Wed, 03 May 2023

Package sass updated to version 0.4.6 with previous version 0.4.5 dated 2023-01-23

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>

Diff between sass versions 0.4.5 dated 2023-01-23 and 0.4.6 dated 2023-05-03

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Package scattermore updated to version 1.0 with previous version 0.8 dated 2022-02-14

Title: Scatterplots with More Points
Description: C-based conversion of large scatterplot data to rasters plus other operations such as data blurring or data alpha blending. Speeds up plotting of data with millions of points.
Author: Tereza Kulichova [aut], Mirek Kratochvil [aut, cre]
Maintainer: Mirek Kratochvil <exa.exa@gmail.com>

Diff between scattermore versions 0.8 dated 2022-02-14 and 1.0 dated 2023-05-03

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Package opa updated to version 0.8.1 with previous version 0.7.4 dated 2023-02-17

Title: An Implementation of Ordinal Pattern Analysis
Description: Quantifies hypothesis to data fit for repeated measures and longitudinal data, as described by Thorngate (1987) <doi:10.1016/S0166-4115(08)60083-7> and Grice et al., (2015) <doi:10.1177/2158244015604192>. Hypothesis and data are encoded as pairwise relative orderings which are then compared to determine the percentage of orderings in the data that are matched by the hypothesis.
Author: Timothy Beechey [aut, cre]
Maintainer: Timothy Beechey <tim.beechey@proton.me>

Diff between opa versions 0.7.4 dated 2023-02-17 and 0.8.1 dated 2023-05-03

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Package bpbounds updated to version 0.1.5 with previous version 0.1.4 dated 2020-01-21

Title: Nonparametric Bounds for the Average Causal Effect Due to Balke and Pearl and Extensions
Description: Implementation of the nonparametric bounds for the average causal effect under an instrumental variable model by Balke and Pearl (Bounds on Treatment Effects from Studies with Imperfect Compliance, JASA, 1997, 92, 439, 1171-1176). The package can calculate bounds for a binary outcome, a binary treatment/phenotype, and an instrument with either 2 or 3 categories. The package implements bounds for situations where these 3 variables are measured in the same dataset (trivariate data) or where the outcome and instrument are measured in one study and the treatment/phenotype and instrument are measured in another study (bivariate data).
Author: Tom Palmer [aut, cre] , Roland Ramsahai [aut] , Vanessa Didelez [aut] , Nuala Sheehan [aut]
Maintainer: Tom Palmer <remlapmot@hotmail.com>

Diff between bpbounds versions 0.1.4 dated 2020-01-21 and 0.1.5 dated 2023-05-03

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New package switchSelection with initial version 1.0.0
Package: switchSelection
Title: Endogenous Switching and Sample Selection Regression Models
Version: 1.0.0
Date: 2023-05-02
Description: Estimate the parameters of multivariate endogenous switching and sample selection models using methods described in Newey (2009) <doi:10.1111/j.1368-423X.2008.00263.x>, E. Kossova, B. Potanin (2018) <https:ideas.repec.org/a/ris/apltrx/0346.html>, E. Kossova, L. Kupriianova, B. Potanin (2020) <https://ideas.repec.org/a/ris/apltrx/0391.html> and E. Kossova, B. Potanin (2022) <https://ideas.repec.org/a/ris/apltrx/0455.html>.
License: GPL (>= 2)
Depends: Rcpp (>= 1.0.6), hpa (>= 1.2.1), mnorm (>= 1.0.0), gena (>= 1.0.0)
LinkingTo: Rcpp, RcppArmadillo, hpa, mnorm
NeedsCompilation: yes
Packaged: 2023-05-02 10:02:44 UTC; Bogdan
Author: Bogdan Potanin [aut, cre, ctb]
Maintainer: Bogdan Potanin <bogdanpotanin@gmail.com>
Repository: CRAN
Date/Publication: 2023-05-03 18:30:02 UTC

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New package ROI.plugin.clarabel with initial version 0.1
Package: ROI.plugin.clarabel
Version: 0.1
Title: 'clarabel' Plug-in for the 'R' Optimization Infrastructure
Author: Benjamin Schwendinger [aut, cre]
Maintainer: Benjamin Schwendinger <benjaminschwe@gmail.com>
Description: Enhances the 'R' Optimization Infrastructure ('ROI') package with the 'clarabel' solver for solving convex cone problems. More information about 'clarabel' can be found at <https://oxfordcontrol.github.io/ClarabelDocs/stable/>.
Imports: stats, methods, slam, ROI (>= 1.0-0), clarabel (>= 0.4.1)
License: GPL-3
URL: https://gitlab.com/roigrp/solver/roi.plugin.clarabel
NeedsCompilation: no
Packaged: 2023-05-02 11:23:15 UTC; bschwendinger
Repository: CRAN
Date/Publication: 2023-05-03 18:30:05 UTC

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New package npsp with initial version 0.7-11
Package: npsp
Title: Nonparametric Spatial Statistics
Version: 0.7-11
Date: 2023-05-01
Maintainer: Ruben Fernandez-Casal <rubenfcasal@gmail.com>
Depends: R (>= 2.14.0), graphics
Imports: sp, methods, quadprog, spam
Suggests: gstat, geoR, fields, DEoptim, knitr
Description: Multidimensional nonparametric spatial (spatio-temporal) geostatistics. S3 classes and methods for multidimensional: linear binning, local polynomial kernel regression (spatial trend estimation), density and variogram estimation. Nonparametric methods for simultaneous inference on both spatial trend and variogram functions (for spatial processes). Nonparametric residual kriging (spatial prediction). For details on these methods see, for example, Fernandez-Casal and Francisco-Fernandez (2014) <doi:10.1007/s00477-013-0817-8> or Castillo-Paez et al. (2019) <doi:10.1016/j.csda.2019.01.017>.
License: GPL (>= 2)
URL: https://github.com/rubenfcasal/npsp
BugReports: https://github.com/rubenfcasal/npsp/issues
LazyData: yes
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2023-05-01 19:14:39 UTC; ruben.fcasal
Author: Ruben Fernandez-Casal [aut, cre]
Repository: CRAN
Date/Publication: 2023-05-03 18:20:02 UTC

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Package kernelshap updated to version 0.3.6 with previous version 0.3.5 dated 2023-03-31

Title: Kernel SHAP
Description: Efficient implementation of Kernel SHAP, see Lundberg and Lee (2017) <https://dl.acm.org/doi/10.5555/3295222.3295230>, and Covert and Lee (2021) <http://proceedings.mlr.press/v130/covert21a>. For models with up to eight features, the results are exact regarding the selected background data. Otherwise, an almost exact hybrid algorithm involving iterative sampling is used. The package plays well together with meta-learning packages like 'tidymodels', 'caret' or 'mlr3'. Visualizations can be done using the R package 'shapviz'.
Author: Michael Mayer [aut, cre], David Watson [aut], Przemyslaw Biecek [ctb]
Maintainer: Michael Mayer <mayermichael79@gmail.com>

Diff between kernelshap versions 0.3.5 dated 2023-03-31 and 0.3.6 dated 2023-05-03

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New package ivDiag with initial version 1.0.4
Package: ivDiag
Title: Estimation and Diagnostic Tools for Instrumental Variables Designs
Version: 1.0.4
Date: 2023-05-01
Maintainer: Yiqing Xu <yiqingxu@stanford.edu>
Description: Estimation and diagnostic tools for instrumental variables designs, which implements the guidelines proposed in Lal et al. (2023) <arXiv:2303.11399>, including bootstrapped standard errors, effective F-statistics, Anderson-Rubin test, valid-t ratio test, and local-to-zero tests.
URL: https://yiqingxu.org/packages/ivDiag/
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Imports: foreach, future, doParallel, lfe, fixest, ggplot2, ggfortify, wCorr, haven, glue, patchwork, testthat
NeedsCompilation: no
Packaged: 2023-05-02 19:18:01 UTC; yiqingxu
Author: Apoorva Lal [aut] , Yiqing Xu [aut, cre]
Repository: CRAN
Date/Publication: 2023-05-03 18:50:02 UTC

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New package GRShiny with initial version 1.0.0
Package: GRShiny
Version: 1.0.0
Title: Graded Response Model
Description: Simulation and analysis of graded response data with different types of estimators. Also, an interactive shiny application is provided with graphics for characteristic and information curves. Samejima (2018) <doi:10.1007/978-1-4757-2691-6_5>.
Depends: R (>= 3.6.0)
Imports: shiny, shinyWidgets, bslib, DT, lavaan, mirt, sirt, ggplot2 (>= 3.4.0), dplyr, readr, tidyr, stringr, magrittr, purrr, data.table, MASS, utils, stats, flextable, gt, officer, openxlsx, sass
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
License: GPL (>= 3)
Encoding: UTF-8
VignetteBuilder: knitr
URL: https://github.com/sooyongl/GRShiny
NeedsCompilation: no
Packaged: 2023-05-02 14:49:53 UTC; sooyong
Author: Sooyong Lee [aut, cre], Tiffany Whittaker [aut], Laura Stapleton [aut]
Maintainer: Sooyong Lee <sooyongl09@gmail.com>
Repository: CRAN
Date/Publication: 2023-05-03 18:40:06 UTC

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New package gor with initial version 1.0
Package: gor
Title: Algorithms for the Subject Graphs and Network Optimization
Version: 1.0
Description: Informal implementation of some algorithms from Graph Theory and Combinatorial Optimization which arise in the subject "Graphs and Network Optimization" from first course of the EUPLA (Escuela Universitaria Politecnica de La Almunia) degree of Data Engineering in Industrial Processes. References used are: Cook et al (1998, ISBN:0-471-55894-X), Korte, Vygen (2018) <doi:10.1007/978-3-662-56039-6>, Hromkovic (2004) <doi:10.1007/978-3-662-05269-3>, Hartmann, Weigt (2005, ISBN:978-3-527-40473-5).
License: GPL-3
Encoding: UTF-8
Depends: igraph, graphics, stats
NeedsCompilation: no
Packaged: 2023-05-02 11:55:32 UTC; admin
Author: Cesar Asensio [aut, cre]
Maintainer: Cesar Asensio <casencha@unizar.es>
Repository: CRAN
Date/Publication: 2023-05-03 18:40:02 UTC

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New package dstabledist with initial version 0.1.0
Package: dstabledist
Title: The Discrete Stable Distribution Functions
Version: 0.1.0
Maintainer: Krutto Annika <annikakrutto@gmail.com>
Description: Probability generating function, formulae for the probabilities (discrete density) and random generation for discrete stable random variables.
License: GPL-3
Encoding: UTF-8
Imports: stabledist, stats, Rdpack
NeedsCompilation: no
Packaged: 2023-05-02 19:57:13 UTC; annikakrutto
Author: Krutto Annika [aut, cre]
Repository: CRAN
Date/Publication: 2023-05-03 18:50:05 UTC

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New package CooccurrenceAffinity with initial version 1.0
Package: CooccurrenceAffinity
Title: Affinity in Co-Occurrence Data
Version: 1.0
Date: 2023-05-02
Description: Computes a novel metric of affinity between two entities based on their co-occurrence (using binary presence/absence data). The metric and its MLE, alpha hat, were advanced in Mainali, Slud, et al, 2021 <doi:10.1126/sciadv.abj9204>. Various types of confidence intervals and median interval were developed in Mainali and Slud, 2022 <doi:10.1101/2022.11.01.514801>.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.1), BiasedUrn (>= 2.0.9)
Imports: cowplot, ggplot2, plyr, reshape
Suggests: cooccur
URL: https://github.com/kpmainali/CooccurrenceAffinity
BugReports: https://github.com/kpmainali/CooccurrenceAffinity/issues
NeedsCompilation: no
Packaged: 2023-05-02 16:46:36 UTC; kpmainali
Author: Kumar Mainali [aut, cre], Eric Slud [aut]
Maintainer: Kumar Mainali <kpmainali@gmail.com>
Repository: CRAN
Date/Publication: 2023-05-03 18:45:42 UTC

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New package BayesRepDesign with initial version 0.42
Package: BayesRepDesign
Version: 0.42
Date: 2023-05-03
Author: Samuel Pawel [aut, cre]
Maintainer: Samuel Pawel <samuel.pawel@uzh.ch>
Title: Bayesian Design of Replication Studies
Description: Provides functionality for determining the sample size of replication studies using Bayesian design approaches in the normal-normal hierarchical model (Pawel et al., 2022) <doi:10.48550/arXiv.2211.02552>.
License: GPL-3
Encoding: UTF-8
Imports: methods, lamW
Suggests: roxygen2, tinytest
NeedsCompilation: no
URL: https://github.com/SamCH93/BayesRepDesign
BugReports: https://github.com/SamCH93/BayesRepDesign/issues
Packaged: 2023-05-03 07:42:49 UTC; sam
Repository: CRAN
Date/Publication: 2023-05-03 18:55:43 UTC

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New package Achilles with initial version 1.7.1
Package: Achilles
Title: Achilles Data Source Characterization
Version: 1.7.1
Date: 2023-05-01
Maintainer: Frank DeFalco <fdefalco@ohdsi.org>
Description: Automated Characterization of Health Information at Large-Scale Longitudinal Evidence Systems. Creates a descriptive statistics summary for an Observational Medical Outcomes Partnership Common Data Model standardized data source. This package includes functions for executing summary queries on the specified data source and exporting reporting content for use across a variety of Observational Health Data Sciences and Informatics community applications.
Depends: DatabaseConnector (>= 2.0.0), R (>= 4.0.0)
Imports: SqlRender (>= 1.6.0), dplyr, jsonlite, ParallelLogger, readr, data.table, lubridate, tseries, rlang
Suggests: DT, magrittr, tidyr, knitr, rmarkdown, testthat (>= 3.0.0), withr
VignetteBuilder: knitr
License: Apache License
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-05-01 19:34:27 UTC; admin_fdefalco
Author: Frank DeFalco [aut, cre], Patrick Ryan [aut], Martijn Schuemie [aut], Vojtech Huser [aut], Chris Knoll [aut], Ajit Londhe [aut], Taha Abdul-Basser [aut], Anthony Molinaro [aut], Observational Health Data Science and Informatics [cph]
Repository: CRAN
Date/Publication: 2023-05-03 18:15:35 UTC

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Package KernSmooth updated to version 2.23-21 with previous version 2.23-20 dated 2021-05-03

Title: Functions for Kernel Smoothing Supporting Wand & Jones (1995)
Description: Functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) "Kernel Smoothing".
Author: Matt Wand [aut], Cleve Moler [ctb] , Brian Ripley [trl, cre, ctb]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between KernSmooth versions 2.23-20 dated 2021-05-03 and 2.23-21 dated 2023-05-03

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Package showtext updated to version 0.9-6 with previous version 0.9-5 dated 2022-02-09

Title: Using Fonts More Easily in R Graphs
Description: Making it easy to use various types of fonts ('TrueType', 'OpenType', Type 1, web fonts, etc.) in R graphs, and supporting most output formats of R graphics including PNG, PDF and SVG. Text glyphs will be converted into polygons or raster images, hence after the plot has been created, it no longer relies on the font files. No external software such as 'Ghostscript' is needed to use this package.
Author: Yixuan Qiu and authors/contributors of the included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>

Diff between showtext versions 0.9-5 dated 2022-02-09 and 0.9-6 dated 2023-05-03

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Package varTestnlme updated to version 1.3.2 with previous version 1.3.1 dated 2022-03-08

Title: Variance Components Testing for Linear and Nonlinear Mixed Effects Models
Description: An implementation of the Likelihood ratio Test (LRT) for testing that, in a (non)linear mixed effects model, the variances of a subset of the random effects are equal to zero. There is no restriction on the subset of variances that can be tested: for example, it is possible to test that all the variances are equal to zero. Note that the implemented test is asymptotic. This package should be used on model fits from packages 'nlme', 'lmer', and 'saemix'. Charlotte Baey, Paul-Henry Cournède and Estelle Kuhn (2019) <doi:10.1016/j.csda.2019.01.014>.
Author: Charlotte Baey [aut, cre] , Estelle Kuhn [aut]
Maintainer: Charlotte Baey <charlotte.baey@univ-lille.fr>

Diff between varTestnlme versions 1.3.1 dated 2022-03-08 and 1.3.2 dated 2023-05-03

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Package OneSampleMR updated to version 0.1.3 with previous version 0.1.2 dated 2022-05-11

Title: One Sample Mendelian Randomization and Instrumental Variable Analyses
Description: Useful functions for one-sample (individual level data) Mendelian randomization and instrumental variable analyses. The package includes implementations of; the Sanderson and Windmeijer (2016) <doi:10.1016/j.jeconom.2015.06.004> conditional F-statistic, the multiplicative structural mean model Hernán and Robins (2006) <doi:10.1097/01.ede.0000222409.00878.37>, and two-stage predictor substitution and two-stage residual inclusion estimators explained by Terza et al. (2008) <doi:10.1016/j.jhealeco.2007.09.009>.
Author: Tom Palmer [aut, cre] , Wes Spiller [aut] , Eleanor Sanderson [aut]
Maintainer: Tom Palmer <remlapmot@hotmail.com>

Diff between OneSampleMR versions 0.1.2 dated 2022-05-11 and 0.1.3 dated 2023-05-03

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Package miscTools updated to version 0.6-28 with previous version 0.6-26 dated 2019-12-08

Title: Miscellaneous Tools and Utilities
Description: Miscellaneous small tools and utilities. Many of them facilitate the work with matrices, e.g. inserting rows or columns, creating symmetric matrices, or checking for semidefiniteness. Other tools facilitate the work with regression models, e.g. extracting the standard errors, obtaining the number of (estimated) parameters, or calculating R-squared values.
Author: Arne Henningsen, Ott Toomet
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>

Diff between miscTools versions 0.6-26 dated 2019-12-08 and 0.6-28 dated 2023-05-03

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Package gcplyr updated to version 1.5.2 with previous version 1.5.1 dated 2023-04-14

Title: Manipulate and Analyze Growth Curve Data
Description: Easy import, manipulation, and model-free analysis of microbial growth curve data, as commonly output by plate readers. Tools for reshaping common plate reader outputs into 'tidy' formats and merging them with design information, making data easy to work with using 'gcplyr' and other packages. Also streamlines common growth curve processing steps, like smoothing and calculating derivatives, and facilitates model-free characterization and analysis of growth data. See methods at <https://mikeblazanin.github.io/gcplyr/>.
Author: Mike Blazanin [aut, cre]
Maintainer: Mike Blazanin <mikeblazanin@gmail.com>

Diff between gcplyr versions 1.5.1 dated 2023-04-14 and 1.5.2 dated 2023-05-03

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Package FIESTA updated to version 3.5.3 with previous version 3.5.2 dated 2023-04-13

Title: Forest Inventory Estimation and Analysis
Description: A research estimation tool for analysts that work with sample-based inventory data from the U.S. Department of Agriculture, Forest Service, Forest Inventory and Analysis (FIA) Program.
Author: Tracey Frescino [aut], Gretchen Moisen [aut], Paul Patterson [aut], Chris Toney [aut], Grayson White [aut, cre]
Maintainer: Grayson White <graysonwhite13@gmail.com>

Diff between FIESTA versions 3.5.2 dated 2023-04-13 and 3.5.3 dated 2023-05-03

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New package wooldridge with initial version 1.4-3
Package: wooldridge
Title: 115 Data Sets from "Introductory Econometrics: A Modern Approach, 7e" by Jeffrey M. Wooldridge
Version: 1.4-3
Description: Students learning both econometrics and R may find the introduction to both challenging. The wooldridge data package aims to lighten the task by efficiently loading any data set found in the text with a single command. Data sets have been compressed to a fraction of their original size. Documentation files contain page numbers, the original source, time of publication, and notes from the author suggesting avenues for further analysis and research. If one needs an introduction to R model syntax, a vignette contains solutions to examples from chapters of the text. Data sets are from the 7th edition (Wooldridge 2020, ISBN-13 978-1-337-55886-0), and are backwards compatible with all previous versions of the text.
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown, stargazer, tinytest, xts, zoo
VignetteBuilder: knitr
LazyDataCompression: xz
URL: https://justinmshea.github.io/wooldridge/
BugReports: https://github.com/JustinMShea/wooldridge/issues/
NeedsCompilation: no
Packaged: 2023-05-03 10:06:55 UTC; impartial-spec
Author: Justin M. Shea [aut, cre], Kennth H. Brown [ctb]
Maintainer: Justin M. Shea <jshea@roosevelt.edu>
Repository: CRAN
Date/Publication: 2023-05-03 11:30:02 UTC

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New package RMediation with initial version 1.2.1
Package: RMediation
Title: Mediation Analysis Confidence Intervals
Version: 1.2.1
Date: 2023-04-28
Depends: R (>= 3.5.0), base (>= 3.5.0), stats (>= 3.5.0), graphics (>= 3.5.0), methods (>= 3.5.0), lavaan (>= 0.5-20), e1071 (>= 1.6-7), OpenMx (>= 2.13), MASS (>= 7.3)
Imports: modelr (>= 0.1.4), doParallel (>= 1.0.0), foreach (>= 1.5.0), iterators (>= 1.0.0), stringr(>= 1.4.0), grDevices (>= 4.3)
Suggests: knitr, rmarkdown
LazyData: true
Description: We provide functions to compute confidence intervals for a well-defined nonlinear function of the model parameters (e.g., product of k coefficients) in single--level and multilevel structural equation models. It also computes a chi-square test statistic for a function of indirect effects. 'Tofighi', D. and 'MacKinnon', D. P. (2011). 'RMediation' An R package for mediation analysis confidence intervals. Behavior Research Methods, 43, 692--700. <doi:10.3758/s13428-011-0076-x>. 'Tofighi', D. (2020). Bootstrap Model-Based Constrained Optimization Tests of Indirect Effects. Frontiers in Psychology, 10, 2989. <doi:10.3389/fpsyg.2019.02989>.
License: GPL-2
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-05-03 01:14:21 UTC; davoodtofighi
Author: Davood Tofighi [aut, cre]
Maintainer: Davood Tofighi <dtofighi@gmail.com>
Repository: CRAN
Date/Publication: 2023-05-03 11:30:12 UTC

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Package pkgmaker updated to version 0.32.10 with previous version 0.32.8 dated 2023-02-14

Title: Development Utilities for R Packages
Description: Provides some low-level utilities to use for package development. It currently provides managers for multiple package specific options and registries, vignette, unit test and bibtex related utilities. It serves as a base package for packages like 'NMF', 'RcppOctave', 'doRNG', and as an incubator package for other general purposes utilities, that will eventually be packaged separately. It is still under heavy development and changes in the interface(s) are more than likely to happen.
Author: Renaud Gaujoux [aut, cre]
Maintainer: Renaud Gaujoux <renozao@protonmail.com>

Diff between pkgmaker versions 0.32.8 dated 2023-02-14 and 0.32.10 dated 2023-05-03

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Package nnet updated to version 7.3-19 with previous version 7.3-18 dated 2022-09-28

Title: Feed-Forward Neural Networks and Multinomial Log-Linear Models
Description: Software for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models.
Author: Brian Ripley [aut, cre, cph], William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between nnet versions 7.3-18 dated 2022-09-28 and 7.3-19 dated 2023-05-03

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Package Infusion updated to version 2.1.0 with previous version 2.0.0 dated 2022-09-28

Title: Inference Using Simulation
Description: Implements functions for simulation-based inference. In particular, implements functions to perform likelihood inference from data summaries whose distributions are simulated. A first approach was described in Rousset et al. (2017 <doi:10.1111/1755-0998.12627>) but the package implements more advanced methods.
Author: Francois Rousset [aut, cre, cph]
Maintainer: Francois Rousset <francois.rousset@umontpellier.fr>

Diff between Infusion versions 2.0.0 dated 2022-09-28 and 2.1.0 dated 2023-05-03

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Package gawdis updated to version 0.1.5 with previous version 0.1.4 dated 2023-04-13

Title: Multi-Trait Dissimilarity with more Uniform Contributions
Description: R function gawdis() produces multi-trait dissimilarity with more uniform contributions of different traits. de Bello et al. (2021) <doi:10.1111/2041-210X.13537> presented the approach based on minimizing the differences in the correlation between the dissimilarity of each trait, or groups of traits, and the multi-trait dissimilarity. This is done using either an analytic or a numerical solution, both available in the function.
Author: Francesco de Bello [aut], Zoltan Botta-Dukat [aut], Jan Leps [aut], Pavel Fibich [aut, cre]
Maintainer: Pavel Fibich <pavel.fibich@prf.jcu.cz>

Diff between gawdis versions 0.1.4 dated 2023-04-13 and 0.1.5 dated 2023-05-03

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Package class updated to version 7.3-22 with previous version 7.3-21 dated 2023-01-23

Title: Functions for Classification
Description: Various functions for classification, including k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.
Author: Brian Ripley [aut, cre, cph], William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between class versions 7.3-21 dated 2023-01-23 and 7.3-22 dated 2023-05-03

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Package baseq updated to version 0.1.4 with previous version 0.1.2 dated 2023-04-28

Title: Basic Sequence Processing Tool for Biological Data
Description: Primarily created as an easy and understanding way to do basic sequences surrounding the central dogma of molecular biology.
Author: Ambu Vijayan [aut, cre] , J. Sreekumar [aut]
Maintainer: Ambu Vijayan <ambuvjyn@gmail.com>

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Package mlr3spatial updated to version 0.4.1 with previous version 0.4.0 dated 2023-02-27

Title: Support for Spatial Objects Within the 'mlr3' Ecosystem
Description: Extends the 'mlr3' ML framework with methods for spatial objects. Data storage and prediction are supported for packages 'terra', 'raster' and 'stars'.
Author: Marc Becker [aut, cre] , Patrick Schratz [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>

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Package diversitree updated to version 0.9-18 with previous version 0.9-16 dated 2021-06-11

Title: Comparative 'Phylogenetic' Analyses of Diversification
Description: Contains a number of comparative 'phylogenetic' methods, mostly focusing on analysing diversification and character evolution. Contains implementations of 'BiSSE' (Binary State 'Speciation' and Extinction) and its unresolved tree extensions, 'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE', 'GeoSSE', and 'BiSSE-ness' Other included methods include Markov models of discrete and continuous trait evolution and constant rate 'speciation' and extinction.
Author: Richard G. FitzJohn [aut, cre], Emma Goldberg [aut], Karen Magnuson-Ford [aut], Roger Sidje [aut]
Maintainer: Richard G. FitzJohn <rich.fitzjohn@gmail.com>

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Package difNLR updated to version 1.4.2-1 with previous version 1.4.1 dated 2022-04-18

Title: DIF and DDF Detection by Non-Linear Regression Models
Description: Detection of differential item functioning (DIF) among dichotomously scored items and differential distractor functioning (DDF) among unscored items with non-linear regression procedures based on generalized logistic regression models (Hladka & Martinkova, 2020, <doi:10.32614/RJ-2020-014>).
Author: Adela Hladka [aut, cre], Patricia Martinkova [aut], Karel Zvara [ctb]
Maintainer: Adela Hladka <hladka@cs.cas.cz>

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Package survey updated to version 4.2-1 with previous version 4.1-1 dated 2021-07-19

Title: Analysis of Complex Survey Samples
Description: Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase subsampling designs. Graphics. PPS sampling without replacement.
Author: Thomas Lumley
Maintainer: "Thomas Lumley" <t.lumley@auckland.ac.nz>

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Package OralOpioids updated to version 1.1.0 with previous version 1.0.1 dated 2023-03-03

Title: Retrieving Oral Opioid Information
Description: Provides details such as Morphine Equivalent Dose (MED), brand name and opioid content which are calculated of all oral opioids authorized for sale by Health Canada based on their Drug Identification Number (DIN). MEDs are calculated based on recommendations by Canadian Institute for Health Information (CIHI) and information obtained from Health Canada's Drug Product Database's monthly data dump. Please note in no way should output from this package be a substitute for medical advise. All medications should only be consumed on prescription from a licensed healthcare provider.
Author: Ankona Banerjee [aut, cre] , Erik Stricker [aut]
Maintainer: Ankona Banerjee <asb426@mail.usask.ca>

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Package fauxpas updated to version 0.5.2 with previous version 0.5.0 dated 2020-04-13

Title: HTTP Error Helpers
Description: HTTP error helpers. Methods included for general purpose HTTP error handling, as well as individual methods for every HTTP status code, both via status code numbers as well as their descriptive names. Supports ability to adjust behavior to stop, message or warning. Includes ability to use custom whisker template to have any configuration of status code, short description, and verbose message. Currently supports integration with 'crul', 'curl', and 'httr'.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package secsse updated to version 2.5.0 with previous version 2.1.7 dated 2021-07-16

Title: Several Examined and Concealed States-Dependent Speciation and Extinction
Description: Simultaneously infers state-dependent diversification across two or more states of a single or multiple traits while accounting for the role of a possible concealed trait. See Herrera-Alsina et al. (2019) <doi:10.1093/sysbio/syy057>.
Author: Leonel Herrera Alsina [aut] , Paul van Els [aut] , Thijs Janzen [ctb] , Hanno Hildenbrandt [ctb] , Rampal S. Etienne [cre, aut]
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>

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Package logistf updated to version 1.25.0 with previous version 1.24.1 dated 2022-01-18

Title: Firth's Bias-Reduced Logistic Regression
Description: Fit a logistic regression model using Firth's bias reduction method, equivalent to penalization of the log-likelihood by the Jeffreys prior. Confidence intervals for regression coefficients can be computed by penalized profile likelihood. Firth's method was proposed as ideal solution to the problem of separation in logistic regression, see Heinze and Schemper (2002) <doi:10.1002/sim.1047>. If needed, the bias reduction can be turned off such that ordinary maximum likelihood logistic regression is obtained. Two new modifications of Firth's method, FLIC and FLAC, lead to unbiased predictions and are now available in the package as well, see Puhr et al (2017) <doi:10.1002/sim.7273>.
Author: Georg Heinze [aut, cre], Meinhard Ploner [aut], Daniela Dunkler [ctb], Harry Southworth [ctb], Lena Jiricka [aut], Gregor Steiner [aut]
Maintainer: Georg Heinze <georg.heinze@meduniwien.ac.at>

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Package blackbox updated to version 1.1.43 with previous version 1.1.32 dated 2020-04-20

Title: Black Box Optimization and Exploration of Parameter Space
Description: Performs prediction of a response function from simulated response values, allowing black-box optimization of functions estimated with some error. Includes a simple user interface for such applications, as well as more specialized functions designed to be called by the Migraine software (Rousset and Leblois, 2012 <doi:10.1093/molbev/MSR262>; Leblois et al., 2014 <doi:10.1093/molbev/msu212>; and see URL). The latter functions are used for prediction of likelihood surfaces and implied likelihood ratio confidence intervals, and for exploration of predictor space of the surface. Prediction of the response is based on ordinary Kriging (with residual error) of the input. Estimation of smoothing parameters is performed by generalized cross-validation.
Author: Francois Rousset [aut, cre, cph] , Raphael Leblois [ctb]
Maintainer: Francois Rousset <francois.rousset@umontpellier.fr>

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Package wooldridge (with last version 1.4-2) was removed from CRAN

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

2021-11-08 1.4-2
2021-06-24 1.4-1
2018-10-10 1.3.1
2018-04-09 1.3.0
2017-09-05 1.2.0
2017-08-29 1.1.0
2017-07-11 1.0.1

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Package lefko3 updated to version 6.0.5 with previous version 6.0.0 dated 2023-03-27

Title: Historical and Ahistorical Population Projection Matrix Analysis
Description: Complete analytical environment for the construction and analysis of matrix population models and integral projection models. Includes the ability to construct historical matrices, which are 2d matrices comprising 3 consecutive times of demographic information. Estimates both raw and function-based forms of historical and standard ahistorical matrices. It also estimates function-based age-by-stage matrices and raw and function-based Leslie matrices.
Author: Richard P. Shefferson [aut, cre] , Johan Ehrlen [aut]
Maintainer: Richard P. Shefferson <cdorm@g.ecc.u-tokyo.ac.jp>

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Package spMC updated to version 0.3.15 with previous version 0.3.12 dated 2022-06-11

Title: Continuous-Lag Spatial Markov Chains
Description: A set of functions is provided for 1) the stratum lengths analysis along a chosen direction, 2) fast estimation of continuous lag spatial Markov chains model parameters and probability computing (also for large data sets), 3) transition probability maps and transiograms drawing, 4) simulation methods for categorical random fields. More details on the methodology are discussed in Sartore (2013) <doi:10.32614/RJ-2013-022> and Sartore et al. (2016) <doi:10.1016/j.cageo.2016.06.001>.
Author: Luca Sartore [aut, cre]
Maintainer: Luca Sartore <drwolf85@gmail.com>

Diff between spMC versions 0.3.12 dated 2022-06-11 and 0.3.15 dated 2023-05-03

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Package bizicount updated to version 1.3.2 with previous version 1.3.1 dated 2023-03-16

Title: Bivariate Zero-Inflated Count Models Using Copulas
Description: Maximum likelihood estimation of copula-based zero-inflated (and non-inflated) Poisson and negative binomial count models. Supports Frank and Gaussian copulas. Allows for mixed margins (e.g., one margin Poisson, the other zero-inflated negative binomial), and several marginal link functions. Built-in methods for publication-quality tables using 'texreg', post-estimation diagnostics using 'DHARMa', and testing for marginal zero-modification via <doi:10.1177/0962280217749991>. For information on copula regression for count data, see Genest and Nešlehová (2007) <doi:10.1017/S0515036100014963> as well as Nikoloulopoulos (2013) <doi:10.1007/978-3-642-35407-6_11>. For information on zero-inflated count regression generally, see Lambert (1992) <https:www.jstor.org/stable/1269547?origin=crossref>. The author acknowledges support by NSF DMS-1925119 and DMS-212324.
Author: John Niehaus [aut, cre]
Maintainer: John Niehaus <jniehaus2257@gmail.com>

Diff between bizicount versions 1.3.1 dated 2023-03-16 and 1.3.2 dated 2023-05-03

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