Wed, 29 Nov 2023

Package LTRCforests updated to version 0.7.0 with previous version 0.6.5 dated 2023-10-19

Title: Ensemble Methods for Survival Data with Time-Varying Covariates
Description: Implements the conditional inference forest and relative risk forest algorithm to modeling left-truncated right-censored data with time-invariant covariates, and (left-truncated) right-censored survival data with time-varying covariates. It also provides functions to tune the parameters and evaluate the model fit. See Yao et al. (2022) <doi:10.1177/09622802221111549>.
Author: Weichi Yao [aut, cre], Halina Frydman [aut], Denis Larocque [aut], Jeffrey S. Simonoff [aut]
Maintainer: Weichi Yao <weichi.yao@gmail.com>

Diff between LTRCforests versions 0.6.5 dated 2023-10-19 and 0.7.0 dated 2023-11-29

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Package agop updated to version 0.2.4 with previous version 0.2-3 dated 2020-01-08

Title: Aggregation Operators and Preordered Sets
Description: Tools supporting multi-criteria and group decision making, including variable number of criteria, by means of aggregation operators, spread measures, fuzzy logic connectives, fusion functions, and preordered sets. Possible applications include, but are not limited to, quality management, scientometrics, software engineering, etc.
Author: Marek Gagolewski [aut, cre] , Anna Cena [ctb]
Maintainer: Marek Gagolewski <marek@gagolewski.com>

Diff between agop versions 0.2-3 dated 2020-01-08 and 0.2.4 dated 2023-11-29

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Package dmm updated to version 2.1-9 with previous version 2.1-8 dated 2023-07-16

Title: Dyadic Mixed Model for Pedigree Data
Description: Dyadic mixed model analysis with multi-trait responses and pedigree-based partitioning of individual variation into a range of environmental and genetic variance components for individual and maternal effects. Method documented in dmmOverview.pdf; dmm is an implementation of dispersion mean model described by Searle et al. (1992) "Variance Components", Wiley, NY.
Author: Neville Jackson
Maintainer: Neville Jackson <nanddjackson@bigpond.com>

Diff between dmm versions 2.1-8 dated 2023-07-16 and 2.1-9 dated 2023-11-29

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Package tdthap updated to version 1.3 with previous version 1.2 dated 2022-10-28

Title: TDT Tests for Extended Haplotypes
Description: Functions and examples are provided for Transmission/disequilibrium tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999) "Transmission/disequilibrium tests for extended marker haplotypes". Amer. J. Hum. Genet., 65:1161-1169, <doi:10.1086/302566>.
Author: David Clayton
Maintainer: Jing Hua Zhao <jinghuazhao@hotmail.com>

Diff between tdthap versions 1.2 dated 2022-10-28 and 1.3 dated 2023-11-29

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Package stringx updated to version 0.2.6 with previous version 0.2.5 dated 2023-05-21

Title: Replacements for Base String Functions Powered by 'stringi'
Description: English is the native language for only 5% of the World population. Also, only 17% of us can understand this text. Moreover, the Latin alphabet is the main one for merely 36% of the total. The early computer era, now a very long time ago, was dominated by the US. Due to the proliferation of the internet, smartphones, social media, and other technologies and communication platforms, this is no longer the case. This package replaces base R string functions (such as grep(), tolower(), sprintf(), and strptime()) with ones that fully support the Unicode standards related to natural language and date-time processing. It also fixes some long-standing inconsistencies, and introduces some new, useful features. Thanks to 'ICU' (International Components for Unicode) and 'stringi', they are fast, reliable, and portable across different platforms.
Author: Marek Gagolewski [aut, cre, cph]
Maintainer: Marek Gagolewski <marek@gagolewski.com>

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Package rcheology updated to version 4.3.2.0 with previous version 4.3.1.1 dated 2023-11-08

Title: Data on Base and Recommended Packages for Current and Previous Versions of R
Description: Provides a dataset of functions in all base and recommended packages of R versions 0.50 onwards.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>

Diff between rcheology versions 4.3.1.1 dated 2023-11-08 and 4.3.2.0 dated 2023-11-29

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Package tikzDevice updated to version 0.12.6 with previous version 0.12.5 dated 2023-08-17

Title: R Graphics Output in LaTeX Format
Description: Provides a graphics output device for R that records plots in a LaTeX-friendly format. The device transforms plotting commands issued by R functions into LaTeX code blocks. When included in a LaTeX document, these blocks are interpreted with the help of 'TikZ'---a graphics package for TeX and friends written by Till Tantau. Using the 'tikzDevice', the text of R plots can contain LaTeX commands such as mathematical formula. The device also allows arbitrary LaTeX code to be inserted into the output stream.
Author: Charlie Sharpsteen [aut], Cameron Bracken [aut], Kirill Mueller [ctb], Yihui Xie [ctb], Ralf Stubner [cre], Nico Bellack [ctb]
Maintainer: Ralf Stubner <ralf.stubner@gmail.com>

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Package negligible updated to version 0.1.5 with previous version 0.1.4 dated 2023-11-11

Title: A Collection of Functions for Negligible Effect/Equivalence Testing
Description: Researchers often want to evaluate whether there is a negligible relationship among variables. The 'negligible' package provides functions that are useful for conducting negligible effect testing (also called equivalence testing). For example, there are functions for evaluating the equivalence of means or the presence of a negligible association (correlation or regression). Beribisky, N., Mara, C., & Cribbie, R. A. (2020) <doi:10.20982/tqmp.16.4.p424>. Beribisky, N., Davidson, H., Cribbie, R. A. (2019) <doi:10.7717/peerj.6853>. Shiskina, T., Farmus, L., & Cribbie, R. A. (2018) <doi:10.20982/tqmp.14.3.p167>. Mara, C. & Cribbie, R. A. (2017) <doi:10.1080/00220973.2017.1301356>. Counsell, A. & Cribbie, R. A. (2015) <doi:10.1111/bmsp.12045>. van Wieringen, K. & Cribbie, R. A. (2014) <doi:10.1111/bmsp.12015>. Goertzen, J. R. & Cribbie, R. A. (2010) <doi:10.1348/000711009x475853>. Cribbie, R. A., Gruman, J. & Arpin-Cribbi [...truncated...]
Author: Robert Cribbie [aut, cre], Udi Alter [aut], Nataly Beribisky [aut], Phil Chalmers [aut], Alyssa Counsell [aut], Linda Farmus [aut], Naomi Martinez Gutierrez [aut], Victoria Ng [ctb]
Maintainer: Robert Cribbie <cribbie@yorku.ca>

Diff between negligible versions 0.1.4 dated 2023-11-11 and 0.1.5 dated 2023-11-29

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Package dqrng updated to version 0.3.2 with previous version 0.3.1 dated 2023-08-30

Title: Fast Pseudo Random Number Generators
Description: Several fast random number generators are provided as C++ header only libraries: The PCG family by O'Neill (2014 <https://www.cs.hmc.edu/tr/hmc-cs-2014-0905.pdf>) as well as Xoroshiro128+ and Xoshiro256+ by Blackman and Vigna (2018 <arXiv:1805.01407>). In addition fast functions for generating random numbers according to a uniform, normal and exponential distribution are included. The latter two use the Ziggurat algorithm originally proposed by Marsaglia and Tsang (2000, <doi:10.18637/jss.v005.i08>). The fast sampling methods support unweighted sampling both with and without replacement. These functions are exported to R and as a C++ interface and are enabled for use with the default 64 bit generator from the PCG family, Xoroshiro128+ and Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry engine (Salmon et al., 2011, <doi:10.1145/2063384.2063405>) as provided by the package 'sitmo'.
Author: Ralf Stubner [aut, cre], daqana GmbH [cph], David Blackman [ctb], Melissa O'Neill [ctb], Sebastiano Vigna [ctb], Aaron Lun [ctb], Kyle Butts [ctb]
Maintainer: Ralf Stubner <ralf.stubner@gmail.com>

Diff between dqrng versions 0.3.1 dated 2023-08-30 and 0.3.2 dated 2023-11-29

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Package coga updated to version 1.2.1 with previous version 1.2.0 dated 2023-08-19

Title: Convolution of Gamma Distributions
Description: Evaluation for density and distribution function of convolution of gamma distributions in R. Two related exact methods and one approximate method are implemented with efficient algorithm and C++ code. A quick guide for choosing correct method and usage of this package is given in package vignette. For the detail of methods used in this package, we refer the user to Mathai(1982)<doi:10.1007/BF02481056>, Moschopoulos(1984)<doi:10.1007/BF02481123>, Barnabani(2017)<doi:10.1080/03610918.2014.963612>, Hu et al.(2020)<doi:10.1007/s00180-019-00924-9>.
Author: Chaoran Hu [aut, cre], Vladimir Pozdnyakov [ths], Jun Yan [ths]
Maintainer: Chaoran Hu <chaoran.hu@uconn.edu>

Diff between coga versions 1.2.0 dated 2023-08-19 and 1.2.1 dated 2023-11-29

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Package scclust updated to version 0.2.4 with previous version 0.2.3 dated 2023-04-24

Title: Size-Constrained Clustering
Description: Provides wrappers for 'scclust', a C library for computationally efficient size-constrained clustering with near-optimal performance. See <https://github.com/fsavje/scclust> for more information.
Author: Fredrik Savje [aut, cre], Michael Higgins [aut], Jasjeet Sekhon [aut]
Maintainer: Fredrik Savje <fredrik.savje@yale.edu>

Diff between scclust versions 0.2.3 dated 2023-04-24 and 0.2.4 dated 2023-11-29

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Package RevGadgets updated to version 1.2.1 with previous version 1.2.0 dated 2023-11-16

Title: Visualization and Post-Processing of 'RevBayes' Analyses
Description: Processes and visualizes the output of complex phylogenetic analyses from the 'RevBayes' phylogenetic graphical modeling software.
Author: Carrie Tribble [aut, cre] , Michael R. May [aut], William A. Freyman [aut], Michael J. Landis [aut], Lim Jun Ying [aut], Joelle Barido-Sottani [aut], Andrew Magee [aut], Bjorn Tore Kopperud [aut], Sebastian Hohna [aut], Nagashima Kengo [ctb], Schliep [...truncated...]
Maintainer: Carrie Tribble <ctribble09@gmail.com>

Diff between RevGadgets versions 1.2.0 dated 2023-11-16 and 1.2.1 dated 2023-11-29

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Package quickmatch updated to version 0.2.2 with previous version 0.2.1 dated 2018-08-24

Title: Quick Generalized Full Matching
Description: Provides functions for constructing near-optimal generalized full matching. Generalized full matching is an extension of the original full matching method to situations with more intricate study designs. The package is made with large data sets in mind and derives matches more than an order of magnitude quicker than other methods.
Author: Fredrik Savje [aut, cre], Jasjeet Sekhon [aut], Michael Higgins [aut]
Maintainer: Fredrik Savje <fredrik.savje@yale.edu>

Diff between quickmatch versions 0.2.1 dated 2018-08-24 and 0.2.2 dated 2023-11-29

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Package FactoClass (with last version 1.2.8) was removed from CRAN

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

2023-09-13 1.2.8
2018-10-01 1.2.7
2018-03-01 1.2.4
2017-09-01 1.1.6
2017-08-09 1.1.4
2017-01-05 1.1.3
2015-08-05 1.1.2
2015-02-03 1.1.1
2013-07-18 1.1.0
2013-06-06 1.0.9
2012-02-01 1.0.8

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Package qha (with last version 0.0.8) was removed from CRAN

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

2016-09-09 0.0.8

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Package RcppSpdlog updated to version 0.0.15 with previous version 0.0.14 dated 2023-07-10

Title: R and C++ Interfaces to 'spdlog' C++ Header Library for Logging
Description: The mature and widely-used C++ logging library 'spdlog' by Gabi Melman provides many desirable features. This package bundles these header files for easy use by R packages from both their R and C or C++ code. Explicit use via 'LinkingTo:' is also supported. Also see the 'spdl' package which enhanced this package with a consistent R and C++ interface.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppSpdlog versions 0.0.14 dated 2023-07-10 and 0.0.15 dated 2023-11-29

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New package HadIBDs with initial version 1.0.0
Package: HadIBDs
Title: Incomplete Block Designs using Hadamard Matrix (HadIBDs)
Version: 1.0.0
Maintainer: Ashutosh Dalal <ashutosh.dalal97@gmail.com>
Description: Hadamard matrix based statistical designs are of immense importance as the resultant designs carry various desirable characterizing properties. Constructing Partially Balanced Incomplete Block Designs (PBIBds) using Kronecker product of incidence matrices of Balanced Incomplete Block (BIB) and Partially Balanced Incomplete Block (PBIB) designs is much evident from literature. Here, we have constructed Incomplete Block Designs (IBDs) based on Hadamard matrices and Kronecker product of Hadamard matrices.
Suggests: MASS, utils
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-11-29 15:39:53 UTC; Ashutosh
Author: Mohd Harun [aut, ctb], Cini Varghese [aut, ctb], Ashutosh Dalal [aut, cre]
Repository: CRAN
Date/Publication: 2023-11-29 19:10:06 UTC

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New package evapoRe with initial version 1.0.0
Package: evapoRe
Title: Evapotranspiration R Recipes
Version: 1.0.0
Description: An R-based application for exploratory data analysis of global EvapoTranspiration (ET) datasets. 'evapoRe' enables users to download, validate, visualize, and analyze multi-source ET data across various spatio-temporal scales. Also, the package offers calculation methods for estimating potential ET (PET), including temperature-based approaches described in : Oudin et al., (2005) <doi:10.1016/j.jhydrol.2004.08.026>. 'evapoRe' supports hydrological modeling, climate studies, agricultural research, and other data-driven fields by facilitating access to ET data and offering powerful analysis capabilities. Users can seamlessly integrate the package into their research applications and explore diverse ET data at different resolutions.
Depends: R (>= 4.0.0), pRecipe
Imports: methods, parallel, utils, data.table, doParallel, foreach, lubridate, raster
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/AkbarR1184/evapoRe
SystemRequirements: PROJ (>= 6, https://proj.org/download.html), GDAL (>= 3, https://gdal.org/download.html), NetCDF(>= 4, https://www.unidata.ucar.edu/software/netcdf/).
Suggests: rmarkdown, ggpubr, knitr, spelling, kableExtra, tibble, testthat (>= 3.0.0)
Language: en-US
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-11-29 14:22:08 UTC; Admin
Author: Akbar Rahmati Ziveh [aut, cre] , Mijael Rodrigo Vargas Godoy [aut] , Vishal Thakur [ctb] , Yannis Markonis [aut, ths]
Maintainer: Akbar Rahmati Ziveh <rahmati_ziveh@fzp.czu.cz>
Repository: CRAN
Date/Publication: 2023-11-29 19:10:02 UTC

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Permanent link

Package epinet updated to version 2.1.11 with previous version 2.1.8 dated 2018-02-13

Title: Epidemic/Network-Related Tools
Description: A collection of epidemic/network-related tools. Simulates transmission of diseases through contact networks. Performs Bayesian inference on network and epidemic parameters, given epidemic data.
Author: Chris Groendyke [aut, cre], David Welch [aut], David Hunter [ctb]
Maintainer: Chris Groendyke <cgroendyke@gmail.com>

Diff between epinet versions 2.1.8 dated 2018-02-13 and 2.1.11 dated 2023-11-29

 DESCRIPTION              |    8 ++++----
 MD5                      |    8 ++++----
 man/Hagelloch.Rd         |    2 +-
 man/ess.Rd               |    2 --
 src/NetworkEpiMCMCSEIR.c |    2 +-
 5 files changed, 10 insertions(+), 12 deletions(-)

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New package pexm with initial version 1.1.3
Package: pexm
Title: Loading a JAGS Module for the Piecewise Exponential Distribution
Version: 1.1.3
Description: Load the Just Another Gibbs Sampling (JAGS) module 'pexm'. The module provides the tools to work with the Piecewise Exponential (PE) distribution in a Bayesian model with the corresponding Markov Chain Monte Carlo algorithm (Gibbs Sampling) implemented via JAGS. Details about the module implementation can be found in Mayrink et al. (2021) <doi:10.18637/jss.v100.i08>.
Depends: coda, rjags
Imports: msm
Encoding: UTF-8
License: GPL-3
URL: https://github.com/vdinizm/pexm
BugReports: https://github.com/vdinizm/pexm/issues
NeedsCompilation: yes
Suggests: testthat
Packaged: 2023-11-29 12:41:45 UTC; vinicius
Author: Vinicius Mayrink [aut, cre] , Joao Duarte [aut], Fabio Demarqui [ctb]
Maintainer: Vinicius Mayrink <vdinizm@gmail.com>
Repository: CRAN
Date/Publication: 2023-11-29 18:50:02 UTC

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New package nexus with initial version 0.1.0
Package: nexus
Title: Sourcing Archaeological Materials by Chemical Composition
Version: 0.1.0
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Description: Exploration and analysis of compositional data in the framework of Aitchison (1986, ISBN: 978-94-010-8324-9). This package provides tools for chemical fingerprinting and source tracking of ancient materials.
License: GPL (>= 3)
URL: https://packages.tesselle.org/nexus/, https://github.com/tesselle/nexus
BugReports: https://github.com/tesselle/nexus/issues
Depends: R (>= 3.5)
Imports: arkhe (>= 1.4.0), dimensio (>= 0.5.0), graphics, grDevices, isopleuros (>= 1.0.0), methods, MASS, stats, utils
Suggests: cluster, folio, igraph, knitr, rmarkdown, rsvg, svglite, tinysnapshot, tinytest
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2023-11-29 08:32:56 UTC; nicolas
Author: Nicolas Frerebeau [aut, cre] , Anne Philippe [aut] , Brice Lebrun [ctb] , Universite Bordeaux Montaigne [fnd], CNRS [fnd]
Repository: CRAN
Date/Publication: 2023-11-29 18:40:02 UTC

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New package KINSIMU with initial version 0.1.1
Package: KINSIMU
Title: Panel Evaluation in Forensic Kinship Analysis
Version: 0.1.1
Date: 2023-11-20
Maintainer: Guanju Ma <mache124@126.com>
Description: Evaluate specific panels in different aspects: i) Simulation tools related to pedigree researches; ii) calculation for systemic effectiveness indicators, such as probability of exclusion (PE).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Imports: utils
NeedsCompilation: no
Packaged: 2023-11-29 14:13:46 UTC; Ma Guanju
Author: Guanju Ma [aut, cre], Shujin Li [ctb]
Repository: CRAN
Date/Publication: 2023-11-29 19:00:06 UTC

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Permanent link

Package htetree updated to version 0.1.18 with previous version 0.1.17 dated 2023-08-12

Title: Causal Inference with Tree-Based Machine Learning Algorithms
Description: Estimating heterogeneous treatment effects with tree-based machine learning algorithms and visualizing estimated results in flexible and presentation-ready ways. For more information, see Brand, Xu, Koch, and Geraldo (2021) <doi:10.1177/0081175021993503>. Our current package first started as a fork of the 'causalTree' package on 'GitHub' and we greatly appreciate the authors for their extremely useful and free package.
Author: Jiahui Xu [cre, aut], Tanvi Shinkre [aut], Jennie Brand [aut]
Maintainer: Jiahui Xu <jiahuixu@ucla.edu>

Diff between htetree versions 0.1.17 dated 2023-08-12 and 0.1.18 dated 2023-11-29

 DESCRIPTION                   |    6 +++---
 MD5                           |   20 ++++++++++----------
 R/causalForest.R              |    2 +-
 R/causalTree.R                |    2 +-
 man/causalForest.Rd           |    2 +-
 man/causalTree.Rd             |    2 +-
 man/causalTree.control.Rd     |    2 +-
 man/honest.causalTree.Rd      |    2 +-
 man/honest.rparttree.Rd       |    2 +-
 man/model.frame.causalTree.Rd |    2 +-
 src/causalTree.c              |    3 ++-
 11 files changed, 23 insertions(+), 22 deletions(-)

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Package fstcore updated to version 0.9.16 with previous version 0.9.14 dated 2023-01-12

Title: R Bindings to the 'Fstlib' Library
Description: The 'fstlib' library provides multithreaded serialization of compressed data frames using the 'fst' format. The 'fst' format allows for random access of stored data and compression with the 'LZ4' and 'ZSTD' compressors.
Author: Mark Klik [aut, cre, cph] , Yuta Mori [ctb, cph] , Przemyslaw Skibinski [ctb, cph] , Tino Reichardt [ctb, cph] , Yann Collet [ctb, cph] , Facebook, Inc. [cph]
Maintainer: Mark Klik <markklik@gmail.com>

Diff between fstcore versions 0.9.14 dated 2023-01-12 and 0.9.16 dated 2023-11-29

 fstcore-0.9.14/fstcore/src/fstlib/CMakeLists.txt                             |only
 fstcore-0.9.14/fstcore/src/fstlib/LZ4/CMakeLists.txt                         |only
 fstcore-0.9.14/fstcore/src/fstlib/ZSTD/CMakeLists.txt                        |only
 fstcore-0.9.14/fstcore/tests/testthat/data                                   |only
 fstcore-0.9.16/fstcore/DESCRIPTION                                           |    8 
 fstcore-0.9.16/fstcore/MD5                                                   |  159 
 fstcore-0.9.16/fstcore/NEWS.md                                               |   13 
 fstcore-0.9.16/fstcore/R/RcppExports.R                                       |    2 
 fstcore-0.9.16/fstcore/README.md                                             |    4 
 fstcore-0.9.16/fstcore/cleanup                                               |    2 
 fstcore-0.9.16/fstcore/configure                                             |    2 
 fstcore-0.9.16/fstcore/man/figures                                           |only
 fstcore-0.9.16/fstcore/src/Makevars.in                                       |    1 
 fstcore-0.9.16/fstcore/src/Makevars.win                                      |    1 
 fstcore-0.9.16/fstcore/src/RcppExports.cpp                                   |   24 
 fstcore-0.9.16/fstcore/src/fstlib/LZ4/LICENSE                                |   48 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/allocations.h                  |only
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/bits.h                         |only
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/bitstream.h                    |   79 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/compiler.h                     |   29 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/cpu.h                          |    2 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/debug.c                        |    2 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/debug.h                        |    2 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/entropy_common.c               |   52 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/error_private.c                |   11 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/error_private.h                |    2 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/fse.h                          |   88 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/fse_decompress.c               |  106 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/huf.h                          |  221 -
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/mem.h                          |   89 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/pool.c                         |   36 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/pool.h                         |    8 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/portability_macros.h           |   27 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/threading.c                    |   82 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/threading.h                    |   15 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/xxhash.c                       |    4 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/xxhash.h                       |   16 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/zstd_common.c                  |   37 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/zstd_deps.h                    |    2 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/zstd_internal.h                |  135 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/common/zstd_trace.h                   |    6 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/clevels.h                    |    2 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/fse_compress.c               |  131 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/hist.c                       |    2 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/hist.h                       |    2 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/huf_compress.c               |  403 +-
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/zstd_compress.c              | 1779 ++++++----
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/zstd_compress_internal.h     |  376 +-
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/zstd_compress_literals.c     |  154 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/zstd_compress_literals.h     |   24 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/zstd_compress_sequences.c    |    6 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/zstd_compress_sequences.h    |    2 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/zstd_compress_superblock.c   |   46 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/zstd_compress_superblock.h   |    2 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/zstd_cwksp.h                 |  190 -
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/zstd_double_fast.c           |  128 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/zstd_double_fast.h           |    5 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/zstd_fast.c                  |  581 ++-
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/zstd_fast.h                  |    5 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/zstd_lazy.c                  |  747 ++--
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/zstd_lazy.h                  |    6 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/zstd_ldm.c                   |   10 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/zstd_ldm.h                   |    2 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/zstd_ldm_geartab.h           |    2 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/zstd_opt.c                   |  186 -
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/zstd_opt.h                   |    2 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/zstdmt_compress.c            |   26 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/compress/zstdmt_compress.h            |    2 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/decompress/huf_decompress.c           |  875 ++--
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/decompress/huf_decompress_amd64.S     |   69 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/decompress/zstd_ddict.c               |    8 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/decompress/zstd_ddict.h               |    2 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/decompress/zstd_decompress.c          |  287 +
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/decompress/zstd_decompress_block.c    |  286 +
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/decompress/zstd_decompress_block.h    |    7 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/decompress/zstd_decompress_internal.h |    6 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/dictBuilder/cover.c                   |   34 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/dictBuilder/cover.h                   |    2 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/dictBuilder/fastcover.c               |    4 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/dictBuilder/zdict.c                   |  100 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/zdict.h                               |   84 
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/zstd.h                                |  715 +++-
 fstcore-0.9.16/fstcore/src/fstlib/ZSTD/zstd_errors.h                         |   35 
 fstcore-0.9.16/fstcore/tests/testthat/test_lintr.R                           |   29 
 84 files changed, 5150 insertions(+), 3529 deletions(-)

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New package bexy with initial version 0.1.2
Package: bexy
Title: Visualize and Parse the Output of 'BeXY'
Version: 0.1.2
Maintainer: Madleina Caduff <madleina.caduff@unifr.ch>
Description: Provides functions for summarizing and plotting the output of the command-line tool 'BeXY' (<https://bitbucket.org/wegmannlab/bexy>), a tool that performs Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data.
License: GPL-2
Encoding: UTF-8
Imports: TeachingDemos,Ternary
NeedsCompilation: no
Packaged: 2023-11-29 13:17:00 UTC; madleina
Author: Madleina Caduff [aut, cre], Raphael Eckel [ctb], Christoph Leuenberger [ctb], Daniel Wegmann [aut]
Repository: CRAN
Date/Publication: 2023-11-29 19:00:02 UTC

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Package streambugs updated to version 1.4 with previous version 1.3 dated 2023-01-27

Title: Parametric Ordinary Differential Equations Model of Growth, Death, and Respiration of Macroinvertebrate and Algae Taxa
Description: Numerically solve and plot solutions of a parametric ordinary differential equations model of growth, death, and respiration of macroinvertebrate and algae taxa dependent on pre-defined environmental factors. The model (version 1.0) is introduced in Schuwirth, N. and Reichert, P., (2013) <DOI:10.1890/12-0591.1>. This package includes model extensions and the core functions introduced and used in Schuwirth, N. et al. (2016) <DOI:10.1111/1365-2435.12605>, Kattwinkel, M. et al. (2016) <DOI:10.1021/acs.est.5b04068>, Mondy, C. P., and Schuwirth, N. (2017) <DOI:10.1002/eap.1530>, and Paillex, A. et al. (2017) <DOI:10.1111/fwb.12927>.
Author: Nele Schuwirth, Peter Reichert, Mikolaj Rybinski
Maintainer: Nele Schuwirth <nele.schuwirth@eawag.ch>

Diff between streambugs versions 1.3 dated 2023-01-27 and 1.4 dated 2023-11-29

 DESCRIPTION                                                           |   10 
 MD5                                                                   |   78 
 NAMESPACE                                                             |   56 
 R/get_par_trait_cond.r                                                |   10 
 R/streambugs-package.r                                                |   14 
 R/streambugs.r                                                        | 1162 
 R/streambugs_aux.r                                                    | 3202 
 R/streambugs_aux_indval_vec.R                                         |  776 
 R/streambugs_aux_proc.r                                               |  982 
 R/streambugs_c.r                                                      |  498 
 R/streambugs_examples.r                                               |  628 
 R/streambugs_plot.r                                                   | 1024 
 inst/extdata/extended_example-pars.tsv                                | 5052 -
 inst/extdata/extended_example-vars_sourcepooltaxa.tsv                 |   74 
 man/construct.statevariables.Rd                                       |   88 
 man/count.feeding.links.Rd                                            |   60 
 man/decode.statevarnames.Rd                                           |   70 
 man/foodweb.plot.Rd                                                   |  162 
 man/plot.streambugs.Rd                                                |   60 
 man/run.streambugs.Rd                                                 |  208 
 man/streambugs-package.Rd                                             |   42 
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 man/streambugs.example.model.toy.Rd                                   |   78 
 man/streambugs.get.sys.def.Rd                                         |   82 
 man/streambugs.write.sys.def.Rd                                       |   52 
 src/streambugs_rhs.c                                                  |   17 
 tests/benchmarks/run_for_toy.R                                        |  348 
 tests/testthat.R                                                      |    8 
 tests/testthat/extended_example_res_C.csv                             |  404 
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 tests/testthat/helper_test_example.R                                  |  172 
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 tests/testthat/run_extended_example.R                                 |   86 
 tests/testthat/run_minimum_example.R                                  |  210 
 tests/testthat/test_aux.R                                             |  688 
 tests/testthat/test_extended_example.R                                |   82 
 tests/testthat/test_minimum_example.R                                 |  112 
 40 files changed, 31608 insertions(+), 31607 deletions(-)

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Package RcppQuantuccia updated to version 0.1.2 with previous version 0.1.1 dated 2022-10-19

Title: R Bindings to the Calendaring Functionality of 'QuantLib'
Description: 'QuantLib' bindings are provided for R using 'Rcpp' via an updated variant of the header-only 'Quantuccia' project (put together initially by Peter Caspers) offering an essential subset of 'QuantLib' (and now maintained separately for the calendaring subset). See the included file 'AUTHORS' for a full list of contributors to both 'QuantLib' and 'Quantuccia'.
Author: Dirk Eddelbuettel; the authors and contributors of QuantLib
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppQuantuccia versions 0.1.1 dated 2022-10-19 and 0.1.2 dated 2023-11-29

 ChangeLog           |   16 ++++++++++++++++
 DESCRIPTION         |    8 ++++----
 MD5                 |   14 +++++++-------
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 src/Makevars        |    5 +++--
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 8 files changed, 52 insertions(+), 28 deletions(-)

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Package quickblock updated to version 0.2.1 with previous version 0.2.0 dated 2018-08-21

Title: Quick Threshold Blocking
Description: Provides functions for assigning treatments in randomized experiments using near-optimal threshold blocking. The package is made with large data sets in mind and derives blocks more than an order of magnitude quicker than other methods.
Author: Fredrik Savje [aut, cre], Jasjeet Sekhon [aut], Michael Higgins [aut]
Maintainer: Fredrik Savje <fredrik.savje@yale.edu>

Diff between quickblock versions 0.2.0 dated 2018-08-21 and 0.2.1 dated 2023-11-29

 DESCRIPTION               |   12 ++++++------
 MD5                       |   16 ++++++++--------
 NEWS.md                   |    5 +++++
 R/quickblock-package.R    |    1 -
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 README.md                 |    7 ++-----
 man/quickblock-package.Rd |    1 -
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 9 files changed, 29 insertions(+), 26 deletions(-)

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Package ProbBreed updated to version 1.0.3.1 with previous version 1.0.3 dated 2023-10-03

Title: Probability Theory for Selecting Candidates in Plant Breeding
Description: Use probability theory under the Bayesian framework for calculating the risk of selecting candidates in a multi-environment context [Dias et al. (2022) <doi:10.1007/s00122-022-04041-y>]. Contained are functions used to fit a Bayesian multi-environment model (based on the available presets), extract posterior values and maximum posterior values, compute the variance components, check the model’s convergence, and calculate the probabilities. For both across and within-environments scopes, the package computes the probability of superior performance and the pairwise probability of superior performance. Furthermore, the probability of superior stability and the pairwise probability of superior stability across environments is estimated. A joint probability of superior performance and stability is also provided.
Author: Saulo Chaves [aut, cre] , Kaio Dias [aut, cph] , Matheus Krause [aut]
Maintainer: Saulo Chaves <saulo.chaves@ufv.br>

Diff between ProbBreed versions 1.0.3 dated 2023-10-03 and 1.0.3.1 dated 2023-11-29

 DESCRIPTION       |    6 
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 R/bayes_met.R     |  459 ++++++++++++++++++++++++++++++++++--------------------
 R/extr_outs.R     |   37 ++--
 R/maize.R         |only
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 16 files changed, 666 insertions(+), 459 deletions(-)

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Package mvMORPH updated to version 1.1.8 with previous version 1.1.7 dated 2023-03-13

Title: Multivariate Comparative Tools for Fitting Evolutionary Models to Morphometric Data
Description: Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees and time series. 'mvMORPH' also proposes high-dimensional multivariate comparative tools (linear models using Generalized Least Squares and multivariate tests) based on penalized likelihood. See Clavel et al. (2015) <DOI:10.1111/2041-210X.12420>, Clavel et al. (2019) <DOI:10.1093/sysbio/syy045>, and Clavel & Morlon (2020) <DOI:10.1093/sysbio/syaa010>.
Author: Julien Clavel, with contributions from Aaron King, and Emmanuel Paradis
Maintainer: Julien Clavel <julien.clavel@hotmail.fr>

Diff between mvMORPH versions 1.1.7 dated 2023-03-13 and 1.1.8 dated 2023-11-29

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 NAMESPACE                       |    5 +
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Package gpboost updated to version 1.2.7 with previous version 1.2.6 dated 2023-10-24

Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre], Pascal Kuendig [aut], Benoit Jacob [cph], Gael Guennebaud [cph], Nicolas Carre [cph], Pierre Zoppitelli [cph], Gauthier Brun [cph], Jean Ceccato [cph], Jitse Niesen [cph], Other authors of Eigen for the included version of E [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>

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Package cpr updated to version 0.3.0 with previous version 0.2.3 dated 2017-03-07

Title: Control Polygon Reduction
Description: Implementation of the Control Polygon Reduction and Control Net Reduction methods for finding parsimonious B-spline regression models.
Author: Peter DeWitt [aut, cre] , Samantha MaWhinney [ths], Nichole Carlson [ths]
Maintainer: Peter DeWitt <dewittpe@gmail.com>

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Package cinterpolate updated to version 1.0.1 with previous version 1.0.0 dated 2019-04-10

Title: Interpolation From C
Description: Simple interpolation methods designed to be used from C code. Supports constant, linear and spline interpolation. An R wrapper is included but this package is primarily designed to be used from C code using 'LinkingTo'. The spline calculations are classical cubic interpolation, e.g., Forsythe, Malcolm and Moler (1977) <ISBN: 9780131653320>.
Author: Rich FitzJohn [aut, cre], Imperial College of Science, Technology and Medicine [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>

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Package updog updated to version 2.1.5 with previous version 2.1.4 dated 2023-11-17

Title: Flexible Genotyping for Polyploids
Description: Implements empirical Bayes approaches to genotype polyploids from next generation sequencing data while accounting for allele bias, overdispersion, and sequencing error. The main functions are flexdog() and multidog(), which allow the specification of many different genotype distributions. Also provided are functions to simulate genotypes, rgeno(), and read-counts, rflexdog(), as well as functions to calculate oracle genotyping error rates, oracle_mis(), and correlation with the true genotypes, oracle_cor(). These latter two functions are useful for read depth calculations. Run browseVignettes(package = "updog") in R for example usage. See Gerard et al. (2018) <doi:10.1534/genetics.118.301468> and Gerard and Ferrao (2020) <doi:10.1093/bioinformatics/btz852> for details on the implemented methods.
Author: David Gerard [aut, cre]
Maintainer: David Gerard <gerard.1787@gmail.com>

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Package tidyAML updated to version 0.0.3 with previous version 0.0.2 dated 2023-04-20

Title: Automatic Machine Learning with 'tidymodels'
Description: The goal of this package will be to provide a simple interface for automatic machine learning that fits the 'tidymodels' framework. The intention is to work for regression and classification problems with a simple verb framework.
Author: Steven Sanderson [aut, cre, cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>

Diff between tidyAML versions 0.0.2 dated 2023-04-20 and 0.0.3 dated 2023-11-29

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Package scoringutils updated to version 1.2.2 with previous version 1.1.0 dated 2023-01-30

Title: Utilities for Scoring and Assessing Predictions
Description: Provides a collection of metrics and proper scoring rules (Tilmann Gneiting & Adrian E Raftery (2007) <doi:10.1198/016214506000001437>, Jordan, A., Krüger, F., & Lerch, S. (2019) <doi:10.18637/jss.v090.i12>) within a consistent framework for evaluation, comparison and visualisation of forecasts. In addition to proper scoring rules, functions are provided to assess bias, sharpness and calibration (Sebastian Funk, Anton Camacho, Adam J. Kucharski, Rachel Lowe, Rosalind M. Eggo, W. John Edmunds (2019) <doi:10.1371/journal.pcbi.1006785>) of forecasts. Several types of predictions (e.g. binary, discrete, continuous) which may come in different formats (e.g. forecasts represented by predictive samples or by quantiles of the predictive distribution) can be evaluated. Scoring metrics can be used either through a convenient data.frame format, or can be applied as individual functions in a vector / matrix format. All functionality has been implemented with a focus on pe [...truncated...]
Author: Nikos Bosse [aut, cre] , Sam Abbott [aut] , Hugo Gruson [aut] , Johannes Bracher [ctb] , Sebastian Funk [aut]
Maintainer: Nikos Bosse <nikosbosse@gmail.com>

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Package qlcal updated to version 0.0.9 with previous version 0.0.8 dated 2023-10-21

Title: R Bindings to the Calendaring Functionality of 'QuantLib'
Description: 'QuantLib' bindings are provided for R using 'Rcpp' via an evolved version of the initial header-only 'Quantuccia' project offering an subset of 'QuantLib' (now maintained separately just for the calendaring subset). See the included file 'AUTHORS' for a full list of contributors to 'QuantLib' (and hence also 'Quantuccia').
Author: Dirk Eddelbuettel; the authors and contributors of QuantLib
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between qlcal versions 0.0.8 dated 2023-10-21 and 0.0.9 dated 2023-11-29

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Package MNM updated to version 1.0-4 with previous version 1.0-3 dated 2018-03-02

Title: Multivariate Nonparametric Methods. An Approach Based on Spatial Signs and Ranks
Description: Multivariate tests, estimates and methods based on the identity score, spatial sign score and spatial rank score are provided. The methods include one and c-sample problems, shape estimation and testing, linear regression and principal components. The methodology is described in Oja (2010) <doi:10.1007/978-1-4419-0468-3> and Nordhausen and Oja (2011) <doi:10.18637/jss.v043.i05>.
Author: Klaus Nordhausen [aut, cre] , Jyrki Mottonen [aut] , Hannu Oja [aut]
Maintainer: Klaus Nordhausen <klausnordhausenR@gmail.com>

Diff between MNM versions 1.0-3 dated 2018-03-02 and 1.0-4 dated 2023-11-29

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New package dsims with initial version 1.0.4
Package: dsims
Depends: dssd (>= 0.2.2)
Imports: mrds, Distance, sf, ggplot2, purrr, dplyr, mgcv, methods, rstudioapi, gridExtra, rlang
Suggests: testthat, parallel, pbapply, knitr, lwgeom, rmarkdown
VignetteBuilder: knitr
Title: Distance Sampling Simulations
Version: 1.0.4
Maintainer: Laura Marshall <lhm@st-and.ac.uk>
Description: Performs distance sampling simulations. 'dsims' repeatedly generates instances of a user defined population within a given survey region. It then generates realisations of a survey design and simulates the detection process. The data are then analysed so that the results can be compared for accuracy and precision across all replications. This process allows users to optimise survey designs for their specific set of survey conditions. The effects of uncertainty in population distribution or parameters can be investigated under a number of simulations so that users can be confident that they have achieved a robust survey design before deploying vessels into the field. The distance sampling designs used in this package from 'dssd' are detailed in Chapter 7 of Advanced Distance Sampling, Buckland et. al. (2008, ISBN-13: 978-0199225873). General distance sampling methods are detailed in Introduction to Distance Sampling: Estimating Abundance of Biological Populations, Buckland et. al. (2004 [...truncated...]
License: GPL (>= 2)
Language: en-GB
URL: https://github.com/DistanceDevelopment/dsims
BugReports: https://github.com/DistanceDevelopment/dsims/issues
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-11-24 13:46:36 UTC; lhm
Author: Laura Marshall [aut, cre], Thomas Len [ctb]
Repository: CRAN
Date/Publication: 2023-11-29 14:10:02 UTC

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New package ivo.table with initial version 0.1
Package: ivo.table
Title: Pretty Contingency Tables and Frequency Tables
Version: 0.1
Description: Nicely formatted frequency tables and contingency tables (cross-tables), that can easily be exported to HTML or 'Office' documents, including 'Excel'. Designed to work with pipes.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: dplyr, flextable, openxlsx, checkmate, officer, purrr, stringr, tidyr
NeedsCompilation: no
Packaged: 2023-11-29 07:53:41 UTC; mans
Author: Mans Thulin [aut, cre], Kajsa Grind [aut], Stefan Furne [aut]
Maintainer: Mans Thulin <mans@statistikkonsult.com>
Repository: CRAN
Date/Publication: 2023-11-29 14:00:02 UTC

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Package image.CannyEdges updated to version 0.1.1 with previous version 0.1.0 dated 2020-08-01

Title: Implementation of the Canny Edge Detector for Images
Description: An implementation of the Canny Edge Detector for detecting edges in images. The package provides an interface to the algorithm available at <https://github.com/Neseb/canny>.
Author: Jan Wijffels [aut, cre, cph], BNOSAC [cph], Vincent Maioli [ctb, cph], IPOL Image Processing On Line [cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>

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New package HDMAADMM with initial version 0.0.1
Package: HDMAADMM
Title: ADMM for High-Dimensional Mediation Models
Version: 0.0.1
Date: 2023-12-01
Maintainer: Pei-Shan Yen <peishan0824@gmail.com>
Description: We use the Alternating Direction Method of Multipliers (ADMM) for parameter estimation in high-dimensional, single-modality mediation models. To improve the sensitivity and specificity of estimated mediation effects, we offer the sure independence screening (SIS) function for dimension reduction. The available penalty options include Lasso, Elastic Net, Pathway Lasso, and Network-constrained Penalty. The methods employed in the package are based on Boyd, S., Parikh, N., Chu, E., Peleato, B., & Eckstein, J. (2011). <doi:10.1561/2200000016>, Fan, J., & Lv, J. (2008) <doi:10.1111/j.1467-9868.2008.00674.x>, Li, C., & Li, H. (2008) <doi:10.1093/bioinformatics/btn081>, Tibshirani, R. (1996) <doi:10.1111/j.2517-6161.1996.tb02080.x>, Zhao, Y., & Luo, X. (2022) <doi:10.4310/21-sii673>, and Zou, H., & Hastie, T. (2005) <doi:10.1111/j.1467-9868.2005.00503.x>.
License: MIT + file LICENSE
Depends: R (>= 4.0.0)
Imports: Rcpp (>= 1.0.0), dqrng, RcppEigen
LinkingTo: Rcpp, RcppEigen
Suggests: roxygen2
Encoding: UTF-8
URL: https://github.com/psyen0824/HDMAADMM
BugReports: https://github.com/psyen0824/HDMAADMM/issues
NeedsCompilation: yes
Packaged: 2023-11-29 01:24:52 UTC; peish
Author: Pei-Shan Yen [aut, cre] , Ching-Chuan Chen [aut]
Repository: CRAN
Date/Publication: 2023-11-29 14:00:16 UTC

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Package gRc updated to version 0.4.6 with previous version 0.4.5 dated 2023-04-30

Title: Inference in Graphical Gaussian Models with Edge and Vertex Symmetries
Description: Estimation, model selection and other aspects of statistical inference in Graphical Gaussian models with edge and vertex symmetries (Graphical Gaussian models with colours). Documentation about 'gRc' is provided in the paper by Hojsgaard and Lauritzen (2007, <doi:10.18637/jss.v023.i06>) and the paper by Hojsgaard and Lauritzen (2008, <doi:10.1111/j.1467-9868.2008.00666.x>).
Author: Soeren Hoejsgaard <sorenh@math.aau.dk>, Steffen L. Lauritzen <lauritzen@math.ku.dk>
Maintainer: Soeren Hoejsgaard <sorenh@math.aau.dk>

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Package gRbase updated to version 2.0.1 with previous version 2.0.0 dated 2023-09-22

Title: A Package for Graphical Modelling in R
Description: The 'gRbase' package provides graphical modelling features used by e.g. the packages 'gRain', 'gRim' and 'gRc'. 'gRbase' implements graph algorithms including (i) maximum cardinality search (for marked and unmarked graphs). (ii) moralization, (iii) triangulation, (iv) creation of junction tree. 'gRbase' facilitates array operations, 'gRbase' implements functions for testing for conditional independence. 'gRbase' illustrates how hierarchical log-linear models may be implemented and describes concept of graphical meta data. The facilities of the package are documented in the book by Højsgaard, Edwards and Lauritzen (2012, <doi:10.1007/978-1-4614-2299-0>) and in the paper by Dethlefsen and Højsgaard, (2005, <doi:10.18637/jss.v014.i17>). Please see 'citation("gRbase")' for citation details.
Author: Soeren Hoejsgaard <sorenh@math.aau.dk>
Maintainer: Soeren Hoejsgaard <sorenh@math.aau.dk>

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New package countts with initial version 0.1.0
Package: countts
Title: Thomson Sampling for Zero-Inflated Count Outcomes
Version: 0.1.0
Description: A specialized tool is designed for assessing contextual bandit algorithms, particularly those aimed at handling overdispersed and zero-inflated count data. It offers a simulated testing environment that includes various models like Poisson, Overdispersed Poisson, Zero-inflated Poisson, and Zero-inflated Overdispersed Poisson. The package is capable of executing five specific algorithms: Linear Thompson sampling with log transformation on the outcome, Thompson sampling Poisson, Thompson sampling Negative Binomial, Thompson sampling Zero-inflated Poisson, and Thompson sampling Zero-inflated Negative Binomial. Additionally, it can generate regret plots to evaluate the performance of contextual bandit algorithms. This package is based on the algorithms by Liu et al. (2023) <arXiv:2311.14359>.
Maintainer: Tanujit Chakraborty <tanujitisi@gmail.com>
License: GPL (>= 2)
Encoding: UTF-8
Imports: MASS, parallel, fastDummies, matrixStats, ggplot2, stats
NeedsCompilation: no
Packaged: 2023-11-29 04:15:35 UTC; mad-s
Author: Xueqing Liu [aut], Nina Deliu [aut], Tanujit Chakraborty [aut, cre, cph] , Lauren Bell [aut], Bibhas Chakraborty [aut]
Repository: CRAN
Date/Publication: 2023-11-29 14:00:10 UTC

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Package convertid updated to version 0.1.8 with previous version 0.1.7 dated 2023-11-04

Title: Convert Gene IDs Between Each Other and Fetch Annotations from Biomart
Description: Gene Symbols or Ensembl Gene IDs are converted using the Bimap interface in 'AnnotationDbi' in convertId2() but that function is only provided as fallback mechanism for the most common use cases in data analysis. The main function in the package is convert.bm() which queries BioMart using the full capacity of the API provided through the 'biomaRt' package. Presets and defaults are provided for convenience but all "marts", "filters" and "attributes" can be set by the user. Function convert.alias() converts Gene Symbols to Aliases and vice versa and function likely_symbol() attempts to determine the most likely current Gene Symbol.
Author: Vidal Fey [aut, cre], Henrik Edgren [aut]
Maintainer: Vidal Fey <vidal.fey@gmail.com>

Diff between convertid versions 0.1.7 dated 2023-11-04 and 0.1.8 dated 2023-11-29

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Package COMPoissonReg updated to version 0.8.1 with previous version 0.8.0 dated 2022-12-02

Title: Conway-Maxwell Poisson (COM-Poisson) Regression
Description: Fit Conway-Maxwell Poisson (COM-Poisson or CMP) regression models to count data (Sellers & Shmueli, 2010) <doi:10.1214/09-AOAS306>. The package provides functions for model estimation, dispersion testing, and diagnostics. Zero-inflated CMP regression (Sellers & Raim, 2016) <doi:10.1016/j.csda.2016.01.007> is also supported.
Author: Kimberly Sellers <kfs7@georgetown.edu> Thomas Lotze <thomas.lotze@thomaslotze.com> Andrew Raim <andrew.raim@gmail.com>
Maintainer: Andrew Raim <andrew.raim@gmail.com>

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Package cauphy updated to version 1.0.2 with previous version 1.0.1 dated 2023-09-19

Title: Trait Evolution on Phylogenies Using the Cauchy Process
Description: The Cauchy Process can model pulsed continuous trait evolution on phylogenies. The likelihood is tractable, and is used for parameter inference and ancestral trait reconstruction. See Bastide and Didier (2023) <doi:10.1093/sysbio/syad053>.
Author: Gilles Didier [aut, cph], Paul Bastide [aut, cre]
Maintainer: Paul Bastide <paul.bastide@cnrs.fr>

Diff between cauphy versions 1.0.1 dated 2023-09-19 and 1.0.2 dated 2023-11-29

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New package admtools with initial version 0.0.1
Package: admtools
Title: Estimate and Manipulate Age-Depth Models
Version: 0.0.1
Description: Estimate age-depth models from stratigraphic and sedimentological data, and transform data between the time and stratigraphic domain.
URL: https://github.com/MindTheGap-ERC/admtools
BugReports: https://github.com/MindTheGap-ERC/admtools/issues
License: Apache License (== 2.0)
Encoding: UTF-8
Depends: R (>= 2.10)
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-11-29 07:08:12 UTC; hohma004
Author: Niklas Hohmann [aut, cre]
Maintainer: Niklas Hohmann <N.H.Hohmann@uu.nl>
Repository: CRAN
Date/Publication: 2023-11-29 14:00:13 UTC

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Package thor updated to version 1.1.5 with previous version 1.1.4 dated 2023-02-07

Title: Interface to 'LMDB'
Description: Key-value store, implemented as a wrapper around 'LMDB'; the "lightning memory-mapped database" <https://www.symas.com/lmdb>. 'LMDB' is a transactional key value store that uses a memory map for efficient access. This package wraps the entire 'LMDB' interface (except duplicated keys), and provides objects for transactions and cursors.
Author: Rich FitzJohn [aut, cre], Howard Chu [aut, cph], Symas Corporation [cph], Martin Hedenfalk [aut, cph], The OpenLDAP Foundation [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>

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Package socialranking updated to version 1.1.0 with previous version 1.0.1 dated 2023-08-23

Title: Social Ranking Solutions for Power Relations on Coalitions
Description: The notion of power index has been widely used in literature to evaluate the influence of individual players (e.g., voters, political parties, nations, stockholders, etc.) involved in a collective decision situation like an electoral system, a parliament, a council, a management board, etc., where players may form coalitions. Traditionally this ranking is determined through numerical evaluation. More often than not however only ordinal data between coalitions is known. The package 'socialranking' offers a set of solutions to rank players based on a transitive ranking between coalitions, including through CP-Majority, ordinal Banzhaf or lexicographic excellence solution summarized by Tahar Allouche, Bruno Escoffier, Stefano Moretti and Meltem Öztürk (2020, <doi:10.24963/ijcai.2020/3>).
Author: Felix Fritz [aut, cre], Jochen Staudacher [aut, cph, ths], Moretti Stefano [aut, cph, ths]
Maintainer: Felix Fritz <felix.fritz@dauphine.eu>

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Package simcross updated to version 0.6 with previous version 0.3-6 dated 2020-09-24

Title: Simulate Experimental Crosses
Description: Simulate and plot general experimental crosses. The focus is on simulating genotypes with an aim towards flexibility rather than speed. Meiosis is simulated following the Stahl model, in which chiasma locations are the superposition of two processes: a proportion p coming from a process exhibiting no interference, and the remainder coming from a process following the chi-square model.
Author: Karl W Broman [aut, cre]
Maintainer: Karl W Broman <broman@wisc.edu>

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Package remstats updated to version 3.2.1 with previous version 3.2.0 dated 2023-11-17

Title: Computes Statistics for Relational Event History Data
Description: Computes a variety of statistics for relational event models. Relational event models enable researchers to investigate both exogenous and endogenous factors influencing the evolution of a time-ordered sequence of events. These models are categorized into tie-oriented models (Butts, C., 2008, <doi:10.1111/j.1467-9531.2008.00203.x>), where the probability of a dyad interacting next is modeled in a single step, and actor-oriented models (Stadtfeld, C., & Block, P., 2017, <doi:10.15195/v4.a14>), which first model the probability of a sender initiating an interaction and subsequently the probability of the sender's choice of receiver. The package is designed to compute a variety of statistics that summarize exogenous and endogenous influences on the event stream for both types of models.
Author: Marlyne Meijerink-Bosman [aut, cre], Giuseppe Arena [ctb], Diana Karimova [ctb], Rumana Lakdawala [ctb], Mahdi Shafiee Kamalabad [ctb], Fabio Generoso Vieira [ctb], Roger Leenders [ctb], Joris Mulder [ctb]
Maintainer: Marlyne Meijerink-Bosman <m.l.meijerink@tilburguniversity.edu>

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Package PoissonBinomial updated to version 1.2.6 with previous version 1.2.5 dated 2022-05-31

Title: Efficient Computation of Ordinary and Generalized Poisson Binomial Distributions
Description: Efficient implementations of multiple exact and approximate methods as described in Hong (2013) <doi:10.1016/j.csda.2012.10.006>, Biscarri, Zhao & Brunner (2018) <doi:10.1016/j.csda.2018.01.007> and Zhang, Hong & Balakrishnan (2018) <doi:10.1080/00949655.2018.1440294> for computing the probability mass, cumulative distribution and quantile functions, as well as generating random numbers for both the ordinary and generalized Poisson binomial distribution.
Author: Florian Junge [aut, cre]
Maintainer: Florian Junge <florian.junge@mailbox.org>

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Package meteoland updated to version 2.2.1 with previous version 2.1.0 dated 2023-08-21

Title: Landscape Meteorology Tools
Description: Functions to estimate weather variables at any position of a landscape [De Caceres et al. (2018) <doi:10.1016/j.envsoft.2018.08.003>].
Author: Miquel De Caceres [aut, cre] , Victor Granda [aut] , Nicolas Martin [aut] , Antoine Cabon [aut]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>

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Package gMCP updated to version 0.8-16 with previous version 0.8-15 dated 2020-03-23

Title: Graph Based Multiple Comparison Procedures
Description: Functions and a graphical user interface for graphical described multiple test procedures.
Author: Kornelius Rohmeyer [aut, cre], Florian Klinglmueller [aut]
Maintainer: Kornelius Rohmeyer <rohmeyer@small-projects.de>

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Package expm updated to version 0.999-8 with previous version 0.999-7 dated 2023-01-09

Title: Matrix Exponential, Log, 'etc'
Description: Computation of the matrix exponential, logarithm, sqrt, and related quantities, using traditional and modern methods.
Author: Martin Maechler [aut, cre] , Christophe Dutang [aut] , Vincent Goulet [aut] , Douglas Bates [ctb] , David Firth [ctb] ), Marina Shapira [ctb] ), Michael Stadelmann [ctb]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>

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Package XML updated to version 3.99-0.16 with previous version 3.99-0.15 dated 2023-11-02

Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an 'XPath' "interpreter".
Author: CRAN Team [ctb, cre] , Duncan Temple Lang [aut] , Tomas Kalibera [ctb]
Maintainer: CRAN Team <CRAN@r-project.org>

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Package WienR updated to version 0.3-15 with previous version 0.3-14 dated 2023-07-04

Title: Derivatives of the First-Passage Time Density and Cumulative Distribution Function, and Random Sampling from the (Truncated) First-Passage Time Distribution
Description: First, we provide functions to calculate the partial derivative of the first-passage time diffusion probability density function (PDF) and cumulative distribution function (CDF) with respect to the first-passage time t (only for PDF), the upper barrier a, the drift rate v, the relative starting point w, the non-decision time t0, the inter-trial variability of the drift rate sv, the inter-trial variability of the rel. starting point sw, and the inter-trial variability of the non-decision time st0. In addition the PDF and CDF themselves are also provided. Most calculations are done on the logarithmic scale to make it more stable. Since the PDF, CDF, and their derivatives are represented as infinite series, we give the user the option to control the approximation errors with the argument 'precision'. For the numerical integration we used the C library cubature by Johnson, S. G. (2005-2013) <https://github.com/stevengj/cubature>. Numerical integration is required whenever sv, sw, and [...truncated...]
Author: Raphael Hartmann [aut, cre], Karl C. Klauer [cph, aut, ctb, ths], Steven G. Johnson [ctb], Jean M. Linhart [ctb], Brian Gough [ctb], Gerard Jungman [ctb], Rudolf Schuerer [ctb], Przemyslaw Sliwa [ctb], Jason H. Stover [ctb]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>

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Package tgstat updated to version 2.3.25 with previous version 2.3.24 dated 2023-06-27

Title: Amos Tanay's Group High Performance Statistical Utilities
Description: A collection of high performance utilities to compute distance, correlation, auto correlation, clustering and other tasks. Contains graph clustering algorithm described in "MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions" (Yael Baran, Akhiad Bercovich, Arnau Sebe-Pedros, Yaniv Lubling, Amir Giladi, Elad Chomsky, Zohar Meir, Michael Hoichman, Aviezer Lifshitz & Amos Tanay, 2019 <doi:10.1186/s13059-019-1812-2>).
Author: Michael Hoichman [aut], Aviezer Lifshitz [aut, cre]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>

Diff between tgstat versions 2.3.24 dated 2023-06-27 and 2.3.25 dated 2023-11-29

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Package tau updated to version 0.0-25 with previous version 0.0-24 dated 2021-07-21

Title: Text Analysis Utilities
Description: Utilities for text analysis.
Author: Christian Buchta [aut], Kurt Hornik [aut, cre] , Ingo Feinerer [aut], David Meyer [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

Diff between tau versions 0.0-24 dated 2021-07-21 and 0.0-25 dated 2023-11-29

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Package simer updated to version 0.9.0.4 with previous version 0.9.0.3 dated 2023-10-12

Title: Data Simulation for Life Science and Breeding
Description: Data simulator including genotype, phenotype, pedigree, selection and reproduction in R. It simulates most of reproduction process of animals or plants and provides data for GS (Genomic Selection), GWAS (Genome-Wide Association Study), and Breeding. For ADI model, please see Kao C and Zeng Z (2002) <doi:10.1093/genetics/160.3.1243>. For build.cov, please see B. D. Ripley (1987) <ISBN:9780470009604>.
Author: Dong Yin [aut], Xuanning Zhang [aut], Lilin Yin [aut], Haohao Zhang [aut], Zhenshuang Tang [aut], Jingya Xu [aut], Xiaohui Yuan [aut], Xiang Zhou [aut], Xinyun Li [aut], Shuhong Zhao [aut], Xiaolei Liu [cre, aut, cph]
Maintainer: Xiaolei Liu <xll198708@gmail.com>

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Package Rogue updated to version 2.1.6 with previous version 2.1.5 dated 2023-03-20

Title: Identify Rogue Taxa in Sets of Phylogenetic Trees
Description: Rogue ("wildcard") taxa are leaves with uncertain phylogenetic position. Their position may vary from tree to tree under inference methods that yield a tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony). The presence of rogue taxa in a tree set can potentially remove all information from a consensus tree. The information content of a consensus tree - a function of its resolution and branch support values - can often be increased by removing rogue taxa. 'Rogue' provides an explicitly information-theoretic approach to rogue detection (Smith 2022) <doi:10.1093/sysbio/syab099>, and an interface to 'RogueNaRok' (Aberer et al. 2013) <doi:10.1093/sysbio/sys078>.
Author: Martin R. Smith [aut, cre, cph] , Andre J. Aberer [aut, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>

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Package ring updated to version 1.0.5 with previous version 1.0.4 dated 2023-04-28

Title: Circular / Ring Buffers
Description: Circular / ring buffers in R and C. There are a couple of different buffers here with different implementations that represent different trade-offs.
Author: Rich FitzJohn [aut, cre], Imperial College of Science, Technology and Medicine [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>

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Package nuggets updated to version 1.0.1 with previous version 1.0.0 dated 2023-11-28

Title: Extensible Data Pattern Searching Framework
Description: Extensible framework for subgroup discovery (Atzmueller (2015) <doi:10.1002/widm.1144>), contrast patterns (Chen (2022) <doi:10.48550/arXiv.2209.13556>), emerging patterns (Dong (1999) <doi:10.1145/312129.312191>) and association rules (Agrawal (1994) <https://www.vldb.org/conf/1994/P487.PDF>). Both crisp (binary) and fuzzy data are supported. It generates conditions in the form of elementary conjunctions, evaluates them on a dataset and checks the induced sub-data for interesting statistical properties. Currently, the package searches for implicative association rules and conditional correlations (Hájek (1978) <doi:10.1007/978-3-642-66943-9>). A user-defined function may be defined to evaluate on each generated condition to search for custom patterns.
Author: Michal Burda [aut, cre]
Maintainer: Michal Burda <michal.burda@osu.cz>

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Package island updated to version 0.2.10 with previous version 0.2.9 dated 2023-01-23

Title: Stochastic Island Biogeography Theory Made Easy
Description: Develops stochastic models based on the Theory of Island Biogeography (TIB) of MacArthur and Wilson (1967) <doi:10.1023/A:1016393430551> and extensions. It implements methods to estimate colonization and extinction rates (including environmental variables) given presence-absence data, simulates community assembly, and performs model selection.
Author: Vicente Jimenez [aut, cre], David Alonso [aut]
Maintainer: Vicente Jimenez <vicente.jimenez.ontiveros@gmail.com>

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Package diffusr (with last version 0.1.4) was removed from CRAN

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

2018-05-17 0.1.4
2018-04-21 0.1.3
2017-10-29 0.1.2
2017-06-05 0.1.1
2016-11-27 0.1.0

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Package openxlsx2 updated to version 1.2 with previous version 1.1 dated 2023-10-23

Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by providing a high level interface to writing, styling and editing worksheets.
Author: Jordan Mark Barbone [aut] , Jan Marvin Garbuszus [aut, cre], Oliver Roy [ctb], openxlsx authors [cph] , Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>

Diff between openxlsx2 versions 1.1 dated 2023-10-23 and 1.2 dated 2023-11-29

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Package AnthropMMD updated to version 4.0.3 with previous version 4.0.2 dated 2023-08-08

Title: An R Package for the Mean Measure of Divergence (MMD)
Description: Offers a graphical user interface for the calculation of the mean measure of divergence, with facilities for trait selection and graphical representations <doi:10.1002/ajpa.23336>.
Author: Frederic Santos [aut, cre]
Maintainer: Frederic Santos <frederic.santos@u-bordeaux.fr>

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Package robustbase updated to version 0.99-1 with previous version 0.99-0 dated 2023-06-16

Title: Basic Robust Statistics
Description: "Essential" Robust Statistics. Tools allowing to analyze data with robust methods. This includes regression methodology including model selections and multivariate statistics where we strive to cover the book "Robust Statistics, Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
Author: Martin Maechler [aut, cre] , Peter Rousseeuw [ctb] , Christophe Croux [ctb] , Valentin Todorov [aut] , Andreas Ruckstuhl [aut] , Matias Salibian-Barrera [aut] , Tobias Verbeke [ctb, fnd] , Manuel Koller [aut] , Eduardo L. T. Conceicao [aut] , Maria A [...truncated...]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>

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Package happign updated to version 0.2.2 with previous version 0.2.1 dated 2023-11-18

Title: R Interface to 'IGN' Web Services
Description: Automatic open data acquisition from resources of IGN ('Institut National de Information Geographique et forestiere') (<https://www.ign.fr/>). Available datasets include various types of raster and vector data, such as digital elevation models, state borders, spatial databases, cadastral parcels, and more. There also access to point clouds data ('LIDAR') and specifics API (<https://apicarto.ign.fr/api/doc/>).
Author: Paul Carteron [aut, cre]
Maintainer: Paul Carteron <carteronpaul@gmail.com>

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Package seriation updated to version 1.5.3 with previous version 1.5.2 dated 2023-11-26

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>

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Package harmony updated to version 1.2.0 with previous version 1.1.0 dated 2023-10-23

Title: Fast, Sensitive, and Accurate Integration of Single Cell Data
Description: Implementation of the Harmony algorithm for single cell integration, described in Korsunsky et al <doi:10.1038/s41592-019-0619-0>. Package includes a standalone Harmony function and interfaces to external frameworks.
Author: Ilya Korsunsky [cre, aut] , Martin Hemberg [aut] , Nikolaos Patikas [aut, ctb] , Hongcheng Yao [aut, ctb] , Nghia Millard [aut] , Jean Fan [aut, ctb] , Kamil Slowikowski [aut, ctb] , Miles Smith [ctb], Soumya Raychaudhuri [aut]
Maintainer: Ilya Korsunsky <ilya.korsunsky@gmail.com>

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Package gdalraster updated to version 1.7.0 with previous version 1.6.0 dated 2023-10-27

Title: Bindings to the 'Geospatial Data Abstraction Library' Raster API
Description: Interface to the Raster API of the 'Geospatial Data Abstraction Library' ('GDAL') supporting manual creation of uninitialized datasets, creation from existing raster as template, low level I/O, configuration of virtual raster (VRT), coordinate transformation, and access to 'gdalwarp' for reprojection. Includes several 'GDAL' algorithms and functions for working with spatial reference systems. Calling signatures resemble the native C, C++ and Python APIs provided by the 'GDAL' project (<https://gdal.org>). Bindings are implemented via exposed C++ class encapsulating a 'GDALDataset' and its associated 'GDALRasterBand' objects, plus several stand-alone functions. Additional functionality includes: class 'RunningStats' for efficient summary statistics on large data streams; class 'CmbTable' for counting unique combinations of integers with a hash table; raster 'combine()' to identify and count unique pixel combinations across multiple input layers; raster 'calc()' to evaluate an R ex [...truncated...]
Author: Chris Toney [aut, cre] , Frank Warmerdam [ctb, cph] , Even Rouault [ctb, cph] , Marius Appel [ctb, cph] , Daniel James [ctb, cph] , Peter Dimov [ctb, cph]
Maintainer: Chris Toney <chris.toney@usda.gov>

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Package arules updated to version 1.7-7 with previous version 1.7-6 dated 2023-03-23

Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing, manipulating and analyzing transaction data and patterns (frequent itemsets and association rules). Also provides C implementations of the association mining algorithms Apriori and Eclat. Hahsler, Gruen and Hornik (2005) <doi:10.18637/jss.v014.i15>.
Author: Michael Hahsler [aut, cre, cph] , Christian Buchta [aut, cph], Bettina Gruen [aut, cph], Kurt Hornik [aut, cph] , Christian Borgelt [ctb, cph], Ian Johnson [ctb], Makhlouf Ledmi [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

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Package rankUncertainty (with last version 1.0.2.0) was removed from CRAN

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

2021-11-15 1.0.2.0
2021-07-27 1.0.1.0
2021-07-12 1.0.0.0

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Package simcdm updated to version 0.1.2 with previous version 0.1.1 dated 2019-03-10

Title: Simulate Cognitive Diagnostic Model ('CDM') Data
Description: Provides efficient R and 'C++' routines to simulate cognitive diagnostic model data for Deterministic Input, Noisy "And" Gate ('DINA') and reduced Reparameterized Unified Model ('rRUM') from Culpepper and Hudson (2017) <doi: 10.1177/0146621617707511>, Culpepper (2015) <doi:10.3102/1076998615595403>, and de la Torre (2009) <doi:10.3102/1076998607309474>.
Author: James Joseph Balamuta [aut, cre, cph] , Steven Andrew Culpepper [aut, cph] , Aaron Hudson [ctb, cph]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>

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Package rrum updated to version 0.2.1 with previous version 0.2.0 dated 2019-02-11

Title: Bayesian Estimation of the Reduced Reparameterized Unified Model with Gibbs Sampling
Description: Implementation of Gibbs sampling algorithm for Bayesian Estimation of the Reduced Reparameterized Unified Model ('rrum'), described by Culpepper and Hudson (2017) <doi: 10.1177/0146621617707511>.
Author: Steven Andrew Culpepper [aut, cph] , Aaron Hudson [aut, cph] , James Joseph Balamuta [aut, cph, cre]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>

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Package MSCMT updated to version 1.3.9 with previous version 1.3.8 dated 2023-11-13

Title: Multivariate Synthetic Control Method Using Time Series
Description: Three generalizations of the synthetic control method (which has already an implementation in package 'Synth') are implemented: first, 'MSCMT' allows for using multiple outcome variables, second, time series can be supplied as economic predictors, and third, a well-defined cross-validation approach can be used. Much effort has been taken to make the implementation as stable as possible (including edge cases) without losing computational efficiency. A detailed description of the main algorithms is given in Becker and Klößner (2018) <doi:10.1016/j.ecosta.2017.08.002>.
Author: Martin Becker [aut, cre] , Stefan Kloessner [aut], Karline Soetaert [com], Jack Dongarra [cph], R.J. Hanson [cph], K.H. Haskell [cph], Cleve Moler [cph], LAPACK authors [cph]
Maintainer: Martin Becker <martin.becker@mx.uni-saarland.de>

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Package mnorm updated to version 1.2.2 with previous version 1.2.1 dated 2023-08-22

Title: Multivariate Normal Distribution
Description: Calculates and differentiates probabilities and density of (conditional) multivariate normal distribution and Gaussian copula (with various marginal distributions) using methods described in A. Genz (2004) <doi:10.1023/B:STCO.0000035304.20635.31>, A. Genz, F. Bretz (2009) <doi:10.1007/978-3-642-01689-9>, H. I. Gassmann (2003) <doi:10.1198/1061860032283> and E. Kossova, B. Potanin (2018) <https://ideas.repec.org/a/ris/apltrx/0346.html>.
Author: Bogdan Potanin [aut, cre, ctb], Sofiia Dolgikh [ctb]
Maintainer: Bogdan Potanin <bogdanpotanin@gmail.com>

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Package vitae updated to version 0.5.4 with previous version 0.5.3 dated 2023-03-21

Title: Curriculum Vitae for R Markdown
Description: Provides templates and functions to simplify the production and maintenance of curriculum vitae.
Author: Mitchell O'Hara-Wild [aut, cre] , Rob Hyndman [aut] , Yihui Xie [ctb] , Albert Krewinkel [cph] , JooYoung Seo [ctb] , Isabelle Greco [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>

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Package trajr updated to version 1.5.1 with previous version 1.5.0 dated 2023-06-24

Title: Animal Trajectory Analysis
Description: A toolbox to assist with statistical analysis of animal trajectories. It provides simple access to algorithms for calculating and assessing a variety of characteristics such as speed and acceleration, as well as multiple measures of straightness or tortuosity. Some support is provided for 3-dimensional trajectories. McLean & Skowron Volponi (2018) <doi:10.1111/eth.12739>.
Author: Jim McLean [aut, cre]
Maintainer: Jim McLean <jim_mclean@optusnet.com.au>

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 trajr-1.5.1/trajr/MD5                                                                            |   39 +--
 trajr-1.5.1/trajr/NEWS.md                                                                        |    4 
 trajr-1.5.1/trajr/R/speed.R                                                                      |    2 
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Package spatstat.random updated to version 3.2-2 with previous version 3.2-1 dated 2023-10-21

Title: Random Generation Functionality for the 'spatstat' Family
Description: Functionality for random generation of spatial data in the 'spatstat' family of packages. Generates random spatial patterns of points according to many simple rules (complete spatial randomness, Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns (thinning, random shift, jittering), simulated realisations of random point processes including simple sequential inhibition, Matern inhibition models, Neyman-Scott cluster processes (using direct, Brix-Kendall, or hybrid algorithms), log-Gaussian Cox processes, product shot noise cluster processes and Gibbs point processes (using Metropolis-Hastings birth-death-shift algorithm, alternating Gibbs sampler, or coupling-from-the-past perfect simulation). Also generates random spatial patterns of line segments, random tessellations, and random images (random noise, random mosaics). Excludes random generation on a linear network, which is covered by the separate package 'spatstat.linnet'.
Author: Adrian Baddeley [aut, cre, cph] , Rolf Turner [aut, cph] , Ege Rubak [aut, cph] , Tilman Davies [aut, cph] , Kasper Klitgaard Berthelsen [ctb, cph], David Bryant [ctb, cph], Ya-Mei Chang [ctb, cph], Ute Hahn [ctb], Abdollah Jalilian [ctb], Dominic Sc [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

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Package mlpack updated to version 4.3.0 with previous version 4.2.1 dated 2023-09-26

Title: 'Rcpp' Integration for the 'mlpack' Library
Description: A fast, flexible machine learning library, written in C++, that aims to provide fast, extensible implementations of cutting-edge machine learning algorithms. See also Curtin et al. (2023) <doi:10.21105/joss.05026>.
Author: Yashwant Singh Parihar [aut, ctb, cph], Ryan Curtin [aut, ctb, cph, cre], Dirk Eddelbuettel [aut, ctb, cph], James Balamuta [aut, ctb, cph], Bill March [ctb, cph], Dongryeol Lee [ctb, cph], Nishant Mehta [ctb, cph], Parikshit Ram [ctb, cph], James Cl [...truncated...]
Maintainer: Ryan Curtin <ryan@ratml.org>

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Package hpa updated to version 1.3.3 with previous version 1.3.1 dated 2023-05-07

Title: Distributions Hermite Polynomial Approximation
Description: Multivariate conditional and marginal densities, moments, cumulative distribution functions as well as binary choice and sample selection models based on Hermite polynomial approximation which was proposed and described by A. Gallant and D. W. Nychka (1987) <doi:10.2307/1913241>.
Author: Potanin Bogdan
Maintainer: Potanin Bogdan <bogdanpotanin@gmail.com>

Diff between hpa versions 1.3.1 dated 2023-05-07 and 1.3.3 dated 2023-11-29

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 MD5                 |    6 +--
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Package wk updated to version 0.9.1 with previous version 0.9.0 dated 2023-10-22

Title: Lightweight Well-Known Geometry Parsing
Description: Provides a minimal R and C++ API for parsing well-known binary and well-known text representation of geometries to and from R-native formats. Well-known binary is compact and fast to parse; well-known text is human-readable and is useful for writing tests. These formats are useful in R only if the information they contain can be accessed in R, for which high-performance functions are provided here.
Author: Dewey Dunnington [aut, cre] , Edzer Pebesma [aut] , Anthony North [ctb]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>

Diff between wk versions 0.9.0 dated 2023-10-22 and 0.9.1 dated 2023-11-29

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 NEWS.md                   |    4 ++++
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 src/wkb-writer.c          |    2 +-
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Package libgeos updated to version 3.11.1-2 with previous version 3.11.1-1 dated 2023-01-19

Title: Open Source Geometry Engine ('GEOS') C API
Description: Provides the Open Source Geometry Engine ('GEOS') as a C API that can be used to write high-performance C and C++ geometry operations using R as an interface. Headers are provided to make linking to and using these functions from C++ code as easy and as safe as possible. This package contains an internal copy of the 'GEOS' library to guarantee the best possible consistency on multiple platforms.
Author: Dewey Dunnington [aut, cre] , GEOS authors [aut], Martin Davis [ctb, cph], Benjamin Campbell [ctb, cph], Tomasz Sowa [ctb, cph], Christian Kaiser [ctb, cph], David Skea [ctb, cph], Daniel Baston [ctb, cph], Sandro Santilli [ctb, cph], Mateusz Loskot [...truncated...]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>

Diff between libgeos versions 3.11.1-1 dated 2023-01-19 and 3.11.1-2 dated 2023-11-29

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Package gam updated to version 1.22-3 with previous version 1.22-2 dated 2023-03-27

Title: Generalized Additive Models
Description: Functions for fitting and working with generalized additive models, as described in chapter 7 of "Statistical Models in S" (Chambers and Hastie (eds), 1991), and "Generalized Additive Models" (Hastie and Tibshirani, 1990).
Author: Trevor Hastie
Maintainer: Trevor Hastie <hastie@stanford.edu>

Diff between gam versions 1.22-2 dated 2023-03-27 and 1.22-3 dated 2023-11-29

 ChangeLog    |    2 ++
 DESCRIPTION  |    8 ++++----
 MD5          |    6 +++---
 src/loessc.c |    6 +++---
 4 files changed, 12 insertions(+), 10 deletions(-)

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Package mgwrsar (with last version 1.0.4) was removed from CRAN

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

2023-04-17 1.0.4
2022-05-05 1.0
2021-05-06 0.1-1
2018-05-11 0.1

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Package qlcMatrix (with last version 0.9.7) was removed from CRAN

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

2018-04-20 0.9.7
2015-10-09 0.9.5
2015-04-27 0.9.4
2014-05-19 0.9.2
2014-05-17 0.9.1

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