Thu, 01 Jun 2023

Package SAPP updated to version 1.0.9-1 with previous version 1.0.8 dated 2020-06-02

Title: Statistical Analysis of Point Processes
Description: Functions for statistical analysis of point processes.
Author: The Institute of Statistical Mathematics
Maintainer: Masami Saga <msaga@mtb.biglobe.ne.jp>

Diff between SAPP versions 1.0.8 dated 2020-06-02 and 1.0.9-1 dated 2023-06-01

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Package disordR updated to version 0.9-5 with previous version 0.9 dated 2023-02-27

Title: Non-Ordered Vectors
Description: Functionality for manipulating values of associative maps. The package is designed to be used with the 'mvp' class of packages that use the STL map class: its purpose is to trap plausible idiom that is ill-defined (implementation-specific) and return an informative error, rather than returning a possibly incorrect result. To cite the package in publications please use Hankin (2022) <doi:10.48550/ARXIV.2210.03856>.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

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Package smooth updated to version 3.2.1 with previous version 3.2.0 dated 2023-01-18

Title: Forecasting Using State Space Models
Description: Functions implementing Single Source of Error state space models for purposes of time series analysis and forecasting. The package includes ADAM (Svetunkov, 2023, <https://openforecast.org/adam/>), Exponential Smoothing (Hyndman et al., 2008, <doi: 10.1007/978-3-540-71918-2>), SARIMA (Svetunkov & Boylan, 2019 <doi: 10.1080/00207543.2019.1600764>), Complex Exponential Smoothing (Svetunkov & Kourentzes, 2018, <doi: 10.13140/RG.2.2.24986.29123>), Simple Moving Average (Svetunkov & Petropoulos, 2018 <doi: 10.1080/00207543.2017.1380326>) and several simulation functions. It also allows dealing with intermittent demand based on the iETS framework (Svetunkov & Boylan, 2019, <doi: 10.13140/RG.2.2.35897.06242>).
Author: Ivan Svetunkov [aut, cre]
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>

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Package WhatsR updated to version 1.0.1 with previous version 1.0 dated 2023-05-26

Title: Parsing, Anonymizing and Visualizing Exported 'WhatsApp' Chat Logs
Description: Imports 'WhatsApp' chat logs and parses them into a usable dataframe object. The parser works on chats exported from Android or iOS phones and on Linux, MacOS and Windows. The parser has multiple options for extracting smilies and emojis from the messages, extracting urls and domains from the messages, extracting names and types of sent media files from the messages, extracting timestamps from messages, extracting and anonymizing author names from messages. Can be used to create anonymized versions of data.
Author: Julian Kohne <julian.kohne@gesis.org>
Maintainer: Julian Kohne <julian.kohne@gesis.org>

Diff between WhatsR versions 1.0 dated 2023-05-26 and 1.0.1 dated 2023-06-01

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Package probably updated to version 1.0.0 with previous version 0.1.0 dated 2022-08-29

Title: Tools for Post-Processing Class Probability Estimates
Description: Models can be improved by post-processing class probabilities, by: recalibration, conversion to hard probabilities, assessment of equivocal zones, and other activities. 'probably' contains tools for conducting these operations as well as calibration tools and conformal inference techniques for regression models.
Author: Max Kuhn [aut, cre], Davis Vaughan [aut], Edgar Ruiz [aut], Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>

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Package jpstat updated to version 0.3.3 with previous version 0.3.2 dated 2023-02-11

Title: Tools for Easy Use of 'e-Stat', 'RESAS' API, Etc
Description: Provides tools to use API such as 'e-Stat' (<https://www.e-stat.go.jp/>), the portal site for Japanese government statistics, and 'RESAS' (Regional Economy and Society Analyzing System, <https://resas.go.jp>).
Author: Mizuki Uchida [aut, cre]
Maintainer: Mizuki Uchida <uchidamizuki@vivaldi.net>

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Package MassWateR updated to version 2.1.0 with previous version 2.0.2 dated 2023-03-21

Title: Quality Control and Analysis of Massachusetts Water Quality Data
Description: Methods for quality control and exploratory analysis of surface water quality data collected in Massachusetts, USA. Functions are developed to facilitate data formatting for the Water Quality Exchange Network <https://www.epa.gov/waterdata/water-quality-data-upload-wqx> and reporting of data quality objectives to state agencies. Quality control methods are from Massachusetts Department of Environmental Protection (2020) <https://www.mass.gov/orgs/massachusetts-department-of-environmental-protection>.
Author: Marcus Beck [aut, cre] , Jill Carr [aut], Ben Wetherill [aut] , Pam DiBona [aut]
Maintainer: Marcus Beck <mbeck@tbep.org>

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Package covidcast updated to version 0.5.0 with previous version 0.4.5 dated 2023-01-07

Title: Client for Delphi's 'COVIDcast Epidata' API
Description: Tools for Delphi's 'COVIDcast Epidata' API: data access, maps and time series plotting, and basic signal processing. The API includes a collection of numerous indicators relevant to the COVID-19 pandemic in the United States, including official reports, de-identified aggregated medical claims data, large-scale surveys of symptoms and public behavior, and mobility data, typically updated daily and at the county level. All data sources are documented at <https://cmu-delphi.github.io/delphi-epidata/api/covidcast.html>.
Author: Taylor Arnold [aut], Jacob Bien [aut], Logan Brooks [aut], Sarah Colquhoun [aut], David Farrow [aut], Jed Grabman [ctb], Pedrito Maynard-Zhang [ctb], Kathryn Mazaitis [aut], Alex Reinhart [aut, cre] , Ryan Tibshirani [aut]
Maintainer: Alex Reinhart <areinhar@stat.cmu.edu>

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Package autoScorecard updated to version 0.2.0 with previous version 0.1.0 dated 2023-05-22

Title: Fully Automatic Generation of Scorecards
Description: Provides an efficient suite of R tools for scorecard modeling, analysis, and visualization. Including equal frequency binning, equidistant binning, K-means binning, chi-square binning, decision tree binning, data screening, manual parameter modeling, fully automatic generation of scorecards, etc. This package is designed to make scorecard development easier and faster. References include: 1. <http://shichen.name/posts/>. 2. Dong-feng Li(Peking University),Class PPT. 3. <https://zhuanlan.zhihu.com/p/389710022>. 4. <https://www.zhangshengrong.com/p/281oqR9JNw/>.
Author: Tai-Sen Zheng [aut, cre]
Maintainer: Tai-Sen Zheng <jc3802201@gmail.com>

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Package RITCH updated to version 0.1.19 with previous version 0.1.18 dated 2023-05-30

Title: R Parser for the ITCH-Protocol
Description: Allows to efficiently parse, filter, and write binary ITCH Files (Version 5.0) containing detailed financial transactions as distributed by NASDAQ to an R data.table.
Author: David Zimmermann-Kollenda [aut, cre]
Maintainer: David Zimmermann-Kollenda <david_j_zimmermann@hotmail.com>

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Package RelimpPCR updated to version 0.3.0 with previous version 0.2.4 dated 2019-05-02

Title: Relative Importance PCA Regression
Description: Performs Principal Components Analysis (also known as PCA) dimensionality reduction in the context of a linear regression. In most cases, PCA dimensionality reduction is performed independent of the response variable for a regression. This captures the majority of the variance of the model's predictors, but may not actually be the optimal dimensionality reduction solution for a regression against the response variable. An alternative method, optimized for a regression against the response variable, is to use both PCA and a relative importance measure. This package applies PCA to a given data frame of predictors, and then calculates the relative importance of each PCA factor against the response variable. It outputs ordered factors that are optimized for model fit. By performing dimensionality reduction with this method, an individual can achieve a the same r-squared value as performing just PCA, but with fewer PCA factors. References: Yuri Balasanov (2017) <https://ilykei.com>.
Author: Michael Hernandez <micahel@hernandez.ai>, Yuri Balasanov
Maintainer: Michael Hernandez <michael@hernandez.ai>

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Package FunnelPlotR updated to version 0.4.2 with previous version 0.4.1 dated 2021-09-30

Title: Funnel Plots for Comparing Institutional Performance
Description: An implementation of methods presented by Spiegelhalter (2005) <doi:10.1002/sim.1970> Funnel plots for comparing institutional performance, for standardised ratios, ratios of counts and proportions with additive overdispersion adjustment.
Author: Chris Mainey [aut, cre] , Andrew Johnson [ctb], Matthew Bass [ctb], NHS-R Community [cph]
Maintainer: Chris Mainey <c.mainey1@nhs.net>

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Package ftsa updated to version 6.2 with previous version 6.1 dated 2021-11-02

Title: Functional Time Series Analysis
Description: Functions for visualizing, modeling, forecasting and hypothesis testing of functional time series. \n Jim\'{e}nez-Var\'{o}n, C., Sun, Y. and Shang, H. L. (2023) <arXiv: 2305.19749>.
Author: Rob Hyndman [aut] , Han Lin Shang [aut, cre, cph]
Maintainer: Han Lin Shang <hanlin.shang@mq.edu.au>

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Package WebGestaltR updated to version 0.4.6 with previous version 0.4.5 dated 2023-02-16

Title: Gene Set Analysis Toolkit WebGestaltR
Description: The web version WebGestalt <https://www.webgestalt.org> supports 12 organisms, 354 gene identifiers and 321,251 function categories. Users can upload the data and functional categories with their own gene identifiers. In addition to the Over-Representation Analysis, WebGestalt also supports Gene Set Enrichment Analysis and Network Topology Analysis. The user-friendly output report allows interactive and efficient exploration of enrichment results. The WebGestaltR package not only supports all above functions but also can be integrated into other pipeline or simultaneously analyze multiple gene lists.
Author: Jing Wang [aut], Yuxing Liao [aut, cre], Eric Jaehnig [ctb], Zhiao Shi [ctb], Quanhu Sheng [ctb]
Maintainer: Yuxing Liao <yuxingliao@gmail.com>

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Package simstudy updated to version 0.7.0 with previous version 0.6.0 dated 2023-02-18

Title: Simulation of Study Data
Description: Simulates data sets in order to explore modeling techniques or better understand data generating processes. The user specifies a set of relationships between covariates, and generates data based on these specifications. The final data sets can represent data from randomized control trials, repeated measure (longitudinal) designs, and cluster randomized trials. Missingness can be generated using various mechanisms (MCAR, MAR, NMAR).
Author: Keith Goldfeld [aut, cre] , Jacob Wujciak-Jens [aut]
Maintainer: Keith Goldfeld <keith.goldfeld@nyulangone.org>

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Package rmarkdown updated to version 2.22 with previous version 2.21 dated 2023-03-26

Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut], Yihui Xie [aut, cre] , Christophe Dervieux [aut] , Jonathan McPherson [aut], Javier Luraschi [aut], Kevin Ushey [aut], Aron Atkins [aut], Hadley Wickham [aut], Joe Cheng [aut], Winston Chang [aut], Richard Iannone [aut] , Andrew Dun [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>

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New package sphereTessellation with initial version 1.0.0
Package: sphereTessellation
Title: Delaunay and Voronoï Tessellations on the Sphere
Version: 1.0.0
Description: Performs Delaunay and Voronoï tessellations on spheres and provides some functions to plot them. The algorithms are mainly performed by the 'C++' library 'CGAL' (<https://www.cgal.org/>).
License: GPL-3
URL: https://github.com/stla/sphereTessellation
BugReports: https://github.com/stla/sphereTessellation/issues
Imports: grDevices, randomcoloR, Rcpp, rgl, s2
LinkingTo: BH, Rcpp, RcppCGAL, RcppEigen
Suggests: cooltools, uniformly
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2023-05-31 09:41:48 UTC; stla
Author: Stephane Laurent [aut, cre]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Repository: CRAN
Date/Publication: 2023-06-01 12:40:02 UTC

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New package RGAP with initial version 0.1.0
Package: RGAP
Title: Production Function Output Gap Estimation
Version: 0.1.0
Depends: R (>= 3.1.0)
Description: The output gap indicates the percentage difference between the actual output of an economy and its potential. Since potential output is a latent process, the estimation of the output gap poses a challenge and numerous filtering techniques have been proposed. 'RGAP' facilitates the estimation of a Cobb-Douglas production function type output gap, as suggested by the European Commission (Havik et al. 2014) <https://ideas.repec.org/p/euf/ecopap/0535.html>. To that end, the non-accelerating wage rate of unemployment (NAWRU) and the trend of total factor productivity (TFP) can be estimated in two bivariate unobserved component models by means of Kalman filtering and smoothing. 'RGAP' features a flexible modeling framework for the appropriate state-space models and offers frequentist as well as Bayesian estimation techniques. Additional functionalities include direct access to the 'AMECO' <https://economy-finance.ec.europa.eu/economic-research-and-databases/economic-databases/ameco- [...truncated...]
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: stats, KFAS, zoo, dlm, openxlsx, ggplot2, gridExtra
Suggests: testthat (>= 3.0.0), R.rsp
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2023-06-01 12:08:30 UTC; sinast
Author: Sina Streicher [aut, cre]
Maintainer: Sina Streicher <streicher@kof.ethz.ch>
Repository: CRAN
Date/Publication: 2023-06-01 12:50:09 UTC

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Package osmdata updated to version 0.2.3 with previous version 0.2.2 dated 2023-04-24

Title: Import 'OpenStreetMap' Data as Simple Features or Spatial Objects
Description: Download and import of 'OpenStreetMap' ('OSM') data as 'sf' or 'sp' objects. 'OSM' data are extracted from the 'Overpass' web server (<https://overpass-api.de/>) and processed with very fast 'C++' routines for return to 'R'.
Author: Mark Padgham [aut, cre], Bob Rudis [aut], Robin Lovelace [aut], Maelle Salmon [aut], Joan Maspons [aut] , Andrew Smith [ctb], James Smith [ctb], Andrea Gilardi [ctb], Enrico Spinielli [ctb], Anthony North [ctb], Martin Machyna [ctb], Marcin Kalicinsk [...truncated...]
Maintainer: Mark Padgham <mark.padgham@email.com>

Diff between osmdata versions 0.2.2 dated 2023-04-24 and 0.2.3 dated 2023-06-01

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New package intrinsicKappa with initial version 0.1
Package: intrinsicKappa
Title: Sample Size Planning Based on Intrinsic Kappa Value
Version: 0.1
Maintainer: David Schindler <dv.schindler@gmail.com>
Description: Kappa statistics is one of the most used methods to evaluate the effectiveness of inpsections based on attribute assessments in industry. However, its estimation by available methods does not provide its "real" or "intrinstic" value. This package provides functions for the computation of the intrinsic kappa value as it is described in: Rafael Sanchez-Marquez, Frank Gerhorst and David Schindler (2023) "Effectiveness of quality inspections of attributive characteristics – A novel and practical method for estimating the “intrinsic” value of kappa based on alpha and beta statistics." <doi:10.1016/j.cie.2023.109006>.
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 4.2.0)
Imports: stats
Suggests: knitr, rmarkdown, utils
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-06-01 11:13:06 UTC; DSCHIND2
Author: David Schindler [aut, cre], Rafael Sanchez-Marquez [aut], Frank Gerhorst [aut]
Repository: CRAN
Date/Publication: 2023-06-01 12:50:07 UTC

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Package FinNet updated to version 0.1.1 with previous version 0.1.0 dated 2023-05-30

Title: Quickly Build and Manipulate Financial Networks
Description: Providing classes, methods, and functions to deal with financial networks. Users can easily store information about both physical and legal persons by using pre-made classes that are studied for integration with scraping packages such as 'rvest' and 'RSelenium'. Moreover, the package assists in creating various types of financial networks depending on the type of relation between its units depending on the relation under scrutiny (ownership, board interlocks, etc.), the desired tie type (valued or binary), and renders them in the most common formats (adjacency matrix, incidence matrix, edge list, 'igraph', 'network').
Author: Fabio Ashtar Telarico [aut, cre]
Maintainer: Fabio Ashtar Telarico <Fabio-Ashtar.Telarico@fdv.uni-lj.si>

Diff between FinNet versions 0.1.0 dated 2023-05-30 and 0.1.1 dated 2023-06-01

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Package distanceto updated to version 0.0.3 with previous version 0.0.2 dated 2021-11-11

Title: Calculate Distance to Features
Description: Calculates distances from point locations to features. The usual approach for eg. resource selection function analyses is to generate a complete distance to features surface then sample it with your observed and random points. Since these raster based approaches can be pretty costly with large areas, and often lead to memory issues in R, the distanceto package opts to compute these distances using efficient, vector based approaches. As a helper, there's a decidedly low-res raster based approach for visually inspecting your region's distance surface. But the workhorse is distance_to.
Author: Alec L. Robitaille [aut, cre]
Maintainer: Alec L. Robitaille <robit.alec@gmail.com>

Diff between distanceto versions 0.0.2 dated 2021-11-11 and 0.0.3 dated 2023-06-01

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New package AFFECT with initial version 0.1.0
Package: AFFECT
Title: Accelerated Functional Failure Time Model with Error-Contaminated Survival Times
Version: 0.1.0
Author: Hsiao-Ting Huang <nikkihuang309700034@gmail.com> [cre,aut] Li-Pang Chen <lchen723@nccu.edu.tw> [aut]
Maintainer: Hsiao-Ting Huang <nikkihuang309700034@gmail.com>
Depends: R (>= 3.3.1)
Imports: stats,ggplot2
Description: We aim to deal with data with measurement error in the response and misclassification censoring status under an AFT model. This package primarily contains three functions, which are used to generate artificial data, correction for error-prone data and estimate the functional covariates for an AFT model.
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-06-01 11:59:46 UTC; nikki
Repository: CRAN
Date/Publication: 2023-06-01 12:50:14 UTC

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Package Statamarkdown updated to version 0.8.0 with previous version 0.7.4 dated 2023-05-25

Title: 'Stata' Markdown
Description: Settings and functions to extend the 'knitr' 'Stata' engine.
Author: Doug Hemken [aut, cre] , Tom Palmer [ctb] , Philipp Lepert [ctb]
Maintainer: Doug Hemken <dehemken@wisc.edu>

Diff between Statamarkdown versions 0.7.4 dated 2023-05-25 and 0.8.0 dated 2023-06-01

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Package simplace updated to version 5.0.12 with previous version 5.0.11 dated 2023-05-09

Title: Interface to Use the Modelling Framework 'SIMPLACE'
Description: Interface to interact with the modelling framework 'SIMPLACE' and to parse the results of simulations.
Author: Gunther Krauss
Maintainer: Gunther Krauss <guntherkrauss@uni-bonn.de>

Diff between simplace versions 5.0.11 dated 2023-05-09 and 5.0.12 dated 2023-06-01

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New package scGOclust with initial version 0.1.0
Package: scGOclust
Title: Measuring Cell Type Similarity with Gene Ontology in Single-Cell RNA-Seq
Version: 0.1.0
Description: Traditional methods for analyzing single cell RNA-seq datasets focus solely on gene expression, but this package introduces a novel approach that goes beyond this limitation. Using Gene Ontology terms as features, the package allows for the functional profile of cell populations, and comparison within and between datasets from the same or different species. Our approach enables the discovery of previously unrecognized functional similarities and differences between cell types and has demonstrated success in identifying cell types' functional correspondence even between evolutionarily distant species.
URL: https://github.com/YY-SONG0718/scGOclust
BugReports: https://github.com/YY-SONG0718/scGOclust/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
LazyDataCompression: bzip2
VignetteBuilder: knitr
Imports: limma, Seurat, biomaRt, dplyr, magrittr, stats, tibble, tidyr, Matrix, utils, networkD3, slanter
Suggests: devtools, knitr, pheatmap, rmarkdown, httr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2023-05-31 13:28:35 UTC; ysong
Author: Yuyao Song [aut, cre, ctb], Irene Papatheodorou [aut, ths]
Maintainer: Yuyao Song <ysong@ebi.ac.uk>
Repository: CRAN
Date/Publication: 2023-06-01 11:50:05 UTC

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New package rwisp with initial version 1.0.1
Package: rwisp
Title: WISP Multiple Criteria Sorting Method
Description: Implementation of the Integrated Simple Weighted Sum Product Method (WISP), a multiple criteria sorting method create by Dragisa Stanujkic (2021) <doi:10.1109/TEM.2021.3075783>.
Version: 1.0.1
Encoding: UTF-8
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2023-05-31 22:59:53 UTC; usuario
Author: Bernardo Silva [aut, cre]
Maintainer: Bernardo Silva <bernardo.silva@furg.br>
Repository: CRAN
Date/Publication: 2023-06-01 12:00:02 UTC

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Package micemd updated to version 1.9.0 with previous version 1.8.0 dated 2021-10-15

Title: Multiple Imputation by Chained Equations with Multilevel Data
Description: Addons for the 'mice' package to perform multiple imputation using chained equations with two-level data. Includes imputation methods dedicated to sporadically and systematically missing values. Imputation of continuous, binary or count variables are available. Following the recommendations of Audigier, V. et al (2018) <doi:10.1214/18-STS646>, the choice of the imputation method for each variable can be facilitated by a default choice tuned according to the structure of the incomplete dataset. Allows parallel calculation and overimputation for 'mice'.
Author: Vincent Audigier [aut, cre] , Matthieu Resche-Rigon [aut] , Johanna Munoz Avila [ctb]
Maintainer: Vincent Audigier <vincent.audigier@cnam.fr>

Diff between micemd versions 1.8.0 dated 2021-10-15 and 1.9.0 dated 2023-06-01

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New package MetricGraph with initial version 1.1.1
Package: MetricGraph
Title: Random Fields on Metric Graphs
Version: 1.1.1
Maintainer: David Bolin <davidbolin@gmail.com>
Description: Facilitates creation and manipulation of metric graphs, such as street or river networks. Further facilitates operations and visualizations of data on metric graphs, and the creation of a large class of random fields and stochastic partial differential equations on such spaces. These random fields can be used for simulation, prediction and inference. In particular, linear mixed effects models including random field components can be fitted to data based on computationally efficient sparse matrix representations. Interfaces to the R packages 'INLA' and 'inlabru' are also provided, which facilitate working with Bayesian statistical models on metric graphs. The main references for the methods are Bolin, Simas and Wallin (2022) <doi:10.48550/arXiv.2205.06163>, Bolin, Kovacs, Kumar and Simas (2023) <doi:10.48550/arXiv.2302.03995> and Bolin, Simas and Wallin (2023) <doi:10.48550/arXiv.2304.03190> and <doi:10.48550/arXiv.2304.10372>.
License: GPL (>= 2)
Imports: stats, ggplot2, igraph, sp, sf, viridis, rSPDE (>= 2.3.1), Matrix, methods, Rcpp (>= 1.0.5)
Suggests: knitr, testthat, INLA (>= 0.0-1468840039), inlabru, osmdata, sn, plotly, tidyr, parallel, optimParallel, numDeriv
Additional_repositories: https://inla.r-inla-download.org/R/testing
BugReports: https://github.com/davidbolin/MetricGraph/issues
URL: https://davidbolin.github.io/MetricGraph/
Copyright: The R package and code, and the main programs, were written by and are Copyright by David Bolin, Alexandre B. Simas and Jonas Wallin, and are redistributable under the GNU Public License, version 2 or later. The package also includes one function from another package, which will be deprecated in 2023, and whose codes are under the GPL-2 license. For details see the COPYRIGHTS file.
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: yes
LinkingTo: Rcpp, RcppEigen
Packaged: 2023-06-01 08:36:14 UTC; debusta
Author: David Bolin [cre, aut], Jonas Wallin [aut], Alexandre Simas [aut]
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2023-06-01 12:00:11 UTC

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Package RoBMA updated to version 3.0.0 with previous version 2.3.2 dated 2023-03-13

Title: Robust Bayesian Meta-Analyses
Description: A framework for estimating ensembles of meta-analytic models (assuming either presence or absence of the effect, heterogeneity, and publication bias). The RoBMA framework uses Bayesian model-averaging to combine the competing meta-analytic models into a model ensemble, weights the posterior parameter distributions based on posterior model probabilities and uses Bayes factors to test for the presence or absence of the individual components (e.g., effect vs. no effect; Bartoš et al., 2022, <doi:10.1002/jrsm.1594>; Maier, Bartoš & Wagenmakers, 2022, <doi:10.1037/met0000405>). Users can define a wide range of non-informative or informative prior distributions for the effect size, heterogeneity, and publication bias components (including selection models and PET-PEESE). The package provides convenient functions for summary, visualizations, and fit diagnostics.
Author: Frantisek Bartos [aut, cre] , Maximilian Maier [aut] , Eric-Jan Wagenmakers [ths] , Joris Goosen [ctb], Matthew Denwood [cph] , Martyn Plummer [cph]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>

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New package bootImpute with initial version 1.2.1
Package: bootImpute
Title: Bootstrap Inference for Multiple Imputation
Version: 1.2.1
Author: Jonathan Bartlett
Maintainer: Jonathan Bartlett <jonathan.bartlett1@lshtm.ac.uk>
Description: Bootstraps and imputes incomplete datasets. Then performs inference on estimates obtained from analysing the imputed datasets as proposed by von Hippel and Bartlett (2021) <doi:10.1214/20-STS793>.
Depends: R (>= 2.10)
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: mice, smcfcs
Suggests: testthat
NeedsCompilation: no
Packaged: 2023-06-01 10:07:56 UTC; jwb13
Repository: CRAN
Date/Publication: 2023-06-01 10:30:02 UTC

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Package watson updated to version 0.4 with previous version 0.3 dated 2023-03-17

Title: Fitting and Simulating Mixtures of Watson Distributions
Description: Tools for fitting and simulating mixtures of Watson distributions. The random sampling scheme of the package offers two sampling algorithms that are based of the results of Sablica, Hornik and Leydold (2022) <https://research.wu.ac.at/en/publications/random-sampling-from-the-watson-distribution>. What is more, the package offers a smart tool to combine these two methods, and based on the selected parameters, it approximates the relative sampling speed for both methods and picks the faster one. In addition, the package offers a fitting function for the mixtures of Watson distribution, that uses the expectation-maximization (EM) algorithm. Special features are the possibility to use multiple variants of the E-step and M-step, sparse matrices for the data representation and state of the art methods for numerical evaluation of needed special functions using the results of Sablica and Hornik (2022) <https://www.ams.org/journals/mcom/2022-91-334/S0025-5718-2021-03690-X/>.
Author: Lukas Sablica [aut, cre] , Kurt Hornik [aut] , Josef Leydold [aut] , Gerard Jungman [ctb, cph] , Brian Gough [ctb, cph]
Maintainer: Lukas Sablica <lsablica@wu.ac.at>

Diff between watson versions 0.3 dated 2023-03-17 and 0.4 dated 2023-06-01

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New package SpiceFP with initial version 0.1.2
Package: SpiceFP
Title: Sparse Method to Identify Joint Effects of Functional Predictors
Version: 0.1.2
Maintainer: Girault Gnanguenon Guesse <girault.gnanguenon@gmail.com>
Description: A set of functions allowing to implement the 'SpiceFP' approach which is iterative. It involves transformation of functional predictors into several candidate explanatory matrices (based on contingency tables), to which relative edge matrices with contiguity constraints are associated. Generalized Fused Lasso regression are performed in order to identify the best candidate matrix, the best class intervals and related coefficients at each iteration. The approach is stopped when the maximal number of iterations is reached or when retained coefficients are zeros. Supplementary functions allow to get coefficients of any candidate matrix or mean of coefficients of many candidates. The methods in this package are describing in Girault Gnanguenon Guesse, Patrice Loisel, Bénedicte Fontez, Thierry Simonneau, Nadine Hilgert (2021) "An exploratory penalized regression to identify combined effects of functional variables -Application to agri-environmental issues" <https://hal.archives-ouvertes. [...truncated...]
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.6.0)
Imports: doParallel, foreach, stringr, tidyr, Matrix, genlasso, purrr
Suggests: fields
NeedsCompilation: no
Packaged: 2023-05-31 14:06:46 UTC; gnanguen
Author: Girault Gnanguenon Guesse [aut, cre], Patrice Loisel [aut], Benedicte Fontez [aut], Nadine Hilgert [aut], Thierry Simonneau [ctr], Isabelle Sanchez [ctr]
Repository: CRAN
Date/Publication: 2023-06-01 09:10:18 UTC

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New package projpred with initial version 2.6.0
Package: projpred
Encoding: UTF-8
Title: Projection Predictive Feature Selection
Version: 2.6.0
Date: 2023-05-25
Description: Performs projection predictive feature selection for generalized linear models (Piironen, Paasiniemi, and Vehtari, 2020, <doi:10.1214/20-EJS1711>) with or without multilevel or additive terms (Catalina, Bürkner, and Vehtari, 2022, <https://proceedings.mlr.press/v151/catalina22a.html>), for some ordinal and nominal regression models (Weber and Vehtari, 2023, <arXiv:2301.01660>), and for many other regression models (using the latent projection by Catalina, Bürkner, and Vehtari, 2021, <arXiv:2109.04702>, which can also be applied to most of the former models). The package is compatible with the 'rstanarm' and 'brms' packages, but other reference models can also be used. See the vignettes and the documentation for more information and examples.
License: GPL-3 | file LICENSE
URL: https://mc-stan.org/projpred/, https://discourse.mc-stan.org
BugReports: https://github.com/stan-dev/projpred/issues/
Depends: R (>= 3.5.0)
Imports: methods, utils, Rcpp, ggplot2, scales, rstantools (>= 2.0.0), loo (>= 2.0.0), lme4 (>= 1.1-28), mvtnorm, mgcv, gamm4, abind, MASS, ordinal, nnet, mclogit
Suggests: ggrepel, rstanarm, brms, nlme, optimx, ucminf, parallel, foreach, iterators, testthat, vdiffr, knitr, rmarkdown, glmnet, cmdstanr, rlang, bayesplot (>= 1.5.0), posterior, doParallel, future, future.callr, doFuture
LinkingTo: Rcpp, RcppArmadillo
Additional_repositories: https://mc-stan.org/r-packages/
LazyData: TRUE
VignetteBuilder: knitr, rmarkdown
NeedsCompilation: yes
Packaged: 2023-05-31 17:46:17 UTC; frank
Author: Juho Piironen [aut], Markus Paasiniemi [aut], Alejandro Catalina [aut], Frank Weber [cre, aut], Aki Vehtari [aut], Jonah Gabry [ctb], Marco Colombo [ctb], Paul-Christian Buerkner [ctb], Hamada S. Badr [ctb], Brian Sullivan [ctb], Soelvi Roegnvaldsson [c [...truncated...]
Maintainer: Frank Weber <fweber144@protonmail.com>
Repository: CRAN
Date/Publication: 2023-06-01 09:10:02 UTC

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Package nonmem2rx updated to version 0.1.1 with previous version 0.1.0 dated 2023-05-26

Title: 'nonmem2rx' Converts 'NONMEM' Models to 'rxode2'
Description: 'NONMEM' has been a tool for running nonlinear mixed effects models since the 80s and is still used today (Bauer 2019 <doi:10.1002/psp4.12404>). This tool allows you to convert 'NONMEM' models to 'rxode2' (Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>) and with simple models 'nlmixr2' syntax (Fidler et al (2019) <doi:10.1002/psp4.12445>). The 'nlmixr2' syntax requires the residual specification to be included and it is not always translated. If available, the 'rxode2' model will read in the 'NONMEM' data and compare the simulation for the population model ('PRED') individual model ('IPRED') and residual model ('IWRES') to immediately show how well the translation is performing. This saves the model development time for people who are creating an 'rxode2' model manually. Additionally, this package reads in all the information to allow simulation with uncertainty (that is the number of observations, the number of subjects, and the covariance matrix) with a 'rx [...truncated...]
Author: Matthew Fidler [aut, cre] , Philip Delff [ctb], Gabriel Staples [ctb]
Maintainer: Matthew Fidler <matt.fidler@novartis.com>

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New package ggPMX with initial version 1.2.9
Package: ggPMX
Title: 'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME Models
Description: At Novartis, we aimed at standardizing the set of diagnostic plots used for modeling activities in order to reduce the overall effort required for generating such plots. For this, we developed a guidance that proposes an adequate set of diagnostics and a toolbox, called 'ggPMX' to execute them. 'ggPMX' is a toolbox that can generate all diagnostic plots at a quality sufficient for publication and submissions using few lines of code. This package focuses on plots recommended by ISoP <doi:10.1002/psp4.12161>. While not required, you can get/install the 'R' 'lixoftConnectors' package in the 'Monolix' installation, as described at the following url <https://monolix.lixoft.com/monolix-api/lixoftconnectors_installation/>. When 'lixoftConnectors' is available, 'R' can use 'Monolix' directly to create the required Chart Data instead of exporting it from the 'Monolix' gui.
Version: 1.2.9
URL: https://github.com/ggPMXdevelopment/ggPMX
BugReports: https://github.com/ggPMXdevelopment/ggPMX/issues
Depends: R (>= 3.5)
Imports: data.table, yaml, R6, gtable, ggplot2 (>= 3.4.0), ggforce, magrittr, stringr, assertthat, GGally, zoo, knitr, rmarkdown, tidyr, dplyr, purrr, readr, rlang, checkmate, scales
License: GPL-2
Suggests: testthat, xtable, vdiffr, rxode2, captioner, nlmixr2, nlmixr2data, lixoftConnectors, xgxr, withr, lifecycle
VignetteBuilder: knitr
NeedsCompilation: no
Encoding: UTF-8
Packaged: 2023-05-31 23:02:17 UTC; matt
Author: Amine Gassem [aut], Bruno Bieth [aut], Irina Baltcheva [aut], Thomas Dumortier [aut], Christian Bartels [aut], Souvik Bhattacharya [aut], Inga Ludwig [aut], Ines Paule [aut], Didier Renard [aut], Matthew Fidler [aut, cre] , Seid Hamzic [aut], Benjami [...truncated...]
Maintainer: Matthew Fidler <matt.fidler@novartis.com>
Repository: CRAN
Date/Publication: 2023-06-01 09:10:11 UTC

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Package eeptools updated to version 1.2.5 with previous version 1.2.4 dated 2020-05-02

Title: Convenience Functions for Education Data
Description: Collection of convenience functions to make working with administrative records easier and more consistent. Includes functions to clean strings, and identify cut points. Also includes three example data sets of administrative education records for learning how to process records with errors.
Author: Jason P. Becker [ctb], Jared E. Knowles [aut, cre]
Maintainer: Jared E. Knowles <jared@civilytics.com>

Diff between eeptools versions 1.2.4 dated 2020-05-02 and 1.2.5 dated 2023-06-01

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Package BayesX updated to version 0.3-2 with previous version 0.3-1.1 dated 2022-07-04

Title: R Utilities Accompanying the Software Package BayesX
Description: Functions for exploring and visualising estimation results obtained with BayesX, a free software for estimating structured additive regression models (<https://www.uni-goettingen.de/de/bayesx/550513.html>). In addition, functions that allow to read, write and manipulate map objects that are required in spatial analyses performed with BayesX.
Author: Nikolaus Umlauf [aut, cre], Thomas Kneib [aut], Nadja Klein [aut], Felix Heinzl [ctb], Andreas Brezger [ctb], Daniel Sabanes Bove [ctb]
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>

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Package BiasedUrn updated to version 2.0.10 with previous version 2.0.9 dated 2023-02-01

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

Diff between BiasedUrn versions 2.0.9 dated 2023-02-01 and 2.0.10 dated 2023-06-01

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Package ggrastr updated to version 1.0.2 with previous version 1.0.1 dated 2021-12-08

Title: Rasterize Layers for 'ggplot2'
Description: Rasterize only specific layers of a 'ggplot2' plot while simultaneously keeping all labels and text in vector format. This allows users to keep plots within the reasonable size limit without loosing vector properties of the scale-sensitive information.
Author: Viktor Petukhov [aut, cph], Teun van den Brand [aut], Evan Biederstedt [cre, aut]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>

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Package mecoturn updated to version 0.2.0 with previous version 0.1.0 dated 2023-02-23

Title: Decipher Microbial Turnover along a Gradient
Description: Two pipelines are provided to study microbial turnover along a gradient, including the beta diversity and microbial abundance change. The 'betaturn' class consists of the steps of community dissimilarity matrix generation, matrix conversion, differential test and visualization. The workflow of 'taxaturn' class includes the taxonomic abundance calculation, abundance transformation, abundance change summary, statistical analysis and visualization. Multiple statistical approaches can contribute to the analysis of microbial turnover.
Author: Chi Liu [aut, cre], Xiangzhen Li [ctb], Minjie Yao [ctb]
Maintainer: Chi Liu <liuchi0426@126.com>

Diff between mecoturn versions 0.1.0 dated 2023-02-23 and 0.2.0 dated 2023-06-01

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Package BIDistances (with last version 0.0.2) was removed from CRAN

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

2023-05-18 0.0.2

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Package R.SamBada (with last version 0.1.3) was removed from CRAN

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

2022-01-04 0.1.3
2019-11-25 0.1.2
2019-05-09 0.1.1
2019-04-12 0.1.0

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Package rsmatrix updated to version 0.2.6 with previous version 0.2.4 dated 2022-08-13

Title: Matrices for Repeat-Sales Price Indexes
Description: A small package for calculating the matrices in Shiller (1991, <doi:10.1016/S1051-1377(05)80028-2>) that serve as the foundation for many repeat-sales price indexes.
Author: Steve Martin [aut, cre, cph]
Maintainer: Steve Martin <stevemartin041@gmail.com>

Diff between rsmatrix versions 0.2.4 dated 2022-08-13 and 0.2.6 dated 2023-06-01

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