Wed, 31 May 2023

Package IDSL.IPA updated to version 2.9 with previous version 2.8 dated 2023-05-18

Title: Intrinsic Peak Analysis (IPA) for HRMS Data
Description: A multi-layered untargeted pipeline for high-throughput LC/HRMS data processing to extract signals of organic small molecules. The package performs ion pairing, peak detection, peak table alignment, retention time correction, aligned peak table gap filling, peak annotation and visualization of extracted ion chromatograms (EICs) and total ion chromatograms (TICs). The 'IDSL.IPA' package was introduced in <doi:10.1021/acs.jproteome.2c00120> .
Author: Sadjad Fakouri-Baygi [aut] , Dinesh Barupal [cre, aut]
Maintainer: Dinesh Barupal <dinesh.barupal@mssm.edu>

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Package zonohedra updated to version 0.2-2 with previous version 0.2-1 dated 2023-05-29

Title: Compute and Plot Zonohedra from Vector Generators
Description: Computes a zonohedron from real vector generators. The package also computes zonogons (2D zonotopes) and zonosegs (1D zonotopes). An elementary S3 class for matroids is included, which supports matroids with rank 3, 2, and 1. Optimization methods are taken from Heckbert (1985) <https://www.cs.cmu.edu/~ph/zono.ps.gz>.
Author: Glenn Davis [aut, cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>

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Package SPARTAAS updated to version 1.2.0 with previous version 1.1.0 dated 2021-10-22

Title: Statistical Pattern Recognition and daTing using Archaeological Artefacts assemblageS
Description: Statistical pattern recognition and dating using archaeological artefacts assemblages. Package of statistical tools for archaeology. hclustcompro(perioclust): Bellanger Lise, Coulon Arthur, Husi Philippe (2021, ISBN:978-3-030-60103-4). mapclust: Bellanger Lise, Coulon Arthur, Husi Philippe (2021) <doi:10.1016/j.jas.2021.105431>. seriograph: Desachy Bruno (2004) <doi:10.3406/pica.2004.2396>. cerardat: Bellanger Lise, Husi Philippe (2012) <doi:10.1016/j.jas.2011.06.031>.
Author: Arthur Coulon [aut, cre], Lise Bellanger [aut], Philippe Husi [aut], Bruno Desachy [ctb], Benjamin Martineau [ctb]
Maintainer: Arthur Coulon <arthur-coulon@outlook.fr>

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Package rgdal updated to version 1.6-7 with previous version 1.6-6 dated 2023-04-18

Title: Bindings for the 'Geospatial' Data Abstraction Library
Description: Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4) and access to projection/transformation operations from the 'PROJ' library. Please note that 'rgdal' will be retired during October 2023, plan transition to sf/stars/'terra' functions using 'GDAL' and 'PROJ' at your earliest convenience (see <https://r-spatial.org/r/2023/05/15/evolution4.html> and earlier blogs for guidance). Use is made of classes defined in the 'sp' package. Raster and vector map data can be imported into R, and raster and vector 'sp' objects exported. The 'GDAL' and 'PROJ' libraries are external to the package, and, when installing the package from source, must be correctly installed first; it is important that 'GDAL' < 3 be matched with 'PROJ' < 6. From 'rgdal' 1.5-8, installed with to 'GDAL' >=3, 'PROJ' >=6 and 'sp' >= 1.4, coordinate reference systems use 'WKT2_2019' strings, not 'PROJ' strings. 'Windows' and 'macOS' binaries (including 'GDAL', 'PROJ' and t [...truncated...]
Author: Roger Bivand [cre, aut] , Tim Keitt [aut], Barry Rowlingson [aut, ctb], Edzer Pebesma [ctb], Michael Sumner [ctb], Robert Hijmans [ctb], Daniel Baston [ctb], Even Rouault [cph, ctb], Frank Warmerdam [cph, ctb], Jeroen Ooms [ctb], Colin Rundel [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

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Package geos updated to version 0.2.3 with previous version 0.2.2 dated 2022-10-22

Title: Open Source Geometry Engine ('GEOS') R API
Description: Provides an R API to the Open Source Geometry Engine ('GEOS') library (<https://libgeos.org/>) and a vector format with which to efficiently store 'GEOS' geometries. High-performance functions to extract information from, calculate relationships between, and transform geometries are provided. Finally, facilities to import and export geometry vectors to other spatial formats are provided.
Author: Dewey Dunnington [aut, cre] , Edzer Pebesma [aut]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>

Diff between geos versions 0.2.2 dated 2022-10-22 and 0.2.3 dated 2023-05-31

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Package downscale updated to version 5.0.0 with previous version 4.2-0 dated 2021-11-24

Title: Downscaling Species Occupancy
Description: Uses species occupancy at coarse grain sizes to predict species occupancy at fine grain sizes. Ten models are provided to fit and extrapolate the occupancy-area relationship, as well as methods for preparing atlas data for modelling. See Marsh et. al. (2018) <doi:10.18637/jss.v086.c03>.
Author: Charles Marsh [aut, cre, cph]
Maintainer: Charles Marsh <charlie.marsh@mailbox.org>

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Package TSCI updated to version 3.0.0 with previous version 2.0.0 dated 2023-04-04

Title: Tools for Causal Inference with Possibly Invalid Instrumental Variables
Description: Two stage curvature identification with machine learning for causal inference in settings when instrumental variable regression is not suitable because of potentially invalid instrumental variables. Based on Guo and Buehlmann (2022) "Two Stage Curvature Identification with Machine Learning: Causal Inference with Possibly Invalid Instrumental Variables" <arXiv:2203.12808>. The vignette is available in Carl, Emmenegger, Bühlmann and Guo (2023) "TSCI: two stage curvature identification for causal inference with invalid instruments" <arXiv:2304.00513>.
Author: David Carl [aut, cre] , Corinne Emmenegger [aut] , Wei Yuan [aut], Mengchu Zheng [aut], Zijian Guo [aut]
Maintainer: David Carl <david.carl@phd.unibocconi.it>

Diff between TSCI versions 2.0.0 dated 2023-04-04 and 3.0.0 dated 2023-05-31

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New package rgoogleclassroom with initial version 0.9
Package: rgoogleclassroom
Title: API Wrapper for Google Classroom and Google Forms
Version: 0.9
Description: This is a Google Forms and Google Classroom API Wrapper for R for managing Google Classrooms from R. The documentation for these APIs is here <https://developers.google.com/forms/api/guides> .
License: GPL-3
URL: https://github.com/datatrail-jhu/rgoogleclassroom
BugReports: https://github.com/datatrail-jhu/rgoogleclassroom/issues
Imports: attempt, curl, httr, jsonlite, purrr, R6, assertthat, lubridate, magrittr, openssl, ottrpal, stringr, dplyr, knitr,
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-05-31 15:25:34 UTC; candacesavonen
Author: Candace Savonen [cre, aut]
Maintainer: Candace Savonen <csavonen@fredhutch.org>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2023-05-31 20:30:02 UTC

More information about rgoogleclassroom at CRAN
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Package mdapack (with last version 0.0.2) was removed from CRAN

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

2020-05-20 0.0.2
2020-03-14 0.0.1

Permanent link
Package bootImpute (with last version 1.2.0) was removed from CRAN

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

2021-04-01 1.2.0
2020-07-10 1.1.0
2019-07-18 1.0.0

Permanent link
Package vaRiskScore updated to version 1.1.0 with previous version 1.0.0 dated 2023-02-16

Title: VA CVD Risk Score
Description: Estimates the predicted 10-year cardiovascular (CVD) risk score (in probability) for women military service members and veterans by inputting patient profiles. The proposed women CVD risk score improves the accuracy of the existing American College of Cardiology/American Heart Association CVD risk assessment tool in predicting long‐term CVD risk for VA women, particularly in young and racial/ethnic minority women. See the reference: Jeon‐Slaughter, H., Chen, X., Tsai, S., Ramanan, B., & Ebrahimi, R. (2021) <doi:10.1161/JAHA.120.019217>.
Author: Xiaofei Chen [aut, cre], Haekyung Jeon-Slaughter [aut]
Maintainer: Xiaofei Chen <bill.nj08873@gmail.com>

Diff between vaRiskScore versions 1.0.0 dated 2023-02-16 and 1.1.0 dated 2023-05-31

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Package varbvs updated to version 2.6-10 with previous version 2.6-8 dated 2023-03-22

Title: Large-Scale Bayesian Variable Selection Using Variational Methods
Description: Fast algorithms for fitting Bayesian variable selection models and computing Bayes factors, in which the outcome (or response variable) is modeled using a linear regression or a logistic regression. The algorithms are based on the variational approximations described in "Scalable variational inference for Bayesian variable selection in regression, and its accuracy in genetic association studies" (P. Carbonetto & M. Stephens, 2012, <DOI:10.1214/12-BA703>). This software has been applied to large data sets with over a million variables and thousands of samples.
Author: Peter Carbonetto [aut, cre], Matthew Stephens [aut], David Gerard [ctb]
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>

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Package LDlinkR updated to version 1.3.0 with previous version 1.2.3 dated 2022-12-15

Title: Calculating Linkage Disequilibrium (LD) in Human Population Groups of Interest
Description: Provides access to the 'LDlink' API (<https://ldlink.nih.gov/?tab=apiaccess>) using the R console. This programmatic access facilitates researchers who are interested in performing batch queries in 1000 Genomes Project (2015) <doi:10.1038/nature15393> data using 'LDlink'. 'LDlink' is an interactive and powerful suite of web-based tools for querying germline variants in human population groups of interest. For more details, please see Machiela et al. (2015) <doi:10.1093/bioinformatics/btv402>.
Author: Timothy A. Myers [aut, cre] , Stephen J. Chanock [aut], Mitchell J. Machiela [aut]
Maintainer: Timothy A. Myers <myersta@mail.nih.gov>

Diff between LDlinkR versions 1.2.3 dated 2022-12-15 and 1.3.0 dated 2023-05-31

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Package entropart updated to version 1.6-12 with previous version 1.6-11 dated 2022-07-11

Title: Entropy Partitioning to Measure Diversity
Description: Measurement and partitioning of diversity, based on Tsallis entropy, following Marcon and Herault (2015) <doi:10.18637/jss.v067.i08>. 'entropart' provides functions to calculate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity. Estimation-bias corrections are available.
Author: Eric Marcon [aut, cre] , Bruno Herault [aut]
Maintainer: Eric Marcon <eric.marcon@agroparistech.fr>

Diff between entropart versions 1.6-11 dated 2022-07-11 and 1.6-12 dated 2023-05-31

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Package attachment updated to version 0.4.0 with previous version 0.3.1 dated 2023-01-27

Title: Deal with Dependencies
Description: Manage dependencies during package development. This can retrieve all dependencies that are used in ".R" files in the "R/" directory, in ".Rmd" files in "vignettes/" directory and in 'roxygen2' documentation of functions. There is a function to update the "DESCRIPTION" file of your package with 'CRAN' packages or any other remote package. All functions to retrieve dependencies of ".R" scripts and ".Rmd" or ".qmd" files can be used independently of a package development.
Author: Sebastien Rochette [cre, aut] , Vincent Guyader [aut] , Murielle Delmotte [aut] , Swann Floc'hlay [aut] , ThinkR [cph, fnd]
Maintainer: Sebastien Rochette <sebastien@thinkr.fr>

Diff between attachment versions 0.3.1 dated 2023-01-27 and 0.4.0 dated 2023-05-31

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Package reproducible updated to version 2.0.4 with previous version 2.0.2 dated 2023-05-07

Title: Enhance Reproducibility of R Code
Description: A collection of high-level, machine- and OS-independent tools for making reproducible and reusable content in R. The two workhorse functions are Cache() and prepInputs(). Cache() allows for nested caching, is robust to environments and objects with environments (like functions), and has deals with some classes of file-backed R objects e.g., from terra and raster packages. Both functions have been developed to be foundational components of data retrieval and processing in continuous workflow situations. In both functions, efforts are made to make the first and subsequent calls of functions have the same result, but faster at subsequent times by way of checksums and digesting. Several features are still under development, including cloud storage of cached objects, allowing for sharing between users. Several advanced options are available, see ?reproducibleOptions().
Author: Eliot J B McIntire [aut, cre] , Alex M Chubaty [aut] , Tati Micheletti [ctb] , Ceres Barros [ctb] , Ian Eddy [ctb] , His Majesty the King in Right of Canada, as represented by the Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>

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Package peramo updated to version 0.1.3 with previous version 0.1.2 dated 2023-03-29

Title: Permutation Tests for Randomization Model
Description: Perform permutation-based hypothesis testing for randomized experiments as suggested in Ludbrook & Dudley (1998) <doi:10.2307/2685470> and Ernst (2004) <doi:10.1214/088342304000000396>, introduced in Pham et al. (2022) <doi:10.1016/j.chemosphere.2022.136736>.
Author: Duy Nghia Pham [aut, cre] , Inna M. Sokolova [ths]
Maintainer: Duy Nghia Pham <nghiapham@yandex.com>

Diff between peramo versions 0.1.2 dated 2023-03-29 and 0.1.3 dated 2023-05-31

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Package asylum updated to version 1.1.0 with previous version 1.0.3 dated 2023-03-11

Title: Data on Asylum and Resettlement for the UK
Description: Data on Asylum and Resettlement for the UK, provided by the Home Office <https://www.gov.uk/government/statistical-data-sets/immigration-system-statistics-data-tables-year-ending-march-2023>.
Author: Matthew Gwynfryn Thomas [cre, aut], Mike Page [aut], British Red Cross [cph]
Maintainer: Matthew Gwynfryn Thomas <matthewgthomas@gmail.com>

Diff between asylum versions 1.0.3 dated 2023-03-11 and 1.1.0 dated 2023-05-31

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Package adabag updated to version 5.0 with previous version 4.3 dated 2023-05-01

Title: Applies Multiclass AdaBoost.M1, SAMME and Bagging
Description: It implements Freund and Schapire's Adaboost.M1 algorithm and Breiman's Bagging algorithm using classification trees as individual classifiers. Once these classifiers have been trained, they can be used to predict on new data. Also, cross validation estimation of the error can be done. Since version 2.0 the function margins() is available to calculate the margins for these classifiers. Also a higher flexibility is achieved giving access to the rpart.control() argument of 'rpart'. Four important new features were introduced on version 3.0, AdaBoost-SAMME (Zhu et al., 2009) is implemented and a new function errorevol() shows the error of the ensembles as a function of the number of iterations. In addition, the ensembles can be pruned using the option 'newmfinal' in the predict.bagging() and predict.boosting() functions and the posterior probability of each class for observations can be obtained. Version 3.1 modifies the relative importance measure to take into account the gain of the Gin [...truncated...]
Author: Alfaro, Esteban; Gamez, Matias and Garcia, Noelia; with contributions from L. Guo, A. Albano, M. Sciandra and A. Plaia
Maintainer: Esteban Alfaro <Esteban.Alfaro@uclm.es>

Diff between adabag versions 4.3 dated 2023-05-01 and 5.0 dated 2023-05-31

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

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

2023-04-10 1.0.1

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Package regsem (with last version 1.9.3) was removed from CRAN

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

2022-08-23 1.9.3
2021-06-03 1.8.0
2020-10-01 1.6.2
2020-02-19 1.5.2
2019-05-22 1.3.9
2019-05-07 1.3.8
2019-03-18 1.3.3
2019-01-02 1.2.3
2018-10-22 1.2.0
2018-03-03 1.1.2
2017-12-05 1.0.6
2017-09-08 0.9.2
2017-06-08 0.8.1
2017-03-02 0.7.0
2016-12-22 0.5.0
2016-12-07 0.4.5
2016-11-15 0.4.3
2016-09-19 0.4.0
2016-08-11 0.2.0
2016-06-13 0.1.3
2016-04-18 0.1.2
2016-04-15 0.1.1
2016-04-04 0.1.0

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Package SVDNF updated to version 0.1.5 with previous version 0.1.4 dated 2023-03-01

Title: Discrete Nonlinear Filtering for Stochastic Volatility Models
Description: Generates simulated paths from various financial stochastic volatility models with jumps and applies the discrete nonlinear filter (DNF) of Kitagawa (1987) <doi:10.1080/01621459.1987.10478534> to compute likelihood evaluations, filtering distribution estimates, and maximum likelihood parameter estimates. The algorithm is implemented following the work of Bégin and Boudreault (2021) <doi:10.1080/10618600.2020.1840995>.
Author: Louis Arsenault-Mahjoubi [aut, cre], Jean-Francois Begin [aut], Mathieu Boudreault [aut]
Maintainer: Louis Arsenault-Mahjoubi <larsenau@sfu.ca>

Diff between SVDNF versions 0.1.4 dated 2023-03-01 and 0.1.5 dated 2023-05-31

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Package r02pro updated to version 0.2 with previous version 0.1 dated 2021-07-05

Title: R Programming: Zero to Pro
Description: This is a companion package of the book "R Programming: Zero to Pro" <https://r02pro.github.io/>. It contains the datasets used in the book and provides interactive exercises corresponding to the book. It covers a wide range of topics including visualization, data transformation, tidying data, data input and output.
Author: Yang Feng [aut, cre], Jianan Zhu [aut]
Maintainer: Yang Feng <yangfengstat@gmail.com>

Diff between r02pro versions 0.1 dated 2021-07-05 and 0.2 dated 2023-05-31

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Package ggPMX (with last version 1.2.8) was removed from CRAN

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

2022-06-17 1.2.8
2022-06-09 1.2.7
2022-02-01 1.2.6
2022-01-15 1.2.5
2021-09-20 1.2.4
2021-05-29 1.2.3
2021-05-28 1.2.2
2021-05-25 1.2.1
2020-06-25 1.1.2
2020-05-14 1.1.1
2020-04-09 1.1

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Package panelr (with last version 0.7.7) was removed from CRAN

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Package projpred (with last version 2.5.0) was removed from CRAN

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2023-04-05 2.5.0
2023-02-12 2.4.0
2023-01-10 2.3.0
2022-11-09 2.2.2
2022-09-20 2.2.1
2022-08-19 2.2.0
2022-05-13 2.1.2
2022-04-03 2.1.1
2022-04-01 2.1.0
2020-10-28 2.0.2
2020-10-26 2.0.0
2020-04-01 1.1.6
2020-01-30 1.1.5

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Package hubeau updated to version 0.4.1 with previous version 0.4.0 dated 2023-03-15

Title: Get Data from the French National Database on Water 'Hub'Eau'
Description: Collection of functions to help retrieving data from 'Hub'Eau' the free and public French National APIs on water <https://hubeau.eaufrance.fr/>.
Author: David Dorchies [aut, cre] , Pascal Irz [ctb], Sebastien Grall [ctb]
Maintainer: David Dorchies <david.dorchies@inrae.fr>

Diff between hubeau versions 0.4.0 dated 2023-03-15 and 0.4.1 dated 2023-05-31

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Package snvecR updated to version 3.7.6 with previous version 3.7.5 dated 2023-05-19

Title: Calculate Earth’s Obliquity and Precession in the Past
Description: Easily calculate precession and obliquity from an orbital solution (defaults to ZB18a from Zeebe and Lourens (2019) <doi:10.1126/science.aax0612>) and assumed or reconstructed values for tidal dissipation (Td) and dynamical ellipticity (Ed). This is a translation and adaptation of the C-code in the supplementary material to Zeebe and Lourens (2022) <doi:10.1029/2021PA004349>, with further details on the methodology described in Zeebe (2022) <doi:10.3847/1538-3881/ac80f8>. The name of the C-routine is snvec, which refers to the key units of computation: spin vector s and orbit normal vector n.
Author: Ilja Kocken [aut, cre, trl, cph] , Richard Zeebe [aut]
Maintainer: Ilja Kocken <ikocken@hawaii.edu>

Diff between snvecR versions 3.7.5 dated 2023-05-19 and 3.7.6 dated 2023-05-31

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Package semptools updated to version 0.2.9.11 with previous version 0.2.9.6 dated 2022-08-25

Title: Customizing Structural Equation Modelling Plots
Description: Most function focus on specific ways to customize a graph. They use a 'qgraph' output as the first argument, and return a modified 'qgraph' object. This allows the functions to be chained by a pipe operator.
Author: Shu Fai Cheung [aut, cre] , Mark Hok Chio Lai [aut]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>

Diff between semptools versions 0.2.9.6 dated 2022-08-25 and 0.2.9.11 dated 2023-05-31

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New package ino with initial version 1.0.0
Package: ino
Title: Initialization of Numerical Optimization
Version: 1.0.0
Description: Analysis of the initialization for numerical optimization of real-valued functions, including likelihood functions of statistical models.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
Imports: cli, crayon, doSNOW, dplyr, forcats, foreach, ggplot2, glue, mvtnorm, reshape2, rlang, scales
Suggests: covr, devtools, DT, fHMM, knitr, markdown, purrr, pracma, rmarkdown, testthat (>= 3.0.0)
URL: https://github.com/loelschlaeger/ino
BugReports: https://github.com/loelschlaeger/ino/issues
VignetteBuilder: knitr
Depends: R (>= 4.0.0), optimizeR (>= 0.3.1)
NeedsCompilation: no
Packaged: 2023-05-31 09:11:05 UTC; loelschlaeger
Author: Lennart Oelschlaeger [aut, cre] , Marius Oetting [aut] , Dietmar Bauer [aut]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Repository: CRAN
Date/Publication: 2023-05-31 10:50:02 UTC

More information about ino at CRAN
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Package hmer updated to version 1.5.0 with previous version 1.4.0 dated 2023-03-29

Title: History Matching and Emulation Package
Description: A set of objects and functions for Bayes Linear emulation and history matching. Core functionality includes automated training of emulators to data, diagnostic functions to ensure suitability, and a variety of proposal methods for generating 'waves' of points. For details on the mathematical background, there are many papers available on the topic (see references attached to function help files); for details of the functions in this package, consult the manual or help files.
Author: Andrew Iskauskas [aut, cre] , TJ McKinley [aut]
Maintainer: Andrew Iskauskas <andrew.iskauskas@durham.ac.uk>

Diff between hmer versions 1.4.0 dated 2023-03-29 and 1.5.0 dated 2023-05-31

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More information about hmer at CRAN
Permanent link

Package visit (with last version 2.1) was removed from CRAN

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

2019-08-26 2.1

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Package mdir (with last version 0.9.0) was removed from CRAN

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

2023-05-17 0.9.0

Permanent link
Package beanz (with last version 2.4) was removed from CRAN

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

2018-11-05 2.4
2018-06-13 2.3
2018-04-25 2.2
2017-05-07 2.1
2017-04-23 2.0
2016-11-14 1.7.1
2016-10-17 1.7
2016-07-29 1.6
2016-07-06 1.5
2016-05-04 1.0

Permanent link
Package dfpk (with last version 3.5.1) was removed from CRAN

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

2018-11-09 3.5.1
2018-07-29 3.5.0
2018-03-28 3.4.1
2017-10-24 3.4.0
2017-09-28 3.3.2
2017-06-30 3.3.1
2017-06-29 3.3.0
2017-06-07 3.2.0
2017-05-14 3.0.1
2017-05-13 3.0.0
2017-03-12 2.1.0
2016-12-15 2.0.0
2016-08-10 1.0

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Package idem (with last version 5.1) was removed from CRAN

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

2021-01-27 5.1

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Package symSEM updated to version 0.2 with previous version 0.1 dated 2020-07-16

Title: Symbolic Computation for Structural Equation Models
Description: A collection of functions for symbolic computation using the 'caracas' package for structural equation models and other statistical analyses. Among its features is the ability to calculate the model-implied covariance (and correlation) matrix and the sampling covariance matrix of variable functions using the delta method.
Author: Mike Cheung [aut, cre]
Maintainer: Mike Cheung <mikewlcheung@nus.edu.sg>

Diff between symSEM versions 0.1 dated 2020-07-16 and 0.2 dated 2023-05-31

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Package catdap updated to version 1.3.7 with previous version 1.3.5 dated 2020-03-12

Title: Categorical Data Analysis Program Package
Description: Categorical data analysis by AIC. The methodology is described in Sakamoto (1992) <ISBN 978-0-7923-1429-5>.
Author: The Institute of Statistical Mathematics
Maintainer: Masami Saga <msaga@mtb.biglobe.ne.jp>

Diff between catdap versions 1.3.5 dated 2020-03-12 and 1.3.7 dated 2023-05-31

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Package BFS updated to version 0.4.8 with previous version 0.4.7 dated 2023-05-19

Title: Get Data from the Swiss Statistical Office
Description: Search and download data from the Swiss Federal Statistical Office (BFS) <https://www.bfs.admin.ch/>.
Author: Felix Luginbuhl [aut, cre]
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>

Diff between BFS versions 0.4.7 dated 2023-05-19 and 0.4.8 dated 2023-05-31

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New package WeibullR.plotly with initial version 0.1.2
Package: WeibullR.plotly
Title: Interactive Weibull Probability Plots with 'WeibullR'
Version: 0.1.2
Description: Build interactive Weibull Probability Plots with 'WeibullR' by David Silkworth and Jurgen Symynck (2022) <https://CRAN.R-project.org/package=WeibullR>, an R package for Weibull analysis, and 'plotly' by Carson Sievert (2020) <https://plotly-r.com>, an interactive web-based graphing library.
URL: https://paulgovan.github.io/WeibullR.plotly/
BugReports: https://github.com/paulgovan/weibullr.plotly/issues
License: Apache License
Imports: WeibullR, plotly
Suggests: knitr, rmarkdown
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-05-31 02:46:49 UTC; paulgovan
Author: Paul Govan [aut, cre, cph]
Maintainer: Paul Govan <pgovan1@aggienetwork.com>
Repository: CRAN
Date/Publication: 2023-05-31 09:00:08 UTC

More information about WeibullR.plotly at CRAN
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New package nimbleHMC with initial version 0.1.0
Package: nimbleHMC
Title: Hamiltonian Monte Carlo and Other Gradient-Based MCMC Sampling Algorithms for 'nimble'
Version: 0.1.0
Date: 2023-05-30
Maintainer: Daniel Turek <danielturek@gmail.com>
Description: Provides gradient-based MCMC sampling algorithms for use with the MCMC engine provided by the 'nimble' package. This includes Hamiltonian Monte Carlo (HMC) and (under development) Langevin samplers. The HMC sampler dynamically determines step size and number of leapfrog steps using the No-U-Turn (NUTS) algorithm as described in Hoffman and Gelman (2014) <arXiv:1111.4246>. In addition, convenience functions are provided for generating and modifying MCMC configuration objects which employ HMC sampling.
Depends: R (>= 3.5.0), nimble (>= 1.0.0)
Imports: methods
Suggests: testthat
License: BSD_3_clause + file LICENSE | GPL (>= 2)
Copyright: See COPYRIGHTS file.
Encoding: UTF-8
LazyData: false
NeedsCompilation: no
Packaged: 2023-05-30 16:13:25 UTC; dturek
Author: Daniel Turek [aut, cre], Perry de Valpine [aut], Christopher Paciorek [aut]
Repository: CRAN
Date/Publication: 2023-05-31 09:00:02 UTC

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New package mirai.promises with initial version 0.1.0
Package: mirai.promises
Title: Make 'Mirai' 'Promises'
Version: 0.1.0
Description: Allows 'mirai' objects encapsulating asynchronous computations, from the 'mirai' package by Gao (2023) <doi:10.5281/zenodo.7912722>, to be used interchangeably with 'promise' objects from the 'promises' package by Cheng (2021) <https://CRAN.R-project.org/package=promises>. This facilitates their use with packages 'plumber' by Schloerke and Allen (2022) <https://CRAN.R-project.org/package=plumber> and 'shiny' by Cheng, Allaire, Sievert, Schloerke, Xie, Allen, McPherson, Dipert and Borges (2022) <https://CRAN.R-project.org/package=shiny>.
License: GPL (>= 3)
BugReports: https://github.com/shikokuchuo/mirai.promises/issues
URL: https://github.com/shikokuchuo/mirai.promises/
Encoding: UTF-8
Depends: R (>= 2.12)
Imports: mirai, later (>= 1.0.0), promises (>= 1.1.0)
NeedsCompilation: no
Packaged: 2023-05-31 07:03:50 UTC; cg334
Author: Charlie Gao [aut, cre] , Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Repository: CRAN
Date/Publication: 2023-05-31 09:00:05 UTC

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New package dfrr with initial version 0.1.5
Package: dfrr
Title: Dichotomized Functional Response Regression
Version: 0.1.5
Maintainer: Fatemeh Asgari <fatemeh.asgari@medisin.uio.no>
Description: Implementing Function-on-Scalar Regression model in which the response function is dichotomized and observed sparsely. This package provides smooth estimations of functional regression coefficients and principal components for the dichotomized functional response regression (dfrr) model.
License: GPL-3
LazyData: TRUE
Encoding: UTF-8
Depends: R (>= 3.5.0), tmvtnorm (>= 1.4-10), fda (>= 5.1.4)
Imports: MASS, ggplot2, plotly
Suggests: car
URL: https://github.com/asgari-fatemeh/dfrr
BugReports: https://github.com/asgari-fatemeh/dfrr/issues
NeedsCompilation: no
Packaged: 2023-05-30 17:14:11 UTC; fatema
Author: Fatemeh Asgari [aut, cre], Saeed Hayati [aut, ctb]
Repository: CRAN
Date/Publication: 2023-05-31 08:30:02 UTC

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Package sp updated to version 1.6-1 with previous version 1.6-0 dated 2023-01-19

Title: Classes and Methods for Spatial Data
Description: Classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma [aut, cre], Roger Bivand [aut], Barry Rowlingson [ctb], Virgilio Gomez-Rubio [ctb], Robert Hijmans [ctb], Michael Sumner [ctb], Don MacQueen [ctb], Jim Lemon [ctb], Finn Lindgren [ctb], Josh O'Brien [ctb], Joseph O'Rourke [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

Diff between sp versions 1.6-0 dated 2023-01-19 and 1.6-1 dated 2023-05-31

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Package sharp updated to version 1.4.1 with previous version 1.4.0 dated 2023-04-18

Title: Stability-enHanced Approaches using Resampling Procedures
Description: In stability selection (N Meinshausen, P Bühlmann (2010) <doi:10.1111/j.1467-9868.2010.00740.x>) and consensus clustering (S Monti et al (2003) <doi:10.1023/A:1023949509487>), resampling techniques are used to enhance the reliability of the results. In this package, hyper-parameters are calibrated by maximising model stability, which is measured under the null hypothesis that all selection (or co-membership) probabilities are identical (B Bodinier et al (2021) <arXiv:2106.02521>). Functions are readily implemented for the use of LASSO regression, sparse PCA, sparse (group) PLS or graphical LASSO in stability selection, and hierarchical clustering, partitioning around medoids, K means or Gaussian mixture models in consensus clustering.
Author: Barbara Bodinier [aut, cre]
Maintainer: Barbara Bodinier <barbara.bodinier@gmail.com>

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Package MultiscaleDTM updated to version 0.8.1 with previous version 0.8 dated 2023-04-25

Title: Multi-Scale Geomorphometric Terrain Attributes
Description: Calculates multi-scale geomorphometric terrain attributes from regularly gridded digital terrain models using a variable focal windows size (Ilich et al. (2023) <doi:10.1111/tgis.13067>).
Author: Alexander Ilich [aut, cre] , Vincent Lecours [aut], Benjamin Misiuk [aut], Steven Murawski [aut]
Maintainer: Alexander Ilich <ailich@usf.edu>

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Package multiocc updated to version 0.2.1 with previous version 0.2.0 dated 2023-05-25

Title: Fits Multivariate Spatio-Temporal Occupancy Model
Description: Spatio-temporal multivariate occupancy models can handle multiple species in occupancy models. This method for fitting such models is described in Hepler and Erhardt (2021) "A spatiotemporal model for multivariate occupancy data" <https://onlinelibrary.wiley.com/doi/abs/10.1002/env.2657>.
Author: Staci Hepler [aut, cre], Rob Erhardt [aut]
Maintainer: Staci Hepler <heplersa@wfu.edu>

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Package ggpicrust2 updated to version 1.7.0 with previous version 1.6.5 dated 2023-05-13

Title: Make 'PICRUSt2' Output Analysis and Visualization Easier
Description: Provides a convenient way to analyze and visualize 'PICRUSt2' output with pre-defined plots and functions. Allows for generating statistical plots about microbiome functional predictions and offers customization options. Features a one-click option for creating publication-level plots, saving time and effort in producing professional-grade figures. Streamlines the 'PICRUSt2' analysis and visualization process. For more details, see Yang et al. (2023) <arXiv:2303.10388>.
Author: Chen Yang [aut, cre], Liangliang Zhang [aut]
Maintainer: Chen Yang <cafferychen7850@gmail.com>

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Package CoxAIPW updated to version 0.0.2 with previous version 0.0.1 dated 2023-02-08

Title: Doubly Robust Inference for Cox Marginal Structural Model with Informative Censoring
Description: Doubly robust estimation and inference of log hazard ratio under the Cox marginal structural model with informative censoring. An augmented inverse probability weighted estimator that involves 3 working models, one for conditional failure time T, one for conditional censoring time C and one for propensity score. Both models for T and C can depend on both a binary treatment A and additional baseline covariates Z, while the propensity score model only depends on Z. With the help of cross-fitting techniques, achieves the rate-doubly robust property that allows the use of most machine learning or non-parametric methods for all 3 working models, which are not permitted in classic inverse probability weighting or doubly robust estimators. Reference: Luo & Xu (2022) <doi:10.48550/arXiv.2206.02296>; Rava (2021) <https://escholarship.org/uc/item/8h1846gs>.
Author: Jiyu Luo [cre, aut], Dennis Rava [aut], Ronghui Xu [aut]
Maintainer: Jiyu Luo <charlesluo1002@gmail.com>

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Package beyondWhittle updated to version 1.2.0 with previous version 1.1.3 dated 2022-04-04

Title: Bayesian Spectral Inference for Time Series
Description: Implementations of Bayesian parametric, nonparametric and semiparametric procedures for univariate and multivariate time series. The package is based on the methods presented in C. Kirch et al (2018) <doi:10.1214/18-BA1126>, A. Meier (2018) <https://opendata.uni-halle.de//handle/1981185920/13470> and Y. Tang et al (2023) <arXiv:2303.11561>. It was supported by DFG grants KI 1443/3-1 and KI 1443/3-2.
Author: Alexander Meier [aut], Claudia Kirch [aut], Matthew C. Edwards [aut], Renate Meyer [aut, cre], Yifu Tang [aut]
Maintainer: Renate Meyer <renate.meyer@auckland.ac.nz>

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New package fdakma with initial version 1.3.1
Package: fdakma
Title: Functional Data Analysis: K-Mean Alignment
Version: 1.3.1
Description: It performs simultaneously clustering and alignment of a multidimensional or unidimensional functional dataset by means of k-mean alignment.
License: GPL (>= 3)
Encoding: UTF-8
URL: https://github.com/astamm/fdakma
BugReports: https://github.com/astamm/fdakma/issues
Imports: cli, fdacluster, rlang
NeedsCompilation: no
Packaged: 2023-05-30 17:30:41 UTC; stamm-a
Author: Laura Sangalli [aut], Piercesare Secchi [aut], Aymeric Stamm [cre, ctb] , Simone Vantini [aut], Valeria Vitelli [aut], Alessandro Zito [ctb]
Maintainer: Aymeric Stamm <aymeric.stamm@cnrs.fr>
Repository: CRAN
Date/Publication: 2023-05-31 07:00:02 UTC

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New package PortalHacienda with initial version 0.1.7
Package: PortalHacienda
Title: Acceder Con R a Los Datos Del Portal De Hacienda
Version: 0.1.7
Description: Obtener listado de datos, acceder y extender series del Portal de Datos de Hacienda.Las proyecciones se realizan con 'forecast', Hyndman RJ, Khandakar Y (2008) <doi:10.18637/jss.v027.i03>. Search, download and forecast time-series from the Ministry of Economy of Argentina. Forecasts are built with the 'forecast' package, Hyndman RJ, Khandakar Y (2008) <doi:10.18637/jss.v027.i03>.
License: GPL-3
Encoding: UTF-8
URL: https://github.com/fmgarciadiaz/PortalHacienda-CRAN
Imports: dplyr (>= 0.8.5), forecast (>= 8.12), timetk (>= 2.0), lubridate (>= 1.7.8), xts (>= 0.12-0), httr, tibble (>= 3.0.1), magrittr (>= 1.5), zoo (>= 1.8-8), curl, purrr
Depends: R (>= 3.6.0)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-05-30 19:48:20 UTC; fmgarciadiaz
Author: Fernando Garcia Diaz [aut, cre]
Maintainer: Fernando Garcia Diaz <fmgarciadiaz78@gmail.com>
Repository: CRAN
Date/Publication: 2023-05-31 06:00:02 UTC

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Package TITAN2 updated to version 2.4.2 with previous version 2.4.1 dated 2020-12-07

Title: Threshold Indicator Taxa Analysis
Description: Uses indicator species scores across binary partitions of a sample set to detect congruence in taxon-specific changes of abundance and occurrence frequency along an environmental gradient as evidence of an ecological community threshold. Relevant references include: Baker, ME and RS King. 2010. A new method for detecting and interpreting biodiversity and ecological community thresholds. Methods in Ecology and Evolution 1(1): 25:37. King, RS and ME Baker. 2010. Considerations for identifying and interpreting ecological community thresholds. Journal of the North American Benthological Association 29(3):998-1008. Baker ME and RS King. 2013. Of TITAN and straw men: an appeal for greater understanding of community data. Freshwater Science 32(2):489-506.
Author: Matthew E. Baker [aut, cph] , Ryan S. King [aut, cph] , David Kahle [aut, cph, cre]
Maintainer: David Kahle <david@kahle.io>

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Package seededlda updated to version 1.0.0 with previous version 0.9.1 dated 2023-05-01

Title: Seeded Sequential LDA for Topic Modeling
Description: Seeded Sequential LDA can classify sentences of texts into pre-define topics with a small number of seed words (Watanabe & Baturo, 2023) <doi:10.1177/08944393231178605>. Implements Seeded LDA (Lu et al., 2010) <doi:10.1109/ICDMW.2011.125> and Sequential LDA (Du et al., 2012) <doi:10.1007/s10115-011-0425-1> with the distributed LDA algorithm (Newman, et al., 2009) for parallel computing.
Author: Kohei Watanabe [aut, cre, cph], Phan Xuan-Hieu [aut, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>

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

Title: Batch Correction of Single Cell Transcriptome Data
Description: Non-linear/linear hybrid method for batch-effect correction that uses Mutual Nearest Neighbors (MNNs) to identify similar cells between datasets. Reference: Loza M. et al. (NAR Genomics and Bioinformatics, 2020) <doi:10.1093/nargab/lqac022>.
Author: Martin Loza [aut, cre] , Diego Diez [aut]
Maintainer: Martin Loza <martin.loza.lopez@gmail.com>

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