Thu, 07 Nov 2024

Package RobinCar updated to version 0.3.2 with previous version 0.3.1 dated 2024-11-06

Title: Robust Inference for Covariate Adjustment in Randomized Clinical Trials
Description: Performs robust estimation and inference when using covariate adjustment and/or covariate-adaptive randomization in randomized clinical trials. Ting Ye, Jun Shao, Yanyao Yi, Qinyuan Zhao (2023) <doi:10.1080/01621459.2022.2049278>. Ting Ye, Marlena Bannick, Yanyao Yi, Jun Shao (2023) <doi:10.1080/24754269.2023.2205802>. Ting Ye, Jun Shao, Yanyao Yi (2023) <doi:10.1093/biomet/asad045>. Marlena Bannick, Jun Shao, Jingyi Liu, Yu Du, Yanyao Yi, Ting Ye (2024) <doi:10.48550/arXiv.2306.10213>.
Author: Marlena Bannick [cre, aut] , Ting Ye [aut], Yanyao Yi [aut], Faith Bian [aut]
Maintainer: Marlena Bannick <mnorwood@uw.edu>

Diff between RobinCar versions 0.3.1 dated 2024-11-06 and 0.3.2 dated 2024-11-07

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Package mlr3data updated to version 0.9.0 with previous version 0.8.0 dated 2024-11-06

Title: Collection of Machine Learning Data Sets for 'mlr3'
Description: A small collection of interesting and educational machine learning data sets which are used as examples in the 'mlr3' book (<https://mlr3book.mlr-org.com>), the use case gallery (<https://mlr3gallery.mlr-org.com>), or in other examples. All data sets are properly preprocessed and ready to be analyzed by most machine learning algorithms. Data sets are automatically added to the dictionary of tasks if 'mlr3' is loaded.
Author: Michel Lang [ctb] , Marc Becker [cre, aut]
Maintainer: Marc Becker <marcbecker@posteo.de>

Diff between mlr3data versions 0.8.0 dated 2024-11-06 and 0.9.0 dated 2024-11-07

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Package fromo updated to version 0.2.3 with previous version 0.2.2 dated 2024-11-03

Title: Fast Robust Moments
Description: Fast, numerically robust computation of weighted moments via 'Rcpp'. Supports computation on vectors and matrices, and Monoidal append of moments. Moments and cumulants over running fixed length windows can be computed, as well as over time-based windows. Moment computations are via a generalization of Welford's method, as described by Bennett et. (2009) <doi:10.1109/CLUSTR.2009.5289161>.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>

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Package CRMetrics updated to version 0.3.2 with previous version 0.3.0 dated 2023-09-01

Title: Cell Ranger Output Filtering and Metrics Visualization
Description: Sample and cell filtering as well as visualisation of output metrics from 'Cell Ranger' by Grace X.Y. Zheng et al. (2017) <doi:10.1038/ncomms14049>. 'CRMetrics' allows for easy plotting of output metrics across multiple samples as well as comparative plots including statistical assessments of these. 'CRMetrics' allows for easy removal of ambient RNA using 'SoupX' by Matthew D Young and Sam Behjati (2020) <doi:10.1093/gigascience/giaa151> or 'CellBender' by Stephen J Fleming et al. (2022) <doi:10.1101/791699>. Furthermore, it is possible to preprocess data using 'Pagoda2' by Nikolas Barkas et al. (2021) <https://github.com/kharchenkolab/pagoda2> or 'Seurat' by Yuhan Hao et al. (2021) <doi:10.1016/j.cell.2021.04.048> followed by embedding of cells using 'Conos' by Nikolas Barkas et al. (2019) <doi:10.1038/s41592-019-0466-z>. Finally, doublets can be detected using 'scrublet' by Samuel L. Wolock et al. (2019) <doi:10.1016/j.cels.2018.11.005> or 'D [...truncated...]
Author: Rasmus Rydbirk [aut, cre], Fabienne Kick [aut], Henrietta Holze [aut], Xian Xin [ctb]
Maintainer: Rasmus Rydbirk <rrydbirk@outlook.dk>

Diff between CRMetrics versions 0.3.0 dated 2023-09-01 and 0.3.2 dated 2024-11-07

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Package Amelia updated to version 1.8.3 with previous version 1.8.2 dated 2024-04-23

Title: A Program for Missing Data
Description: A tool that "multiply imputes" missing data in a single cross-section (such as a survey), from a time series (like variables collected for each year in a country), or from a time-series-cross-sectional data set (such as collected by years for each of several countries). Amelia II implements our bootstrapping-based algorithm that gives essentially the same answers as the standard IP or EMis approaches, is usually considerably faster than existing approaches and can handle many more variables. Unlike Amelia I and other statistically rigorous imputation software, it virtually never crashes (but please let us know if you find to the contrary!). The program also generalizes existing approaches by allowing for trends in time series across observations within a cross-sectional unit, as well as priors that allow experts to incorporate beliefs they have about the values of missing cells in their data. Amelia II also includes useful diagnostics of the fit of multiple imputation models. The p [...truncated...]
Author: James Honaker [aut], Gary King [aut], Matthew Blackwell [aut, cre]
Maintainer: Matthew Blackwell <mblackwell@gmail.com>

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Package SAMtool updated to version 1.8.0 with previous version 1.7.0 dated 2024-08-29

Title: Stock Assessment Methods Toolkit
Description: Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform data-rich fisheries. 'SAMtool' provides a conditioning model, assessment models of varying complexity with standardized reporting, model-based management procedures, and diagnostic tools for evaluating assessments inside closed-loop simulation.
Author: Quang Huynh [aut, cre], Tom Carruthers [aut], Adrian Hordyk [aut]
Maintainer: Quang Huynh <quang@bluematterscience.com>

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Package vglmer updated to version 1.0.6 with previous version 1.0.5 dated 2024-09-12

Title: Variational Inference for Hierarchical Generalized Linear Models
Description: Estimates hierarchical models using variational inference. At present, it can estimate logistic, linear, and negative binomial models. It can accommodate models with an arbitrary number of random effects and requires no integration to estimate. It also provides the ability to improve the quality of the approximation using marginal augmentation. Goplerud (2022) <doi:10.1214/21-BA1266> and Goplerud (2024) <doi:10.1017/S0003055423000035> provide details on the variational algorithms.
Author: Max Goplerud [aut, cre]
Maintainer: Max Goplerud <mgoplerud@austin.utexas.edu>

Diff between vglmer versions 1.0.5 dated 2024-09-12 and 1.0.6 dated 2024-11-07

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Package gKRLS updated to version 1.0.4 with previous version 1.0.3 dated 2024-09-04

Title: Generalized Kernel Regularized Least Squares
Description: Kernel regularized least squares, also known as kernel ridge regression, is a flexible machine learning method. This package implements this method by providing a smooth term for use with 'mgcv' and uses random sketching to facilitate scalable estimation on large datasets. It provides additional functions for calculating marginal effects after estimation and for use with ensembles ('SuperLearning'), double/debiased machine learning ('DoubleML'), and robust/clustered standard errors ('sandwich'). Chang and Goplerud (2024) <doi:10.1017/pan.2023.27> provide further details.
Author: Qing Chang [aut], Max Goplerud [aut, cre]
Maintainer: Max Goplerud <mgoplerud@austin.utexas.edu>

Diff between gKRLS versions 1.0.3 dated 2024-09-04 and 1.0.4 dated 2024-11-07

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Package bbotk updated to version 1.3.0 with previous version 1.2.0 dated 2024-10-25

Title: Black-Box Optimization Toolkit
Description: Features highly configurable search spaces via the 'paradox' package and optimizes every user-defined objective function. The package includes several optimization algorithms e.g. Random Search, Iterated Racing, Bayesian Optimization (in 'mlr3mbo') and Hyperband (in 'mlr3hyperband'). bbotk is the base package of 'mlr3tuning', 'mlr3fselect' and 'miesmuschel'.
Author: Marc Becker [cre, aut] , Jakob Richter [aut] , Michel Lang [aut] , Bernd Bischl [aut] , Martin Binder [aut], Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>

Diff between bbotk versions 1.2.0 dated 2024-10-25 and 1.3.0 dated 2024-11-07

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Package msm updated to version 1.8.2 with previous version 1.8.1 dated 2024-10-04

Title: Multi-State Markov and Hidden Markov Models in Continuous Time
Description: Functions for fitting continuous-time Markov and hidden Markov multi-state models to longitudinal data. Designed for processes observed at arbitrary times in continuous time (panel data) but some other observation schemes are supported. Both Markov transition rates and the hidden Markov output process can be modelled in terms of covariates, which may be constant or piecewise-constant in time.
Author: Christopher Jackson [aut, cre]
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>

Diff between msm versions 1.8.1 dated 2024-10-04 and 1.8.2 dated 2024-11-07

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Package mlr3viz updated to version 0.10.0 with previous version 0.9.0 dated 2024-07-01

Title: Visualizations for 'mlr3'
Description: Visualization package of the 'mlr3' ecosystem. It features plots for mlr3 objects such as tasks, learners, predictions, benchmark results, tuning instances and filters via the 'autoplot()' generic of 'ggplot2'. The package draws plots with the 'viridis' color palette and applies the minimal theme. Visualizations include barplots, boxplots, histograms, ROC curves, and Precision-Recall curves.
Author: Michel Lang [aut] , Patrick Schratz [aut] , Raphael Sonabend [aut] , Marc Becker [cre, aut] , Jakob Richter [aut] , Damir Pulatov [ctb], John Zobolas [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>

Diff between mlr3viz versions 0.9.0 dated 2024-07-01 and 0.10.0 dated 2024-11-07

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Package mlr3fselect updated to version 1.2.1 with previous version 1.2.0 dated 2024-10-25

Title: Feature Selection for 'mlr3'
Description: Feature selection package of the 'mlr3' ecosystem. It selects the optimal feature set for any 'mlr3' learner. The package works with several optimization algorithms e.g. Random Search, Recursive Feature Elimination, and Genetic Search. Moreover, it can automatically optimize learners and estimate the performance of optimized feature sets with nested resampling.
Author: Marc Becker [aut, cre] , Patrick Schratz [aut] , Michel Lang [aut] , Bernd Bischl [aut] , John Zobolas [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>

Diff between mlr3fselect versions 1.2.0 dated 2024-10-25 and 1.2.1 dated 2024-11-07

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Package charcuterie updated to version 0.0.6 with previous version 0.0.4 dated 2024-09-13

Title: Handle Strings as Vectors of Characters
Description: Creates a new chars class which looks like a string but is actually a vector of individual characters, making 'strings' iterable. This class enables vector operations on 'strings' such as reverse, sort, head, and set operations.
Author: Jonathan Carroll [aut, cre]
Maintainer: Jonathan Carroll <rpkg@jcarroll.com.au>

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Package waldo updated to version 0.6.1 with previous version 0.6.0 dated 2024-11-04

Title: Find Differences Between R Objects
Description: Compare complex R objects and reveal the key differences. Designed particularly for use in testing packages where being able to quickly isolate key differences makes understanding test failures much easier.
Author: Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>

Diff between waldo versions 0.6.0 dated 2024-11-04 and 0.6.1 dated 2024-11-07

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Package stars updated to version 0.6-7 with previous version 0.6-6 dated 2024-07-16

Title: Spatiotemporal Arrays, Raster and Vector Data Cubes
Description: Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL' bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.
Author: Edzer Pebesma [aut, cre] , Michael Sumner [ctb] , Etienne Racine [ctb], Adriano Fantini [ctb], David Blodgett [ctb], Krzysztof Dyba [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

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Package smcfcs updated to version 1.9.0 with previous version 1.8.0 dated 2024-06-04

Title: Multiple Imputation of Covariates by Substantive Model Compatible Fully Conditional Specification
Description: Implements multiple imputation of missing covariates by Substantive Model Compatible Fully Conditional Specification. This is a modification of the popular FCS/chained equations multiple imputation approach, and allows imputation of missing covariate values from models which are compatible with the user specified substantive model.
Author: Jonathan Bartlett [aut, cre], Ruth Keogh [aut], Edouard F. Bonneville [aut], Claus Thorn Ekstroem [ctb]
Maintainer: Jonathan Bartlett <jonathan.bartlett1@lshtm.ac.uk>

Diff between smcfcs versions 1.8.0 dated 2024-06-04 and 1.9.0 dated 2024-11-07

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Package parallelly updated to version 1.39.0 with previous version 1.38.0 dated 2024-07-27

Title: Enhancing the 'parallel' Package
Description: Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.
Author: Henrik Bengtsson [aut, cre, cph] , Mike Cheng [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between parallelly versions 1.38.0 dated 2024-07-27 and 1.39.0 dated 2024-11-07

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Package arkhe updated to version 1.8.0 with previous version 1.7.0 dated 2024-07-29

Title: Tools for Cleaning Rectangular Data
Description: A dependency-free collection of simple functions for cleaning rectangular data. This package allows to detect, count and replace values or discard rows/columns using a predicate function. In addition, it provides tools to check conditions and return informative error messages.
Author: Nicolas Frerebeau [aut, cre] , Brice Lebrun [ctb] , Universite Bordeaux Montaigne [fnd], CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>

Diff between arkhe versions 1.7.0 dated 2024-07-29 and 1.8.0 dated 2024-11-07

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Package yulab.utils updated to version 0.1.8 with previous version 0.1.7 dated 2024-08-26

Title: Supporting Functions for Packages Maintained by 'YuLab-SMU'
Description: Miscellaneous functions commonly used by 'YuLab-SMU'.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between yulab.utils versions 0.1.7 dated 2024-08-26 and 0.1.8 dated 2024-11-07

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Package Q2q updated to version 0.1.1 with previous version 0.1.0 dated 2020-11-23

Title: Interpolating Age-Specific Mortality Rates at All Ages
Description: Mortality rates are typically provided in an abridged format, i.e., by age groups 0, [1, 5], [5, 10]', '[10, 15]', and so on. Some applications necessitate a detailed (single) age description. Despite the large number of proposed approaches in the literature, only a few methods ensure great performance at both younger and higher ages. For example, the 6-term 'Lagrange' interpolation function is well suited to mortality interpolation at younger ages (with irregular intervals), but not at older ages. The 'Karup-King' method, on the other hand, performs well at older ages but is not suitable for younger ones. Interested readers can find a full discussion of the two stated methods in the book Shryock, Siegel, and Associates (1993).The Q2q package combines the two methods to allow for the interpolation of mortality rates across all age groups. It begins by implementing each method independently, and then the resulting curves are linked using a 5-age averaged error between the two partial cu [...truncated...]
Author: Farid FLICI [aut, cre]
Maintainer: Farid FLICI <farid.flici@cread.dz>

Diff between Q2q versions 0.1.0 dated 2020-11-23 and 0.1.1 dated 2024-11-07

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Package mda updated to version 0.5-5 with previous version 0.5-4 dated 2023-06-22

Title: Mixture and Flexible Discriminant Analysis
Description: Mixture and flexible discriminant analysis, multivariate adaptive regression splines (MARS), BRUTO, and vector-response smoothing splines. Hastie, Tibshirani and Friedman (2009) "Elements of Statistical Learning (second edition, chap 12)" Springer, New York.
Author: Trevor Hastie [aut, cre] , Robert Tibshirani [aut] , Balasubramanian Narasimhan [ctb] , Friedrich Leisch [ctb] , Kurt Hornik [ctb] , Brian Ripley [ctb]
Maintainer: Trevor Hastie <hastie@stanford.edu>

Diff between mda versions 0.5-4 dated 2023-06-22 and 0.5-5 dated 2024-11-07

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Package GGIR updated to version 3.1-5 with previous version 3.1-4 dated 2024-09-03

Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from 'GENEActiv' <https://activinsights.com/>, binary (.gt3x) and .csv-export data from 'Actigraph' <https://theactigraph.com> devices, and binary (.cwa) and .csv-export data from 'Axivity' <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format. Also the package allows for external function embedding.
Author: Vincent T van Hees [aut, cre], Jairo H Migueles [aut] , Severine Sabia [ctb], Matthew R Patterson [ctb], Zhou Fang [ctb], Joe Heywood [ctb], Joan Capdevila Pujol [ctb], Lena Kushleyeva [ctb], Mathilde Chen [ctb], Manasa Yerramalla [ctb], Patrick Bos [...truncated...]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>

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Package fr updated to version 0.5.2 with previous version 0.5.1 dated 2023-11-30

Title: Frictionless Standards
Description: A "tabular-data-resource" (<https://specs.frictionlessdata.io/tabular-data-resource/>) is a simple format to describe a singular tabular data resource such as a CSV file. It includes support both for metadata such as author and title and a schema to describe the data, for example the types of the fields/columns in the data. Create a tabular-data-resource by providing a data.frame and specifying metadata. Write and read tabular-data-resources to and from disk.
Author: Cole Brokamp [aut, cre, cph] , Tomasz Kalinowski [ctb]
Maintainer: Cole Brokamp <cole@colebrokamp.com>

Diff between fr versions 0.5.1 dated 2023-11-30 and 0.5.2 dated 2024-11-07

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Package CVXR updated to version 1.0-15 with previous version 1.0-14 dated 2024-06-27

Title: Disciplined Convex Optimization
Description: An object-oriented modeling language for disciplined convex programming (DCP) as described in Fu, Narasimhan, and Boyd (2020, <doi:10.18637/jss.v094.i14>). It allows the user to formulate convex optimization problems in a natural way following mathematical convention and DCP rules. The system analyzes the problem, verifies its convexity, converts it into a canonical form, and hands it off to an appropriate solver to obtain the solution. Interfaces to solvers on CRAN and elsewhere are provided, both commercial and open source.
Author: Anqi Fu [aut, cre], Balasubramanian Narasimhan [aut], David W Kang [aut], Steven Diamond [aut], John Miller [aut], Stephen Boyd [ctb], Paul Kunsberg Rosenfield [ctb]
Maintainer: Anqi Fu <anqif@alumni.stanford.edu>

Diff between CVXR versions 1.0-14 dated 2024-06-27 and 1.0-15 dated 2024-11-07

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New package WMAP with initial version 1.0.0
Package: WMAP
Title: Weighted Meta-Analysis with Pseudo-Populations
Version: 1.0.0
Description: Implementation of integrative weighting approaches for multiple observational studies and causal inferences. The package features three weighting approaches, each representing a special case of the unified weighting framework, introduced by Guha and Li (2024) <doi:10.1093/biomtc/ujae070>, which includes an extension of inverse probability weights for data integration settings.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: pkgcond, ggplot2, zeallot, caret, randomForest, forcats, utils, stats, grDevices
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2024-11-06 02:25:33 UTC; doggydoggy
Author: Subharup Guha [aut, cre], Mengqi Xu [aut], Kashish Priyam [aut], Yi Li [aut]
Maintainer: Subharup Guha <s.guha@ufl.edu>
Repository: CRAN
Date/Publication: 2024-11-07 18:40:02 UTC

More information about WMAP at CRAN
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Package validmind updated to version 0.1.2 with previous version 0.1.1 dated 2024-04-08

Title: Interface to the 'ValidMind' Platform
Description: Deploy, execute, and analyze the results of models hosted on the 'ValidMind' platform <https://validmind.com>. This package interfaces with the 'Python' client library in order to allow advanced diagnostics and insight into trained models all from an 'R' environment.
Author: Andres Rodriguez [aut, cre, cph]
Maintainer: Andres Rodriguez <andres@validmind.ai>

Diff between validmind versions 0.1.1 dated 2024-04-08 and 0.1.2 dated 2024-11-07

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New package threeBrain with initial version 1.2.0
Package: threeBrain
Title: Your Advanced 3D Brain Visualization
Version: 1.2.0
Description: A fast, interactive cross-platform, and easy to share 'WebGL'-based 3D brain viewer that visualizes 'FreeSurfer' and/or 'AFNI/SUMA' surfaces. The viewer widget can be either standalone or embedded into 'R-shiny' applications. The standalone version only require a web browser with 'WebGL2' support (for example, 'Chrome', 'Firefox', 'Safari'), and can be inserted into any websites. The 'R-shiny' support allows the 3D viewer to be dynamically generated from reactive user inputs. Please check the publication by Wang, Magnotti, Zhang, and Beauchamp (2023, <doi:10.1523/ENEURO.0328-23.2023>) for electrode localization. This viewer has been fully adopted by 'RAVE' <https://openwetware.org/wiki/RAVE>, an interactive toolbox to analyze 'iEEG' data by Magnotti, Wang, and Beauchamp (2020, <doi:10.1016/j.neuroimage.2020.117341>). Please check 'citation("threeBrain")' for details.
License: MPL-2.0
Encoding: UTF-8
Language: en-US
URL: https://dipterix.org/threeBrain/, https://github.com/dipterix/threeBrain
BugReports: https://github.com/dipterix/threeBrain/issues
Imports: utils, grDevices, graphics, dipsaus, xml2, servr, png, knitr, shiny (>= 1.2.0), digest (>= 0.6.22), freesurferformats (>= 0.1.7), jsonlite (>= 1.5), stringr (>= 1.3.1), htmlwidgets (>= 1.3), R6 (>= 2.3.0), gifti (>= 0.7.5), oro.nifti (>= 0.9.1)
Suggests: rmarkdown, DT, ravetools, htmltools
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-05 16:10:27 UTC; dipterix
Author: Zhengjia Wang [aut, cre, cph], John Magnotti [ctb, res], Xiang Zhang [ctb, res], Brian Metzger [res], Elizabeth Nesbitt [res], Meng Li [ths], Michael Beauchamp [ths, ctb, dtc]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-07 18:20:03 UTC

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New package shelter with initial version 0.1.1
Package: shelter
Title: Support for Secure API Key Management
Version: 0.1.1
Maintainer: Shawn Garbett <Shawn.Garbett@vumc.org>
Description: Secure handling of API keys can be difficult. This package provides secure convenience functions for entering / handling API keys and opening connections via inversion of control on those keys. Works seamlessly between production and developer environments.
Depends: R (>= 4.1.0)
License: GPL-3
Encoding: UTF-8
Imports: checkmate, getPass, yaml, filelock, rappdirs, sodium
Suggests: testthat (>= 3.0.0), rstudioapi, mockery
URL: https://github.com/vubiostat/shelter
BugReports: https://github.com/vubiostat/shelter/issues
NeedsCompilation: no
Packaged: 2024-11-05 21:06:37 UTC; garbetsp
Author: Benjamin Nutter [ctb, aut], Shawn Garbett [cre, ctb] , Hui Wu [aut], Cole Beck [aut], Savannah Obregon [aut]
Repository: CRAN
Date/Publication: 2024-11-07 18:30:02 UTC

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Package riverdist updated to version 0.17.1 with previous version 0.17.0 dated 2024-10-15

Title: River Network Distance Computation and Applications
Description: Reads river network shape files and computes network distances. Also included are a variety of computation and graphical tools designed for fisheries telemetry research, such as minimum home range, kernel density estimation, and clustering analysis using empirical k-functions with a bootstrap envelope. Tools are also provided for editing the river networks, meaning there is no reliance on external software.
Author: Matt Tyers [aut, cre]
Maintainer: Matt Tyers <matttyersstat@gmail.com>

Diff between riverdist versions 0.17.0 dated 2024-10-15 and 0.17.1 dated 2024-11-07

 DESCRIPTION                      |   18 +++++++++---------
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Package jagshelper updated to version 0.4.1 with previous version 0.4.0 dated 2024-10-21

Title: Extracting and Visualizing Output from 'jagsUI'
Description: Tools are provided to streamline Bayesian analyses in 'JAGS' using the 'jagsUI' package. Included are functions for extracting output in simpler format, functions for streamlining assessment of convergence, and functions for producing summary plots of output. Also included is a function that provides a simple template for running 'JAGS' from 'R'. Referenced materials can be found at <DOI:10.1214/ss/1177011136>.
Author: Matt Tyers [aut, cre]
Maintainer: Matt Tyers <matttyersstat@gmail.com>

Diff between jagshelper versions 0.4.0 dated 2024-10-21 and 0.4.1 dated 2024-11-07

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New package washr with initial version 1.0.1
Package: washr
Title: Publication Toolkit for Water, Sanitation and Hygiene (WASH) Data
Version: 1.0.1
Description: A toolkit to set up an R data package in a consistent structure. Automates tasks like tidy data export, data dictionary documentation, README and website creation, and citation management.
License: GPL (>= 3)
Encoding: UTF-8
Imports: desc (>= 1.4.3), devtools (>= 2.4.5), cffr (>= 1.0.1), pkgdown (>= 2.0.7), rlang (>= 1.1.3), usethis (>= 2.2.3), utils (>= 4.3.3)
Language: en-GB
Date: 2024-11-01
URL: https://openwashdata.github.io/washr/
BugReports: https://github.com/openwashdata/washr/issues
Suggests: knitr, rmarkdown, testthat (>= 3.2.1), withr (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-05 12:05:48 UTC; cwalder
Author: Mian Zhong [aut] , Margaux Goetschmann [aut] , Colin Walder [aut, cre] , Lars Schoebitz [aut] , Global Health Engineering, ETH Zurich [cph]
Maintainer: Colin Walder <cwalder@ethz.ch>
Repository: CRAN
Date/Publication: 2024-11-07 17:50:02 UTC

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Package CCMMR updated to version 0.2.1 with previous version 0.2 dated 2023-12-21

Title: Minimization of the Convex Clustering Loss Function
Description: Implements the convex clustering through majorization-minimization (CCMM) algorithm described in Touw, Groenen, and Terada (2022) <doi:10.48550/arXiv.2211.01877> to perform minimization of the convex clustering loss function.
Author: Daniel Touw [aut, cre] , Patrick Groenen [aut] , Yoshikazu Terada [aut]
Maintainer: Daniel Touw <touw@ese.eur.nl>

Diff between CCMMR versions 0.2 dated 2023-12-21 and 0.2.1 dated 2024-11-07

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Package Rnest updated to version 0.0.0.2 with previous version 0.0.0.1 dated 2024-05-21

Title: Next Eigenvalue Sufficiency Test
Description: Determine the number of dimensions to retain in exploratory factor analysis. The main function, nest(), returns the solution and the plot(nest()) returns a plot.
Author: P.-O. Caron [aut, cre, cph]
Maintainer: P.-O. Caron <pocaron19@gmail.com>

Diff between Rnest versions 0.0.0.1 dated 2024-05-21 and 0.0.0.2 dated 2024-11-07

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Package plotthis updated to version 0.3.6 with previous version 0.3.5 dated 2024-11-05

Title: High-Level Plotting Built Upon 'ggplot2' and Other Plotting Packages
Description: Provides high-level API and a wide range of options to create stunning, publication-quality plots effortlessly. It is built upon 'ggplot2' and other plotting packages, and is designed to be easy to use and to work seamlessly with 'ggplot2' objects. It is particularly useful for creating complex plots with multiple layers, facets, and annotations. It also provides a set of functions to create plots for specific types of data, such as Venn diagrams, alluvial diagrams, and phylogenetic trees. The package is designed to be flexible and customizable, and to work well with the 'ggplot2' ecosystem. The API can be found at <https://pwwang.github.io/plotthis/reference/index.html>.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>

Diff between plotthis versions 0.3.5 dated 2024-11-05 and 0.3.6 dated 2024-11-07

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Package digiRhythm updated to version 2.3 with previous version 2.2 dated 2024-07-31

Title: Analyzing Animal's Rhythmicity
Description: Analyze and visualize the rhythmic behavior of animals using the degree of functional coupling (See Scheibe (1999) <doi:10.1076/brhm.30.2.216.1420>), compute and visualize harmonic power, actograms, average activity and diurnality index.
Author: Hassan-Roland Nasser [aut, cre], Marie Schneider [aut, ctb], Joanna Stachowicz [aut, rev], Christina Umstaetter [aut, ths]
Maintainer: Hassan-Roland Nasser <hassan.nasser@me.com>

Diff between digiRhythm versions 2.2 dated 2024-07-31 and 2.3 dated 2024-11-07

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Package translated (with last version 0.1.1) was removed from CRAN

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

2023-04-25 0.1.1
2023-01-31 0.1.0

Permanent link
Package table.glue (with last version 0.0.4) was removed from CRAN

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

2024-09-20 0.0.4
2023-02-07 0.0.3
2020-10-31 0.0.2
2020-09-30 0.0.1

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Package flowr (with last version 0.9.11) was removed from CRAN

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

2021-03-02 0.9.11
2016-04-18 0.9.10
2015-12-03 0.9.9.5
2015-10-03 0.9.8.2
2015-08-22 0.9.7.10

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Package good (with last version 1.0.2) was removed from CRAN

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

2024-05-17 1.0.2
2021-05-10 1.0.1
2021-05-06 1.0.0

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Package params (with last version 0.7.3) was removed from CRAN

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

2021-03-01 0.7.3
2016-04-18 0.6.1
2016-02-22 0.5.0
2015-12-01 0.4
2015-09-22 0.3.0
2015-08-22 0.2.5
2015-08-14 0.2.4
2015-07-27 0.2

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Package MetaNLP updated to version 0.1.3 with previous version 0.1.2 dated 2024-05-23

Title: Natural Language Processing for Meta Analysis
Description: Given a CSV file with titles and abstracts, the package creates a document-term matrix that is lemmatized and stemmed and can directly be used to train machine learning methods for automatic title-abstract screening in the preparation of a meta analysis.
Author: Nico Bruder [aut] , Samuel Zimmermann [aut] , Johannes Vey [aut] , Maximilian Pilz [aut, cre] , Institute of Medical Biometry - University of Heidelberg [cph]
Maintainer: Maximilian Pilz <maximilian.pilz@itwm.fraunhofer.de>

Diff between MetaNLP versions 0.1.2 dated 2024-05-23 and 0.1.3 dated 2024-11-07

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New package visualpred with initial version 0.1.1
Package: visualpred
Title: Visualization 2D of Binary Classification Models
Version: 0.1.1
Description: Visual contour and 2D point and contour plots for binary classification modeling under algorithms such as 'glm', 'rf', 'gbm', 'nnet' and 'svm', presented over two dimensions generated by 'famd' and 'mca' methods. Package 'FactoMineR' for multivariate reduction functions and package 'MBA' for interpolation functions are used. The package can be used to visualize the discriminant power of input variables and algorithmic modeling, explore outliers, compare algorithm behaviour, etc. It has been created initially for teaching purposes, but it has also many practical uses under the 'XAI' paradigm.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: gbm, randomForest, nnet (>= 7.3.12), e1071, MASS (>= 7.3.51.4), magrittr, FactoMineR (>= 2.3), ggplot2 (>= 3.3.0), mltools, dplyr, data.table, MBA, pROC, ggrepel
Suggests: knitr, markdown,egg
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
NeedsCompilation: no
Maintainer: Javier Portela <javipgm@gmail.com>
Packaged: 2024-11-07 10:23:39 UTC; TrendingPC
Author: Javier Portela [aut, cre]
Repository: CRAN
Date/Publication: 2024-11-07 12:30:02 UTC

More information about visualpred at CRAN
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Package S7 updated to version 0.2.0 with previous version 0.1.1 dated 2023-09-17

Title: An Object Oriented System Meant to Become a Successor to S3 and S4
Description: A new object oriented programming system designed to be a successor to S3 and S4. It includes formal class, generic, and method specification, and a limited form of multiple dispatch. It has been designed and implemented collaboratively by the R Consortium Object-Oriented Programming Working Group, which includes representatives from R-Core, 'Bioconductor', 'Posit'/'tidyverse', and the wider R community.
Author: Object-Oriented Programming Working Group [cph], Davis Vaughan [aut], Jim Hester [aut] , Tomasz Kalinowski [aut], Will Landau [aut], Michael Lawrence [aut], Martin Maechler [aut] , Luke Tierney [aut], Hadley Wickham [aut, cre]
Maintainer: Hadley Wickham <hadley@posit.co>

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Package ergm.ego updated to version 1.1.1 with previous version 1.1.0 dated 2023-05-30

Title: Fit, Simulate and Diagnose Exponential-Family Random Graph Models to Egocentrically Sampled Network Data
Description: Utilities for managing egocentrically sampled network data and a wrapper around the 'ergm' package to facilitate ERGM inference and simulation from such data. See Krivitsky and Morris (2017) <doi:10.1214/16-AOAS1010>.
Author: Pavel N. Krivitsky [aut, cre] , Steven M. Goodreau [ctb], Martina Morris [ctb], Kirk Li [ctb], Emily N. Beylerian [ctb], Michal Bojanowski [ctb] , Chad Klumb [ctb]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>

Diff between ergm.ego versions 1.1.0 dated 2023-05-30 and 1.1.1 dated 2024-11-07

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Permanent link

Package cryptoQuotes updated to version 1.3.2 with previous version 1.3.1 dated 2024-05-31

Title: Open Access to Cryptocurrency Market Data, Sentiment Indicators and Interactive Charts
Description: This high-level API client provides open access to cryptocurrency market data, sentiment indicators, and interactive charting tools. The data is sourced from major cryptocurrency exchanges via 'curl' and returned in 'xts'-format. The data comes in open, high, low, and close (OHLC) format with flexible granularity, ranging from seconds to months. This flexibility makes it ideal for developing and backtesting trading strategies or conducting detailed market analysis.
Author: Serkan Korkmaz [cre, aut, ctb, cph] , Jonas Cuzulan Hirani [ctb]
Maintainer: Serkan Korkmaz <serkor1@duck.com>

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Package vistributions updated to version 0.2.0 with previous version 0.1.2 dated 2021-05-20

Title: Visualize Probability Distributions
Description: Visualize and compute percentiles/probabilities of normal, t, f, chi square and binomial distributions.
Author: Aravind Hebbali [aut, cre]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>

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Package tidyllm updated to version 0.2.0 with previous version 0.1.0 dated 2024-10-10

Title: Tidy Integration of Large Language Models
Description: A tidy interface for integrating large language model (LLM) APIs such as 'Claude', 'Openai', 'Groq','Mistral' and local models via 'Ollama' into R workflows. The package supports text and media-based interactions, interactive message history, batch request APIs, and a tidy, pipeline-oriented interface for streamlined integration into data workflows. Web services are available at <https://www.anthropic.com>, <https://openai.com>, <https://groq.com>, <https://mistral.ai/> and <https://ollama.com>.
Author: Eduard Bruell [aut, cre]
Maintainer: Eduard Bruell <eduard.bruell@zew.de>

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Package siren updated to version 1.0.5 with previous version 1.0.4 dated 2023-10-25

Title: Hybrid FA-CFA for Controlling Acquiescence in Restricted Factorial Solutions
Description: Performs hybrid multi-stage factor analytic procedure for controlling acquiescence in restricted solutions (Ferrando & Lorenzo-Seva, 2000 <https://www.uv.es/revispsi/articulos3.00/ferran7.pdf>).
Author: David Navarro-Gonzalez [aut, cre], Pere J. Ferrando [aut], Fabia Morales-Vives [aut], Ana Hernandez-Dorado [aut]
Maintainer: David Navarro-Gonzalez <david.navarro@udl.cat>

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Package RJSDMX updated to version 3.5-0 with previous version 3.4-0 dated 2024-09-13

Title: R Interface to SDMX Web Services
Description: Provides functions to retrieve data and metadata from providers that disseminate data by means of SDMX web services. SDMX (Statistical Data and Metadata eXchange) is a standard that has been developed with the aim of simplifying the exchange of statistical information. More about the SDMX standard and the SDMX Web Services can be found at: <https://sdmx.org>.
Author: Attilio Mattiocco [aut, cre]
Maintainer: Attilio Mattiocco <attilio.mattiocco@bancaditalia.it>

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Package graphicalEvidence updated to version 1.1 with previous version 1.0 dated 2024-10-25

Title: Graphical Evidence
Description: Computes marginal likelihood in Gaussian graphical models through a novel telescoping block decomposition of the precision matrix which allows estimation of model evidence. The top level function used to estimate marginal likelihood is called evidence(), which expects the prior name, data, and relevant prior specific parameters. This package also provides an MCMC prior sampler using the same underlying approach, implemented in prior_sampling(), which expects a prior name and prior specific parameters. Both functions also expect the number of burn-in iterations and the number of sampling iterations for the underlying MCMC sampler.
Author: David Rowe [aut, cre]
Maintainer: David Rowe <david@rowe-stats.com>

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Package SPARRAfairness updated to version 0.0.0.2 with previous version 0.0.0.1 dated 2023-04-20

Title: Analysis of Differential Behaviour of SPARRA Score Across Demographic Groups
Description: The SPARRA risk score (Scottish Patients At Risk of admission and Re-Admission) estimates yearly risk of emergency hospital admission using electronic health records on a monthly basis for most of the Scottish population. This package implements a suite of functions used to analyse the behaviour and performance of the score, focusing particularly on differential performance over demographically-defined groups. It includes useful utility functions to plot receiver-operator-characteristic, precision-recall and calibration curves, draw stock human figures, estimate counterfactual quantities without the need to re-compute risk scores, to simulate a semi-realistic dataset.
Author: Ioanna Thoma [aut] , Catalina Vallejos [ctb] , Louis Aslett [ctb] , Jill Ireland [ctb] , Simon Rogers [ctb] , James Liley [cre, aut]
Maintainer: James Liley <james.liley@durham.ac.uk>

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Package hgwrr updated to version 0.6-0 with previous version 0.5-0 dated 2024-07-28

Title: Hierarchical and Geographically Weighted Regression
Description: This model divides coefficients into three types, i.e., local fixed effects, global fixed effects, and random effects (Hu et al., 2022)<doi:10.1177/23998083211063885>. If data have spatial hierarchical structures (especially are overlapping on some locations), it is worth trying this model to reach better fitness.
Author: Yigong Hu [aut, cre], Richard Harris [aut], Richard Timmerman [aut]
Maintainer: Yigong Hu <yigong.hu@bristol.ac.uk>

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Package zipangu updated to version 0.3.3 with previous version 0.3.2 dated 2022-12-09

Title: Japanese Utility Functions and Data
Description: Some data treated by the Japanese R user require unique operations and processing. These are caused by address, Kanji, and traditional year representations. 'zipangu' transforms specific to Japan into something more general one.
Author: Shinya Uryu [aut, cre] , Hiroaki Yutani [ctb] , Kazuhiro Maeda [ctb], Mao Kobayashi [ctb], Akiru Kato [ctb]
Maintainer: Shinya Uryu <suika1127@gmail.com>

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Title: Analysis of Spatial Stratified Heterogeneity
Description: Analyzing spatial factors and exploring spatial associations based on the concept of spatial stratified heterogeneity, and also takes into account local spatial dependencies, spatial interpretability, potential spatial interactions, and robust spatial stratification. Additionally, it supports geographical detector models established in academic literature.
Author: Wenbo Lv [aut, cre, cph] , Yangyang Lei [aut] , Fangmei Liu [aut] , Wufan Zhao [aut] , Yongze Song [aut] , Jianwu Yan [aut]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>

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 gdverse-1.2/gdverse/vignettes/spade.Rmd                  |  444 ++---
 70 files changed, 6516 insertions(+), 6505 deletions(-)

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