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 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>

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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>

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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>

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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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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>

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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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 116 files changed, 9791 insertions(+), 8754 deletions(-)

More information about rempsyc at CRAN
Permanent link

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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 RcppAlgos-2.6.0/RcppAlgos/src/PollardRho.cpp                                 |only
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 RcppAlgos-2.7.1/RcppAlgos/inst/doc/GeneralCombinatorics.html                 |  575 +++---
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 RcppAlgos-2.7.1/RcppAlgos/inst/include/CheckReturn.h                         |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/ClassUtils/ClassUtils.h               |   41 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/ClassUtils/ComboApplyClass.h          |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/ClassUtils/ComboClass.h               |   13 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/ClassUtils/ComboResClass.h            |    9 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/ClassUtils/GetPrevCombPerm.h          |    7 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/ClassUtils/GetPrevCombPermApply.h     |    7 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/ClassUtils/NextCombinatorics.h        |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/ClassUtils/PrevCombinatorics.h        |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/BigComboCount.h          |   13 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/CombinationResults.h     |   30 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/CombinationsDistinct.h   |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/CombinationsMultiset.h   |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/CombinationsRep.h        |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/ComboCount.h             |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/ComboDistinctApply.h     |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/ComboManager.h           |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/ComboMultisetApply.h     |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/ComboRepApply.h          |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/ComboResGlue.h           |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/ComboResMain.h           |    9 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/NextComboSection.h       |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/NthCombination.h         |   16 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/RankCombination.h        |    9 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Combinations/ThreadSafeComb.h         |    9 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/CombinatoricsResGlue.h                |    7 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/ComboCartesian.h                      |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/ComboGroupsUtils.h                    |   12 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/ComputedCount.h                       |   13 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Constraints/CnstrntsSpecialClass.h    |    7 
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 RcppAlgos-2.7.1/RcppAlgos/inst/include/GetCombPerm.h                         |    9 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/GetCombPermApply.h                    |    7 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/NthResult.h                           |   11 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/NumbersUtils/Eratosthenes.h           |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/NumbersUtils/EulerPhiSieve.h          |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/NumbersUtils/MotleyStartIndex.h       |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/NumbersUtils/PhiTinyLookup.h          |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/NumbersUtils/PollardRhoDepends.h      |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/NumbersUtils/PollardRhoUtils.h        |   18 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/NumbersUtils/PrimeFactorizeSieve.h    |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/NumbersUtils/PrimesPolRho.h           |   63 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/NumbersUtils/PrimesSegSieve.h         |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/NumbersUtils/Wheel.h                  |  493 ++---
 RcppAlgos-2.7.1/RcppAlgos/inst/include/NumbersUtils/libdivide.h              |  377 ++-
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/BigPartsCountDistinct.h    |   30 
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 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/PartitionsMultiset.h       |    7 
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 RcppAlgos-2.7.1/RcppAlgos/inst/include/Partitions/ThreadSafeParts.h          |   15 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/BigPermuteCount.h        |   13 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/NextPermSectionRep.h     |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/NextPermutation.h        |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/NthPermutation.h         |   10 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermutationResults.h     |   32 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermutationsDistinct.h   |   57 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermutationsMultiset.h   |   67 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermutationsRep.h        |   25 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermuteCount.h           |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermuteDistinctApply.h   |   10 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermuteHelper.h          |    7 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermuteManager.h         |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermuteMultisetApply.h   |   10 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermuteOptimized.h       |    8 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermuteRepApply.h        |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermuteResGlue.h         |    5 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/PermuteResMain.h         |   10 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/RankPermutation.h        |    9 
 RcppAlgos-2.7.1/RcppAlgos/inst/include/Permutations/ThreadSafePerm.h         |    9 
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 RcppAlgos-2.7.1/RcppAlgos/man/comboGroups.Rd                                 |    2 
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 RcppAlgos-2.7.1/RcppAlgos/man/primeSieve.Rd                                  |    3 
 RcppAlgos-2.7.1/RcppAlgos/src/BigComboCount.cpp                              |   99 -
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 RcppAlgos-2.7.1/RcppAlgos/src/BigPermuteCount.cpp                            |   80 
 RcppAlgos-2.7.1/RcppAlgos/src/CartesianContainer.cpp                         |    2 
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 RcppAlgos-2.7.1/RcppAlgos/src/CombinatoricsApply.cpp                         |   29 
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 RcppAlgos-2.7.1/RcppAlgos/src/ComboApplyClass.cpp                            |   75 
 RcppAlgos-2.7.1/RcppAlgos/src/ComboCartesian.cpp                             |   57 
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 RcppAlgos-2.7.1/RcppAlgos/src/ComboCount.cpp                                 |   15 
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 RcppAlgos-2.7.1/RcppAlgos/src/ComboGroupsUtils.cpp                           |   63 
 RcppAlgos-2.7.1/RcppAlgos/src/ComboResClass.cpp                              |   58 
 RcppAlgos-2.7.1/RcppAlgos/src/ComboResMain.cpp                               |   10 
 RcppAlgos-2.7.1/RcppAlgos/src/CompositionsRep.cpp                            |   67 
 RcppAlgos-2.7.1/RcppAlgos/src/ComputedCount.cpp                              |    6 
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 RcppAlgos-2.7.1/RcppAlgos/src/ConstraintsSpecial.cpp                         |    6 
 RcppAlgos-2.7.1/RcppAlgos/src/ConstraintsUtils.cpp                           |   15 
 RcppAlgos-2.7.1/RcppAlgos/src/ConvertUtils.cpp                               |only
 RcppAlgos-2.7.1/RcppAlgos/src/DivNumSieve.cpp                                |  110 -
 RcppAlgos-2.7.1/RcppAlgos/src/ExposeClass.cpp                                |   38 
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 RcppAlgos-2.7.1/RcppAlgos/src/GetClassVals.cpp                               |   30 
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 RcppAlgos-2.7.1/RcppAlgos/src/GetCombPermApply.cpp                           |    2 
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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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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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Sun, 05 Feb 2023

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>

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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/DESCRIPTION                                                                    |   14 
 JSmediation-0.2.1/JSmediation/LICENSE                                                                        |    4 
 JSmediation-0.2.1/JSmediation/MD5                                                                            |  180 
 JSmediation-0.2.1/JSmediation/NAMESPACE                                                                      |  112 
 JSmediation-0.2.1/JSmediation/NEWS.md                                                                        |   96 
 JSmediation-0.2.1/JSmediation/R/JSmediation-package.R                                                        |only
 JSmediation-0.2.1/JSmediation/R/add_index.R                                                                  |   48 
 JSmediation-0.2.1/JSmediation/R/apastylr.R                                                                   |  118 
 JSmediation-0.2.1/JSmediation/R/build_contrast.R                                                             |  112 
 JSmediation-0.2.1/JSmediation/R/check_assumptions.R                                                          |  188 
 JSmediation-0.2.1/JSmediation/R/check_variables.R                                                            |  100 
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 JSmediation-0.2.1/JSmediation/R/create_path.R                                                                |   48 
 JSmediation-0.2.1/JSmediation/R/display_models.R                                                             |   74 
 JSmediation-0.2.1/JSmediation/R/dohle_siegrist.R                                                             |   58 
 JSmediation-0.2.1/JSmediation/R/dohle_siegrist_w.R                                                           |   58 
 JSmediation-0.2.1/JSmediation/R/extract_models.R                                                             |  250 
 JSmediation-0.2.1/JSmediation/R/ho_et_al.R                                                                   |   70 
 JSmediation-0.2.1/JSmediation/R/indirect_effect-methods.R                                                    |   48 
 JSmediation-0.2.1/JSmediation/R/indirect_effect_class.R                                                      |   54 
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 JSmediation-0.2.1/JSmediation/R/mdt_simple.R                                                                 |  330 
 JSmediation-0.2.1/JSmediation/R/mdt_simple_index.R                                                           |  134 
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 JSmediation-0.2.1/JSmediation/R/mdt_within_index.R                                                           |  134 
 JSmediation-0.2.1/JSmediation/R/mdt_within_wide.R                                                            |  316 
 JSmediation-0.2.1/JSmediation/R/mediation_model_class.R                                                      |   62 
 JSmediation-0.2.1/JSmediation/R/mediation_model_print.R                                                      |  116 
 JSmediation-0.2.1/JSmediation/R/plot_assumptions.R                                                           |  262 
 JSmediation-0.2.1/JSmediation/R/standarize_variable.R                                                        |  134 
 JSmediation-0.2.1/JSmediation/R/utils-glue.R                                                                 |   34 
 JSmediation-0.2.1/JSmediation/R/utils-pipe.R                                                                 |   22 
 JSmediation-0.2.1/JSmediation/R/utils-tidy-eval.R                                                            |   80 
 JSmediation-0.2.1/JSmediation/R/zzz.R                                                                        |   64 
 JSmediation-0.2.1/JSmediation/README.md                                                                      |  318 
 JSmediation-0.2.1/JSmediation/build/vignette.rds                                                             |binary
 JSmediation-0.2.1/JSmediation/inst/apa.csl                                                                   | 3832 +++----
 JSmediation-0.2.1/JSmediation/inst/doc/jsmediation.R                                                         |   94 
 JSmediation-0.2.1/JSmediation/inst/doc/jsmediation.Rmd                                                       |  498 
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 JSmediation-0.2.1/JSmediation/man/apastylr.Rd                                                                |   54 
 JSmediation-0.2.1/JSmediation/man/build_contrast.Rd                                                          |   86 
 JSmediation-0.2.1/JSmediation/man/check_assumptions.Rd                                                       |  104 
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 JSmediation-0.2.1/JSmediation/man/display_models.Rd                                                          |   66 
 JSmediation-0.2.1/JSmediation/man/dohle_siegrist.Rd                                                          |   74 
 JSmediation-0.2.1/JSmediation/man/dohle_siegrist_wide.Rd                                                     |   76 
 JSmediation-0.2.1/JSmediation/man/extract_model.Rd                                                           |   88 
 JSmediation-0.2.1/JSmediation/man/extract_models.Rd                                                          |   78 
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 JSmediation-0.2.1/JSmediation/man/pipe.Rd                                                                    |   24 
 JSmediation-0.2.1/JSmediation/man/plot_assumptions.Rd                                                        |   98 
 JSmediation-0.2.1/JSmediation/man/print.indirect_index.Rd                                                    |   39 
 JSmediation-0.2.1/JSmediation/man/print.mediation_model.Rd                                                   |   38 
 JSmediation-0.2.1/JSmediation/man/standardize_variable.Rd                                                    |   96 
 JSmediation-0.2.1/JSmediation/man/tidyeval.Rd                                                                |   94 
 JSmediation-0.2.1/JSmediation/tests/testthat.R                                                               |    8 
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 JSmediation-0.2.1/JSmediation/tests/testthat/test-apastylr.R                                                 |   34 
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 JSmediation-0.2.1/JSmediation/tests/testthat/test-display_models.R                                           |   26 
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 JSmediation-0.2.1/JSmediation/tests/testthat/test-indirect_effect-methods.R                                  |   30 
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 JSmediation-0.2.1/JSmediation/tests/testthat/test-mdt_within_wide.R                                          |   56 
 JSmediation-0.2.1/JSmediation/tests/testthat/test-plot_assumptions.R                                         |   96 
 JSmediation-0.2.1/JSmediation/tests/testthat/test-standarize_variable.R                                      |  150 
 JSmediation-0.2.1/JSmediation/vignettes/jsmediation.Rmd                                                      |  498 
 JSmediation-0.2.1/JSmediation/vignettes/moderated-mediation.Rmd                                              |  312 
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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>

Diff between AirMonitor versions 0.2.2 dated 2022-03-31 and 0.3.9 dated 2023-02-05

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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 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 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>

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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>

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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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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>

Diff between RItools versions 0.3-1 dated 2022-08-10 and 0.3-2 dated 2023-02-03

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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>

Diff between UKFE versions 0.2.6 dated 2023-01-23 and 0.2.7 dated 2023-02-03

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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>

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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>

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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>

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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>

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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>

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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>

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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>

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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>

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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>

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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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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>

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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>

Diff between CSMES versions 1.0.0 dated 2020-02-22 and 1.0.1 dated 2023-02-03

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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>

Diff between chronicler versions 0.2.0 dated 2022-05-17 and 0.2.1 dated 2023-02-03

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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>

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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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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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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>

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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>

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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>

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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>

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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>

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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>

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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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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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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>

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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>

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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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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>

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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>

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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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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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Package lpSolve updated to version 5.6.18 with previous version 5.6.17 dated 2022-10-10

Title: Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs
Description: Lp_solve is freely available (under LGPL 2) software for solving linear, integer and mixed integer programs. In this implementation we supply a "wrapper" function in C and some R functions that solve general linear/integer problems, assignment problems, and transportation problems. This version calls lp_solve version 5.5.
Author: Michel Berkelaar and others
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>

Diff between lpSolve versions 5.6.17 dated 2022-10-10 and 5.6.18 dated 2023-02-01

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Package geoelectrics updated to version 0.2.2 with previous version 0.2.0 dated 2018-08-28

Title: 3D-Visualization of Geoelectric Resistivity Measurement Profiles
Description: Visualizes two-dimensional geoelectric resistivity measurement profiles in three dimensions.
Author: Anja Kleebaum <kleebaum@informatik.uni-heidelberg.de>
Maintainer: Anja Kleebaum <kleebaum@informatik.uni-heidelberg.de>

Diff between geoelectrics versions 0.2.0 dated 2018-08-28 and 0.2.2 dated 2023-02-01

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Package nmslibR updated to version 1.0.7 with previous version 1.0.6 dated 2021-09-11

Title: Non Metric Space (Approximate) Library
Description: A Non-Metric Space Library ('NMSLIB' <https://github.com/nmslib/nmslib>) wrapper, which according to the authors "is an efficient cross-platform similarity search library and a toolkit for evaluation of similarity search methods. The goal of the 'NMSLIB' <https://github.com/nmslib/nmslib> Library is to create an effective and comprehensive toolkit for searching in generic non-metric spaces. Being comprehensive is important, because no single method is likely to be sufficient in all cases. Also note that exact solutions are hardly efficient in high dimensions and/or non-metric spaces. Hence, the main focus is on approximate methods". The wrapper also includes Approximate Kernel k-Nearest-Neighbor functions based on the 'NMSLIB' <https://github.com/nmslib/nmslib> 'Python' Library.
Author: Lampros Mouselimis [aut, cre] , B. Naidan [cph] ), L. Boytsov [cph] ), Yu. Malkov [cph] ), B. Frederickson [cph] ), D. Novak [cph] )
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>

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Package visachartR updated to version 3.0.0 with previous version 2.2.0 dated 2023-01-20

Title: Wrapper for 'Visa Chart Components'
Description: Provides a set of wrapper functions for 'Visa Chart Components'. 'Visa Chart Components' <https://github.com/visa/visa-chart-components> is an accessibility focused, framework agnostic set of data experience design systems components for the web.
Author: Christopher DeMartini [aut, cre], Stephanie Modica [aut], David Kutas [aut], Jaime Tanner [aut], Frank Elavsky [aut], Wojtek Kostelecki [ctb], Visa Data Experience Team [aut, fnd], Visa, Inc. [cph]
Maintainer: Christopher DeMartini <chris.demartini.npm@gmail.com>

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Package tinytex updated to version 0.44 with previous version 0.43 dated 2022-12-13

Title: Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform, portable, and easy-to-maintain version of 'TeX Live'. This package also contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] , RStudio, PBC [cph], Christophe Dervieux [ctb] , Devon Ryan [ctb] , Ethan Heinzen [ctb], Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

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Package MachineShop updated to version 3.6.1 with previous version 3.6.0 dated 2022-09-05

Title: Machine Learning Models and Tools
Description: Meta-package for statistical and machine learning with a unified interface for model fitting, prediction, performance assessment, and presentation of results. Approaches for model fitting and prediction of numerical, categorical, or censored time-to-event outcomes include traditional regression models, regularization methods, tree-based methods, support vector machines, neural networks, ensembles, data preprocessing, filtering, and model tuning and selection. Performance metrics are provided for model assessment and can be estimated with independent test sets, split sampling, cross-validation, or bootstrap resampling. Resample estimation can be executed in parallel for faster processing and nested in cases of model tuning and selection. Modeling results can be summarized with descriptive statistics; calibration curves; variable importance; partial dependence plots; confusion matrices; and ROC, lift, and other performance curves.
Author: Brian J Smith [aut, cre]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>

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Package ISRaD updated to version 2.4.7 with previous version 1.7.8 dated 2021-01-06

Title: Tools and Data for the International Soil Radiocarbon Database
Description: This is the central location for data and tools for the development, maintenance, analysis, and deployment of the International Soil Radiocarbon Database (ISRaD). ISRaD was developed as a collaboration between the U.S. Geological Survey Powell Center and the Max Planck Institute for Biogeochemistry. This R package provides tools for accessing and manipulating ISRaD data, compiling local data using the ISRaD data structure, and simple query and reporting functions for ISRaD. For more detailed information visit the ISRaD website at: <https://soilradiocarbon.org/>.
Author: Alison Hoyt [aut], Jeffrey Beem-Miller [aut, cre], Shane Stoner [aut], J. Grey Monroe [aut], Caitlin Hicks-Pries [aut], Paul A. Levine [aut]
Maintainer: Jeffrey Beem-Miller <jbeem@bgc-jena.mpg.de>

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Package healthyR.ai updated to version 0.0.12 with previous version 0.0.11 dated 2023-01-12

Title: The Machine Learning and AI Modeling Companion to 'healthyR'
Description: Hospital machine learning and ai data analysis workflow tools, modeling, and automations. This library provides many useful tools to review common administrative hospital data. Some of these include predicting length of stay, and readmits. The aim is to provide a simple and consistent verb framework that takes the guesswork out of everything.
Author: Steven Sanderson [aut, cre, cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>

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Package RTransferEntropy updated to version 0.2.21 with previous version 0.2.14 dated 2021-04-02

Title: Measuring Information Flow Between Time Series with Shannon and Renyi Transfer Entropy
Description: Measuring information flow between time series with Shannon and Rényi transfer entropy. See also Dimpfl and Peter (2013) <doi:10.1515/snde-2012-0044> and Dimpfl and Peter (2014) <doi:10.1016/j.intfin.2014.03.004> for theory and applications to financial time series. Additional references can be found in the theory part of the vignette.
Author: David Zimmermann [aut, cre], Simon Behrendt [aut], Thomas Dimpfl [aut], Franziska Peter [aut]
Maintainer: David Zimmermann <david_j_zimmermann@hotmail.com>

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Package rstac updated to version 0.9.2-2 with previous version 0.9.2-1 dated 2023-01-21

Title: Client Library for SpatioTemporal Asset Catalog
Description: Provides functions to access, search and download spacetime earth observation data via SpatioTemporal Asset Catalog (STAC). This package supports the version 1.0.0 (and older) of the STAC specification (<https://github.com/radiantearth/stac-spec>). For further details see Simoes et al. (2021) <doi:10.1109/IGARSS47720.2021.9553518>.
Author: Rolf Simoes [aut], Felipe Carvalho [aut, cre], Brazil Data Cube Team [aut], National Institute for Space Research [cph]
Maintainer: Felipe Carvalho <lipecaso@gmail.com>

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Package RNeXML updated to version 2.4.11 with previous version 2.4.10 dated 2023-01-09

Title: Semantically Rich I/O for the 'NeXML' Format
Description: Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.
Author: Carl Boettiger [cre, aut] , Scott Chamberlain [aut] , Hilmar Lapp [aut] , Kseniia Shumelchyk [aut], Rutger Vos [aut]
Maintainer: Carl Boettiger <cboettig@gmail.com>

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Package revss updated to version 1.0.5 with previous version 1.0.4 dated 2022-04-04

Title: Robust Estimation in Very Small Samples
Description: Implements the estimation techniques described in Rousseeuw & Verboven (2002) <doi:10.1016/S0167-9473(02)00078-6> for the location and scale of very small samples.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>

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Package Ravages updated to version 1.1.2 with previous version 1.1.1 dated 2022-11-11

Title: Rare Variant Analysis and Genetic Simulations
Description: Rare variant association tests: burden tests (Bocher et al. 2019 <doi:10.1002/gepi.22210>) and the Sequence Kernel Association Test (Bocher et al. 2021 <doi:10.1038/s41431-020-00792-8>) in the whole genome; and genetic simulations.
Author: Ozvan Bocher and Herve Perdry
Maintainer: Ozvan Bocher <bocherozvan@gmail.com>

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Package rapidphylo updated to version 0.1.2 with previous version 0.1.1 dated 2022-12-19

Title: Rapidly Estimates Phylogeny from Large Allele Frequency Data Using Root Distances Method
Description: Rapidly estimates tree-topology from large allele frequency data using Root Distances Method, under a Brownian Motion Model. See Peng et al. (2021) <doi:10.1016/j.ympev.2021.107142>.
Author: Arindam RoyChoudhury [aut, cre, cph], Jing Peng [aut], Ying Li [aut], Laura Kubatko [aut, ths]
Maintainer: Arindam RoyChoudhury <arr2014@med.cornell.edu>

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Package PSS.Health updated to version 0.6.1 with previous version 0.5.1 dated 2022-07-06

Title: Power and Sample Size for Health Researchers via Shiny
Description: Power and Sample Size for Health Researchers is a Shiny application that brings together a series of functions related to sample size and power calculations for common analysis in the healthcare field. There are functionalities to calculate the power, sample size to estimate or test hypotheses for means and proportions (including test for correlated groups, equivalence, non-inferiority and superiority), association, correlations coefficients, regression coefficients (linear, logistic and Cox), linear mixed model, Cronbach's alpha, interobserver agreement, intraclass correlation coefficients, limit of agreement on Bland-Altman plots, area under the curve, sensitivity and specificity incorporating the prevalence of disease. You can also use the online version at <https://hcpa-unidade-bioestatistica.shinyapps.io/PSS_Health/>.
Author: Rogerio Boff Borges [aut, cre] , Guilherme Serpa Azambuja [aut] , Aline Castello Branco Mancuso [aut] , Vanessa Bielefeldt Leotti [aut] , Vânia Naomi Hirakata [aut] , Suzi Alves Camey [aut] , Stela Maris de Jezus Castro [aut] , Hospital de Clinicas d [...truncated...]
Maintainer: Rogerio Boff Borges <roborges@hcpa.edu.br>

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Package ggblanket updated to version 1.6.3 with previous version 1.6.2 dated 2022-12-19

Title: Simplify 'ggplot2' Visualisation
Description: Simplify 'ggplot2' visualisation with 'ggblanket' wrapper functions.
Author: David Hodge [aut, cre]
Maintainer: David Hodge <davidhodge931@gmail.com>

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Package FSA updated to version 0.9.4 with previous version 0.9.3 dated 2022-02-18

Title: Simple Fisheries Stock Assessment Methods
Description: A variety of simple fish stock assessment methods.
Author: Derek H. Ogle [aut, cre] , Jason C. Doll [aut], A. Powell Wheeler [aut], Alexis Dinno [aut] )
Maintainer: Derek H. Ogle <DerekOgle51@gmail.com>

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Package eHDPrep updated to version 1.3.2 with previous version 1.2.1 dated 2022-09-07

Title: Quality Control and Semantic Enrichment of Datasets
Description: A tool for the preparation and enrichment of health datasets for analysis. Provides functionality for assessing data quality and for improving the reliability and machine interpretability of a dataset. 'eHDPrep' also enables semantic enrichment of a dataset where metavariables are discovered from the relationships between input variables determined from user-provided ontologies.
Author: Tom Toner [aut] , Ian Overton [aut, cre]
Maintainer: Ian Overton <I.Overton@qub.ac.uk>

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Permanent link

Package Delaporte updated to version 8.1.0 with previous version 8.0.3 dated 2022-09-06

Title: Statistical Functions for the Delaporte Distribution
Description: Provides probability mass, distribution, quantile, random-variate generation, and method-of-moments parameter-estimation functions for the Delaporte distribution with parameterization based on Vose (2008) <isbn:9780470512845>. The Delaporte is a discrete probability distribution which can be considered the convolution of a negative binomial distribution with a Poisson distribution. Alternatively, it can be considered a counting distribution with both Poisson and negative binomial components. It has been studied in actuarial science as a frequency distribution which has more variability than the Poisson, but less than the negative binomial.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>

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Package CEOdata updated to version 1.3.0.1 with previous version 1.2.0.1 dated 2022-05-17

Title: Datasets of the CEO (Centre d'Estudis d'Opinio) for Opinion Polls in Catalonia
Description: Easy and convenient access to the datasets of the "Centre d'Estudis d'Opinio", the Catalan institution for polling and public opinion. The package uses the data stored in the servers of the CEO and returns it in a tidy format.
Author: Xavier Fernandez-i-Marin [aut, cre]
Maintainer: Xavier Fernandez-i-Marin <xavier.fim@gmail.com>

Diff between CEOdata versions 1.2.0.1 dated 2022-05-17 and 1.3.0.1 dated 2023-02-01

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Package terrainr updated to version 0.7.3 with previous version 0.7.2 dated 2022-12-07

Title: Landscape Visualizations in R and 'Unity'
Description: Functions for the retrieval, manipulation, and visualization of 'geospatial' data, with an aim towards producing '3D' landscape visualizations in the 'Unity' '3D' rendering engine. Functions are also provided for retrieving elevation data and base map tiles from the 'USGS' National Map <https://apps.nationalmap.gov/services/>.
Author: Michael Mahoney [aut, cre] , Mike Johnson [rev] for rOpenSci, see <https://github.com/ropensci/software-review/issues/416>), Sydney Foks [rev] for rOpenSci, see <https://github.com/ropensci/software-review/issues/416>)
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>

Diff between terrainr versions 0.7.2 dated 2022-12-07 and 0.7.3 dated 2023-02-01

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Permanent link

Package suddengains updated to version 0.6.1 with previous version 0.6.0 dated 2023-01-31

Title: Identify Sudden Gains in Longitudinal Data
Description: Identify sudden gains based on the three criteria outlined by Tang and DeRubeis (1999) <doi:10.1037/0022-006X.67.6.894> to a selection of repeated measures. Sudden losses, defined as the opposite of sudden gains can also be identified. Two different datasets can be created, one including all sudden gains/losses and one including one selected sudden gain/loss for each case. It can extract scores around sudden gains/losses. It can plot the average change around sudden gains/losses and trajectories of individual cases.
Author: Milan Wiedemann [aut, cre] , Graham M Thew [aut] , Richard Stott [ctb] , Anke Ehlers [ctb, ths] , Mental Health Research UK [fnd], Wellcome Trust [fnd]
Maintainer: Milan Wiedemann <milan.wiedemann@gmail.com>

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Package RInside updated to version 0.2.18 with previous version 0.2.17 dated 2022-04-01

Title: C++ Classes to Embed R in C++ (and C) Applications
Description: C++ classes to embed R in C++ (and C) applications A C++ class providing the R interpreter is offered by this package making it easier to have "R inside" your C++ application. As R itself is embedded into your application, a shared library build of R is required. This works on Linux, OS X and even on Windows provided you use the same tools used to build R itself. Numerous examples are provided in the nine subdirectories of the examples/ directory of the installed package: standard, 'mpi' (for parallel computing), 'qt' (showing how to embed 'RInside' inside a Qt GUI application), 'wt' (showing how to build a "web-application" using the Wt toolkit), 'armadillo' (for 'RInside' use with 'RcppArmadillo'), 'eigen' (for 'RInside' use with 'RcppEigen'), and 'c_interface' for a basic C interface and 'Ruby' illustration. The examples use 'GNUmakefile(s)' with GNU extensions, so a GNU make is required (and will use the 'GNUmakefile' automatically). 'Doxygen'-generated documentation of the C++ cl [...truncated...]
Author: Dirk Eddelbuettel, Romain Francois, and Lance Bachmeier
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RInside versions 0.2.17 dated 2022-04-01 and 0.2.18 dated 2023-02-01

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Package PBSddesolve updated to version 1.13.3 with previous version 1.13.1 dated 2022-11-09

Title: Solver for Delay Differential Equations
Description: Functions for solving systems of delay differential equations by interfacing with numerical routines written by Simon N. Wood, including contributions from Benjamin J. Cairns. These numerical routines first appeared in Simon Wood's 'solv95' program. This package includes a vignette and a complete user's guide. 'PBSddesolve' originally appeared on CRAN under the name 'ddesolve'. That version is no longer supported. The current name emphasizes a close association with other 'PBS' packages, particularly 'PBSmodelling'.
Author: Alex Couture-Beil [aut], Jon T. Schnute [aut], Rowan Haigh [aut, cre], Simon N. Wood [aut], Benjamin J. Cairns [aut], Nicholas Boers [ctb]
Maintainer: Rowan Haigh <rowan.haigh@dfo-mpo.gc.ca>

Diff between PBSddesolve versions 1.13.1 dated 2022-11-09 and 1.13.3 dated 2023-02-01

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Package Pade updated to version 1.0.5 with previous version 1.0.4 dated 2022-01-18

Title: Padé Approximant Coefficients
Description: Given a vector of Taylor series coefficients of sufficient length as input, the function returns the numerator and denominator coefficients for the Padé approximant of appropriate order (Baker, 1975) <ISBN:9780120748556>.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>

Diff between Pade versions 1.0.4 dated 2022-01-18 and 1.0.5 dated 2023-02-01

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Package ndi updated to version 0.1.4 with previous version 0.1.3 dated 2022-12-01

Title: Neighborhood Deprivation Indices
Description: Computes various metrics of socio-economic deprivation and disparity in the United States. Some metrics are considered "spatial" because they consider the values of neighboring (i.e., adjacent) census geographies in their computation, while other metrics are "aspatial" because they only consider the value within each census geography. Two types of aspatial neighborhood deprivation indices (NDI) are available: including: (1) based on Messer et al. (2006) <doi:10.1007/s11524-006-9094-x> and (2) based on Andrews et al. (2020) <doi:10.1080/17445647.2020.1750066> and Slotman et al. (2022) <doi:10.1016/j.dib.2022.108002> who use variables chosen by Roux and Mair (2010) <doi:10.1111/j.1749-6632.2009.05333.x>. Both are a decomposition of multiple demographic characteristics from the U.S. Census Bureau American Community Survey 5-year estimates (ACS-5; 2006-2010 onward). Using data from the ACS-5 (2005-2009 onward), the package can also (1) compute the spatial Racial Iso [...truncated...]
Author: Ian D. Buller [aut, cre, cph] , NCI [cph, fnd]
Maintainer: Ian D. Buller <ian.buller@alumni.emory.edu>

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Package SimDesign updated to version 2.10.1 with previous version 2.10 dated 2023-01-24

Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to safely and efficiently organize and execute Monte Carlo simulation experiments in R. The package controls the structure and back-end of Monte Carlo simulation experiments by utilizing a generate-analyse-summarise workflow. The workflow safeguards against common simulation coding issues, such as automatically re-simulating non-convergent results, prevents inadvertently overwriting simulation files, catches error and warning messages during execution, and implicitly supports parallel processing. For a pedagogical introduction to the package see Sigal and Chalmers (2016) <doi:10.1080/10691898.2016.1246953>. For a more in-depth overview of the package and its design philosophy see Chalmers and Adkins (2020) <doi:10.20982/tqmp.16.4.p248>.
Author: Phil Chalmers [aut, cre] , Matthew Sigal [ctb], Ogreden Oguzhan [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>

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Package lcsm updated to version 0.3.1 with previous version 0.1.2 dated 2020-07-24

Title: Univariate and Bivariate Latent Change Score Modelling
Description: Helper functions to implement univariate and bivariate latent change score models in R using the 'lavaan' package. For details about Latent Change Score Modeling (LCSM) see McArdle (2009) <doi:10.1146/annurev.psych.60.110707.163612> and Grimm, An, McArdle, Zonderman and Resnick (2012) <doi:10.1080/10705511.2012.659627>. The package automatically generates 'lavaan' syntax for different model specifications and varying timepoints. The 'lavaan' syntax generated by this package can be returned and further specifications can be added manually. Longitudinal plots as well as simplified path diagrams can be created to visualise data and model specifications. Estimated model parameters and fit statistics can be extracted as data frames. Data for different univariate and bivariate LCSM can be simulated by specifying estimates for model parameters to explore their effects. This package combines the strengths of other R packages like 'lavaan', 'broom', and 'semPlot' by generating 'lava [...truncated...]
Author: Milan Wiedemann [aut, cre] , Graham M Thew [ctb] , Urska Kosir [ctb] , Anke Ehlers [ths] , Mental Health Research UK [fnd]
Maintainer: Milan Wiedemann <milan.wiedemann@gmail.com>

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Package vcd updated to version 1.4-11 with previous version 1.4-10 dated 2022-06-09

Title: Visualizing Categorical Data
Description: Visualization techniques, data sets, summary and inference procedures aimed particularly at categorical data. Special emphasis is given to highly extensible grid graphics. The package was package was originally inspired by the book "Visualizing Categorical Data" by Michael Friendly and is now the main support package for a new book, "Discrete Data Analysis with R" by Michael Friendly and David Meyer (2015).
Author: David Meyer [aut, cre] , Achim Zeileis [aut] , Kurt Hornik [aut] , Florian Gerber [ctb], Michael Friendly [ctb]
Maintainer: David Meyer <David.Meyer@R-project.org>

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Package sets updated to version 1.0-22 with previous version 1.0-21 dated 2022-02-09

Title: Sets, Generalized Sets, Customizable Sets and Intervals
Description: Data structures and basic operations for ordinary sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets, customizable sets, and intervals.
Author: David Meyer [aut, cre] , Kurt Hornik [aut] , Christian Buchta [ctb]
Maintainer: David Meyer <David.Meyer@R-project.org>

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Package e1071 updated to version 1.7-13 with previous version 1.7-12 dated 2022-10-24

Title: Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien
Description: Functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, generalized k-nearest neighbour ...
Author: David Meyer [aut, cre] , Evgenia Dimitriadou [aut, cph], Kurt Hornik [aut] , Andreas Weingessel [aut], Friedrich Leisch [aut], Chih-Chung Chang [ctb, cph] , Chih-Chen Lin [ctb, cph]
Maintainer: David Meyer <David.Meyer@R-project.org>

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Package codetools updated to version 0.2-19 with previous version 0.2-18 dated 2020-11-04

Title: Code Analysis Tools for R
Description: Code analysis tools for R.
Author: Luke Tierney <luke-tierney@uiowa.edu>
Maintainer: Luke Tierney <luke-tierney@uiowa.edu>

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Package winch updated to version 0.0.12 with previous version 0.0.11 dated 2022-10-31

Title: Portable Native and Joint Stack Traces
Description: Obtain the native stack trace and fuse it with R's stack trace for easier debugging of R packages with native code.
Author: Kirill Mueller [aut, cre] , R Consortium [fnd], Ian Lance Taylor [aut] , Free Software Foundation [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>

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Package tidytransit updated to version 1.4.1 with previous version 1.4 dated 2022-08-26

Title: Read, Validate, Analyze, and Map GTFS Feeds
Description: Read General Transit Feed Specification (GTFS) zipfiles into a list of R dataframes. Perform validation of the data structure against the specification. Analyze the headways and frequencies at routes and stops. Create maps and perform spatial analysis on the routes and stops. Please see the GTFS documentation here for more detail: <https://gtfs.org/>.
Author: Flavio Poletti [aut, cre], Daniel Herszenhut [aut] , Mark Padgham [aut], Tom Buckley [aut], Danton Noriega-Goodwin [aut], Angela Li [ctb], Elaine McVey [ctb], Charles Hans Thompson [ctb], Michael Sumner [ctb], Patrick Hausmann [ctb], Bob Rudis [ctb], [...truncated...]
Maintainer: Flavio Poletti <flavio.poletti@hotmail.ch>

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Package stevemisc updated to version 1.5.0 with previous version 1.4.1 dated 2022-04-12

Title: Steve's Miscellaneous Functions
Description: These are miscellaneous functions that I find useful for my research and teaching. The contents include themes for plots, functions for simulating quantities of interest from regression models, functions for simulating various forms of fake data for instructional/research purposes, and many more. All told, the functions provided here are broadly useful for data organization, data presentation, data recoding, and data simulation.
Author: Steve Miller [aut, cre], Ben Bolker [ctb], Dave Armstrong [ctb], John Fox [ctb], Winston Chang [ctb], Brian Ripley [ctb], Bill Venables [ctb], Pascal van Kooten [ctb], Gerko Vink [ctb], Paul Williamson [ctb], Andreas Beger [ctb] , Vincent Arel-Bundoc [...truncated...]
Maintainer: Steve Miller <steven.v.miller@gmail.com>

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Package NADA2 updated to version 1.1.3 with previous version 1.1.2 dated 2023-01-27

Title: Data Analysis for Censored Environmental Data
Description: Contains methods described by Dennis Helsel in his book "Statistics for Censored Environmental Data using Minitab and R" (2011) and courses and videos at <https://practicalstats.com>. This package adds new functions to the `NADA` Package.
Author: Paul Julian [aut, cre], Dennis Helsel [aut, cph]
Maintainer: Paul Julian <pauljulianphd@gmail.com>

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Package mockr updated to version 0.2.1 with previous version 0.2.0 dated 2022-04-02

Title: Mocking in R
Description: Provides a means to mock a package function, i.e., temporarily substitute it for testing. Designed as a drop-in replacement for the now deprecated 'testthat::with_mock()' and 'testthat::local_mock()'.
Author: Kirill Mueller [aut, cre]
Maintainer: Kirill Mueller <kirill@cynkra.com>

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Package IIProductionUnknown updated to version 0.0.3 with previous version 0.0.2 dated 2022-10-11

Title: Analyzing Data Through of Percentage of Importance Indice (Production Unknown) and Its Derivations
Description: The Importance Index (I.I.) can determine the loss and solution sources for a system in certain knowledge areas (e.g., agronomy), when production (e.g., fruits) is known (Demolin-Leite, 2021). Events (e.g., agricultural pest) can have different magnitudes (numerical measurements), frequencies, and distributions (aggregate, random, or regular) of event occurrence, and I.I. bases in this triplet (Demolin-Leite, 2021) <https://cjascience.com/index.php/CJAS/article/view/1009/1319>. Usually, the higher the magnitude and frequency of aggregated distribution, the greater the problem or the solution (e.g., natural enemies versus pests) for the system (Demolin-Leite, 2021). However, the final production of the system is not always known or is difficult to determine (e.g., degraded area recovery). A derivation of the I.I. is the percentage of Importance Index-Production Unknown (% I.I.-PU) that can detect the loss or solution sources, when production is unknown for the system (Demolin-Leit [...truncated...]
Author: Germano Leao Demolin-Leite [aut] , Alcinei Mistico Azevedo [aut, cre]
Maintainer: Alcinei Mistico Azevedo <alcineimistico@hotmail.com>

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Package flexsurv updated to version 2.2.2 with previous version 2.2.1 dated 2022-12-22

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

Diff between flexsurv versions 2.2.1 dated 2022-12-22 and 2.2.2 dated 2023-02-01

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Package Arothron updated to version 2.0.5 with previous version 2.0.3 dated 2021-10-01

Title: Geometric Morphometric Methods and Virtual Anthropology Tools
Description: Tools for geometric morphometric analysis. The package includes tools of virtual anthropology to align two not articulated parts belonging to the same specimen, to build virtual cavities as endocast (Profico et al, 2021 <doi:10.1002/ajpa.24340>).
Author: Antonio Profico, Costantino Buzi, Silvia Castiglione, Marina Melchionna, Paolo Piras, Pasquale Raia, Alessio Veneziano
Maintainer: Antonio Profico <antonio.profico@gmail.com>

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Package sourcetools updated to version 0.1.7-1 with previous version 0.1.7 dated 2018-04-24

Title: Tools for Reading, Tokenizing and Parsing R Code
Description: Tools for the reading and tokenization of R code. The 'sourcetools' package provides both an R and C++ interface for the tokenization of R code, and helpers for interacting with the tokenized representation of R code.
Author: Kevin Ushey
Maintainer: Kevin Ushey <kevinushey@gmail.com>

Diff between sourcetools versions 0.1.7 dated 2018-04-24 and 0.1.7-1 dated 2023-02-01

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Package FRK updated to version 2.1.5 with previous version 2.1.3 dated 2022-12-20

Title: Fixed Rank Kriging
Description: A tool for spatial/spatio-temporal modelling and prediction with large datasets. The approach models the field, and hence the covariance function, using a set of basis functions. This fixed-rank basis-function representation facilitates the modelling of big data, and the method naturally allows for non-stationary, anisotropic covariance functions. Discretisation of the spatial domain into so-called basic areal units (BAUs) facilitates the use of observations with varying support (i.e., both point-referenced and areal supports, potentially simultaneously), and prediction over arbitrary user-specified regions. `FRK` also supports inference over various manifolds, including the 2D plane and 3D sphere, and it provides helper functions to model, fit, predict, and plot with relative ease. Version 2.0.0 and above also supports the modelling of non-Gaussian data (e.g., Poisson, binomial, negative-binomial, gamma, and inverse-Gaussian) by employing a generalised linear mixed model (GLMM) framew [...truncated...]
Author: Andrew Zammit-Mangion [aut, cre], Matthew Sainsbury-Dale [aut]
Maintainer: Andrew Zammit-Mangion <andrewzm@gmail.com>

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Package BiasedUrn updated to version 2.0.9 with previous version 2.0.8 dated 2022-10-22

Title: Biased Urn Model Distributions
Description: Statistical models of biased sampling in the form of univariate and multivariate noncentral hypergeometric distributions, including Wallenius' noncentral hypergeometric distribution and Fisher's noncentral hypergeometric distribution. See vignette("UrnTheory") for explanation of these distributions. Literature: Fog, A. (2008a). Calculation Methods for Wallenius' Noncentral Hypergeometric Distribution, Communications in Statistics, Simulation and Computation, 37(2) <doi:10.1080/03610910701790269>. Fog, A. (2008b). Sampling methods for Wallenius’ and Fisher’s noncentral hypergeometric distributions, Communications in Statistics—Simulation and Computation, 37(2) <doi:10.1080/03610910701790236>.
Author: Agner Fog
Maintainer: Agner Fog <agner@agner.org>

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Package proffer updated to version 0.1.6 with previous version 0.1.5 dated 2021-07-26

Title: Profile R Code and Visualize with 'Pprof'
Description: Like similar profiling tools, the 'proffer' package automatically detects sources of slowness in R code. The distinguishing feature of 'proffer' is its utilization of 'pprof', which supplies interactive visualizations that are efficient and easy to interpret. Behind the scenes, the 'profile' package converts native Rprof() data to a protocol buffer that 'pprof' understands. For the documentation of 'proffer', visit <https://r-prof.github.io/proffer/>. To learn about the implementations and methodologies of 'pprof', 'profile', and protocol buffers, visit <https://github.com/google/pprof>. <https://developers.google.com/protocol-buffers>, and <https://github.com/r-prof/profile>, respectively.
Author: William Michael Landau [aut, cre] , Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>

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Package samc updated to version 3.0.2 with previous version 2.0.1 dated 2022-06-11

Title: Spatial Absorbing Markov Chains
Description: Implements functions for working with absorbing Markov chains. The implementation is based on the framework described in "Toward a unified framework for connectivity that disentangles movement and mortality in space and time" by Fletcher et al. (2019) <doi:10.1111/ele.13333>, which applies them to spatial ecology. This framework incorporates both resistance and absorption with spatial absorbing Markov chains (SAMC) to provide several short-term and long-term predictions for metrics related to connectivity in landscapes. Despite the ecological context of the framework, this package can be used in any application of absorbing Markov chains.
Author: Andrew Marx [aut, cre, cph] , Robert Fletcher [ctb] , Miguel Acevedo [ctb] , Jorge Sefair [ctb] , Chao Wang [ctb]
Maintainer: Andrew Marx <ajm.rpackages@gmail.com>

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More information about samc at CRAN
Permanent link

Package MSCMT updated to version 1.3.5 with previous version 1.3.4 dated 2019-11-14

Title: Multivariate Synthetic Control Method Using Time Series
Description: Three generalizations of the synthetic control method (which has already an implementation in package 'Synth') are implemented: first, 'MSCMT' allows for using multiple outcome variables, second, time series can be supplied as economic predictors, and third, a well-defined cross-validation approach can be used. Much effort has been taken to make the implementation as stable as possible (including edge cases) without losing computational efficiency. A detailed description of the main algorithms is given in Becker and Klößner (2018) <doi:10.1016/j.ecosta.2017.08.002>.
Author: Martin Becker [aut, cre] , Stefan Kloeßner [aut], Karline Soetaert [com], Jack Dongarra [cph], R.J. Hanson [cph], K.H. Haskell [cph], Cleve Moler [cph], LAPACK authors [cph]
Maintainer: Martin Becker <martin.becker@mx.uni-saarland.de>

Diff between MSCMT versions 1.3.4 dated 2019-11-14 and 1.3.5 dated 2023-02-01

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More information about MSCMT at CRAN
Permanent link

Package marginaleffects updated to version 0.9.0 with previous version 0.8.1 dated 2022-11-23

Title: Predictions, Comparisons, Slopes, Marginal Means, and Hypothesis Tests
Description: Compute and plot predictions, slopes, marginal means, and comparisons (contrasts, risk ratios, odds, etc.) for over 70 classes of statistical models in R. Conduct linear and non-linear hypothesis tests, or equivalence tests. Calculate uncertainty estimates using the delta method, bootstrapping, or simulation-based inference.
Author: Vincent Arel-Bundock [aut, cre, cph] , Marcio Augusto Diniz [ctb] , Noah Greifer [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>

Diff between marginaleffects versions 0.8.1 dated 2022-11-23 and 0.9.0 dated 2023-02-01

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 marginaleffects-0.9.0/marginaleffects/DESCRIPTION                                                           |   90 -
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 marginaleffects-0.9.0/marginaleffects/NAMESPACE                                                             |   54 
 marginaleffects-0.9.0/marginaleffects/NEWS.md                                                               |   52 
 marginaleffects-0.9.0/marginaleffects/R/backtransform.R                                                     |    2 
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 marginaleffects-0.9.0/marginaleffects/R/get_group_names.R                                                   |    2 
 marginaleffects-0.9.0/marginaleffects/R/get_hypothesis.R                                                    |   56 
 marginaleffects-0.9.0/marginaleffects/R/get_jacobian.R                                                      |    2 
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 marginaleffects-0.9.0/marginaleffects/R/get_predict.R                                                       |   25 
 marginaleffects-0.9.0/marginaleffects/R/get_se_delta.R                                                      |   24 
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 marginaleffects-0.9.0/marginaleffects/R/github_issue.R                                                      |    2 
 marginaleffects-0.9.0/marginaleffects/R/hush.R                                                              |    6 
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 marginaleffects-0.9.0/marginaleffects/R/mean_or_mode.R                                                      |   41 
 marginaleffects-0.9.0/marginaleffects/R/methods_MASS.R                                                      |    2 
 marginaleffects-0.9.0/marginaleffects/R/methods_afex.R                                                      |    2 
 marginaleffects-0.9.0/marginaleffects/R/methods_aod.R                                                       |   15 
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 marginaleffects-0.9.0/marginaleffects/R/methods_bife.R                                                      |    2 
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 marginaleffects-0.9.0/marginaleffects/R/methods_brms.R                                                      |   24 
 marginaleffects-0.9.0/marginaleffects/R/methods_crch.R                                                      |    2 
 marginaleffects-0.9.0/marginaleffects/R/methods_fixest.R                                                    |   15 
 marginaleffects-0.9.0/marginaleffects/R/methods_gamlss.R                                                    |    4 
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 marginaleffects-0.9.0/marginaleffects/R/methods_mlogit.R                                                    |    9 
 marginaleffects-0.9.0/marginaleffects/R/methods_nnet.R                                                      |    2 
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 marginaleffects-0.9.0/marginaleffects/R/methods_plm.R                                                       |   10 
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 marginaleffects-0.9.0/marginaleffects/R/methods_robustlmm.R                                                 |    2 
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 marginaleffects-0.9.0/marginaleffects/R/package.R                                                           |    2 
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Package ip2location updated to version 8.1.2 with previous version 8.1.1 dated 2023-01-23

Title: Lookup for IP Address Information
Description: Enables the user to find the country, region, city, coordinates, zip code, time zone, ISP, domain name, connection type, area code, weather station code, weather station name, mobile, usage type, address type and IAB category that any IP address or hostname originates from. Supported IPv4 and IPv6. Please visit <https://www.ip2location.com> to learn more. You may also want to visit <https://lite.ip2location.com> for free database download. This package requires 'IP2Location Python' module. At the terminal, please run 'pip install IP2Location' to install the module.
Author: IP2Location
Maintainer: IP2Location <support@ip2location.com>

Diff between ip2location versions 8.1.1 dated 2023-01-23 and 8.1.2 dated 2023-02-01

 DESCRIPTION             |    6 +++---
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Package injurytools updated to version 1.0.1 with previous version 1.0.0 dated 2023-01-26

Title: A Toolkit for Sports Injury Data Analysis
Description: Sports Injury Data analysis aims to identify and describe the magnitude of the injury problem, and to gain more insights (e.g. determine potential risk factors) by statistical modelling approaches. The 'injurytools' package provides standardized routines and utilities that simplify such analyses. It offers functions for data preparation, informative visualizations and descriptive and model-based analyses.
Author: Lore Zumeta Olaskoaga [aut, cre] , Dae-Jin Lee [aut]
Maintainer: Lore Zumeta Olaskoaga <lzumeta@bcamath.org>

Diff between injurytools versions 1.0.0 dated 2023-01-26 and 1.0.1 dated 2023-02-01

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Package IDSL.MXP updated to version 1.9 with previous version 1.8 dated 2023-01-06

Title: Parser for mzML, mzXML, and netCDF Files (Mass Spectrometry Data)
Description: A tiny parser to extract mass spectra data and metadata table of mass spectrometry acquisition properties from mzML, mzXML and netCDF files introduced in <doi:10.1021/acs.jproteome.2c00120>.
Author: Sadjad Fakouri-Baygi [cre, aut] , Dinesh Barupal [aut]
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>

Diff between IDSL.MXP versions 1.8 dated 2023-01-06 and 1.9 dated 2023-02-01

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