description: Import data from 'Excel' binary (.xlsb) workbooks into R.
Author: Michael Allen [aut, cre]
Maintainer: Michael Allen <michael@velofrog.com>

Diff between readxlsb versions 0.1.4 dated 2020-09-29 and 0.1.5 dated 2023-02-03

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Package Luminescence updated to version 0.9.21 with previous version 0.9.20 dated 2022-07-16

Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc] , Christoph Burow [aut, trl, dtc] , Michael Dietze [aut] , Margret C. Fuchs [aut] , Christoph Schmidt [aut] , Manfred Fischer [aut, trl], Johannes Friedrich [aut] , Norbert Mercier [aut] , Rachel K. Smedley [ct [...truncated...]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@uni-heidelberg.de>

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More information about Luminescence at CRAN
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Package InflectSSP updated to version 1.5 with previous version 1.4.5 dated 2022-10-03

Title: Melt Curve Fitting and Melt Shift Analysis
Description: Analyzes raw abundance data from a cellular thermal shift experiment and calculates melt temperatures and melt shifts for each protein in the experiment. McCracken (2022) <doi:10.1101/2022.12.30.522131>.
Author: Neil McCracken [aut], Hao Liu [ctb], Amber Mosley [cre]
Maintainer: Amber Mosley <almosley@iu.edu>

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Package eq5d updated to version 0.14.0 with previous version 0.13.0 dated 2022-11-11

Title: Methods for Analysing 'EQ-5D' Data and Calculating 'EQ-5D' Index Scores
Description: EQ-5D is a popular health related quality of life instrument used in the clinical and economic evaluation of health care. Developed by the EuroQol group <https://euroqol.org/>, the instrument consists of two components: health state description and evaluation. For the description component a subject self-rates their health in terms of five dimensions; mobility, self-care, usual activities, pain/discomfort, and anxiety/depression using either a three-level (EQ-5D-3L, <https://euroqol.org/eq-5d-instruments/eq-5d-3l-about/>) or a five-level (EQ-5D-5L, <https://euroqol.org/eq-5d-instruments/eq-5d-5l-about/>) scale. Frequently the scores on these five dimensions are converted to a single utility index using country specific value sets, which can be used in the clinical and economic evaluation of health care as well as in population health surveys. The eq5d package provides methods to calculate index scores from a subject's dimension scores. 29 TTO and 11 VAS EQ-5D-3L value [...truncated...]
Author: Fraser Morton [aut, cre], Jagtar Singh Nijjar [aut]
Maintainer: Fraser Morton <fraser.morton@glasgow.ac.uk>

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Package clarify updated to version 0.1.1 with previous version 0.1.0 dated 2023-01-25

Title: Simulation-Based Inference for Regression Models
Description: Performs simulation-based inference as an alternative to the delta method for obtaining valid confidence intervals and p-values for regression post-estimation quantities, such as average marginal effects and predictions at representative values. This framework for simulation-based inference is especially useful when the resulting quantity is not normally distributed and the delta method approximation fails. The methodology is described in King, Tomz, and Wittenberg (2000) <doi:10.2307/2669316>. 'clarify' is meant to replace some of the functionality of the archived package 'Zelig'; see the vignette "Translating Zelig to clarify" for replicating this functionality.
Author: Noah Greifer [aut, cre] , Steven Worthington [aut] , Stefano Iacus [aut] , Gary King [aut]
Maintainer: Noah Greifer <ngreifer@iq.harvard.edu>

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More information about clarify at CRAN
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Package BayesXsrc updated to version 3.0-4 with previous version 3.0-3 dated 2022-11-03

Title: Distribution of the 'BayesX' C++ Sources
Description: 'BayesX' performs Bayesian inference in structured additive regression (STAR) models. The R package BayesXsrc provides the 'BayesX' command line tool for easy installation. A convenient R interface is provided in package R2BayesX.
Author: Nikolaus Umlauf [aut, cre] , Daniel Adler [aut], Thomas Kneib [aut], Stefan Lang [aut], Achim Zeileis [aut]
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>

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Package BayesMallows updated to version 1.2.2 with previous version 1.2.1 dated 2022-11-04

Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model (Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>; Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>). Both Metropolis-Hastings and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule, Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the posterior distributions of parameters are provided. The package also provides functions for estimating the partition function (normalizing constant) of the Mallows rank model, both with the importance sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm (Mukherjee, Annals of Sta [...truncated...]
Author: Oystein Sorensen [aut, cre] , Valeria Vitelli [aut] , Marta Crispino [aut], Qinghua Liu [aut], Cristina Mollica [aut], Luca Tardella [aut], Anja Stein [aut], Waldir Leoncio [ctr]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>

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Package batchtools updated to version 0.9.16 with previous version 0.9.15 dated 2021-01-11

Title: Tools for Computation on Batch Systems
Description: As a successor of the packages 'BatchJobs' and 'BatchExperiments', this package provides a parallel implementation of the Map function for high performance computing systems managed by schedulers 'IBM Spectrum LSF' (<https://www.ibm.com/products/hpc-workload-management>), 'OpenLava' (<https://www.openlava.org/>), 'Univa Grid Engine'/'Oracle Grid Engine' (<https://www.univa.com/>), 'Slurm' (<https://slurm.schedmd.com/>), 'TORQUE/PBS' (<https://adaptivecomputing.com/cherry-services/torque-resource-manager/>), or 'Docker Swarm' (<https://docs.docker.com/engine/swarm/>). A multicore and socket mode allow the parallelization on a local machines, and multiple machines can be hooked up via SSH to create a makeshift cluster. Moreover, the package provides an abstraction mechanism to define large-scale computer experiments in a well-organized and reproducible way.
Author: Michel Lang [cre, aut] , Bernd Bischl [aut], Dirk Surmann [ctb]
Maintainer: Michel Lang <michellang@gmail.com>

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Package vegan3d updated to version 1.2-0 with previous version 1.1-2 dated 2018-10-25

Title: Static and Dynamic 3D Plots for the 'vegan' Package
Description: Static and dynamic 3D plots to be used with ordination results and in diversity analysis, especially with the vegan package.
Author: Jari Oksanen [aut, cre], Roeland Kindt [aut], Gavin L. Simpson [aut], Duncan Murdoch [ctb]
Maintainer: Jari Oksanen <jhoksane@gmail.com>

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Package shapviz updated to version 0.5.0 with previous version 0.4.1 dated 2023-01-11

Title: SHAP Visualizations
Description: Visualizations for SHAP (SHapley Additive exPlanations), such as waterfall plots, force plots, various types of importance plots, dependence plots, and interaction plots. These plots act on a 'shapviz' object created from a matrix of SHAP values and a corresponding feature dataset. Wrappers for the R packages 'xgboost', 'lightgbm', 'fastshap', 'shapr', 'h2o', 'treeshap', and 'kernelshap' are added for convenience. By separating visualization and computation, it is possible to display factor variables in graphs, even if the SHAP values are calculated by a model that requires numerical features. The plots are inspired by those provided by the 'shap' package in Python, but there is no dependency on it.
Author: Michael Mayer [aut, cre]
Maintainer: Michael Mayer <mayermichael79@gmail.com>

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Package dynamite updated to version 1.1.1 with previous version 1.0.1 dated 2022-12-23

Title: Bayesian Modeling and Causal Inference for Multivariate Longitudinal Data
Description: Easy-to-use and efficient interface for Bayesian inference of complex panel (time series) data using dynamic multivariate panel models by Helske and Tikka (2022) <doi:10.31235/osf.io/mdwu5>. The package supports joint modeling of multiple measurements per individual, time-varying and time-invariant effects, and a wide range of discrete and continuous distributions. Estimation of these dynamic multivariate panel models is carried out via 'Stan'.
Author: Santtu Tikka [aut, cre] , Jouni Helske [aut] , Nicholas Clark [rev], Lucy D’Agostino McGowan [rev]
Maintainer: Santtu Tikka <santtuth@gmail.com>

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Package dsfa updated to version 2.0.0 with previous version 1.0.1 dated 2022-11-04

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

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New package stxplore with initial version 0.1.0
Package: stxplore
Title: Exploration of Spatio-Temporal Data
Version: 0.1.0
Maintainer: Sevvandi Kandanaarachchi <sevvandik@gmail.com>
Description: A set of statistical tools for spatio-temporal data exploration. Includes simple plotting functions, covariance calculations and computations similar to principal component analysis for spatio-temporal data. Can use both dataframes and stars objects for all plots and computations. For more details refer 'Spatio-Temporal Statistics with R' (Christopher K. Wikle, Andrew Zammit-Mangion, Noel Cressie, 2019, ISBN:9781138711136).
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
LazyDataCompression: gzip
Imports: fields, ggmap, ggplot2, ggridges, gridExtra, gstat, lubridate, magrittr, RColorBrewer, rlang, sp, spacetime, stars, stats, tidyr
Depends: R (>= 2.10)
Suggests: dplyr, knitr, rmarkdown, ncmeta, units, maps, cubelyr
VignetteBuilder: knitr
URL: https://sevvandi.github.io/stxplore/
NeedsCompilation: no
Packaged: 2023-02-02 08:58:08 UTC; kan092
Author: Sevvandi Kandanaarachchi [aut, cre] , Petra Kunhert [aut] , Andrew Zammit-Mangion [ctb]
Repository: CRAN
Date/Publication: 2023-02-03 10:10:02 UTC

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New package smallsets with initial version 1.0.0
Package: smallsets
Title: The Smallset Timeline Builder
Version: 1.0.0
Maintainer: Lydia R. Lucchesi <Lydia.Lucchesi@anu.edu.au>
Description: Data practitioners regularly use the 'R' and 'Python' programming languages to prepare data for analyses. Thus, they encode data preprocessing decisions in 'R' and 'Python' scripts. The 'smallsets' package subsequently decodes these decisions into a Smallset Timeline, a visualisation proposed in Lucchesi et al. (2022) <doi:10.1145/3531146.3533175>. A Smallset Timeline is a series of small data snapshots of different preprocessing steps. The 'smallsets' package builds this figure from a user's dataset and 'R'/'Python' preprocessing script, which contains structured comments with snapshot instructions.
URL: https://github.com/lydialucchesi/smallsets
License: GPL (>= 3)
Encoding: UTF-8
LazyData: TRUE
Depends: R (>= 3.5.0)
Imports: colorspace, flextable, ggplot2, ggtext, patchwork, plotrix, reticulate
Suggests: gurobi, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-02-02 05:53:14 UTC; luc093
Author: Lydia R. Lucchesi [aut, cre] , Petra M. Kuhnert [ths], Jenny L. Davis [ths], Lexing Xie [ths]
Repository: CRAN
Date/Publication: 2023-02-03 10:10:06 UTC

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Package miesmuschel updated to version 0.0.3 with previous version 0.0.2 dated 2022-11-16

Title: Mixed Integer Evolution Strategies
Description: Evolutionary black box optimization algorithms building on the 'bbotk' package. 'miesmuschel' offers both ready-to-use optimization algorithms, as well as their fundamental building blocks that can be used to manually construct specialized optimization loops. The Mixed Integer Evolution Strategies as described by Li et al. (2013) <doi:10.1162/EVCO_a_00059> can be implemented, as well as the multi-objective optimization algorithms NSGA-II by Deb, Pratap, Agarwal, and Meyarivan (2002) <doi:10.1109/4235.996017>.
Author: Martin Binder [aut, cre], Lennart Schneider [ctb] , Susanne Dandl [ctb] , Andreas Hofheinz [ctb]
Maintainer: Martin Binder <mlr.developer@mb706.com>

Diff between miesmuschel versions 0.0.2 dated 2022-11-16 and 0.0.3 dated 2023-02-03

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New package gcplyr with initial version 1.1.0
Package: gcplyr
Title: Manipulate and Analyze Growth Curve Data
Version: 1.1.0
Date: 2023-02-02
Description: Easy import, manipulation, and model-free analysis of bacterial growth curve data, as commonly output by plate readers. Tools for reshaping common plate reader outputs into 'tidy' formats and merging them with design information, making data easy to work with using 'gcplyr' and other packages. Also streamlines common growth curve processing steps, like smoothing and calculating derivatives, and facilitates model-free characterization and analysis of growth data. See methods at <https://mikeblazanin.github.io/gcplyr/>.
License: MIT + file LICENSE
URL: https://mikeblazanin.github.io/gcplyr/, https://github.com/mikeblazanin/gcplyr/
Depends: R (>= 2.10)
Imports: dplyr, stats, tidyr, tools, utils
Suggests: cowplot, ggplot2, knitr, lubridate, mgcv, readxl, rmarkdown, testthat (>= 3.0.0), xlsx
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2023-02-02 19:24:58 UTC; mikeb
Author: Mike Blazanin [aut, cre]
Maintainer: Mike Blazanin <mikeblazanin@gmail.com>
Repository: CRAN
Date/Publication: 2023-02-03 10:32:31 UTC

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New package eselect with initial version 1.1
Package: eselect
Title: Adaptive Clinical Trial Designs with Endpoint Selection and Sample Size Reassessment
Version: 1.1
Maintainer: Marta Bofill Roig <marta.bofillroig@meduniwien.ac.at>
Description: Endpoint selection and sample size reassessment for multiple binary endpoints based on blinded and/or unblinded data. Trial design that allows an adaptive modification of the primary endpoint based on blinded information obtained at an interim analysis. The decision rule chooses the endpoint with the lower estimated required sample size. Additionally, the sample size is reassessed using the estimated event probabilities and correlation between endpoints. The implemented design is proposed in Bofill Roig, M., Gómez Melis, G., Posch, M., and Koenig, F. (2022). <doi:10.48550/arXiv.2206.09639>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: stats, CompAREdesign
NeedsCompilation: no
Packaged: 2023-02-02 13:22:06 UTC; marta.bofill
Author: Marta Bofill Roig [aut, cre] , Guadalupe Gomez Melis [ctb], Franz Koenig [ctb], Martin Posch [ctb]
Repository: CRAN
Date/Publication: 2023-02-03 10:22:32 UTC

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New package CARM with initial version 1.0.0
Package: CARM
Title: Covariate-Adjusted Adaptive Randomization via Mahalanobis-Distance
Version: 1.0.0
Author: Haoyu Yang [aut], Fanglu Chen [aut, cre], Yichen Qin [aut], Yang Li [aut]
Maintainer: Fanglu Chen <chenfanglu1031@qq.com>
Description: In randomized controlled trial (RCT), balancing covariate is often one of the most important concern. CARM package provides functions to balance the covariates and generate allocation sequence by covariate-adjusted Adaptive Randomization via Mahalanobis-distance (ARM) for RCT. About what ARM is and how it works please see Y. Qin, Y. Li, W. Ma, H. Yang, and F. Hu (2022). "Adaptive randomization via Mahalanobis distance" Statistica Sinica. <doi:10.5705/ss.202020.0440>. In addition, the package is also suitable for the randomization process of multi-arm trials. For details, please see Yang H, Qin Y, Wang F, et al. (2023). "Balancing covariates in multi-arm trials via adaptive randomization" Computational Statistics & Data Analysis.<doi:10.1016/j.csda.2022.107642>.
License: GPL (>= 2)
Encoding: UTF-8
Depends: R(>= 3.6.0),stats
Imports: arrangements,dplyr,MASS
NeedsCompilation: no
Packaged: 2023-02-02 16:52:06 UTC; star
Repository: CRAN
Date/Publication: 2023-02-03 10:22:35 UTC

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New package animate with initial version 0.3.9.4
Package: animate
Title: A Web-Based Graphics Device for Animated Visualisations
Version: 0.3.9.4
Description: Implements a web-based graphics device for animated visualisations. Modelled on the 'base' syntax, it extends the 'base' graphics functions to support frame-by-frame animation and keyframes animation. The target use cases are real-time animated visualisations, including agent-based models, dynamical systems, and animated diagrams. The generated visualisations can be deployed as GIF images / MP4 videos, as 'Shiny' apps (with interactivity) or as HTML documents through embedding into R Markdown documents.
License: MIT + file LICENSE
URL: https://kcf-jackson.github.io/animate/
BugReports: https://github.com/kcf-jackson/animate/issues
Encoding: UTF-8
Imports: R6, httpuv, base64enc, jsonlite, glue, R.utils
Suggests: rmarkdown, knitr, shiny, htmltools, pryr, V8, servr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-02-03 06:57:49 UTC; jkwok
Author: Chun Fung Kwok [aut, cre] , Davis McCarthy [ctb]
Maintainer: Chun Fung Kwok <kcf.jackson@gmail.com>
Repository: CRAN
Date/Publication: 2023-02-03 10:42:32 UTC

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Package tidydice updated to version 1.0.0 with previous version 0.1.1 dated 2021-04-19

Title: Simulates Dice Rolls and Coin Flips
Description: Utils for basic statistical experiments, that can be used for teaching introductory statistics. Each experiment generates a tibble. Dice rolls and coin flips are simulated using sample(). The properties of the dice can be changed, like the number of sides. A coin flip is simulated using a two sided dice. Experiments can be combined with the pipe-operator.
Author: Roland Krasser [aut, cre], Giovanni Marco Dall'Olio [aut]
Maintainer: Roland Krasser <roland.krasser@gmail.com>

Diff between tidydice versions 0.1.1 dated 2021-04-19 and 1.0.0 dated 2023-02-03

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Package opalr updated to version 3.3.0 with previous version 3.2.0 dated 2022-10-13

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

Diff between opalr versions 3.2.0 dated 2022-10-13 and 3.3.0 dated 2023-02-03

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Package HMDHFDplus updated to version 2.0.1 with previous version 1.9.19 dated 2022-11-06

Title: Read Human Mortality Database and Human Fertility Database Data from the Web
Description: Utilities for reading data from the Human Mortality Database (<https://www.mortality.org>), Human Fertility Database (<https://www.humanfertility.org>), and similar databases from the web or locally into an R session as data.frame objects. These are the two most widely used sources of demographic data to study basic demographic change, trends, and develop new demographic methods. Other supported databases at this time include the Human Fertility Collection (<https://www.fertilitydata.org>), The Japanese Mortality Database (<https://www.ipss.go.jp/p-toukei/JMD/index-en.html>), and the Canadian Human Mortality Database (<http://www.bdlc.umontreal.ca/chmd/>). Arguments and data are standardized.
Author: Tim Riffe [aut, cre], Carl Boe [aut], Jason Hilton [aut], Josh Goldstein [ctb], Stephen Holzman [ctb]
Maintainer: Tim Riffe <tim.riffe@gmail.com>

Diff between HMDHFDplus versions 1.9.19 dated 2022-11-06 and 2.0.1 dated 2023-02-03

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Package roger updated to version 1.4-0 with previous version 1.3-1 dated 2022-11-19

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

Diff between roger versions 1.3-1 dated 2022-11-19 and 1.4-0 dated 2023-02-03

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Package ggrepel updated to version 0.9.3 with previous version 0.9.2 dated 2022-11-06

Title: Automatically Position Non-Overlapping Text Labels with 'ggplot2'
Description: Provides text and label geoms for 'ggplot2' that help to avoid overlapping text labels. Labels repel away from each other and away from the data points.
Author: Kamil Slowikowski [aut, cre] , Alicia Schep [ctb] , Sean Hughes [ctb] , Trung Kien Dang [ctb] , Saulius Lukauskas [ctb], Jean-Olivier Irisson [ctb] , Zhian N Kamvar [ctb] , Thompson Ryan [ctb] , Dervieux Christophe [ctb] , Yutani Hiroaki [ctb], Pierr [...truncated...]
Maintainer: Kamil Slowikowski <kslowikowski@gmail.com>

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Package GE updated to version 0.3.5 with previous version 0.3.4 dated 2023-01-06

Title: General Equilibrium Modeling
Description: Some tools for developing general equilibrium models and some general equilibrium models. These models can be used for teaching economic theory and are built by the methods of new structural economics (see <https://www.nse.pku.edu.cn/> and LI Wu, 2019, ISBN: 9787521804225, General Equilibrium and Structural Dynamics: Perspectives of New Structural Economics. Beijing: Economic Science Press). The model form and mathematical methods can be traced back to J. von Neumann (1945, A Model of General Economic Equilibrium. The Review of Economic Studies, 13. pp. 1-9), J. G. Kemeny, O. Morgenstern and G. L. Thompson (1956, A Generalization of the von Neumann Model of an Expanding Economy, Econometrica, 24, pp. 115-135) et al. By the way, J. G. Kemeny is a co-inventor of the computer language BASIC.
Author: LI Wu <liwu@staff.shu.edu.cn>
Maintainer: LI Wu <liwu@staff.shu.edu.cn>

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Thu, 02 Feb 2023

Package slendr updated to version 0.5.0 with previous version 0.4.0 dated 2022-09-30

Title: A Simulation Framework for Spatiotemporal Population Genetics
Description: A framework for simulating spatially explicit genomic data which leverages real cartographic information for programmatic and visual encoding of spatiotemporal population dynamics on real geographic landscapes. Population genetic models are then automatically executed by the 'SLiM' software by Haller et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom built-in simulation 'SLiM' script. Additionally, fully abstract spatial models not tied to a specific geographic location are supported, and users can also simulate data from standard, non-spatial, random-mating models. These can be simulated either with the 'SLiM' built-in back-end script, or using an efficient coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022) <doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the R package. Simulated genomic data is saved in a tree-sequence format and can be loaded, manipulated, and summarised using tree-sequen [...truncated...]
Author: Martin Petr [aut, cre]
Maintainer: Martin Petr <contact@bodkan.net>

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Package romic updated to version 1.1.1 with previous version 1.0.0 dated 2021-07-20

Title: R for High-Dimensional Omic Data
Description: Represents high-dimensional data as tables of features, samples and measurements, and a design list for tracking the meaning of individual variables. Using this format, filtering, normalization, and other transformations of a dataset can be carried out in a flexible manner. 'romic' takes advantage of these transformations to create interactive 'shiny' apps for exploratory data analysis such as an interactive heatmap.
Author: Sean Hackett [aut, cre] , Calico Life Sciences LLC [cph, fnd]
Maintainer: Sean Hackett <sean@calicolabs.com>

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Package nzilbb.labbcat updated to version 1.2-0 with previous version 1.1-1 dated 2022-05-19

Title: Accessing Data Stored in 'LaBB-CAT' Instances
Description: 'LaBB-CAT' is a web-based language corpus management system developed by the New Zealand Institute of Language, Brain and Behaviour (NZILBB) - see <https://labbcat.canterbury.ac.nz>. This package defines functions for accessing corpus data in a 'LaBB-CAT' instance. You must have at least version 20230202.1600 of 'LaBB-CAT' to use this package. For more information about 'LaBB-CAT', see Robert Fromont and Jennifer Hay (2008) <doi:10.3366/E1749503208000142> or Robert Fromont (2017) <doi:10.1016/j.csl.2017.01.004>.
Author: Robert Fromont [aut, cre]
Maintainer: Robert Fromont <robert.fromont@canterbury.ac.nz>

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Package kyotil updated to version 2023.2-2 with previous version 2022.12-20 dated 2022-12-20

Title: Utility Functions for Statistical Analysis Report Generation and Monte Carlo Studies
Description: Helper functions for creating formatted summary of regression models, writing publication-ready tables to latex files, and running Monte Carlo experiments.
Author: Youyi Fong [cre], Krisztian Sebestyen [aut], Han Sunwoo [aut], Jason Becker [ctb], Bendix Carstensen [ctb], Daryl Morris [ctb], Josh Pasek [ctb], Dennis Chao [ctb], Andri Signorell [ctb], Sue Li [ctb], Jonathan Bartlett [ctb], Christophe Dutang [ctb]
Maintainer: Youyi Fong <youyifong@gmail.com>

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Package imager updated to version 0.42.18 with previous version 0.42.16 dated 2022-12-19

Title: Image Processing Library Based on 'CImg'
Description: Fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one colour dimension). Provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analysing image data using R. The package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image processing.
Author: Simon Barthelme [aut], David Tschumperle [ctb], Jan Wijffels [ctb], Haz Edine Assemlal [ctb], Shota Ochi [cre]
Maintainer: Shota Ochi <shotaochi1990@gmail.com>

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Package video updated to version 0.1.1 with previous version 0.1.0 dated 2022-07-21

Title: 'Shiny' Extension of 'video.js'
Description: Video interactivity within 'shiny' applications using 'video.js'. Enables the status of the video to be sent from the UI to the server, and allows events such as playing and pausing the video to be triggered from the server.
Author: Ashley Baldry [aut, cre], Steve Heffernan [aut]
Maintainer: Ashley Baldry <arbaldry91@gmail.com>

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Package appler updated to version 0.2.0 with previous version 0.1.4 dated 2022-10-06

Title: 'Apple App Store' and 'iTunes' Data Extraction
Description: Using 'Apple App Store' <https://www.apple.com/app-store/> web scraping and 'iTunes' API <https://performance-partners.apple.com/search-api> to extract content information, app ratings and reviews.
Author: Ashley Baldry [aut, cre]
Maintainer: Ashley Baldry <arbaldry91@gmail.com>

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Package gausscov updated to version 1.0.2 with previous version 1.0.1 dated 2023-01-17

Title: The Gaussian Covariate Method for Variable Selection
Description: Given the standard linear model the traditional way of deciding whether to include the jth covariate is to apply the F-test to decide whether the corresponding beta coefficient is zero. The Gaussian covariate method is completely different. The question as to whether the beta coefficient is or is not zero is replaced by the question as to whether the covariate is better or worse than i.i.d. Gaussian noise. The P-value for the covariate is the probability that Gaussian noise is better. Surprisingly this can be given exactly and it is the same a the P-value for the classical model based on the F-distribution. The Gaussian covariate P-value is model free, it is the same for any data set. Using the idea it is possible to do covariate selection for a small number of covariates 25 by considering all subsets. Post selection inference causes no problems as the P-values hold whatever the data. The idea extends to stepwise regression again with exact probabilities. In the simplest version the [...truncated...]
Author: Laurie Davies [aut, cre]
Maintainer: Laurie Davies <pldavies44@cantab.net>

Diff between gausscov versions 1.0.1 dated 2023-01-17 and 1.0.2 dated 2023-02-02

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Package sivs updated to version 0.2.6 with previous version 0.2.5 dated 2021-07-20

Title: Stable Iterative Variable Selection
Description: An iterative feature selection method (manuscript submitted) that internally utilizes various Machine Learning methods that have embedded feature reduction in order to shrink down the feature space into a small and yet robust set.
Author: Mehrad Mahmoudian [aut, cre] , Mikko Venaelaeinen [aut, rev] , Riku Klen [aut, ths] , Laura Elo [aut, ths, fnd]
Maintainer: Mehrad Mahmoudian <mehrad.mahmoudian@utu.fi>

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Package opentripplanner updated to version 0.5.1 with previous version 0.5 dated 2023-01-06

Title: Setup and connect to 'OpenTripPlanner'
Description: Setup and connect to 'OpenTripPlanner' (OTP) <http://www.opentripplanner.org/>. OTP is an open source platform for multi-modal and multi-agency journey planning written in 'Java'. The package allows you to manage a local version or connect to remote OTP server to find walking, cycling, driving, or transit routes. This package has been peer-reviewed by rOpenSci (v. 0.2.0.0).
Author: Malcolm Morgan [aut, cre] , Marcus Young [aut] , Robin Lovelace [aut] , Layik Hama [ctb]
Maintainer: Malcolm Morgan <m.morgan1@leeds.ac.uk>

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Package omu updated to version 1.0.9 with previous version 1.0.7 dated 2022-08-27

Title: A Metabolomics Analysis Tool for Intuitive Figures and Convenient Metadata Collection
Description: Facilitates the creation of intuitive figures to describe metabolomics data by utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG) hierarchy data, and gathers functional orthology and gene data from the KEGG-REST API.
Author: Connor Tiffany [aut, cre]
Maintainer: Connor Tiffany <crtiffany@ucdavis.edu>

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New package roads with initial version 1.1.0
Package: roads
Title: Road Network Projection
Version: 1.1.0
Date: 2023-03-11
URL: https://github.com/LandSciTech/roads, https://landscitech.github.io/roads/
Description: Project road network development based on an existing road network, target locations to be connected by roads and a cost surface. Road projection methods include minimum spanning tree with least cost path (Kruskal's algorithm (1956) <doi:10.2307/2033241>), least cost path (Dijkstra's algorithm (1959) <doi:10.1007/BF01386390>) or snapping. These road network projection methods are ideal for use with land cover change projection models.
License: Apache License (>= 2)
Encoding: UTF-8
LazyData: true
Imports: raster, dplyr, igraph, sp, data.table, sf, units, rlang, methods, tidyselect, terra
Suggests: testthat (>= 2.1.0), knitr, rmarkdown, viridis, tmap, bench
VignetteBuilder: knitr
Depends: R (>= 2.10)
BugReports: https://github.com/LandSciTech/roads/issues
NeedsCompilation: no
Packaged: 2023-02-01 17:18:51 UTC; EndicottS
Author: Sarah Endicott [aut, cre] , Kyle Lochhead [aut], Josie Hughes [aut], Patrick Kirby [aut], Her Majesty the Queen in Right of Canada as represented by the Minister of the Environment [cph] , Province of British Columbia [cph]
Maintainer: Sarah Endicott <sarah.endicott@ec.gc.ca>
Repository: CRAN
Date/Publication: 2023-02-02 16:10:02 UTC

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New package rda with initial version 1.2-1
Package: rda
Version: 1.2-1
VersionNote: Archived on 2020-01-01 on CRAN
Title: Shrunken Centroids Regularized Discriminant Analysis
Depends: R (>= 2.10)
Imports: methods
Suggests: covr
Description: Provides functions implementing the shrunken centroids regularized discriminant analysis for classification purpose in high dimensional data. The method is described in Guo at al. (2013) <doi:10.1093/biostatistics/kxj035>.
License: GPL (>= 3)
URL: https://github.com/valentint/rda
BugReports: https://github.com/valentint/rda/issues
Repository: CRAN
Date/Publication: 2023-02-02 16:20:02 UTC
Author: Yaqian Guo [aut], Trevor Hastie [aut], Robert Tibshirani [aut], Valentin Todorov [cre]
Maintainer: Valentin Todorov <valentin@todorov.at>
NeedsCompilation: no
Packaged: 2023-02-01 21:21:44 UTC; valen

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Package mapbayr updated to version 0.9.0 with previous version 0.8.0 dated 2022-09-29

Title: MAP-Bayesian Estimation of PK Parameters
Description: Performs maximum a posteriori Bayesian estimation of individual pharmacokinetic parameters from a model defined in 'mrgsolve', typically for model-based therapeutic drug monitoring. Internally computes an objective function value from model and data, performs optimization and returns predictions in a convenient format. The performance of the package was described by Le Louedec et al (2021) <doi:10.1002/psp4.12689>.
Author: Felicien Le Louedec [aut, cre] , Kyle T Baron [ctb]
Maintainer: Felicien Le Louedec <felicienlelouedec@proton.me>

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Package janitor updated to version 2.2.0 with previous version 2.1.0 dated 2021-01-04

Title: Simple Tools for Examining and Cleaning Dirty Data
Description: The main janitor functions can: perfectly format data.frame column names; provide quick counts of variable combinations (i.e., frequency tables and crosstabs); and explore duplicate records. Other janitor functions nicely format the tabulation results. These tabulate-and-report functions approximate popular features of SPSS and Microsoft Excel. This package follows the principles of the "tidyverse" and works well with the pipe function %>%. janitor was built with beginning-to-intermediate R users in mind and is optimized for user-friendliness.
Author: Sam Firke [aut, cre], Bill Denney [ctb], Chris Haid [ctb], Ryan Knight [ctb], Malte Grosser [ctb], Jonathan Zadra [ctb]
Maintainer: Sam Firke <samuel.firke@gmail.com>

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Package gratia updated to version 0.8.1 with previous version 0.7.3 dated 2022-05-10

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

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 gratia-0.8.1/gratia/NAMESPACE                                                                                     |   98 
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 gratia-0.8.1/gratia/R/compare-smooths.R                                                                           |    2 
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 gratia-0.8.1/gratia/R/data-sim.R                                                                                  |    2 
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New package GFDmcv with initial version 0.1.0
Package: GFDmcv
Title: General Hypothesis Testing Problems for Multivariate Coefficients of Variation
Version: 0.1.0
Date: 2023-02-02
Description: Performs test procedures for general hypothesis testing problems for four multivariate coefficients of variation (Ditzhaus and Smaga, 2023 <arXiv:2301.12009>). We can verify the global hypothesis about equality as well as the particular hypotheses defined by contrasts, e.g., we can conduct post hoc tests. We also provide the simultaneous confidence intervals for contrasts.
License: LGPL-2 | LGPL-3 | GPL-2 | GPL-3
Imports: Rcpp (>= 1.0.9), mvtnorm, doParallel, MASS, foreach, Matrix, stringr, HSAUR
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2023-02-02 13:54:19 UTC; ls
Author: Marc Ditzhaus [aut], Lukasz Smaga [aut, cre]
Maintainer: Lukasz Smaga <ls@amu.edu.pl>
Repository: CRAN
Date/Publication: 2023-02-02 17:00:02 UTC

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New package cols4all with initial version 0.6
Package: cols4all
License: GPL-3
Title: Colors for all
LazyLoad: yes
Description: Color palettes for all people, including those with color vision deficiency. Popular color palette series have been organized by type and have been scored on several properties such as color-blind-friendliness and fairness (i.e. do colors stand out equally?). Own palettes can also be loaded and analysed. Besides the common palette types (categorical, sequential, and diverging) it also includes bivariate color palettes. Furthermore, a color for missing values is assigned to each palette.
Version: 0.6
Date: 2023-01-30
Encoding: UTF-8
Depends: R (>= 3.5.0),
Imports: methods, grDevices, stats, abind, png, stringdist, colorspace (>= 2.1)
Suggests: colorblindcheck, kableExtra, knitr, shiny, shinyjs, ggplot2, scales, rmarkdown
URL: https://github.com/mtennekes/cols4all
BugReports: https://github.com/mtennekes/cols4all/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-02-01 21:38:33 UTC; mtes
Author: Martijn Tennekes [aut, cre], Marco Puts [ctb], Achim Zeileis [ctb], Jakub Nowosad [ctb], Robin Lovelace [ctb], Helgasoft [ctb], Matthew Petroff [ctb]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Repository: CRAN
Date/Publication: 2023-02-02 16:30:02 UTC

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Package cdrcR updated to version 0.1.0 with previous version 0.0.1 dated 2021-11-19

Title: Load 'CDRC' Data
Description: A wrapper for the 'CDRC' 'API' that returns data frames or 'sf' of 'CDRC' data. The 'API' web reference is:<https://api.cdrc.ac.uk/swagger/index.html>.
Author: Alessia Calafiore [aut, cre]
Maintainer: Alessia Calafiore <aelissa3388@gmail.com>

Diff between cdrcR versions 0.0.1 dated 2021-11-19 and 0.1.0 dated 2023-02-02

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New package BayesDIP with initial version 0.1.1
Package: BayesDIP
Title: Bayesian Decreasingly Informative Priors for Early Termination Phase II Trials
Version: 0.1.1
Date: 2023-1-31
Maintainer: Chen Wang <wangc10@vcu.edu>
Description: Provide early termination phase II trial designs with a decreasingly informative prior (DIP) or a regular Bayesian prior chosen by the user. The program can determine the minimum planned sample size necessary to achieve the user-specified admissible designs. The program can also perform power and expected sample size calculations for the tests in early termination Phase II trials. See Wang C and Sabo RT (2022) <doi:10.18203/2349-3259.ijct20221110>; Sabo RT (2014) <doi:10.1080/10543406.2014.888441>.
License: GPL (>= 2)
URL: <https://github.com/chenw10/BayesDIP>
Imports: stats
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2023-02-01 18:44:53 UTC; chen
Author: Chen Wang [cre, aut], Roy Sabo [aut]
Repository: CRAN
Date/Publication: 2023-02-02 16:20:05 UTC

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Package DecomposeR updated to version 1.0.6 with previous version 1.0.5 dated 2022-12-02

Title: Empirical Mode Decomposition for Cyclostratigraphy
Description: Tools to apply Ensemble Empirical Mode Decomposition (EEMD) for cyclostratigraphy purposes. Mainly: a new algorithm, extricate, that performs EEMD in seconds, a linear interpolation algorithm using the greatest rational common divisor of depth or time, different algorithms to compute instantaneous amplitude, frequency and ratios of frequencies, and functions to verify and visualise the outputs. The functions were developed during the CRASH project (Checking the Reproducibility of Astrochronology in the Hauterivian). When using for publication please cite Wouters, S., Crucifix, M., Sinnesael, M., Da Silva, A.C., Zeeden, C., Zivanovic, M., Boulvain, F., Devleeschouwer, X., 2022, "A decomposition approach to cyclostratigraphic signal processing". Earth-Science Reviews 225 (103894). <doi:10.1016/j.earscirev.2021.103894>.
Author: Sebastien Wouters [aut, cre]
Maintainer: Sebastien Wouters <wouterseb@gmail.com>

Diff between DecomposeR versions 1.0.5 dated 2022-12-02 and 1.0.6 dated 2023-02-02

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Package chatgpt updated to version 0.1.5 with previous version 0.1.4 dated 2023-01-16

Title: Interface to 'ChatGPT' from R
Description: 'OpenAI's 'ChatGPT' <https://chat.openai.com/> coding assistant for 'RStudio'. A set of functions and 'RStudio' addins that aim to help the R developer in tedious coding tasks.
Author: Juan Cruz Rodriguez [aut, cre]
Maintainer: Juan Cruz Rodriguez <jcrodriguez@unc.edu.ar>

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Package presenter updated to version 0.1.2 with previous version 0.1.1 dated 2021-11-18

Title: Present Data with Style
Description: Consists of custom wrapper functions using packages 'openxlsx', 'flextable', and 'officer' to create highly formatted MS office friendly output of your data frames. These viewer friendly outputs are intended to match expectations of professional looking presentations in business and consulting scenarios. The functions are opinionated in the sense that they expect the input data frame to have certain properties in order to take advantage of the automated formatting.
Author: Harrison Tietze [aut, cre]
Maintainer: Harrison Tietze <Harrison4192@gmail.com>

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New package SampleSizeMeans with initial version 1.2
Package: SampleSizeMeans
Title: Sample Size Calculations for Normal Means
Version: 1.2
Date: 2023-02-01
Description: Sample size requirements calculation using three different Bayesian criteria in the context of designing an experiment to estimate a normal mean or the difference between two normal means. Functions for calculation of required sample sizes for the Average Length Criterion, the Average Coverage Criterion and the Worst Outcome Criterion in the context of normal means are provided. Functions for both the fully Bayesian and the mixed Bayesian/likelihood approaches are provided. For reference see Joseph L. and B\'elisle P. (1997) <https://www.jstor.org/stable/2988525>.
Imports: stats
License: GPL (>= 2)
Repository: CRAN
NeedsCompilation: no
Packaged: 2023-02-01 10:59:00 UTC; Patrick
Author: Lawrence Joseph [aut], Patrick Belisle [aut, cre]
Maintainer: Patrick Belisle <patrickb.stat@gmail.com>
Date/Publication: 2023-02-02 13:10:06 UTC

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New package echoice2 with initial version 0.2.0
Package: echoice2
Title: Choice Models with Economic Foundation
Version: 0.2.0
Date: 2023-01-02
Maintainer: Nino Hardt <me@ninohardt.com>
Description: Implements choice models based on economic theory, including estimation using Markov chain Monte Carlo (MCMC), prediction, and more. Its usability is inspired by ideas from 'tidyverse'. Models include versions of the Hierarchical Multinomial Logit and Multiple Discrete-Continous (Volumetric) models with and without screening. The foundations of these models are described in Allenby, Hardt and Rossi (2019) <doi:10.1016/bs.hem.2019.04.002>. Models with conjunctive screening are described in Kim, Hardt, Kim and Allenby (2022) <doi:10.1016/j.ijresmar.2022.04.001>. Models with set-size variation are described in Hardt and Kurz (2020) <doi:10.2139/ssrn.3418383>.
License: MIT + file LICENSE
URL: http://ninohardt.de/echoice2/
Imports: Rcpp (>= 1.0.1), parallel (>= 4.0), magrittr, stats, graphics, stringr, purrr, tibble (>= 2.1.3), tidyselect (>= 1.2.0), tidyr, rlang (>= 1.0.6), forcats
Depends: R (>= 3.5), dplyr, ggplot2
Suggests: testthat (>= 3.0.0)
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
SystemRequirements: OpenMP
NeedsCompilation: yes
Packaged: 2023-02-01 11:34:28 UTC; myself
Author: Nino Hardt [aut, cre]
Repository: CRAN
Date/Publication: 2023-02-02 13:10:02 UTC

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New package OlympicRshiny with initial version 1.0.0
Package: OlympicRshiny
Title: 'Shiny' Application for Olympic Data
Version: 1.0.0
Description: 'Shiny' Application to visualize Olympic Data. From 1896 to 2016. Even Winter Olympics events are included. Data is from Kaggle at <https://www.kaggle.com/heesoo37/120-years-of-olympic-history-athletes-and-results>.
License: MIT + file LICENSE
URL: https://github.com/Amalan-ConStat/OlympicRshiny, https://amalan-con-stat.shinyapps.io/OlympicRshiny/, https://amalan-con-stat.shinyapps.io/olympic/
BugReports: https://github.com/Amalan-ConStat/OlympicRshiny/issues
Depends: R (>= 2.10)
Imports: config (>= 0.3.1), dplyr, forcats, ggplot2, golem (>= 0.3.5), shiny (>= 1.7.4), shinybusy, shinythemes, summarytools
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2023-02-01 06:36:04 UTC; amala
Author: Amalan Mahendran [cre, aut]
Maintainer: Amalan Mahendran <amalan0595@gmail.com>
Repository: CRAN
Date/Publication: 2023-02-02 13:00:03 UTC

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New package MetChem with initial version 0.2
Package: MetChem
Version: 0.2
Date: 2023-02-01
Maintainer: Stefano Cacciatore <tkcaccia@gmail.com>
Title: Chemical Structural Similarity Analysis
Description: A new pipeline to explore chemical structural similarity across metabolite. It allows to classify metabolites in structurally-related modules and identify common shared functional groups. KODAMA algorithm is used to highlight structural similarity between metabolites. See Cacciatore S, Tenori L, Luchinat C, Bennett PR, MacIntyre DA. (2017) Bioinformatics <doi:10.1093/bioinformatics/btw705> and Cacciatore S, Luchinat C, Tenori L. (2014) Proc Natl Acad Sci USA <doi:10.1073/pnas.1220873111>.
Depends: R (>= 3.5.0), stats, KODAMA (>= 2.3), httr, XML, fingerprint, rcdk (>= 3.4.3)
Suggests: knitr, rmarkdown, readxl, impute, pheatmap, RColorBrewer
VignetteBuilder: knitr
SuggestsNote: No suggestions
License: GPL (>= 2)
Packaged: 2023-02-01 07:26:50 UTC; stefano
NeedsCompilation: no
Repository: CRAN
Author: Ebtesam Abdel-Shafy [aut], Tadele Melak [aut], David A. MacIntyre [aut], Giorgia Zadra [aut], Luiz F. Zerbini [aut], Silvano Piazza [aut], Stefano Cacciatore [aut, cre]
Date/Publication: 2023-02-02 13:00:05 UTC

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New package connectapi with initial version 0.1.3.1
Package: connectapi
Title: Utilities for Interacting with the 'Posit Connect' Server API
Version: 0.1.3.1
Description: Provides a helpful 'R6' class and methods for interacting with the 'Posit Connect' Server API along with some meaningful utility functions for regular tasks. API documentation varies by 'Posit Connect' installation and version, but the latest documentation is also hosted publicly at <https://docs.posit.co/connect/api/>.
License: MIT + file LICENSE
URL: https://github.com/rstudio/connectapi
Imports: config, dplyr, fs, glue, httr, lifecycle, magrittr, progress, purrr, R6, rlang (>= 0.4.2), tibble, uuid, vctrs (>= 0.3.0), yaml, bit64, jsonlite
Suggests: crayon, flexdashboard, ggplot2, gridExtra, htmltools, knitr, lubridate, processx, rmarkdown, rprojroot, spelling, testthat, rsconnect, webshot2, covr, mockery, devtools
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2023-02-01 00:02:36 UTC; colearendt
Author: Sean Lopp [aut], Cole Arendt [aut, cre], Posit, PBC [cph, fnd]
Maintainer: Cole Arendt <cole@posit.co>
Repository: CRAN
Date/Publication: 2023-02-02 12:50:02 UTC

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Package SoilHyP updated to version 0.1.7 with previous version 0.1.6 dated 2022-05-25

Title: Soil Hydraulic Properties
Description: Provides functions for (1) soil water retention (SWC) and unsaturated hydraulic conductivity (Ku) (van Genuchten-Mualem (vGM or vG) [1, 2], Peters-Durner-Iden (PDI) [3, 4, 5], Brooks and Corey (bc) [8]), (2) fitting of parameter for SWC and/or Ku using Shuffled Complex Evolution (SCE) optimisation and (3) calculation of soil hydraulic properties (Ku and soil water contents) based on the simplified evaporation method (SEM) [6, 7]. Main references: [1] van Genuchten (1980) <doi:10.2136/sssaj1980.03615995004400050002x>, [2] Mualem (1976) <doi:10.1029/WR012i003p00513>, [3] Peters (2013) <doi:10.1002/wrcr.20548>, [4] Iden and Durner (2013) <doi:10.1002/2014WR015937>, [5] Peters (2014) <doi:10.1002/2014WR015937>, [6] Wind G. P. (1966), [7] Peters and Durner (2008) <doi:10.1016/j.jhydrol.2008.04.016> and [8] Brooks and Corey (1964).
Author: Ullrich Dettmann [aut, cre], Felix Andrews [ctb] which is not on r-cran . The SCEoptim function is adapted, and substantially revised from Brecht Donckels MATLAB code which is in turn adopted from Qingyun Duans MATLAB code), Brecht Donckels [ctb] , [...truncated...]
Maintainer: Ullrich Dettmann <ullrich.dettmann@thuenen.de>

Diff between SoilHyP versions 0.1.6 dated 2022-05-25 and 0.1.7 dated 2023-02-02

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Package rlibkriging updated to version 0.7-4.2 with previous version 0.7-4.1 dated 2023-01-17

Title: Kriging Models using the 'libKriging' Library
Description: Interface to 'libKriging' 'C++' library <https://github.com/libKriging> that should provide most standard Kriging / Gaussian process regression features (like in 'DiceKriging', 'kergp' or 'RobustGaSP' packages). 'libKriging' relies on Armadillo linear algebra library (Apache 2 license) by Conrad Sanderson, and 'lbfgsb_cpp' is a 'C++' wrapper by Colin Fang around 'lbfgsb' library (BSD-3 license) by Ciyou Zhu, Richard Byrd, Jorge Nocedal and Jose Luis Morales used for hyperparameters optimization.
Author: Pascal Have [aut], Yann Richet [aut, cre] , Yves Deville [aut], Conrad Sanderson [ctb], Colin Fang [ctb], Ciyou Zhu [ctb], Richard Byrd [ctb], Jorge Nocedal [ctb], Jose Luis Morales [ctb]
Maintainer: Yann Richet <yann.richet@irsn.fr>

Diff between rlibkriging versions 0.7-4.1 dated 2023-01-17 and 0.7-4.2 dated 2023-02-02

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Package OCNet updated to version 0.6.0 with previous version 0.5.1 dated 2022-12-15

Title: Optimal Channel Networks
Description: Generate and analyze Optimal Channel Networks (OCNs): oriented spanning trees reproducing all scaling features characteristic of real, natural river networks. As such, they can be used in a variety of numerical experiments in the fields of hydrology, ecology and epidemiology. See Carraro et al. (2020) <doi:10.1002/ece3.6479> for a presentation of the package; Rinaldo et al. (2014) <doi:10.1073/pnas.1322700111> for a theoretical overview on the OCN concept; Furrer and Sain (2010) <doi:10.18637/jss.v036.i10> for the construct used.
Author: Luca Carraro [aut, cre], Florian Altermatt [ctb], Emanuel A. Fronhofer [ctb], Reinhard Furrer [ctb], Isabelle Gounand [ctb], Andrea Rinaldo [ctb], Enrico Bertuzzo [aut]
Maintainer: Luca Carraro <luca.carraro@hotmail.it>

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Package stevetemplates updated to version 0.9.0 with previous version 0.8.0 dated 2022-09-29

Title: Steve's R Markdown Templates
Description: These are my collection of 'R Markdown' templates, mostly for compilation to PDF. These are useful for all things academic and professional, if you are using 'R Markdown' for things like your CV or your articles and manuscripts.
Author: Steven V. Miller
Maintainer: Steven V. Miller <steven.v.miller@gmail.com>

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Package paws.common updated to version 0.5.5 with previous version 0.5.4 dated 2023-01-11

Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services <https://aws.amazon.com>. The functions handle building, signing, and sending requests, and receiving responses. They are designed to help build higher-level interfaces to individual services, such as Simple Storage Service (S3).
Author: David Kretch [aut], Adam Banker [aut], Dyfan Jones [cre], Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>

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Package schemr updated to version 0.2.0 with previous version 0.1.0 dated 2021-03-10

Title: Convert Images to Usable Color Schemes
Description: A fast and adaptable tool to convert photos and images into usable colour schemes for data visualisation. Contains functionality to extract colour palettes from images, as well for the conversion of images between colour spaces.
Author: Stuart Morrison [aut, cre]
Maintainer: Stuart Morrison <smorrison@ucdavis.edu>

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Package naniar updated to version 1.0.0 with previous version 0.6.1 dated 2021-05-14

Title: Data Structures, Summaries, and Visualisations for Missing Data
Description: Missing values are ubiquitous in data and need to be explored and handled in the initial stages of analysis. 'naniar' provides data structures and functions that facilitate the plotting of missing values and examination of imputations. This allows missing data dependencies to be explored with minimal deviation from the common work patterns of 'ggplot2' and tidy data. The work is fully discussed at Tierney & Cook (2023) <doi:10.18637/jss.v105.i07>.
Author: Nicholas Tierney [aut, cre] , Di Cook [aut] , Miles McBain [aut] , Colin Fay [aut] , Mitchell O'Hara-Wild [ctb], Jim Hester [ctb], Luke Smith [ctb], Andrew Heiss [ctb]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>

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Package LMfilteR updated to version 0.1.3.1 with previous version 0.1.3 dated 2020-10-12

Title: Filter Methods for Parameter Estimation in Linear and Non Linear Regression Models
Description: We present a method based on filtering algorithms to estimate the parameters of linear, i.e. the coefficients and the variance of the error term. The proposed algorithms make use of Particle Filters following Ristic, B., Arulampalam, S., Gordon, N. (2004, ISBN: 158053631X) resampling methods. Parameters of logistic regression models are also estimated using an evolutionary particle filter method.
Author: Christian Llano Robayo [aut, cre], Nazrul Shaikh [aut], Pegu Nilutpal [aut]
Maintainer: Christian Llano Robayo <info@cecareus.com>

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Package emhawkes updated to version 0.9.7 with previous version 0.9.5 dated 2021-02-16

Title: Exponential Multivariate Hawkes Model
Description: Simulate and fitting exponential multivariate Hawkes model. This package simulates a multivariate Hawkes model, introduced by Hawkes (1971) <doi:10.2307/2334319>, with an exponential kernel and fits the parameters from the data. Models with the constant parameters, as well as complex dependent structures, can also be simulated and estimated. The estimation is based on the maximum likelihood method, introduced by introduced by Ozaki (1979) <doi:10.1007/BF02480272>, with 'maxLik' package.
Author: Kyungsub Lee [aut, cre]
Maintainer: Kyungsub Lee <kyungsub@gmail.com>

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Package diemr updated to version 1.1.1 with previous version 1.1 dated 2022-10-19

Title: Diagnostic Index Expectation Maximisation in R
Description: Likelihood-based genome polarisation finds which alleles of genomic markers belong to which side of the barrier. Co-estimates which individuals belong to either side of the barrier and barrier strength. Uses expectation maximisation in likelihood framework. The method is described in Baird et al. (2022) <doi:10.1111/2041-210X.14010>.
Author: Natalia Martinkova [aut, cre] , Stuart Baird [aut]
Maintainer: Natalia Martinkova <martinkova@ivb.cz>

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Package barplot3d (with last version 1.0.1) was removed from CRAN

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Package animalTrack (with last version 1.0.0) was removed from CRAN

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Package AIG (with last version 0.1.9) was removed from CRAN

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Wed, 01 Feb 2023

Package visdat updated to version 0.6.0 with previous version 0.5.3 dated 2019-02-15

Title: Preliminary Visualisation of Data
Description: Create preliminary exploratory data visualisations of an entire dataset to identify problems or unexpected features using 'ggplot2'.
Author: Nicholas Tierney [aut, cre] , Sean Hughes [rev] , Mara Averick [rev] , Stuart Lee [ctb], Earo Wang [ctb], Nic Crane [ctb], Christophe Regouby [ctb]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>

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Package sparrpowR updated to version 0.2.7 with previous version 0.2.6 dated 2022-12-02

Title: Power Analysis to Detect Spatial Relative Risk Clusters
Description: Calculate the statistical power to detect clusters using kernel-based spatial relative risk functions that are estimated using the 'sparr' package. Details about the 'sparr' package methods can be found in the tutorial: Davies et al. (2018) <doi:10.1002/sim.7577>. Details about kernel density estimation can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>. More information about relative risk functions using kernel density estimation can be found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.
Author: Ian D. Buller [aut, cre, cph] , Derek W. Brown [aut, cph] , Mitchell J. Machiela [ctb] , Timothy A. Myers [ctb], NCI [cph, fnd]
Maintainer: Ian D. Buller <ian.buller@alumni.emory.edu>

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Package r2rtf updated to version 1.0.1 with previous version 1.0.0 dated 2023-01-11

Title: Easily Create Production-Ready Rich Text Format (RTF) Table and Figure
Description: Create production-ready Rich Text Format (RTF) table and figure with flexible format.
Author: Yilong Zhang [aut, cre], Siruo Wang [aut], Simiao Ye [aut], Fansen Kong [aut], Brian Lang [aut], Nan Xiao [ctb], Madhusudhan Ginnaram [ctb], Ruchitbhai Patel [ctb], Huei-Ling Chen [ctb], Peikun Wu [ctb], Uday Preetham Palukuru [ctb], Daniel Woodie [c [...truncated...]
Maintainer: Yilong Zhang <elong0527@gmail.com>

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Package envi updated to version 0.1.17 with previous version 0.1.15 dated 2022-08-30

Title: Environmental Interpolation using Spatial Kernel Density Estimation
Description: Estimates an ecological niche using occurrence data, covariates, and kernel density-based estimation methods. For a single species with presence and absence data, the 'envi' package uses the spatial relative risk function that is estimated using the 'sparr' package. Details about the 'sparr' package methods can be found in the tutorial: Davies et al. (2018) <doi:10.1002/sim.7577>. Details about kernel density estimation can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>. More information about relative risk functions using kernel density estimation can be found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.
Author: Ian D. Buller [aut, cre, cph] , Lance A. Waller [ctb, ths] , Emory University [cph]
Maintainer: Ian D. Buller <ian.buller@alumni.emory.edu>

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Package not updated to version 1.5 with previous version 1.4 dated 2022-10-06

Title: Narrowest-Over-Threshold Change-Point Detection
Description: Provides efficient implementation of the Narrowest-Over-Threshold methodology for detecting an unknown number of change-points occurring at unknown locations in one-dimensional data following 'deterministic signal + noise' model. Currently implemented scenarios are: piecewise-constant signal, piecewise-constant signal with a heavy-tailed noise, piecewise-linear signal, piecewise-quadratic signal, piecewise-constant signal and with piecewise-constant variance of the noise. For details, see Baranowski, Chen and Fryzlewicz (2019) <doi:10.1111/rssb.12322>.
Author: Rafal Baranowski, Yining Chen, Piotr Fryzlewicz
Maintainer: Yining Chen <Y.Chen101@lse.ac.uk>

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Package gateR updated to version 0.1.13 with previous version 0.1.12 dated 2022-12-01

Title: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation
Description: Estimates statistically significant marker combination values within which one immunologically distinctive group (i.e., disease case) is more associated than another group (i.e., healthy control), successively, using various combinations (i.e., "gates") of markers to examine features of cells that may be different between groups. For a two-group comparison, the 'gateR' package uses the spatial relative risk function estimated using the 'sparr' package. Details about the 'sparr' package methods can be found in the tutorial: Davies et al. (2018) <doi:10.1002/sim.7577>. Details about kernel density estimation can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>. More information about relative risk functions using kernel density estimation can be found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.
Author: Ian D. Buller [aut, cre, cph] , Elena Hsieh [ctb] , Debashis Ghosh [ctb] , Lance A. Waller [ctb] , NCI [cph]
Maintainer: Ian D. Buller <ian.buller@alumni.emory.edu>

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Package taskscheduleR updated to version 1.7 with previous version 1.6 dated 2022-03-16

Title: Schedule R Scripts and Processes with the Windows Task Scheduler
Description: Schedule R scripts/processes with the Windows task scheduler. This allows R users to automate R processes on specific time points from R itself.
Author: Jan Wijffels [aut, cre, cph], BNOSAC [cph], Oliver Belmans [cph, aut]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>

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Package epanet2toolkit updated to version 0.6.2 with previous version 0.5.1 dated 2021-04-22

Title: Call 'EPANET' Functions to Simulate Pipe Networks
Description: Enables simulation of water piping networks using 'EPANET'. The package provides functions from the 'EPANET' programmer's toolkit as R functions so that basic or customized simulations can be carried out from R. The package uses 'EPANET' version 2.2 from Open Water Analytics <https://github.com/OpenWaterAnalytics/EPANET/releases/tag/v2.2>.
Author: Ernesto Arandia [aut], Bradley Eck [aut, cre], Lew Rossman [aut], Michael Tryby [ctb], Sam Hatchett [ctb], Feng Shang [ctb], James Uber [ctb], Tom Taxon [ctb], Hyoungmin Woo [ctb], Jinduan Chen [ctb], Yunier Soad [ctb], Mike Kane [ctb], Demetrios Eli [...truncated...]
Maintainer: Bradley Eck <brad@bradeck.net>

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Package tidygraph updated to version 1.2.3 with previous version 1.2.2 dated 2022-08-22

Title: A Tidy API for Graph Manipulation
Description: A graph, while not "tidy" in itself, can be thought of as two tidy data frames describing node and edge data respectively. 'tidygraph' provides an approach to manipulate these two virtual data frames using the API defined in the 'dplyr' package, as well as provides tidy interfaces to a lot of common graph algorithms.
Author: Thomas Lin Pedersen [cre, aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>

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Package rstatix updated to version 0.7.2 with previous version 0.7.1 dated 2022-11-09

Title: Pipe-Friendly Framework for Basic Statistical Tests
Description: Provides a simple and intuitive pipe-friendly framework, coherent with the 'tidyverse' design philosophy, for performing basic statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses. The output of each test is automatically transformed into a tidy data frame to facilitate visualization. Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix. Functions are also included to facilitate the analysis of factorial experiments, including purely 'within-Ss' designs (repeated measures), purely 'between-Ss' designs, and mixed 'within-and-between-Ss' designs. It's also possible to compute several effect size metrics, including "eta squared" for ANOVA, "Cohen's d" for t-test and 'Cramer V' for the association between categorical variables. The package contains helper functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances.
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>

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Package morphomap updated to version 1.4 with previous version 1.3 dated 2020-12-16

Title: Morphometric Maps, Bone Landmarking and Cross Sectional Geometry
Description: Extract cross sections from long bone meshes at specified intervals along the diaphysis. Calculate two and three-dimensional morphometric maps, cross-sectional geometric parameters, and semilandmarks on the periosteal and endosteal contours of each cross section.
Author: Antonio Profico [aut, cre], Luca Bondioli [aut], Pasquale Raia [aut], Julien Claude [ctb], Paul O'Higgins [aut], Damiano Marchi [aut]
Maintainer: Antonio Profico <antonio.profico@gmail.com>

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Package cat2cat updated to version 0.4.6 with previous version 0.4.5 dated 2022-09-25

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

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Package umap updated to version 0.2.10.0 with previous version 0.2.9.0 dated 2022-08-25

Title: Uniform Manifold Approximation and Projection
Description: Uniform manifold approximation and projection is a technique for dimension reduction. The algorithm was described by McInnes and Healy (2018) in <arXiv:1802.03426>. This package provides an interface for two implementations. One is written from scratch, including components for nearest-neighbor search and for embedding. The second implementation is a wrapper for 'python' package 'umap-learn' (requires separate installation, see vignette for more details).
Author: Tomasz Konopka [aut, cre]
Maintainer: Tomasz Konopka <tokonopka@gmail.com>

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