Mon, 10 Jul 2023

Package secr updated to version 4.6.1 with previous version 4.6.0 dated 2023-05-23

Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford [aut, cre] , Philipp Jund [ctb] ), David Fletcher [ctb] )
Maintainer: Murray Efford <murray.efford@otago.ac.nz>

Diff between secr versions 4.6.0 dated 2023-05-23 and 4.6.1 dated 2023-07-10

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Package RcppSpdlog updated to version 0.0.14 with previous version 0.0.13 dated 2023-06-17

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 0.0.13 dated 2023-06-17 and 0.0.14 dated 2023-07-10

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Package RcppAlgos updated to version 2.8.0 with previous version 2.7.2 dated 2023-02-11

Title: High Performance Tools for Combinatorics and Computational Mathematics
Description: Provides optimized functions and flexible combinatorial iterators implemented in C++ for solving problems in combinatorics and computational mathematics. Utilizes the RMatrix class from 'RcppParallel' for thread safety. There are combination/permutation functions with constraint parameters that allow for generation of all results of a vector meeting specific criteria (e.g. generating integer partitions/compositions or finding all combinations such that the sum is between two bounds). Capable of generating specific combinations/permutations (e.g. retrieve only the nth lexicographical result) which sets up nicely for parallelization as well as random sampling. Gmp support permits exploration where the total number of results is large (e.g. comboSample(10000, 500, n = 4)). Additionally, there are several high performance number theoretic functions that are useful for problems common in computational mathematics. Some of these functions make use of the fast integer division library 'libdiv [...truncated...]
Author: Joseph Wood
Maintainer: Joseph Wood <jwood000@gmail.com>

Diff between RcppAlgos versions 2.7.2 dated 2023-02-11 and 2.8.0 dated 2023-07-10

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Permanent link

Package PTXQC updated to version 1.0.17 with previous version 1.0.16 dated 2023-05-17

Title: Quality Report Generation for MaxQuant and mzTab Results
Description: Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the MaxQuant software suite (from .txt files) or mzTab files (ideally from OpenMS 'QualityControl' tool). Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format. Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) <doi:10.1021/acs.jproteome.5b00780>.
Author: Chris Bielow [aut, cre], Juliane Schmachtenberg [ctb], Swenja Wagner [ctb], Patricia Scheil [ctb], Tom Waschischek [ctb], Guido Mastrobuoni [dtc, rev]
Maintainer: Chris Bielow <chris.bielow@bsc.fu-berlin.de>

Diff between PTXQC versions 1.0.16 dated 2023-05-17 and 1.0.17 dated 2023-07-10

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Package piggyback updated to version 0.1.5 with previous version 0.1.4 dated 2022-07-19

Title: Managing Larger Data on a GitHub Repository
Description: Because larger (> 50 MB) data files cannot easily be committed to git, a different approach is required to manage data associated with an analysis in a GitHub repository. This package provides a simple work-around by allowing larger (up to 2 GB) data files to piggyback on a repository as assets attached to individual GitHub releases. These files are not handled by git in any way, but instead are uploaded, downloaded, or edited directly by calls through the GitHub API. These data files can be versioned manually by creating different releases. This approach works equally well with public or private repositories. Data can be uploaded and downloaded programmatically from scripts. No authentication is required to download data from public repositories.
Author: Carl Boettiger [aut, cre, cph] , Tan Ho [aut] , Mark Padgham [ctb] , Jeffrey O Hanson [ctb] , Kevin Kuo [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>

Diff between piggyback versions 0.1.4 dated 2022-07-19 and 0.1.5 dated 2023-07-10

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Package meteor updated to version 0.4-4 with previous version 0.3-4 dated 2019-08-08

Title: Meteorological Data Manipulation
Description: A set of functions for weather and climate data manipulation, and other helper functions, to support dynamic ecological modeling, particularly crop and crop disease modeling.
Author: Robert J. Hijmans [cre, aut], Gerald Nelson [ctb], Maarten Waterloo [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>

Diff between meteor versions 0.3-4 dated 2019-08-08 and 0.4-4 dated 2023-07-10

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Package MatrixModels updated to version 0.5-2 with previous version 0.5-1 dated 2022-09-11

Title: Modelling with Sparse and Dense Matrices
Description: Modelling with sparse and dense 'Matrix' matrices, using modular prediction and response module classes.
Author: Douglas Bates <bates@stat.wisc.edu> and Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>

Diff between MatrixModels versions 0.5-1 dated 2022-09-11 and 0.5-2 dated 2023-07-10

 ChangeLog             |   10 ++++++++
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 MD5                   |   14 +++++------
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Package FIESTAutils updated to version 1.1.8 with previous version 1.1.7 dated 2023-05-27

Title: Utility Functions for Forest Inventory Estimation and Analysis
Description: A set of tools for data wrangling, spatial data analysis, statistical modeling (including direct, model-assisted, photo-based, and small area tools), and USDA Forest Service data base tools. These tools are aimed to help Foresters, Analysts, and Scientists extract and perform analyses on USDA Forest Service data.
Author: Tracey Frescino [aut], Chris Toney [aut], Grayson White [aut, cre]
Maintainer: Grayson White <graysonwhite13@gmail.com>

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Package DDD updated to version 5.2.2 with previous version 5.2.1 dated 2023-02-22

Title: Diversity-Dependent Diversification
Description: Implements maximum likelihood and bootstrap methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent, under various models including various types of key innovations. See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, <DOI:10.1098/rspb.2011.1439>, Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, <DOI:10.1086/667574>, Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099, <DOI:10.1111/2041-210X.12565> and Laudanno et al. 2021. Syst. Biol. 70: 389–407, <DOI:10.1093/sysbio/syaa048>. Also contains functions to simulate the diversity-dependent process.
Author: Rampal S. Etienne [aut, cre] , Bart Haegeman [aut] , Hanno Hildenbrandt [ctb] , Giovanni Laudanno [ctb]
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>

Diff between DDD versions 5.2.1 dated 2023-02-22 and 5.2.2 dated 2023-07-10

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Package DCchoice updated to version 0.2.0 with previous version 0.1.1 dated 2022-08-19

Title: Analyzing Dichotomous Choice Contingent Valuation Data
Description: Functions for analyzing dichotomous choice contingent valuation (CV) data. It provides functions for estimating parametric and nonparametric models for single-, one-and-one-half-, and double-bounded CV data. For details, see Aizaki et al. (2022) <doi:10.1007/s42081-022-00171-1>.
Author: Tomoaki Nakatani [aut, cph] , Hideo Aizaki [aut, cre], Kazuo Sato [ctb]
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>

Diff between DCchoice versions 0.1.1 dated 2022-08-19 and 0.2.0 dated 2023-07-10

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Package crew updated to version 0.4.0 with previous version 0.3.0 dated 2023-06-26

Title: A Distributed Worker Launcher Framework
Description: In computationally demanding analysis projects, statisticians and data scientists asynchronously deploy long-running tasks to distributed systems, ranging from traditional clusters to cloud services. The 'NNG'-powered 'mirai' R package by Gao (2023) <https://CRAN.R-project.org/package=mirai> is a sleek and sophisticated scheduler that efficiently processes these intense workloads. The 'crew' package extends 'mirai' with a unifying interface for third-party worker launchers. Inspiration also comes from packages. 'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>, 'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>, 'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>), and 'batchtools' by Lang, Bischel, and Surmann (2017) <doi:10.21105/joss.00135>.
Author: William Michael Landau [aut, cre] , Daniel Woodie [ctb], Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>

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Package compound.Cox updated to version 3.30 with previous version 3.29 dated 2023-06-18

Title: Univariate Feature Selection and Compound Covariate for Predicting Survival
Description: Univariate feature selection and compound covariate methods under the Cox model with high-dimensional features (e.g., gene expressions). Available are survival data for non-small-cell lung cancer patients with gene expressions (Chen et al 2007 New Engl J Med) <DOI:10.1056/NEJMoa060096>, statistical methods in Emura et al (2012 PLoS ONE) <DOI:10.1371/journal.pone.0047627>, Emura & Chen (2016 Stat Methods Med Res) <DOI:10.1177/0962280214533378>, and Emura et al (2019)<DOI:10.1016/j.cmpb.2018.10.020>. Algorithms for generating correlated gene expressions are also available. Estimation of survival functions via copula-graphic (CG) estimators is also implemented, which is useful for sensitivity analyses under dependent censoring (Yeh et al 2023) <DOI:10.3390/biomedicines11030797>.
Author: Takeshi Emura, Hsuan-Yu Chen, Shigeyuki Matsui, Yi-Hau Chen
Maintainer: Takeshi Emura <takeshiemura@gmail.com>

Diff between compound.Cox versions 3.29 dated 2023-06-18 and 3.30 dated 2023-07-10

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Package vivid updated to version 0.2.8 with previous version 0.2.7 dated 2023-04-11

Title: Variable Importance and Variable Interaction Displays
Description: A suite of plots for displaying variable importance and two-way variable interaction jointly. Can also display partial dependence plots laid out in a pairs plot or 'zenplots' style.
Author: Alan Inglis [aut, cre], Andrew Parnell [aut], Catherine Hurley [aut]
Maintainer: Alan Inglis <alan.n.inglis@gmail.com>

Diff between vivid versions 0.2.7 dated 2023-04-11 and 0.2.8 dated 2023-07-10

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Package swipeR updated to version 1.0.0 with previous version 0.1.0 dated 2022-12-12

Title: Carousels using the 'JavaScript' Library 'Swiper'
Description: Create carousels using the 'JavaScript' library 'Swiper' and the package 'htmlwidgets'. The carousels can be displayed in the 'RStudio' viewer pane, in 'Shiny' applications and in 'R markdown' documents. The package also provides a 'RStudio' addin allowing to choose image files and to display them in the viewer pane.
Author: Stephane Laurent [aut, cre], Vladimir Kharlampidi [cph]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>

Diff between swipeR versions 0.1.0 dated 2022-12-12 and 1.0.0 dated 2023-07-10

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New package subselect with initial version 0.15.5
Package: subselect
Version: 0.15.5
Date: 2023-07-10
Title: Selecting Variable Subsets
Author: Jorge Orestes Cerdeira [aut], Pedro Duarte Silva [aut], Jorge Cadima [aut, cre], Manuel Minhoto [aut]
Maintainer: Jorge Cadima <jcadima@isa.ulisboa.pt>
Description: A collection of functions which (i) assess the quality of variable subsets as surrogates for a full data set, in either an exploratory data analysis or in the context of a multivariate linear model, and (ii) search for subsets which are optimal under various criteria. Theoretical support for the heuristic search methods and exploratory data analysis criteria is in Cadima, Cerdeira, Minhoto (2003, <doi:10.1016/j.csda.2003.11.001>). Theoretical support for the leap and bounds algorithm and the criteria for the general multivariate linear model is in Duarte Silva (2001, <doi:10.1006/jmva.2000.1920>). There is a package vignette "subselect", which includes additional references.
Depends: R (>= 3.5.0)
Imports: MASS, ISwR, corpcor
License: GPL (>= 2)
Repository: CRAN
LazyData: TRUE
NeedsCompilation: yes
Packaged: 2023-07-10 09:41:40 UTC; jcadima
Date/Publication: 2023-07-10 22:30:12 UTC

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New package ppmSuite with initial version 0.3.3
Package: ppmSuite
Title: A Collection of Models that Employ Product Partition Distributions as a Prior on Partitions
Version: 0.3.3
Maintainer: Garritt L. Page <page@stat.byu.edu>
Description: Provides a suite of functions that fit models that use PPM type priors for partitions. Models include hierarchical Gaussian and probit ordinal models with a (covariate dependent) PPM. If a covariate dependent product partition model is selected, then all the options detailed in Page, G.L.; Quintana, F.A. (2018) <doi:10.1007/s11222-017-9777-z> are available. If covariate values are missing, then the approach detailed in Page, G.L.; Quintana, F.A.; Mueller, P (2020) <doi:10.1080/10618600.2021.1999824> is employed. Also included in the package is a function that fits a Gaussian likelihood spatial product partition model that is detailed in Page, G.L.; Quintana, F.A. (2016) <doi:10.1214/15-BA971>, and multivariate PPM change point models that are detailed in Quinlan, J.J.; Page, G.L.; Castro, L.M. (2023) <doi:10.1214/22-BA1344>. In addition, a function that fits a univariate or bivariate functional data model that employs a PPM or a PPMx to cluster curves bas [...truncated...]
Depends: R (>= 3.5.0)
License: GPL
Encoding: UTF-8
LazyData: true
Suggests: cluster
Imports: Matrix
NeedsCompilation: yes
Packaged: 2023-07-09 11:59:37 UTC; gpage
Author: Garritt L. Page [aut, cre, cph], Jose J. Quinlan [aut, cph], S. McKay Curtis [ctb, cph], Radford M. Neal [ctb, cph]
Repository: CRAN
Date/Publication: 2023-07-10 22:30:17 UTC

More information about ppmSuite at CRAN
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Package designmatch updated to version 0.5.3 with previous version 0.5.1 dated 2023-06-26

Title: Matched Samples that are Balanced and Representative by Design
Description: Includes functions for the construction of matched samples that are balanced and representative by design. Among others, these functions can be used for matching in observational studies with treated and control units, with cases and controls, in related settings with instrumental variables, and in discontinuity designs. Also, they can be used for the design of randomized experiments, for example, for matching before randomization. By default, 'designmatch' uses the 'highs' optimization solver, but its performance is greatly enhanced by the 'Gurobi' optimization solver and its associated R interface. For their installation, please follow the instructions at <https://www.gurobi.com/documentation/quickstart.html> and <https://www.gurobi.com/documentation/7.0/refman/r_api_overview.html>. We have also included directions in the gurobi_installation file in the inst folder.
Author: Jose R. Zubizarreta <zubizarreta@hcp.med.harvard.edu>, Cinar Kilcioglu <ckilcioglu16@gsb.columbia.edu>, Juan P. Vielma <jvielma@mit.edu>, Eric R. Cohn <ericcohn@g.harvard.edu>
Maintainer: Jose R. Zubizarreta <zubizarreta@hcp.med.harvard.edu>

Diff between designmatch versions 0.5.1 dated 2023-06-26 and 0.5.3 dated 2023-07-10

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Package cthist updated to version 2.1.0 with previous version 2.0.0 dated 2023-07-09

Title: Clinical Trial Registry History
Description: Retrieves historical versions of clinical trial registry entries from <https://ClinicalTrials.gov>. Package functionality and implementation is documented in Carlisle (2022) <DOI:10.1371/journal.pone.0270909>.
Author: Benjamin Gregory Carlisle [aut, cre]
Maintainer: Benjamin Gregory Carlisle <murph@bgcarlisle.com>

Diff between cthist versions 2.0.0 dated 2023-07-09 and 2.1.0 dated 2023-07-10

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Package canadianmaps updated to version 1.3.0 with previous version 1.0.0 dated 2022-02-01

Title: Effortlessly Create Stunning Canadian Maps
Description: Simple and seamless access to a variety of 'StatCan' shapefiles for mapping Canadian provinces, regions, forward sortation areas, census divisions, and subdivisions using the popular 'ggplot2' package.
Author: Joelle Cayen [aut, cre]
Maintainer: Joelle Cayen <joelle.cayen@phac-aspc.gc.ca>

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Package stevedore updated to version 0.9.6 with previous version 0.9.5 dated 2022-11-11

Title: Docker Client
Description: Work with containers over the Docker API. Rather than using system calls to interact with a docker client, using the API directly means that we can receive richer information from docker. The interface in the package is automatically generated using the 'OpenAPI' (a.k.a., 'swagger') specification, and all return values are checked in order to make them type stable.
Author: Rich FitzJohn [aut, cre]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>

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Package safetensors updated to version 0.1.1 with previous version 0.1.0 dated 2023-06-13

Title: Safetensors File Format
Description: A file format for storing tensors that is secure (doesn't allow for code execution), fast and simple to implement. 'safetensors' also enables cross language and cross frameworks compatibility making it an ideal format for storing machine learning model weights.
Author: Daniel Falbel [aut, cre], Posit [cph]
Maintainer: Daniel Falbel <daniel@posit.co>

Diff between safetensors versions 0.1.0 dated 2023-06-13 and 0.1.1 dated 2023-07-10

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Package TCGAretriever updated to version 1.7 with previous version 1.5 dated 2019-12-17

Title: Retrieve Genomic and Clinical Data from CBioPortal Including TCGA Data
Description: The Cancer Genome Atlas (TCGA) is a program aimed at improving our understanding of Cancer Biology. Several TCGA Datasets are available online. 'TCGAretriever' helps accessing and downloading TCGA data hosted on 'cBioPortal' via its Web Interface (see <http://www.cbioportal.org/> for more information).
Author: Damiano Fantini
Maintainer: Damiano Fantini <damiano.fantini@gmail.com>

Diff between TCGAretriever versions 1.5 dated 2019-12-17 and 1.7 dated 2023-07-10

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Package sleev updated to version 1.0.3 with previous version 1.0.2 dated 2022-05-24

Title: Semiparametric Likelihood Estimation with Errors in Variables
Description: Efficient regression analysis under general two-phase sampling, where Phase I includes error-prone data and Phase II contains validated data on a subset.
Author: Sarah Lotspeich [aut], Ran Tao [aut, cre], Joey Sherrill [prg], Jiangmei Xiong [ctb]
Maintainer: Ran Tao <r.tao@vanderbilt.edu>

Diff between sleev versions 1.0.2 dated 2022-05-24 and 1.0.3 dated 2023-07-10

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Package sasLM updated to version 0.9.10 with previous version 0.9.9 dated 2023-06-05

Title: 'SAS' Linear Model
Description: This is a core implementation of 'SAS' procedures for linear models - GLM, REG, ANOVA, TTEST, FREQ, and UNIVARIATE. Some R packages provide type II and type III SS. However, the results of nested and complex designs are often different from those of 'SAS.' Different results does not necessarily mean incorrectness. However, many wants the same results to SAS. This package aims to achieve that. Reference: Littell RC, Stroup WW, Freund RJ (2002, ISBN:0-471-22174-0).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>

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Package proteus updated to version 1.1.1 with previous version 1.1.0 dated 2023-03-08

Title: Multiform Seq2Seq Model for Time-Feature Analysis
Description: Seq2seq time-feature analysis based on variational model, with a wide range of distributions available for the latent variable.
Author: Giancarlo Vercellino
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>

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Package pRecipe updated to version 3.0.0 with previous version 2.5.0 dated 2023-06-13

Title: Precipitation R Recipes
Description: An open-access tool/framework to download, validate, visualize, and analyze multi-source precipitation data. More information and an example of implementation can be found in Vargas Godoy and Markonis (2023, <doi:10.1016/j.envsoft.2023.105711>).
Author: Mijael Rodrigo Vargas Godoy [aut, cre] , Yannis Markonis [aut, ths]
Maintainer: Mijael Rodrigo Vargas Godoy <mirovago@gmail.com>

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Package NutrienTrackeR updated to version 1.3.0 with previous version 1.2.0 dated 2021-11-14

Title: Food Composition Information and Dietary Assessment
Description: Provides a tool set for food information and dietary assessment. It uses food composition data from several reference databases, including: 'USDA' (United States), 'CIQUAL' (France), 'BEDCA' (Spain), 'CNF' (Canada) and 'STFCJ' (Japan). 'NutrienTrackeR' calculates the intake levels for both macronutrient and micronutrients, and compares them with the recommended dietary allowances (RDA). It includes a number of visualization tools, such as time series plots of nutrient intake, and pie-charts showing the main foods contributing to the intake level of a given nutrient. A shiny app exposing the main functionalities of the package is also provided.
Author: Andrea Rodriguez-Martinez [aut], Rafael Ayala [aut, cre] , Mark Balchunas [aut], Daniel Gutierrez-Del-Rio [aut] , Ting-Hua Chen [aut] , Yacine Debbabi [aut], Lara Selles Vidal [aut]
Maintainer: Rafael Ayala <rafael.ayala@oist.jp>

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New package KSgeneral with initial version 1.1.2
Package: KSgeneral
Version: 1.1.2
Title: Computing P-Values of the K-S Test for (Dis)Continuous Null Distribution
Author: Dimitrina S. Dimitrova <D.Dimitrova@city.ac.uk>, Vladimir K. Kaishev <Vladimir.Kaishev.1@city.ac.uk> and Senren Tan <raymondtsrtsr@outlook.com>
Maintainer: Senren Tan <raymondtsrtsr@outlook.com>
Depends: R (>= 3.3.0)
SystemRequirements: fftw3 (>=3.3.4)
Copyright: Copyright holders of FFTW3: Copyright (c) 2003, 2007-11 Matteo Frigo; Copyright (c) 2003, 2007-11 Massachusetts Institute of Technology
Description: Computes a p-value of the one-sample two-sided (or one-sided, as a special case) Kolmogorov-Smirnov (KS) statistic, for any fixed critical level, and an arbitrary, possibly large sample size for a pre-specified purely discrete, mixed or continuous cumulative distribution function (cdf) under the null hypothesis. If a data sample is supplied, 'KSgeneral' computes the p-value corresponding to the value of the KS test statistic computed based on the user provided data sample. The package 'KSgeneral' implements a novel, accurate and efficient method named Exact-KS-FFT, expressing the p-value as a double-boundary non-crossing probability for a homogeneous Poisson process, which is then efficiently computed using Fast Fourier Transform (FFT). The package can also be used to compute and plot the complementary cdf of the KS statistic which is known to depend on the hypothesized distribution when the latter is discontinuous (i.e. purely discrete or mixed). To cite this package in publication us [...truncated...]
License: GPL (>= 2.0)
URL: https://github.com/raymondtsr/KSgeneral
Encoding: UTF-8
LazyData: true
Imports: Rcpp (>= 0.12.12), MASS, dgof
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2023-07-09 16:03:11 UTC; hedgehog
Repository: CRAN
Date/Publication: 2023-07-10 19:10:09 UTC

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Package hclust1d updated to version 0.1.0 with previous version 0.0.1 dated 2023-04-11

Title: Hierarchical Clustering of Univariate (1d) Data
Description: Univariate agglomerative hierarchical clustering with a comprehensive list of choices of a linkage function in O(n*log n) time. The better algorithmic time complexity is paired with an efficient 'C++' implementation.
Author: Szymon Nowakowski [aut, cre]
Maintainer: Szymon Nowakowski <s.nowakowski@mimuw.edu.pl>

Diff between hclust1d versions 0.0.1 dated 2023-04-11 and 0.1.0 dated 2023-07-10

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Package geonapi updated to version 0.7 with previous version 0.6-1 dated 2022-08-19

Title: 'GeoNetwork' API R Interface
Description: Provides an R interface to the 'GeoNetwork' API (<https://geonetwork-opensource.org/#api>) allowing to upload and publish metadata in a 'GeoNetwork' web-application and expose it to OGC CSW.
Author: Emmanuel Blondel [aut, cre]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>

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Package epca updated to version 1.1.0 with previous version 1.0.1 dated 2023-02-07

Title: Exploratory Principal Component Analysis
Description: Exploratory principal component analysis for large-scale dataset, including sparse principal component analysis and sparse matrix approximation.
Author: Fan Chen [aut, cre]
Maintainer: Fan Chen <fan.chen@wisc.edu>

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Package BrailleR updated to version 1.0.2 with previous version 0.32.1 dated 2021-10-22

Title: Improved Access for Blind Users
Description: Blind users do not have access to the graphical output from R without printing the content of graphics windows to an embosser of some kind. This is not as immediate as is required for efficient access to statistical output. The functions here are created so that blind people can make even better use of R. This includes the text descriptions of graphs, convenience functions to replace the functionality offered in many GUI front ends, and experimental functionality for optimising graphical content to prepare it for embossing as tactile images.
Author: A. Jonathan R. Godfrey [aut, cre] , Debra Warren [aut], Donal Fitzpatrick [ctb] , Duncan Murdoch [ctb], Greg Snow [ctb] , Henrik Bengtsson [ctb] , James Curtis [ctb], James Thompson [aut] , JooYoung Seo [ctb], Marshall Flax [ctb], Paul Murrell [aut] [...truncated...]
Maintainer: A. Jonathan R. Godfrey <a.j.godfrey@massey.ac.nz>

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Package VineCopula updated to version 2.5.0 with previous version 2.4.5 dated 2023-01-19

Title: Statistical Inference of Vine Copulas
Description: Provides tools for the statistical analysis of regular vine copula models, see Aas et al. (2009) <doi:10.1016/j.insmatheco.2007.02.001> and Dissman et al. (2013) <doi:10.1016/j.csda.2012.08.010>. The package includes tools for parameter estimation, model selection, simulation, goodness-of-fit tests, and visualization. Tools for estimation, selection and exploratory data analysis of bivariate copula models are also provided.
Author: Thomas Nagler [aut, cre], Ulf Schepsmeier [aut], Jakob Stoeber [aut], Eike Christian Brechmann [aut], Benedikt Graeler [aut], Tobias Erhardt [aut], Carlos Almeida [ctb], Aleksey Min [ctb, ths], Claudia Czado [ctb, ths], Mathias Hofmann [ctb], Matthia [...truncated...]
Maintainer: Thomas Nagler <mail@tnagler.com>

Diff between VineCopula versions 2.4.5 dated 2023-01-19 and 2.5.0 dated 2023-07-10

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Package RAFS updated to version 0.2.3 with previous version 0.2.2 dated 2023-05-30

Title: Robust Aggregative Feature Selection
Description: A cross-validated minimal-optimal feature selection algorithm. It utilises popularity counting, hierarchical clustering with feature dissimilarity measures, and prefiltering with all-relevant feature selection method to obtain the minimal-optimal set of features.
Author: Radoslaw Piliszek [aut, cre]
Maintainer: Radoslaw Piliszek <radoslaw.piliszek@gmail.com>

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Package r2rtf updated to version 1.1.0 with previous version 1.0.4 dated 2023-06-18

Title: Easily Create Production-Ready Rich Text Format (RTF) Table and Figure
Description: Create production-ready Rich Text Format (RTF) table and figure with flexible format.
Author: Yilong Zhang [aut, cre], Siruo Wang [aut], Simiao Ye [aut], Fansen Kong [aut], Brian Lang [aut], Nan Xiao [ctb], Madhusudhan Ginnaram [ctb], Ruchitbhai Patel [ctb], Huei-Ling Chen [ctb], Peikun Wu [ctb], Uday Preetham Palukuru [ctb], Daniel Woodie [c [...truncated...]
Maintainer: Yilong Zhang <elong0527@gmail.com>

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Package declared updated to version 0.22 with previous version 0.21 dated 2023-05-16

Title: Functions for Declared Missing Values
Description: A zero dependency package containing functions to declare labels and missing values, coupled with associated functions to create (weighted) tables of frequencies and various other summary measures. Some of the base functions have been rewritten to make use of the specific information about the missing values, most importantly to distinguish between empty and declared missing values. Some functions have similar functionality with the corresponding ones from packages "haven" and "labelled". The aim is to ensure as much compatibility as possible with these packages, while offering an alternative in the objects of class "declared".
Author: Adrian Dusa [aut, cre, cph] , Daniel Antal [ctb]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>

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 declared-0.22/declared/vignettes/b_Added_value.Rmd                               |   60 +--
 declared-0.22/declared/vignettes/c_Weighting.Rmd                                 |   18 
 declared-0.22/declared/vignettes/declared.theme                                  |    2 
 38 files changed, 954 insertions(+), 363 deletions(-)

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Package BayesTools updated to version 0.2.16 with previous version 0.2.15 dated 2023-06-23

Title: Tools for Bayesian Analyses
Description: Provides tools for conducting Bayesian analyses and Bayesian model averaging (Kass and Raftery, 1995, <doi:10.1080/01621459.1995.10476572>, Hoeting et al., 1999, <doi:10.1214/ss/1009212519>). The package contains functions for creating a wide range of prior distribution objects, mixing posterior samples from 'JAGS' and 'Stan' models, plotting posterior distributions, and etc... The tools for working with prior distribution span from visualization, generating 'JAGS' and 'bridgesampling' syntax to basic functions such as rng, quantile, and distribution functions.
Author: Frantisek Bartos [aut, cre]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>

Diff between BayesTools versions 0.2.15 dated 2023-06-23 and 0.2.16 dated 2023-07-10

 DESCRIPTION                      |    6 -
 MD5                              |   34 ++++----
 NAMESPACE                        |    1 
 NEWS.md                          |    5 +
 R/JAGS-fit.R                     |  127 ++++++++++++++++++++++++++++++---
 R/tools.R                        |    2 
 build/partial.rdb                |binary
 inst/doc/ComparisonR.html        |    4 -
 inst/doc/SpikeAndSlab.html       |    4 -
 man/JAGS_check_and_list.Rd       |    2 
 man/JAGS_fit.Rd                  |   20 ++++-
 man/Savage_Dickey_BF.Rd          |   62 ++++++++--------
 man/marginal_inference.Rd        |  130 +++++++++++++++++-----------------
 man/mpoint.Rd                    |   98 ++++++++++++-------------
 man/plot_marginal.Rd             |  148 +++++++++++++++++++--------------------
 man/remove_column.Rd             |   42 +++++------
 man/transform_factor_samples.Rd  |   48 ++++++------
 man/transform_meandif_samples.Rd |   48 ++++++------
 18 files changed, 455 insertions(+), 326 deletions(-)

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New package TML with initial version 0.1.0
Package: TML
Title: Tropical Geometry Tools for Machine Learning
Version: 0.1.0
Description: Suite of tropical geometric tools for use in machine learning applications. These methods may be summarized in the following references: Yoshida, et al. (2022) <arxiv:2209.15045>, Barnhill et al. (2023) <arxiv:2303.02539>, Barnhill and Yoshida (2023) <doi:10.21203/rs.3.rs-3047827/v1>, Yoshida et al. (2022) <arXiv:2206.04206>, and Yoshida et al. (2019) <doi:10.1007/s11538-018-0493-4>.
License: MIT + file LICENSE
Maintainer: David Barnhill <david.barnhill@nps.edu>
URL: https://github.com/barnhilldave/TML
BugReports: https://github.com/barnhilldave/TML/issues
Depends: R (>= 3.5.0)
Imports: MASS, Matrix, RcppAlgos, Rfast, combinat, gtools, lpSolve, lpSolveAPI, magick, miscTools, phangorn, rcdd, rgl, ape, phytools, maps, cluster
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2023-07-08 16:23:05 UTC; davidbarnhill
Author: David Barnhill [aut, cre] , Ruriko Yoshida [aut], Keiji Miura [aut]
Repository: CRAN
Date/Publication: 2023-07-10 16:10:02 UTC

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New package PolarCAP with initial version 1.0.1
Package: PolarCAP
Title: Access the Polarization in Comparative Attitudes Project
Version: 1.0.1
Description: Distributes data from the Polarization in Comparative Attitudes Project. Helper functions enable data retrieval in wide and tidy formats for user-defined countries and years. Provides support for case-insensitive country names in many languages. Mehlhaff (2022) <https://imehlhaff.net/files/Polarization%20and%20Democracy.pdf>.
License: CC0
Encoding: UTF-8
URL: https://github.com/imehlhaff/PolarCAP
BugReports: https://github.com/imehlhaff/PolarCAP/issues
Depends: R (>= 2.10)
Imports: tidyr, countrycode
NeedsCompilation: no
Packaged: 2023-07-08 16:00:33 UTC; IsaacMehlhaff
Author: Isaac Mehlhaff [aut, cre, cph]
Maintainer: Isaac Mehlhaff <isaac.mehlhaff@gmail.com>
Repository: CRAN
Date/Publication: 2023-07-10 16:10:12 UTC

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New package mixvlmc with initial version 0.1.1
Package: mixvlmc
Title: Variable Length Markov Chains with Covariates
Version: 0.1.1
Description: Estimates Variable Length Markov Chains (VLMC) models and VLMC with covariates models from discrete sequences. Supports model selection via information criteria and simulation of new sequences from an estimated model. See Bühlmann, P. and Wyner, A. J. (1999) <doi:10.1214/aos/1018031204> for VLMC and Zanin Zambom, A., Kim, S. and Lopes Garcia, N. (2022) <doi:10.1111/jtsa.12615> for VLMC with covariates.
License: GPL (>= 3)
URL: https://github.com/fabrice-rossi/mixvlmc, https://fabrice-rossi.github.io/mixvlmc/
BugReports: https://github.com/fabrice-rossi/mixvlmc/issues
Encoding: UTF-8
LazyData: true
Imports: assertthat, butcher, nnet, pROC, Rcpp (>= 1.0.8.3), rlang, stats, stringr, VGAM, withr
LinkingTo: Rcpp
Suggests: data.table, geodist, ggplot2, knitr, rmarkdown, testthat (>= 3.0.0), tibble
Depends: R (>= 2.10)
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2023-07-08 18:13:52 UTC; fabrice
Author: Fabrice Rossi [aut, cre, cph] , Hugo Le Picard [ctb] , Guenole Joubioux [ctb]
Maintainer: Fabrice Rossi <Fabrice.Rossi@apiacoa.org>
Repository: CRAN
Date/Publication: 2023-07-10 16:20:02 UTC

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Package KernSmooth updated to version 2.23-22 with previous version 2.23-21 dated 2023-05-03

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

Diff between KernSmooth versions 2.23-21 dated 2023-05-03 and 2.23-22 dated 2023-07-10

 DESCRIPTION  |    8 ++++----
 MD5          |    6 +++---
 PORTING      |   11 +++++++++++
 src/Makevars |    2 +-
 4 files changed, 19 insertions(+), 8 deletions(-)

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Package dwctaxon (with last version 2.0.2) was removed from CRAN

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

2023-05-30 2.0.2

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Package texPreview (with last version 2.0.0) was removed from CRAN

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

2022-03-31 2.0.0
2020-12-10 1.5
2020-09-18 1.4.6
2020-02-16 1.4.4
2019-12-12 1.4.3
2019-12-05 1.4.2
2019-10-29 1.4.1
2019-10-23 1.4.0
2019-05-05 1.3.2
2018-10-25 1.2.3
2018-10-02 1.2.2
2018-08-15 1.1.5
2018-06-07 1.1.4
2017-08-29 1.1.0
2017-04-03 1.0.0

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Package rgudhi (with last version 0.2.0) was removed from CRAN

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

2023-03-24 0.2.0
2023-01-19 0.1.0

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Package mathpix (with last version 0.5.0) was removed from CRAN

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

2022-04-02 0.5.0
2020-06-19 0.4.0
2018-04-27 0.3.0
2017-10-18 0.2.0
2017-09-27 0.1.0

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Package literanger (with last version 0.0.1) was removed from CRAN

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

2023-06-26 0.0.1

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