Sun, 26 Nov 2023

Package formods updated to version 0.1.2 with previous version 0.1.1 dated 2023-08-17

Title: 'Shiny' Modules for General Tasks
Description: 'Shiny' apps can often make use of the same key elements, this package provides modules for common tasks (data upload, wrangling data, figure generation and saving the app state). These modules can react and interact as well as generate code to create reproducible analyses.
Author: John Harrold [aut, cre]
Maintainer: John Harrold <john.m.harrold@gmail.com>

Diff between formods versions 0.1.1 dated 2023-08-17 and 0.1.2 dated 2023-11-26

 DESCRIPTION                            |    8 
 MD5                                    |   70 +
 NAMESPACE                              |    5 
 NEWS.md                                |   11 
 R/ASM_Server.R                         |   28 
 R/DW_Server.R                          |   12 
 R/UD_Server.R                          |    2 
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Package stratallo updated to version 2.2.1 with previous version 2.2.0 dated 2023-06-24

Title: Optimum Sample Allocation in Stratified Sampling
Description: Functions in this package provide solution to classical problem in survey methodology - an optimum sample allocation in stratified sampling. In this context, the optimum allocation is in the classical Tschuprow-Neyman's sense and it satisfies additional lower or upper bounds restrictions imposed on sample sizes in strata. There are few different algorithms available to use, and one them is based on popular sample allocation method that applies Neyman allocation to recursively reduced set of strata. This package also provides the function that computes a solution to the minimum cost allocation problem, which is a minor modification of the classical optimum sample allocation. This problem lies in the determination of a vector of strata sample sizes that minimizes total cost of the survey, under assumed fixed level of the stratified estimator's variance. As in the case of the classical optimum allocation, the problem of minimum cost allocation can be complemented by imposing upper-bounds [...truncated...]
Author: Wojciech Wojciak [aut, cre], Jacek Wesolowski [sad], Robert Wieczorkowski [ctb]
Maintainer: Wojciech Wojciak <wojciech.wojciak@gmail.com>

Diff between stratallo versions 2.2.0 dated 2023-06-24 and 2.2.1 dated 2023-11-26

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 stratallo-2.2.1/stratallo/NEWS.md                                  |    9 
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 stratallo-2.2.1/stratallo/tests/testthat/test-algorithms_rna_rec.R |   42 
 stratallo-2.2.1/stratallo/tests/testthat/test-algorithms_rnabox.R  |  216 ++++-
 stratallo-2.2.1/stratallo/tests/testthat/test-algorithms_sga.R     |   22 
 stratallo-2.2.1/stratallo/tests/testthat/test-algorithms_sgaplus.R |   22 
 stratallo-2.2.1/stratallo/tests/testthat/test-helpers.R            |   22 
 stratallo-2.2.1/stratallo/tests/testthat/test-opt.R                |  272 +++---
 stratallo-2.2.1/stratallo/tests/testthat/test-optcost.R            |  240 ++---
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 40 files changed, 2010 insertions(+), 1576 deletions(-)

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Package stochvol updated to version 3.2.3 with previous version 3.2.1 dated 2023-03-10

Title: Efficient Bayesian Inference for Stochastic Volatility (SV) Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models with and without asymmetry (leverage) via Markov chain Monte Carlo (MCMC) methods. Methodological details are given in Kastner and Fr├╝hwirth-Schnatter (2014) <doi:10.1016/j.csda.2013.01.002> and Hosszejni and Kastner (2019) <doi:10.1007/978-3-030-30611-3_8>; the most common use cases are described in Hosszejni and Kastner (2021) <doi:10.18637/jss.v100.i12> and Kastner (2016) <doi:10.18637/jss.v069.i05> and the package examples.
Author: Darjus Hosszejni [aut, cre] , Gregor Kastner [aut]
Maintainer: Darjus Hosszejni <darjus.hosszejni@icloud.com>

Diff between stochvol versions 3.2.1 dated 2023-03-10 and 3.2.3 dated 2023-11-26

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Package sp updated to version 2.1-2 with previous version 2.1-1 dated 2023-10-16

Title: Classes and Methods for Spatial Data
Description: Classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc. From this version, 'rgdal', 'maptools', and 'rgeos' are no longer used at all, see <https://r-spatial.org/r/2023/05/15/evolution4.html> for details.
Author: Edzer Pebesma [aut, cre], Roger Bivand [aut], Barry Rowlingson [ctb], Virgilio Gomez-Rubio [ctb], Robert Hijmans [ctb], Michael Sumner [ctb], Don MacQueen [ctb], Jim Lemon [ctb], Finn Lindgren [ctb], Josh O'Brien [ctb], Joseph O'Rourke [ctb], Patrick [...truncated...]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

Diff between sp versions 2.1-1 dated 2023-10-16 and 2.1-2 dated 2023-11-26

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 MD5                                 |   24 ++++++++++++------------
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 src/sp.h                            |    2 +-
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 src/zerodist.c                      |    8 ++++----
 13 files changed, 36 insertions(+), 23 deletions(-)

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New package simEd with initial version 2.0.1
Package: simEd
Title: Simulation Education
Version: 2.0.1
Imports: graphics, grDevices, methods, stats, utils, shape
Depends: rstream
Suggests: magick
Description: Contains various functions to be used for simulation education, including simple Monte Carlo simulation functions, queueing simulation functions, variate generation functions capable of producing independent streams and antithetic variates, functions for illustrating random variate generation for various discrete and continuous distributions, and functions to compute time-persistent statistics. Also contains functions for visualizing: event-driven details of a single-server queue model; a Lehmer random number generator; variate generation via acceptance-rejection; and of generating a non-homogeneous Poisson process via thinning. Also contains two queueing data sets (one fabricated, one real-world) to facilitate input modeling. More details on the use of these functions can be found in Lawson and Leemis (2015) <doi:10.1109/WSC.2017.8248124>, in Kudlay, Lawson, and Leemis (2020) <doi:10.1109/WSC48552.2020.9384010>, and in Lawson and Leemis (2021) <doi:10.1109/WSC52266.2 [...truncated...]
License: MIT + file LICENSE
LazyData: true
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-11-26 13:08:36 UTC; blawson
Author: Barry Lawson [aut, cre, cph], Larry Leemis [aut], Vadim Kudlay [aut]
Maintainer: Barry Lawson <blawson@bates.edu>
Repository: CRAN
Date/Publication: 2023-11-26 23:20:13 UTC

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Package seriation updated to version 1.5.2 with previous version 1.5.1 dated 2023-07-20

Title: Infrastructure for Ordering Objects Using Seriation
Description: Infrastructure for ordering objects with an implementation of several seriation/sequencing/ordination techniques to reorder matrices, dissimilarity matrices, and dendrograms. Also provides (optimally) reordered heatmaps, color images and clustering visualizations like dissimilarity plots, and visual assessment of cluster tendency plots (VAT and iVAT). Hahsler et al (2008) <doi:10.18637/jss.v025.i03>.
Author: Michael Hahsler [aut, cre, cph] , Christian Buchta [aut, cph], Kurt Hornik [aut, cph] , David Barnett [ctb], Michael Brusco [ctb, cph], Michael Friendly [ctb], Hans-Friedrich Koehn [ctb, cph], Fionn Murtagh [ctb, cph], Stephanie Stahl [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

Diff between seriation versions 1.5.1 dated 2023-07-20 and 1.5.2 dated 2023-11-26

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 seriation-1.5.2/seriation/NEWS.md                               |   22 +-
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 seriation-1.5.2/seriation/R/AAA_registry_criterion.R            |    4 
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 seriation-1.5.2/seriation/R/Zoo.R                               |    9 
 seriation-1.5.2/seriation/R/criterion.dist.R                    |    5 
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 seriation-1.5.2/seriation/src/init.c                            |    4 
 seriation-1.5.2/seriation/src/nextperm.c                        |    2 
 seriation-1.5.2/seriation/src/optimal.c                         |    7 
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 53 files changed, 486 insertions(+), 292 deletions(-)

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Package nleqslv updated to version 3.3.5 with previous version 3.3.4 dated 2023-01-14

Title: Solve Systems of Nonlinear Equations
Description: Solve a system of nonlinear equations using a Broyden or a Newton method with a choice of global strategies such as line search and trust region. There are options for using a numerical or user supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a singular or ill-conditioned Jacobian.
Author: Berend Hasselman
Maintainer: Berend Hasselman <bhh@xs4all.nl>

Diff between nleqslv versions 3.3.4 dated 2023-01-14 and 3.3.5 dated 2023-11-26

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New package accrual with initial version 1.4
Package: accrual
Title: Bayesian Accrual Prediction
Version: 1.4
Date: 2023-11-23
Maintainer: Junhao Liu <liujunhao2008@gmail.com>
Depends: R(>= 3.1.3), tcltk2
Imports: fgui, SMPracticals
Description: Participant recruitment for medical research is challenging. Slow accrual leads to delays in research. Accrual monitoring during the process of recruitment is critical. Researchers need reliable tools to manage the accrual rate. We developed a Bayesian method that integrates the researcher's experience with previous trials and data from the current study, providing reliable predictions on accrual rate for clinical studies. For more details and background on these methodologies, see the publications of Byron, Stephen and Susan (2008) <doi:10.1002/sim.3128>, and Yu et al. (2015) <doi:10.1002/sim.6359>. In this R package, Bayesian accrual prediction functions are presented, which can be easily used by statisticians and clinical researchers.
License: GPL-2
Encoding: UTF-8
LazyLoad: true
NeedsCompilation: no
Packaged: 2023-11-26 18:08:02 UTC; disne
Author: Junhao Liu [aut, cre] , Yu Jiang [aut] , Cen Wu [aut], Steve Simon [aut], Matthew S. Mayo [aut], Rama Raghavan [aut], Byron J. Gajewski [aut]
Repository: CRAN
Date/Publication: 2023-11-26 23:20:19 UTC

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Package bskyr updated to version 0.1.0 with previous version 0.0.4 dated 2023-11-10

Title: Interact with 'Bluesky' Social
Description: Collect data from and make posts on 'Bluesky' Social via the Hypertext Transfer Protocol (HTTP) Application Programming Interface (API), as documented at <https://atproto.com/specs/xrpc>. This further supports broader queries to the Authenticated Transfer (AT) Protocol <https://atproto.com/> which 'Bluesky' Social relies on. Data is returned in a tidy format and posts can be made using a simple interface.
Author: Christopher T. Kenny [aut, cre]
Maintainer: Christopher T. Kenny <christopherkenny@fas.harvard.edu>

Diff between bskyr versions 0.0.4 dated 2023-11-10 and 0.1.0 dated 2023-11-26

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 bskyr-0.1.0/bskyr/R/graph_actor_lists.R                                 |   33 +
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 bskyr-0.1.0/bskyr/R/graph_blocks.R                                      |   83 ++--
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 bskyr-0.1.0/bskyr/R/graph_follows.R                                     |  119 +++---
 bskyr-0.1.0/bskyr/R/graph_list.R                                        |  120 +++---
 bskyr-0.1.0/bskyr/R/graph_muted_lists.R                                 |   69 +--
 bskyr-0.1.0/bskyr/R/graph_mutes.R                                       |   83 ++--
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Package RQuantLib updated to version 0.4.20 with previous version 0.4.19 dated 2023-08-07

Title: R Interface to the 'QuantLib' Library
Description: The 'RQuantLib' package makes parts of 'QuantLib' accessible from R The 'QuantLib' project aims to provide a comprehensive software framework for quantitative finance. The goal is to provide a standard open source library for quantitative analysis, modeling, trading, and risk management of financial assets.
Author: Dirk Eddelbuettel, Khanh Nguyen , Terry Leitch
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RQuantLib versions 0.4.19 dated 2023-08-07 and 0.4.20 dated 2023-11-26

 ChangeLog               |   22 ++++++++++
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More information about RQuantLib at CRAN
Permanent link

Package PMCMRplus updated to version 1.9.9 with previous version 1.9.8 dated 2023-10-09

Title: Calculate Pairwise Multiple Comparisons of Mean Rank Sums Extended
Description: For one-way layout experiments the one-way ANOVA can be performed as an omnibus test. All-pairs multiple comparisons tests (Tukey-Kramer test, Scheffe test, LSD-test) and many-to-one tests (Dunnett test) for normally distributed residuals and equal within variance are available. Furthermore, all-pairs tests (Games-Howell test, Tamhane's T2 test, Dunnett T3 test, Ury-Wiggins-Hochberg test) and many-to-one (Tamhane-Dunnett Test) for normally distributed residuals and heterogeneous variances are provided. Van der Waerden's normal scores test for omnibus, all-pairs and many-to-one tests is provided for non-normally distributed residuals and homogeneous variances. The Kruskal-Wallis, BWS and Anderson-Darling omnibus test and all-pairs tests (Nemenyi test, Dunn test, Conover test, Dwass-Steele-Critchlow- Fligner test) as well as many-to-one (Nemenyi test, Dunn test, U-test) are given for the analysis of variance by ranks. Non-parametric trend tests (Jonckheere test, Cuzick test, Johnson-Mehr [...truncated...]
Author: Thorsten Pohlert [aut, cre]
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>

Diff between PMCMRplus versions 1.9.8 dated 2023-10-09 and 1.9.9 dated 2023-11-26

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Package foreign updated to version 0.8-86 with previous version 0.8-85 dated 2023-09-09

Title: Read Data Stored by 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', 'dBase', ...
Description: Reading and writing data stored by some versions of 'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', and for reading and writing some 'dBase' files.
Author: R Core Team [aut, cph, cre], Roger Bivand [ctb, cph], Vincent J. Carey [ctb, cph], Saikat DebRoy [ctb, cph], Stephen Eglen [ctb, cph], Rajarshi Guha [ctb, cph], Swetlana Herbrandt [ctb], Nicholas Lewin-Koh [ctb, cph], Mark Myatt [ctb, cph], Michael N [...truncated...]
Maintainer: R Core Team <R-core@R-project.org>

Diff between foreign versions 0.8-85 dated 2023-09-09 and 0.8-86 dated 2023-11-26

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Package shinyTempSignal updated to version 0.0.4 with previous version 0.0.3 dated 2022-07-06

Title: Explore Temporal Signal of Molecular Phylogenies
Description: Sequences sampled at different time points can be used to infer molecular phylogenies on natural time scales, but if the sequences records inaccurate sampling times, that are not the actual sampling times, then it will affect the molecular phylogenetic analysis. This shiny application helps exploring temporal characteristics of the evolutionary trees through linear regression analysis and with the ability to identify and remove incorrect labels.
Author: Guangchuang Yu [aut, cre, cph] , Xuanan Zhu [aut], Jianfeng Lin [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between shinyTempSignal versions 0.0.3 dated 2022-07-06 and 0.0.4 dated 2023-11-26

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Package git2r updated to version 0.33.0 with previous version 0.32.0 dated 2023-04-12

Title: Provides Access to Git Repositories
Description: Interface to the 'libgit2' library, which is a pure C implementation of the 'Git' core methods. Provides access to 'Git' repositories to extract data and running some basic 'Git' commands.
Author: See AUTHORS file.
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>

Diff between git2r versions 0.32.0 dated 2023-04-12 and 0.33.0 dated 2023-11-26

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Package actxps updated to version 1.4.0 with previous version 1.3.0 dated 2023-09-15

Title: Create Actuarial Experience Studies: Prepare Data, Summarize Results, and Create Reports
Description: Experience studies are used by actuaries to explore historical experience across blocks of business and to inform assumption setting activities. This package provides functions for preparing data, creating studies, visualizing results, and beginning assumption development. Experience study methods, including exposure calculations, are described in: Atkinson & McGarry (2016) "Experience Study Calculations" <https://www.soa.org/49378a/globalassets/assets/files/research/experience-study-calculations.pdf>. The limited fluctuation credibility method used by the 'exp_stats()' function is described in: Herzog (1999, ISBN:1-56698-374-6) "Introduction to Credibility Theory".
Author: Matt Heaphy [aut, cre]
Maintainer: Matt Heaphy <mattrmattrs@gmail.com>

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Package phylosem updated to version 1.1.1 with previous version 1.1.0 dated 2023-10-06

Title: Phylogenetic Structural Equation Model
Description: Applies phylogenetic comparative methods (PCM) and phylogenetic trait imputation using structural equation models (SEM), extending methods from Thorson et al. (2023) <doi:10.1111/2041-210X.14076>. This implementation includes a minimal set of features, to allow users to easily read all of the documentation and source code. PCM using SEM includes phylogenetic linear models and structural equation models as nested submodels, but also allows imputation of missing values. Features and comparison with other packages are described in Thorson and van der Bijl (In press).
Author: James Thorson [aut, cre] , Wouter van der Bijl [ctb]
Maintainer: James Thorson <James.Thorson@noaa.gov>

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Package semtree updated to version 0.9.19 with previous version 0.9.18 dated 2022-05-13

Title: Recursive Partitioning for Structural Equation Models
Description: SEM Trees and SEM Forests -- an extension of model-based decision trees and forests to Structural Equation Models (SEM). SEM trees hierarchically split empirical data into homogeneous groups each sharing similar data patterns with respect to a SEM by recursively selecting optimal predictors of these differences. SEM forests are an extension of SEM trees. They are ensembles of SEM trees each built on a random sample of the original data. By aggregating over a forest, we obtain measures of variable importance that are more robust than measures from single trees. A description of the method was published by Brandmaier, von Oertzen, McArdle, & Lindenberger (2013) <doi:10.1037/a0030001> and Arnold, Voelkle, & Brandmaier (2020) <doi:10.3389/fpsyg.2020.564403>.
Author: Andreas M. Brandmaier [aut, cre], John J. Prindle [aut], Manuel Arnold [aut], Caspar J. Van Lissa [aut]
Maintainer: Andreas M. Brandmaier <andy@brandmaier.de>

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Package insight updated to version 0.19.7 with previous version 0.19.6 dated 2023-10-12

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 snowfall updated to version 1.84-6.3 with previous version 1.84-6.2 dated 2022-07-05

Title: Easier Cluster Computing (Based on 'snow')
Description: Usability wrapper around snow for easier development of parallel R programs. This package offers e.g. extended error checks, and additional functions. All functions work in sequential mode, too, if no cluster is present or wished. Package is also designed as connector to the cluster management tool sfCluster, but can also used without it.
Author: Jochen Knaus
Maintainer: Jochen Knaus <jo@imbi.uni-freiburg.de>

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Package FD updated to version 1.0-12.3 with previous version 1.0-12.2 dated 2023-11-17

Title: Measuring Functional Diversity (FD) from Multiple Traits, and Other Tools for Functional Ecology
Description: Computes different multidimensional FD indices. Implements a distance-based framework to measure FD that allows any number and type of functional traits, and can also consider species relative abundances. Also contains other useful tools for functional ecology.
Author: Etienne Laliberte, Pierre Legendre, Bill Shipley
Maintainer: Etienne Laliberte <etiennelaliberte@gmail.com>

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Package NonlinearRDD updated to version 0.0.4 with previous version 0.0.3 dated 2023-10-27

Title: Nonlinear Regression Discontinuity Design
Description: Estimation of the possibly nonlinear and non separable structural function in regression discontinuity designs with a continuous treatment variable. The method is based on Xie (2022) <arXiv:2204.08168>.
Author: Haitian Xie [aut, cre, cph]
Maintainer: Haitian Xie <xht@gsm.pku.edu.cn>

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Package ezplot updated to version 0.7.11 with previous version 0.7.10 dated 2023-10-20

Title: Functions for Common Chart Types
Description: Wrapper for the 'ggplot2' package that creates a variety of common charts (e.g. bar, line, area, ROC, waterfall, pie) while aiming to reduce typing.
Author: Wojtek Kostelecki
Maintainer: Wojtek Kostelecki <wojtek.kostelecki@gmail.com>

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Package allomr updated to version 0.3.0 with previous version 0.2.0 dated 2023-02-18

Title: Removing Allometric Effects of Body Size in Morphological Analysis
Description: Implementation of the technique of Lleonart et al. (2000) <doi:10.1006/jtbi.2000.2043> to scale body measurements that exhibit an allometric growth. This procedure is a theoretical generalization of the technique used by Thorpe (1975) <doi:10.1111/j.1095-8312.1975.tb00732.x> and Thorpe (1976) <doi:10.1111/j.1469-185X.1976.tb01063.x>.
Author: Saemi Schaer [aut, cre, cph]
Maintainer: Saemi Schaer <saemi.schaer@gmail.com>

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Package GeneralizedHyperbolic updated to version 0.8-6 with previous version 0.8-4 dated 2018-05-15

Title: The Generalized Hyperbolic Distribution
Description: Functions for the hyperbolic and related distributions. Density, distribution and quantile functions and random number generation are provided for the hyperbolic distribution, the generalized hyperbolic distribution, the generalized inverse Gaussian distribution and the skew-Laplace distribution. Additional functionality is provided for the hyperbolic distribution, normal inverse Gaussian distribution and generalized inverse Gaussian distribution, including fitting of these distributions to data. Linear models with hyperbolic errors may be fitted using hyperblmFit.
Author: David Scott <d.scott@auckland.ac.nz>
Maintainer: David Scott <d.scott@auckland.ac.nz>

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Package jstable updated to version 1.1.3 with previous version 1.1.2 dated 2023-10-18

Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] , Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>

Diff between jstable versions 1.1.2 dated 2023-10-18 and 1.1.3 dated 2023-11-26

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Package HyperbolicDist updated to version 0.6-5 with previous version 0.6-4 dated 2022-02-21

Title: The Hyperbolic Distribution
Description: Maintenance has been discontinued for this package. It has been superseded by 'GeneralizedHyperbolic'. 'GeneralizedHyperbolic' includes all the functionality of 'HyperbolicDist' and more and is based on a more rational design. 'HyperbolicDist' provides functions for the hyperbolic and related distributions. Density, distribution and quantile functions and random number generation are provided for the hyperbolic distribution, the generalized hyperbolic distribution, the generalized inverse Gaussian distribution and the skew-Laplace distribution. Additional functionality is provided for the hyperbolic distribution, including fitting of the hyperbolic to data.
Author: David Scott <d.scott@auckland.ac.nz>
Maintainer: David Scott <d.scott@auckland.ac.nz>

Diff between HyperbolicDist versions 0.6-4 dated 2022-02-21 and 0.6-5 dated 2023-11-26

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