Thu, 18 Nov 2021

Package isoreader updated to version 1.3.2 with previous version 1.3.1 dated 2021-10-15

Title: Read Stable Isotope Data Files
Description: Interface to the raw data file formats commonly encountered in scientific disciplines that make use of stable isotopes.
Author: Sebastian Kopf [aut, cre] (<https://orcid.org/0000-0002-2044-0201>), Brett Davidheiser-Kroll [aut] (<https://orcid.org/0000-0002-6153-7851>), Ilja Kocken [aut] (<https://orcid.org/0000-0003-2196-8718>)
Maintainer: Sebastian Kopf <sebastian.kopf@colorado.edu>

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Package clifford updated to version 1.0-5 with previous version 1.0-2 dated 2020-03-08

Title: Arbitrary Dimensional Clifford Algebras
Description: A suite of routines for Clifford algebras, using the 'Map' class of the Standard Template Library. Canonical reference: Hestenes (1987, ISBN 90-277-1673-0, "Clifford algebra to geometric calculus"). Special cases including Lorentz transforms, quaternion multiplication, and Grassman algebra, are discussed. Conformal geometric algebra theory is implemented.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

Diff between clifford versions 1.0-2 dated 2020-03-08 and 1.0-5 dated 2021-11-18

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Package tiledb updated to version 0.10.0 with previous version 0.9.7 dated 2021-10-07

Title: Universal Storage Engine for Sparse and Dense Multidimensional Arrays
Description: The universal storage engine 'TileDB' introduces a powerful on-disk format for multi-dimensional arrays. It supports dense and sparse arrays, dataframes and key-values stores, cloud storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression, encryption and checksum filters, uses a fully multi-threaded implementation, supports parallel I/O, data versioning ('time travel'), metadata and groups. It is implemented as an embeddable cross-platform C++ library with APIs from several languages, and integrations.
Author: TileDB, Inc. [aut, cph], Dirk Eddelbuettel [cre]
Maintainer: Dirk Eddelbuettel <dirk@tiledb.com>

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Package lessR updated to version 4.0.8 with previous version 4.0.6 dated 2021-10-25

Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting including the introduced here Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, Trellis graphics and a built-in help system. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, and generation and rendering of R markdown instructions for interpretative output.
Author: David Gerbing, The School of Business, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>

Diff between lessR versions 4.0.6 dated 2021-10-25 and 4.0.8 dated 2021-11-18

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Package PL94171 updated to version 1.0.1 with previous version 0.3.2 dated 2021-08-06

Title: Tabulate P.L. 94-171 Redistricting Data Summary Files
Description: Tools to process legacy format summary redistricting data files produced by the United States Census Bureau pursuant to P.L. 94-171. These files are generally available earlier but are difficult to work with as-is.
Author: Cory McCartan [aut, cre], Christopher T. Kenny [aut]
Maintainer: Cory McCartan <cmccartan@g.harvard.edu>

Diff between PL94171 versions 0.3.2 dated 2021-08-06 and 1.0.1 dated 2021-11-18

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Package autothresholdr updated to version 1.3.12 with previous version 1.3.11 dated 2021-05-12

Title: An R Port of the 'ImageJ' Plugin 'Auto Threshold'
Description: Algorithms for automatically finding appropriate thresholds for numerical data, with special functions for thresholding images. Provides the 'ImageJ' 'Auto Threshold' plugin functionality to R users. See <https://imagej.net/plugins/auto-threshold> and Landini et al. (2017) <DOI:10.1111/jmi.12474>.
Author: Rory Nolan [aut, cre, trl] (<https://orcid.org/0000-0002-5239-4043>), Luis Alvarez [ctb] (<https://orcid.org/0000-0003-1316-1906>), Sergi Padilla-Parra [ctb, ths] (<https://orcid.org/0000-0002-8010-9481>), Gabriel Landini [ctb, cph] (<https://orcid.org/0000-0002-9689-0989>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>

Diff between autothresholdr versions 1.3.11 dated 2021-05-12 and 1.3.12 dated 2021-11-18

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Package clustrd updated to version 1.3.8 with previous version 1.3.7-2 dated 2020-02-29

Title: Methods for Joint Dimension Reduction and Clustering
Description: A class of methods that combine dimension reduction and clustering of continuous, categorical or mixed-type data (Markos, Iodice D'Enza and van de Velden 2019; <DOI:10.18637/jss.v091.i10>). For continuous data, the package contains implementations of factorial K-means (Vichi and Kiers 2001; <DOI:10.1016/S0167-9473(00)00064-5>) and reduced K-means (De Soete and Carroll 1994; <DOI:10.1007/978-3-642-51175-2_24>); both methods that combine principal component analysis with K-means clustering. For categorical data, the package provides MCA K-means (Hwang, Dillon and Takane 2006; <DOI:10.1007/s11336-004-1173-x>), i-FCB (Iodice D'Enza and Palumbo 2013, <DOI:10.1007/s00180-012-0329-x>) and Cluster Correspondence Analysis (van de Velden, Iodice D'Enza and Palumbo 2017; <DOI:10.1007/s11336-016-9514-0>), which combine multiple correspondence analysis with K-means. For mixed-type data, it provides mixed Reduced K-means and mixed Factorial K-means (van de Velden, Iodice D'Enza and Markos 2019; <DOI:10.1002/wics.1456>), which combine PCA for mixed-type data with K-means.
Author: Angelos Markos [aut, cre], Alfonso Iodice D'Enza [aut], Michel van de Velden [aut]
Maintainer: Angelos Markos <amarkos@gmail.com>

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Package anthro updated to version 1.0.0 with previous version 0.9.4 dated 2020-10-30

Title: Computation of the WHO Child Growth Standards
Description: Provides WHO Child Growth Standards (z-scores) with confidence intervals and standard errors around the prevalence estimates, taking into account complex sample designs. More information on the methods is available online: <https://www.who.int/tools/child-growth-standards>.
Author: Dirk Schumacher [aut, cre], Elaine Borghi [ctb], Jonathan Polonsky [ctb], World Health Organization [cph]
Maintainer: Dirk Schumacher <mail@dirk-schumacher.net>

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Package suppdata updated to version 1.1-8 with previous version 1.1-7 dated 2021-09-13

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

Diff between suppdata versions 1.1-7 dated 2021-09-13 and 1.1-8 dated 2021-11-18

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New package SignacX with initial version 2.2.5
Package: SignacX
Version: 2.2.5
Date: 2021-11-17
Title: Cell Type Identification and Discovery from Single Cell Gene Expression Data
Maintainer: Mathew Chamberlain <chamberlainphd@gmail.com>
URL: https://github.com/mathewchamberlain/SignacX
BugReports: https://github.com/mathewchamberlain/SignacX/issues
Imports: neuralnet, lme4, methods, Matrix, pbmcapply, Seurat(>= 3.2.0), RJSONIO, igraph (>= 1.2.1), jsonlite (>= 1.5), RColorBrewer (>= 1.1.2), stats
Suggests: hdf5r, rhdf5, knitr, rmarkdown, formatR
Description: An implementation of neural networks trained with flow-sorted gene expression data to classify cellular phenotypes in single cell RNA-sequencing data. See Chamberlain M et al. (2021) <doi:10.1101/2021.02.01.429207> for more details.
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-11-18 02:53:21 UTC; ubuntu
Author: Mathew Chamberlain [aut, cre], Virginia Savova [aut], Richa Hanamsagar [aut], Frank Nestle [aut], Emanuele de Rinaldis [aut], Sanofi US [fnd]
Repository: CRAN
Date/Publication: 2021-11-18 16:20:03 UTC

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Package opdisDownsampling updated to version 0.8.0 with previous version 0.7.0 dated 2021-10-18

Title: Optimal Distribution Preserving Down-Sampling of Bio-Medical Data
Description: An optimized method for distribution-preserving class-proportional down-sampling of bio-medical data.
Author: Jorn Lotsch [aut,cre] (<https://orcid.org/0000-0002-5818-6958>), Sebastian Malkusch [aut] (<https://orcid.org/0000-0001-6766-140X>), Alfred Ultsch [aut] (<https://orcid.org/0000-0002-7845-3283>)
Maintainer: Jorn Lotsch <j.lotsch@em.uni-frankfurt.de>

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Package gdm updated to version 1.5.0-1 with previous version 1.5.0 dated 2021-11-16

Title: Generalized Dissimilarity Modeling
Description: A toolkit with functions to fit, plot, summarize, and apply Generalized Dissimilarity Models.
Author: Matt Fitzpatrick [aut, cre] (<https://orcid.org/0000-0003-1911-8407>), Karel Mokany [aut] (<https://orcid.org/0000-0003-4199-3697>), Glenn Manion [aut], Diego Nieto-Lugilde [aut] (<https://orcid.org/0000-0003-4135-2881>), Simon Ferrier [aut] (<https://orcid.org/0000-0001-7884-2388>), Matthew Lisk [ctb], Chris Ware [ctb], Skip Woolley [ctb], Tom Harwood [ctb]
Maintainer: Matt Fitzpatrick <mfitzpatrick@umces.edu>

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Package bbl updated to version 0.4.1 with previous version 0.4.0 dated 2021-02-03

Title: Boltzmann Bayes Learner
Description: Supervised learning using Boltzmann Bayes model inference, which extends naive Bayes model to include interactions. Enables classification of data into multiple response groups based on a large number of discrete predictors that can take factor values of heterogeneous levels. Either pseudo-likelihood or mean field inference can be used with L2 regularization, cross-validation, and prediction on new data. Woo et al. (2016) <doi:10.1186/s12864-016-2871-3>.
Author: Jun Woo [aut, cre] (<https://orcid.org/0000-0003-3220-2064>)
Maintainer: Jun Woo <junwoo035@gmail.com>

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Package starsExtra updated to version 0.2.7 with previous version 0.2.6 dated 2021-09-06

Title: Miscellaneous Functions for Working with 'stars' Rasters
Description: Miscellaneous functions for working with 'stars' objects, mainly single-band rasters. Currently includes functions for: (1) focal filtering, (2) detrending of Digital Elevation Models, (3) calculating flow length, (4) calculating the Convergence Index, (5) calculating topographic aspect and topographic slope.
Author: Michael Dorman [aut, cre]
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>

Diff between starsExtra versions 0.2.6 dated 2021-09-06 and 0.2.7 dated 2021-11-18

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Package rnoaa updated to version 1.3.7 with previous version 1.3.4 dated 2021-05-19

Title: 'NOAA' Weather Data from R
Description: Client for many 'NOAA' data sources including the 'NCDC' climate 'API' at <https://www.ncdc.noaa.gov/cdo-web/webservices/v2>, with functions for each of the 'API' 'endpoints': data, data categories, data sets, data types, locations, location categories, and stations. In addition, we have an interface for 'NOAA' sea ice data, the 'NOAA' severe weather inventory, 'NOAA' Historical Observing 'Metadata' Repository ('HOMR') data, 'NOAA' storm data via 'IBTrACS', tornado data via the 'NOAA' storm prediction center, and more.
Author: Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>), Daniel Hocking [ctb, cre] (<https://orcid.org/0000-0003-1889-9184>), Brooke Anderson [ctb], Maëlle Salmon [ctb], Adam Erickson [ctb], Nicholas Potter [ctb], Joseph Stachelek [ctb], Alex Simmons [ctb], Karthik Ram [ctb], Hart Edmund [ctb], rOpenSci [fnd] (https://ropensci.org)
Maintainer: Daniel Hocking <djhocking@gmail.com>

Diff between rnoaa versions 1.3.4 dated 2021-05-19 and 1.3.7 dated 2021-11-18

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Package pARI updated to version 1.1.0 with previous version 1.0.0 dated 2021-11-17

Title: Permutation-Based All-Resolutions Inference Method
Description: It computes the All-Resolution Inference method in the permutation framework, i.e., simultaneous lower confidence bounds for the number of true discoveries. <arXiv:2012.00368>.
Author: Angela Andreella [aut, cre] (Main author, <https://orcid.org/0000-0002-1141-3041>)
Maintainer: Angela Andreella <angela.andreella@unipd.it>

Diff between pARI versions 1.0.0 dated 2021-11-17 and 1.1.0 dated 2021-11-18

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Package onlineBcp updated to version 0.1.2 with previous version 0.1.1 dated 2021-04-28

Title: Online Bayesian Methods for Change Point Analysis
Description: It implements the online Bayesian methods for change point analysis. It can also perform missing data imputation with methods from 'VIM'. The reference is Yigiter A, Chen J, An L, Danacioglu N (2015) <doi:10.1080/02664763.2014.1001330>.
Author: Hongyan Xu [cre, aut], Ayten Yigiter [aut], Jie Chen [aut]
Maintainer: Hongyan Xu <hxu@augusta.edu>

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Package jfa updated to version 0.6.1 with previous version 0.6.0 dated 2021-09-22

Title: Bayesian and Classical Audit Sampling
Description: Implements the audit sampling workflow as discussed in Derks et al. (2019) <doi:10.31234/osf.io/9f6ub>. The package makes it easy for an auditor to plan a statistical sample, select the sample from the population, and evaluate the misstatement in the sample compliant with the International Standards on Auditing. Next to classical audit sampling methodology, the package implements Bayesian equivalents of these methods whose statistical underpinnings are described in Derks et al. (2021) <doi:10.1111/ijau.12240> and Derks et al. (2021) <doi:10.31234/osf.io/kzqp5>.
Author: Koen Derks [aut, cre] (<https://orcid.org/0000-0002-5533-9349>)
Maintainer: Koen Derks <k.derks@nyenrode.nl>

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New package filterNHP with initial version 0.1.2
Package: filterNHP
Title: Non-Human Primate Search Filters
Version: 0.1.2
Date: 2021-11-17
Description: Generate search filters to query scientific bibliographic sources, such as PubMed and Web of Science, for non-human primate related publications.
License: AGPL (>= 3)
Encoding: UTF-8
Depends: R (>= 3.5.0)
Suggests: testthat, knitr, rmarkdown
Imports: data.tree (>= 1.0.0), shiny, shinyWidgets, shinyjs, shinyBS, rclipboard
NeedsCompilation: no
Packaged: 2021-11-17 18:36:58 UTC; avrincon
Author: Lauren C. Cassidy [aut], Cathalijn H. C. Leenaars [aut], Alan V. Rincon [aut, cre], Dana Pfefferle [aut]
Maintainer: Alan V. Rincon <avrincon1@gmail.com>
Repository: CRAN
Date/Publication: 2021-11-18 15:10:03 UTC

More information about filterNHP at CRAN
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New package knnwtsim with initial version 0.1.0
Package: knnwtsim
Title: K Nearest Neighbor Forecasting with a Tailored Similarity Metric
Version: 0.1.0
Author: Matthew Trupiano
Maintainer: Matthew Trupiano <matthew.trupiano.professional@gmail.com>
Description: Functions to implement K Nearest Neighbor forecasting using a weighted similarity metric tailored to the problem of forecasting univariate time series where recent observations, seasonal patterns, and exogenous predictors are all relevant in predicting future observations of the series in question. For more information on the formulation of this similarity metric please see Trupiano (2021) <https://github.com/mtrupiano1/knnwtsim/blob/main/README.md>.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
URL: https://github.com/mtrupiano1/knnwtsim
BugReports: https://github.com/mtrupiano1/knnwtsim/issues
Suggests: testthat (>= 3.0.0)
Imports: stats
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2021-11-16 23:30:36 UTC; mtrup
Repository: CRAN
Date/Publication: 2021-11-18 14:30:02 UTC

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New package fastCorrDiff with initial version 0.5
Package: fastCorrDiff
Title: Fast Differential Correlation Matrix Screening
Version: 0.5
Date: 2021-11-10
Author: Tianxi Li and Xiwei Tang
Maintainer: Tianxi Li <tianxili@virginia.edu>
Description: Fast spectral algorithms for differential analysis on large-scale correlation matrices of Li et. al. (2021) <arXiv:2111.03721> are implemented. The methods can identify a group of genes exhibiting differential correlation patterns between two groups. For high-dimensional matrices, compressed spectral screening methods are also provided based on random subsampling. The work to build this package is partially supported by the NSF grant DMS-2015298.
License: GPL (>= 2)
Depends: Matrix,irlba,plyr
Imports: stats,RSpectra
NeedsCompilation: no
Packaged: 2021-11-17 04:07:14 UTC; tianxili
Repository: CRAN
Date/Publication: 2021-11-18 14:40:02 UTC

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New package excluder with initial version 0.3.2
Package: excluder
Title: Checks for Exclusion Criteria in Online Data
Version: 0.3.2
Description: Data that are collected through online sources such as Mechanical Turk may require excluding rows because of IP address duplication, geolocation, or completion duration. This package facilitates exclusion of these data for Qualtrics datasets.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
URL: https://docs.ropensci.org/excluder/, https://github.com/ropensci/excluder/
BugReports: https://github.com/ropensci/excluder/issues/
Imports: cli, curl, dplyr, iptools, janitor, lubridate, magrittr, maps, rlang, stringr, tidyr, tidyselect
Depends: R (>= 3.5.0)
Suggests: covr, knitr, lifecycle, readr, rmarkdown, testthat (>= 3.0.0), withr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-11-10 14:41:09 UTC; jstevens
Author: Jeffrey R. Stevens [aut, cre, cph] (<https://orcid.org/0000-0003-2375-1360>), Joseph O'Brien [rev] (<https://orcid.org/0000-0001-9851-5077>), Julia Silge [rev] (<https://orcid.org/0000-0002-3671-836X>)
Maintainer: Jeffrey R. Stevens <jeffrey.r.stevens@gmail.com>
Repository: CRAN
Date/Publication: 2021-11-18 14:30:05 UTC

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New package adass with initial version 1.0.0
Package: adass
Title: Adaptive Smoothing Spline (AdaSS) Estimator for the Function-on-Function Linear Regression
Version: 1.0.0
Description: Implements the adaptive smoothing spline estimator for the function-on-function linear regression model described in Centofanti et al. (2020) <arXiv:2011.12036>.
License: GPL-3
Encoding: UTF-8
Imports: fda, parallel, matrixcalc, SparseM, mvtnorm, Rfast, plot3D
URL: https://github.com/unina-sfere/adass
BugReports: https://github.com/unina-sfere/adass
SystemRequirements: GNU make
Suggests: knitr, rmarkdown, testthat
NeedsCompilation: no
Packaged: 2021-11-17 12:02:24 UTC; fabio
Author: Fabio Centofanti [cre, aut], Antonio Lepore [aut], Alessandra Menafoglio [aut], Biagio Palumbo [aut], Simone Vantini [aut]
Maintainer: Fabio Centofanti <fabio.centofanti@unina.it>
Repository: CRAN
Date/Publication: 2021-11-18 14:40:05 UTC

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New package mapscanner with initial version 0.0.5
Package: mapscanner
Title: Print Maps, Draw on Them, Scan Them Back in
Version: 0.0.5
Description: Enables preparation of maps to be printed and drawn on. Modified maps can then be scanned back in, and hand-drawn marks converted to spatial objects.
License: GPL-3 | BSD_2_clause + file LICENSE
URL: https://github.com/ropensci/mapscanner
BugReports: https://github.com/ropensci/mapscanner/issues
Depends: R (>= 3.5.0)
Imports: cli, curl, fs, glue, magick, magrittr, memoise, pdftools, png, purrr, raster, Rcpp, reproj, RNiftyReg, sf, slippymath, tibble
Suggests: dplyr, ggplot2, gibble, jpeg, knitr, lwgeom, mapview, mmand, osmdata, polyclip, rmarkdown, spelling, testthat
LinkingTo: Rcpp
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-GB
NeedsCompilation: yes
SystemRequirements: C++11
Packaged: 2021-11-16 12:46:13 UTC; smexus
Author: Mark Padgham [aut, cre], Michael D. Sumner [aut], Kelly Hondula [rev] (Kelly reviewed the package for rOpenSci, see https://github.com/ropensci/software-review/issues/330), Nicholas Potter [rev] (Nichola reviewed the package for rOpenSci, see https://github.com/ropensci/software-review/issues/330), Stanislaw Adaszewski [cph] (author of include concaveman-cpp code)
Maintainer: Mark Padgham <mark.padgham@email.com>
Repository: CRAN
Date/Publication: 2021-11-18 13:30:02 UTC

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New package GPSeqClus with initial version 1.2.0
Package: GPSeqClus
Title: Sequential Clustering Algorithm for Location Data
Version: 1.2.0
Date: 2021-11-12
Author: Clapp, J. G.
Maintainer: Justin Clapp <justin.clapp@wyo.gov>
Description: Applies sequential clustering algorithm to animal location data based on user-defined parameters. Plots interactive cluster maps and provides a summary dataframe with attributes for each cluster commonly used as covariates in subsequent modeling efforts. Additional functions provide individual keyhole markup language plots for quick assessment, and export of global positioning system exchange format files for navigation purposes. Methods can be found at <doi:10.1111/2041-210X.13572>.
Depends: R (>= 3.5)
Imports: geosphere, htmlwidgets, leaflet, leaflet.extras, plotKML, plyr, purrr, rgdal, sp, spacetime, stats, suncalc, tcltk, utils
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2021-11-16 15:57:13 UTC; Jugclapp
Repository: CRAN
Date/Publication: 2021-11-18 13:40:02 UTC

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New package dynr with initial version 0.1.16-27
Package: dynr
Date: 2021-11-16
Title: Dynamic Models with Regime-Switching
Maintainer: Michael D. Hunter <mike.dynr@gmail.com>
URL: https://dynrr.github.io/, https://github.com/mhunter1/dynr
Contact: <dynr@googlegroups.com>
Depends: R (>= 3.0.0), ggplot2
Imports: MASS, Matrix, numDeriv, xtable, latex2exp, grid, reshape2, plyr, mice, magrittr, Rdpack, methods, fda, car, stringi, tibble, deSolve
Suggests: testthat, roxygen2 (>= 3.1), knitr, rmarkdown
VignetteBuilder: knitr
Description: Intensive longitudinal data have become increasingly prevalent in various scientific disciplines. Many such data sets are noisy, multivariate, and multi-subject in nature. The change functions may also be continuous, or continuous but interspersed with periods of discontinuities (i.e., showing regime switches). The package 'dynr' (Dynamic Modeling in R) is an R package that implements a set of computationally efficient algorithms for handling a broad class of linear and nonlinear discrete- and continuous-time models with regime-switching properties under the constraint of linear Gaussian measurement functions. The discrete-time models can generally take on the form of a state- space or difference equation model. The continuous-time models are generally expressed as a set of ordinary or stochastic differential equations. All estimation and computations are performed in C, but users are provided with the option to specify the model of interest via a set of simple and easy-to-learn model specification functions in R. Model fitting can be performed using single- subject time series data or multiple-subject longitudinal data. Ou, Hunter, & Chow (2019) <doi:10.32614/RJ-2019-012> provided a detailed introduction to the interface and more information on the algorithms.
SystemRequirements: GNU make
NeedsCompilation: yes
License: GPL-3
LazyLoad: yes
LazyData: yes
RdMacros: Rdpack
Biarch: true
Version: 0.1.16-27
Packaged: 2021-11-16 16:03:16 UTC; mhunter
Author: Lu Ou [aut], Michael D. Hunter [aut, cre] (<https://orcid.org/0000-0002-3651-6709>), Sy-Miin Chow [aut] (<https://orcid.org/0000-0003-1938-027X>), Linying Ji [aut], Meng Chen [aut], Hui-Ju Hung [aut], Jungmin Lee [aut], Yanling Li [aut], Jonathan Park [aut], Massachusetts Institute of Technology [cph], S. G. Johnson [cph], Benoit Scherrer [cph], Dieter Kraft [cph]
Repository: CRAN
Date/Publication: 2021-11-18 13:50:02 UTC

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Package corrplot updated to version 0.92 with previous version 0.91 dated 2021-11-10

Title: Visualization of a Correlation Matrix
Description: Provides a visual exploratory tool on correlation matrix that supports automatic variable reordering to help detect hidden patterns among variables.
Author: Taiyun Wei [cre, aut], Viliam Simko [aut], Michael Levy [ctb], Yihui Xie [ctb], Yan Jin [ctb], Jeff Zemla [ctb], Moritz Freidank [ctb], Jun Cai [ctb], Tomas Protivinsky [ctb]
Maintainer: Taiyun Wei <weitaiyun@gmail.com>

Diff between corrplot versions 0.91 dated 2021-11-10 and 0.92 dated 2021-11-18

 DESCRIPTION                         |    6 
 LICENSE                             |    4 
 MD5                                 |   82 -
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 NEWS.md                             |  297 ++--
 R/colorlegend.R                     |  226 +--
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 tests/testthat/test-corrRect.R      |  126 +-
 tests/testthat/test-corrplot.R      |  576 ++++-----
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 vignettes/example-colorlegend.R     |  108 -
 vignettes/example-corrMatOrder.R    |   56 
 vignettes/example-corrRect.R        |  146 +-
 vignettes/example-corrRect.hclust.R |   70 -
 vignettes/example-corrplot.R        |  458 +++----
 vignettes/example-corrplot.mixed.R  |   26 
 42 files changed, 5750 insertions(+), 5526 deletions(-)

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Package AgroReg updated to version 1.2.1 with previous version 1.2.0 dated 2021-10-11

Title: Regression Analysis Linear and Nonlinear for Agriculture
Description: Linear and nonlinear regression analysis common in agricultural science articles (Archontoulis & Miguez (2015). <doi:10.2134/agronj2012.0506>). The package includes polynomial, exponential, gaussian, logistic, logarithmic, segmented, non-parametric models, among others. The functions return the model coefficients and their respective p values, coefficient of determination, root mean square error, AIC, BIC, as well as graphs with the equations automatically.
Author: Gabriel Danilo Shimizu [aut, cre] (<https://orcid.org/0000-0001-8524-508X>), Leandro Simoes Azeredo Goncalves [aut, ctb] (<https://orcid.org/0000-0001-9700-9375>)
Maintainer: Gabriel Danilo Shimizu <shimizu@uel.br>

Diff between AgroReg versions 1.2.0 dated 2021-10-11 and 1.2.1 dated 2021-11-18

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 NAMESPACE                     |   12 ++
 NEWS.md                       |   12 ++
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 R/BIEXP_analysis.R            |   11 +-
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 R/N_analysis.R                |   17 ++-
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 R/asymptotic_i_sup_analysis.R |   12 +-
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 R/correlation_analysis.R      |only
 R/extractmodel_analysis.R     |only
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 R/linearlinear_analysis.R     |   21 +++-
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 R/mitscherlich_analysis.R     |   11 +-
 R/newton_analysis.R           |   14 +-
 R/peleg_analysis.R            |   14 +-
 R/plot_arrange.R              |   25 +++--
 R/pltLN_analysis.R            |   19 ++-
 R/pltQD_analysis.R            |   19 ++-
 R/potential_analysis.R        |   10 +-
 R/quadraticplateau_analysis.R |   19 ++-
 R/regression.R                |   24 ++--
 R/thompson_analysis.R         |   11 +-
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 man/GP.Rd                     |    5 -
 man/LL.Rd                     |    5 -
 man/LM.Rd                     |   14 ++
 man/LM13.Rd                   |    8 +
 man/LM13i.Rd                  |    8 +
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 104 files changed, 1049 insertions(+), 582 deletions(-)

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Package impactr updated to version 0.3.0 with previous version 0.2.0 dated 2021-09-03

Title: Mechanical Loading Prediction Through Accelerometer Data
Description: Functions to read, process and analyse accelerometer data related to mechanical loading variables. This package is developed and tested for use with raw accelerometer data from triaxial 'ActiGraph' <https://actigraphcorp.com> accelerometers.
Author: Lucas Veras [aut, cre] (<https://orcid.org/0000-0003-0562-5803>)
Maintainer: Lucas Veras <lucasdsveras@gmail.com>

Diff between impactr versions 0.2.0 dated 2021-09-03 and 0.3.0 dated 2021-11-18

 DESCRIPTION                   |    8 +-
 MD5                           |   32 +++++-----
 NEWS.md                       |    6 +
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 src/acceleration_rate.cpp     |   22 -------
 src/compute_loading.cpp       |   12 ++-
 tests/testthat/test-predict.R |   46 +++++++++++---
 17 files changed, 219 insertions(+), 105 deletions(-)

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Package datacleanr updated to version 1.0.3 with previous version 1.0.2 dated 2021-11-03

Title: Interactive and Reproducible Data Cleaning
Description: Flexible and efficient cleaning of data with interactivity. 'datacleanr' facilitates best practices in data analyses and reproducibility with built-in features and by translating interactive/manual operations to code. The package is designed for interoperability, and so seamlessly fits into reproducible analyses pipelines in 'R'.
Author: Alexander Hurley [cre, aut, cph] (<https://orcid.org/0000-0002-9641-2805>), Richard Peters [ctb] (<https://orcid.org/0000-0002-7441-1297>), Christoforos Pappas [ctb] (<https://orcid.org/0000-0001-5721-557X>)
Maintainer: Alexander Hurley <agl.hurley@gmail.com>

Diff between datacleanr versions 1.0.2 dated 2021-11-03 and 1.0.3 dated 2021-11-18

 DESCRIPTION                         |    6 +++---
 MD5                                 |    6 +++---
 NEWS.md                             |    4 ++++
 tests/testthat/test-filter_scoped.R |    4 +---
 4 files changed, 11 insertions(+), 9 deletions(-)

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Package spant updated to version 1.16.0 with previous version 1.15.0 dated 2021-10-22

Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.
Author: Martin Wilson [cre, aut] (<https://orcid.org/0000-0002-2089-3956>), Yong Wang [ctb], John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>

Diff between spant versions 1.15.0 dated 2021-10-22 and 1.16.0 dated 2021-11-18

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 81 files changed, 1975 insertions(+), 1899 deletions(-)

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Package opGMMassessment updated to version 0.3 with previous version 0.2.1 dated 2021-11-01

Title: Optimized Automated Gaussian Mixture Assessment
Description: Necessary functions for optimized automated evaluation of the number and parameters of Gaussian mixtures in one-dimensional data. Various methods are available for parameter estimation and for determining the number of modes in the mixture.
Author: Jorn Lotsch [aut,cre] (<https://orcid.org/0000-0002-5818-6958>), Sebastian Malkusch [aut] (<https://orcid.org/0000-0001-6766-140X>), Martin Maechler [ctb], Peter Rousseeuw [ctb], Anja Struyf [ctb], Mia Hubert [ctb], Kurt Hornik [ctb]
Maintainer: Jorn Lotsch <j.lotsch@em.uni-frankfurt.de>

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Package spmoran updated to version 0.2.2.1 with previous version 0.2.2 dated 2021-09-13

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

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Package DatabaseConnector updated to version 5.0.0 with previous version 4.0.2 dated 2021-04-15

Title: Connecting to Various Database Platforms
Description: An R 'DataBase Interface' ('DBI') compatible interface to various database platforms ('PostgreSQL', 'Oracle', 'Microsoft SQL Server', 'Amazon Redshift', 'Microsoft Parallel Database Warehouse', 'IBM Netezza', 'Apache Impala', 'Google BigQuery', 'Spark', and 'SQLite'). Also includes support for fetching data as 'Andromeda' objects. Uses 'Java Database Connectivity' ('JDBC') to connect to databases (except SQLite).
Author: Martijn Schuemie [aut, cre], Marc Suchard [aut], Observational Health Data Science and Informatics [cph], Microsoft Inc. [cph] (SQL Server JDBC driver), PostgreSQL Global Development Group [cph] (PostgreSQL JDBC driver), Oracle Inc. [cph] (Oracle JDBC driver), Amazon Inc. [cph] (RedShift JDBC driver)
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>

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Package briskaR updated to version 1.0.3 with previous version 1.0.2 dated 2021-01-11

Title: Biological Risk Assessment
Description: A spatio-temporal exposure-hazard model for assessing biological risk and impact. The model is based on stochastic geometry for describing the landscape and the exposed individuals, a dispersal kernel for the dissemination of contaminants, a set of tools to handle spatio-temporal dataframe and ecotoxicological equations. Walker E, Leclerc M, Rey JF, Beaudouin R, Soubeyrand S, and Messean A, (2017), A Spatio-Temporal Exposure-Hazard Model for Assessing Biological Risk and Impact, Risk Analysis, <doi:10.1111/risa.12941>. Leclerc M, Walker E, Messean A, Soubeyrand S (2018), Spatial exposure-hazard and landscape models for assessing the impact of GM crops on non-target organisms, Science of the Total Environment, 624, 470-479.
Author: Virgile Baudrot [aut], Emily Walker [aut], Jean-Francois Rey [aut, cre], Melen Leclerc [aut], Samuel Soubeyrand [ctb], Marc Bourotte [ctb]
Maintainer: Jean-Francois Rey <jean-francois.rey@inrae.fr>

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Package antaresViz (with last version 0.16) was removed from CRAN

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

2021-06-21 0.16
2021-01-12 0.15.4
2020-11-13 0.15.3
2020-05-26 0.15.2
2020-02-24 0.15.1
2018-10-11 0.15.0
2018-06-12 0.14.0
2018-05-22 0.13.0

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Package safedata (with last version 1.0.9) was removed from CRAN

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

2020-11-18 1.0.9
2020-10-09 1.0.8
2020-08-03 1.0.7
2020-07-07 1.0.5
2020-06-02 1.0.1

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Package MAGEE updated to version 1.0.1 with previous version 1.0.0 dated 2021-05-10

Title: Mixed Model Association Test for GEne-Environment Interaction
Description: Use a 'glmmkin' class object (GMMAT package) from the null model to perform generalized linear mixed model-based single-variant and variant set main effect tests, gene-environment interaction tests, and joint tests for association, as proposed in Wang et al. (2020) <DOI:10.1002/gepi.22351>.
Author: Xinyu Wang [aut], Han Chen [aut, cre], Duy Pham [aut]
Maintainer: Han Chen <han.chen.2@uth.tmc.edu>

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Package dipm updated to version 1.4 with previous version 1.3 dated 2021-11-17

Title: Depth Importance in Precision Medicine (DIPM) Method
Description: An implementation of the Depth Importance in Precision Medicine (DIPM) method in Chen and Zhang (2020) <doi:10.1093/biostatistics/kxaa021> and Chen and Zhang (2020) <doi:10.1007/978-3-030-46161-4_16>. The DIPM method is a classification tree that searches for subgroups with especially poor or strong performance in a given treatment group.
Author: Cai Li [aut, cre], Victoria Chen [aut], Heping Zhang [aut]
Maintainer: Cai Li <cli9@ncsu.edu>

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Package rcdd updated to version 1.5 with previous version 1.4 dated 2021-10-19

Title: Computational Geometry
Description: R interface to (some of) cddlib (<https://github.com/cddlib/cddlib>). Converts back and forth between two representations of a convex polytope: as solution of a set of linear equalities and inequalities and as convex hull of set of points and rays. Also does linear programming and redundant generator elimination (for example, convex hull in n dimensions). All functions can use exact infinite-precision rational arithmetic.
Author: Charles J. Geyer <charlie@stat.umn.edu> and Glen D. Meeden <glen@stat.umn.edu>, incorporates code from cddlib (ver 0.94f) written by Komei Fukuda <fukuda@ifor.math.ethz.ch>
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>

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Package radiant.design updated to version 1.4.1 with previous version 1.3.5 dated 2020-03-24

Title: Design Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Design menu includes interfaces for design of experiments, sampling, and sample size calculation. The application extends the functionality in 'radiant.data'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>

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Package radiant.basics updated to version 1.4.1 with previous version 1.4.0 dated 2021-06-03

Title: Basics Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Basics menu includes interfaces for probability calculation, central limit theorem simulation, comparing means and proportions, goodness-of-fit testing, cross-tabs, and correlation. The application extends the functionality in 'radiant.data'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>

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Package presenter updated to version 0.1.1 with previous version 0.1.0 dated 2021-10-08

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 imager updated to version 0.42.11 with previous version 0.42.10 dated 2021-06-10

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 iForecast updated to version 1.0.4 with previous version 1.0.3 dated 2021-07-30

Title: Machine Learning Time Series Forecasting
Description: Compute both static and recursive time series forecasts of machine learning models.
Author: Ho Tsung-wu
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>

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Package fmtr updated to version 1.5.4 with previous version 1.5.3 dated 2021-10-09

Title: Easily Apply Formats to Data
Description: Contains a set of functions that can be used to apply formats to data frames or vectors. The package aims to provide to functionality similar to that of SAS® formats. Formats are assigned to the format attribute on data frame columns. Then when the fdata() function is called, a new data frame is created with the column data formatted as specified. The package also contains a value() function to create a user-defined format, similar to a SAS® user-defined format.
Author: David Bosak
Maintainer: David Bosak <dbosak01@gmail.com>

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Package exiftoolr updated to version 0.1.7 with previous version 0.1.6 dated 2021-11-06

Title: ExifTool Functionality from R
Description: Reads, writes, and edits EXIF and other file metadata using ExifTool <https://exiftool.org/>, returning read results as a data frame. ExifTool supports many different metadata formats including EXIF, GPS, IPTC, XMP, JFIF, GeoTIFF, ICC Profile, Photoshop IRB, FlashPix, AFCP and ID3, Lyrics3, as well as the maker notes of many digital cameras by Canon, Casio, DJI, FLIR, FujiFilm, GE, GoPro, HP, JVC/Victor, Kodak, Leaf, Minolta/Konica-Minolta, Motorola, Nikon, Nintendo, Olympus/Epson, Panasonic/Leica, Pentax/Asahi, Phase One, Reconyx, Ricoh, Samsung, Sanyo, Sigma/Foveon and Sony.
Author: Joshua O'Brien [aut, cre]
Maintainer: Joshua O'Brien <joshmobrien@gmail.com>

Diff between exiftoolr versions 0.1.6 dated 2021-11-06 and 0.1.7 dated 2021-11-18

 DESCRIPTION      |    8 ++---
 MD5              |   10 +++---
 NEWS.md          |    9 +++++
 R/exif_read.R    |    4 +-
 R/utils.R        |   86 +++++++++++++++++++++++++++++++------------------------
 man/exif_call.Rd |    2 -
 6 files changed, 71 insertions(+), 48 deletions(-)

More information about exiftoolr at CRAN
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