Wed, 14 Dec 2022

Package SimplyAgree updated to version 0.1.2 with previous version 0.1.0 dated 2022-08-24

Title: Flexible and Robust Agreement and Reliability Analyses
Description: Reliability and agreement analyses often have limited software support. Therefore, this package was created to make agreement and reliability analyses easier for the average researcher. The functions within this package include simple tests of agreement, agreement analysis for nested and replicate data, and provide robust analyses of reliability. In addition, this package contains a set of functions to help when planning studies looking to assess measurement agreement. For robust analyses of agreement, limits of agreement through a bootstrap method can also be calculated.
Author: Aaron Caldwell [aut, cre]
Maintainer: Aaron Caldwell <arcaldwell49@gmail.com>

Diff between SimplyAgree versions 0.1.0 dated 2022-08-24 and 0.1.2 dated 2022-12-14

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More information about SimplyAgree at CRAN
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Package jsmodule updated to version 1.3.4 with previous version 1.3.3 dated 2022-10-18

Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] , Zarathu [cph, fnd], Hyunki Lee [aut], Changwoo Lim [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>

Diff between jsmodule versions 1.3.3 dated 2022-10-18 and 1.3.4 dated 2022-12-14

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More information about jsmodule at CRAN
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Package SDMtune updated to version 1.2.0 with previous version 1.1.6 dated 2022-08-25

Title: Species Distribution Model Selection
Description: User-friendly framework that enables the training and the evaluation of species distribution models (SDMs). The package implements functions for data driven variable selection and model tuning and includes numerous utilities to display the results. All the functions used to select variables or to tune model hyperparameters have an interactive real-time chart displayed in the 'RStudio' viewer pane during their execution.
Author: Sergio Vignali [aut, cre] , Arnaud Barras [aut] , Veronika Braunisch [aut] , Conservation Biology - University of Bern [fnd]
Maintainer: Sergio Vignali <sergio.vignali@unibe.ch>

Diff between SDMtune versions 1.1.6 dated 2022-08-25 and 1.2.0 dated 2022-12-14

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Package phers updated to version 1.0.0 with previous version 0.0.3 dated 2022-05-31

Title: Calculate Phenotype Risk Scores
Description: Use phenotype risk scores based on linked clinical and genetic data to study Mendelian disease and rare genetic variants. See Bastarache et al. 2018 <doi:10.1126/science.aal4043>.
Author: Jake Hughey [aut, cre], Layla Aref [aut]
Maintainer: Jake Hughey <jakejhughey@gmail.com>

Diff between phers versions 0.0.3 dated 2022-05-31 and 1.0.0 dated 2022-12-14

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Package maptools updated to version 1.1-6 with previous version 1.1-5 dated 2022-10-21

Title: Tools for Handling Spatial Objects
Description: Please note that 'maptools' will be retired during 2023, plan transition at your earliest convenience; some functionality will be moved to 'sp'. Set of tools for manipulating geographic data. It includes binary access to 'GSHHG' shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as 'PBSmapping', 'spatstat.geom', 'maps', and others.
Author: Roger Bivand [cre, aut] , Nicholas Lewin-Koh [aut], Edzer Pebesma [ctb], Eric Archer [ctb], Adrian Baddeley [ctb], Nick Bearman [ctb], Hans-Joerg Bibiko [ctb], Steven Brey [ctb], Jonathan Callahan [ctb], German Carrillo [ctb], Stephane Dray [ctb], Dav [...truncated...]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

Diff between maptools versions 1.1-5 dated 2022-10-21 and 1.1-6 dated 2022-12-14

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Package grf updated to version 2.2.1 with previous version 2.2.0 dated 2022-08-06

Title: Generalized Random Forests
Description: Forest-based statistical estimation and inference. GRF provides non-parametric methods for heterogeneous treatment effects estimation (optionally using right-censored outcomes, multiple treatment arms or outcomes, or instrumental variables), as well as least-squares regression, quantile regression, and survival regression, all with support for missing covariates.
Author: Julie Tibshirani [aut, cre], Susan Athey [aut], Rina Friedberg [ctb], Vitor Hadad [ctb], David Hirshberg [ctb], Luke Miner [ctb], Erik Sverdrup [aut], Stefan Wager [aut], Marvin Wright [ctb]
Maintainer: Julie Tibshirani <jtibs@cs.stanford.edu>

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Package gmp updated to version 0.6-9 with previous version 0.6-8 dated 2022-11-09

Title: Multiple Precision Arithmetic
Description: Multiple Precision Arithmetic (big integers and rationals, prime number tests, matrix computation), "arithmetic without limitations" using the C library GMP (GNU Multiple Precision Arithmetic).
Author: Antoine Lucas, Immanuel Scholz, Rainer Boehme <rb-gmp@reflex-studio.de>, Sylvain Jasson <Sylvain.Jasson@inrae.fr>, Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Antoine Lucas <antoinelucas@gmail.com>

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Package DEET updated to version 1.0.7 with previous version 1.0.6 dated 2022-10-09

Title: Differential Expression Enrichment Tool
Description: Abstract of Manuscript. Differential gene expression analysis using RNA sequencing (RNA-seq) data is a standard approach for making biological discoveries. Ongoing large-scale efforts to process and normalize publicly available gene expression data enable rapid and systematic reanalysis. While several powerful tools systematically process RNA-seq data, enabling their reanalysis, few resources systematically recompute differentially expressed genes (DEGs) generated from individual studies. We developed a robust differential expression analysis pipeline to recompute 3162 human DEG lists from The Cancer Genome Atlas, Genotype-Tissue Expression Consortium, and 142 studies within the Sequence Read Archive. After measuring the accuracy of the recomputed DEG lists, we built the Differential Expression Enrichment Tool (DEET), which enables users to interact with the recomputed DEG lists. DEET, available through CRAN and RShiny, systematically queries which of the recomputed DEG lists share sim [...truncated...]
Author: Dustin Sokolowski [aut, cre], Jedid Ahn [aut], Lauren Erdman [aut], Kai Ellis [aut], Huayun Hou [aut], Anna Goldenberg [aut], Michael Wilson [aut]
Maintainer: Dustin Sokolowski <dustin.sokolowski@sickkids.ca>

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Package datawizard updated to version 0.6.5 with previous version 0.6.4 dated 2022-11-19

Title: Easy Data Wrangling and Statistical Transformations
Description: A lightweight package to assist in key steps involved in any data analysis workflow: (1) wrangling the raw data to get it in the needed form, (2) applying preprocessing steps and statistical transformations, and (3) compute statistical summaries of data properties and distributions. It is also the data wrangling backend for packages in 'easystats' ecosystem. References: Patil et al. (2022) <doi:10.21105/joss.04684>.
Author: Indrajeet Patil [aut] , Etienne Bacher [aut, cre] , Dominique Makowski [aut] , Daniel Luedecke [aut] , Mattan S. Ben-Shachar [aut] , Brenton M. Wiernik [aut] , Remi Theriault [ctb] , Thomas J. Faulkenberry [rev], Robert Garrett [rev]
Maintainer: Etienne Bacher <etienne.bacher@protonmail.com>

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Package dataset updated to version 0.2.0 with previous version 0.1.9 dated 2022-12-02

Title: Create Data Frames that are Easier to Exchange and Reuse
Description: The aim of the 'dataset' package is to make tidy datasets easier to release, exchange and reuse. It organizes and formats data frame 'R' objects into well-referenced, well-described, interoperable datasets into release and reuse ready form. A subjective interpretation of the W3C DataSet recommendation and the datacube model <https://www.w3.org/TR/vocab-data-cube/>, which is also used in the global Statistical Data and Metadata eXchange standards, the application of the connected Dublin Core <https://www.dublincore.org/specifications/dublin-core/dcmi-terms/> and DataCite <https://support.datacite.org/docs/datacite-metadata-schema-44/> standards preferred by European open science repositories to improve the findability, accessibility, interoperability and reusability of the datasets.
Author: Daniel Antal [aut, cre] , Marcelo Perlin [rev]
Maintainer: Daniel Antal <daniel.antal@dataobservatory.eu>

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Package spdl updated to version 0.0.3 with previous version 0.0.2 dated 2022-12-01

Title: Wrapper for 'RcppSpdlog' Functions
Description: Logging functions in 'RcppSpdlog' provide access to the logging functionality from the 'spdlog' 'C++' library. This package offers shorter convenience wrappers for the 'R' functions which match the 'C++' functions, namely via, say, 'spdl::debug()' at the debug level. The actual formatting is done by the 'fmt::format()' function from the 'fmtlib' library (that is also 'std::format()' in 'C++20' or later).
Author: Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package safetyGraphics updated to version 2.1.1 with previous version 2.1.0 dated 2022-04-08

Title: Interactive Graphics for Monitoring Clinical Trial Safety
Description: A framework for evaluation of clinical trial safety. Users can interactively explore their data using the included 'Shiny' application.
Author: Jeremy Wildfire [cre, aut], Becca Krouse [aut], Preston Burns [aut], Xiao Ni [aut], James Buchanan [aut], Susan Duke [aut]
Maintainer: Jeremy Wildfire <jwildfire@gmail.com>

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Package RaMS updated to version 1.3.1 with previous version 1.3.0 dated 2022-11-28

Title: R Access to Mass-Spec Data
Description: R-based access to mass-spectrometry (MS) data. While many packages exist to process MS data, many of these make it difficult to access the underlying mass-to-charge ratio (m/z), intensity, and retention time of the files themselves. This package is designed to format MS data in a tidy fashion and allows the user perform the plotting and analysis.
Author: William Kumler [aut, cre, cph], Ricardo Cunha [ctb], Ethan Bass [ctb]
Maintainer: William Kumler <wkumler@uw.edu>

Diff between RaMS versions 1.3.0 dated 2022-11-28 and 1.3.1 dated 2022-12-14

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Package future.batchtools updated to version 0.11.0 with previous version 0.10.0 dated 2021-01-04

Title: A Future API for Parallel and Distributed Processing using 'batchtools'
Description: Implementation of the Future API on top of the 'batchtools' package. This allows you to process futures, as defined by the 'future' package, in parallel out of the box, not only on your local machine or ad-hoc cluster of machines, but also via high-performance compute ('HPC') job schedulers such as 'LSF', 'OpenLava', 'Slurm', 'SGE', and 'TORQUE' / 'PBS', e.g. 'y <- future.apply::future_lapply(files, FUN = process)'.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

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Package BI updated to version 1.2.0 with previous version 1.1.0 dated 2022-09-30

Title: Blinding Assessment Indexes for Randomized, Controlled, Clinical Trials
Description: Generate the James Blinding Index, as described in James et al (1996) <https://pubmed.ncbi.nlm.nih.gov/8841652/> and the Bang Blinding Index, as described in Bang et al (2004) <https://pubmed.ncbi.nlm.nih.gov/15020033/>. These are measures to assess whether or not satisfactory blinding has been maintained in a randomized, controlled, clinical trial. These can be generated for trial subjects, research coordinators and principal investigators, based upon standardized questionnaires that have been administered, to assess whether or not they can correctly guess to which treatment arm (e.g. placebo or treatment) subjects were assigned at randomization.
Author: Marc Schwartz [aut, cre], Nate Mercaldo [aut]
Maintainer: Marc Schwartz <marc_schwartz@me.com>

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Package SNPassoc updated to version 2.1-0 with previous version 2.0-18 dated 2022-11-15

Title: SNPs-Based Whole Genome Association Studies
Description: Functions to perform most of the common analysis in genome association studies are implemented. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented. Max-statistic and genetic risk-allele score exact distributions are also possible to be estimated. The methods are described in Gonzalez JR et al., 2007 <doi: 10.1093/bioinformatics/btm025>.
Author: Victor Moreno [aut], Juan R Gonzalez [aut] , Dolors Pelegri [aut, cre]
Maintainer: Dolors Pelegri <dolors.pelegri@isglobal.org>

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Package parallelly updated to version 1.33.0 with previous version 1.32.1 dated 2022-07-21

Title: Enhancing the 'parallel' Package
Description: Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between parallelly versions 1.32.1 dated 2022-07-21 and 1.33.0 dated 2022-12-14

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Package tm updated to version 0.7-10 with previous version 0.7-9 dated 2022-10-19

Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut, cre] , Kurt Hornik [aut] , Artifex Software, Inc. [ctb, cph]
Maintainer: Ingo Feinerer <feinerer@logic.at>

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Package overlapping updated to version 2.1 with previous version 2.0 dated 2022-10-20

Title: Estimation of Overlapping in Empirical Distributions
Description: Functions for estimating the overlapping area of two or more kernel density estimations from empirical data.
Author: Massimiliano Pastore [aut,cre], Pierfrancesco Alaimo Di Loro [ctb], Marco Mingione [ctb], Antonio Calcagni' [ctb]
Maintainer: Massimiliano Pastore <massimiliano.pastore@unipd.it>

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Package clustMixType updated to version 0.3-9 with previous version 0.2-15 dated 2021-08-18

Title: k-Prototypes Clustering for Mixed Variable-Type Data
Description: Functions to perform k-prototypes partitioning clustering for mixed variable-type data according to Z.Huang (1998): Extensions to the k-Means Algorithm for Clustering Large Data Sets with Categorical Variables, Data Mining and Knowledge Discovery 2, 283-304.
Author: Gero Szepannek [aut, cre], Rabea Aschenbruck [aut]
Maintainer: Gero Szepannek <gero.szepannek@web.de>

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Package castor updated to version 1.7.6 with previous version 1.7.5 dated 2022-11-10

Title: Efficient Phylogenetics on Large Trees
Description: Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>

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Package aricode updated to version 1.0.2 with previous version 1.0.1 dated 2022-09-05

Title: Efficient Computations of Standard Clustering Comparison Measures
Description: Implements an efficient O(n) algorithm based on bucket-sorting for fast computation of standard clustering comparison measures. Available measures include adjusted Rand index (ARI), normalized information distance (NID), normalized mutual information (NMI), adjusted mutual information (AMI), normalized variation information (NVI) and entropy, as described in Vinh et al (2009) <doi:10.1145/1553374.1553511>. Include AMI (Adjusted Mutual Information) since version 0.1.2, a modified version of ARI (MARI), as described in Sundqvist et al. <doi:10.1007/s00180-022-01230-7> and simple Chi-square distance since version 1.0.0.
Author: Julien Chiquet [aut, cre] , Guillem Rigaill [aut], Martina Sundqvist [aut], Valentin Dervieux [ctb], Florent Bersani [ctb]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>

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Package nimble updated to version 0.13.1 with previous version 0.13.0 dated 2022-11-15

Title: MCMC, Particle Filtering, and Programmable Hierarchical Modeling
Description: A system for writing hierarchical statistical models largely compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models and do basic R-style math, and compiling both models and nimbleFunctions via custom-generated C++. 'NIMBLE' includes default methods for MCMC, Monte Carlo Expectation Maximization, and some other tools. The nimbleFunction system makes it easy to do things like implement new MCMC samplers from R, customize the assignment of samplers to different parts of a model from R, and compile the new samplers automatically via C++ alongside the samplers 'NIMBLE' provides. 'NIMBLE' extends the 'BUGS'/'JAGS' language by making it extensible: New distributions and functions can be added, including as calls to external compiled code. Although most people think of MCMC as the main goal of the 'BUGS'/'JAGS' language for writing models, one can use 'NIMBLE' for writing arbitrary other kinds of model-generic algorithms as well. A full User Manual is available at <htt [...truncated...]
Author: Perry de Valpine [aut], Christopher Paciorek [aut, cre], Daniel Turek [aut], Nick Michaud [aut], Cliff Anderson-Bergman [aut], Fritz Obermeyer [aut], Claudia Wehrhahn Cortes [aut] , Abel Rodrìguez [aut] , Duncan Temple Lang [aut] , Sally Paganin [aut [...truncated...]
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>

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Package leidenbase updated to version 0.1.14 with previous version 0.1.12 dated 2022-09-29

Title: R and C/C++ Wrappers to Run the Leiden find_partition() Function
Description: An R to C/C++ interface that runs the Leiden community detection algorithm to find a basic partition (). It runs the equivalent of the 'leidenalg' find_partition() function, which is given in the 'leidenalg' distribution file 'leiden/src/functions.py'. This package includes the required source code files from the official 'leidenalg' distribution and functions from the R 'igraph' package. The 'leidenalg' distribution is available from <https://github.com/vtraag/leidenalg/> and the R 'igraph' package is available from <https://igraph.org/r/>. The Leiden algorithm is described in the article by Traag et al. (2019) <doi:10.1038/s41598-019-41695-z>.
Author: Brent Ewing [aut, cre], Vincent Traag [ctb], Gabor Csardi [ctb], Tamas Nepusz [ctb], Szabolcs Horvat [ctb], Fabio Zanini [ctb]
Maintainer: Brent Ewing <bge@uw.edu>

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Package httpuv updated to version 1.6.7 with previous version 1.6.6 dated 2022-09-08

Title: HTTP and WebSocket Server Library
Description: Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)
Author: Joe Cheng [aut], Winston Chang [aut, cre], RStudio, PBC [cph], Hector Corrada Bravo [ctb], Jeroen Ooms [ctb], Andrzej Krzemienski [cph]
Maintainer: Winston Chang <winston@rstudio.com>

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Package future.callr updated to version 0.8.1 with previous version 0.8.0 dated 2022-04-01

Title: A Future API for Parallel Processing using 'callr'
Description: Implementation of the Future API on top of the 'callr' package. This allows you to process futures, as defined by the 'future' package, in parallel out of the box, on your local (Linux, macOS, Windows, ...) machine. Contrary to backends relying on the 'parallel' package (e.g. 'future::multisession') and socket connections, the 'callr' backend provided here can run more than 125 parallel R processes.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

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Package forsearch updated to version 3.0.0 with previous version 2.3.0 dated 2022-04-24

Title: Diagnostic Analysis Using Forward Search Procedure for Various Models
Description: Identifies potential data outliers and their impact on estimates and analyses. Uses the forward search approach of Atkinson and Riani, "Robust Diagnostic Regression Analysis", 2000,<ISBN: o-387-95017-6>) to prepare descriptive statistics of a dataset that is to be analyzed by stats::lm(), stats::glm(), or nlme::lme(). Includes graphics functions to display the descriptive statistics.
Author: William Fairweather [aut, cre]
Maintainer: William Fairweather <wrf343@flowervalleyconsulting.com>

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New package csmaps with initial version 2022.12.15
Package: csmaps
Title: Preformatted Maps of Norway that Don't Need Geolibraries
Version: 2022.12.15
Description: Provides datasets containing preformatted maps of Norway at the county, municipality, and ward (Oslo only) level for redistricting in 2017, 2018, and 2020. Multiple layouts are provided (normal, split, and with an insert for Oslo), allowing the user to rapidly create choropleth maps of Norway without any geolibraries.
Depends: R (>= 3.5.0)
License: MIT + file LICENSE
URL: https://www.csids.no/csmaps/, https://github.com/csids/csmaps
BugReports: https://github.com/csids/csmaps/issues
LazyData: true
Imports: data.table, utils
Suggests: testthat, knitr, rmarkdown, ggplot2, magrittr, ggrepel, leaflet, sf, csdata
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-12-14 08:52:56 UTC; rstudio
Author: Richard Aubrey White [aut, cre] , Chi Zhang [aut] , Geonorge [ctb], CSIDS [cph]
Maintainer: Richard Aubrey White <hello@rwhite.no>
Repository: CRAN
Date/Publication: 2022-12-14 17:20:09 UTC

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Package butcher updated to version 0.3.1 with previous version 0.3.0 dated 2022-08-25

Title: Model Butcher
Description: Provides a set of S3 generics to axe components of fitted model objects and help reduce the size of model objects saved to disk.
Author: Joyce Cahoon [aut] , Davis Vaughan [aut], Max Kuhn [aut], Alex Hayes [aut], Julia Silge [cre, aut] , RStudio [cph, fnd]
Maintainer: Julia Silge <julia.silge@rstudio.com>

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Package stacks updated to version 1.0.1 with previous version 1.0.0 dated 2022-07-06

Title: Tidy Model Stacking
Description: Model stacking is an ensemble technique that involves training a model to combine the outputs of many diverse statistical models, and has been shown to improve predictive performance in a variety of settings. 'stacks' implements a grammar for 'tidymodels'-aligned model stacking.
Author: Simon Couch [aut, cre], Max Kuhn [aut], RStudio [cph, fnd]
Maintainer: Simon Couch <simonpatrickcouch@gmail.com>

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Package qad updated to version 1.0.4 with previous version 1.0.3 dated 2022-07-05

Title: Quantification of Asymmetric Dependence
Description: A copula-based measure for quantifying asymmetry in dependence and associations. Documentation and theory about 'qad' is provided by the paper by Junker, Griessenberger & Trutschnig (2021, <doi:10.1016/j.csda.2020.107058>), and the paper by Trutschnig (2011, <doi:10.1016/j.jmaa.2011.06.013>).
Author: Thimo Kasper <thimo.kasper@plus.ac.at>, Florian Griessenberger <florian.griessenberger@plus.ac.at>, Robert R. Junker <>, Valentin Petzel <valetin.petzel@sbg.ac.at>, Wolfgang Trutschnig <wolfgang.trutschnig@plus.ac.at>
Maintainer: Nicolas Dietrich <nicolaspascal.dietrich@plus.ac.at>

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Package FactoMineR updated to version 2.7 with previous version 2.6 dated 2022-09-09

Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis. F. Husson, S. Le and J. Pages (2017).
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson <francois.husson@agrocampus-ouest.fr>

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Package clmplus updated to version 0.1.0 with previous version 0.0.1 dated 2022-09-01

Title: Tool-Box of Chain Ladder Plus Models
Description: Implementation of the chain ladder model under the reverse time framework introduced in Hiabu (2017) <doi:10.1080/03461238.2016.1240709>. It also implements extensions that add flexibility to the individual development factors modeling by allowing practitioners to set their own hazard rate model.
Author: Gabriele Pittarello [aut, cre, cph] , Munir Hiabu [aut, cph] , Andres Villegas [aut, cph]
Maintainer: Gabriele Pittarello <gabriele.pittarello@uniroma1.it>

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Package sdmpredictors updated to version 0.2.14 with previous version 0.2.13 dated 2022-09-13

Title: Species Distribution Modelling Predictor Datasets
Description: Terrestrial and marine predictors for species distribution modelling from multiple sources, including WorldClim <https://www.worldclim.org/>,, ENVIREM <https://envirem.github.io/>, Bio-ORACLE <https://bio-oracle.org/> and MARSPEC <http://www.marspec.org/>.
Author: Samuel Bosch [aut], Lennert Tyberghein [ctb], Olivier De Clerck [ctb], Salvador Fernandez [aut, cre], Lennert Schepers [ctb], LifeWatch Belgium [fnd]
Maintainer: Salvador Fernandez <salvador.fernandez@vliz.be>

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Package eurodata updated to version 1.6.0 with previous version 1.5.0 dated 2022-08-31

Title: Fast and Easy Eurostat Data Import and Search
Description: Interface to Eurostat’s Bulk Download Facility with fast data.table-based import of data, labels, and metadata. On top of the core functionality, data search and data description/comparison functions are also provided.
Author: Aleksander Rutkowski [aut, cre]
Maintainer: Aleksander Rutkowski <alek.rutkowski@gmail.com>

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Package csodata updated to version 1.4.0 with previous version 1.3.0 dated 2022-10-21

Title: Download Data from the CSO 'PxStat' API
Description: Imports 'PxStat' data in JSON-stat format and (optionally) reshapes it into wide format. The Central Statistics Office (CSO) is the national statistical institute of Ireland and 'PxStat' is the CSOs online database of Official Statistics. This database contains current and historical data series compiled from CSO statistical releases and is accessed at <http://data.cso.ie>. The CSO 'PxStat' Application Programming Interface (API), which is accessed in this package, provides access to 'PxStat' data in JSON-stat format at <http://data.cso.ie>. This dissemination tool allows developers machine to machine access to CSO 'PxStat' data.
Author: Eoin Horgan [aut] , Conor Crowley [aut, cre], Vytas Vaiciulis [aut], Mervyn O'Luing [aut], James O'Rourke [aut]
Maintainer: Conor Crowley <conor.crowley@cso.ie>

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Package BlockmodelingGUI updated to version 1.8.4 with previous version 1.8.3 dated 2022-05-31

Title: GUI for the Generalised Blockmodeling of Valued Networks
Description: This app provides some useful tools for Offering an accessible GUI for generalised blockmodeling of single-relation, one-mode networks. The user can execute blockmodeling without having to write a line code by using the app's visual helps. Moreover, there are several ways to visualisations networks and their partitions. Finally, the results can be exported as if they were produced by writing code. The development of this package is financially supported by the Slovenian Research Agency (www.arrs.gov.si) within the research project J5-2557 (Comparison and evaluation of different approaches to blockmodeling dynamic networks by simulations with application to Slovenian co-authorship networks).
Author: Fabio Ashtar Telarico [aut, cre] , Ales Ziberna [aut]
Maintainer: Fabio Ashtar Telarico <telaricof@fdv.uni-lj.si>

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Package BFS updated to version 0.4.4 with previous version 0.4.3 dated 2022-09-07

Title: Get Data from the Swiss Statistical Office
Description: Search and download data from the Swiss Federal Statistical Office (BFS) <https://www.bfs.admin.ch/>.
Author: Felix Luginbuhl [aut, cre]
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>

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Package EpiInvert updated to version 0.3.1 with previous version 0.3.0 dated 2022-12-08

Title: Variational Techniques in Epidemiology
Description: Using variational techniques we address some epidemiological problems as the incidence curve decomposition by inverting the renewal equation as described in Alvarez et al. (2021) <doi:10.1073/pnas.2105112118> and Alvarez et al. (2022) <doi:10.3390/biology11040540> or the estimation of the functional relationship between epidemiological indicators. We also propose a learning method for the short time forecast of the trend incidence curve as described in Morel et al. (2022) <doi:10.1101/2022.11.05.22281904>.
Author: Luis Alvarez [aut, cre] , Jean-David Morel [ctb] , Jean-Michel Morel [ctb]
Maintainer: Luis Alvarez <lalvarez@ulpgc.es>

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Package aorsf updated to version 0.0.5 with previous version 0.0.4 dated 2022-11-07

Title: Accelerated Oblique Random Survival Forests
Description: Fit, interpret, and make predictions with oblique random survival forests. Oblique decision trees are notoriously slow compared to their axis based counterparts, but 'aorsf' runs as fast or faster than axis-based decision tree algorithms for right-censored time-to-event outcomes. Methods to accelerate and interpret the oblique random survival forest are described in Jaeger et al., (2022) <arXiv:2208.01129>.
Author: Byron Jaeger [aut, cre] , Nicholas Pajewski [ctb], Sawyer Welden [ctb], Christopher Jackson [rev], Marvin Wright [rev], Lukas Burk [rev]
Maintainer: Byron Jaeger <bjaeger@wakehealth.edu>

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Package nemBM updated to version 1.00.01 with previous version 1.00.00 dated 2022-12-13

Title: Using Network Evolution Models to Generate Networks with Selected Blockmodel Type
Description: To study network evolution models and different blockmodeling approaches. Various functions enable generating (temporal) networks with a selected blockmodel type, taking into account selected local network mechanisms. The development of this package is financially supported the Slovenian Research Agency (www.arrs.gov.si) within the research program P5<96>0168 and the research project J5-2557 (Comparison and evaluation of different approaches to blockmodeling dynamic networks by simulations with application to Slovenian co-authorship networks).
Author: Marjan Cugmas [aut, cre], Ales Ziberna [aut]
Maintainer: Marjan Cugmas <marjan.cugmas@fdv.uni-lj.si>

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Package bcfrailphdv updated to version 0.1.1 with previous version 0.1.0 dated 2020-11-30

Title: Bivariate Correlated Frailty Models with Varied Variances
Description: Fit and simulate bivariate correlated frailty models with proportional hazard structure. Frailty distributions, such as gamma and lognormal models are supported for semiparametric procedures. Frailty variances of the two subjects can be varied or equal. Details on the models are available in book of Wienke (2011,ISBN:978-1-4200-7388-1). Bivariate gamma fit is obtained using the approach given in Iachine (1995) with modifications. Lognormal fit is based on the approach by Ripatti and Palmgren (2000) <doi:10.1111/j.0006-341X.2000.01016.x>. Frailty distributions, such as gamma, inverse gaussian and power variance frailty models are supported for parametric approach.
Author: Mesfin Tsegaye [aut, cre], Yehenew Kifle [aut, ctb]
Maintainer: Mesfin Tsegaye <mesfin.tsegaye@ddu.edu.et>

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Package aisoph updated to version 0.3 with previous version 0.2 dated 2022-11-19

Title: Additive Isotonic Proportional Hazards Model
Description: Nonparametric estimation of additive isotonic covariate effects for proportional hazards model.
Author: Yunro Chung [aut, cre]
Maintainer: Yunro Chung <yunro.chung@asu.edu>

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More information about aisoph at CRAN
Permanent link

New package glmnetr with initial version 0.1-1
Title: Relaxed Lasso Model for Data Which Might Have Long Run Times Using 'glmnet'
Package: glmnetr
Version: 0.1-1
Date: 2022-12-10
Depends: R (>= 3.4.0)
Suggests: R.rsp
VignetteBuilder: R.rsp
Imports: glmnet, survival, Matrix
ByteCompile: Yes
Author: Walter K Kremers [aut, cre]
Maintainer: Walter K Kremers <kremers.walter@mayo.edu>
Description: For some datasets, for example when the design matrix is not of full rank, 'glmnet' may have very long run times when fitting the relaxed lasso model, in particular when fitting a Cox based model, making it difficult to get solutions either from glmnet() or cv.glmnet(). In this package, 'glmnetr', we provide a workaround and solve for the non penalized relaxed model where gamma=0 for model structures analogue to R functions like glm() or coxph() of the survival package. If you are not fitting relaxed lasso models, or if you are able to get convergence using 'glmnet', then this package may not be of much benefit to you. Note, while this package may allow one to fit relaxed lasso models that have difficulties converging using 'glmnet', this package does not afford the full function and versatility of 'glmnet'. In addition to fitting the relaxed lasso model this package also includes the function cv.glmnetr() to perform a cross validation to identify hyper-parameters for a lasso fit, m [...truncated...]
License: GPL-3
NeedsCompilation: no
Copyright: Mayo Foundation for Medical Education and Research
Encoding: UTF-8
Packaged: 2022-12-14 04:55:24 UTC; KREMERS
Repository: CRAN
Date/Publication: 2022-12-14 12:10:02 UTC

More information about glmnetr at CRAN
Permanent link

New package tRophicPosition with initial version 0.8.0
Package: tRophicPosition
Title: Bayesian Trophic Position Estimation with Stable Isotopes
Version: 0.8.0
Date: 2022-12-11
Depends: R (>= 3.4.0)
Imports: coda, data.table, ggplot2, gridExtra, hdrcde, MCMCglmm, methods, plyr, rjags, RColorBrewer, stats
Author: Claudio Quezada-Romegialli, Andrew L Jackson, Chris Harrod
URL: https://github.com/clquezada/tRophicPosition
BugReports: https://groups.google.com/d/forum/trophicposition-support
Maintainer: Claudio Quezada-Romegialli <clquezada@ug.uchile.cl>
Description: Estimates the trophic position of a consumer relative to a baseline species. It implements a Bayesian approach which combines an interface to the 'JAGS' MCMC library of 'rjags' and stable isotopes. Users are encouraged to test the package and send bugs and/or errors to trophicposition-support@googlegroups.com.
License: GPL (>= 2)
LazyData: TRUE
Suggests: dplyr, knitr, rmarkdown, testthat, covr
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-GB
NeedsCompilation: no
Packaged: 2022-12-12 13:49:27 UTC; ASUS
Repository: CRAN
Date/Publication: 2022-12-14 11:40:02 UTC

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Package sars updated to version 1.3.6 with previous version 1.3.5 dated 2021-08-05

Title: Fit and Compare Species-Area Relationship Models Using Multimodel Inference
Description: Implements the basic elements of the multi-model inference paradigm for up to twenty species-area relationship models (SAR), using simple R list-objects and functions, as in Triantis et al. 2012 <DOI:10.1111/j.1365-2699.2011.02652.x>. The package is scalable and users can easily create their own model and data objects. Additional SAR related functions are provided.
Author: Thomas J. Matthews [aut, cre] , Francois Guilhaumon [aut] , Kevin Cazelles [rev]
Maintainer: Thomas J. Matthews <txm676@gmail.com>

Diff between sars versions 1.3.5 dated 2021-08-05 and 1.3.6 dated 2022-12-14

 DESCRIPTION                              |    8 
 MD5                                      |   22 
 NEWS.md                                  |   18 
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New package RGCxGC with initial version 1.2.0
Package: RGCxGC
Title: Preprocessing and Multivariate Analysis of Bidimensional Gas Chromatography Data
Version: 1.2.0
Date: 2022-12-13
Maintainer: Cristian Quiroz-Moreno <cristianquirozd1997@gmail.com>
Description: Toolbox for chemometrics analysis of bidimensional gas chromatography data. This package import data for common scientific data format (NetCDF) and fold it to 2D chromatogram. Then, it can perform preprocessing and multivariate analysis. In the preprocessing algorithms, baseline correction, smoothing, and peak alignment are available. While in multivariate analysis, multiway principal component analysis is incorporated.
License: MIT + file LICENSE
URL: https://github.com/DanielQuiroz97/RGCxGC, https://danielquiroz97.github.io/RGCxGC/
BugReports: https://github.com/DanielQuiroz97/RGCxGC/issues
Imports: colorRamps, Rdpack, stats, methods, graphics
Depends: R (>= 4.2.0), RNetCDF, ptw
LazyData: true
Encoding: UTF-8
Suggests: knitr, rmarkdown, lattice, prettydoc,
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-12-13 20:44:01 UTC; quirozmoreno.1
Author: Cristian Quiroz-Moreno [aut, cre] , Guilherme L. Alexandrino [aut] , Noroska G.S. Mogollon [aut]
Repository: CRAN
Date/Publication: 2022-12-14 11:30:02 UTC

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Package pkgdown updated to version 2.0.7 with previous version 2.0.6 dated 2022-07-16

Title: Make Static HTML Documentation for a Package
Description: Generate an attractive and useful website from a source package. 'pkgdown' converts your documentation, vignettes, 'README', and more to 'HTML' making it easy to share information about your package online.
Author: Hadley Wickham [aut, cre] , Jay Hesselberth [aut] , Maelle Salmon [aut] , RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>

Diff between pkgdown versions 2.0.6 dated 2022-07-16 and 2.0.7 dated 2022-12-14

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New package POMS with initial version 1.0.1
Package: POMS
Title: Phylogenetic Organization of Metagenomic Signals
Version: 1.0.1
Description: Code to identify functional enrichments across diverse taxa in phylogenetic tree, particularly where these taxa differ in abundance across samples in a non-random pattern. The motivation for this approach is to identify microbial functions encoded by diverse taxa that are at higher abundance in certain samples compared to others, which could indicate that such functions are broadly adaptive under certain conditions. See 'GitHub' repository for tutorial and examples: <https://github.com/gavinmdouglas/POMS/wiki>. Citation: Gavin M. Douglas, Molly G. Hayes, Morgan G. I. Langille, Elhanan Borenstein (2022) <doi:10.1093/bioinformatics/btac655>.
License: GPL-3
Imports: ape (>= 3.0), data.table, MASS, parallel (>= 3.3.0), phangorn (>= 2.0.0), phylolm (>= 2.6), utils, XNomial (>= 1.0.4)
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-12-13 14:44:20 UTC; gavin
Author: Gavin Douglas [aut, cre]
Maintainer: Gavin Douglas <gavinmdouglas@gmail.com>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2022-12-14 11:40:11 UTC

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New package hdcate with initial version 0.1.0
Package: hdcate
Title: Estimation of Conditional Average Treatment Effects with High-Dimensional Data
Version: 0.1.0
Imports: KernSmooth, R6, hdm, locpol, caret
Description: A two-step double-robust method to estimate the conditional average treatment effects (CATE) with potentially high-dimensional covariate(s). In the first stage, the nuisance functions necessary for identifying CATE are estimated by machine learning methods, allowing the number of covariates to be comparable to or larger than the sample size. The second stage consists of a low-dimensional local linear regression, reducing CATE to a function of the covariate(s) of interest. The CATE estimator implemented in this package not only allows for high-dimensional data, but also has the “double robustness” property: either the model for the propensity score or the models for the conditional means of the potential outcomes are allowed to be misspecified (but not both). This package is based on the paper by Fan et al., "Estimation of Conditional Average Treatment Effects With High-Dimensional Data" (2022), Journal of Business & Economic Statistics <doi:10.1080/07350015.2020.1811102>.
License: GPL (>= 3)
Encoding: UTF-8
Suggests: knitr, rmarkdown, xfun, randomForest, dplyr, ggplot2, ggthemes
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-12-13 19:08:51 UTC; hengzhaohong
Author: Qingliang Fan [aut, cre], Hengzhao Hong [aut]
Maintainer: Qingliang Fan <michaelqfan@cuhk.edu.hk>
Repository: CRAN
Date/Publication: 2022-12-14 11:50:02 UTC

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Package Ghat updated to version 0.2.0 with previous version 0.1.0 dated 2019-08-02

Title: Quantifying Evolution and Selection on Complex Traits
Description: Functions are provided for quantifying evolution and selection on complex traits. The package implements effective handling and analysis algorithms scaled for genome-wide data and calculates a composite statistic, denoted Ghat, which is used to test for selection on a trait. The package provides a number of simple examples for handling and analysing the genome data and visualising the output and results. Beissinger et al., (2018) <doi:10.1534/genetics.118.300857>.
Author: Medhat Mahmoud [aut], Ngoc-Thuy Ha [aut], Tim Beissinger [aut, cre]
Maintainer: Tim Beissinger <timbeissinger@gmail.com>

Diff between Ghat versions 0.1.0 dated 2019-08-02 and 0.2.0 dated 2022-12-14

 DESCRIPTION      |   18 +-
 LICENSE          |    4 
 MD5              |   19 +-
 NAMESPACE        |   46 +++---
 R/Ghat.R         |  400 +++++++++++++++++++++++++++----------------------------
 R/Maiz_wqs.R     |   40 ++---
 R/ld_decay.R     |  218 ++++++++++++++---------------
 README.md        |only
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 man/Maize_wqs.Rd |   66 ++++-----
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 11 files changed, 548 insertions(+), 547 deletions(-)

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New package ExNRuleEnsemble with initial version 0.1.0
Package: ExNRuleEnsemble
Title: A k Nearest Neibour Ensemble Based on Extended Neighbourhood Rule
Version: 0.1.0
Description: The extended neighbourhood rule for the k nearest neighbour ensemble where the neighbours are determined in k steps. Starting from the first nearest observation of the test point, the algorithm identifies a single observation that is closest to the observation at the previous step. At each base learner in the ensemble, this search is extended to k steps on a random bootstrap sample with a random subset of features selected from the feature space. The final predicted class of the test point is determined by using a majority vote in the predicted classes given by all base models. Amjad Ali, Muhammad Hamraz, Naz Gul, Dost Muhammad Khan, Saeed Aldahmani, Zardad Khan (2022) <doi:10.48550/arXiv.2205.15111>.
License: GPL (>= 3)
Encoding: UTF-8
Imports: FNN
LazyData: true
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2022-12-13 15:39:08 UTC; aaliu
Author: Amjad Ali [aut, cre, cph], Muhammad Hamraz [aut], Saeed Aldahmani [aut], Zardad Khan [aut]
Maintainer: Amjad Ali <Amjad.ali@awkum.edu.pk>
Repository: CRAN
Date/Publication: 2022-12-14 11:50:05 UTC

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New package etwfe with initial version 0.1.0
Package: etwfe
Title: Extended Two-Way Fixed Effects
Version: 0.1.0
Date: 2022-12-12
Description: Convenience functions for implementing extended two-way fixed effect regressions a la Wooldridge (2021, 2022) <doi:10.2139/ssrn.3906345>, <doi:10.2139/ssrn.4183726>.
License: MIT + file LICENSE
Imports: fixest (>= 0.11.0), stats, Formula, marginaleffects (>= 0.8.1)
Suggests: did, modelsummary, ggplot2, knitr, rmarkdown, tinytest
Encoding: UTF-8
URL: https://grantmcdermott.com/etwfe/
BugReports: https://github.com/grantmcdermott/etwfe/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-12-14 01:26:42 UTC; grant
Author: Grant McDermott [aut, cre]
Maintainer: Grant McDermott <grantmcd@uoregon.edu>
Repository: CRAN
Date/Publication: 2022-12-14 12:00:02 UTC

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New package ddc with initial version 1.0.1
Package: ddc
Title: Distance Density Clustering Algorithm
Version: 1.0.1
Date: 2022-12-13
Maintainer: Ruizhe Ma <maruizhe.cs@gmail.com>
Description: A distance density clustering (DDC) algorithm in R. DDC uses dynamic time warping (DTW) to compute a similarity matrix, based on which cluster centers and cluster assignments are found. DDC inherits dynamic time warping (DTW) arguments and constraints. The cluster centers are centroid points that are calculated using the DTW Barycenter Averaging (DBA) algorithm. The clustering process is divisive. At each iteration, cluster centers are updated and data is reassigned to cluster centers. Early stopping is possible. The output includes cluster centers and clustering assignment, as described in the paper (Ma et al (2017) <doi:10.1109/ICDMW.2017.11>).
License: GPL (>= 2)
Depends: R (>= 4.2)
Imports: dtw (>= 1.22), dtwclust (>= 5.5), parallel (>= 4.2), magrittr (>= 2.0), utils
Encoding: UTF-8
ByteCompile: yes
BuildResaveData: no
NeedsCompilation: yes
Suggests: knitr, rmarkdown, spelling, testthat (>= 3.0.0)
Language: en-US
VignetteBuilder: knitr
Packaged: 2022-12-14 04:11:40 UTC; bingjiang
Author: Ruizhe Ma [cre, aut], Bing Jiang [aut]
Repository: CRAN
Date/Publication: 2022-12-14 12:00:05 UTC

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Package CRMetrics updated to version 0.2.3 with previous version 0.2.2 dated 2022-11-30

Title: Cell Ranger Output Filtering and Metrics Visualization
Description: Sample and cell filtering as well as visualisation of output metrics from 'Cell Ranger' by Grace X.Y. Zheng et al. (2017) <doi:10.1038/ncomms14049>. 'CRMetrics' allows for easy plotting of output metrics across multiple samples as well as comparative plots including statistical assessments of these. 'CRMetrics' allows for easy removal of ambient RNA using 'SoupX' by Matthew D Young and Sam Behjati (2020) <doi:10.1093/gigascience/giaa151> or 'CellBender' by Stephen J Fleming et al. (2022) <doi:10.1101/791699>. Furthermore, it is possible to preprocess data using 'Pagoda2' by Nikolas Barkas et al. (2021) <https://github.com/kharchenkolab/pagoda2> or 'Seurat' by Yuhan Hao et al. (2021) <doi:10.1016/j.cell.2021.04.048> followed by embedding of cells using 'Conos' by Nikolas Barkas et al. (2019) <doi:10.1038/s41592-019-0466-z>. Finally, doublets can be detected using 'scrublet' by Samuel L. Wolock et al. (2019) <doi:10.1016/j.cels.2018.11.005> or 'D [...truncated...]
Author: Rasmus Rydbirk [aut, cre], Fabienne Kick [aut], Henrietta Holze [aut], Xian Xin [ctb]
Maintainer: Rasmus Rydbirk <rasmus.rydbirk@bric.ku.dk>

Diff between CRMetrics versions 0.2.2 dated 2022-11-30 and 0.2.3 dated 2022-12-14

 DESCRIPTION                |    8 -
 MD5                        |   14 -
 NEWS.md                    |    4 
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 R/inner_functions.R        |    3 
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 man/addPlotStatsSamples.Rd |    2 
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 8 files changed, 273 insertions(+), 197 deletions(-)

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New package condorOptions with initial version 1.0.1
Package: condorOptions
Title: Trading Condor Options Strategies
Version: 1.0.1
Author: MaheshP Kumar [aut, cre]
Maintainer: MaheshP Kumar <maheshparamjitkumar@gmail.com>
Imports: ggplot2, dplyr, magrittr, tibble
Description: Trading of Condor Options Strategies is represented here through their Graphs. The graphic indicators, strategies, calculations, functions and all the discussions are for academic, research, and educational purposes only and should not be construed as investment advice and come with absolutely no Liability. Guy Cohen (“The Bible of Options Strategies (2nd ed.)”, 2015, ISBN: 9780133964028). Zura Kakushadze, Juan A. Serur (“151 Trading Strategies”, 2018, ISBN: 9783030027919). John C. Hull (“Options, Futures, and Other Derivatives (11th ed.)”, 2022, ISBN: 9780136939979).
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-12-13 03:42:48 UTC; mahes
Repository: CRAN
Date/Publication: 2022-12-14 11:40:08 UTC

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New package trip with initial version 1.8.7
Package: trip
Title: Tracking Data
Version: 1.8.7
Depends: R (>= 3.3.0)
Imports: geodist, MASS, methods, raster, reproj, sp, spatstat.geom, spatstat.explore, glue, viridis, traipse (>= 0.2.0), crsmeta, dplyr, rlang
Suggests: adehabitatLT, knitr, testthat, covr, rmarkdown, lubridate, maps, spelling, lattice
Description: Access and manipulate spatial tracking data, with straightforward coercion from and to other formats. Filter for speed and create time spent maps from tracking data. There are coercion methods to convert between 'trip' and 'ltraj' from 'adehabitatLT', and between 'trip' and 'psp' and 'ppp' from 'spatstat'. Trip objects can be created from raw or grouped data frames, and from types in the 'sp', sf', 'amt', 'trackeR', 'mousetrap', and other packages, Sumner, MD (2011) <https://eprints.utas.edu.au/12273/3/sumner.pdf>.
URL: https://github.com/Trackage/trip
BugReports: https://github.com/Trackage/trip/issues
NeedsCompilation: no
ByteCompile: yes
License: GPL-3
LazyData: yes
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
Packaged: 2022-12-14 05:11:35 UTC; mdsumner
Author: Michael D. Sumner [aut, cre], Sebastian Luque [ctb], Anthony Fischbach [ctb], Tomislav Hengl [ctb]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Repository: CRAN
Date/Publication: 2022-12-14 09:10:02 UTC

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Package rminqa updated to version 0.2.1 with previous version 0.1.1 dated 2022-05-10

Title: Derivative-Free Optimization in R using C++
Description: Perform derivative-free optimization algorithms in R using C++. A wrapper interface is provided to call C function of the 'bobyqa' implementation (See <https://github.com/emmt/Algorithms/tree/master/bobyqa>).
Author: Sam Watson [aut], Yi Pan [aut, cre], Éric Thiebaut [aut], Mike Powell [aut]
Maintainer: Yi Pan <ypan1988@gmail.com>

Diff between rminqa versions 0.1.1 dated 2022-05-10 and 0.2.1 dated 2022-12-14

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More information about rminqa at CRAN
Permanent link

Package rb3 updated to version 0.0.7 with previous version 0.0.6 dated 2022-08-19

Title: Download and Parse Public Data Released by B3 Exchange
Description: Download and parse public files released by B3 and convert them into useful formats and data structures common to data analysis practitioners.
Author: Wilson Freitas [aut, cre], Marcelo Perlin [aut]
Maintainer: Wilson Freitas <wilson.freitas@gmail.com>

Diff between rb3 versions 0.0.6 dated 2022-08-19 and 0.0.7 dated 2022-12-14

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More information about rb3 at CRAN
Permanent link

New package nser with initial version 1.4.4
Package: nser
Title: Bhavcopy and Live Market Data from National Stock Exchange (NSE) & Bombay Stock Exchange (BSE) India
Version: 1.4.4
Date: 2022-12-11
Description: Download Current & Historical Bhavcopy. Get Live Market data from NSE India of Equities and Derivatives (F&O) segment. Data source <https://www.nseindia.com/>.
URL: https://github.com/nandp1/nser/
BugReports: https://github.com/nandp1/nser/issues
Language: en-US
License: GPL-3
Depends: R (>= 3.0)
Encoding: UTF-8
LazyData: true
Imports: stats, utils, readr, magrittr, rvest, tidyverse, stringr, jsonlite, RSelenium, googleVis, dplyr, lubridate, purrr, curl
Suggests: rmarkdown, testthat (>= 3.0.0), knitr, reshape2
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-12-14 05:27:43 UTC; FCI
Author: Nandan Patil [cre, aut]
Maintainer: Nandan Patil <tryanother609@gmail.com>
Repository: CRAN
Date/Publication: 2022-12-14 10:00:02 UTC

More information about nser at CRAN
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New package gutenbergr with initial version 0.2.3
Package: gutenbergr
Title: Download and Process Public Domain Works from Project Gutenberg
Version: 0.2.3
Description: Download and process public domain works in the Project Gutenberg collection <http://www.gutenberg.org/>. Includes metadata for all Project Gutenberg works, so that they can be searched and retrieved.
License: GPL-2
LazyData: TRUE
Maintainer: Myfanwy Johnston <mrowlan1@gmail.com>
URL: https://docs.ropensci.org/gutenbergr/, https://github.com/ropensci/gutenbergr
BugReports: https://github.com/ropensci/gutenbergr/issues
VignetteBuilder: knitr
Depends: R (>= 2.10)
Imports: cli, dplyr, glue, lazyeval, magrittr, purrr, readr, stringr, urltools
Encoding: UTF-8
Suggests: curl, ggplot2, knitr, rmarkdown, testthat, tidyr, tidytext
Language: en-US
NeedsCompilation: no
Packaged: 2022-12-13 23:41:35 UTC; myfanwyjohnston
Author: Myfanwy Johnston [aut, cre], David Robinson [aut, cph]
Repository: CRAN
Date/Publication: 2022-12-14 10:00:06 UTC

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Package StrucDiv updated to version 0.2.1 with previous version 0.2.0 dated 2022-12-13

Title: Spatial Structural Diversity Quantification in Raster Data
Description: Spatial structural diversity refers to the spatial, i.e. horizontal arrangement of landscape elements and can reveal itself as landscape features, such as patches and linear features. The 'R' package 'StrucDiv' provides methods to quantify spatial structural diversity in continuous remote sensing data, or in other data in raster format. Structure is based on the spatial arrangement of value pairs. The 'R' package 'StrucDiv' includes methods to combine information from different spatial scales, which allows to quantify multi-scale spatial structural diversity.
Author: Leila Schuh [aut, cre] , Reinhard Furrer [aut] , Kalina Cherneva [ctb, ctr], Kirill Mueller [ctr], Patrick Schratz [ctr], University Research Priority Progam Global Change and Biodiversity of the University of Zurich [fnd]
Maintainer: Leila Schuh <l.schuh@posteo.net>

Diff between StrucDiv versions 0.2.0 dated 2022-12-13 and 0.2.1 dated 2022-12-14

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Package rgeos updated to version 0.6-1 with previous version 0.5-9 dated 2021-12-14

Title: Interface to Geometry Engine - Open Source ('GEOS')
Description: Interface to Geometry Engine - Open Source ('GEOS') using the C 'API' for topology operations on geometries. Please note that 'rgeos' will be retired during 2023, plan transition to sf functions using 'GEOS' at your earliest convenience. The 'GEOS' library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on 'CRAN'. ('rgeos' >= 0.5-1): Up to and including 'GEOS' 3.7.1, topological operations succeeded with some invalid geometries for which the same operations fail from and including 'GEOS' 3.7.2. The 'checkValidity=' argument defaults and structure have been changed, from default FALSE to integer default '0L' for 'GEOS' < 3.7.2 (no check), '1L' 'GEOS' >= 3.7.2 (check and warn). A value of '2L' is also provided that may be used, assigned globally using 'set_RGEOS_CheckValidity(2L)', or locally using the 'checkValidity=2L' argument, to attempt zero-width buffer repair if i [...truncated...]
Author: Roger Bivand [cre, aut] , Colin Rundel [aut], Edzer Pebesma [ctb], Rainer Stuetz [ctb], Karl Ove Hufthammer [ctb], Patrick Giraudoux [ctb], Martin Davis [cph, ctb], Sandro Santilli [cph, ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

Diff between rgeos versions 0.5-9 dated 2021-12-14 and 0.6-1 dated 2022-12-14

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Package rgdal updated to version 1.6-3 with previous version 1.6-2 dated 2022-11-08

Title: Bindings for the 'Geospatial' Data Abstraction Library
Description: Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4) and access to projection/transformation operations from the 'PROJ' library. Please note that 'rgdal' will be retired by the end of 2023, plan transition to sf/stars/'terra' functions using 'GDAL' and 'PROJ' at your earliest convenience. Use is made of classes defined in the 'sp' package. Raster and vector map data can be imported into R, and raster and vector 'sp' objects exported. The 'GDAL' and 'PROJ' libraries are external to the package, and, when installing the package from source, must be correctly installed first; it is important that 'GDAL' < 3 be matched with 'PROJ' < 6. From 'rgdal' 1.5-8, installed with to 'GDAL' >=3, 'PROJ' >=6 and 'sp' >= 1.4, coordinate reference systems use 'WKT2_2019' strings, not 'PROJ' strings. 'Windows' and 'macOS' binaries (including 'GDAL', 'PROJ' and their dependencies) are provided on 'CRAN'.
Author: Roger Bivand [cre, aut] , Tim Keitt [aut], Barry Rowlingson [aut, ctb], Edzer Pebesma [ctb], Michael Sumner [ctb], Robert Hijmans [ctb], Daniel Baston [ctb], Even Rouault [cph, ctb], Frank Warmerdam [cph, ctb], Jeroen Ooms [ctb], Colin Rundel [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

Diff between rgdal versions 1.6-2 dated 2022-11-08 and 1.6-3 dated 2022-12-14

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Package pwrss updated to version 0.2.0 with previous version 0.1.0 dated 2022-11-09

Title: Power and Sample Size Calculation Tools
Description: Statistical power and minimum required sample size calculations for (1) testing a proportion (one-sample) against a constant, (2) testing a mean (one-sample) against a constant, (3) testing difference between two proportions (independent samples), (4) testing difference between two means (independent and paired samples), (5) testing a correlation (one-sample) against a constant, (6) testing difference between two correlations (independent samples), (7) testing a coefficient against a constant in multiple linear regression, (8) testing an indirect effect in the mediation analysis (Sobel, Joint, and Monte Carlo), (9) testing an R-squared against zero in linear regression, (10) testing an R-squared difference against zero in hierarchical regression, (11) testing an eta-squared or f-squared (for main and interaction effects) against zero in analysis of variance (could be one-way, two-way, and three-way), (12) testing an eta-squared or f-squared (for main and interaction effects) ag [...truncated...]
Author: Metin Bulus [aut, cre]
Maintainer: Metin Bulus <bulusmetin@gmail.com>

Diff between pwrss versions 0.1.0 dated 2022-11-09 and 0.2.0 dated 2022-12-14

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Package naryn updated to version 2.6.13 with previous version 2.6.12 dated 2022-11-22

Title: Native Access Medical Record Retriever for High Yield Analytics
Description: A toolkit for medical records data analysis. The 'naryn' package implements an efficient data structure for storing medical records, and provides a set of functions for data extraction, manipulation and analysis.
Author: Misha Hoichman [aut], Aviezer Lifshitz [aut, cre], Ben Gilat [aut], Netta Mendelson-Cohen [ctb], Rami Jaschek [ctb], Weizmann Institute of Science [cph]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>

Diff between naryn versions 2.6.12 dated 2022-11-22 and 2.6.13 dated 2022-12-14

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New package nlmm with initial version 1.0.2
Package: nlmm
Title: Generalized Laplace Mixed-Effects Models
Version: 1.0.2
Date: 2022-12-14
Maintainer: Marco Geraci <marco.geraci@uniroma1.it>
Depends: R (>= 3.0.0), nlme
Imports: utils, lqmm, mvtnorm, MASS, numDeriv, statmod, stats, Matrix, Qtools, Rcpp (>= 0.12.13)
LinkingTo: Rcpp, RcppArmadillo, BH
Description: Provides functions to fit linear mixed models based on convolutions of the generalized Laplace (GL) distribution. The GL mixed-effects model includes four special cases with normal random effects and normal errors (NN), normal random effects and Laplace errors (NL), Laplace random effects and normal errors (LN), and Laplace random effects and Laplace errors (LL). The methods are described in Geraci and Farcomeni (2020, Statistical Methods in Medical Research) <doi:10.1177/0962280220903763>.
License: GPL (>= 2)
LazyLoad: yes
NeedsCompilation: yes
Packaged: 2022-12-14 08:41:56 UTC; marco
Author: Marco Geraci [aut, cph, cre] , Alessio Farcomeni [ctb]
Repository: CRAN
Date/Publication: 2022-12-14 09:00:02 UTC

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Package GARCOM updated to version 1.2.1 with previous version 1.2.0 dated 2020-10-16

Title: Gene and Region Counting of Mutations ("GARCOM")
Description: Gene and Region Counting of Mutations (GARCOM) package computes mutation (or alleles) counts per gene per individuals based on gene annotation or genomic base pair boundaries. It comes with features to accept data formats in plink(.raw) and VCF. It provides users flexibility to extract and filter individuals, mutations and genes of interest.
Author: Sanjeev Sariya [aut, cre, cph], Giuseppe Tosto [aut, cph]
Maintainer: Sanjeev Sariya <sanjeevsariya@gmail.com>

Diff between GARCOM versions 1.2.0 dated 2020-10-16 and 1.2.1 dated 2022-12-14

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Package freegroup updated to version 1.1-6 with previous version 1.1-3 dated 2021-11-20

Title: The Free Group
Description: The free group in R; juxtaposition is represented by a plus. Includes inversion, multiplication by a scalar, group-theoretic power operation, and Tietze forms. To cite the package in publications please use Hankin (2022) <doi:10.48550/ARXIV.2212.05883>.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

Diff between freegroup versions 1.1-3 dated 2021-11-20 and 1.1-6 dated 2022-12-14

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Package proverbs updated to version 0.3.0 with previous version 0.2.0 dated 2022-11-16

Title: Print a Daily Bible Proverb to Console
Description: A simple package to grab a Bible proverb corresponding to the day of the month.
Author: Brad Lindblad [aut, cre, cph]
Maintainer: Brad Lindblad <me@bradlindblad.com>

Diff between proverbs versions 0.2.0 dated 2022-11-16 and 0.3.0 dated 2022-12-14

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Package persDx updated to version 0.2.0 with previous version 0.1.0 dated 2022-05-30

Title: Estimating Personalized Diagnostics Rules
Description: Recommend the optimal biomarker for disease screening or diagnosis based on patients' individual characteristics.
Author: Yunro Chung [aut, cre]
Maintainer: Yunro Chung <yunro.chung@asu.edu>

Diff between persDx versions 0.1.0 dated 2022-05-30 and 0.2.0 dated 2022-12-14

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Package ggrcs updated to version 0.2.7 with previous version 0.2.6 dated 2022-11-28

Title: Draw Histograms and Restricted Cubic Splines (RCS)
Description: You can use this function to easily draw a combined histogram and restricted cubic spline. The function draws the graph through 'ggplot2'. RCS fitting requires the use of the rcs() function of the 'rms' package. Can fit cox regression, logistic regression. This method was described by Per Kragh (2003) <doi:10.1002/sim.1497>.
Author: Qiang LIU [aut, cre]
Maintainer: Qiang LIU <dege857@163.com>

Diff between ggrcs versions 0.2.6 dated 2022-11-28 and 0.2.7 dated 2022-12-14

 DESCRIPTION        |    6 +++---
 MD5                |    8 ++++----
 R/ggrcs.R          |   12 +++++++-----
 R/predata.ols.R    |    2 +-
 man/predata.ols.Rd |    2 +-
 5 files changed, 16 insertions(+), 14 deletions(-)

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Package ccml updated to version 1.2.0 with previous version 1.1.0 dated 2022-08-29

Title: Consensus Clustering for Different Sample Coverage Data
Description: Consensus clustering, also called meta-clustering or cluster ensembles, has been increasingly used in clinical data. Current consensus clustering methods tend to ensemble a number of different clusters from mathematical replicates with similar sample coverage. As the fact of common variety of sample coverage in the real-world data, a new consensus clustering strategy dealing with such biological replicates is required. This is a two-step consensus clustering package, which is used to input multiple predictive labels with different sample coverage (missing labels).
Author: Chuanxing Li [aut, cre], Meng Zhou [aut]
Maintainer: Chuanxing Li <chuan-xing.li@ki.se>

Diff between ccml versions 1.1.0 dated 2022-08-29 and 1.2.0 dated 2022-12-14

 DESCRIPTION                    |    6 +++---
 MD5                            |   14 +++++++-------
 NEWS.md                        |   39 ++++++++++++++++++++++++---------------
 R/callNCW.R                    |   10 ++++++++--
 R/ccml.R                       |    4 ++--
 R/plotCompareCW.R              |    6 +++---
 R/spectralClusteringAffinity.R |    2 +-
 man/callNCW.Rd                 |    2 +-
 8 files changed, 49 insertions(+), 34 deletions(-)

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Package bayesMRM updated to version 2.4.0 with previous version 2.3.0 dated 2022-11-29

Title: Bayesian Multivariate Receptor Modeling
Description: Bayesian analysis of multivariate receptor modeling. The package consists of implementations of the methods of Park and Oh (2015) <doi:10.1016/j.chemolab.2015.08.021>.The package uses 'JAGS'(Just Another Gibbs Sampler) to generate Markov chain Monte Carlo samples of parameters.
Author: Man-Suk Oh [aut, cre], Eun-Kyung Lee [aut], Eun Sug Park [aut]
Maintainer: Man-Suk Oh <msoh@ewha.ac.kr>

Diff between bayesMRM versions 2.3.0 dated 2022-11-29 and 2.4.0 dated 2022-12-14

 DESCRIPTION |   12 ++++++------
 MD5         |    2 +-
 2 files changed, 7 insertions(+), 7 deletions(-)

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Package Rcsdp updated to version 0.1.57.4 with previous version 0.1.57.2 dated 2021-11-02

Title: R Interface to the CSDP Semidefinite Programming Library
Description: R interface to the CSDP semidefinite programming library. Installs version 6.1.1 of CSDP from the COIN-OR website if required. An existing installation of CSDP may be used by passing the proper configure arguments to the installation command. See the INSTALL file for further details.
Author: Hector Corrada Bravo [aut, cre], Florian Schwendinger [ctb], Brian Borchers [aut], Don van den Bergh [ctb]
Maintainer: Hector Corrada Bravo <hcorrada@gmail.com>

Diff between Rcsdp versions 0.1.57.2 dated 2021-11-02 and 0.1.57.4 dated 2022-12-14

 Rcsdp-0.1.57.2/Rcsdp/src/Csdp/lib/Csdp.ts            |only
 Rcsdp-0.1.57.4/Rcsdp/DESCRIPTION                     |   10 +
 Rcsdp-0.1.57.4/Rcsdp/MD5                             |   87 ++++++++---------
 Rcsdp-0.1.57.4/Rcsdp/R/Rcsdp.R                       |    2 
 Rcsdp-0.1.57.4/Rcsdp/README.md                       |    2 
 Rcsdp-0.1.57.4/Rcsdp/man/csdp.Rd                     |    2 
 Rcsdp-0.1.57.4/Rcsdp/man/csdp.control.Rd             |    4 
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/include/declarations.h |   96 +++++++------------
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/Fnorm.c            |   16 ---
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/add_mat.c          |    5 
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/addscaledmat.c     |   10 -
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/allocmat.c         |    9 -
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/calc_dobj.c        |   10 -
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/calc_pobj.c        |    8 -
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/chol.c             |   23 ----
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/copy_mat.c         |    4 
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/easysdp.c          |   46 +++------
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/freeprob.c         |   12 --
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/initparams.c       |    5 
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/initsoln.c         |   18 +--
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/linesearch.c       |   23 ++--
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/make_i.c           |    4 
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/makefill.c         |   14 +-
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/mat_mult.c         |   37 +++----
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/mat_multsp.c       |   33 +++---
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/matvec.c           |    6 -
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/norms.c            |   15 --
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/op_a.c             |   10 -
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/op_at.c            |   10 -
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/op_o.c             |   18 +--
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/packed.c           |   21 ----
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/psd_feas.c         |   40 +++----
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/qreig.c            |    6 -
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/readprob.c         |   56 ++---------
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/readsol.c          |   18 +--
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/sdp.c              |   85 +++++++---------
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/solvesys.c         |    7 -
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/sortentries.c      |    6 -
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/sym_mat.c          |    4 
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/trace_prod.c       |    5 
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/tweakgap.c         |   20 +--
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/user_exit.c        |   56 ++++-------
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/writeprob.c        |   14 +-
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/writesol.c         |   14 +-
 Rcsdp-0.1.57.4/Rcsdp/src/Csdp/lib/zero_mat.c         |    4 
 45 files changed, 355 insertions(+), 540 deletions(-)

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Package metaMix (with last version 0.3) was removed from CRAN

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

2019-02-11 0.3

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Package r.proxy (with last version 0.1.0) was removed from CRAN

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

2021-11-17 0.1.0

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