Thu, 04 May 2023

Package rtika updated to version 2.7.0 with previous version 2.4.1 dated 2022-09-26

Title: R Interface to 'Apache Tika'
Description: Extract text or metadata from over a thousand file types, using Apache Tika <https://tika.apache.org/>. Get either plain text or structured XHTML content.
Author: Sasha Goodman [aut, cre], The Apache Software Foundation [aut, cph], Julia Silge [rev] , David Gohel [rev]
Maintainer: Sasha Goodman <goodmansasha@gmail.com>

Diff between rtika versions 2.4.1 dated 2022-09-26 and 2.7.0 dated 2023-05-04

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Package MSclust updated to version 1.0.3 with previous version 1.0.2 dated 2022-08-31

Title: Multiple-Scaled Clustering
Description: Model based clustering using the multivariate multiple Scaled t (MST) and multivariate multiple scaled contaminated normal (MSCN) distributions. The MST is an extension of the multivariate Student-t distribution to include flexible tail behaviors, Forbes, F. & Wraith, D. (2014) <doi:10.1007/s11222-013-9414-4>. The MSCN represents a heavy-tailed generalization of the multivariate normal (MN) distribution to model elliptical contoured scatters in the presence of mild outliers (also referred to as "bad" points) and automatically detect bad points, Punzo, A. & Tortora, C. (2021) <doi:10.1177/1471082X19890935>.
Author: Cristina Tortora [aut, cre, cph] , Antonio Punzo [aut] , Louis Tran [aut]
Maintainer: Cristina Tortora <grikris1@gmail.com>

Diff between MSclust versions 1.0.2 dated 2022-08-31 and 1.0.3 dated 2023-05-04

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Package mlr3fairness updated to version 0.3.2 with previous version 0.3.1 dated 2022-08-16

Title: Fairness Auditing and Debiasing for 'mlr3'
Description: Integrates fairness auditing and bias mitigation methods for the 'mlr3' ecosystem. This includes fairness metrics, reporting tools, visualizations and bias mitigation techniques such as "Reweighing" described in 'Kamiran, Calders' (2012) <doi:10.1007/s10115-011-0463-8> and "Equalized Odds" described in 'Hardt et al.' (2016) <https://papers.nips.cc/paper/2016/file/9d2682367c3935defcb1f9e247a97c0d-Paper.pdf>. Integration with 'mlr3' allows for auditing of ML models as well as convenient joint tuning of machine learning algorithms and debiasing methods.
Author: Florian Pfisterer [cre, aut] , Wei Siyi [aut], Michel Lang [aut]
Maintainer: Florian Pfisterer <pfistererf@googlemail.com>

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Package canaper updated to version 1.0.1 with previous version 1.0.0 dated 2022-10-04

Title: Categorical Analysis of Neo- And Paleo-Endemism
Description: Provides functions to analyze the spatial distribution of biodiversity, in particular categorical analysis of neo- and paleo-endemism (CANAPE) as described in Mishler et al (2014) <doi:10.1038/ncomms5473>. 'canaper' conducts statistical tests to determine the types of endemism that occur in a study area while accounting for the evolutionary relationships of species.
Author: Joel H. Nitta [aut, cre] , Shawn W. Laffan [ctb, dtc], Brent D. Mishler [ctb, dtc], Wataru Iwasaki [ctb] , Klaus Schliep [rev]
Maintainer: Joel H. Nitta <joelnitta@gmail.com>

Diff between canaper versions 1.0.0 dated 2022-10-04 and 1.0.1 dated 2023-05-04

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Package tablaxlsx updated to version 1.2.5 with previous version 1.2.4 dated 2020-10-19

Title: Write Formatted Tables in Excel Workbooks
Description: For writing tables with custom formats in a Excel file ready to be distributed.
Author: Jesus Maria Rodriguez Rodriguez
Maintainer: Jesus Maria Rodriguez Rodriguez <jesusmro@gmail.com>

Diff between tablaxlsx versions 1.2.4 dated 2020-10-19 and 1.2.5 dated 2023-05-04

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Package mdgc updated to version 0.1.7 with previous version 0.1.6 dated 2022-09-10

Title: Missing Data Imputation Using Gaussian Copulas
Description: Provides functions to impute missing values using Gaussian copulas for mixed data types as described by Christoffersen et al. (2021) <arXiv:2102.02642>. The method is related to Hoff (2007) <doi:10.1214/07-AOAS107> and Zhao and Udell (2019) <arXiv:1910.12845> but differs by making a direct approximation of the log marginal likelihood using an extended version of the Fortran code created by Genz and Bretz (2002) <doi:10.1198/106186002394> in addition to also support multinomial variables.
Author: Benjamin Christoffersen [cre, aut] , Alan Genz [cph], Frank Bretz [cph], Torsten Hothorn [cph], R-core [cph], Ross Ihaka [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>

Diff between mdgc versions 0.1.6 dated 2022-09-10 and 0.1.7 dated 2023-05-04

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Package h2otools updated to version 0.3 with previous version 0.1 dated 2022-10-02

Title: Machine Learning Model Evaluation for 'h2o' Package
Description: Several functions are provided that simplify using 'h2o' package. Currently, a function for extracting the AutoML model parameter is provided, alongside a function for computing F-Measure statistics at any given threshold. For more information about 'h2o' package see <https://h2o.ai/>.
Author: E. F. Haghish [aut, cre, cph]
Maintainer: E. F. Haghish <haghish@uio.no>

Diff between h2otools versions 0.1 dated 2022-10-02 and 0.3 dated 2023-05-04

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New package survstan with initial version 0.0.1
Package: survstan
Title: Fitting Survival Regression Models via 'Stan'
Version: 0.0.1
Description: Parametric survival regression models under the maximum likelihood approach via 'Stan'. Implemented regression models include accelerated failure time models, proportional hazards models, proportional odds models, and accelerated hazard models. Available baseline survival distributions include exponential, Weibull, log-normal, and log-logistic distributions. References: Lawless (2002) <ISBN:9780471372158>; Bennett (1982) <doi:10.1002/sim.4780020223>; Chen and Wang(2000) <doi:10.1080/01621459.2000.10474236>.
License: MIT + file LICENSE
Encoding: UTF-8
Biarch: true
Depends: R (>= 3.4.0), survival
Imports: actuar (>= 3.0.0), dplyr, ggplot2, gridExtra, methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), Rdpack, rlang, rstan (>= 2.18.1), rstantools (>= 2.3.1), tibble
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
SystemRequirements: GNU make
URL: https://github.com/fndemarqui/survstan, https://fndemarqui.github.io/survstan/
BugReports: https://github.com/fndemarqui/survstan/issues
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2023-05-03 22:17:52 UTC; fndemarqui
Author: Fabio Demarqui [aut, cre, cph]
Maintainer: Fabio Demarqui <fndemarqui@est.ufmg.br>
Repository: CRAN
Date/Publication: 2023-05-04 19:10:02 UTC

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New package pseudohouseholds with initial version 0.1.0
Package: pseudohouseholds
Title: Generate Pseudohouseholds on Road Networks in Regions
Version: 0.1.0
Description: Given an arbitrary set of spatial regions and road networks, generate a set of representative points, or pseudohouseholds, that can be used for travel burden analysis. Parallel processing is supported.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: dplyr, furrr, sf
Depends: R (>= 2.10)
Suggests: covr, future, ggplot2, ggspatial, knitr, purrr, rmarkdown, testthat (>= 3.0.0)
URL: https://github.com/chris31415926535/pseudohouseholds
BugReports: https://github.com/chris31415926535/pseudohouseholds/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-05-03 14:07:04 UTC; rstudio
Author: Christopher Belanger [aut, cre, cph]
Maintainer: Christopher Belanger <christopher.a.belanger@gmail.com>
Repository: CRAN
Date/Publication: 2023-05-04 19:10:06 UTC

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New package HMTL with initial version 0.1.0
Package: HMTL
Title: Heterogeneous Multi-Task Feature Learning
Version: 0.1.0
Description: The heterogeneous multi-task feature learning is a data integration method to conduct joint feature selection across multiple related data sets with different distributions. The algorithm can combine different types of learning tasks, including linear regression, Huber regression, adaptive Huber, and logistic regression. The modified version of Bayesian Information Criterion (BIC) is produced to measure the model performance. Package is based on Yuan Zhong, Wei Xu, and Xin Gao (2022) <https://www.fields.utoronto.ca/talk-media/1/53/65/slides.pdf>.
Depends: R (>= 3.5.0), stats, graphics, Matrix, pROC
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2023-05-04 01:46:00 UTC; adamzhong
Author: Yuan Zhong [aut, cre], Wei Xu [aut], Xin Gao [aut]
Maintainer: Yuan Zhong <aqua.zhong@gmail.com>
Repository: CRAN
Date/Publication: 2023-05-04 19:20:02 UTC

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Package SEMgraph updated to version 1.2.0 with previous version 1.1.3 dated 2022-10-12

Title: Network Analysis and Causal Inference Through Structural Equation Modeling
Description: Estimate networks and causal relationships in complex systems through Structural Equation Modeling. This package also includes functions to import, weight, manipulate, and fit biological network models within the Structural Equation Modeling framework described in Grassi M, Palluzzi F, Tarantino B (2022) <doi:10.1093/bioinformatics/btac567>.
Author: Mario Grassi [aut], Fernando Palluzzi [aut], Barbara Tarantino [aut, cre]
Maintainer: Barbara Tarantino <barbara.tarantino01@universitadipavia.it>

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Package bench updated to version 1.1.3 with previous version 1.1.2 dated 2021-11-30

Title: High Precision Timing of R Expressions
Description: Tools to accurately benchmark and analyze execution times for R expressions.
Author: Jim Hester [aut], Davis Vaughan [aut, cre], Drew Schmidt [ctb] , Posit Software, PBC [cph, fnd]
Maintainer: Davis Vaughan <davis@posit.co>

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Package xQTLbiolinks updated to version 1.4.2 with previous version 1.2.2 dated 2022-08-27

Title: Integrative Analysis of Quantitative Trait Locus Data of 'xQTL'
Description: Enables users-customized data retrieval, processing, analysis, and data visualization of molecular quantitative trait locus and gene expression data from public resources through the application programming interface <https://gtexportal.org/home/api-docs/index.html> of 'GTEx' and <http://www.ebi.ac.uk/eqtl/api> of 'eQTL cagalogue'.
Author: Ruofan Ding [aut, cre], Xudong Zou [aut, ctb], Yangmei Qin [aut, ctb], Gao Wang [aut, ctb], Lei Li [aut, ctb, cph]
Maintainer: Ruofan Ding <dingruofan1@foxmail.com>

Diff between xQTLbiolinks versions 1.2.2 dated 2022-08-27 and 1.4.2 dated 2023-05-04

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Package unittest updated to version 1.6-0 with previous version 1.5-3 dated 2022-09-25

Title: TAP-Compliant Unit Testing
Description: Concise TAP <http://testanything.org/> compliant unit testing package. Authored tests can be run using CMD check with minimal implementation overhead.
Author: Jamie Lentin [aut, cre], Anthony Hennessey [aut]
Maintainer: Jamie Lentin <jm@ravingmantis.com>

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Package shapr updated to version 0.2.2 with previous version 0.2.1 dated 2023-02-27

Title: Prediction Explanation with Dependence-Aware Shapley Values
Description: Complex machine learning models are often hard to interpret. However, in many situations it is crucial to understand and explain why a model made a specific prediction. Shapley values is the only method for such prediction explanation framework with a solid theoretical foundation. Previously known methods for estimating the Shapley values do, however, assume feature independence. This package implements the method described in Aas, Jullum and Løland (2019) <arXiv:1903.10464>, which accounts for any feature dependence, and thereby produces more accurate estimates of the true Shapley values.
Author: Nikolai Sellereite [aut] , Martin Jullum [cre, aut] , Annabelle Redelmeier [aut], Anders Loeland [ctb], Jens Christian Wahl [ctb], Camilla Lingjaerde [ctb], Norsk Regnesentral [cph, fnd]
Maintainer: Martin Jullum <Martin.Jullum@nr.no>

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Package pointRes updated to version 2.0.2 with previous version 2.0.1 dated 2022-05-07

Title: Analyzing Pointer Years and Components of Resilience
Description: Functions to calculate and plot event and pointer years as well as resilience indices. Designed for dendroecological applications, but also suitable to analyze patterns in other ecological time series.
Author: Marieke van der Maaten-Theunissen [aut, cph, cre, trl], Ernst van der Maaten [aut, trl], Gottfried Jetsckhe [aut, trl], Mario Trouillier [aut, trl]
Maintainer: Marieke van der Maaten-Theunissen <marieke.theunissen@tu-dresden.de>

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Package pedquant updated to version 0.2.2 with previous version 0.2.1 dated 2022-11-12

Title: Public Economic Data and Quantitative Analysis
Description: Provides an interface to access public economic and financial data for economic research and quantitative analysis. The data sources including NBS, FRED, Sina, Eastmoney and etc. It also provides quantitative functions for trading strategies based on the 'data.table', 'TTR', 'PerformanceAnalytics' and etc packages.
Author: Shichen Xie [aut, cre]
Maintainer: Shichen Xie <xie@shichen.name>

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Package mlmpower updated to version 1.0.1 with previous version 1.0.0 dated 2023-04-26

Title: Power Analysis and Data Simulation for Multilevel Models
Description: A declarative language for specifying multilevel models, solving for population parameters based on specified variance-explained effect size measures, generating data, and conducting power analyses to determine sample size recommendations. The specification allows for any number of within-cluster effects, between-cluster effects, covariate effects at either level, and random coefficients. Moreover, the models do not assume orthogonal effects, and predictors can correlate at either level and accommodate models with multiple interaction effects.
Author: Brian T. Keller [aut, cre, cph]
Maintainer: Brian T. Keller <bk@utexas.edu>

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Package indicspecies updated to version 1.7.13 with previous version 1.7.12 dated 2022-03-06

Title: Relationship Between Species and Groups of Sites
Description: Functions to assess the strength and statistical significance of the relationship between species occurrence/abundance and groups of sites [De Caceres & Legendre (2009) <doi:10.1890/08-1823.1>]. Also includes functions to measure species niche breadth using resource categories [De Caceres et al. (2011) <doi:10.1111/J.1600-0706.2011.19679.x>].
Author: Miquel De Caceres [aut, cre] , Florian Jansen [aut], Noah Dell [aut]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>

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Package causalweight updated to version 1.0.4 with previous version 1.0.3 dated 2022-08-12

Title: Estimation Methods for Causal Inference Based on Inverse Probability Weighting
Description: Various estimators of causal effects based on inverse probability weighting, doubly robust estimation, and double machine learning. Specifically, the package includes methods for estimating average treatment effects, direct and indirect effects in causal mediation analysis, and dynamic treatment effects. The models refer to studies of Froelich (2007) <doi:10.1016/j.jeconom.2006.06.004>, Huber (2012) <doi:10.3102/1076998611411917>, Huber (2014) <doi:10.1080/07474938.2013.806197>, Huber (2014) <doi:10.1002/jae.2341>, Froelich and Huber (2017) <doi:10.1111/rssb.12232>, Hsu, Huber, Lee, and Lettry (2020) <doi:10.1002/jae.2765>, and others.
Author: Hugo Bodory [aut, cre] , Martin Huber [aut] , Jannis Kueck [aut]
Maintainer: Hugo Bodory <hugo.bodory@unisg.ch>

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New package UComp with initial version 4.0.0
Package: UComp
Title: Automatic Unobserved Components and Other Time Series Models
Version: 4.0.0
Date: 2023-05-02
Author: Diego J. Pedregal [aut, cre]
Maintainer: Diego J. Pedregal <Diego.Pedregal@uclm.es>
Description: Comprehensive analysis and forecasting of univariate time series using automatic unobserved components models and algorithms. Harvey, AC (1989) <doi:10.1017/CBO9781107049994>. Pedregal DJ and Young PC (2002) <doi:10.1002/9780470996430>. Durbin J and Koopman SJ (2012) <doi:10.1093/acprof:oso/9780199641178.001.0001>. Hyndman RJ, Koehler AB, Ord JK, and Snyder RD (2008) <doi:10.1007/9783540719182>.
License: GPL-3
Encoding: UTF-8
Imports: ggplot2, gridExtra, tsibble, tsoutliers, stats, ggforce, utils, parallel
LinkingTo: Rcpp, RcppArmadillo
Depends: Rcpp (>= 1.0.3), R (>= 3.5.0)
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2023-05-04 11:25:35 UTC; diego.pedregal
Repository: CRAN
Date/Publication: 2023-05-04 13:20:06 UTC

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Package saccadr updated to version 0.1.2 with previous version 0.1.1 dated 2022-09-20

Title: Extract Saccades via an Ensemble of Methods Approach
Description: A modular and extendable approach to extract (micro)saccades from gaze samples via an ensemble of methods. Although there is an agreement about a general definition of a saccade, the more specific details are harder to agree upon. Therefore, there are numerous algorithms that extract saccades based on various heuristics, which differ in the assumptions about velocity, acceleration, etc. The package uses three methods (Engbert and Kliegl (2003) <doi:10.1016/S0042-6989(03)00084-1>, Otero-Millan et al. (2014)<doi:10.1167/14.2.18>, and Nyström and Holmqvist (2010) <doi:10.3758/BRM.42.1.188>) to label individual samples and then applies a majority vote approach to identify saccades. The package includes three methods but can be extended via custom functions. It also uses a modular approach to compute velocity and acceleration from noisy samples. Finally, you can obtain methods votes per gaze sample instead of saccades.
Author: Alexander Pastukhov [aut, cre]
Maintainer: Alexander Pastukhov <pastukhov.alexander@gmail.com>

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Package openalexR updated to version 1.1.0 with previous version 1.0.2.9 dated 2023-04-01

Title: Getting Bibliographic Records from 'OpenAlex' Database Using 'DSL' API
Description: A set of tools to extract bibliographic content from 'OpenAlex' database using API <https://docs.openalex.org>.
Author: Massimo Aria [aut, cre, cph] , Corrado Cuccurullo [ctb] , Trang Le [aut] , June Choe [ctb]
Maintainer: Massimo Aria <aria@unina.it>

Diff between openalexR versions 1.0.2.9 dated 2023-04-01 and 1.1.0 dated 2023-05-04

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Package goeveg updated to version 0.6.1 with previous version 0.6.0 dated 2023-04-19

Title: Functions for Community Data and Ordinations
Description: A collection of functions useful in (vegetation) community analyses and ordinations. Includes automatic species selection for ordination diagrams, NMDS stress/scree plots, species response curves and rank-abundance curves as well as calculation and sorting of synoptic tables.
Author: Friedemann von Lampe [aut, cre], Jenny Schellenberg [aut]
Maintainer: Friedemann von Lampe <fvonlampe@uni-goettingen.de>

Diff between goeveg versions 0.6.0 dated 2023-04-19 and 0.6.1 dated 2023-05-04

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Package nodiv updated to version 1.4.1 with previous version 1.4.0 dated 2020-05-26

Title: Compares the Distribution of Sister Clades Through a Phylogeny
Description: An implementation of the nodiv algorithm, see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. <DOI:10.1111/2041-210X.12283>. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped.
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard <mkborregaard@sund.ku.dk>

Diff between nodiv versions 1.4.0 dated 2020-05-26 and 1.4.1 dated 2023-05-04

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Package sparseSEM updated to version 3.8-1 with previous version 3.8 dated 2023-04-21

Title: Sparse-Aware Maximum Likelihood for Structural Equation Models
Description: Provides Sparse-aware maximum likelihood for structural equation models in inferring network structure (topology).
Author: Anhui Huang [aut, ctb, cre]
Maintainer: Anhui Huang <anhuihuang@gmail.com>

Diff between sparseSEM versions 3.8 dated 2023-04-21 and 3.8-1 dated 2023-05-04

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More information about sparseSEM at CRAN
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Package rswipl updated to version 9.1.9 with previous version 9.1.8 dated 2023-03-24

Title: Embed 'SWI'-'Prolog'
Description: Interface to 'SWI'-'Prolog', <https://www.swi-prolog.org/>. This package is normally not loaded directly, please refer to package 'rolog' instead. The purpose of this package is to provide the 'Prolog' runtime on systems that do not have a software installation of 'SWI'-'Prolog'.
Author: Matthias Gondan [aut, com, cre] , Jan Wielemaker [ctb, cph] , European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>

Diff between rswipl versions 9.1.8 dated 2023-03-24 and 9.1.9 dated 2023-05-04

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More information about rswipl at CRAN
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Package leaflegend updated to version 1.1.0 with previous version 1.0.0 dated 2022-08-05

Title: Add Custom Legends to 'leaflet' Maps
Description: Provides extensions to the 'leaflet' package to customize legends with images, text styling, orientation, sizing, and symbology and functions to create symbols to plot on maps.
Author: Thomas Roh [aut, cre], Ricardo Rodrigo Basa [ctb]
Maintainer: Thomas Roh <thomas@roh.engineering>

Diff between leaflegend versions 1.0.0 dated 2022-08-05 and 1.1.0 dated 2023-05-04

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Package ggeffects updated to version 1.2.2 with previous version 1.2.1 dated 2023-04-02

Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from Model Outputs
Description: Compute marginal effects and adjusted predictions from statistical models and returns the result as tidy data frames. These data frames are ready to use with the 'ggplot2'-package. Effects and predictions can be calculated for many different models. Interaction terms, splines and polynomial terms are also supported. The main functions are ggpredict(), ggemmeans() and ggeffect(). There is a generic plot()-method to plot the results using 'ggplot2'.
Author: Daniel Luedecke [aut, cre] , Frederik Aust [ctb] , Sam Crawley [ctb] , Mattan S. Ben-Shachar [ctb]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>

Diff between ggeffects versions 1.2.1 dated 2023-04-02 and 1.2.2 dated 2023-05-04

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New package gsMAMS with initial version 0.7.1
Package: gsMAMS
Title: Group Sequential Designs of Multi-Arm Multi-Stage Trials
Version: 0.7.1
Imports: mvtnorm, stats, survival
Description: It provides functions to generate operating characteristics and to calculate Sequential Conditional Probability Ratio Tests(SCPRT) efficacy and futility boundary values along with sample/event size of Multi-Arm Multi-Stage(MAMS) trials for different outcomes. The package is based on Jianrong Wu, Yimei Li, Liang Zhu (2023) <doi:10.1002/sim.9682>, Jianrong Wu, Yimei Li (2023) "Group Sequential Multi-Arm Multi-Stage Survival Trial Design with Treatment Selection"(Manuscript accepted for publication) and Jianrong Wu, Yimei Li, Shengping Yang (2023) "Group Sequential Multi-Arm Multi-Stage Trial Design with Ordinal Endpoints"(In preparation).
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-05-03 20:43:04 UTC; tpatni
Author: Tushar Patni [aut, cre], Yimei Li [aut], Jianrong Wu [aut]
Maintainer: Tushar Patni <tushar.patni006@gmail.com>
Repository: CRAN
Date/Publication: 2023-05-04 09:00:02 UTC

More information about gsMAMS at CRAN
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New package snplinkage with initial version 1.0.0
Package: snplinkage
Title: Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations
Version: 1.0.0
Description: Linkage disequilibrium visualizations of up to several hundreds of single nucleotide polymorphisms (SNPs), annotated with chromosomic positions and gene names. Two types of plots are available for small numbers of SNPs (<40) and for large numbers (tested up to 500). Both can be extended by combining other ggplots, e.g. association studies results, and functions enable to directly visualize the effect of SNP selection methods, as minor allele frequency filtering and TagSNP selection, with a second correlation heatmap. The SNPs correlations are computed on Genotype Data objects from the 'GWASTools' package using the 'SNPRelate' package, and the plots are customizable 'ggplot2' and 'gtable' objects and are annotated using the 'biomaRt' package. Usage is detailed in the vignette with example data and results from up to 500 SNPs of 1,200 scans are in Charlon T. (2019) <doi:10.13097/archive-ouverte/unige:161795>.
Imports: gdsfmt, ggplot2, gtable, magrittr, stats, utils
Depends: R (>= 2.15), GWASTools (>= 1.10.1)
Suggests: biomaRt, cowplot, data.table, dplyr, ggrepel, grid, grDevices, knitr, methods, plyr, SNPRelate, testthat
URL: https://gitlab.com/thomaschln/snplinkage
BugReports: https://gitlab.com/thomaschln/snplinkage/-/issues
VignetteBuilder: knitr
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-05-03 06:43:57 UTC; root
Author: Thomas Charlon [aut, cre] , Karl Forner [aut], Alessandro Di Cara [aut], Jerome Wojcik [aut]
Maintainer: Thomas Charlon <charlon@protonmail.com>
Repository: CRAN
Date/Publication: 2023-05-04 08:10:02 UTC

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New package MDEI with initial version 1.0
Package: MDEI
Title: Implementing the Method of Direct Estimation and Inference
Version: 1.0
Date: 2023-05-03
Description: Causal and statistical inference on an arbitrary treatment effect curve requires care in both estimation and inference. This package, implements the Method of Direct Estimation and Inference as introduced in "Estimation and Inference on Nonlinear and Heterogeneous Effects" by Ratkovic and Tingley (2023) <doi:10.1086/723811>. The method takes an outcome, variable of theoretical interest (treatment), and set of variables and then returns a partial derivative (marginal effect) of the treatment variable at each point along with uncertainty intervals. The approach offers two advances. First, a split-sample approach is used as a guard against over-fitting. Second, the method uses a data-driven interval derived from conformal inference, rather than relying on a normality assumption on the error terms.
License: GPL (>= 2)
Depends: R (>= 3.6.0)
Imports: grDevices, MASS, ranger, Rcpp (>= 1.0.6), splines2
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2023-05-03 13:37:22 UTC; ratkovic
Author: Marc Ratkovic [aut, cre], Dustin Tingley [ctb], Nithin Kavi [aut]
Maintainer: Marc Ratkovic <ratkovic@princeton.edu>
Repository: CRAN
Date/Publication: 2023-05-04 08:30:11 UTC

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Package Lahman updated to version 11.0-0 with previous version 10.0-1 dated 2022-04-26

Title: Sean 'Lahman' Baseball Database
Description: Provides the tables from the 'Sean Lahman Baseball Database' as a set of R data.frames. It uses the data on pitching, hitting and fielding performance and other tables from 1871 through 2022, as recorded in the 2023 version of the database. Documentation examples show how many baseball questions can be investigated.
Author: Michael Friendly [aut], Chris Dalzell [cre, aut], Martin Monkman [aut], Dennis Murphy [aut], Vanessa Foot [ctb], Justeena Zaki-Azat [ctb], Sean Lahman [cph]
Maintainer: Chris Dalzell <cdalzell@gmail.com>

Diff between Lahman versions 10.0-1 dated 2022-04-26 and 11.0-0 dated 2023-05-04

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Permanent link

Package iemisc updated to version 1.0.3 with previous version 1.0.2 dated 2023-03-07

Title: Irucka Embry's Miscellaneous Functions
Description: A collection of Irucka Embry's miscellaneous functions (Engineering Economics, Civil & Environmental/Water Resources Engineering, Construction Measurements, GNU Octave compatible functions, Python compatible function, Trigonometric functions in degrees and function in radians, Geometry, Statistics, Mortality Calculators, Quick Search, etc.).
Author: Irucka Embry [aut, cre], Felix Andrews [aut, ctb] , Hans Werner Borchers [aut, ctb] , Samit Basu [aut, ctb] , David Bateman [aut, ctb] , Rik Wehbring [aut, ctb] , Didier Clamond [aut, ctb] , Berry Boessenkool [aut, ctb] , Tyler Rinker [aut, ctb] , Co [...truncated...]
Maintainer: Irucka Embry <iembry@ecoccs.com>

Diff between iemisc versions 1.0.2 dated 2023-03-07 and 1.0.3 dated 2023-05-04

 DESCRIPTION                                               |   19 
 MD5                                                       |  433 +++++++-------
 NAMESPACE                                                 |    8 
 NEWS.md                                                   |   13 
 R/AgivenF.R                                               |    2 
 R/AgivenFcont.R                                           |   12 
 R/AgivenP.R                                               |    2 
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 R/Manningpara.R                                           |    2 
 R/Manningtrap.R                                           |    4 
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 R/PgivenFivary.R                                          |    2 
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 README.md                                                 |   85 ++
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 221 files changed, 922 insertions(+), 771 deletions(-)

More information about iemisc at CRAN
Permanent link

New package HybridMicrobiomes with initial version 0.1.0
Package: HybridMicrobiomes
Title: Analysis of Host-Associated Microbiomes from Hybrid Organisms
Version: 0.1.0
Description: Provides tools to analyze and visualize the relationships between host-associated microbiomes of hybrid organisms and those of their progenitor species.
License: GPL-2
Encoding: UTF-8
Imports: rgl, compositions,phyloseq, rlang, PERMANOVA, graphics, stats
NeedsCompilation: no
Packaged: 2023-05-02 19:33:07 UTC; sbewick
Author: Benjamin Camper [aut], Zachary Lauglin [ctb], Daniel Malagon [ctb], Robert Denton [ctb], Sharon Bewick [aut, cre], National Science Foundation Division of Integrative Organismal Systems [fnd], Clemson University Support for Early Exploration and Dev [...truncated...]
Maintainer: Sharon Bewick <sbewick@clemson.edu>
Repository: CRAN
Date/Publication: 2023-05-04 08:10:05 UTC

More information about HybridMicrobiomes at CRAN
Permanent link

New package gdi with initial version 1.1.1
Package: gdi
Title: Volumetric Analysis using Graphic Double Integration
Version: 1.1.1
Date: 2023-05-03
Author: Darius Nau [aut, cre]
Maintainer: Darius Nau <dariusnau@gmx.at>
Description: Tools implementing an automated version of the graphic double integration technique first employed by Jerison (1973) <ISBN:9780323141086> and Hurlburt (1999) <doi:10.1080/02724634.1999.10011145>. Graphic double integration is primarily used for volume or mass estimation of (extinct) animals, and the package 'gdi' aims to make this technique as convenient and versatile as possible. The main functions of 'gdi' provide utilities for automatically measuring diameters from digital silhouettes provided as image files, and for calculating volume via graphic double integration with a simple elliptical superelliptical (following Motani 2001 <doi:10.1666/0094-8373(2001)027%3C0735:EBMFST%3E2.0.CO;2>) or complex cross-sectional model.
Depends: jpeg, png
License: GPL (>= 3)
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-05-03 10:55:16 UTC; suirad
Repository: CRAN
Date/Publication: 2023-05-04 08:20:02 UTC

More information about gdi at CRAN
Permanent link

Package CodelistGenerator updated to version 1.2.0 with previous version 1.1.0 dated 2023-04-01

Title: Generate Code Lists for the OMOP Common Data Model
Description: Generate a candidate code list for the Observational Medical Outcomes Partnership (OMOP) common data model based on string matching. For a given search strategy, a candidate code list will be returned.
Author: Edward Burn [aut, cre]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>

Diff between CodelistGenerator versions 1.1.0 dated 2023-04-01 and 1.2.0 dated 2023-05-04

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More information about CodelistGenerator at CRAN
Permanent link

Package MASS updated to version 7.3-60 with previous version 7.3-59 dated 2023-04-21

Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph], Bill Venables [ctb], Douglas M. Bates [ctb], Kurt Hornik [trl] , Albrecht Gebhardt [trl] , David Firth [ctb]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

Diff between MASS versions 7.3-59 dated 2023-04-21 and 7.3-60 dated 2023-05-04

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More information about MASS at CRAN
Permanent link

Package testthat updated to version 3.1.8 with previous version 3.1.7 dated 2023-03-12

Title: Unit Testing for R
Description: Software testing is important, but, in part because it is frustrating and boring, many of us avoid it. 'testthat' is a testing framework for R that is easy to learn and use, and integrates with your existing 'workflow'.
Author: Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd], R Core team [ctb] )
Maintainer: Hadley Wickham <hadley@posit.co>

Diff between testthat versions 3.1.7 dated 2023-03-12 and 3.1.8 dated 2023-05-04

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Package samc updated to version 3.2.0 with previous version 3.1.0 dated 2023-04-07

Title: Spatial Absorbing Markov Chains
Description: Implements functions for working with absorbing Markov chains. The implementation is based on the framework described in "Toward a unified framework for connectivity that disentangles movement and mortality in space and time" by Fletcher et al. (2019) <doi:10.1111/ele.13333>, which applies them to spatial ecology. This framework incorporates both resistance and absorption with spatial absorbing Markov chains (SAMC) to provide several short-term and long-term predictions for metrics related to connectivity in landscapes. Despite the ecological context of the framework, this package can be used in any application of absorbing Markov chains.
Author: Andrew Marx [aut, cre, cph] , Robert Fletcher [ctb] , Miguel Acevedo [ctb] , Jorge Sefair [ctb] , Chao Wang [ctb] , Hughes Josie [ctb] , Barrett Griffin [ctb]
Maintainer: Andrew Marx <ajm.rpackages@gmail.com>

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Package clarify updated to version 0.1.3 with previous version 0.1.2 dated 2023-02-22

Title: Simulation-Based Inference for Regression Models
Description: Performs simulation-based inference as an alternative to the delta method for obtaining valid confidence intervals and p-values for regression post-estimation quantities, such as average marginal effects and predictions at representative values. This framework for simulation-based inference is especially useful when the resulting quantity is not normally distributed and the delta method approximation fails. The methodology is described in King, Tomz, and Wittenberg (2000) <doi:10.2307/2669316>. 'clarify' is meant to replace some of the functionality of the archived package 'Zelig'; see the vignette "Translating Zelig to clarify" for replicating this functionality.
Author: Noah Greifer [aut, cre] , Steven Worthington [aut] , Stefano Iacus [aut] , Gary King [aut]
Maintainer: Noah Greifer <ngreifer@iq.harvard.edu>

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Package bignum updated to version 0.3.2 with previous version 0.3.1 dated 2023-04-02

Title: Arbitrary-Precision Integer and Floating-Point Mathematics
Description: Classes for storing and manipulating arbitrary-precision integer vectors and high-precision floating-point vectors. These extend the range and precision of the 'integer' and 'double' data types found in R. This package utilizes the 'Boost.Multiprecision' C++ library. It is specifically designed to work well with the 'tidyverse' collection of R packages.
Author: David Hall [aut, cre, cph]
Maintainer: David Hall <david.hall.physics@gmail.com>

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Package TCIU (with last version 1.2.2) was removed from CRAN

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

2023-02-27 1.2.2

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Package FIESTAutils updated to version 1.1.6 with previous version 1.1.5 dated 2023-03-21

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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