Tue, 19 Mar 2024

Package easy.utils updated to version 0.0.4 with previous version 0.0.3 dated 2023-10-17

Title: Frequently Used Functions for Easy R Programming
Description: Some utility functions for validation, data manipulation or color palettes. These functions can be helpful to reduce internal codes everywhere in package development.
Author: Yuchen Li [aut, cre]
Maintainer: Yuchen Li <ycli1995@outlook.com>

Diff between easy.utils versions 0.0.3 dated 2023-10-17 and 0.0.4 dated 2024-03-19

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More information about easy.utils at CRAN
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Package qtlpoly (with last version 0.2.3) was removed from CRAN

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

2022-01-12 0.2.3
2021-11-10 0.2.2

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Mon, 18 Mar 2024

Package Seurat updated to version 5.0.3 with previous version 5.0.2 dated 2024-02-28

Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Author: Andrew Butler [ctb] , Saket Choudhary [ctb] , Charlotte Darby [ctb] , Jeff Farrell [ctb], Isabella Grabski [ctb] , Christoph Hafemeister [ctb] , Yuhan Hao [ctb] , Austin Hartman [ctb] , Paul Hoffman [ctb] , Jaison Jain [ctb] , Longda Jiang [ctb] , Ma [...truncated...]
Maintainer: Rahul Satija <seurat@nygenome.org>

Diff between Seurat versions 5.0.2 dated 2024-02-28 and 5.0.3 dated 2024-03-18

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Package psych updated to version 2.4.3 with previous version 2.4.1 dated 2024-01-18

Title: Procedures for Psychological, Psychometric, and Personality Research
Description: A general purpose toolbox developed originally for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Validation and cross validation of scales developed using basic machine learning algorithms are provided, as are functions for simulating and testing particular item and test structures. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, including mediation models, factor analysis and structural equation models are created using basic graphics. Some of the fu [...truncated...]
Author: William Revelle [aut, cre]
Maintainer: William Revelle <revelle@northwestern.edu>

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Package phylopath updated to version 1.2.1 with previous version 1.2.0 dated 2023-10-09

Title: Perform Phylogenetic Path Analysis
Description: A comprehensive and easy to use R implementation of confirmatory phylogenetic path analysis as described by Von Hardenberg and Gonzalez-Voyer (2012) <doi:10.1111/j.1558-5646.2012.01790.x>.
Author: Wouter van der Bijl [aut, cre]
Maintainer: Wouter van der Bijl <wouter@zoology.ubc.ca>

Diff between phylopath versions 1.2.0 dated 2023-10-09 and 1.2.1 dated 2024-03-18

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Package LadderFuelsR updated to version 0.0.4 with previous version 0.0.3 dated 2024-01-26

Title: Automated Tool for Vertical Fuel Continuity Analysis using Airborne Laser Scanning Data
Description: Set of tools for analyzing vertical fuel continuity at the tree level using Airborne Laser Scanning data. The workflow consisted of: 1) calculating the vertical height profiles of each segmented tree; 2) identifying gaps and fuel layers; 3) estimating the distance between fuel layers; and 4) retrieving the fuel layers base height and depth. Additionally, other functions recalculate previous metrics after considering distances greater than 1 m and calculate the canopy base height as the fuel base height located at the largest- and at the last-distance. Moreover, the package calculates: i) the percentage of Leaf Area Density comprised in each fuel layer, ii) remove fuel layers with Leaf Area Density percentage less than 25, iii) recalculate the distances among the reminder ones, and iv) identify the canopy base height as the fuel base height with the highest Leaf Area Density percentage. On the other hand, when there is only one fuel layer, it identifies the canopy base height performing [...truncated...]
Author: Olga Viedma [aut, cph, cre], Carlos Alberto Silva [aut, cph], Jose Manuel Moreno [aut, cph]
Maintainer: Olga Viedma <olga.viedma@uclm.es>

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Package ODMeans updated to version 0.2.1 with previous version 0.2.0 dated 2024-01-10

Title: OD-Means: k-Means for Origin-Destination
Description: OD-means is a hierarchical adaptive k-means algorithm based on origin-destination pairs. In the first layer of the hierarchy, the clusters are separated automatically based on the variation of the within-cluster distance of each cluster until convergence. The second layer of the hierarchy corresponds to the sub clustering process of small clusters based on the distance between the origin and destination of each cluster.
Author: Sebastian Moreno [aut, cre], Cristobal Heredia [aut], Wilfredo Yushimito [ths], Gonzalo Huerta [ths]
Maintainer: Sebastian Moreno <sebastian.moreno.araya@gmail.com>

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Package mlr3cluster updated to version 0.1.9 with previous version 0.1.8 dated 2023-03-12

Title: Cluster Extension for 'mlr3'
Description: Extends the 'mlr3' package with cluster analysis.
Author: Damir Pulatov [cre, aut], Michel Lang [aut]
Maintainer: Damir Pulatov <damirpolat@protonmail.com>

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Package GSNA updated to version 0.1.4.2 with previous version 0.1.4.1 dated 2024-02-14

Title: Gene Set Networking Analysis Package
Description: Create networks of gene sets, infer clusters of functionally-related gene sets based on similarity statistics, and visualize the results. This package simplifies and accelerates interpretation of pathways analysis data sets. It is designed to work in tandem with standard pathways analysis methods, such as the 'GSEA' program (Gene Set Enrichment Analysis), CERNO (Coincident Extreme Ranks in Numerical Observations, implemented in the 'tmod' package) and others. Inputs to 'GSNA' are the outputs of pathways analysis methods: a list of gene sets (or "modules"), pathways or GO-terms with associated p-values. Since pathways analysis methods may be used to analyze many different types of data including transcriptomic, epigenetic, and high-throughput screen data sets, the 'GSNA' pipeline is applicable to these data as well. The use of 'GSNA' has been described in the following papers: Collins DR, Urbach JM, Racenet ZJ, Arshad U, Power KA, Newman RM, et al. (2021) <doi:10.1016/j.immuni.2021.0 [...truncated...]
Author: Jonathan M Urbach [aut, cre]
Maintainer: Jonathan M Urbach <jurbach@mgh.harvard.edu>

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Package cito updated to version 1.1 with previous version 1.0.2 dated 2023-10-06

Title: Building and Training Neural Networks
Description: The 'cito' package provides a user-friendly interface for training and interpreting deep neural networks (DNN). 'cito' simplifies the fitting of DNNs by supporting the familiar formula syntax, hyperparameter tuning under cross-validation, and helps to detect and handle convergence problems. DNNs can be trained on CPU, GPU and MacOS GPUs. In addition, 'cito' has many downstream functionalities such as various explainable AI (xAI) metrics (e.g. variable importance, partial dependence plots, accumulated local effect plots, and effect estimates) to interpret trained DNNs. 'cito' optionally provides confidence intervals (and p-values) for all xAI metrics and predictions. At the same time, 'cito' is computationally efficient because it is based on the deep learning framework 'torch'. The 'torch' package is native to R, so no Python installation or other API is required for this package.
Author: Christian Amesoeder [aut], Maximilian Pichler [aut, cre] , Florian Hartig [ctb] , Armin Schenk [ctb]
Maintainer: Maximilian Pichler <maximilian.pichler@biologie.uni-regensburg.de>

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Package QHScrnomo updated to version 3.0.1 with previous version 3.0.0 dated 2023-04-18

Title: Construct Nomograms for Competing Risks Regression Models
Description: Nomograms are constructed to predict the cumulative incidence rate which is calculated after adjusting for competing causes to the event of interest. K-fold cross-validation is implemented to validate predictive accuracy using a competing-risk version of the concordance index. Methods are as described in: Kattan MW, Heller G, Brennan MF (2003).
Author: Michael Kattan [aut], Changhong Yu [aut], Xinge Ji [aut], Zajichek Alex [cre]
Maintainer: Zajichek Alex <zajicha2@ccf.org>

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Package ghibli updated to version 0.3.4 with previous version 0.3.3 dated 2022-08-26

Title: Studio Ghibli Colour Palettes
Description: Colour palettes inspired by Studio Ghibli <https://en.wikipedia.org/wiki/Studio_Ghibli> films, ported to R for your enjoyment.
Author: Ewen Henderson [aut, cre] , Danielle Desrosiers [ctb], Michael Chirico [ctb]
Maintainer: Ewen Henderson <ewenhenderson@gmail.com>

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Package wflo updated to version 1.9 with previous version 1.8 dated 2023-01-15

Title: Data Set and Helper Functions for Wind Farm Layout Optimization Problems
Description: Provides a convenient data set, a set of helper functions, and a benchmark function for economically (profit) driven wind farm layout optimization. This enables researchers in the field of the NP-hard (non-deterministic polynomial-time hard) problem of wind farm layout optimization to focus on their optimization methodology contribution and also provides a realistic benchmark setting for comparability among contributions. See Croonenbroeck, Carsten & Hennecke, David (2020) <doi:10.1016/j.energy.2020.119244>.
Author: Carsten Croonenbroeck [aut, cre], David Hennecke [ctb]
Maintainer: Carsten Croonenbroeck <carsten.croonenbroeck@uni-rostock.de>

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Package causalsens updated to version 0.1.3 with previous version 0.1.2 dated 2018-06-18

Title: Selection Bias Approach to Sensitivity Analysis for Causal Effects
Description: The causalsens package provides functions to perform sensitivity analyses and to study how various assumptions about selection bias affects estimates of causal effects.
Author: Matthew Blackwell <mblackwell@gov.harvard.edu.edu>
Maintainer: Matthew Blackwell <mblackwell@gov.harvard.edu>

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Package tsmethods updated to version 1.0.1 with previous version 1.0.0 dated 2024-03-09

Title: Time Series Methods
Description: Generic methods for use in a time series probabilistic framework, allowing for a common calling convention across packages. Additional methods for time series prediction ensembles and probabilistic plotting of predictions is included. A more detailed description is available at <https://www.nopredict.com/packages/tsmethods> which shows the currently implemented methods in the 'tsmodels' framework.
Author: Alexios Galanos [aut, cre, cph]
Maintainer: Alexios Galanos <alexios@4dscape.com>

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Package smcryptoR updated to version 0.1.2 with previous version 0.1.1 dated 2024-02-26

Title: ShangMi(SM) Cryptographic Algorithms(SM2/SM3/SM4)
Description: Bindings to 'smcrypto' <https://github.com/zhuobie/smcrypto>: a 'Rust' implementation of China's Standards of Encryption Algorithms, which is usually called 'ShangMi(SM)' algorithms. It contains 'SM3' message digest algorithm, 'SM2' asymmetric encryption algorithm and 'SM4' symmetric encryption algorithm. Users can do message hash, encrypt/decrypt, sign/verify, key exchange and more.
Author: Meng Yu [aut, cre]
Maintainer: Meng Yu <610074@gmail.com>

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Package PowerTOST updated to version 1.5-6 with previous version 1.5-4 dated 2022-02-21

Title: Power and Sample Size for (Bio)Equivalence Studies
Description: Contains functions to calculate power and sample size for various study designs used in bioequivalence studies. Use known.designs() to see the designs supported. Power and sample size can be obtained based on different methods, amongst them prominently the TOST procedure (two one-sided t-tests). See README and NEWS for further information.
Author: Detlew Labes [aut, cre] , Helmut Schuetz [aut] , Benjamin Lang [aut]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>

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New package immunarch with initial version 0.9.1
Package: immunarch
Title: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires
Version: 0.9.1
Contact: support@immunomind.io
Description: A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq) and single-cell sequencing (scRNAseq). Immunarch implements most of the widely used AIRR analysis methods, such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor databases and clonotype tracking in vaccination and cancer studies. A successor to our previously published 'tcR' immunoinformatics package (Nazarov 2015) <doi:10.1186/s12859-015-0613-1>.
License: Apache License (== 2.0)
URL: https://immunarch.com/, https://github.com/immunomind/immunarch
BugReports: https://github.com/immunomind/immunarch/issues
Imports: factoextra (>= 1.0.4), fpc, UpSetR (>= 1.4.0), pheatmap (>= 1.0.12), ggrepel (>= 0.8.0), reshape2 (>= 1.4.2), circlize, MASS (>= 7.3), Rtsne (>= 0.15), readxl (>= 1.3.1), shiny (>= 1.4.0), shinythemes, airr, ggseqlogo, ggalluvial (>= 0.10.0), Rcpp (>= 1.0), magrittr, methods, scales, ggpubr (>= 0.2), rlang (>= 0.4), plyr, purrr, stringdist, jsonlite, readr, stringr, tibble, tidyselect, tidyr, igraph, ape, doParallel, rlist, utils, glue, phangorn, uuid, stringi, ggraph
Depends: R (>= 4.0.0), ggplot2 (>= 3.1.0), dplyr (>= 0.8.0), dtplyr (>= 1.0.0), data.table (>= 1.12.6), patchwork
LinkingTo: Rcpp
Suggests: knitr (>= 1.8), roxygen2 (>= 3.0.0), testthat (>= 2.1.0), pkgdown (>= 0.1.0), assertthat, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
NeedsCompilation: yes
Packaged: 2024-03-18 18:22:17 UTC; vdn
Author: Vadim I. Nazarov [aut, cre], Vasily O. Tsvetkov [aut], Siarhei Fiadziushchanka [aut], Eugene Rumynskiy [aut], Aleksandr A. Popov [aut], Ivan Balashov [aut], Maria Samokhina [aut], Anna Lorenc [ctb], Daniel J. Moore [ctb], Victor Greiff [ctb], ImmunoM [...truncated...]
Maintainer: Vadim I. Nazarov <support@immunomind.io>
Repository: CRAN
Date/Publication: 2024-03-18 19:10:06 UTC

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Package tarchetypes updated to version 0.8.0 with previous version 0.7.12 dated 2024-02-06

Title: Archetypes for Targets
Description: Function-oriented Make-like declarative pipelines for Statistics and data science are supported in the 'targets' R package. As an extension to 'targets', the 'tarchetypes' package provides convenient user-side functions to make 'targets' easier to use. By establishing reusable archetypes for common kinds of targets and pipelines, these functions help express complicated reproducible pipelines concisely and compactly. The methods in this package were influenced by the 'drake' R package by Will Landau (2018) <doi:10.21105/joss.00550>.
Author: William Michael Landau [aut, cre] , Samantha Oliver [rev] , Tristan Mahr [rev] , Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>

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New package sgapi with initial version 1.0.0
Package: sgapi
Title: Aid Querying 'nomis' and 'Office for National Statistics Open Geography' APIs
Version: 1.0.0
Description: Facilitates extraction of geospatial data from the 'Office for National Statistics Open Geography' and 'nomis' Application Programming Interfaces (APIs). Simplifies process of querying 'nomis' datasets <https://www.nomisweb.co.uk/> and extracting desired datasets in dataframe format. Extracts area shapefiles at chosen resolution from 'Office for National Statistics Open Geography' <https://geoportal.statistics.gov.uk/>.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://defra-data-science-centre-of-excellence.github.io/sgapi/, https://github.com/Defra-Data-Science-Centre-of-Excellence/sgapi
BugReports: https://github.com/Defra-Data-Science-Centre-of-Excellence/sgApi/issues
Imports: magrittr, sf, dplyr, httr, readr, xml2, methods
Suggests: testthat (>= 3.0.0)
Depends: R (>= 3.6)
LazyData: true
NeedsCompilation: no
Packaged: 2024-03-18 10:30:00 UTC; andrewchristy
Author: Andrew Christy [aut, cre], James Macpherson [aut], Hadyn Jenkins [aut], Crown Copyright [cph]
Maintainer: Andrew Christy <OR_Hub@defra.gov.uk>
Repository: CRAN
Date/Publication: 2024-03-18 18:10:02 UTC

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New package QTE.RD with initial version 1.0.0
Package: QTE.RD
Title: Quantile Treatment Effects under the Regression Discontinuity Design
Version: 1.0.0
Author: Zhongjun Qu [aut, cph], Jungmo Yoon [aut, cre, cph]
Maintainer: Jungmo Yoon <jmyoon@hanyang.ac.kr>
Description: Provides comprehensive methods for testing, estimating, and conducting uniform inference on quantile treatment effects (QTEs) in sharp regression discontinuity (RD) designs, incorporating covariates and implementing robust bias correction methods of Qu, Yoon, Perron (2024) <doi:10.1162/rest_a_01168>.
Encoding: UTF-8
Imports: quantreg, plotrix, stats
License: GPL (>= 3)
Suggests: spelling
Language: en-US
NeedsCompilation: no
Packaged: 2024-03-18 10:27:49 UTC; jyoon
Repository: CRAN
Date/Publication: 2024-03-18 18:10:05 UTC

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New package tf with initial version 0.3.2
Package: tf
Title: S3 Classes and Methods for Tidy Functional Data
Version: 0.3.2
Description: Defines S3 vector data types for vectors of functional data (grid-based, spline-based or functional principal components-based) with all arithmetic and summary methods, derivation, integration and smoothing, plotting, data import and export, and data wrangling, such as re-evaluating, subsetting, sub-assigning, zooming into sub-domains, or extracting functional features like minima/maxima and their locations. The implementation allows including such vectors in data frames for joint analysis of functional and scalar variables.
License: AGPL (>= 3)
URL: https://tidyfun.github.io/tf/, https://github.com/tidyfun/tf/
BugReports: https://github.com/tidyfun/tf/issues
Depends: R (>= 4.1)
Imports: checkmate, methods, mgcv, mvtnorm, pracma, purrr, rlang, stats, vctrs (>= 0.2.4), zoo
Suggests: covr, dplyr, knitr, refund, testthat (>= 3.0.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-03-15 13:18:58 UTC; fabians
Author: Fabian Scheipl [aut, cre] , Jeff Goldsmith [aut], Julia Wrobel [ctb] , Maximilian Muecke [ctb] , Sebastian Fischer [ctb] , Trevor Hastie [ctb] , Rahul Mazumder [ctb] , Chen Meng [ctb]
Maintainer: Fabian Scheipl <fabian.scheipl@googlemail.com>
Repository: CRAN
Date/Publication: 2024-03-18 17:30:02 UTC

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Package hyperbolicDEA updated to version 1.0.0 with previous version 0.1.1 dated 2024-02-22

Title: Hyperbolic DEA Estimation
Description: Implements Data Envelopment Analysis (DEA) with a hyperbolic orientation using a non-linear programming solver. It enables flexible estimations with weight restrictions, non-discretionary variables, and a generalized distance function. Additionally, it allows for the calculation of slacks and super-efficiency scores. The methods are detailed in Öttl et al. (2023), <doi:10.1016/j.dajour.2023.100343>. Furthermore, the package provides a non-linear profitability estimation built upon the DEA framework.
Author: Alexander Oettl [cre, aut] , Daniel Gulde [aut]
Maintainer: Alexander Oettl <alexoettl34@gmail.com>

Diff between hyperbolicDEA versions 0.1.1 dated 2024-02-22 and 1.0.0 dated 2024-03-18

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Package configural updated to version 0.1.5 with previous version 0.1.4 dated 2021-01-18

Title: Multivariate Profile Analysis
Description: R functions for criterion profile analysis, Davison and Davenport (2002) <doi:10.1037/1082-989X.7.4.468> and meta-analytic criterion profile analysis, Wiernik, Wilmot, Davison, and Ones (2020) <doi:10.1037/met0000305>. Sensitivity analyses to aid in interpreting criterion profile analysis results are also included.
Author: Brenton M. Wiernik [aut, cre]
Maintainer: Brenton M. Wiernik <brenton@wiernik.org>

Diff between configural versions 0.1.4 dated 2021-01-18 and 0.1.5 dated 2024-03-18

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New package cepumd with initial version 2.1.0
Package: cepumd
Title: Calculate Consumer Expenditure Survey (CE) Annual Estimates
Version: 2.1.0
Description: Provides functions and data files to help CE Public-Use Microdata (PUMD) users calculate annual estimated expenditure means, standard errors, and quantiles according to the methods used by the CE with PUMD. For more information on the CE please visit <https://www.bls.gov/cex>. For further reading on CE estimate calculations please see the CE Calculation section of the U.S. Bureau of Labor Statistics (BLS) Handbook of Methods at <https://www.bls.gov/opub/hom/cex/calculation.htm>. For further information about CE PUMD please visit <https://www.bls.gov/cex/pumd.htm>.
License: GPL (>= 3)
URL: https://arcenis-r.github.io/cepumd/, https://github.com/arcenis-r/cepumd
BugReports: https://github.com/arcenis-r/cepumd/issues
Depends: R (>= 3.5.0)
Imports: dplyr (>= 1.0.0), janitor, purrr, readr, readxl, rlang, stringr, tidyr, tidyselect (>= 1.2.0), utils
Suggests: covr, knitr, rmarkdown, spelling, testthat (>= 2.1.0)
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2024-03-17 14:55:20 UTC; arcen
Author: Arcenis Rojas [aut, cre, cph]
Maintainer: Arcenis Rojas <arcenis.rojas@gmail.com>
Repository: CRAN
Date/Publication: 2024-03-18 17:50:02 UTC

More information about cepumd at CRAN
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Package MigConnectivity updated to version 0.4.6 with previous version 0.4.5 dated 2024-01-16

Title: Estimate Migratory Connectivity for Migratory Animals
Description: Allows the user to estimate transition probabilities for migratory animals between any two phases of the annual cycle, using a variety of different data types. Also quantifies the strength of migratory connectivity (MC), a standardized metric to quantify the extent to which populations co-occur between two phases of the annual cycle. Includes functions to estimate MC and the more traditional metric of migratory connectivity strength (Mantel correlation) incorporating uncertainty from multiple sources of sampling error. For cross-species comparisons, methods are provided to estimate differences in migratory connectivity strength, incorporating uncertainty. See Cohen et al. (2018) <doi:10.1111/2041-210X.12916>, Cohen et al. (2019) <doi:10.1111/ecog.03974>, and Roberts et al. (2023) <doi:10.1002/eap.2788> for details on some of these methods.
Author: Jeffrey A. Hostetler [cre, aut], Michael T. Hallworth [aut], Clark S. Rushing [ctb], Emily B. Cohen [ctb], Valentine Herrmann [ctb]
Maintainer: Jeffrey A. Hostetler <jhostetler@usgs.gov>

Diff between MigConnectivity versions 0.4.5 dated 2024-01-16 and 0.4.6 dated 2024-03-18

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Package mcmsupply updated to version 1.1.1 with previous version 1.0.1 dated 2024-03-12

Title: Estimating Public and Private Sector Contraceptive Market Supply Shares
Description: Family Planning programs and initiatives typically use nationally representative surveys to estimate key indicators of a country’s family planning progress. However, in recent years, routinely collected family planning services data (Service Statistics) have been used as a supplementary data source to bridge gaps in the surveys. The use of service statistics comes with the caveat that adjustments need to be made for missing private sector contributions to the contraceptive method supply chain. Evaluating the supply source of modern contraceptives often relies on Demographic Health Surveys (DHS), where many countries do not have recent data beyond 2015/16. Fortunately, in the absence of recent surveys we can rely on statistical model-based estimates and projections to fill the knowledge gap. We present a Bayesian, hierarchical, penalized-spline model with multivariate-normal spline coefficients, to account for across method correlations, to produce country-specific,annual estimates for [...truncated...]
Author: Hannah Comiskey [aut, cre], Niamh Cahill [aut], Leontine Alkema [aut]
Maintainer: Hannah Comiskey <hannah.comiskey.2015@mumail.ie>

Diff between mcmsupply versions 1.0.1 dated 2024-03-12 and 1.1.1 dated 2024-03-18

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 mcmsupply-1.1.1/mcmsupply/NEWS.md                                                   |   11 
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Package konfound updated to version 0.5.0 with previous version 0.4.0 dated 2021-06-01

Title: Quantify the Robustness of Causal Inferences
Description: Statistical methods that quantify the conditions necessary to alter inferences, also known as sensitivity analysis, are becoming increasingly important to a variety of quantitative sciences. A series of recent works, including Frank (2000) <doi:10.1177/0049124100029002001> and Frank et al. (2013) <doi:10.3102/0162373713493129> extend previous sensitivity analyses by considering the characteristics of omitted variables or unobserved cases that would change an inference if such variables or cases were observed. These analyses generate statements such as "an omitted variable would have to be correlated at xx with the predictor of interest (e.g., treatment) and outcome to invalidate an inference of a treatment effect". Or "one would have to replace pp percent of the observed data with null hypothesis cases to invalidate the inference". We implement these recent developments of sensitivity analysis and provide modules to calculate these two robustness indices and generate such [...truncated...]
Author: Joshua M Rosenberg [aut, cre], Ran Xu [ctb], Qinyun Lin [ctb], Spiro Maroulis [ctb], Sarah Narvaiz [ctb], Kenneth A Frank [ctb], Wei Wang [ctb]
Maintainer: Joshua M Rosenberg <jmrosen48@gmail.com>

Diff between konfound versions 0.4.0 dated 2021-06-01 and 0.5.0 dated 2024-03-18

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New package cardx with initial version 0.1.0
Package: cardx
Title: Extra Analysis Results Data Utilities
Version: 0.1.0
Description: Create extra Analysis Results Data (ARD) summary objects. The package supplements the simple ARD functions from the 'cards' package, exporting functions to put statistical results in the ARD format. These objects are used and re-used to construct summary tables, visualizations, and written reports.
License: Apache License 2.0
URL: https://github.com/insightsengineering/cardx
BugReports: https://github.com/insightsengineering/cardx/issues
Depends: R (>= 4.1)
Imports: cards (>= 0.1.0), cli (>= 3.6.1), dplyr (>= 1.1.2), glue (>= 1.6.2), rlang (>= 1.1.1), tidyr (>= 1.3.0)
Suggests: broom (>= 1.0.5), broom.helpers (>= 1.13.0), spelling, testthat (>= 3.2.0), withr
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2024-03-15 17:35:50 UTC; sjobergd
Author: Daniel Sjoberg [aut, cre], F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Daniel Sjoberg <danield.sjoberg@gmail.com>
Repository: CRAN
Date/Publication: 2024-03-18 14:30:02 UTC

More information about cardx at CRAN
Permanent link

Package Rtapas (with last version 1.1) was removed from CRAN

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

2022-09-28 1.1
2022-09-19 1.0
2022-06-14 0.9

Permanent link
Package zstdlite (with last version 0.2.7) was removed from CRAN

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

2024-03-17 0.2.7

Permanent link
Package CooRTweet updated to version 2.0.1 with previous version 2.0.0 dated 2024-01-15

Title: Coordinated Networks Detection on Social Media
Description: Detects a variety of coordinated actions on social media and outputs the network of coordinated users along with related information.
Author: Nicola Righetti [aut, cre] , Paul Balluff [aut]
Maintainer: Nicola Righetti <nicola.righetti@univie.ac.at>

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Package maraca updated to version 0.7 with previous version 0.6 dated 2023-10-24

Title: The Maraca Plot: Visualization of Hierarchical Composite Endpoints in Clinical Trials
Description: Library that supports visual interpretation of hierarchical composite endpoints (HCEs). HCEs are complex constructs used as primary endpoints in clinical trials, combining outcomes of different types into ordinal endpoints, in which each patient contributes the most clinically important event (one and only one) to the analysis. See Karpefors M et al. (2022) <doi:10.1177/17407745221134949>.
Author: Martin Karpefors [aut] , Samvel B. Gasparyan [aut] , Stefano Borini [ctb], Monika Huhn [aut, cre]
Maintainer: Monika Huhn <monika.huhn@astrazeneca.com>

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Package diffeqr updated to version 2.0.1 with previous version 2.0.0 dated 2023-10-20

Title: Solving Differential Equations (ODEs, SDEs, DDEs, DAEs)
Description: An interface to 'DifferentialEquations.jl' <https://diffeq.sciml.ai/dev/> from the R programming language. It has unique high performance methods for solving ordinary differential equations (ODE), stochastic differential equations (SDE), delay differential equations (DDE), differential-algebraic equations (DAE), and more. Much of the functionality, including features like adaptive time stepping in SDEs, are unique and allow for multiple orders of magnitude speedup over more common methods. Supports GPUs, with support for CUDA (NVIDIA), AMD GPUs, Intel oneAPI GPUs, and Apple's Metal (M-series chip GPUs). 'diffeqr' attaches an R interface onto the package, allowing seamless use of this tooling by R users. For more information, see Rackauckas and Nie (2017) <doi:10.5334/jors.151>.
Author: Christopher Rackauckas [aut, cre, cph]
Maintainer: Christopher Rackauckas <me@chrisrackauckas.com>

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Package VirtualPop updated to version 2.0.2 with previous version 1.0.2 dated 2022-06-23

Title: Simulation of Populations by Sampling Waiting-Time Distributions
Description: Constructs a virtual population from fertility and mortality rates for any country, calendar year and birth cohort in the Human Mortality Database <https://www.mortality.org> and the Human Fertility Database <https://www.humanfertility.org>. Fertility histories are simulated for every individual and their offspring, producing a multi-generation virtual population.
Author: Frans Willekens [aut, cre] , Tim Riffe [ctb]
Maintainer: Frans Willekens <willekens@nidi.nl>

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Package cheapr updated to version 0.3.0 with previous version 0.2.0 dated 2024-03-06

Title: Simple Functions to Save Time and Memory
Description: Fast and memory-efficient (or 'cheap') tools to facilitate efficient programming, saving time and memory. It aims to provide 'cheaper' alternatives to common base R functions, as well as some additional functions.
Author: Nick Christofides [aut, cre]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>

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Package DrugExposureDiagnostics updated to version 1.0.4 with previous version 1.0.3 dated 2024-01-31

Title: Diagnostics for OMOP Common Data Model Drug Records
Description: Ingredient specific diagnostics for drug exposure records in the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Ger Inberg [aut, cre] , Edward Burn [aut] , Yuchen Guo [ctb] , Marti Catala [ctb] , Mike Du [ctb] , Theresa Burkard [ctb] , Xintong Li [ctb] , Ross Williams [ctb] , Erasmus MC [cph]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>

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Package bamlss updated to version 1.2-3 with previous version 1.2-2 dated 2023-10-29

Title: Bayesian Additive Models for Location, Scale, and Shape (and Beyond)
Description: Infrastructure for estimating probabilistic distributional regression models in a Bayesian framework. The distribution parameters may capture location, scale, shape, etc. and every parameter may depend on complex additive terms (fixed, random, smooth, spatial, etc.) similar to a generalized additive model. The conceptual and computational framework is introduced in Umlauf, Klein, Zeileis (2019) <doi:10.1080/10618600.2017.1407325> and the R package in Umlauf, Klein, Simon, Zeileis (2021) <doi:10.18637/jss.v100.i04>.
Author: Nikolaus Umlauf [aut, cre] , Nadja Klein [aut] , Achim Zeileis [aut] , Meike Koehler [ctb], Thorsten Simon [aut] , Stanislaus Stadlmann [ctb], Alexander Volkmann [ctb]
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>

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Package rolog updated to version 0.9.15 with previous version 0.9.14 dated 2023-06-29

Title: Query 'SWI'-'Prolog' from R
Description: This R package connects to SWI-Prolog, <https://www.swi-prolog.org/>, so that R can send deterministic and non-deterministic queries to prolog (consult, query/submit, once, findall).
Author: Matthias Gondan [aut, com, cre] , European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>

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Package psSubpathway updated to version 0.1.3 with previous version 0.1.2 dated 2023-08-09

Title: Flexible Identification of Phenotype-Specific Subpathways
Description: A network-based systems biology tool for flexible identification of phenotype-specific subpathways in the cancer gene expression data with multiple categories (such as multiple subtype or developmental stages of cancer). Subtype Set Enrichment Analysis (SubSEA) and Dynamic Changed Subpathway Analysis (DCSA) are developed to flexible identify subtype specific and dynamic changed subpathways respectively. The operation modes include extraction of subpathways from biological pathways, inference of subpathway activities in the context of gene expression data, identification of subtype specific subpathways with SubSEA, identification of dynamic changed subpathways associated with the cancer developmental stage with DCSA, and visualization of the activities of resulting subpathways by using box plots and heat maps. Its capabilities render the tool could find the specific abnormal subpathways in the cancer dataset with multi-phenotype samples.
Author: Xudong Han, Junwei Han, Qing Fei
Maintainer: Junwei Han <hanjunwei1981@163.com>

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Package ProFAST updated to version 1.4 with previous version 1.3 dated 2024-01-11

Title: Probabilistic Factor Analysis for Spatially-Aware Dimension Reduction
Description: Probabilistic factor analysis for spatially-aware dimension reduction across multi-section spatial transcriptomics data with millions of spatial locations. More details can be referred to Wei Liu, et al. (2023) <doi:10.1101/2023.07.11.548486>.
Author: Wei Liu [aut, cre], Xiao Zhang [aut], Jin Liu [aut]
Maintainer: Wei Liu <liuweideng@gmail.com>

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Package parameters updated to version 0.21.6 with previous version 0.21.5 dated 2024-02-07

Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various statistical models. Beyond computing p values, CIs, and other indices for a wide variety of models (see list of supported models using the function 'insight::supported_models()'), this package implements features like bootstrapping or simulating of parameters and models, feature reduction (feature extraction and variable selection) as well as functions to describe data and variable characteristics (e.g. skewness, kurtosis, smoothness or distribution).
Author: Daniel Luedecke [aut, cre] , Dominique Makowski [aut] , Mattan S. Ben-Shachar [aut] , Indrajeet Patil [aut] , Soeren Hoejsgaard [aut], Brenton M. Wiernik [aut] , Zen J. Lau [ctb], Vincent Arel-Bundock [ctb] , Jeffrey Girard [ctb] , Christina Maimone [re [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>

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Package eudract updated to version 1.0.0 with previous version 0.10.2 dated 2023-08-09

Title: Creates Safety Results Summary in XML to Upload to EudraCT, or ClinicalTrials.gov
Description: The remit of the European Clinical Trials Data Base (EudraCT <https://eudract.ema.europa.eu/> ), or ClinicalTrials.gov <https://clinicaltrials.gov/>, is to provide open access to summaries of all registered clinical trial results; thus aiming to prevent non-reporting of negative results and provide open-access to results to inform future research. The amount of information required and the format of the results, however, imposes a large extra workload at the end of studies on clinical trial units. In particular, the adverse-event-reporting component requires entering: each unique combination of treatment group and safety event; for every such event above, a further 4 pieces of information (body system, number of occurrences, number of subjects, number exposed) for non-serious events, plus an extra three pieces of data for serious adverse events (numbers of causally related events, deaths, causally related deaths). This package prepares the required statistics needed by Eudr [...truncated...]
Author: Simon Bond [cre], Beatrice Pantaleo [aut]
Maintainer: Simon Bond <simon.bond7@nhs.net>

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Package bsamGP updated to version 1.2.5 with previous version 1.2.4 dated 2022-03-17

Title: Bayesian Spectral Analysis Models using Gaussian Process Priors
Description: Contains functions to perform Bayesian inference using a spectral analysis of Gaussian process priors. Gaussian processes are represented with a Fourier series based on cosine basis functions. Currently the package includes parametric linear models, partial linear additive models with/without shape restrictions, generalized linear additive models with/without shape restrictions, and density estimation model. To maximize computational efficiency, the actual Markov chain Monte Carlo sampling for each model is done using codes written in FORTRAN 90. This software has been developed using funding supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (no. NRF-2016R1D1A1B03932178 and no. NRF-2017R1D1A3B03035235).
Author: Seongil Jo [aut, cre], Taeryon Choi [aut], Beomjo Park [aut, cre], Peter J. Lenk [ctb]
Maintainer: Beomjo Park <beomjop@gmail.com>

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Package tictoc updated to version 1.2.1 with previous version 1.2 dated 2023-04-23

Title: Functions for Timing R Scripts, as Well as Implementations of "Stack" and "StackList" Structures
Description: Code execution timing functions 'tic' and 'toc' that can be nested. One can record all timings while a complex script is running, and examine the values later. It is also possible to instrument the timing calls with custom callbacks. In addition, this package provides class 'Stack', implemented as a vector, and class 'StackList', which is a stack implemented as a list, both of which support operations 'push', 'pop', 'first_element', 'last_element' and 'clear'.
Author: Sergei Izrailev
Maintainer: Sergei Izrailev <sizrailev@jabiruventures.com>

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Package SubtypeDrug updated to version 0.1.8 with previous version 0.1.7 dated 2024-01-21

Title: Prioritization of Candidate Cancer Subtype Specific Drugs
Description: A systematic biology tool was developed to prioritize cancer subtype-specific drugs by integrating genetic perturbation, drug action, biological pathway, and cancer subtype. The capabilities of this tool include inferring patient-specific subpathway activity profiles in the context of gene expression profiles with subtype labels, calculating differentially expressed subpathways based on cultured human cells treated with drugs in the 'cMap' (connectivity map) database, prioritizing cancer subtype specific drugs according to drug-disease reverse association score based on subpathway, and visualization of results (Castelo (2013) <doi:10.1186/1471-2105-14-7>; Han et al (2019) <doi:10.1093/bioinformatics/btz894>; Lamb and Justin (2006) <doi:10.1126/science.1132939>). Please cite using <doi:10.1093/bioinformatics/btab011>.
Author: Xudong Han, Junwei Han, Chonghui Liu
Maintainer: Junwei Han <hanjunwei1981@163.com>

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Package rnndescent updated to version 0.1.4 with previous version 0.1.3 dated 2023-12-07

Title: Nearest Neighbor Descent Method for Approximate Nearest Neighbors
Description: The Nearest Neighbor Descent method for finding approximate nearest neighbors by Dong and co-workers (2010) <doi:10.1145/1963405.1963487>. Based on the 'Python' package 'PyNNDescent' <https://github.com/lmcinnes/pynndescent>.
Author: James Melville [aut, cre, cph], Vitalie Spinu [ctb]
Maintainer: James Melville <jlmelville@gmail.com>

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Sun, 17 Mar 2024

Package ggsci updated to version 3.0.2 with previous version 3.0.1 dated 2024-03-02

Title: Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2'
Description: A collection of 'ggplot2' color palettes inspired by plots in scientific journals, data visualization libraries, science fiction movies, and TV shows.
Author: Nan Xiao [aut, cre] , Joshua Cook [ctb], Clara Jegousse [ctb], Miaozhu Li [ctb]
Maintainer: Nan Xiao <me@nanx.me>

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Permanent link

Package mcp updated to version 0.3.4 with previous version 0.3.3 dated 2023-03-22

Title: Regression with Multiple Change Points
Description: Flexible and informed regression with Multiple Change Points. 'mcp' can infer change points in means, variances, autocorrelation structure, and any combination of these, as well as the parameters of the segments in between. All parameters are estimated with uncertainty and prediction intervals are supported - also near the change points. 'mcp' supports hypothesis testing via Savage-Dickey density ratio, posterior contrasts, and cross-validation. 'mcp' is described in Lindeløv (submitted) <doi:10.31219/osf.io/fzqxv> and generalizes the approach described in Carlin, Gelfand, & Smith (1992) <doi:10.2307/2347570> and Stephens (1994) <doi:10.2307/2986119>.
Author: Jonas Kristoffer Lindeloev [aut, cre]
Maintainer: Jonas Kristoffer Lindeloev <jonas@lindeloev.dk>

Diff between mcp versions 0.3.3 dated 2023-03-22 and 0.3.4 dated 2024-03-17

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More information about mcp at CRAN
Permanent link

Package duckplyr updated to version 0.3.2 with previous version 0.3.1 dated 2024-03-10

Title: A 'DuckDB'-Backed Version of 'dplyr'
Description: A drop-in replacement for 'dplyr', powered by 'DuckDB' for performance. Also defines a set of generics that provide a low-level implementer's interface for the high-level user interface of 'dplyr'.
Author: Hannes Muehleisen [aut] , Kirill Mueller [aut, cre] , Posit Software, PBC [cph, fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>

Diff between duckplyr versions 0.3.1 dated 2024-03-10 and 0.3.2 dated 2024-03-17

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Permanent link

Package stoppingrule updated to version 0.4.0 with previous version 0.3.0 dated 2023-09-01

Title: Create and Evaluate Stopping Rules for Safety Monitoring
Description: Provides functions for creating, displaying, and evaluating stopping rules for safety monitoring in clinical studies. Implements stopping rule methods described in Goldman (1987) <doi:10.1016/0197-2456(87)90153-X>; Geller et al. (2003, ISBN:9781135524388); Ivanova, Qaqish, and Schell (2005) <doi:10.1111/j.1541-0420.2005.00311.x>; Chen and Chaloner (2006) <doi:10.1002/sim.2429>; and Kulldorff et al. (2011) <doi:10.1080/07474946.2011.539924>.
Author: Michael J. Martens [aut,cre], Qinghua Lian [aut], Brent R. Logan [ctb]
Maintainer: Michael J. Martens <mmartens@mcw.edu>

Diff between stoppingrule versions 0.3.0 dated 2023-09-01 and 0.4.0 dated 2024-03-17

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More information about stoppingrule at CRAN
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Package semmcci updated to version 1.1.4 with previous version 1.1.3 dated 2023-10-14

Title: Monte Carlo Confidence Intervals in Structural Equation Modeling
Description: Monte Carlo confidence intervals for free and defined parameters in models fitted in the structural equation modeling package 'lavaan' can be generated using the 'semmcci' package. 'semmcci' has three main functions, namely, MC(), MCMI(), and MCStd(). The output of 'lavaan' is passed as the first argument to the MC() function or the MCMI() function to generate Monte Carlo confidence intervals. Monte Carlo confidence intervals for the standardized estimates can also be generated by passing the output of the MC() function or the MCMI() function to the MCStd() function. A description of the package and code examples are presented in Pesigan and Cheung (2023) <doi:10.3758/s13428-023-02114-4>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph] , Shu Fai Cheung [ctb]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>

Diff between semmcci versions 1.1.3 dated 2023-10-14 and 1.1.4 dated 2024-03-17

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Package pak updated to version 0.7.2 with previous version 0.7.1 dated 2023-12-10

Title: Another Approach to Package Installation
Description: The goal of 'pak' is to make package installation faster and more reliable. In particular, it performs all HTTP operations in parallel, so metadata resolution and package downloads are fast. Metadata and package files are cached on the local disk as well. 'pak' has a dependency solver, so it finds version conflicts before performing the installation. This version of 'pak' supports CRAN, 'Bioconductor' and 'GitHub' packages as well.
Author: Gabor Csardi [aut, cre], Jim Hester [aut], Posit Software, PBC [cph, fnd], Winston Chang [ctb] , Ascent Digital Services [cph, fnd] , Hadley Wickham [ctb, cph] , Jeroen Ooms [ctb] , Maelle Salmon [ctb] , Duncan Temple Lang [ctb] , Lloyd Hilaiel [cph] [...truncated...]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>

Diff between pak versions 0.7.1 dated 2023-12-10 and 0.7.2 dated 2024-03-17

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More information about pak at CRAN
Permanent link

Package pkgdepends updated to version 0.7.2 with previous version 0.7.1 dated 2023-12-10

Title: Package Dependency Resolution and Downloads
Description: Find recursive dependencies of 'R' packages from various sources. Solve the dependencies to obtain a consistent set of packages to install. Download packages, and install them. It supports packages on 'CRAN', 'Bioconductor' and other 'CRAN-like' repositories, 'GitHub', package 'URLs', and local package trees and files. It caches metadata and package files via the 'pkgcache' package, and performs all 'HTTP' requests, downloads, builds and installations in parallel. 'pkgdepends' is the workhorse of the 'pak' package.
Author: Gabor Csardi [aut, cre], Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>

Diff between pkgdepends versions 0.7.1 dated 2023-12-10 and 0.7.2 dated 2024-03-17

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More information about pkgdepends at CRAN
Permanent link

Package pkgbuild updated to version 1.4.4 with previous version 1.4.3 dated 2023-12-10

Title: Find Tools Needed to Build R Packages
Description: Provides functions used to build R packages. Locates compilers needed to build R packages on various platforms and ensures the PATH is configured appropriately so R can use them.
Author: Hadley Wickham [aut], Jim Hester [aut], Gabor Csardi [aut, cre], Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>

Diff between pkgbuild versions 1.4.3 dated 2023-12-10 and 1.4.4 dated 2024-03-17

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Permanent link

Package remotes updated to version 2.5.0 with previous version 2.4.2.1 dated 2023-07-18

Title: R Package Installation from Remote Repositories, Including 'GitHub'
Description: Download and install R packages stored in 'GitHub', 'GitLab', 'Bitbucket', 'Bioconductor', or plain 'subversion' or 'git' repositories. This package provides the 'install_*' functions in 'devtools'. Indeed most of the code was copied over from 'devtools'.
Author: Gabor Csardi [aut, cre], Jim Hester [aut], Hadley Wickham [aut], Winston Chang [aut], Martin Morgan [aut], Dan Tenenbaum [aut], Posit Software, PBC [cph, fnd], Ascent Digital Services [cph]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>

Diff between remotes versions 2.4.2.1 dated 2023-07-18 and 2.5.0 dated 2024-03-17

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Package rgrass updated to version 0.4-2 with previous version 0.4-1 dated 2024-01-08

Title: Interface Between 'GRASS' Geographical Information System and 'R'
Description: An interface between the 'GRASS' geographical information system ('GIS') and 'R', based on starting 'R' from within the 'GRASS' 'GIS' environment, or running a free-standing 'R' session in a temporary 'GRASS' location; the package provides facilities for using all 'GRASS' commands from the 'R' command line. The original interface package for 'GRASS 5' (2000-2010) is described in Bivand (2000) <doi:10.1016/S0098-3004(00)00057-1> and Bivand (2001) <https://www.r-project.org/conferences/DSC-2001/Proceedings/Bivand.pdf>. This was succeeded by 'spgrass6' for 'GRASS 6' (2006-2016) and 'rgrass7' for 'GRASS 7' (2015-present). The 'rgrass' package modernizes the interface for 'GRASS 8' while still permitting the use of 'GRASS 7'.
Author: Roger Bivand [cre, aut] , Rainer Krug [ctb] , Robin Lovelace [ctb] , Markus Neteler [ctb] , Sebastian Jeworutzki [ctb] , Floris Vanderhaeghe [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

Diff between rgrass versions 0.4-1 dated 2024-01-08 and 0.4-2 dated 2024-03-17

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Package dupNodes updated to version 0.2.0 with previous version 0.1.0 dated 2024-02-05

Title: Creates an 'igraph' Object that Duplicates Nodes with Self-Loops
Description: Creates a new graph from an existing one, duplicating nodes with self-loops. This can be used for a computation of betweenness centrality that does not drop this essential information. Implements Merelo & Molinari (2024) <doi:10.1007/s42001-023-00245-4>.
Author: Juan Julian Merelo-Guervos
Maintainer: Juan Julian Merelo-Guervos <jjmerelo@gmail.com>

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New package zstdlite with initial version 0.2.7
Package: zstdlite
Title: Fast Compression and Serialization with 'Zstandard' Algorithm
Version: 0.2.7
Maintainer: Mike Cheng <mikefc@coolbutuseless.com>
Description: Fast, compressed serialization of R objects using the 'Zstandard' algorithm. R objects can be compressed and decompressed quickly using the standard serialization mechanism in R. Raw byte vectors and strings are also handled directly for compatibility with compressed data created by other systems and programs supporting 'Zstandard' compression. Dictionaries are supported for more effective compression of small data, and functions are provided for training these dictionaries. This implementation provides an R interface to advanced features of the 'Zstandard' 'C' library (available from <https://github.com/facebook/zstd>).
URL: https://github.com/coolbutuseless/zstdlite
BugReports: https://github.com/coolbutuseless/zstdlite/issues
License: MIT + file LICENSE
Encoding: UTF-8
Copyright: This package includes code from the 'Zstandard' library owned by Meta Platforms, Inc. and affiliates. and created by Yann Collet. See file 'inst/COPYRIGHTS' for details.
Suggests: knitr, rmarkdown, testthat, bench
Depends: R (>= 3.4.0)
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-03-14 08:14:36 UTC; mike
Author: Mike Cheng [aut, cre, cph], Yann Collet [aut] , Meta Platforms, Inc. and affiliates. [cph]
Repository: CRAN
Date/Publication: 2024-03-17 09:10:02 UTC

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New package tsdistributions with initial version 1.0.0
Package: tsdistributions
Title: Location Scale Standardized Distributions
Version: 1.0.0
Maintainer: Alexios Galanos <alexios@4dscape.com>
Depends: R (>= 3.5.0), methods, tsmethods
LinkingTo: TMB, RcppEigen
Imports: TMB (>= 1.7.20), GeneralizedHyperbolic, SkewHyperbolic, stats, utils, data.table, zoo, Rsolnp, sandwich, future.apply, future, progressr
Description: Location-Scale based distributions parameterized in terms of mean, standard deviation, skew and shape parameters and estimation using automatic differentiation. Distributions include the Normal, Student and GED as well as their skewed variants ('Fernandez and Steel'), the 'Johnson SU', and the Generalized Hyperbolic.
License: GPL-2
Encoding: UTF-8
VignetteBuilder: knitr
URL: https://www.nopredict.com/packages/tsdistributions, https://github.com/tsmodels/tsdistributions
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
NeedsCompilation: yes
Packaged: 2024-03-14 17:36:20 UTC; alexios
Author: Alexios Galanos [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-03-17 09:10:05 UTC

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New package confcons with initial version 0.3.1
Package: confcons
Title: Confidence and Consistency of Predictive Distribution Models
Version: 0.3.1
Date: 2024-03-12
Description: Calculate confidence and consistency that measure the goodness-of-fit and transferability of predictive/potential distribution models (including species distribution models) as described by Somodi & Bede-Fazekas et al. (2024) <doi:10.1016/j.ecolmodel.2024.110667>.
License: GPL (>= 3)
Encoding: UTF-8
URL: https://github.com/bfakos/confcons, https://bfakos.github.io/confcons/
BugReports: https://github.com/bfakos/confcons/issues
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), mockery, vctrs, withr, ROCR, covr, terra, sf, blockCV (>= 3.1-3), ggplot2, ranger
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-03-15 16:37:26 UTC; Ákos
Author: Akos Bede-Fazekas [aut, cre] , Imelda Somodi [aut] , Zoltan Botta-Dukat [ctb]
Maintainer: Akos Bede-Fazekas <bfakos@ecolres.hu>
Repository: CRAN
Date/Publication: 2024-03-17 09:40:02 UTC

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New package blscrapeR with initial version 4.0.1
Package: blscrapeR
Title: An API Wrapper for the United States Bureau of Labor Statistics
Version: 4.0.1
Description: Scrapes various data from <https://www.bls.gov/>. The Bureau of Labor Statistics is the statistical branch of the United States Department of Labor. The package has additional functions to help parse, analyze and visualize the data.
Depends: R (>= 3.5.0)
Imports: httr, jsonlite, magrittr, utils, stats, dplyr, purrr, tibble, stringr
Suggests: testthat, knitr, rmarkdown
License: MIT + file LICENSE
URL: https://github.com/keberwein/blscrapeR
BugReports: https://github.com/keberwein/blscrapeR/issues
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-03-14 22:53:33 UTC; anon
Author: Kris Eberwein [aut, cre]
Maintainer: Kris Eberwein <kris.eberwein@gmail.com>
Repository: CRAN
Date/Publication: 2024-03-17 09:20:02 UTC

More information about blscrapeR at CRAN
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Package fsMTS (with last version 0.1.7) was removed from CRAN

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

2022-04-26 0.1.7

Permanent link
Package survML updated to version 1.1.0 with previous version 1.0.0 dated 2023-07-08

Title: Flexible Estimation of Conditional Survival Functions Using Machine Learning
Description: Tools for flexible estimation of conditional survival functions using off-the-shelf machine learning tools. Implements both global and local survival stacking. See Wolock CJ, Gilbert PB, Simon N, and Carone M (2024) <doi:10.1080/10618600.2024.2304070>.
Author: Charles Wolock [aut, cre, cph]
Maintainer: Charles Wolock <cwolock@gmail.com>

Diff between survML versions 1.0.0 dated 2023-07-08 and 1.1.0 dated 2024-03-17

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Package sommer updated to version 4.3.4 with previous version 4.3.3 dated 2023-11-13

Title: Solving Mixed Model Equations in R
Description: Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., heterogeneous and unstructured) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>; Jensen et al., 1997). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms for the problems r x r (r being the number of records) or using the Henderson-based average information algorithm for the problem c x c (c being the number of coefficients to estimate). Spatial models can also be fitted using the two-dimensional spline functionality available.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>

Diff between sommer versions 4.3.3 dated 2023-11-13 and 4.3.4 dated 2024-03-17

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Package bivariatemaps updated to version 1.3 with previous version 1.2 dated 2023-11-21

Title: Creates Bivariate Maps
Description: Contains functions to plot bivariate maps. For more info, see: Hidasi-Neto, J (2015) <https://rfunctions.blogspot.com/2015/03/bivariate-maps-bivariatemap-function.html>.
Author: Jose Hidasi-Neto [aut, cre]
Maintainer: Jose Hidasi-Neto <hidasineto@gmail.com>

Diff between bivariatemaps versions 1.2 dated 2023-11-21 and 1.3 dated 2024-03-17

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Sat, 16 Mar 2024

Package extrafrail updated to version 1.9 with previous version 1.8 dated 2023-09-26

Title: Estimation and Additional Tools for Alternative Shared Frailty Models
Description: Provide estimation and data generation tools for some new multivariate frailty models. This version includes the gamma, inverse Gaussian, weighted Lindley, Birnbaum-Saunders, truncated normal and mixture of inverse Gaussian as the distribution for the frailty terms. For the basal model, it is considered a parametric approach based on the exponential, Weibull and the piecewise exponential distributions as well as a semiparametric approach. For details, see Gallardo and Bourguignon (2022) <arXiv:2206.12973>.
Author: Diego Gallardo [aut, cre], Marcelo Bourguignon [aut]
Maintainer: Diego Gallardo <dgallardo@ubiobio.cl>

Diff between extrafrail versions 1.8 dated 2023-09-26 and 1.9 dated 2024-03-16

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Package FedData updated to version 4.0.1 with previous version 4.0.0 dated 2023-10-03

Title: Functions to Automate Downloading Geospatial Data Available from Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from several federated data sources (mainly sources maintained by the US Federal government). Currently, the package enables extraction from nine datasets: The National Elevation Dataset digital elevation models (1 and 1/3 arc-second; USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic (SSURGO) database from the National Cooperative Soil Survey (NCSS), which is led by the Natural Resources Conservation Service (NRCS) under the USDA; the Global Historical Climatology Network (GHCN), coordinated by National Climatic Data Center at NOAA; the Daymet gridded estimates of daily weather parameters for North America, version 4, available from the Oak Ridge National Laboratory's Distributed Active Archive Center (DAAC); the International Tree Ring Data Bank; the National Land Cover Database (NLCD); the Cropland Data Layer from the National Agricultural Statistics Service; and the PAD-US dataset of protected area [...truncated...]
Author: R. Kyle Bocinsky [aut, cre, cph] , Dylan Beaudette [ctb], Scott Chamberlain [ctb, rev], Jeffrey Hollister [ctb], Julia Gustavsen [rev]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>

Diff between FedData versions 4.0.0 dated 2023-10-03 and 4.0.1 dated 2024-03-16

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Package LipidomicsR updated to version 0.1.6 with previous version 0.1.0 dated 2024-03-14

Title: Elegant Tools for Processing and Visualization of Lipidomics Data
Description: An elegant tool for processing and visualizing lipidomics data generated by mass spectrometry. 'LipidomicsR' simplifies channel and replicate handling while providing thorough lipid species annotation. Its visualization capabilities encompass principal components analysis plots, heatmaps, volcano plots, and radar plots, enabling concise data summarization and quality assessment. Additionally, it can generate bar plots and line plots to visualize the abundance of each lipid species.
Author: Mingshi Li [aut], Hengyu Zhu [aut, cre]
Maintainer: Hengyu Zhu <hengyu.21@intl.zju.edu.cn>

Diff between LipidomicsR versions 0.1.0 dated 2024-03-14 and 0.1.6 dated 2024-03-16

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Package ARPALData updated to version 1.5.2 with previous version 1.5.1 dated 2024-02-24

Title: Retrieving and Analyzing Air Quality and Weather Data from ARPA Lombardia
Description: Contains functions for retrieving, managing and analysing air quality and weather data from Regione Lombardia open database (<https://www.dati.lombardia.it/>). Data are collected by ARPA Lombardia (Lombardia Environmental Protection Agency), Italy, through its ground monitoring network. See the webpage <https://www.arpalombardia.it/> for further information on ARPA Lombardia's activities and history. Data quality (e.g. missing values, exported values, graphical mapping) has been checked involving members of the ARPA Lombardia's office for air quality control. The package makes available observations since 1989 (for weather) and 1968 (for air quality) and are updated with daily frequency by the regional agency. Full description of the package can be retrieved in the companion paper Maranzano \& Algieri (2024), "ARPALData: an R package for retrieving and analyzing air quality and weather data from ARPA Lombardia (Italy)", Environmental and Ecological Statistics, <doi:1 [...truncated...]
Author: Paolo Maranzano [aut, cre, cph] , Andrea Algieri [aut, cph]
Maintainer: Paolo Maranzano <pmaranzano.ricercastatistica@gmail.com>

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Package shide updated to version 0.2.0 with previous version 0.1.3 dated 2024-02-04

Title: Date/Time Classes Based on Jalali Calendar
Description: Implements S3 classes for storing dates and date-times based on the Jalali calendar. The main design goal of 'shide' is consistency with base R's 'Date' and 'POSIXct'. It provide features such as: date-time parsing, formatting and arithmetic.
Author: Mohsen Mollayi [aut, cre, cph]
Maintainer: Mohsen Mollayi <mmollayi@gmail.com>

Diff between shide versions 0.1.3 dated 2024-02-04 and 0.2.0 dated 2024-03-16

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Package RNAmf updated to version 0.1.1 with previous version 0.1.0 dated 2023-12-06

Title: Recursive Non-Additive Emulator for Multi-Fidelity Data
Description: Performs RNA emulation and active learning proposed by Heo and Sung (2023+) <arXiv:2309.11772> for multi-fidelity computer experiments. The RNA emulator is particularly useful when the simulations with different fidelity level are nonlinearly correlated. The hyperparameters in the model are estimated by maximum likelihood estimation.
Author: Junoh Heo [aut, cre], Chih-Li Sung [aut]
Maintainer: Junoh Heo <heojunoh@msu.edu>

Diff between RNAmf versions 0.1.0 dated 2023-12-06 and 0.1.1 dated 2024-03-16

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Package wrappedtools updated to version 0.9.5 with previous version 0.9.3 dated 2023-09-24

Title: Useful Wrappers Around Commonly Used Functions
Description: The main functionalities of 'wrappedtools' are: adding backticks to variable names; rounding to desired precision with special case for p-values; selecting columns based on pattern and storing their position, name, and backticked name; computing and formatting of descriptive statistics (e.g. mean±SD), comparing groups and creating publication-ready tables with descriptive statistics and p-values; creating specialized plots for correlation matrices. Functions were mainly written for my own daily work or teaching, but may be of use to others as well.
Author: Andreas Busjahn [cre, aut] , Bilal Asser [aut]
Maintainer: Andreas Busjahn <andreas@busjahn.net>

Diff between wrappedtools versions 0.9.3 dated 2023-09-24 and 0.9.5 dated 2024-03-16

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Package rswipl updated to version 9.3.3 with previous version 9.1.22 dated 2024-01-25

Title: Embed 'SWI'-'Prolog'
Description: Interface to 'SWI'-'Prolog', <https://www.swi-prolog.org/>. This package is normally not loaded directly, please refer to package 'rolog' instead. The purpose of this package is to provide the 'Prolog' runtime on systems that do not have a software installation of 'SWI'-'Prolog'.
Author: Matthias Gondan [aut, com, cre] , Jan Wielemaker [ctb, cph] , European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>

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Package processx updated to version 3.8.4 with previous version 3.8.3 dated 2023-12-10

Title: Execute and Control System Processes
Description: Tools to run system processes in the background. It can check if a background process is running; wait on a background process to finish; get the exit status of finished processes; kill background processes. It can read the standard output and error of the processes, using non-blocking connections. 'processx' can poll a process for standard output or error, with a timeout. It can also poll several processes at once.
Author: Gabor Csardi [aut, cre, cph] , Winston Chang [aut], Posit Software, PBC [cph, fnd], Ascent Digital Services [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>

Diff between processx versions 3.8.3 dated 2023-12-10 and 3.8.4 dated 2024-03-16

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Package naivebayes updated to version 1.0.0 with previous version 0.9.7 dated 2020-03-08

Title: High Performance Implementation of the Naive Bayes Algorithm
Description: In this implementation of the Naive Bayes classifier following class conditional distributions are available: 'Bernoulli', 'Categorical', 'Gaussian', 'Poisson', 'Multinomial' and non-parametric representation of the class conditional density estimated via Kernel Density Estimation. Implemented classifiers handle missing data and can take advantage of sparse data.
Author: Michal Majka [aut, cre]
Maintainer: Michal Majka <michalmajka@hotmail.com>

Diff between naivebayes versions 0.9.7 dated 2020-03-08 and 1.0.0 dated 2024-03-16

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Package BiodiversityR updated to version 2.16-1 with previous version 2.15-4 dated 2023-10-22

Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt [cre, aut]
Maintainer: Roeland Kindt <RoelandCEKindt@gmail.com>

Diff between BiodiversityR versions 2.15-4 dated 2023-10-22 and 2.16-1 dated 2024-03-16

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Package visachartR updated to version 3.3.0 with previous version 3.2.0 dated 2023-10-06

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

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New package mosaicCalc with initial version 0.6.1
Package: mosaicCalc
Title: R-Language Based Calculus Operations for Teaching
Description: Software to support the introductory *MOSAIC Calculus* textbook <https://www.mosaic-web.org/MOSAIC-Calculus/>), one of many data- and modeling-oriented educational resources developed by Project MOSAIC (<https://www.mosaic-web.org/>). Provides symbolic and numerical differentiation and integration, as well as support for applied linear algebra (for data science), and differential equations/dynamics. Includes grammar-of-graphics-based functions for drawing vector fields, trajectories, etc. The software is suitable for general use, but intended mainly for teaching calculus.
Version: 0.6.1
Depends: R (>= 3.5.0), mosaic, mosaicCore (>= 0.9.2),
Imports: cubature, Deriv, dplyr, ggformula, ggplot2, glue, grDevices, MASS, Matrix, metR (>= 0.11.0), orthopolynom, plotly, rlang, Ryacas, sp, stats, tibble
Suggests: testthat, knitr, palmerpenguins, rmarkdown, mosaicData
Author: Daniel T. Kaplan <kaplan@macalester.edu>, Randall Pruim <rpruim@calvin.edu>, Nicholas J. Horton <nhorton@amherst.edu>
Maintainer: Daniel Kaplan <kaplan@macalester.edu>
VignetteBuilder: knitr
NeedsCompilation: no
License: GPL (>= 2)
LazyLoad: yes
LazyData: yes
URL: https://github.com/ProjectMOSAIC/mosaicCalc
BugReports: https://github.com/ProjectMOSAIC/mosaicCalc/issues
Encoding: UTF-8
Packaged: 2024-03-16 00:51:14 UTC; kaplan
Repository: CRAN
Date/Publication: 2024-03-16 07:10:06 UTC

More information about mosaicCalc at CRAN
Permanent link

Package DImodelsMulti updated to version 1.0.1 with previous version 1.0 dated 2024-01-16

Title: Fit Multivariate Diversity-Interactions Models with Repeated Measures
Description: An add-on package to 'DImodels' for the fitting of biodiversity and ecosystem function relationship study data with multiple ecosystem function responses and/or time points. This package uses the multivariate and repeated measures Diversity-Interactions (DI) methods developed by Kirwan et al. (2009) <doi:10.1890/08-1684.1>, Finn et al. (2013) <doi:10.1111/1365-2664.12041>, and Dooley et al. (2015) <doi:10.1111/ele.12504>.
Author: Laura Byrne [aut, cre] , Rishabh Vishwakarma [aut], Rafael de Andrade Moral [aut], Caroline Brophy [aut]
Maintainer: Laura Byrne <ByrneL54@tcd.ie>

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Package caschrono (with last version 2.4) was removed from CRAN

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

2023-11-01 2.4
2022-11-15 2.3

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Package tinytex updated to version 0.50 with previous version 0.49 dated 2023-11-22

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

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Package GenTwoArmsTrialSize updated to version 0.0.5 with previous version 0.0.4.5 dated 2023-12-11

Title: Generalized Two Arms Clinical Trial Sample Size Calculation
Description: Two arms clinical trials required sample size is calculated in the comprehensive parametric context. The calculation is based on the type of endpoints(continuous/binary/time-to-event/ordinal), design (parallel/crossover), hypothesis tests (equality/noninferiority/superiority/equivalence), trial arms noncompliance rates and expected loss of follow-up. Methods are described in: Chow SC, Shao J, Wang H, Lokhnygina Y (2017) <doi:10.1201/9781315183084>, Wittes, J (2002) <doi:10.1093/epirev/24.1.39>, Sato, T (2000) <doi:10.1002/1097-0258(20001015)19:19%3C2689::aid-sim555%3E3.0.co;2-0>, Lachin J M, Foulkes, M A (1986) <doi:10.2307/2531201>, Whitehead J(1993) <doi:10.1002/sim.4780122404>, Julious SA (2023) <doi:10.1201/9780429503658>.
Author: Mohsen Soltanifar [aut] , Chel Hee Lee [cre, aut]
Maintainer: Chel Hee Lee <chelhee.lee@ucalgary.ca>

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Fri, 15 Mar 2024

Package BTSPAS updated to version 2024.4.1 with previous version 2021.11.2 dated 2021-10-25

Title: Bayesian Time-Stratified Population Analysis
Description: Provides advanced Bayesian methods to estimate abundance and run-timing from temporally-stratified Petersen mark-recapture experiments. Methods include hierarchical modelling of the capture probabilities and spline smoothing of the daily run size. Theory described in Bonner and Schwarz (2011) <doi:10.1111/j.1541-0420.2011.01599.x>.
Author: Carl J Schwarz <cschwarz.stat.sfu.ca@gmail.com> and Simon J Bonner <sbonner6@uwo.ca>
Maintainer: Carl J Schwarz <cschwarz.stat.sfu.ca@gmail.com>

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Package teal.reporter updated to version 0.3.1 with previous version 0.3.0 dated 2024-02-16

Title: Reporting Tools for 'shiny' Modules
Description: Prebuilt 'shiny' modules containing tools for the generation of 'rmarkdown' reports, supporting reproducible research and analysis.
Author: Dawid Kaledkowski [aut, cre] , Kartikeya Kirar [aut] , Marcin Kosinski [aut], Maciej Nasinski [aut], Konrad Pagacz [aut], Mahmoud Hallal [aut], Chendi Liao [rev], Dony Unardi [rev], F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>

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Package SpatialDDLS updated to version 1.0.1 with previous version 1.0.0 dated 2023-12-06

Title: Deconvolution of Spatial Transcriptomics Data Based on Neural Networks
Description: Deconvolution of spatial transcriptomics data based on neural networks and single-cell RNA-seq data. SpatialDDLS implements a workflow to create neural network models able to make accurate estimates of cell composition of spots from spatial transcriptomics data using deep learning and the meaningful information provided by single-cell RNA-seq data. See Torroja and Sanchez-Cabo (2019) <doi:10.3389/fgene.2019.00978> and Mañanes et al. (2024) <doi:10.1093/bioinformatics/btae072> to get an overview of the method and see some examples of its performance.
Author: Diego Mananes [aut, cre] , Carlos Torroja [aut] , Fatima Sanchez-Cabo [aut]
Maintainer: Diego Mananes <dmananesc@cnic.es>

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Package sass updated to version 0.4.9 with previous version 0.4.8 dated 2023-12-05

Title: Syntactically Awesome Style Sheets ('Sass')
Description: An 'SCSS' compiler, powered by the 'LibSass' library. With this, R developers can use variables, inheritance, and functions to generate dynamic style sheets. The package uses the 'Sass CSS' extension language, which is stable, powerful, and CSS compatible.
Author: Joe Cheng [aut], Timothy Mastny [aut], Richard Iannone [aut] , Barret Schloerke [aut] , Carson Sievert [aut, cre] , Christophe Dervieux [ctb] , RStudio [cph, fnd], Sass Open Source Foundation [ctb, cph] , Greter Marcel [ctb, cph] , Mifsud Michael [ct [...truncated...]
Maintainer: Carson Sievert <carson@rstudio.com>

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Package KSgeneral updated to version 1.1.3 with previous version 1.1.2 dated 2023-07-10

Title: Computing P-Values of the K-S Test for (Dis)Continuous Null Distribution
Description: Computes a p-value of the one-sample two-sided (or one-sided, as a special case) Kolmogorov-Smirnov (KS) statistic, for any fixed critical level, and an arbitrary, possibly large sample size for a pre-specified purely discrete, mixed or continuous cumulative distribution function (cdf) under the null hypothesis. If a data sample is supplied, 'KSgeneral' computes the p-value corresponding to the value of the KS test statistic computed based on the user provided data sample. The package 'KSgeneral' implements a novel, accurate and efficient method named Exact-KS-FFT, expressing the p-value as a double-boundary non-crossing probability for a homogeneous Poisson process, which is then efficiently computed using Fast Fourier Transform (FFT). The package can also be used to compute and plot the complementary cdf of the KS statistic which is known to depend on the hypothesized distribution when the latter is discontinuous (i.e. purely discrete or mixed). To cite this package in publication us [...truncated...]
Author: Dimitrina S. Dimitrova <D.Dimitrova@city.ac.uk>, Yun Jia <yunjia2019@gmail.com>, Vladimir K. Kaishev <Vladimir.Kaishev.1@city.ac.uk> and Senren Tan <raymondtsrtsr@outlook.com>
Maintainer: Dimitrina S. Dimitrova <D.Dimitrova@city.ac.uk>

Diff between KSgeneral versions 1.1.2 dated 2023-07-10 and 1.1.3 dated 2024-03-15

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Package insight updated to version 0.19.9 with previous version 0.19.8 dated 2024-01-31

Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent access to information contained in various R models, like model formulas, model terms, information about random effects, data that was used to fit the model or data from response variables. 'insight' mainly revolves around two types of functions: Functions that find (the names of) information, starting with 'find_', and functions that get the underlying data, starting with 'get_'. The package has a consistent syntax and works with many different model objects, where otherwise functions to access these information are missing.
Author: Daniel Luedecke [aut, cre] , Dominique Makowski [aut, ctb] , Indrajeet Patil [aut, ctb] , Philip Waggoner [aut, ctb] , Mattan S. Ben-Shachar [aut, ctb] , Brenton M. Wiernik [aut, ctb] , Vincent Arel-Bundock [aut, ctb] , Etienne Bacher [aut, ctb] , Ale [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>

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Package emuR updated to version 2.5.0 with previous version 2.4.2 dated 2023-11-03

Title: Main Package of the EMU Speech Database Management System
Description: Provide the EMU Speech Database Management System (EMU-SDMS) with database management, data extraction, data preparation and data visualization facilities. See <https://ips-lmu.github.io/The-EMU-SDMS-Manual/> for more details.
Author: Markus Jochim [aut, cre] , Raphael Winkelmann [aut], Klaus Jaensch [aut, ctb], Steve Cassidy [aut, ctb], Jonathan Harrington [aut, ctb]
Maintainer: Markus Jochim <markusjochim@phonetik.uni-muenchen.de>

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Package AMAPVox updated to version 2.2.1 with previous version 1.0.1 dated 2023-06-22

Title: LiDAR Data Voxelisation
Description: Read, manipulate and write voxel spaces. Voxel spaces are read from text-based output files of the 'AMAPVox' software. 'AMAPVox' is a LiDAR point cloud voxelisation software that aims at estimating leaf area through several theoretical/numerical approaches. See more in the article Vincent et al. (2017) <doi:10.23708/1AJNMP> and the technical note Vincent et al. (2021) <doi:10.23708/1AJNMP>.
Author: Gregoire Vincent [aut], Julien Heurtebize [aut], Philippe Verley [aut, cre]
Maintainer: Philippe Verley <philippe.verley@ird.fr>

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Package visR updated to version 0.4.1 with previous version 0.4.0 dated 2023-11-20

Title: Clinical Graphs and Tables Adhering to Graphical Principles
Description: To enable fit-for-purpose, reusable clinical and medical research focused visualizations and tables with sensible defaults and based on graphical principles as described in: "Vandemeulebroecke et al. (2018)" <doi:10.1002/pst.1912>, "Vandemeulebroecke et al. (2019)" <doi:10.1002/psp4.12455>, and "Morris et al. (2019)" <doi:10.1136/bmjopen-2019-030215>.
Author: Mark Baillie [aut, cre, cph], Diego Saldana [aut], Charlotta Fruechtenicht [aut], Marc Vandemeulebroecke [aut], Thanos Siadimas [aut], Pawel Kawski [aut], Steven Haesendonckx [aut], James Black [aut], Pelagia Alexandra Papadopoulou [aut], Tim Treis [ [...truncated...]
Maintainer: Mark Baillie <bailliem@gmail.com>

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Package frailtypack updated to version 3.6.0 with previous version 3.5.1 dated 2023-11-25

Title: Shared, Joint (Generalized) Frailty Models; Surrogate Endpoints
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package: 1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied. 2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope). 3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects. 4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed. 5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms. 6) Joint Nested fra [...truncated...]
Author: Virginie Rondeau [aut, cre] , Juan R. Gonzalez [aut], Yassin Mazroui [aut], Audrey Mauguen [aut], Amadou Diakite [aut], Alexandre Laurent [aut], Myriam Lopez [aut], Agnieszka Krol [aut], Casimir L. Sofeu [aut], Julien Dumerc [aut], Denis Rustand [aut [...truncated...]
Maintainer: Virginie Rondeau <virginie.rondeau@u-bordeaux.fr>

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Package folders updated to version 0.1.0 with previous version 0.0.6 dated 2023-03-14

Title: Standardized Folder Names
Description: Supports the use of standardized folder names.
Author: Brian High [aut, cre], University of Washington [cph, fnd]
Maintainer: Brian High <bhigh@live.com>

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Package aifeducation updated to version 0.3.2 with previous version 0.3.1 dated 2024-02-18

Title: Artificial Intelligence for Education
Description: In social and educational settings, the use of Artificial Intelligence (AI) is a challenging task. Relevant data is often only available in handwritten forms, or the use of data is restricted by privacy policies. This often leads to small data sets. Furthermore, in the educational and social sciences, data is often unbalanced in terms of frequencies. To support educators as well as educational and social researchers in using the potentials of AI for their work, this package provides a unified interface for neural nets in 'keras', 'tensorflow', and 'pytorch' to deal with natural language problems. In addition, the package ships with a shiny app, providing a graphical user interface. This allows the usage of AI for people without skills in writing python/R scripts. The tools integrate existing mathematical and statistical methods for dealing with small data sets via pseudo-labeling (e.g. Lee (2013) <https://www.researchgate.net/publication/280581078_Pseudo-Label_The_Simple_and_Efficie [...truncated...]
Author: Berding Florian [aut, cre] , Pargmann Julia [ctb], Riebenbauer Elisabeth [ctb], Rebmann Karin [ctb], Slopinski Andreas [ctb]
Maintainer: Berding Florian <florian.berding@uni-hamburg.de>

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Package PCMBase updated to version 1.2.14 with previous version 1.2.13 dated 2022-11-18

Title: Simulation and Likelihood Calculation of Phylogenetic Comparative Models
Description: Phylogenetic comparative methods represent models of continuous trait data associated with the tips of a phylogenetic tree. Examples of such models are Gaussian continuous time branching stochastic processes such as Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes, which regard the data at the tips of the tree as an observed (final) state of a Markov process starting from an initial state at the root and evolving along the branches of the tree. The PCMBase R package provides a general framework for manipulating such models. This framework consists of an application programming interface for specifying data and model parameters, and efficient algorithms for simulating trait evolution under a model and calculating the likelihood of model parameters for an assumed model and trait data. The package implements a growing collection of models, which currently includes BM, OU, BM/OU with jumps, two-speed OU as well as mixed Gaussian models, in which different types of the above model [...truncated...]
Author: Venelin Mitov [aut, cre, cph] , Krzysztof Bartoszek [ctb], Georgios Asimomitis [ctb], Tanja Stadler [ths]
Maintainer: Venelin Mitov <vmitov@gmail.com>

Diff between PCMBase versions 1.2.13 dated 2022-11-18 and 1.2.14 dated 2024-03-15

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More information about PCMBase at CRAN
Permanent link

Package dinamic updated to version 1.0.1 with previous version 1.0 dated 2011-11-09

Title: A Method to Analyze Recurrent DNA Copy Number Aberrations in Tumors
Description: In tumor tissue, underlying genomic instability can lead to DNA copy number alterations, e.g., copy number gains or losses. Sporadic copy number alterations occur randomly throughout the genome, whereas recurrent alterations are observed in the same genomic region across multiple independent samples, perhaps because they provide a selective growth advantage. This package implements the DiNAMIC procedure for assessing the statistical significance of recurrent DNA copy number aberrations (Bioinformatics (2011) 27(5) 678 - 685).
Author: Vonn Walter [aut, cre] , Andrew B. Nobel [aut], Fred A. Wright [aut]
Maintainer: Vonn Walter <vwalter1@pennstatehealth.psu.edu>

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More information about dinamic at CRAN
Permanent link

Package tfrmt updated to version 0.1.1 with previous version 0.1.0 dated 2023-10-17

Title: Applies Display Metadata to Analysis Results Datasets
Description: Creates a framework to store and apply display metadata to Analysis Results Datasets (ARDs). The use of 'tfrmt' allows users to define table format and styling without the data, and later apply the format to the data.
Author: Becca Krouse [aut, cre], Christina Fillmore [aut] , GlaxoSmithKline Research & Development Limited [cph, fnd], Atorus Research LLC [cph, fnd], Ellis Hughes [aut] , Karima Ahmad [aut] , Shannon Haughton [aut]
Maintainer: Becca Krouse <becca.z.krouse@gsk.com>

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Package moodlequizR updated to version 2.0.2 with previous version 1.0.3 dated 2023-09-12

Title: Easily Create Fully Randomized 'Moodle' Test Questions
Description: Routines to generate fully randomized 'moodle' quizzes. It also contains 12 examples and a 'shiny' app.
Author: Wolfgang Rolke [aut, cre]
Maintainer: Wolfgang Rolke <wolfgang.rolke@upr.edu>

Diff between moodlequizR versions 1.0.3 dated 2023-09-12 and 2.0.2 dated 2024-03-15

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Package manynet updated to version 0.4.4 with previous version 0.4.1 dated 2024-01-24

Title: Many Ways to Make, Modify, Mark, and Map Myriad Networks
Description: A set of tools for making, modifying, marking, and mapping many different types of networks. All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects, and on one-mode, two-mode (bipartite), and sometimes three-mode networks. The package includes functions for importing and exporting, creating and generating networks, modifying networks and node and tie attributes, and describing and visualizing networks with sensible defaults.
Author: James Hollway [cre, aut, ctb] , Henrique Sposito [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>

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Package flashr updated to version 0.1.2 with previous version 0.1.1 dated 2023-03-28

Title: Create Flashcards of Terms and Definitions
Description: Provides functions for creating flashcard decks of terms and definitions. This package creates HTML slides using 'revealjs' that can be viewed in the 'RStudio' viewer or a web browser. Users can create flashcards from either existing built-in decks or create their own from CSV files or vectors of function names.
Author: Jeffrey R. Stevens [aut, cre, cph]
Maintainer: Jeffrey R. Stevens <jeffrey.r.stevens@protonmail.com>

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Package rirods updated to version 0.2.0 with previous version 0.1.2 dated 2023-11-02

Title: R Client for 'iRODS'
Description: The open sourced data management software 'Integrated Rule-Oriented Data System' ('iRODS') offers solutions for the whole data life cycle (<https://irods.org/>). The loosely constructed and highly configurable architecture of 'iRODS' frees the user from strict formatting constraints and single-vendor solutions. This package provides an interface to the 'iRODS' HTTP API, allowing you to manage your data and metadata in 'iRODS' with R. Storage of annotated files and R objects in 'iRODS' ensures findability, accessibility, interoperability, and reusability of data.
Author: Martin Schobben [aut, cre, cph] , Mariana Montes [aut], Terrell Russell [ctb], Christine Staiger [ctb], Ton Smeele [ctb], Alan King [ctb]
Maintainer: Martin Schobben <schobbenmartin@gmail.com>

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Title: Power Analysis and Data Simulation for Multilevel Models
Description: A declarative language for specifying multilevel models, solving for population parameters based on specified variance-explained effect size measures, generating data, and conducting power analyses to determine sample size recommendations. The specification allows for any number of within-cluster effects, between-cluster effects, covariate effects at either level, and random coefficients. Moreover, the models do not assume orthogonal effects, and predictors can correlate at either level and accommodate models with multiple interaction effects.
Author: Brian T. Keller [aut, cre, cph]
Maintainer: Brian T. Keller <btkeller@missouri.edu>

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Title: Genetic Analysis of Populations with Mixed Reproduction
Description: Population genetic analyses for hierarchical analysis of partially clonal populations built upon the architecture of the 'adegenet' package. Originally described in Kamvar, Tabima, and Grünwald (2014) <doi:10.7717/peerj.281> with version 2.0 described in Kamvar, Brooks, and Grünwald (2015) <doi:10.3389/fgene.2015.00208>.
Author: Zhian N. Kamvar [cre, aut] , Javier F. Tabima [aut] , Sydney E. Everhart [ctb, dtc] , Jonah C. Brooks [aut], Stacy A. Krueger-Hadfield [ctb] , Erik Sotka [ctb], Brian J. Knaus [ctb] , Patrick G. Meirmans [ctb] , Frederic D. Chevalier [ctb] , David Fo [...truncated...]
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>

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Title: Create Custom Plots for Viewing Genetic Association Results
Description: A collection of functions for visualizing,exploring and annotating genetic association results.Association results from multiple traits can be viewed simultaneously along with gene annotation, over the entire genome (Manhattan plot) or in the more detailed regional view.
Author: Thorhildur Juliusdottir [cph, aut, cre], Andri Stefansson [aut]
Maintainer: Thorhildur Juliusdottir <totajuliusd@gmail.com>

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Title: Data Visualization for QTL Experiments
Description: Functions to plot QTL (quantitative trait loci) analysis results and related diagnostics. Part of 'qtl2', an upgrade of the 'qtl' package to better handle high-dimensional data and complex cross designs.
Author: Brian S Yandell [aut, cre], Karl W Broman [aut]
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Package giscoR updated to version 0.4.1 with previous version 0.4.0 dated 2023-10-30

Title: Download Map Data from GISCO API - Eurostat
Description: Tools to download data from the GISCO (Geographic Information System of the Commission) Eurostat database <https://ec.europa.eu/eurostat/web/gisco>. Global and European map data available. This package is in no way officially related to or endorsed by Eurostat.
Author: Diego Hernangomez [aut, cre, cph] , EuroGeographics [cph] , Vincent Arel-Bundock [cph]
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Package formatdown updated to version 0.1.3 with previous version 0.1.2 dated 2023-06-21

Title: Formatting Tools for 'rmarkdown' Documents
Description: Provides a small set of tools for formatting tasks when creating documents in R Markdown or Quarto Markdown. Convert the elements of a numerical vector to character strings in one of several forms: powers-of-ten notation in engineering or scientific form delimited for rendering as inline equations; integer or decimal notation delimited for equation rendering; numbers with measurement units (non-delimited) where units are selected to eliminate the need for powers-of-ten or scientific notation. Useful for rendering a numerical scalar in an inline R code chunk as well as formatting columns of data frames displayed in a table.
Author: Richard Layton [aut, cre]
Maintainer: Richard Layton <graphdoctor@gmail.com>

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Package saeRobust updated to version 0.5.0 with previous version 0.4.0 dated 2023-01-18

Title: Robust Small Area Estimation
Description: Methods to fit robust alternatives to commonly used models used in Small Area Estimation. The methods here used are based on best linear unbiased predictions and linear mixed models. At this time available models include area level models incorporating spatial and temporal correlation in the random effects.
Author: Sebastian Warnholz [aut, cre]
Maintainer: Sebastian Warnholz <wahani@gmail.com>

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Package howManyImputations updated to version 0.2.5 with previous version 0.2.4 dated 2023-02-05

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

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Package finbif updated to version 0.9.5 with previous version 0.9.4 dated 2024-01-12

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

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Package fable updated to version 0.3.4 with previous version 0.3.3 dated 2023-03-22

Title: Forecasting Models for Tidy Time Series
Description: Provides a collection of commonly used univariate and multivariate time series forecasting models including automatically selected exponential smoothing (ETS) and autoregressive integrated moving average (ARIMA) models. These models work within the 'fable' framework provided by the 'fabletools' package, which provides the tools to evaluate, visualise, and combine models in a workflow consistent with the tidyverse.
Author: Mitchell O'Hara-Wild [aut, cre], Rob Hyndman [aut], Earo Wang [aut], Gabriel Caceres [ctb] , Christoph Bergmeir [ctb] , Tim-Gunnar Hensel [ctb], Timothy Hyndman [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>

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Package ripc updated to version 0.2.1 with previous version 0.2.0 dated 2023-09-06

Title: Download and Tidy IPC and CH Data
Description: Utilities to access Integrated Food Security Phase Classification (IPC) and Cadre Harmonisé (CH) food security data. Wrapper functions are available for all of the 'IPC-CH' Public API (<https://docs.api.ipcinfo.org>) simplified and advanced endpoints to easily download the data in a clean and tidy format.
Author: Seth Caldwell [aut, cre, cph]
Maintainer: Seth Caldwell <caldwellst@gmail.com>

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Package EGAnet updated to version 2.0.5 with previous version 2.0.4 dated 2024-01-22

Title: Exploratory Graph Analysis – a Framework for Estimating the Number of Dimensions in Multivariate Data using Network Psychometrics
Description: Implements the Exploratory Graph Analysis (EGA) framework for dimensionality and psychometric assessment. EGA estimates the number of dimensions in psychological data using network estimation methods and community detection algorithms. A bootstrap method is provided to assess the stability of dimensions and items. Fit is evaluated using the Entropy Fit family of indices. Unique Variable Analysis evaluates the extent to which items are locally dependent (or redundant). Network loadings provide similar information to factor loadings and can be used to compute network scores. A bootstrap and permutation approach are available to assess configural and metric invariance. Hierarchical structures can be detected using Hierarchical EGA. Time series and intensive longitudinal data can be analyzed using Dynamic EGA, supporting individual, group, and population level assessments.
Author: Hudson Golino [aut, cre] , Alexander Christensen [aut] , Robert Moulder [ctb] , Luis E. Garrido [ctb] , Laura Jamison [ctb] , Dingjing Shi [ctb]
Maintainer: Hudson Golino <hfg9s@virginia.edu>

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Package bnlearn updated to version 4.9.3 with previous version 4.9.2 dated 2024-03-12

Title: Bayesian Network Structure Learning, Parameter Learning and Inference
Description: Bayesian network structure learning, parameter learning and inference. This package implements constraint-based (PC, GS, IAMB, Inter-IAMB, Fast-IAMB, MMPC, Hiton-PC, HPC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing and Tabu Search) and hybrid (MMHC, RSMAX2, H2PC) structure learning algorithms for discrete, Gaussian and conditional Gaussian networks, along with many score functions and conditional independence tests. The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also implemented. Some utility functions (model comparison and manipulation, random data generation, arc orientation testing, simple and advanced plots) are included, as well as support for parameter estimation (maximum likelihood and Bayesian) and inference, conditional probability queries, cross-validation, bootstrap and model averaging. Development snapshots with the latest bugfixes are available from <https://www.bnlearn.com/>.
Author: Marco Scutari [aut, cre], Tomi Silander [ctb], Robert Ness [ctb]
Maintainer: Marco Scutari <scutari@bnlearn.com>

Diff between bnlearn versions 4.9.2 dated 2024-03-12 and 4.9.3 dated 2024-03-15

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Package BayesXsrc updated to version 3.0-5 with previous version 3.0-4 dated 2023-02-03

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

Diff between BayesXsrc versions 3.0-4 dated 2023-02-03 and 3.0-5 dated 2024-03-15

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Package BayesMallows updated to version 2.1.1 with previous version 2.1.0 dated 2024-03-13

Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model (Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>; Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>; Sorensen et al., R Journal, 2020 <doi:10.32614/RJ-2020-026>; Stein, PhD Thesis, 2023 <https://eprints.lancs.ac.uk/id/eprint/195759>). Both Metropolis-Hastings and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule, Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the posterior distributions of parameters are provided. The package also provides functions for estimating the partition function (normalizing constant) of the Mallows rank mo [...truncated...]
Author: Oystein Sorensen [aut, cre] , Waldir Leoncio [aut], Valeria Vitelli [aut] , Marta Crispino [aut], Qinghua Liu [aut], Cristina Mollica [aut], Luca Tardella [aut], Anja Stein [aut]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>

Diff between BayesMallows versions 2.1.0 dated 2024-03-13 and 2.1.1 dated 2024-03-15

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Package templates updated to version 0.4.0 with previous version 0.3.0 dated 2018-05-22

Title: A System for Working with Templates
Description: Provides tools to work with template code and text in R. It aims to provide a simple substitution mechanism for R-expressions inside these templates. Templates can be written in other languages like 'SQL', can simply be represented by characters in R, or can themselves be R-expressions or functions.
Author: Sebastian Warnholz [aut, cre]
Maintainer: Sebastian Warnholz <wahani@gmail.com>

Diff between templates versions 0.3.0 dated 2018-05-22 and 0.4.0 dated 2024-03-15

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Package s3fs updated to version 0.1.5 with previous version 0.1.4 dated 2023-10-23

Title: 'Amazon Web Service S3' File System
Description: Access 'Amazon Web Service Simple Storage Service' ('S3') <https://aws.amazon.com/s3/> as if it were a file system. Interface based on the R package 'fs'.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>

Diff between s3fs versions 0.1.4 dated 2023-10-23 and 0.1.5 dated 2024-03-15

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New package rlandfire with initial version 1.0.0
Package: rlandfire
Title: Interface to 'LANDFIRE Product Service' API
Version: 1.0.0
Maintainer: Mark Buckner <mab677@cornell.edu>
Description: Provides access to a suite of geospatial data layers for wildfire management, fuel modeling, ecology, natural resource management, climate, conservation, etc., via the 'LANDFIRE' (<https://www.landfire.gov/index.php>) Product Service ('LFPS') API.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/bcknr/rlandfire
BugReports: https://github.com/bcknr/rlandfire/issues
Imports: httr, sf, utils
Suggests: knitr, raster, rmarkdown, stars, terra, testthat (>= 3.0.0)
VignetteBuilder: knitr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-03-14 20:56:57 UTC; mark
Author: Mark Buckner [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-03-15 11:20:02 UTC

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New package pensynth with initial version 0.3.0
Package: pensynth
Title: Penalized Synthetic Control Estimation
Version: 0.3.0
Description: Estimate penalized synthetic control models and perform hold-out validation to determine their penalty parameter. This method is based on the work by Abadie & L'Hour (2021) <doi:10.1080/01621459.2021.1971535>. Penalized synthetic controls smoothly interpolate between one-to-one matching and the synthetic control method.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: geometry, clarabel
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-03-15 08:54:50 UTC; erikj
Author: Erik-Jan van Kesteren [cre, aut] , Isaac Slaughter [ctb]
Maintainer: Erik-Jan van Kesteren <e.vankesteren1@uu.nl>
Repository: CRAN
Date/Publication: 2024-03-15 11:50:05 UTC

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Package NeuroDecodeR updated to version 0.2.0 with previous version 0.1.0 dated 2022-09-29

Title: Decode Information from Neural Activity
Description: Neural decoding is method of analyzing neural data that uses a pattern classifiers to predict experimental conditions based on neural activity. 'NeuroDecodeR' is a system of objects that makes it easy to run neural decoding analyses. For more information on neural decoding see Meyers & Kreiman (2011) <doi:10.7551/mitpress/8404.003.0024>.
Author: Ethan Meyers [aut, cre]
Maintainer: Ethan Meyers <ethan.meyers@gmail.com>

Diff between NeuroDecodeR versions 0.1.0 dated 2022-09-29 and 0.2.0 dated 2024-03-15

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 NeuroDecodeR-0.2.0/NeuroDecodeR/NAMESPACE                                                                               |  138 
 NeuroDecodeR-0.2.0/NeuroDecodeR/R/NeuroDecodeR.R                                                                        |  120 
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 NeuroDecodeR-0.2.0/NeuroDecodeR/R/cl_poisson_naive_bayes.R                                                              |  374 +-
 NeuroDecodeR-0.2.0/NeuroDecodeR/R/cl_svm.R                                                                              |  412 +-
 NeuroDecodeR-0.2.0/NeuroDecodeR/R/create_binned_data.R                                                                  |  566 +--
 NeuroDecodeR-0.2.0/NeuroDecodeR/R/cv_standard.R                                                                         | 1046 +++---
 NeuroDecodeR-0.2.0/NeuroDecodeR/R/ds_basic.R                                                                            |  950 +++---
 NeuroDecodeR-0.2.0/NeuroDecodeR/R/ds_generalization.R                                                                   |  578 +--
 NeuroDecodeR-0.2.0/NeuroDecodeR/R/fp_select_k_features.R                                                                |  332 +-
 NeuroDecodeR-0.2.0/NeuroDecodeR/R/fp_zscore.R                                                                           |  212 -
 NeuroDecodeR-0.2.0/NeuroDecodeR/R/generic_functions.R                                                                   |  486 +--
 NeuroDecodeR-0.2.0/NeuroDecodeR/R/get_num_label_repetitions.R                                                           | 1052 +++---
 NeuroDecodeR-0.2.0/NeuroDecodeR/R/log_and_save_decoding_results.R                                                       |  733 ++--
 NeuroDecodeR-0.2.0/NeuroDecodeR/R/ndr_container.R                                                                       |  276 -
 NeuroDecodeR-0.2.0/NeuroDecodeR/R/private_helper_functions.R                                                            |  526 +--
 NeuroDecodeR-0.2.0/NeuroDecodeR/R/raster_data_functions.R                                                               | 1305 ++++----
 NeuroDecodeR-0.2.0/NeuroDecodeR/R/rm_confusion_matrix.R                                                                 | 1100 +++----
 NeuroDecodeR-0.2.0/NeuroDecodeR/R/rm_main_results.R                                                                     | 1566 +++++-----
 NeuroDecodeR-0.2.0/NeuroDecodeR/R/test_valid_NDR_objects.R                                                              | 1006 +++---
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 NeuroDecodeR-0.2.0/NeuroDecodeR/build/vignette.rds                                                                      |binary
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 NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/NDR_object_specification.Rmd                                                   |  836 ++---
 NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/NDR_object_specification.html                                                  | 1459 ++++-----
 NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/data_formats.R                                                                 |   56 
 NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/data_formats.Rmd                                                               |  350 +-
 NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/data_formats.html                                                              | 1091 +++---
 NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/datasets.R                                                                     |   28 
 NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/datasets.Rmd                                                                   |  288 -
 NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/datasets.html                                                                  |  917 ++---
 NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/generalization_tutorial.R                                                      |  360 +-
 NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/generalization_tutorial.Rmd                                                    |  716 ++--
 NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/generalization_tutorial.html                                                   | 1447 ++++-----
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 NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/introduction_tutorial.Rmd                                                      |  992 +++---
 NeuroDecodeR-0.2.0/NeuroDecodeR/inst/doc/introduction_tutorial.html                                                     | 1461 ++++-----
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 NeuroDecodeR-0.2.0/NeuroDecodeR/man/NeuroDecodeR.Rd                                                                     |   82 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/aggregate_CV_split_results.Rd                                                       |   74 
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 NeuroDecodeR-0.2.0/NeuroDecodeR/man/aggregate_resample_run_results.Rd                                                   |   52 
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 NeuroDecodeR-0.2.0/NeuroDecodeR/man/cl_max_correlation.Rd                                                               |  156 
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 NeuroDecodeR-0.2.0/NeuroDecodeR/man/cl_svm.Rd                                                                           |  154 
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 NeuroDecodeR-0.2.0/NeuroDecodeR/man/figures/README-TCD_plot-1.png                                                       |binary
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 NeuroDecodeR-0.2.0/NeuroDecodeR/man/fp_select_k_features.Rd                                                             |  124 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/fp_zscore.Rd                                                                        |  102 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_data.Rd                                                                         |   70 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_data.ds_basic.Rd                                                                |   70 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_data.ds_generalization.Rd                                                       |   70 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_num_label_repetitions.Rd                                                        |  112 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_num_label_repetitions_each_site.Rd                                              |   68 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_parameters.Rd                                                                   |   64 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_parameters.cl_max_correlation.Rd                                                |   64 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_parameters.cl_poisson_naive_bayes.Rd                                            |   64 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_parameters.cl_svm.Rd                                                            |   64 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_parameters.cv_standard.Rd                                                       |   62 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_parameters.ds_basic.Rd                                                          |   64 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_parameters.ds_generalization.Rd                                                 |   64 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_parameters.fp_select_k_features.Rd                                              |   64 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_parameters.fp_zscore.Rd                                                         |   64 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_parameters.rm_confusion_matrix.Rd                                               |   64 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_parameters.rm_main_results.Rd                                                   |   64 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_predictions.Rd                                                                  |   94 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_predictions.cl_max_correlation.Rd                                               |   94 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_predictions.cl_poisson_naive_bayes.Rd                                           |   94 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_predictions.cl_svm.Rd                                                           |   94 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/get_siteIDs_with_k_label_repetitions.Rd                                             |   86 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/log_check_results_already_exist.Rd                                                  |   44 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/log_load_results_from_params.Rd                                                     |   48 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/log_load_results_from_result_name.Rd                                                |   54 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/log_save_results.Rd                                                                 |   66 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/plot.label_repetition.Rd                                                            |   56 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/plot.raster_data.Rd                                                                 |   54 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/plot.rm_confusion_matrix.Rd                                                         |  120 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/plot.rm_main_results.Rd                                                             |   91 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/plot_main_results.Rd                                                                |  126 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/preprocess_data.Rd                                                                  |   86 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/preprocess_data.fp_select_k_features.Rd                                             |   86 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/preprocess_data.fp_zscore.Rd                                                        |   86 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/read_matlab_raster_data.Rd                                                          |  138 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/read_raster_data.Rd                                                                 |   94 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/rm_confusion_matrix.Rd                                                              |  132 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/rm_main_results.Rd                                                                  |  134 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/run_decoding.Rd                                                                     |   60 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/run_decoding.cv_standard.Rd                                                         |   58 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/test_valid_binned_format.Rd                                                         |   48 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/test_valid_ndr_object.Rd                                                            |   50 
 NeuroDecodeR-0.2.0/NeuroDecodeR/man/test_valid_raster_format.Rd                                                         |   87 
 NeuroDecodeR-0.2.0/NeuroDecodeR/tests/testthat.R                                                                        |    8 
 NeuroDecodeR-0.2.0/NeuroDecodeR/tests/testthat/example_DECODING_RESULTS.Rda                                             |binary
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 NeuroDecodeR-0.2.0/NeuroDecodeR/tests/testthat/test-bin_convert_data.R                                                  |  622 +--
 NeuroDecodeR-0.2.0/NeuroDecodeR/tests/testthat/test-classifiers.R                                                       |  344 +-
 NeuroDecodeR-0.2.0/NeuroDecodeR/tests/testthat/test-datasources.R                                                       |  849 ++---
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 NeuroDecodeR-0.2.0/NeuroDecodeR/tests/testthat/test-full_decoding.R                                                     |  152 
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 NeuroDecodeR-0.2.0/NeuroDecodeR/tests/testthat/test-ndr_container.R                                                     |   74 
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 NeuroDecodeR-0.2.0/NeuroDecodeR/vignettes/NDR_object_specification.Rmd                                                  |  836 ++---
 NeuroDecodeR-0.2.0/NeuroDecodeR/vignettes/data_formats.Rmd                                                              |  350 +-
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 NeuroDecodeR-0.2.0/NeuroDecodeR/vignettes/generalization_tutorial.Rmd                                                   |  716 ++--
 NeuroDecodeR-0.2.0/NeuroDecodeR/vignettes/introduction_tutorial.Rmd                                                     |  992 +++---
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Permanent link

New package dySEM with initial version 1.0.0
Package: dySEM
Title: Dyadic Structural Equation Modeling
Version: 1.0.0
Description: Scripting of structural equation models via 'lavaan' for Dyadic Data Analysis, and helper functions for supplemental calculations, tabling, and model visualization. Current models supported include Dyadic Confirmatory Factor Analysis, the Actor–Partner Interdependence Model (observed and latent), the Common Fate Model (observed and latent), Mutual Influence Model (latent), and the Bifactor Dyadic Model (latent).
License: GPL-3
Encoding: UTF-8
URL: https://github.com/jsakaluk/dySEM, https://jsakaluk.github.io/dySEM/
BugReports: https://github.com/jsakaluk/dySEM/issues
Imports: dplyr, gt, lavaan, lifecycle, magrittr, rlang, semPlot, stringr, tibble
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
LazyData: true
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-03-14 17:49:18 UTC; johnsakaluk
Author: John Sakaluk [aut, cre, cph] , Omar Camanto [aut], Robyn Kilshaw [ctb], Alexandra Fisher [ctb]
Maintainer: John Sakaluk <jksakaluk@gmail.com>
Repository: CRAN
Date/Publication: 2024-03-15 11:10:02 UTC

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Package databraryr updated to version 0.6.2 with previous version 0.6.1 dated 2024-02-22

Title: Interact with the 'Databrary.org' API
Description: 'Databrary.org' is a restricted access repository for research data, especially video and audio. This package provides commands to interact with the data stored on 'Databrary.org'.
Author: Rick O. Gilmore [aut, cre, cph], Jeffrey Spies [aut], National Science Foundation OAC-2032713 [fnd], National Institutes of Health R01HD094830 [fnd]
Maintainer: Rick O. Gilmore <rog1@psu.edu>

Diff between databraryr versions 0.6.1 dated 2024-02-22 and 0.6.2 dated 2024-03-15

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New package palette with initial version 0.0.2
Package: palette
Title: Color Scheme Helpers
Version: 0.0.2
Description: Hexadecimal codes are typically used to represent colors in R. Connecting these codes to their colors requires practice or memorization. 'palette' provides a 'vctrs' class for working with color palettes, including printing and plotting functions. The goal of the class is to place visual representations of color palettes directly on or, at least, next to their corresponding character representations. Palette extensions also are provided for data frames using 'pillar'.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/christopherkenny/palette, https://christophertkenny.com/palette/
BugReports: https://github.com/christopherkenny/palette/issues
Imports: cli, pillar, vctrs
Suggests: ggplot2, spelling, testthat (>= 3.0.0), vdiffr
Language: en-US
Depends: R (>= 3.5)
NeedsCompilation: no
Packaged: 2024-03-14 17:07:36 UTC; chris
Author: Christopher T. Kenny [aut, cre]
Maintainer: Christopher T. Kenny <christopherkenny@fas.harvard.edu>
Repository: CRAN
Date/Publication: 2024-03-15 10:40:02 UTC

More information about palette at CRAN
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Package FinePop updated to version 1.5.2 with previous version 1.5.1 dated 2018-10-26

Title: Fine-Scale Population Analysis
Description: Statistical tool set for population genetics. The package provides following functions: 1) empirical Bayes estimator of Fst and other measures of genetic differentiation, 2) regression analysis of environmental effects on genetic differentiation using bootstrap method, 3) interfaces to read and manipulate 'GENEPOP' format data files and allele/haplotype frequency format files.
Author: Reiichiro Nakamichi, Hirohisa Kishino, Shuichi Kitada
Maintainer: Reiichiro Nakamichi <nakamichi_reiichiro33@fra.go.jp>

Diff between FinePop versions 1.5.1 dated 2018-10-26 and 1.5.2 dated 2024-03-15

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Package epos updated to version 1.1 with previous version 1.0 dated 2021-02-19

Title: Epilepsy Ontologies' Similarities
Description: Analysis and visualization of similarities between epilepsy ontologies based on text mining results by comparing ranked lists of co-occurring drug terms in the BioASQ corpus. The ranked result lists of neurological drug terms co-occurring with terms from the epilepsy ontologies EpSO, ESSO, EPILONT, EPISEM and FENICS undergo further analysis. The source data to create the ranked lists of drug names is produced using the text mining workflows described in Mueller, Bernd and Hagelstein, Alexandra (2016) <doi:10.4126/FRL01-006408558>, Mueller, Bernd et al. (2017) <doi:10.1007/978-3-319-58694-6_22>, Mueller, Bernd and Rebholz-Schuhmann, Dietrich (2020) <doi:10.1007/978-3-030-43887-6_52>, and Mueller, Bernd et al. (2022) <doi:10.1186/s13326-021-00258-w>.
Author: Bernd Mueller
Maintainer: Bernd Mueller <bernd.mueller@zbmed.de>

Diff between epos versions 1.0 dated 2021-02-19 and 1.1 dated 2024-03-15

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Package QCA updated to version 3.22 with previous version 3.21 dated 2023-09-18

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

Diff between QCA versions 3.21 dated 2023-09-18 and 3.22 dated 2024-03-15

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Package feasts updated to version 0.3.2 with previous version 0.3.1 dated 2023-03-22

Title: Feature Extraction and Statistics for Time Series
Description: Provides a collection of features, decomposition methods, statistical summaries and graphics functions for the analysing tidy time series data. The package name 'feasts' is an acronym comprising of its key features: Feature Extraction And Statistics for Time Series.
Author: Mitchell O'Hara-Wild [aut, cre], Rob Hyndman [aut], Earo Wang [aut], Di Cook [ctb], Thiyanga Talagala [ctb] , Leanne Chhay [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>

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Package WRS2 updated to version 1.1-6 with previous version 1.1-5 dated 2023-10-30

Title: A Collection of Robust Statistical Methods
Description: A collection of robust statistical methods based on Wilcox' WRS functions. It implements robust t-tests (independent and dependent samples), robust ANOVA (including between-within subject designs), quantile ANOVA, robust correlation, robust mediation, and nonparametric ANCOVA models based on robust location measures.
Author: Patrick Mair [cre, aut], Rand Wilcox [aut], Indrajeet Patil [ctb]
Maintainer: Patrick Mair <mair@fas.harvard.edu>

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Package eRm updated to version 1.0-6 with previous version 1.0-5 dated 2024-03-01

Title: Extended Rasch Modeling
Description: Fits Rasch models (RM), linear logistic test models (LLTM), rating scale model (RSM), linear rating scale models (LRSM), partial credit models (PCM), and linear partial credit models (LPCM). Missing values are allowed in the data matrix. Additional features are the ML estimation of the person parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test, nonparametric Monte-Carlo Tests, itemfit and personfit statistics including infit and outfit measures, ICC and other plots, automated stepwise item elimination, simulation module for various binary data matrices.
Author: Patrick Mair [cre, aut], Thomas Rusch [aut], Reinhold Hatzinger [aut], Marco J. Maier [aut], Rudolf Debelak [ctb]
Maintainer: Patrick Mair <mair@fas.harvard.edu>

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Package cfa updated to version 0.10-1 with previous version 0.10-0 dated 2017-05-01

Title: Configural Frequency Analysis (CFA)
Description: Analysis of configuration frequencies for simple and repeated measures, multiple-samples CFA, hierarchical CFA, bootstrap CFA, functional CFA, Kieser-Victor CFA, and Lindner's test using a conventional and an accelerated algorithm.
Author: Patrick Mair [aut, cre], Stefan Funke [aut], Joachim Harloff [ctb], Alexander von Eye [ctb]
Maintainer: Patrick Mair <mair@fas.harvard.edu>

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Package misha (with last version 4.2.9) was removed from CRAN

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

2024-01-15 4.2.9
2023-12-05 4.2.8

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Package vcfppR (with last version 0.4.0) was removed from CRAN

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

2024-02-26 0.4.0
2024-01-14 0.3.8
2023-12-14 0.3.5

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Package inferCSN updated to version 1.0.1 with previous version 1.0.0 dated 2024-02-09

Title: Inferring Cell-Specific Gene Regulatory Network
Description: A method for inferring cell-specific gene regulatory network from single-cell sequencing data.
Author: Meng Xu [aut, cre]
Maintainer: Meng Xu <mengxu98@qq.com>

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Package framecleaner updated to version 0.2.1 with previous version 0.2.0 dated 2021-11-17

Title: Clean Data Frames
Description: Provides a friendly interface for modifying data frames with a sequence of piped commands built upon the 'tidyverse' Wickham et al., (2019) <doi:10.21105/joss.01686> . The majority of commands wrap 'dplyr' mutate statements in a convenient way to concisely solve common issues that arise when tidying small to medium data sets. Includes smart defaults and allows flexible selection of columns via 'tidyselect'.
Author: Harrison Tietze [aut, cre]
Maintainer: Harrison Tietze <Harrison4192@gmail.com>

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Thu, 14 Mar 2024

Package Rwhois updated to version 1.0.16 with previous version 1.0.14 dated 2023-05-24

Title: WHOIS Server Querying
Description: Queries data from WHOIS servers.
Author: Brad Cable
Maintainer: Brad Cable <brad@bcable.net>

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Package Rrdap updated to version 1.0.7 with previous version 1.0.6 dated 2022-07-14

Title: RDAP Server Querying
Description: Queries data from RDAP servers.
Author: Brad Cable
Maintainer: Brad Cable <brad@bcable.net>

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Package StructFDR updated to version 1.4 with previous version 1.3 dated 2018-05-29

Title: False Discovery Control Procedure Integrating the Prior Structure Information
Description: Perform more powerful false discovery control (FDR) for microbiome data, taking into account the prior phylogenetic relationship among bacteria species. As a general methodology, it is applicable to any type of (genomic) data with prior structure information.
Author: Jun Chen
Maintainer: Jun Chen <chen.jun2@mayo.edu>

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Package PriceIndices updated to version 0.1.9 with previous version 0.1.8 dated 2023-06-26

Title: Calculating Bilateral and Multilateral Price Indexes
Description: Preparing a scanner data set for price dynamics calculations (data selecting, data classification, data matching, data filtering). Computing bilateral and multilateral indexes. For details on these methods see: Diewert and Fox (2020) <doi:10.1080/07350015.2020.1816176>, Białek (2019) <doi:10.2478/jos-2019-0014> or Białek (2020) <doi:10.2478/jos-2020-0037>.
Author: Jacek Bialek [aut, cre]
Maintainer: Jacek Bialek <jacek.bialek@uni.lodz.pl>

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Package OpenSpecy updated to version 1.0.8 with previous version 1.0.7 dated 2024-03-11

Title: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra
Description: Raman and (FT)IR spectral analysis tool for plastic particles and other environmental samples (Cowger et al. 2021, <doi:10.1021/acs.analchem.1c00123>). With read_any(), Open Specy provides a single function for reading individual, batch, or map spectral data files like .asp, .csv, .jdx, .spc, .spa, .0, and .zip. process_spec() simplifies processing spectra, including smoothing, baseline correction, range restriction and flattening, intensity conversions, wavenumber alignment, and min-max normalization. Spectra can be identified in batch using an onboard reference library (Cowger et al. 2020, <doi:10.1177/0003702820929064>) using match_spec(). A Shiny app is available via run_app() or online at <https://openanalysis.org/openspecy/>.
Author: Win Cowger [cre, aut, dtc] , Zacharias Steinmetz [aut] , Nick Leong [aut] , Andrea Faltynkova [aut, dtc] , Hannah Sherrod [aut] , Andrew B Gray [ctb] , Hannah Hapich [ctb] , Jennifer Lynch [ctb, dtc] , Hannah De Frond [ctb, dtc] , Keenan Munno [ctb, [...truncated...]
Maintainer: Win Cowger <wincowger@gmail.com>

Diff between OpenSpecy versions 1.0.7 dated 2024-03-11 and 1.0.8 dated 2024-03-14

 DESCRIPTION                             |    8 +-
 MD5                                     |   48 +++++++-------
 NAMESPACE                               |    4 -
 NEWS.md                                 |    6 +
 R/manage_na.R                           |   32 +++++----
 R/manage_spec.R                         |    2 
 R/read_multi.R                          |   82 +++++++++++++-----------
 R/sig_noise.R                           |    2 
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 tests/testthat/test-adj_range.R         |    2 
 tests/testthat/test-interactive_plots.R |    2 
 tests/testthat/test-manage_na.R         |   11 ++-
 tests/testthat/test-manage_spec.R       |    2 
 tests/testthat/test-match_spec.R        |    4 -
 tests/testthat/test-read_envi.R         |    4 -
 tests/testthat/test-read_multi.R        |    2 
 tests/testthat/test-share_spec.R        |    3 
 tests/testthat/test-smooth_intens.R     |   12 +--
 tests/testthat/test-spec_res.R          |    2 
 tests/testthat/test-workflows.R         |   84 +++++++++++++-----------
 25 files changed, 254 insertions(+), 211 deletions(-)

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Package EnrichIntersect updated to version 0.7 with previous version 0.6 dated 2023-02-26

Title: Enrichment Analysis and Intersecting Sankey Diagram
Description: A flexible tool for enrichment analysis based on user-defined sets. It allows users to perform over-representation analysis of the custom sets among any specified ranked feature list, hence making enrichment analysis applicable to various types of data from different scientific fields. 'EnrichIntersect' also enables an interactive means to visualize identified associations based on, for example, the mix-lasso model (Zhao et al., 2022 <doi:10.1016/j.isci.2022.104767>) or similar methods.
Author: Zhi Zhao [aut, cre], Manuela Zucknick [aut], Tero Aittokallio [ctb]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>

Diff between EnrichIntersect versions 0.6 dated 2023-02-26 and 0.7 dated 2024-03-14

 DESCRIPTION                   |    8 ++--
 MD5                           |   21 ++++++-----
 NEWS.md                       |    5 ++
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 inst/doc/EnrichIntersect.Rmd  |    4 +-
 inst/doc/EnrichIntersect.html |   78 +++++++++++++++++++++---------------------
 man/figures                   |only
 vignettes/EnrichIntersect.Rmd |    4 +-
 12 files changed, 78 insertions(+), 61 deletions(-)

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Package ABM updated to version 0.4.1 with previous version 0.3 dated 2023-03-24

Title: Agent Based Model Simulation Framework
Description: A high-performance, flexible and extensible framework to develop continuous-time agent based models. Its high performance allows it to simulate millions of agents efficiently. Agents are defined by their states (arbitrary R lists). The events are handled in chronological order. This avoids the multi-event interaction problem in a time step of discrete-time simulations, and gives precise outcomes. The states are modified by provided or user-defined events. The framework provides a flexible and customizable implementation of state transitions (either spontaneous or caused by agent interactions), making the framework suitable to apply to epidemiology and ecology, e.g., to model life history stages, competition and cooperation, and disease and information spread. The agent interactions are flexible and extensible. The framework provides random mixing and network interactions, and supports multi-level mixing patterns. It can be easily extended to other interactions such as inter- and intra [...truncated...]
Author: Junling Ma [aut, cre]
Maintainer: Junling Ma <junlingm@uvic.ca>

Diff between ABM versions 0.3 dated 2023-03-24 and 0.4.1 dated 2024-03-14

 ABM-0.3/ABM/R/ABM.R                     |only
 ABM-0.3/ABM/man/ABM.Rd                  |only
 ABM-0.4.1/ABM/DESCRIPTION               |    8 +--
 ABM-0.4.1/ABM/MD5                       |   78 ++++++++++++++++----------------
 ABM-0.4.1/ABM/R/ABM-package.R           |only
 ABM-0.4.1/ABM/R/Agent.R                 |   26 ++--------
 ABM-0.4.1/ABM/R/Contact.R               |   14 ++++-
 ABM-0.4.1/ABM/R/Population.R            |   18 ++-----
 ABM-0.4.1/ABM/R/RcppExports.R           |   20 ++++----
 ABM-0.4.1/ABM/R/Simulation.R            |   10 ++--
 ABM-0.4.1/ABM/README.md                 |    2 
 ABM-0.4.1/ABM/inst/include/Agent.h      |   39 ++++++++++++++--
 ABM-0.4.1/ABM/inst/include/Contact.h    |   18 ++++---
 ABM-0.4.1/ABM/inst/include/Counter.h    |    4 -
 ABM-0.4.1/ABM/inst/include/Network.h    |   12 ++--
 ABM-0.4.1/ABM/inst/include/Population.h |   24 ++++-----
 ABM-0.4.1/ABM/inst/include/RNG.h        |    1 
 ABM-0.4.1/ABM/inst/include/Simulation.h |   20 ++++++++
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 ABM-0.4.1/ABM/src/Contact.cpp           |   17 ++----
 ABM-0.4.1/ABM/src/Counter.cpp           |    9 +--
 ABM-0.4.1/ABM/src/Network.cpp           |   42 ++++++++---------
 ABM-0.4.1/ABM/src/Population.cpp        |   70 ++++++++++++++--------------
 ABM-0.4.1/ABM/src/RNG.cpp               |    2 
 ABM-0.4.1/ABM/src/RcppExports.cpp       |   70 ++++++++++++----------------
 ABM-0.4.1/ABM/src/Simulation.cpp        |   20 ++++++--
 ABM-0.4.1/ABM/src/Transition.cpp        |    5 +-
 42 files changed, 355 insertions(+), 297 deletions(-)

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Package GCPBayes updated to version 4.2.0 with previous version 4.1.0 dated 2023-12-04

Title: Bayesian Meta-Analysis of Pleiotropic Effects Using Group Structure
Description: Run a Gibbs sampler for a multivariate Bayesian sparse group selection model with Dirac, continuous and hierarchical spike prior for detecting pleiotropy on the traits. This package is designed for summary statistics containing estimated regression coefficients and its estimated covariance matrix. The methodology is available from: Baghfalaki, T., Sugier, P. E., Truong, T., Pettitt, A. N., Mengersen, K., & Liquet, B. (2021) <doi:10.1002/sim.8855>.
Author: Yazdan Asgari [aut, cre], Taban Baghfalaki [aut], Benoit Liquet [aut], Pierre-Emmanuel Sugier [aut], Mohammed Sedki [aut], Therese Truong [aut]
Maintainer: Yazdan Asgari <yazdan.asgari@inserm.fr>

Diff between GCPBayes versions 4.1.0 dated 2023-12-04 and 4.2.0 dated 2024-03-14

 DESCRIPTION                       |   24 +++++++++++++++++++-----
 MD5                               |   20 ++++++++++----------
 NEWS.md                           |   19 +++++++++++++++++++
 R/CS.R                            |    2 +-
 R/DS.R                            |    2 +-
 R/GCPBayes.R                      |    4 ++--
 R/HS.R                            |   30 +++++++++++++++++++++++-------
 R/Simulated_individual_survival.R |   33 +++++++++++++++++----------------
 R/summaryCS.R                     |    4 ++--
 R/summaryDS.R                     |    2 +-
 R/summaryHS.R                     |    4 ++--
 11 files changed, 97 insertions(+), 47 deletions(-)

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Package DTRreg updated to version 2.1 with previous version 2.0 dated 2023-11-19

Title: DTR Estimation and Inference via G-Estimation, Dynamic WOLS, Q-Learning, and Dynamic Weighted Survival Modeling (DWSurv)
Description: Dynamic treatment regime estimation and inference via G-estimation, dynamic weighted ordinary least squares (dWOLS) and Q-learning. Inference via bootstrap and recursive sandwich estimation. Estimation and inference for survival outcomes via Dynamic Weighted Survival Modeling (DWSurv). Extension to continuous treatment variables. Wallace et al. (2017) <DOI:10.18637/jss.v080.i02>; Simoneau et al. (2020) <DOI:10.1080/00949655.2020.1793341>.
Author: Michael Wallace, Erica E M Moodie, David A Stephens, Gabrielle Simoneau, Shannon T. Holloway and Juliana Schulz
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>

Diff between DTRreg versions 2.0 dated 2023-11-19 and 2.1 dated 2024-03-14

 DESCRIPTION           |   10 ++---
 MD5                   |   37 ++++++++++-----------
 NEWS                  |   10 +++++
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 R/chooseM.R           |    2 -
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 R/s3-methods.R        |    2 -
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 R/treatmentClasses.R  |   36 +++++++++++++-------
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 R/varest.R            |    5 +-
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 20 files changed, 194 insertions(+), 118 deletions(-)

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New package updateme with initial version 0.1.0
Package: updateme
Title: Informative Messages About Outdated Packages
Version: 0.1.0
Description: When a package is loaded, the source repository is checked for new versions and a message is shown in the console indicating whether the package is out of date.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/wurli/updateme, https://wurli.github.io/updateme/
BugReports: https://github.com/wurli/updateme/issues
Imports: cachem, cli (>= 3.6.0), curl, memoise, rlang, utils
Suggests: BiocManager, gitcreds, knitr, rmarkdown, testthat (>= 3.0.0), withr
NeedsCompilation: no
Packaged: 2024-03-13 11:51:58 UTC; JSCOTT4
Author: Jacob Scott [aut, cre]
Maintainer: Jacob Scott <jscott2718@gmail.com>
Repository: CRAN
Date/Publication: 2024-03-14 20:10:02 UTC

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New package theftdlc with initial version 0.1.0
Package: theftdlc
Title: Analyse and Interpret Time Series Features
Version: 0.1.0
Date: 2024-03-14
Maintainer: Trent Henderson <then6675@uni.sydney.edu.au>
Description: Provides a suite of functions for analysing, interpreting, and visualising time-series features calculated from different feature sets from the 'theft' package. Implements statistical learning methodologies described in Henderson, T., Bryant, A., and Fulcher, B. (2023) <arXiv:2303.17809>.
BugReports: https://github.com/hendersontrent/theftdlc/issues
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.5.0), theft (>= 0.6.1)
Imports: rlang, stats, tibble, dplyr, ggplot2, tidyr, purrr, reshape2, scales, broom, Rtsne, e1071, janitor, umap, MASS, mclust, normaliseR, correctR
Suggests: lifecycle, cachem, bslib, knitr, markdown, rmarkdown, pkgdown, testthat
VignetteBuilder: knitr
URL: https://hendersontrent.github.io/theftdlc/
NeedsCompilation: no
Packaged: 2024-03-14 11:38:13 UTC; trenthenderson
Author: Trent Henderson [cre, aut]
Repository: CRAN
Date/Publication: 2024-03-14 20:40:02 UTC

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Package rqPen updated to version 3.2.2 with previous version 3.2.1 dated 2023-08-24

Title: Penalized Quantile Regression
Description: Performs penalized quantile regression with LASSO, elastic net, SCAD and MCP penalty functions including group penalties. Provides a function that automatically generates lambdas and evaluates different models with cross validation or BIC, including a large p version of BIC. Below URL provides a link to a work in progress vignette.
Author: Ben Sherwood [aut, cre], Adam Maidman [ctb], Shaobo Li [ctb]
Maintainer: Ben Sherwood <ben.sherwood@ku.edu>

Diff between rqPen versions 3.2.1 dated 2023-08-24 and 3.2.2 dated 2024-03-14

 DESCRIPTION                     |    8 
 LICENSE                         |    4 
 MD5                             |   98 -
 NAMESPACE                       |  102 -
 NEWS                            |  310 +--
 R/QICD_functions.R              | 1366 ++++++++---------
 R/mainFunctions.R               |   43 
 R/rqPen.R                       |   52 
 R/workHorse.R                   | 2934 ++++++++++++++++++------------------
 README.md                       |  116 -
 build/partial.rdb               |binary
 inst/REFERENCES.bib             | 3202 ++++++++++++++++++++--------------------
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 man/rqPen.Rd                    |   34 
 50 files changed, 6047 insertions(+), 6051 deletions(-)

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New package LipidomicsR with initial version 0.1.0
Package: LipidomicsR
Title: Elegant Tools for Processing and Visualization of Lipidomics Data
Version: 0.1.0
Maintainer: Hengyu Zhu <hengyu.21@intl.zju.edu.cn>
Description: An elegant tool for processing and visualizing lipidomics data generated by mass spectrometry. 'LipidomicsR' simplifies channel and replicate handling while providing thorough lipid species annotation. Its visualization capabilities encompass principal components analysis plots, heatmaps, volcano plots, and radar plots, enabling concise data summarization and quality assessment. Additionally, it can generate bar plots and line plots to visualize the abundance of each lipid species.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: broom, car, ggiraph, rcompanion, tidyr, cowplot, dplyr, fmsb, ggplot2, ggplotify, ggrepel, pheatmap, RColorBrewer, reshape2, scales, stringr, tidyselect
Depends: tidyverse
NeedsCompilation: no
Packaged: 2024-03-14 14:53:00 UTC; zhy11
Author: Mingshi Li [aut], Hengyu Zhu [aut, cre]
Repository: CRAN
Date/Publication: 2024-03-14 20:40:05 UTC

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New package ggbrick with initial version 0.3.0
Package: ggbrick
Title: Waffle Style Chart with a Brick Layout in 'ggplot2'
Version: 0.3.0
Maintainer: Daniel Oehm <danieloehm@gmail.com>
Description: A new take on the bar chart. Similar to a waffle style chart but instead of squares the layout resembles a brick wall.
Depends: R (>= 3.5.0)
Imports: ggplot2, dplyr, purrr, glue
License: MIT + file LICENSE
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-03-14 05:41:08 UTC; danie
Author: Daniel Oehm [aut, cre]
Repository: CRAN
Date/Publication: 2024-03-14 20:20:02 UTC

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New package dnn with initial version 0.0.6
Package: dnn
Title: Deep Neural Network Tools for Probability and Statistic Models
Version: 0.0.6
Date: 2024-03-12
Author: Bingshu E. Chen [aut, cre], Patrick Norman [aut, ctb], Wenyu Jiang [ctb], Wanlu Li [ctb]
Maintainer: Bingshu E. Chen <bingshu.chen@queensu.ca>
Depends: R (>= 3.5.0), ggplot2, survival, Rcpp
Imports: methods
LinkingTo: Rcpp, RcppArmadillo
Description: Contains tools to build deep neural network with flexible users define loss function and probability models. Several applications included in this package are, 1) The (deepAFT) model, a deep neural network model for accelerated failure time (AFT) model for survival data. 2) The (deepGLM) model, a deep neural network model for generalized linear model (glm) for continuous, categorical and Poisson data.
License: GPL (>= 2)
LazyLoad: yes
NeedsCompilation: yes
Packaged: 2024-03-14 15:42:28 UTC; b3chen
Repository: CRAN
Date/Publication: 2024-03-14 20:50:05 UTC

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New package cucumber with initial version 1.0.0
Package: cucumber
Title: Behavior-Driven Development for R
Version: 1.0.0
Description: Write executable specifications in a natural language that describes how your code should behave. Write specifications in feature files using 'Gherkin' language and execute them using functions implemented in R. Use them as an extension to your 'testthat' tests to provide a high level description of how your code works.
License: MIT + file LICENSE
URL: https://github.com/jakubsob/cucumber, https://jakubsob.github.io/cucumber/
BugReports: https://github.com/jakubsob/cucumber
Encoding: UTF-8
Suggests: mockery, box, shinytest2, chromote, covr, knitr, rmarkdown
Imports: checkmate, dplyr, fs, glue, purrr, rlang, stringr, testthat (>= 3.0.0), tibble, withr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-03-14 08:50:51 UTC; jakub
Author: Jakub Sobolewski [aut, cre]
Maintainer: Jakub Sobolewski <jakupsob@gmail.com>
Repository: CRAN
Date/Publication: 2024-03-14 20:30:02 UTC

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New package cpmr with initial version 0.0.8
Package: cpmr
Title: Connectome Predictive Modelling in R
Version: 0.0.8
Description: Connectome Predictive Modelling (CPM) (Shen et al. (2017) <doi:10.1038/nprot.2016.178>) is a method to predict individual differences in behaviour from brain functional connectivity. 'cpmr' provides a simple yet efficient implementation of this method.
License: MIT + file LICENSE
URL: https://github.com/psychelzh/cpmr, https://psychelzh.github.io/cpmr/
BugReports: https://github.com/psychelzh/cpmr/issues
Imports: Rfast, stats
Suggests: testthat (>= 3.0.0), withr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-03-14 00:58:04 UTC; lenovo
Author: Liang Zhang [aut, cre]
Maintainer: Liang Zhang <psychelzh@outlook.com>
Repository: CRAN
Date/Publication: 2024-03-14 20:20:05 UTC

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New package calmr with initial version 0.6.1
Package: calmr
Title: Canonical Associative Learning Models and their Representations
Version: 0.6.1
Description: Implementations of canonical associative learning models, with tools to run experiment simulations, estimate model parameters, and compare model representations. Experiments and results are represented using S4 classes and methods.
License: GPL (>= 3)
URL: https://github.com/victor-navarro/calmr, https://victornavarro.org/calmr/
BugReports: https://github.com/victor-navarro/calmr/issues
Depends: R (>= 3.5)
Imports: data.table, future, future.apply, GA, ggnetwork, ggplot2, grid, methods, network, patchwork, progressr, rlang, stats
Suggests: knitr, rmarkdown, spelling, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2024-03-12 23:00:59 UTC; Victor
Author: Victor Navarro [aut, cre, cph]
Maintainer: Victor Navarro <navarrov@cardiff.ac.uk>
Repository: CRAN
Date/Publication: 2024-03-14 20:10:05 UTC

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New package bgev with initial version 0.1
Package: bgev
Title: Bimodal GEV Distribution with Location Parameter
Version: 0.1
Date: 2024-03-07
Depends: EnvStats, DEoptim, stats, MASS
Description: Density, distribution function, quantile function random generation and estimation of bimodal GEV distribution given in Otiniano et al. (2023) <doi:10.1007/s10651-023-00566-7>. This new generalization of the well-known GEV (Generalized Extreme Value) distribution is useful for modeling heterogeneous bimodal data from different areas.
License: GPL-3
NeedsCompilation: no
Packaged: 2024-03-14 15:36:27 UTC; thiagosousa
Author: Cira Otiniano Author [aut], Yasmin Lirio Author [aut], Thiago Sousa Developer [cre]
Maintainer: Thiago Sousa Developer <thiagoestatistico@gmail.com>
Repository: CRAN
Date/Publication: 2024-03-14 20:50:08 UTC

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New package DiSCos with initial version 0.0.1
Package: DiSCos
Title: Distributional Synthetic Controls Estimation
Version: 0.0.1
Description: The method of synthetic controls is a widely-adopted tool for evaluating causal effects of policy changes in settings with observational data. In many settings where it is applicable, researchers want to identify causal effects of policy changes on a treated unit at an aggregate level while having access to data at a finer granularity. This package implements a simple extension of the synthetic controls estimator, developed in Gunsilius (2023) <doi:10.3982/ECTA18260>, that takes advantage of this additional structure and provides nonparametric estimates of the heterogeneity within the aggregate unit. The idea is to replicate the quantile function associated with the treated unit by a weighted average of quantile functions of the control units. The package contains tools for aggregating and plotting the resulting distributional estimates, as well as for carrying out inference on them.
License: MIT + file LICENSE
BugReports: https://github.com/
URL: <link href="https://github.com/" rel="canonical">, <link href="http://www.davidvandijcke.com/DiSCos/" rel="canonical">
LazyData: TRUE
Imports: CVXR, pracma, Rdpack, parallel, evmix, utils, extremeStat, MASS
Depends: data.table, R (>= 2.10), ggplot2
Suggests: haven, latex2exp, knitr, rmarkdown, maps, testthat (>= 3.0.0), quadprog
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-03-12 20:10:29 UTC; davidvandijcke
Author: David Van Dijcke [aut, cre] , Florian Gunsilius [aut] , Siyun He [aut]
Maintainer: David Van Dijcke <dvdijcke@umich.edu>
Repository: CRAN
Date/Publication: 2024-03-14 20:00:02 UTC

More information about DiSCos at CRAN
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Package CDCPLACES updated to version 1.1.5 with previous version 1.1.4 dated 2024-01-24

Title: Access the 'CDC PLACES' API
Description: Allows users to seamlessly query several 'CDC PLACES' APIs (<https://data.cdc.gov/browse?q=PLACES%20&sortBy=relevance>) by geography, state, measure, and release year. This package also contains a function to explore the available measures for each release year.
Author: Brenden Smith [aut, cre]
Maintainer: Brenden Smith <smit2535@msu.edu>

Diff between CDCPLACES versions 1.1.4 dated 2024-01-24 and 1.1.5 dated 2024-03-14

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Package vivainsights updated to version 0.5.2 with previous version 0.5.1 dated 2024-01-10

Title: Analyze and Visualize Data from 'Microsoft Viva Insights'
Description: Provides a versatile range of functions, including exploratory data analysis, time-series analysis, organizational network analysis, and data validation, whilst at the same time implements a set of best practices in analyzing and visualizing data specific to 'Microsoft Viva Insights'.
Author: Martin Chan [aut, cre], Carlos Morales [aut]
Maintainer: Martin Chan <martin.chan@microsoft.com>

Diff between vivainsights versions 0.5.1 dated 2024-01-10 and 0.5.2 dated 2024-03-14

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Package bigrquery updated to version 1.5.1 with previous version 1.5.0 dated 2024-01-22

Title: An Interface to Google's 'BigQuery' 'API'
Description: Easily talk to Google's 'BigQuery' database from R.
Author: Hadley Wickham [aut, cre] , Jennifer Bryan [aut] , Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>

Diff between bigrquery versions 1.5.0 dated 2024-01-22 and 1.5.1 dated 2024-03-14

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Package R6causal updated to version 0.8.3 with previous version 0.8.2 dated 2023-12-18

Title: R6 Class for Structural Causal Models
Description: The implemented R6 class 'SCM' aims to simplify working with structural causal models. The missing data mechanism can be defined as a part of the structural model. The class contains methods for 1) defining a structural causal model via functions, text or conditional probability tables, 2) printing basic information on the model, 3) plotting the graph for the model using packages 'igraph' or 'qgraph', 4) simulating data from the model, 5) applying an intervention, 6) checking the identifiability of a query using the R packages 'causaleffect' and 'dosearch', 7) defining the missing data mechanism, 8) simulating incomplete data from the model according to the specified missing data mechanism and 9) checking the identifiability in a missing data problem using the R package 'dosearch'. In addition, there are functions for running experiments and doing counterfactual inference using simulation.
Author: Juha Karvanen [aut, cre]
Maintainer: Juha Karvanen <juha.karvanen@iki.fi>

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Package gamlss.data updated to version 6.0-6 with previous version 6.0-2 dated 2021-11-07

Title: Data for Generalised Additive Models for Location Scale and Shape
Description: Data used as examples in the current two books on Generalised Additive Models for Location Scale and Shape introduced by Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>.
Author: Mikis Stasinopoulos <d.stasinopoulos@gre.ac.uk>, Bob Rigby, Fernanda De Bastiani
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@gre.ac.uk>

Diff between gamlss.data versions 6.0-2 dated 2021-11-07 and 6.0-6 dated 2024-03-14

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Package tramicp updated to version 0.0-2 with previous version 0.0-1 dated 2023-09-29

Title: Model-Based Causal Feature Selection for General Response Types
Description: Extends invariant causal prediction (Peters et al., 2016, <doi:10.1111/rssb.12167>) to generalized linear and transformation models (Hothorn et al., 2018, <doi:10.1111/sjos.12291>). The methodology is described in Kook et al. (2023, <doi:10.48550/arXiv.2309.12833>).
Author: Lucas Kook [aut, cre] , Sorawit Saengkyongam [ctb], Anton Rask Lundborg [ctb], Torsten Hothorn [ctb], Jonas Peters [ctb]
Maintainer: Lucas Kook <lucasheinrich.kook@gmail.com>

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Package contingencytables updated to version 3.0.0 with previous version 2.2.1 dated 2024-01-11

Title: Statistical Analysis of Contingency Tables
Description: Provides functions to perform statistical inference of data organized in contingency tables. This package is a companion to the "Statistical Analysis of Contingency Tables" book by Fagerland et al. <ISBN 9781466588172>.
Author: Morten Wang Fagerland [aut], Stian Lydersen [ctb], Petter Laake [ctb], Waldir Leoncio [cre], Ole Christian Lingjaerde [trl], Brad J. Biggerstaff [ctb]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>

Diff between contingencytables versions 2.2.1 dated 2024-01-11 and 3.0.0 dated 2024-03-14

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Package comstab updated to version 0.0.2 with previous version 0.0.1 dated 2024-02-20

Title: Partitioning the Drivers of Stability of Ecological Communities
Description: Contains the basic functions to apply the unified framework for partitioning the drivers of stability of ecological communities. Segrestin et al. (2024) <doi:10.1111/geb.13828>.
Author: Jules Segrestin [aut, cre, cph]
Maintainer: Jules Segrestin <jsegrestin@gmail.com>

Diff between comstab versions 0.0.1 dated 2024-02-20 and 0.0.2 dated 2024-03-14

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Package cliot updated to version 0.2.0 with previous version 0.1.0 dated 2024-01-22

Title: Clinical Indices and Outcomes Tools
Description: Collection of indices and tools relating to cardiovascular, nephrology, and hepatic research that aid epidemiological chort or retrospective chart review with big data. All indices and tools take commonly used lab values and patient demographics and measurements to compute various risk and predictive values for survival. References to original literature and validation contained in each function documentation.
Author: Neel Agarwal <nxa357@case.edu>
Maintainer: Neel Agarwal <neel.agarwal.216@gmail.com>

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Package Ropj updated to version 0.3-5 with previous version 0.3-4 dated 2023-03-14

Title: Import Origin(R) Project Files
Description: Read the data from Origin(R) project files ('*.opj') <https://www.originlab.com/doc/User-Guide/Origin-File-Types>. No write support is planned.
Author: Miquel Garriga [aut, cph], Stefan Gerlach [aut, cph], Ion Vasilief [aut, cph], Alex Kargovsky [aut, cph], Knut Franke [ctb, cph], Alexander Semke [ctb, cph], Tilman Benkert [ctb, cph], Kasper Peeters [ctb, cph], Russell Standish [ctb, cph], Ivan Kryl [...truncated...]
Maintainer: Ivan Krylov <krylov.r00t@gmail.com>

Diff between Ropj versions 0.3-4 dated 2023-03-14 and 0.3-5 dated 2024-03-14

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Package evsim updated to version 1.4.0 with previous version 1.3.0 dated 2024-02-04

Title: Electric Vehicle Charging Sessions Simulation
Description: Simulation of Electric Vehicles charging sessions using Gaussian models, together with time-series power demand calculations. The simulation methodology is published in Cañigueral et al. (2023, ISBN:0957-4174) <doi:10.1016/j.eswa.2023.120318>.
Author: Marc Canigueral [aut, cre]
Maintainer: Marc Canigueral <marc.canigueral@udg.edu>

Diff between evsim versions 1.3.0 dated 2024-02-04 and 1.4.0 dated 2024-03-14

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Package evprof updated to version 1.1.2 with previous version 1.1.1 dated 2024-02-05

Title: Electric Vehicle Charging Sessions Profiling and Modelling
Description: Tools for modelling electric vehicle charging sessions into generic groups with similar connection patterns called "user profiles", using Gaussian Mixture Models clustering. The clustering and profiling methodology is described in Cañigueral and Meléndez (2021, ISBN:0142-0615) <doi:10.1016/j.ijepes.2021.107195>.
Author: Marc Canigueral [aut, cre, cph]
Maintainer: Marc Canigueral <marc.canigueral@udg.edu>

Diff between evprof versions 1.1.1 dated 2024-02-05 and 1.1.2 dated 2024-03-14

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Package cmstatr updated to version 0.9.3 with previous version 0.9.2 dated 2023-09-09

Title: Statistical Methods for Composite Material Data
Description: An implementation of the statistical methods commonly used for advanced composite materials in aerospace applications. This package focuses on calculating basis values (lower tolerance bounds) for material strength properties, as well as performing the associated diagnostic tests. This package provides functions for calculating basis values assuming several different distributions, as well as providing functions for non-parametric methods of computing basis values. Functions are also provided for testing the hypothesis that there is no difference between strength and modulus data from an alternate sample and that from a "qualification" or "baseline" sample. For a discussion of these statistical methods and their use, see the Composite Materials Handbook, Volume 1 (2012, ISBN: 978-0-7680-7811-4). Additional details about this package are available in the paper by Kloppenborg (2020, <doi:10.21105/joss.02265>).
Author: Stefan Kloppenborg [aut, cre] , Billy Cheng [ctb], Ally Fraser [ctb], Jeffrey Borlik [ctb], Comtek Advanced Structures, Ltd. [fnd]
Maintainer: Stefan Kloppenborg <stefan@kloppenborg.ca>

Diff between cmstatr versions 0.9.2 dated 2023-09-09 and 0.9.3 dated 2024-03-14

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New package gam.hp with initial version 0.0-1
Package: gam.hp
Title: Hierarchical Partitioning of Adjusted R2 and Explained Deviance for Generalized Additive Models
Version: 0.0-1
Date: 2024-3-12
Depends: R (>= 3.4.0),mgcv,ggplot2
Maintainer: Jiangshan Lai <lai@njfu.edu.cn>
Description: Conducts hierarchical partitioning to calculate individual contributions of each predictor towards adjusted R2 and explained deviance for generalized additive models based on output of gam()in 'mgcv' package, applying the algorithm in this paper: Lai(2022) <doi:10.1093/jpe/rtac096>.
License: GPL
Encoding: UTF-8
URL: https://github.com/laijiangshan/gam.hp
NeedsCompilation: no
Packaged: 2024-03-13 13:46:50 UTC; lai
Author: Jiangshan Lai [aut, cre] , Jing Tang [aut]
Repository: CRAN
Date/Publication: 2024-03-14 13:00:03 UTC

More information about gam.hp at CRAN
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New package CompositionalML with initial version 1.0
Package: CompositionalML
Title: Machine Learning with Compositional Data
Version: 1.0
Date: 2024-03-13
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Depends: R (>= 4.0)
Imports: Boruta, Compositional, doParallel, e1071, foreach, graphics, ranger, Rfast, Rfast2, stats
Description: Machine learning algorithms for predictor variables that are compositional data and the response variable is either continuous or categorical. Specifically, the Boruta variable selection algorithm, random forest, support vector machines and projection pursuit regression are included. Relevant papers include: Tsagris M.T., Preston S. and Wood A.T.A. (2011). "A data-based power transformation for compositional data". Fourth International International Workshop on Compositional Data Analysis. <doi:10.48550/arXiv.1106.1451> and Alenazi, A. (2023). "A review of compositional data analysis and recent advances". Communications in Statistics--Theory and Methods, 52(16): 5535--5567. <doi:10.1080/03610926.2021.2014890>.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2024-03-13 12:23:56 UTC; mtsag
Repository: CRAN
Date/Publication: 2024-03-14 12:40:02 UTC

More information about CompositionalML at CRAN
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Package bfp updated to version 0.0-48 with previous version 0.0-47 dated 2023-12-06

Title: Bayesian Fractional Polynomials
Description: Implements the Bayesian paradigm for fractional polynomial models under the assumption of normally distributed error terms, see Sabanes Bove, D. and Held, L. (2011) <doi:10.1007/s11222-010-9170-7>.
Author: Daniel Sabanes Bove [aut, cre], Isaac Gravestock [aut], Robert Davies [cph], Stephen Moshier [cph], Gareth Ambler [cph], Axel Benner [cph]
Maintainer: Daniel Sabanes Bove <daniel.sabanesbove@gmx.net>

Diff between bfp versions 0.0-47 dated 2023-12-06 and 0.0-48 dated 2024-03-14

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Package smotefamily updated to version 1.4.0 with previous version 1.3.1 dated 2019-05-30

Title: A Collection of Oversampling Techniques for Class Imbalance Problem Based on SMOTE
Description: A collection of various oversampling techniques developed from SMOTE is provided. SMOTE is a oversampling technique which synthesizes a new minority instance between a pair of one minority instance and one of its K nearest neighbor. Other techniques adopt this concept with other criteria in order to generate balanced dataset for class imbalance problem.
Author: Wacharasak Siriseriwan [aut, cre]
Maintainer: Wacharasak Siriseriwan <wacharasak.s@gmail.com>

Diff between smotefamily versions 1.3.1 dated 2019-05-30 and 1.4.0 dated 2024-03-14

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Package rnames updated to version 1.0.1 with previous version 1.0.0 dated 2024-03-11

Title: Recursive Display of Items in Nested Lists
Description: Recursive display of names and paths of all the items nested within sublists of a list object.
Author: Diego Ciccia [aut, cre]
Maintainer: Diego Ciccia <cicciadiego99@gmail.com>

Diff between rnames versions 1.0.0 dated 2024-03-11 and 1.0.1 dated 2024-03-14

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Package FuzzySimRes updated to version 0.4.0 with previous version 0.3.0 dated 2023-08-10

Title: Simulation and Resampling Methods for Epistemic Fuzzy Data
Description: Random simulations of fuzzy numbers are still a challenging problem. The aim of this package is to provide the respective procedures to simulate fuzzy random variables, especially in the case of the piecewise linear fuzzy numbers (PLFNs, see Coroianua et al. (2013) <doi:10.1016/j.fss.2013.02.005> for the further details). Additionally, the special resampling algorithms known as the epistemic bootstrap are provided (see Grzegorzewski and Romaniuk (2022) <doi:10.34768/amcs-2022-0021>, Grzegorzewski and Romaniuk (2022) <doi:10.1007/978-3-031-08974-9_39>) together with the functions to apply statistical tests and estimate various characteristics based on the epistemic bootstrap. The package also includes a real-life data set of epistemic fuzzy triangular numbers. The fuzzy numbers used in this package are consistent with the 'FuzzyNumbers' package.
Author: Maciej Romaniuk [cre, aut] , Przemyslaw Grzegorzewski [aut] , Abbas Parchami [aut] , Luis Carvalho [ctb, cph]
Maintainer: Maciej Romaniuk <mroman@ibspan.waw.pl>

Diff between FuzzySimRes versions 0.3.0 dated 2023-08-10 and 0.4.0 dated 2024-03-14

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Wed, 13 Mar 2024

Package UCSCXenaShiny updated to version 2.0.0 with previous version 1.1.10 dated 2023-02-28

Title: Interactive Analysis of UCSC Xena Data
Description: Provides functions and a Shiny application for downloading, analyzing and visualizing datasets from UCSC Xena (<http://xena.ucsc.edu/>), which is a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Author: Shixiang Wang [aut, cre] , Shensuo Li [aut], Yi Xiong [aut] , Longfei Zhao [aut] , Kai Gu [aut] , Yin Li [aut], Fei Zhao [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>

Diff between UCSCXenaShiny versions 1.1.10 dated 2023-02-28 and 2.0.0 dated 2024-03-13

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Package ruminate updated to version 0.2.2 with previous version 0.2.1 dated 2023-12-11

Title: A Pharmacometrics Data Transformation and Analysis Tool
Description: Exploration of pharmacometrics data involves both general tools (transformation and plotting) and specific techniques (non-compartmental analysis). This kind of exploration is generally accomplished by utilizing different packages. The purpose of 'ruminate' is to create a 'shiny' interface to make these tools more broadly available while creating reproducible results.
Author: John Harrold [aut, cre]
Maintainer: John Harrold <john.m.harrold@gmail.com>

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Package ggscidca updated to version 0.1.9 with previous version 0.1.0 dated 2024-03-04

Title: Plotting Decision Curve Analysis with Coloured Bars
Description: Decision curve analysis is a method for evaluating and comparing prediction models that incorporates clinical consequences, requires only the data set on which the models are tested, and can be applied to models that have either continuous or dichotomous results. The 'ggscidca' package adds coloured bars of discriminant relevance to the traditional decision curve. Improved practicality and aesthetics. This method was described by Balachandran VP (2015) <doi:10.1016/S1470-2045(14)71116-7>.
Author: Qiang Liu [aut, cre]
Maintainer: Qiang Liu <dege857@163.com>

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Package DDPNA updated to version 0.3.3 with previous version 0.3.1 dated 2022-05-17

Title: Disease-Drived Differential Proteins Co-Expression Network Analysis
Description: Functions designed to connect disease-related differential proteins and co-expression network. It provides the basic statics analysis included t test, ANOVA analysis. The network construction is not offered by the package, you can used 'WGCNA' package which you can learn in Peter et al. (2008) <doi:10.1186/1471-2105-9-559>. It also provides module analysis included PCA analysis, two enrichment analysis, Planner maximally filtered graph extraction and hub analysis.
Author: Kefu Liu [aut, cre]
Maintainer: Kefu Liu <liukefu19@163.com>

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Package mlflow updated to version 2.11.1 with previous version 2.10.2 dated 2024-02-16

Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for the complete machine learning life cycle, see <https://mlflow.org/>. This package supports installing 'MLflow', tracking experiments, creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre], Javier Luraschi [aut], Kevin Kuo [aut] , RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>

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Package florabr updated to version 1.1.0 with previous version 1.0.1 dated 2023-12-10

Title: Explore Brazilian Flora 2020 Database
Description: A collection of functions designed to retrieve, filter and spatialize data from the Brazilian Flora 2020 dataset. For more information about the dataset, please visit <https://floradobrasil.jbrj.gov.br/consulta/>.
Author: Weverton Trindade [aut, cre]
Maintainer: Weverton Trindade <wevertonf1993@gmail.com>

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Package verbalisr updated to version 0.5.2 with previous version 0.5.1 dated 2023-08-19

Title: Describe Pedigree Relationships in Words
Description: Describe in words the genealogical relationship between two members of a given pedigree, using the algorithm in Vigeland (2022) <doi:10.1186/s12859-022-04759-y>. 'verbalisr' is part of the 'pedsuite' collection of packages for pedigree analysis. For a demonstration of 'verbalisr', see the online app 'QuickPed' at <https://magnusdv.shinyapps.io/quickped>.
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>

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New package scAnnotate with initial version 0.3
Package: scAnnotate
Title: An Automated Cell Type Annotation Tool for Single-Cell RNA-Sequencing Data
Version: 0.3
Description: An entirely data-driven cell type annotation tools, which requires training data to learn the classifier, but not biological knowledge to make subjective decisions. It consists of three steps: preprocessing training and test data, model fitting on training data, and cell classification on test data. See Xiangling Ji,Danielle Tsao, Kailun Bai, Min Tsao, Li Xing, Xuekui Zhang.(2022)<doi:10.1101/2022.02.19.481159> for more details.
Depends: R(>= 4.0.0)
License: GPL-3
URL: https://doi.org/10.1101/2022.02.19.481159
Encoding: UTF-8
LazyData: true
Suggests: knitr, testthat (>= 3.0.0), rmarkdown
VignetteBuilder: knitr
Imports: glmnet, stats, Seurat (>= 5.0.1), harmony, SeuratObject
NeedsCompilation: no
Packaged: 2024-03-13 22:29:52 UTC; xzhang
Author: Xiangling Ji [aut], Danielle Tsao [aut], Kailun Bai [ctb], Min Tsao [aut], Li Xing [aut], Xuekui Zhang [aut, cre]
Maintainer: Xuekui Zhang <xuekui@uvic.ca>
Repository: CRAN
Date/Publication: 2024-03-14 00:00:02 UTC

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Package maximin updated to version 1.0-5 with previous version 1.0-4 dated 2021-01-10

Title: Space-Filling Design under Maximin Distance
Description: Constructs a space-filling design under the criterion of maximum-minimum distance. Both discrete and continuous searches are provided.
Author: Furong Sun <furong.sun@gmail.com>, Robert B. Gramacy <rbg@vt.edu>
Maintainer: Furong Sun <furong.sun@gmail.com>

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Package GofCens updated to version 0.97 with previous version 0.92 dated 2022-01-05

Title: Goodness-of-Fit Methods for Complete and Right-Censored Data
Description: Graphical tools and goodness-of-fit tests for complete and right-censored data: 1. Kolmogorov-Smirnov, Cramér-von Mises, and Anderson-Darling tests, which use the empirical distribution function for complete data and are extended for right-censored data. 2. Generalized chi-squared-type test, which is based on the squared differences between observed and expected counts using random cells with right-censored data. 3. A series of graphical tools such as probability or cumulative hazard plots to guide the decision about the most suitable parametric model for the data.
Author: Klaus Langohr [aut, cre], Mireia Besalu [aut], Matilde Francisco [aut], Guadalupe Gomez [aut]
Maintainer: Klaus Langohr <klaus.langohr@upc.edu>

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Package correctR updated to version 0.2.1 with previous version 0.1.3 dated 2023-08-20

Title: Corrected Test Statistics for Comparing Machine Learning Models on Correlated Samples
Description: Calculate a set of corrected test statistics for cases when samples are not independent, such as when classification accuracy values are obtained over resamples or through k-fold cross-validation, as proposed by Nadeau and Bengio (2003) <doi:10.1023/A:1024068626366> and presented in Bouckaert and Frank (2004) <doi:10.1007/978-3-540-24775-3_3>.
Author: Trent Henderson [cre, aut]
Maintainer: Trent Henderson <then6675@uni.sydney.edu.au>

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Package saeczi updated to version 0.1.1 with previous version 0.1.0 dated 2024-02-13

Title: Small Area Estimation for Continuous Zero Inflated Data
Description: Provides functionality to fit a zero-inflated estimator for small area estimation. This estimator is a combines a linear mixed effects regression model and a logistic mixed effects regression model via a two-stage modeling approach. The estimator's mean squared error is estimated via a parametric bootstrap method. Chandra and others (2012, <doi:10.1080/03610918.2011.598991>) introduce and describe this estimator and mean squared error estimator. White and others (2024+, <arXiv:2402.03263>) describe the applicability of this estimator to estimation of forest attributes and further assess the estimator's properties.
Author: Josh Yamamoto [aut, cre], Dinan Elsyad [aut], Grayson White [aut], Julian Schmitt [aut], Niels Korsgaard [aut], Kelly McConville [aut], Kate Hu [aut]
Maintainer: Josh Yamamoto <joshuayamamoto5@gmail.com>

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Package nestedcv updated to version 0.7.8 with previous version 0.7.4 dated 2024-01-30

Title: Nested Cross-Validation with 'glmnet' and 'caret'
Description: Implements nested k*l-fold cross-validation for lasso and elastic-net regularised linear models via the 'glmnet' package and other machine learning models via the 'caret' package. Cross-validation of 'glmnet' alpha mixing parameter and embedded fast filter functions for feature selection are provided. Described as double cross-validation by Stone (1977) <doi:10.1111/j.2517-6161.1977.tb01603.x>. Also implemented is a method using outer CV to measure unbiased model performance metrics when fitting Bayesian linear and logistic regression shrinkage models using the horseshoe prior over parameters to encourage a sparse model as described by Piironen & Vehtari (2017) <doi:10.1214/17-EJS1337SI>.
Author: Myles Lewis [aut, cre] , Athina Spiliopoulou [aut] , Cankut Cubuk [ctb] , Katriona Goldmann [ctb]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>

Diff between nestedcv versions 0.7.4 dated 2024-01-30 and 0.7.8 dated 2024-03-13

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Package ragg updated to version 1.3.0 with previous version 1.2.7 dated 2023-12-11

Title: Graphic Devices Based on AGG
Description: Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D drawing library. The 'ragg' package provides a set of graphic devices based on AGG to use as alternative to the raster devices provided through the 'grDevices' package.
Author: Thomas Lin Pedersen [cre, aut] , Maxim Shemanarev [aut, cph] , Tony Juricic [ctb, cph] , Milan Marusinec [ctb, cph] , Spencer Garrett [ctb] , Posit, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>

Diff between ragg versions 1.2.7 dated 2023-12-11 and 1.3.0 dated 2024-03-13

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More information about ragg at CRAN
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Package datarobot updated to version 2.18.6 with previous version 2.18.5 dated 2023-11-02

Title: 'DataRobot' Predictive Modeling API
Description: For working with the 'DataRobot' predictive modeling platform's API <https://www.datarobot.com/>.
Author: Ron Pearson [aut], Zachary Deane-Mayer [aut], David Chudzicki [aut], Dallin Akagi [aut], Sergey Yurgenson [aut], Thakur Raj Anand [aut], Peter Hurford [aut], Chester Ismay [aut], AJ Alon [aut], Andrew Watson [aut], Gregory Williams [aut], Anastasiia [...truncated...]
Maintainer: AJ Alon <api-maintainer@datarobot.com>

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Package esmtools updated to version 1.0.1 with previous version 1.0.0 dated 2024-01-11

Title: Preprocessing Experience Sampling Method (ESM) Data
Description: Tailored explicitly for Experience Sampling Method (ESM) data, it contains a suite of functions designed to simplify preprocessing steps and create subsequent reporting. It empowers users with capabilities to extract critical insights during preprocessing, conducts thorough data quality assessments (e.g., design and sampling scheme checks, compliance rate, careless responses), and generates visualizations and concise summary tables tailored specifically for ESM data. Additionally, it streamlines the creation of informative and interactive preprocessing reports, enabling researchers to transparently share their dataset preprocessing methodologies. Finally, it is part of a larger ecosystem which includes a framework and a web gallery (<https://preprocess.esmtools.com/>).
Author: Jordan Revol [aut, cre, cph] , Koen Niemeijer [ctb]
Maintainer: Jordan Revol <jordan.revol@kuleuven.be>

Diff between esmtools versions 1.0.0 dated 2024-01-11 and 1.0.1 dated 2024-03-13

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Package beyondWhittle updated to version 1.2.1 with previous version 1.2.0 dated 2023-05-31

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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Package targets updated to version 1.6.0 with previous version 1.5.1 dated 2024-02-15

Title: Dynamic Function-Oriented 'Make'-Like Declarative Pipelines
Description: Pipeline tools coordinate the pieces of computationally demanding analysis projects. The 'targets' package is a 'Make'-like pipeline tool for statistics and data science in R. The package skips costly runtime for tasks that are already up to date, orchestrates the necessary computation with implicit parallel computing, and abstracts files as R objects. If all the current output matches the current upstream code and data, then the whole pipeline is up to date, and the results are more trustworthy than otherwise. The methodology in this package borrows from GNU 'Make' (2015, ISBN:978-9881443519) and 'drake' (2018, <doi:10.21105/joss.00550>).
Author: William Michael Landau [aut, cre] , Matthew T. Warkentin [ctb], Mark Edmondson [ctb] , Samantha Oliver [rev] , Tristan Mahr [rev] , Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>

Diff between targets versions 1.5.1 dated 2024-02-15 and 1.6.0 dated 2024-03-13

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Permanent link

Package geofi updated to version 1.0.15 with previous version 1.0.14 dated 2024-02-05

Title: Access Finnish Geospatial Data
Description: Designed to simplify geospatial data access from the Statistics Finland Web Feature Service API <https://geo.stat.fi/geoserver/index.html>, the geofi package offers researchers and analysts a set of tools to obtain and harmonize administrative spatial data for a wide range of applications, from urban planning to environmental research. The package contains annually updated time series of municipality key datasets that can be used for data aggregation and language translations.
Author: Markus Kainu [aut, cre] , Joona Lehtomaki [aut] , Juuso Parkkinen [ctb] , Jani Miettinen [ctb], Pyry Kantanen [ctb], Sampo Vesanen [ctb], Leo Lahti [aut]
Maintainer: Markus Kainu <markus.kainu@kapsi.fi>

Diff between geofi versions 1.0.14 dated 2024-02-05 and 1.0.15 dated 2024-03-13

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Package excessmort updated to version 0.7.0 with previous version 0.6.1 dated 2021-10-11

Title: Excess Mortality
Description: Implementation of method for estimating excess mortality and other health related outcomes from weekly or daily count data described in Acosta and Irizarry (2021) "A Flexible Statistical Framework for Estimating Excess Mortality".
Author: Rafael A. Irizarry [aut, cre], Rolando Acosta [aut], Ferenci Tamas [ctb]
Maintainer: Rafael A. Irizarry <rafael_irizarry@dfci.harvard.edu>

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Package Benchmarking updated to version 0.32 with previous version 0.31 dated 2022-11-04

Title: Benchmark and Frontier Analysis Using DEA and SFA
Description: Methods for frontier analysis, Data Envelopment Analysis (DEA), under different technology assumptions (fdh, vrs, drs, crs, irs, add/frh, and fdh+), and using different efficiency measures (input based, output based, hyperbolic graph, additive, super, and directional efficiency). Peers and slacks are available, partial price information can be included, and optimal cost, revenue and profit can be calculated. Evaluation of mergers is also supported. Methods for graphing the technology sets are also included. There is also support for comparative methods based on Stochastic Frontier Analyses (SFA) and for convex nonparametric least squares of convex functions (STONED). In general, the methods can be used to solve not only standard models, but also many other model variants. It complements the book, Bogetoft and Otto, Benchmarking with DEA, SFA, and R, Springer-Verlag, 2011, but can of course also be used as a stand-alone package.
Author: Peter Bogetoft and Lars Otto
Maintainer: Lars Otto <larsot23@gmail.com>

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Package easybgm updated to version 0.1.2 with previous version 0.1.1 dated 2023-11-14

Title: Extracting and Visualizing Bayesian Graphical Models
Description: Fit and visualize the results of a Bayesian analysis of networks commonly found in psychology. The package supports fitting cross-sectional network models fitted using the packages 'BDgraph', 'bgms' and 'BGGM'. The package provides the parameter estimates, posterior inclusion probabilities, inclusion Bayes factor, and the posterior density of the parameters. In addition, for 'BDgraph' and 'bgms' it allows to assess the posterior structure space. Furthermore, the package comes with an extensive suite for visualizing results.
Author: Karoline Huth [aut, cre] , Sara Keetelaar [ctb]
Maintainer: Karoline Huth <k.huth@uva.nl>

Diff between easybgm versions 0.1.1 dated 2023-11-14 and 0.1.2 dated 2024-03-13

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Package baskexact updated to version 1.0.0 with previous version 0.1.0 dated 2021-09-15

Title: Analytical Calculation of Basket Trial Operating Characteristics
Description: Analytically calculates the operating characteristics of single-stage and two-stage basket trials with equal sample sizes using the power prior design by Baumann et al. (2024) <doi:10.48550/arXiv.2309.06988> and the design by Fujikawa et al. (2020) <doi:10.1002/bimj.201800404>.
Author: Lukas Baumann [aut, cre]
Maintainer: Lukas Baumann <baumann@imbi.uni-heidelberg.de>

Diff between baskexact versions 0.1.0 dated 2021-09-15 and 1.0.0 dated 2024-03-13

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Package zCompositions updated to version 1.5.0-3 with previous version 1.5.0-2 dated 2024-03-09

Title: Treatment of Zeros, Left-Censored and Missing Values in Compositional Data Sets
Description: Principled methods for the imputation of zeros, left-censored and missing data in compositional data sets (Palarea-Albaladejo and Martin-Fernandez (2015) <doi:10.1016/j.chemolab.2015.02.019>).
Author: Javier Palarea-Albaladejo [cre, aut] , Josep Antoni Martin-Fernandez [aut]
Maintainer: Javier Palarea-Albaladejo <javier.palarea@udg.edu>

Diff between zCompositions versions 1.5.0-2 dated 2024-03-09 and 1.5.0-3 dated 2024-03-13

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Package PROreg updated to version 1.3 with previous version 1.2 dated 2022-07-12

Title: Patient Reported Outcomes Regression Analysis
Description: It offers a wide variety of techniques, such as graphics, recoding, or regression models, for a comprehensive analysis of patient-reported outcomes (PRO). Especially novel is the broad range of regression models based on the beta-binomial distribution useful for analyzing binomial data with over-dispersion in cross-sectional, longitudinal, or multidimensional response studies (see Najera-Zuloaga J., Lee D.-J. and Arostegui I. (2019) <doi:10.1002/bimj.201700251>).
Author: Josu Najera-Zuloaga <josu.najera@ehu.eus>, Dae-Jin Lee <Dae-Jin.Lee@ie.edu>, Inmaculada Arostegui <inmaculada.arostegui@ehu.eus>
Maintainer: Josu Najera-Zuloaga <josu.najera@ehu.eus>

Diff between PROreg versions 1.2 dated 2022-07-12 and 1.3 dated 2024-03-13

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More information about PROreg at CRAN
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