Wed, 25 May 2022

Package rpartScore updated to version 1.0-2 with previous version 1.0-1 dated 2012-12-08

Title: Classification Trees for Ordinal Responses
Description: Recursive partitioning methods to build classification trees for ordinal responses within the CART framework. Trees are grown using the Generalized Gini impurity function, where the misclassification costs are given by the absolute or squared differences in scores assigned to the categories of the response. Pruning is based on the total misclassification rate or on the total misclassification cost.
Author: Giuliano Galimberti, Gabriele Soffritti, Matteo Di Maso
Maintainer: Giuliano Galimberti <giuliano.galimberti@unibo.it>

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Package MapGAM updated to version 1.2-6 with previous version 1.2-5 dated 2019-07-27

Title: Mapping Smoothed Effect Estimates from Individual-Level Data
Description: Contains functions for mapping odds ratios, hazard ratios, or other effect estimates using individual-level data such as case-control study data, using generalized additive models (GAMs) or Cox models for smoothing with a two-dimensional predictor (e.g., geolocation or exposure to chemical mixtures) while adjusting linearly for confounding variables, using methods described by Kelsall and Diggle (1998), Webster at al. (2006), and Bai et al. (2020). Includes convenient functions for mapping point estimates and confidence intervals, efficient control sampling, and permutation tests for the null hypothesis that the two-dimensional predictor is not associated with the outcome variable (adjusting for confounders).
Author: Lu Bai, Scott Bartell, Robin Bliss, and Veronica Vieira
Maintainer: Scott Bartell <sbartell@uci.edu>

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Package dcurves updated to version 0.3.0 with previous version 0.2.0 dated 2021-07-20

Title: Decision Curve Analysis for Model Evaluation
Description: Diagnostic and prognostic models are typically evaluated with measures of accuracy that do not address clinical consequences. Decision-analytic techniques allow assessment of clinical outcomes, but often require collection of additional information may be cumbersome to apply to models that yield a continuous result. Decision curve analysis is a method for evaluating and comparing prediction models that incorporates clinical consequences, requires only the data set on which the models are tested, and can be applied to models that have either continuous or dichotomous results. See the following references for details on the methods: Vickers (2006) <doi:10.1177/0272989X06295361>, Vickers (2008) <doi:10.1186/1472-6947-8-53>, and Pfeiffer (2020) <doi:10.1002/bimj.201800240>.
Author: Daniel D. Sjoberg [aut, cre, cph], Emily Vertosick [ctb]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>

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Package catIrt updated to version 0.5.1 with previous version 0.5-0 dated 2014-10-05

Title: Simulate IRT-Based Computerized Adaptive Tests
Description: Functions designed to simulate data that conform to basic unidimensional IRT models (for now 3-parameter binary response models and graded response models) along with Post-Hoc CAT simulations of those models given various item selection methods, ability estimation methods, and termination criteria. See Wainer (2000) <doi:10.4324/9781410605931>, van der Linden & Pashley (2010) <doi:10.1007/978-0-387-85461-8_1>, and Eggen (1999) <doi:10.1177/01466219922031365> for more details.
Author: Steven Nydick [cre, aut]
Maintainer: Steven Nydick <swnydick@gmail.com>

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Package usethis updated to version 2.1.6 with previous version 2.1.5 dated 2021-12-09

Title: Automate Package and Project Setup
Description: Automate package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio' projects, and more.
Author: Hadley Wickham [aut] , Jennifer Bryan [aut, cre] , Malcolm Barrett [aut] , RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>

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Package hapassoc updated to version 1.2-9 with previous version 1.2-8 dated 2015-05-10

Title: Inference of Trait Associations with SNP Haplotypes and Other Attributes using the EM Algorithm
Description: The following R functions are used for inference of trait associations with haplotypes and other covariates in generalized linear models. The functions are developed primarily for data collected in cohort or cross-sectional studies. They can accommodate uncertain haplotype phase and handle missing genotypes at some SNPs.
Author: K. Burkett <kburkett@uottawa.ca>, B. McNeney <mcneney@sfu.ca>, J. Graham <jgraham@stat.sfu.ca>, with code for case-control data contributed by Zhijian Chen <z11chen@math.uwaterloo.ca>
Maintainer: K. Burkett <kburkett@uottawa.ca>

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Package vetiver updated to version 0.1.5 with previous version 0.1.4 dated 2022-04-28

Title: Version, Share, Deploy, and Monitor Models
Description: The goal of 'vetiver' is to provide fluent tooling to version, share, deploy, and monitor a trained model. Functions handle both recording and checking the model's input data prototype, and predicting from a remote API endpoint. The 'vetiver' package is extensible, with generics that can support many kinds of models.
Author: Julia Silge [cre, aut] , RStudio [cph, fnd]
Maintainer: Julia Silge <julia.silge@rstudio.com>

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Package tidypredict updated to version 0.4.9 with previous version 0.4.8 dated 2020-10-28

Title: Run Predictions Inside the Database
Description: It parses a fitted 'R' model object, and returns a formula in 'Tidy Eval' code that calculates the predictions. It works with several databases back-ends because it leverages 'dplyr' and 'dbplyr' for the final 'SQL' translation of the algorithm. It currently supports lm(), glm(), randomForest(), ranger(), earth(), xgb.Booster.complete(), cubist(), and ctree() models.
Author: Max Kuhn [aut, cre], Edgar Ruiz [aut]
Maintainer: Max Kuhn <max@rstudio.com>

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Package swCRTdesign updated to version 3.2 with previous version 3.1 dated 2019-10-25

Title: Stepped Wedge Cluster Randomized Trial (SW CRT) Design
Description: A set of tools for examining the design and analysis aspects of stepped wedge cluster randomized trials (SW CRT) based on a repeated cross-sectional sampling scheme (Hussey MA and Hughes JP (2007) Contemporary Clinical Trials 28:182-191. <doi:10.1016/j.cct.2006.05.007>).
Author: Jim Hughes, Navneet R. Hakhu, Emily Voldal, and Fan Xia
Maintainer: Jim Hughes <jphughes@uw.edu>

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Package PUPAIM updated to version 0.3.1 with previous version 0.3.0 dated 2022-05-12

Title: A Collection of Physical and Chemical Adsorption Isotherm Models
Description: The PUPAIM R package can generally fit any adsorption experimental data to any of the 55 available adsorption isotherm models - 32 nonlinear models and 23 linear models. This package provides parameter estimation, model accuracy analysis, model error analysis, and adsorption plot created using the package 'ggplot2'. This package will help the users for a much easier way of adsorption model data fitting.
Author: Keith T. Ostan [aut] , Paul Angelo C. Manlapaz [aut] , Jemimah Christine L. Mesias [aut] , Chester C. Deocaris [aut, ths, cre]
Maintainer: Chester C. Deocaris <ccdeocaris@pup.edu.ph>

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Package StereoMorph updated to version 1.6.7 with previous version 1.6.5 dated 2022-05-12

Title: Stereo Camera Calibration and Reconstruction
Description: Functions for the collection of 3D points and curves using a stereo camera setup.
Author: Aaron Olsen, Annat Haber
Maintainer: Aaron Olsen <aarolsen@gmail.com>

Diff between StereoMorph versions 1.6.5 dated 2022-05-12 and 1.6.7 dated 2022-05-25

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Package pogit updated to version 1.3.0 with previous version 1.2.0 dated 2019-01-17

Title: Bayesian Variable Selection for a Poisson-Logistic Model
Description: Bayesian variable selection for regression models of under-reported count data as well as for (overdispersed) Poisson, negative binomal and binomial logit regression models using spike and slab priors.
Author: Michaela Dvorzak [aut, cre], Helga Wagner [aut]
Maintainer: Michaela Dvorzak <m.dvorzak@gmx.at>

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Package habCluster updated to version 1.0.5 with previous version 1.0.3 dated 2022-05-18

Title: Detecting Spatial Clustering Based on Connection Cost Between Grids
Description: Based on landscape connectivity, spatial boundaries were identified using community detection algorithm at grid level. Methods using raster as input and the value of each cell of the raster is the "smoothness" to indicate how easy the cell connecting with neighbor cells. Details about the 'habCluster' package methods can be found in Zhang et al. <bioRxiv:2022.05.06.490926>.
Author: Qiang Dai
Maintainer: Qiang Dai <daiqiang@cib.ac.cn>

Diff between habCluster versions 1.0.3 dated 2022-05-18 and 1.0.5 dated 2022-05-25

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Package GeneralizedUmatrix updated to version 1.2.4 with previous version 1.2.2 dated 2021-01-12

Title: Credible Visualization for Two-Dimensional Projections of Data
Description: Projections are common dimensionality reduction methods, which represent high-dimensional data in a two-dimensional space. However, when restricting the output space to two dimensions, which results in a two dimensional scatter plot (projection) of the data, low dimensional similarities do not represent high dimensional distances coercively [Thrun, 2018] <DOI: 10.1007/978-3-658-20540-9>. This could lead to a misleading interpretation of the underlying structures [Thrun, 2018]. By means of the 3D topographic map the generalized Umatrix is able to depict errors of these two-dimensional scatter plots. The package is derived from the book of Thrun, M.C.: "Projection Based Clustering through Self-Organization and Swarm Intelligence" (2018) <DOI:10.1007/978-3-658-20540-9> and the main algorithm called simplified self-organizing map for dimensionality reduction methods is published in <DOI: 10.1016/j.mex.2020.101093>.
Author: Michael Thrun [aut, cre, cph] , Felix Pape [ctb, ctr], Tim Schreier [ctb, ctr], Luis Winckelman [ctb, ctr], Quirin Stier [ctb, ctr], Alfred Ultsch [ths]
Maintainer: Michael Thrun <m.thrun@gmx.net>

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Package bpr updated to version 1.0.5 with previous version 1.0.4 dated 2021-09-22

Title: Fitting Bayesian Poisson Regression
Description: Posterior sampling and inference for Bayesian Poisson regression models. The model specification makes use of Gaussian (or conditionally Gaussian) prior distributions on the regression coefficients. Details on the algorithm are found in D'Angelo and Canale (2021) <arXiv:2109.09520>.
Author: Laura D'Angelo
Maintainer: Laura D'Angelo <laura.dangelo@live.com>

Diff between bpr versions 1.0.4 dated 2021-09-22 and 1.0.5 dated 2022-05-25

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Package RFpredInterval updated to version 1.0.6 with previous version 1.0.5 dated 2022-01-20

Title: Prediction Intervals with Random Forests and Boosted Forests
Description: Implements various prediction interval methods with random forests and boosted forests. The package has two main functions: pibf() produces prediction intervals with boosted forests (PIBF) as described in Alakus et al. (2021) <arXiv:2106.08217> and rfpi() builds 15 distinct variations of prediction intervals with random forests (RFPI) proposed by Roy and Larocque (2020) <doi:10.1177/0962280219829885>.
Author: Cansu Alakus [aut, cre], Denis Larocque [aut], Aurelie Labbe [aut], Hemant Ishwaran [ctb] , Udaya B. Kogalur [ctb]
Maintainer: Cansu Alakus <cansu.alakus@hec.ca>

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Package GAIPE updated to version 1.1 with previous version 1.0 dated 2013-04-17

Title: Graphical Extension with Accuracy in Parameter Estimation (GAIPE)
Description: Implements graphical extension with accuracy in parameter estimation (AIPE) on RMSEA for sample size planning in structural equation modeling based on Lin, T.-Z. & Weng, L.-J. (2014) <doi: 10.1080/10705511.2014.915380>. And, it can also implement AIPE on RMSEA and power analysis on RMSEA.
Author: Tzu-Yao Lin
Maintainer: Yao Lin <zaiyaolin@gmail.com>

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Package RcppAPT updated to version 0.0.9 with previous version 0.0.8 dated 2021-12-04

Title: 'Rcpp' Interface to the APT Package Manager
Description: The 'APT Package Management System' provides Debian and Debian-derived Linux systems with a powerful system to resolve package dependencies. This package offers access directly from R. This can only work on a system with a suitable 'libapt-pkg-dev' installation so functionality is curtailed if such a library is not found.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package monotone updated to version 0.1.2 with previous version 0.1.1 dated 2022-05-25

Title: Performs Monotone Regression
Description: The monotone package contains a fast up-and-down-blocks implementation for the pool-adjacent-violators algorithm for simple linear ordered monotone regression, including two spin-off functions for unimodal and bivariate monotone regression (see <doi:10.18637/jss.v102.c01>).
Author: Frank Busing [aut, cre], Juan Claramunt Gonzalez [aut]
Maintainer: Frank Busing <busing@fsw.leidenuniv.nl>

Diff between monotone versions 0.1.1 dated 2022-05-25 and 0.1.2 dated 2022-05-25

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Package MLGL updated to version 0.6.7 with previous version 0.6.5 dated 2020-11-28

Title: Multi-Layer Group-Lasso
Description: It implements a new procedure of variable selection in the context of redundancy between explanatory variables, which holds true with high dimensional data (Grimonprez et al. (2018) <https://hal.inria.fr/hal-01857242>).
Author: Quentin Grimonprez [aut, cre], Samuel Blanck [ctb], Alain Celisse [ths], Guillemette Marot [ths], Yi Yang [ctb], Hui Zou [ctb]
Maintainer: Quentin Grimonprez <quentingrim@yahoo.fr>

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Package mlr3viz updated to version 0.5.9 with previous version 0.5.8 dated 2022-04-04

Title: Visualizations for 'mlr3'
Description: Provides visualizations for 'mlr3' objects such as tasks, predictions, resample results or benchmark results via the autoplot() generic of 'ggplot2'. The returned 'ggplot' objects are intended to provide sensible defaults, yet can easily be customized to create camera-ready figures. Visualizations include barplots, boxplots, histograms, ROC curves, and Precision-Recall curves.
Author: Michel Lang [cre, aut] , Patrick Schratz [aut] , Raphael Sonabend [aut] , Marc Becker [aut] , Jakob Richter [aut] , Damir Pulatov [ctb]
Maintainer: Michel Lang <michellang@gmail.com>

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Package mlr3learners updated to version 0.5.3 with previous version 0.5.2 dated 2022-01-22

Title: Recommended Learners for 'mlr3'
Description: Recommended Learners for 'mlr3'. Extends 'mlr3' with interfaces to essential machine learning packages on CRAN. This includes, but is not limited to: (penalized) linear and logistic regression, linear and quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support vector machines, and gradient boosting.
Author: Michel Lang [cre, aut] , Quay Au [aut] , Stefan Coors [aut] , Patrick Schratz [aut]
Maintainer: Michel Lang <michellang@gmail.com>

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Package seqHMM updated to version 1.2.1-1 with previous version 1.2.0 dated 2021-10-18

Title: Mixture Hidden Markov Models for Social Sequence Data and Other Multivariate, Multichannel Categorical Time Series
Description: Designed for fitting hidden (latent) Markov models and mixture hidden Markov models for social sequence data and other categorical time series. Also some more restricted versions of these type of models are available: Markov models, mixture Markov models, and latent class models. The package supports models for one or multiple subjects with one or multiple parallel sequences (channels). External covariates can be added to explain cluster membership in mixture models. The package provides functions for evaluating and comparing models, as well as functions for visualizing of multichannel sequence data and hidden Markov models. Models are estimated using maximum likelihood via the EM algorithm and/or direct numerical maximization with analytical gradients. All main algorithms are written in C++ with support for parallel computation. Documentation is available via several vignettes in this page, and the paper by Helske and Helske (2019, <doi:10.18637/jss.v088.i03>).
Author: Jouni Helske [aut, cre] , Satu Helske [aut]
Maintainer: Jouni Helske <jouni.helske@iki.fi>

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Package r2spss updated to version 0.3.2 with previous version 0.3.1 dated 2022-03-23

Title: Format R Output to Look Like SPSS
Description: Create plots and LaTeX tables that look like SPSS output for use in teaching materials. Rather than copying-and-pasting SPSS output into documents, R code that mocks up SPSS output can be integrated directly into dynamic LaTeX documents with tools such as knitr. Functionality includes statistical techniques that are typically covered in introductory statistics classes: descriptive statistics, common hypothesis tests, ANOVA, and linear regression, as well as box plots, histograms, scatter plots, and line plots (including profile plots).
Author: Andreas Alfons [aut, cre]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>

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Package list updated to version 9.2.2 with previous version 9.2.1 dated 2022-05-10

Title: Statistical Methods for the Item Count Technique and List Experiment
Description: Allows researchers to conduct multivariate statistical analyses of survey data with list experiments. This survey methodology is also known as the item count technique or the unmatched count technique and is an alternative to the commonly used randomized response method. The package implements the methods developed by Imai (2011) <doi:10.1198/jasa.2011.ap10415>, Blair and Imai (2012) <doi:10.1093/pan/mpr048>, Blair, Imai, and Lyall (2013) <doi:10.1111/ajps.12086>, Imai, Park, and Greene (2014) <doi:10.1093/pan/mpu017>, Aronow, Coppock, Crawford, and Green (2015) <doi:10.1093/jssam/smu023>, Chou, Imai, and Rosenfeld (2017) <doi:10.1177/0049124117729711>, and Blair, Chou, and Imai (2018) <https://imai.fas.harvard.edu/research/files/listerror.pdf>. This includes a Bayesian MCMC implementation of regression for the standard and multiple sensitive item list experiment designs and a random effects setup, a Bayesian MCMC hierarchical regression model with up to three hierarchical groups, the combined list experiment and endorsement experiment regression model, a joint model of the list experiment that enables the analysis of the list experiment as a predictor in outcome regression models, a method for combining list experiments with direct questions, and methods for diagnosing and adjusting for response error. In addition, the package implements the statistical test that is designed to detect certain failures of list experiments, and a placebo test for the list experiment using data from direct questions.
Author: Graeme Blair [aut, cre], Winston Chou [aut], Kosuke Imai [aut], Bethany Park [ctb], Alexander Coppock [ctb]
Maintainer: Graeme Blair <graeme.blair@gmail.com>

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Package GMSE updated to version 1.0.0.1 with previous version 0.7.0.0 dated 2021-08-02

Title: Generalised Management Strategy Evaluation Simulator
Description: Integrates game theory and ecological theory to construct social-ecological models that simulate the management of populations and stakeholder actions. These models build off of a previously developed management strategy evaluation (MSE) framework to simulate all aspects of management: population dynamics, manager observation of populations, manager decision making, and stakeholder responses to management decisions. The newly developed generalised management strategy evaluation (GMSE) framework uses genetic algorithms to mimic the decision-making process of managers and stakeholders under conditions of change, uncertainty, and conflict. Simulations can be run using gmse(), gmse_apply(), and gmse_gui() functions.
Author: A. Bradley Duthie [aut, cre] , Adrian Bach [aut], Nils Bunnefeld [aut, fnd] , Jeremy Cusack [ctb] , Isabel Jones [ctb] , Jeroen Minderman [aut] , Erlend Nilsen [ctb] , Ochoa Gabriela [aut] , Rocio Pozo [ctb] , Sarobidy Rakotonarivo [ctb] , Bram Van M [...truncated...]
Maintainer: A. Bradley Duthie <brad.duthie@gmail.com>

Diff between GMSE versions 0.7.0.0 dated 2021-08-02 and 1.0.0.1 dated 2022-05-25

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Package eurlex updated to version 0.4.2 with previous version 0.4.1 dated 2022-03-31

Title: Retrieve Data on European Union Law
Description: Access to data on European Union laws and court decisions made easy with pre-defined 'SPARQL' queries and 'GET' requests.
Author: Michal Ovadek [aut, cre, cph]
Maintainer: Michal Ovadek <michal.ovadek@gmail.com>

Diff between eurlex versions 0.4.1 dated 2022-03-31 and 0.4.2 dated 2022-05-25

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Package binGroup2 updated to version 1.2.4 with previous version 1.2.3 dated 2022-05-16

Title: Identification and Estimation using Group Testing
Description: Methods for the group testing identification problem: 1) Operating characteristics (e.g., expected number of tests) for commonly used hierarchical and array-based algorithms, and 2) Optimal testing configurations for these same algorithms. Methods for the group testing estimation problem: 1) Estimation and inference procedures for an overall prevalence, and 2) Regression modeling for commonly used hierarchical and array-based algorithms.
Author: Brianna Hitt [aut, cre] , Christopher Bilder [aut] , Frank Schaarschmidt [aut] , Brad Biggerstaff [aut] , Christopher McMahan [aut] , Joshua Tebbs [aut] , Boan Zhang [ctb], Michael Black [ctb], Peijie Hou [ctb], Peng Chen [ctb]
Maintainer: Brianna Hitt <brianna.hitt@afacademy.af.edu>

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Package monotone updated to version 0.1.1 with previous version 0.1.0 dated 2021-03-10

Title: Performs Monotone Regression
Description: The monotone package contains a fast up-and-down-blocks implementation for the pool-adjacent-violators algorithm for simple linear ordered monotone regression, including two spin-off functions for unimodal and bivariate monotone regression (see <doi:10.18637/jss.v102.c01>).
Author: Frank Busing [aut, cre], Juan Claramunt Gonzalez [aut]
Maintainer: Frank Busing <busing@fsw.leidenuniv.nl>

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Package epiR updated to version 2.0.48 with previous version 2.0.46 dated 2022-03-31

Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> and Evan Sergeant <evansergeant@gmail.com> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>

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Package SoilHyP updated to version 0.1.6 with previous version 0.1.5 dated 2021-01-08

Title: Soil Hydraulic Properties
Description: Provides functions for (1) soil water retention (SWC) and unsaturated hydraulic conductivity (Ku) (van Genuchten-Mualem (vGM or vG) [1, 2], Peters-Durner-Iden (PDI) [3, 4, 5], Brooks and Corey (bc) [8]), (2) fitting of parameter for SWC and/or Ku using Shuffled Complex Evolution (SCE) optimisation and (3) calculation of soil hydraulic properties (Ku and soil water contents) based on the simplified evaporation method (SEM) [6, 7]. Main references: [1] van Genuchten (1980) <doi:10.2136/sssaj1980.03615995004400050002x>, [2] Mualem (1976) <doi:10.1029/WR012i003p00513>, [3] Peters (2013) <doi:10.1002/wrcr.20548>, [4] Iden and Durner (2013) <doi:10.1002/2014WR015937>, [5] Peters (2014) <doi:10.1002/2014WR015937>, [6] Wind G. P. (1966), [7] Peters and Durner (2008) <doi:10.1016/j.jhydrol.2008.04.016> and [8] Brooks and Corey (1964).
Author: Ullrich Dettmann [aut, cre], Felix Andrews [ctb] which is not on r-cran . The SCEoptim function is adapted, and substantially revised from Brecht Donckels MATLAB code which is in turn adopted from Qingyun Duans MATLAB code), Brecht Donckels [ctb] , [...truncated...]
Maintainer: Ullrich Dettmann <ullrich.dettmann@thuenen.de>

Diff between SoilHyP versions 0.1.5 dated 2021-01-08 and 0.1.6 dated 2022-05-25

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Package SecDim updated to version 2.2 with previous version 1.3 dated 2022-05-02

Title: The Second Dimension of Spatial Association
Description: Most of the current methods explore spatial association using observations at sample locations, which are defined as the first dimension of spatial association (FDA). The proposed concept of the second dimension of spatial association (SDA) aims to extract in-depth information about the geographical environment from locations outside sample locations for exploring spatial association.
Author: Yongze Song [aut, cre]
Maintainer: Yongze Song <yongze.song@postgrad.curtin.edu.au>

Diff between SecDim versions 1.3 dated 2022-05-02 and 2.2 dated 2022-05-25

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Package radiant.model updated to version 1.4.4 with previous version 1.4.3 dated 2021-12-21

Title: Model Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Model menu includes interfaces for linear and logistic regression, naive Bayes, neural networks, classification and regression trees, model evaluation, collaborative filtering, decision analysis, and simulation. The application extends the functionality in 'radiant.data'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>

Diff between radiant.model versions 1.4.3 dated 2021-12-21 and 1.4.4 dated 2022-05-25

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Package radiant.data updated to version 1.4.2 with previous version 1.4.1 dated 2021-11-12

Title: Data Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Data menu includes interfaces for loading, saving, viewing, visualizing, summarizing, transforming, and combining data. It also contains functionality to generate reproducible reports of the analyses conducted in the application.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>

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Package ORKM updated to version 0.1.1.1 with previous version 0.0.2.1 dated 2022-04-25

Title: The Online Regularized K-Means Clustering Algorithm
Description: Algorithm of online regularized k-means to deal with online multi(single) view data. The philosophy of the package is described in Guo G. (2020) <doi:10.1080/02331888.2020.1823979>.
Author: Guangbao Guo [aut, cre] , Miao Yu [aut], Haoyue Song [aut], Ruiling Niu [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>

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Package MeTo updated to version 0.1.1 with previous version 0.1.0 dated 2019-01-11

Title: Meteorological Tools
Description: Meteorological Tools following the FAO56 irrigation paper of Allen et al. (1998) [1]. Functions for calculating: reference evapotranspiration (ETref), extraterrestrial radiation (Ra), net radiation (Rn), saturation vapor pressure (satVP), global radiation (Rs), soil heat flux (G), daylight hours, and more. [1] Allen, R. G., Pereira, L. S., Raes, D., & Smith, M. (1998). Crop evapotranspiration-Guidelines for computing crop water requirements-FAO Irrigation and drainage paper 56. FAO, Rome, 300(9).
Author: Ullrich Dettmann [aut, cre], R. Grima [aut]
Maintainer: Ullrich Dettmann <ullrich.dettmann@thuenen.de>

Diff between MeTo versions 0.1.0 dated 2019-01-11 and 0.1.1 dated 2022-05-25

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Package basefun updated to version 1.1-3 with previous version 1.1-2 dated 2022-01-14

Title: Infrastructure for Computing with Basis Functions
Description: Some very simple infrastructure for basis functions.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between basefun versions 1.1-2 dated 2022-01-14 and 1.1-3 dated 2022-05-25

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Package shadowr updated to version 0.0.2 with previous version 0.0.1 dated 2022-04-22

Title: Selenium Plugin to Manage Multi Level Shadow Elements on Web Page
Description: Shadow Document Object Model is a web standard that offers component style and markup encapsulation. It is a critically important piece of the Web Components story as it ensures that a component will work in any environment even if other CSS or JavaScript is at play on the page. Custom HTML tags can't be directly identified with selenium tools, because Selenium doesn't provide any way to deal with shadow elements. Using this plugin you can handle any custom HTML tags.
Author: Ricardo Landolt [cre, aut], Sushil Gupta [ctb]
Maintainer: Ricardo Landolt <ricardo.landolt1@gmail.com>

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Package relliptical updated to version 1.2.0 with previous version 1.1.0 dated 2022-01-07

Title: The Truncated Elliptical Family of Distributions
Description: It offers random numbers generation from members of the truncated multivariate elliptical family of distribution such as the truncated versions of the Normal, Student-t, Pearson VII, Slash, Logistic, among others. Particular distributions can be provided by specifying the density generating function. It also computes the first two moments (covariance matrix as well) for some particular distributions. References used for this package: Galarza, C. E., Matos, L. A., Castro, L. M., & Lachos, V. H. (2022). Moments of the doubly truncated selection elliptical distributions with emphasis on the unified multivariate skew-t distribution. Journal of Multivariate Analysis, 189, 104944 <doi:10.1016/j.jmva.2021.104944>; Ho, H. J., Lin, T. I., Chen, H. Y., & Wang, W. L. (2012). Some results on the truncated multivariate t distribution. Journal of Statistical Planning and Inference, 142(1), 25-40 <doi:10.1016/j.jspi.2011.06.006>; Valeriano, K. A., Galarza, C. E., & Matos, L. A. (2021). Moments and random number generation for the truncated elliptical family of distributions. arXiv preprint <arXiv:2112.09319>.
Author: Katherine A. L. Valeriano [aut, cre] , Larissa Avila Matos [ctb] , Christian Galarza Morales [ctb]
Maintainer: Katherine A. L. Valeriano <katandreina@gmail.com>

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Package radiant updated to version 1.4.2 with previous version 1.4.1 dated 2021-11-22

Title: Business Analytics using R and Shiny
Description: A platform-independent browser-based interface for business analytics in R, based on the shiny package. The application combines the functionality of 'radiant.data', 'radiant.design', 'radiant.basics', 'radiant.model', and 'radiant.multivariate'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>

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Package meteospain updated to version 0.0.4 with previous version 0.0.3 dated 2021-11-05

Title: Access to Spanish Meteorological Stations Services
Description: Access to different Spanish meteorological stations data services and APIs (AEMET, SMC, MG, Meteoclimatic...).
Author: Victor Granda [aut, cre] , Miquel de Caceres [ctb] , Aitor Ameztegui [ctb]
Maintainer: Victor Granda <victorgrandagarcia@gmail.com>

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Package ergm.count updated to version 4.1.1 with previous version 4.0.2 dated 2021-06-18

Title: Fit, Simulate and Diagnose Exponential-Family Models for Networks with Count Edges
Description: A set of extensions for the 'ergm' package to fit weighted networks whose edge weights are counts. See Krivitsky (2012) <doi:10.1214/12-EJS696> and Krivitsky, Hunter, Morris, and Klumb (2021) <arXiv:2106.04997>.
Author: Pavel N. Krivitsky [aut, cre] , Mark S. Handcock [ctb], David R. Hunter [ctb], Joyce Cheng [ctb]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>

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Package dycdtools updated to version 0.4.2 with previous version 0.4.1 dated 2022-05-08

Title: Tools for DYRESM-CAEDYM Model Development: Calibration Assistant and Post-Processing
Description: Tools for DYRESM-CAEDYM model development, including assisting with calibrating selected model parameters and visualising model output through time series plot, profile plot, contour plot, and scatter plot.
Author: Songyan Yu [aut, cre] , Christopher McBride [ctb], Marieke Frassl [ctb]
Maintainer: Songyan Yu <sunny.yu@griffith.edu.au>

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Package AlgDesign updated to version 1.2.1 with previous version 1.2.0 dated 2019-11-29

Title: Algorithmic Experimental Design
Description: Algorithmic experimental designs. Calculates exact and approximate theory experimental designs for D,A, and I criteria. Very large designs may be created. Experimental designs may be blocked or blocked designs created from a candidate list, using several criteria. The blocking can be done when whole and within plot factors interact.
Author: Bob Wheeler <bwheelerg@gmail.com>
Maintainer: Jerome Braun <jvbraun.statistics@gmail.com>

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Package hibayes updated to version 1.1.0 with previous version 1.0.1 dated 2022-01-13

Title: Individual-Level, Summary-Level and Single-Step Bayesian Regression Model
Description: A user-friendly tool to fit Bayesian regression models. It can fit 3 types of Bayesian models using individual-level, summary-level, and individual plus pedigree-level (single-step) data for both Genomic prediction/selection (GS) and Genome-Wide Association Study (GWAS), it was designed to estimate joint effects and genetic parameters for a complex trait, including: (1) fixed effects and coefficients of covariates, (2) environmental random effects, and its corresponding variance, (3) genetic variance, (4) residual variance, (5) heritability, (6) genomic estimated breeding values (GEBV) for both genotyped and non-genotyped individuals, (7) SNP effect size, (8) phenotype/genetic variance explained (PVE) for single or multiple SNPs, (9) posterior probability of association of the genomic window (WPPA), (10) posterior inclusive probability (PIP). The functions are not limited, we will keep on going in enriching it with more features. References: Meuwissen et al. (2001) <doi:10.1093/genetics/157.4.1819>; Gustavo et al. (2013) <doi:10.1534/genetics.112.143313>; Habier et al. (2011) <doi:10.1186/1471-2105-12-186>; Yi et al. (2008) <doi:10.1534/genetics.107.085589>; Zhou et al. (2013) <doi:10.1371/journal.pgen.1003264>; Moser et al. (2015) <doi:10.1371/journal.pgen.1004969>; Lloyd-Jones et al. (2019) <doi:10.1038/s41467-019-12653-0>; Henderson (1976) <doi:10.2307/2529339>; Fernando et al. (2014) <doi:10.1186/1297-9686-46-50>.
Author: Lilin Yin [aut, cre, cph], Haohao Zhang [aut, cph], Xiaolei Liu [aut, cph]
Maintainer: Lilin Yin <ylilin@163.com>

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Package AzureStor updated to version 3.7.0 with previous version 3.6.1 dated 2022-02-03

Title: Storage Management in 'Azure'
Description: Manage storage in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/en-us/product-categories/storage/>. On the admin side, 'AzureStor' includes features to create, modify and delete storage accounts. On the client side, it includes an interface to blob storage, file storage, and 'Azure Data Lake Storage Gen2': upload and download files and blobs; list containers and files/blobs; create containers; and so on. Authenticated access to storage is supported, via either a shared access key or a shared access signature (SAS). Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre], Microsoft [cph]
Maintainer: Hong Ooi <hongooi73@gmail.com>

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Tue, 24 May 2022

Package timedeppar updated to version 1.0.2 with previous version 1.0.1 dated 2020-10-01

Title: Infer Constant and Stochastic, Time-Dependent Model Parameters
Description: Infer constant and stochastic, time-dependent parameters to consider intrinsic stochasticity of a dynamic model and/or to analyze model structure modifications that could reduce model deficits. The concept is based on inferring time-dependent parameters as stochastic processes in the form of Ornstein-Uhlenbeck processes jointly with inferring constant model parameters and parameters of the Ornstein-Uhlenbeck processes. The package also contains functions to sample from and calculate densities of Ornstein-Uhlenbeck processes. References: Tomassini, L., Reichert, P., Kuensch, H.-R. Buser, C., Knutti, R. and Borsuk, M.E. (2009), A smoothing algorithm for estimating stochastic, continuous-time model parameters and its application to a simple climate model, Journal of the Royal Statistical Society: Series C (Applied Statistics) 58, 679-704, <doi:10.1111/j.1467-9876.2009.00678.x> Reichert, P., and Mieleitner, J. (2009), Analyzing input and structural uncertainty of nonlinear dynamic models with stochastic, time-dependent parameters. Water Resources Research, 45, W10402, <doi:10.1029/2009WR007814> Reichert, P., Ammann, L. and Fenicia, F. (2021), Potential and challenges of investigating intrinsic uncertainty of hydrological models with time-dependent, stochastic parameters. Water Resources Research 57(8), e2020WR028311, <doi:10.1029/2020WR028311> Reichert, P. (2022), timedeppar: An R package for inferring stochastic, time-dependent model parameters, in preparation.
Author: Peter Reichert <peter.reichert@eawag.ch>
Maintainer: Peter Reichert <peter.reichert@eawag.ch>

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Package sleev updated to version 1.0.2 with previous version 1.0.1 dated 2022-02-01

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

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Package omu updated to version 1.0.5 with previous version 1.0.4 dated 2020-05-18

Title: A Metabolomics Analysis Tool for Intuitive Figures and Convenient Metadata Collection
Description: Facilitates the creation of intuitive figures to describe metabolomics data by utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG) hierarchy data, and gathers functional orthology and gene data from the KEGG-REST API.
Author: Connor Tiffany [aut, cre]
Maintainer: Connor Tiffany <crtiffany@ucdavis.edu>

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Package IFC updated to version 0.1.5 with previous version 0.1.2 dated 2021-10-13

Title: Tools for Imaging Flow Cytometry
Description: Contains several tools to treat imaging flow cytometry data from 'ImageStream®' and 'FlowSight®' cytometers ('Amnis®', part of 'Luminex®'). Provides an easy and simple way to read and write .fcs, .rif, .cif and .daf files. Information such as masks, features, regions and populations set within these files can be retrieved for each single cell. In addition, raw data such as images stored can also be accessed. Users, may hopefully increase their productivity thanks to dedicated functions to extract, visualize, manipulate and export 'IFC' data. Toy data example can be installed through the 'IFCdata' package of approximately 32 MB, which is available in a 'drat' repository <https://gitdemont.github.io/IFCdata/>. See file 'COPYRIGHTS' and file 'AUTHORS' for a list of copyright holders and authors.
Author: Yohann Demont [aut, cre], Gautier Stoll [ctb], Guido Kroemer [ldr], Jean-Pierre Marolleau [ldr], Loïc Garcon [ldr]
Maintainer: Yohann Demont <git.demont@gmail.com>

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More information about IFC at CRAN
Permanent link

Package gtfstools updated to version 1.1.0 with previous version 1.0.0 dated 2021-11-16

Title: General Transit Feed Specification (GTFS) Editing and Analysing Tools
Description: Utility functions to read, manipulate, analyse and write transit feeds in the General Transit Feed Specification (GTFS) data format.
Author: Daniel Herszenhut [aut, cre] , Rafael H. M. Pereira [aut] , Pedro R. Andrade [aut] , Joao Bazzo [aut] , Mark Padgham [ctb], Marcus Saraiva [ctb] , Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Daniel Herszenhut <dhersz@gmail.com>

Diff between gtfstools versions 1.0.0 dated 2021-11-16 and 1.1.0 dated 2022-05-24

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More information about gtfstools at CRAN
Permanent link

Package GeoWeightedModel updated to version 1.0.2 with previous version 1.0.0 dated 2022-05-11

Title: User-Friendly Interface for Geographically-Weighted Models
Description: Contains the development of a tool that provides a web-based graphical user interface (GUI) to perform Techniques from a subset of spatial statistics known as geographically weighted (GW) models. Contains methods described by Brunsdon et al., 1996 <doi:10.1111/j.1538-4632.1996.tb00936.x>, Brunsdon et al., 2002 <doi:10.1016/s0198-9715(01)00009-6>, Harris et al., 2011 <doi:10.1080/13658816.2011.554838>, Brunsdon et al., 2007 <doi:10.1111/j.1538-4632.2007.00709.x>.
Author: Javier De La Hoz Maestre [cre, aut] , Maria Jose Fernandez Gomez [aut] , Susana Mendez [aut]
Maintainer: Javier De La Hoz Maestre <jdelahozmaestre@gmail.com>

Diff between GeoWeightedModel versions 1.0.0 dated 2022-05-11 and 1.0.2 dated 2022-05-24

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 MD5                                                    |   22 -
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 12 files changed, 1721 insertions(+), 355 deletions(-)

More information about GeoWeightedModel at CRAN
Permanent link

Package composits updated to version 0.1.1 with previous version 0.1.0 dated 2020-09-30

Title: Compositional, Multivariate and Univariate Time Series Outlier Ensemble
Description: A compositional, multivariate and univariate time series outlier ensemble. It uses the four R packages 'forecast', 'tsoutliers', 'otsad' and 'anomalize' to detect time series outliers (Kandanaarachchi, Menendez 2020) <doi:10.13140/RG.2.2.32217.95845>.
Author: Sevvandi Kandanaarachchi [aut, cre] , Patricia Menendez [aut] , Ursula Laa [aut] , Ruben Loaiza-Maya [aut]
Maintainer: Sevvandi Kandanaarachchi <sevvandik@gmail.com>

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Package clusterSim updated to version 0.50-1 with previous version 0.49-2 dated 2021-01-06

Title: Searching for Optimal Clustering Procedure for a Data Set
Description: Distance measures (GDM1, GDM2, Sokal-Michener, Bray-Curtis, for symbolic interval-valued data), cluster quality indices (Calinski-Harabasz, Baker-Hubert, Hubert-Levine, Silhouette, Krzanowski-Lai, Hartigan, Gap, Davies-Bouldin), data normalization formulas (metric data, interval-valued symbolic data), data generation (typical and non-typical data), HINoV method, replication analysis, linear ordering methods, spectral clustering, agreement indices between two partitions, plot functions (for categorical and symbolic interval-valued data). (MILLIGAN, G.W., COOPER, M.C. (1985) <doi:10.1007/BF02294245>, HUBERT, L., ARABIE, P. (1985) <doi:10.1007%2FBF01908075>, RAND, W.M. (1971) <doi:10.1080/01621459.1971.10482356>, JAJUGA, K., WALESIAK, M. (2000) <doi:10.1007/978-3-642-57280-7_11>, MILLIGAN, G.W., COOPER, M.C. (1988) <doi:10.1007/BF01897163>, JAJUGA, K., WALESIAK, M., BAK, A. (2003) <doi:10.1007/978-3-642-55721-7_12>, DAVIES, D.L., BOULDIN, D.W. (1979) <doi:10.1109/TPAMI.1979.4766909>, CALINSKI, T., HARABASZ, J. (1974) <doi:10.1080/03610927408827101>, HUBERT, L. (1974) <doi:10.1080/01621459.1974.10480191>, TIBSHIRANI, R., WALTHER, G., HASTIE, T. (2001) <doi:10.1111/1467-9868.00293>, BRECKENRIDGE, J.N. (2000) <doi:10.1207/S15327906MBR3502_5>, WALESIAK, M., DUDEK, A. (2008) <doi:10.1007/978-3-540-78246-9_11>).
Author: Marek Walesiak <marek.walesiak@ue.wroc.pl>, Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Maintainer: Andrzej Dudek <andrzej.dudek@ue.wroc.pl>

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Package bcdata updated to version 0.3.1 with previous version 0.3.0 dated 2021-10-28

Title: Search and Retrieve Data from the BC Data Catalogue
Description: Search, query, and download tabular and 'geospatial' data from the British Columbia Data Catalogue (<https://catalogue.data.gov.bc.ca/>). Search catalogue data records based on keywords, data licence, sector, data format, and B.C. government organization. View metadata directly in R, download many data formats, and query 'geospatial' data available via the B.C. government Web Feature Service ('WFS') using 'dplyr' syntax.
Author: Andy Teucher [aut, cre] , Sam Albers [aut, ctb] , Stephanie Hazlitt [aut, ctb] , Province of British Columbia [cph]
Maintainer: Andy Teucher <andy.teucher@gov.bc.ca>

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Package BayesMallows updated to version 1.2.0 with previous version 1.1.2 dated 2022-04-11

Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model (Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>; Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>). Both Metropolis-Hastings and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule, Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the posterior distributions of parameters are provided. The package also provides functions for estimating the partition function (normalizing constant) of the Mallows rank model, both with the importance sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm (Mukherjee, Annals of Statistics, 2016 <doi:10.1214/15-AOS1389>).
Author: Oystein Sorensen [aut, cre] , Valeria Vitelli [aut] , Marta Crispino [aut], Qinghua Liu [aut], Cristina Mollica [aut], Luca Tardella [aut], Anja Stein [aut], Waldir Leoncio [ctr]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>

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Package nanostringr updated to version 0.3.0 with previous version 0.2.0 dated 2021-02-06

Title: Performs Quality Control, Data Normalization, and Batch Effect Correction for 'NanoString nCounter' Data
Description: Provides quality control (QC), normalization, and batch effect correction operations for 'NanoString nCounter' data, Talhouk et al. (2016) <doi:10.1371/journal.pone.0153844>. Various metrics are used to determine which samples passed or failed QC. Gene expression should first be normalized to housekeeping genes, before a reference-based approach is used to adjust for batch effects. Raw NanoString data can be imported in the form of Reporter Code Count (RCC) files.
Author: Derek Chiu [aut, cre], Aline Talhouk [aut], Samuel Leung [aut]
Maintainer: Derek Chiu <dchiu@bccrc.ca>

Diff between nanostringr versions 0.2.0 dated 2021-02-06 and 0.3.0 dated 2022-05-24

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Package TBEST updated to version 5.2 with previous version 5.0 dated 2014-12-29

Title: Tree Branches Evaluated Statistically for Tightness
Description: Our method introduces mathematically well-defined measures for tightness of branches in a hierarchical tree. Statistical significance of the findings is determined, for all branches of the tree, by performing permutation tests, optionally with generalized Pareto p-value estimation.
Author: Guoli Sun, Alex Krasnitz
Maintainer: Guoli Sun <guolisun87@gmail.com>

Diff between TBEST versions 5.0 dated 2014-12-29 and 5.2 dated 2022-05-24

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Package ZetaSuite updated to version 1.0.1 with previous version 1.0.0 dated 2022-03-31

Title: Analyze High-Dimensional High-Throughput Dataset and Quality Control Single-Cell RNA-Seq
Description: The advent of genomic technologies has enabled the generation of two-dimensional or even multi-dimensional high-throughput data, e.g., monitoring multiple changes in gene expression in genome-wide siRNA screens across many different cell types (E Robert McDonald 3rd (2017) <doi: 10.1016/j.cell.2017.07.005> and Tsherniak A (2017) <doi: 10.1016/j.cell.2017.06.010>) or single cell transcriptomics under different experimental conditions. We found that simple computational methods based on a single statistical criterion is no longer adequate for analyzing such multi-dimensional data. We herein introduce 'ZetaSuite', a statistical package initially designed to score hits from two-dimensional RNAi screens.We also illustrate a unique utility of 'ZetaSuite' in analyzing single cell transcriptomics to differentiate rare cells from damaged ones (Vento-Tormo R (2018) <doi: 10.1038/s41586-018-0698-6>). In 'ZetaSuite', we have the following steps: QC of input datasets, normalization using Z-transformation, Zeta score calculation and hits selection based on defined Screen Strength.
Author: Yajing Hao [aut] , Shuyang Zhang [ctb] , Junhui Li [cre], Guofeng Zhao [ctb], Xiang-Dong Fu [cph, fnd]
Maintainer: Junhui Li <ljh.biostat@gmail.com>

Diff between ZetaSuite versions 1.0.0 dated 2022-03-31 and 1.0.1 dated 2022-05-24

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Package wTO updated to version 2.0.1 with previous version 2.0 dated 2022-05-10

Title: Computing Weighted Topological Overlaps (wTO) & Consensus wTO Network
Description: Computes the Weighted Topological Overlap with positive and negative signs (wTO) networks given a data frame containing the mRNA count/ expression/ abundance per sample, and a vector containing the interested nodes of interaction (a subset of the elements of the full data frame). It also computes the cut-off threshold or p-value based on the individuals bootstrap or the values reshuffle per individual. It also allows the construction of a consensus network, based on multiple wTO networks. The package includes a visualization tool for the networks. More about the methodology can be found at <arXiv:1711.04702>.
Author: Deisy Morselli Gysi, Andre Voigt, Tiago Miranda Fragoso, Eivind Almaas and Katja Nowick.
Maintainer: Deisy Morselli Gysi <deisy.ccnr@gmail.com>

Diff between wTO versions 2.0 dated 2022-05-10 and 2.0.1 dated 2022-05-24

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Package VineCopula updated to version 2.4.4 with previous version 2.4.3 dated 2021-10-07

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

Diff between VineCopula versions 2.4.3 dated 2021-10-07 and 2.4.4 dated 2022-05-24

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Package TreeTools updated to version 1.7.2 with previous version 1.7.1 dated 2022-03-25

Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) <doi:10.1371/journal.pone.0212942>; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2021) <doi:10.1093/sysbio/syab072>, and of tree balance (Mir et al. 2013) <doi:10.1016/j.mbs.2012.10.005>; artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <http://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph] , Emmanuel Paradis [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>

Diff between TreeTools versions 1.7.1 dated 2022-03-25 and 1.7.2 dated 2022-05-24

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Package shinyFiles updated to version 0.9.2 with previous version 0.9.1 dated 2021-11-10

Title: A Server-Side File System Viewer for Shiny
Description: Provides functionality for client-side navigation of the server side file system in shiny apps. In case the app is running locally this gives the user direct access to the file system without the need to "download" files to a temporary location. Both file and folder selection as well as file saving is available.
Author: Thomas Lin Pedersen [cre, aut] , Vincent Nijs [aut], Thomas Schaffner [aut], Eric Nantz [aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>

Diff between shinyFiles versions 0.9.1 dated 2021-11-10 and 0.9.2 dated 2022-05-24

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Package Rdsdp updated to version 1.0.5.2 with previous version 1.0.5.1 dated 2021-11-02

Title: R Interface to DSDP Semidefinite Programming Library
Description: R interface to DSDP semidefinite programming library. The DSDP software is a free open source implementation of an interior-point method for semidefinite programming. It provides primal and dual solutions, exploits low-rank structure and sparsity in the data, and has relatively low memory requirements for an interior-point method.
Author: Zhisu Zhu, Yinyu Ye
Maintainer: Zhisu Zhu <zhuzhisu@alumni.stanford.edu>

Diff between Rdsdp versions 1.0.5.1 dated 2021-11-02 and 1.0.5.2 dated 2022-05-24

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Package RcppXPtrUtils updated to version 0.1.2 with previous version 0.1.1 dated 2019-01-21

Title: XPtr Add-Ons for 'Rcpp'
Description: Provides the means to compile user-supplied C++ functions with 'Rcpp' and retrieve an 'XPtr' that can be passed to other C++ components.
Author: Inaki Ucar [aut, cph, cre]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>

Diff between RcppXPtrUtils versions 0.1.1 dated 2019-01-21 and 0.1.2 dated 2022-05-24

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Package parameters updated to version 0.18.0 with previous version 0.17.0 dated 2022-03-10

Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various statistical models. Beyond computing p values, CIs, and other indices for a wide variety of models (see list of supported models using the function 'insight::supported_models()'), this package implements features like bootstrapping or simulating of parameters and models, feature reduction (feature extraction and variable selection) as well as functions to describe data and variable characteristics (e.g. skewness, kurtosis, smoothness or distribution).
Author: Daniel Luedecke [aut, cre] , Dominique Makowski [aut] , Mattan S. Ben-Shachar [aut] , Indrajeet Patil [aut] , Soeren Hoejsgaard [aut], Brenton M. Wiernik [aut] , Zen J. Lau [ctb], Vincent Arel-Bundock [ctb] , Jeffrey Girard [ctb] , Christina Maimone [re [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>

Diff between parameters versions 0.17.0 dated 2022-03-10 and 0.18.0 dated 2022-05-24

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Package openssl updated to version 2.0.2 with previous version 2.0.1 dated 2022-05-14

Title: Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers. Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] , Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package dexter updated to version 1.2.1 with previous version 1.1.5 dated 2022-02-19

Title: Data Management and Analysis of Tests
Description: A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Author: Gunter Maris [aut], Timo Bechger [aut], Jesse Koops [aut, cre], Ivailo Partchev [aut]
Maintainer: Jesse Koops <jesse.koops@cito.nl>

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Package Andromeda updated to version 0.6.1 with previous version 0.6.0 dated 2022-01-25

Title: Asynchronous Disk-Based Representation of Massive Data
Description: Storing very large data objects on a local drive, while still making it possible to manipulate the data in an efficient manner.
Author: Adam Black [aut, cre], Martijn Schuemie [aut], Marc A. Suchard [aut], Observational Health Data Science and Informatics [cph]
Maintainer: Adam Black <black@ohdsi.org>

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Package HostSwitch updated to version 0.1.1 with previous version 0.1.0 dated 2021-09-27

Title: Simulate the Extent of Host Switching by Consumers
Description: Using a simulation-based approach, the 'HostSwitch' package provides functions to investigate host switches by consumers. The individual-based model is based on the concept of ecological fitting. The mockup model is published by Araujo et al. 2015. Understanding Host-Switching by Ecological Fitting (<doi:10.1371/journal.pone.0139225>). The package provides an R-friendly and modified version of this model which can be applied to different consumer-resource scenarios.
Author: Valeria Trivellone [aut], Sabrina B.L. Araujo [aut], Bernd Panassiti [cre, aut]
Maintainer: Bernd Panassiti <bernd.panassiti@gmail.com>

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Package GaussSuppression updated to version 0.3.0 with previous version 0.2.0 dated 2022-04-05

Title: Tabular Data Suppression using Gaussian Elimination
Description: A statistical disclosure control tool to protect tables by suppression using the Gaussian elimination secondary suppression algorithm. Primary suppression functions for the minimum frequency rule, the dominance rule and a directly-disclosive rule are included. General primary suppression functions can be supplied as input. Suppressed frequencies can be replaced by synthetic decimal numbers as described in Langsrud (2019) <doi:10.1007/s11222-018-9848-9>.
Author: Oyvind Langsrud [aut, cre], Daniel Lupp [aut], Hege Boevelstad [ctb]
Maintainer: Oyvind Langsrud <oyl@ssb.no>

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Package campfin updated to version 1.0.9 with previous version 1.0.8 dated 2021-09-02

Title: Wrangle Campaign Finance Data
Description: Explore and normalize American campaign finance data. Created by the Investigative Reporting Workshop to facilitate work on The Accountability Project, an effort to collect public data into a central, standard database that is more easily searched: <https://publicaccountability.org/>.
Author: Kiernan Nicholls [aut, cre, cph], Investigative Reporting Workshop [cph], Yanqi Xu [aut], Schuyler Erle [cph]
Maintainer: Kiernan Nicholls <kiernann@protonmail.com>

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Package POSetR updated to version 1.1.0 with previous version 1.0.4 dated 2021-11-24

Title: Partially Ordered Sets in R
Description: Provides a set of basic tools for generating, analyzing, summarizing and visualizing finite partially ordered sets. In particular, it implements flexible and very efficient algorithms for the extraction of linear extensions and for the computation of mutual ranking probabilities and other user-defined functionals, over them. The package is meant as a computationally efficient "engine", for the implementation of data analysis procedures, on systems of multidimensional ordinal indicators and partially ordered data, in the spirit of Fattore, M. (2016) "Partially ordered sets and the measurement of multidimensional ordinal deprivation", Social Indicators Research <DOI:10.1007/s11205-015-1059-6>, and Fattore M. and Arcagni, A. (2018) "A reduced posetic approach to the measurement of multidimensional ordinal deprivation", Social Indicators Research <DOI:10.1007/s11205-016-1501-4>.
Author: Alberto Arcagni [aut, cre], Alessandro Avellone [aut], Marco Fattore [aut]
Maintainer: Alberto Arcagni <alberto.arcagni@uniroma1.it>

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Package audubon updated to version 0.2.0 with previous version 0.1.2 dated 2022-04-02

Title: Japanese Text Processing Tools
Description: A collection of Japanese text processing tools for filling Japanese iteration marks, Japanese character type conversions, segmentation by phrase, and text normalization which is based on rules for the 'Sudachi' morphological analyzer and the 'NEologd' (Neologism dictionary for 'MeCab'). These features are specific to Japanese and are not implemented in 'ICU' (International Components for Unicode).
Author: Akiru Kato [cre, aut], Koki Takahashi [cph] , Shuhei Iitsuka [cph] , Taku Kudo [cph]
Maintainer: Akiru Kato <paithiov909@gmail.com>

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Package mpathsenser updated to version 1.0.2 with previous version 1.0.1 dated 2022-05-19

Title: Process and Analyse Data from m-Path Sense
Description: Overcomes one of the major challenges in mobile (passive) sensing, namely being able to pre-process the raw data that comes from a mobile sensing app, specifically "m-Path Sense" <https://m-path.io>. The main task of 'mpathsenser' is therefore to read "m-Path Sense" JSON files into a database and provide several convenience functions to aid in data processing.
Author: Koen Niemeijer [aut, cre]
Maintainer: Koen Niemeijer <koen.niemeijer@kuleuven.be>

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Package npphen updated to version 1.5.0 with previous version 1.1.1 dated 2021-11-19

Title: Vegetation Phenological Cycle and Anomaly Detection using Remote Sensing Data
Description: Calculates phenological cycle and anomalies using a non-parametric approach applied to time series of vegetation indices derived from remote sensing data or field measurements. The package implements basic and high-level functions for manipulating vector data (numerical series) and raster data (satellite derived products). Processing of very large raster files is supported. For more information, please check the following paper: Estay, S., Chávez, R.O. (2018) <doi:10.1101/301143>.
Author: Roberto O. Chavez [cre, aut], Sergio A. Estay [cre, aut], Jose A. Lastra [cre,ctb] & Carlos G. Riquelme [ctb]
Maintainer: Jose A. Lastra <jose.lastra@pucv.cl>

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Package mand updated to version 1.1 with previous version 1.0 dated 2021-06-29

Title: Multivariate Analysis for Neuroimaging Data
Description: Several functions can be used to analyze neuroimaging data using multivariate methods based on the 'msma' package. The functions used in the book entitled "Multivariate Analysis for Neuroimaging Data" (2021, ISBN-13: 978-0367255329) are contained.
Author: Atsushi Kawaguchi [aut, cre]
Maintainer: Atsushi Kawaguchi <kawa_a24@yahoo.co.jp>

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Package IPEC updated to version 1.0.3 with previous version 1.0.1 dated 2022-05-17

Title: Root Mean Square Curvature Calculation
Description: Calculates the RMS intrinsic and parameter-effects curvatures of a nonlinear regression model. The curvatures are global measures of assessing whether a model/data set combination is close-to-linear or not. See Bates and Watts (1980) <doi:10.1002/9780470316757> and Ratkowsky and Reddy (2017) <doi:10.1093/aesa/saw098> for details.
Author: Peijian Shi [aut, cre], Peter M. Ridland [aut], David A. Ratkowsky [aut], Yang Li [aut]
Maintainer: Peijian Shi <pjshi@njfu.edu.cn>

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Package cosinor updated to version 1.2.2 with previous version 1.1 dated 2014-07-28

Title: Tools for Estimating and Predicting the Cosinor Model
Description: A set of simple functions that transforms longitudinal data to estimate the cosinor linear model as described in Tong (1976). Methods are given to summarize the mean, amplitude and acrophase, to predict the mean annual outcome value, and to test the coefficients.
Author: Michael Sachs <sachsmc@gmail.com>
Maintainer: Michael Sachs <sachsmc@gmail.com>

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Package CoOL updated to version 1.1.2 with previous version 1.0.3 dated 2021-07-16

Title: Causes of Outcome Learning
Description: Implementing the computational phase of the Causes of Outcome Learning approach as described in Rieckmann, Dworzynski, Arras, Lapuschkin, Samek, Arah, Rod, Ekstrom. 2022. Causes of outcome learning: A causal inference-inspired machine learning approach to disentangling common combinations of potential causes of a health outcome. International Journal of Epidemiology <doi:10.1093/ije/dyac078>. The optional 'ggtree' package can be obtained through Bioconductor.
Author: Andreas Rieckmann [aut, cre], Piotr Dworzynski [aut], Leila Arras [ctb], Claus Thorn Ekstrom [aut]
Maintainer: Andreas Rieckmann <aric@sund.ku.dk>

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Package rspa updated to version 0.2.6 with previous version 0.2.5 dated 2019-06-19

Title: Adapt Numerical Records to Fit (in)Equality Restrictions
Description: Minimally adjust the values of numerical records in a data.frame, such that each record satisfies a predefined set of equality and/or inequality constraints. The constraints can be defined using the 'validate' package. The core algorithms have recently been moved to the 'lintools' package, refer to 'lintools' for a more basic interface and access to a version of the algorithm that works with sparse matrices.
Author: Mark van der Loo
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>

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Package rsae updated to version 0.2 with previous version 0.1-5 dated 2014-02-13

Title: Robust Small Area Estimation
Description: Empirical best linear unbiased prediction (EBLUP) and robust prediction of the area-level means under the basic unit-level model. The model can be fitted by maximum likelihood or a (robust) M-estimator. Mean square prediction error is computed by a parametric bootstrap.
Author: Tobias Schoch [aut, cre] , Brent Richard [cph]
Maintainer: Tobias Schoch <tobias.schoch@fhnw.ch>

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Package languageserver updated to version 0.3.13 with previous version 0.3.12 dated 2021-10-19

Title: Language Server Protocol
Description: An implementation of the Language Server Protocol for R. The Language Server protocol is used by an editor client to integrate features like auto completion. See <https://microsoft.github.io/language-server-protocol/> for details.
Author: Randy Lai [aut, cre], Kun Ren [ctb]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>

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Package wowa updated to version 1.0.2 with previous version 1.0.1 dated 2021-02-05

Title: Weighted Ordered Weighted Average
Description: Introduce weights into Ordered Weighted Averages and extend bivariate means based on n-ary tree construction. Please refer to the following: G. Beliakov, H. Bustince, and T. Calvo (2016, ISBN: 978-3-319-24753-3), G. Beliakov(2018) <doi:10.1002/int.21913>, G. Beliakov, J.J. Dujmovic (2016) <doi:10.1016/j.ins.2015.10.040>, J.J. Dujmovic and G. Beliakov (2017) <doi:10.1002/int.21828>.
Author: Gleb Beliakov [aut, cre], Daniela Calderon [aut]
Maintainer: Gleb Beliakov <gleb@deakin.edu.au>

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Package opdisDownsampling updated to version 0.8.2 with previous version 0.8.1 dated 2021-12-21

Title: Optimal Distribution Preserving Down-Sampling of Bio-Medical Data
Description: An optimized method for distribution-preserving class-proportional down-sampling of bio-medical data.
Author: Jorn Lotsch [aut,cre] , Sebastian Malkusch [aut] , Alfred Ultsch [aut]
Maintainer: Jorn Lotsch <j.lotsch@em.uni-frankfurt.de>

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Package Directional updated to version 5.5 with previous version 5.4 dated 2022-05-15

Title: A Collection of Functions for Directional Data Analysis
Description: A collection of functions for directional data (including massive data, with millions of observations) analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000). Other references include a) Phillip J. Paine, Simon P. Preston Michail Tsagris and Andrew T. A. Wood (2018). An elliptically symmetric angular Gaussian distribution. Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>. b) Tsagris M. and Alenazi A. (2019). Comparison of discriminant analysis methods on the sphere. Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>. c) P. J. Paine, S. P. Preston, M. Tsagris and Andrew T. A. Wood (2020). Spherical regression models with general covariates and anisotropic errors. Statistics and Computing 30(1): 153--165. <doi:10.1007/s11222-019-09872-2>. d) Tsagris M. and Alenazi A. (2022). An investigation of hypothesis testing procedures for circular and spherical mean vectors. Communications in Statistics-Simulation and Computation (Accepted for publication). <doi:10.1080/03610918.2022.2045499>.
Author: Michail Tsagris, Giorgos Athineou, Christos Adam, Anamul Sajib, Eli Amson, Micah J. Waldstein
Maintainer: Michail Tsagris <mtsagris@uoc.gr>

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Package digitalDLSorteR updated to version 0.3.0 with previous version 0.2.0 dated 2022-03-10

Title: Deconvolution of Bulk RNA-Seq Data Based on Deep Learning
Description: Deconvolution of bulk RNA-Seq data using context-specific deconvolution models based on Deep Neural Networks using scRNA-Seq data as input. These models are able to make accurate estimates of the cell composition of bulk RNA-Seq samples from the same context using the advances provided by Deep Learning and the meaningful information provided by scRNA-Seq data. See Torroja and Sanchez-Cabo (2019) <doi:10.3389/fgene.2019.00978> for more details.
Author: Diego Mananes [aut, cre] , Carlos Torroja [aut] , Fatima Sanchez-Cabo [aut]
Maintainer: Diego Mananes <dmananesc@cnic.es>

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Package campsismod updated to version 0.8.1 with previous version 0.8.0 dated 2022-02-14

Title: Generic Implementation of a PK/PD Model
Description: A generic, easy-to-use and expandable implementation of a pharmacokinetic (PK) / pharmacodynamic (PD) model based on the S4 class system. This package allows the user to read/write a pharmacometric model from/to files and adapt it further on the fly in the R environment. For this purpose, this package provides an intuitive API to add, modify or delete equations, ordinary differential equations (ODE's), model parameters or compartment properties (like infusion duration or rate, bioavailability and initial values). Finally, this package also provides a useful export of the model for use with simulation packages 'RxODE' and 'mrgsolve'. This package is designed and intended to be used with package 'campsis', a PK/PD simulation platform built on top of 'RxODE' and 'mrgsolve'.
Author: Nicolas Luyckx [aut, cre]
Maintainer: Nicolas Luyckx <nicolas.luyckx@calvagone.com>

Diff between campsismod versions 0.8.0 dated 2022-02-14 and 0.8.1 dated 2022-05-24

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Package CausCor updated to version 0.1.2 with previous version 0.1.1 dated 2022-05-13

Title: Calculate Correlations and Estimate Causality
Description: This tool performs pairwise correlation analysis and estimate causality. Particularly, it is useful for detecting the metabolites that would be altered by the gut bacteria.
Author: Tomomi Sugiyama [aut, cre]
Maintainer: Tomomi Sugiyama <sugiyama.t.am@m.titech.ac.jp>

Diff between CausCor versions 0.1.1 dated 2022-05-13 and 0.1.2 dated 2022-05-24

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Package nseval updated to version 0.4.2 with previous version 0.4 dated 2018-08-06

Title: Tools for Lazy and Non-Standard Evaluation
Description: Functions to capture, inspect, manipulate, and create lazy values (promises), "..." lists, and active calls.
Author: Peter Meilstrup <peter.meilstrup@gmail.com>
Maintainer: Peter Meilstrup <peter.meilstrup@gmail.com>

Diff between nseval versions 0.4 dated 2018-08-06 and 0.4.2 dated 2022-05-24

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Permanent link

Package gt updated to version 0.6.0 with previous version 0.5.0 dated 2022-04-21

Title: Easily Create Presentation-Ready Display Tables
Description: Build display tables from tabular data with an easy-to-use set of functions. With its progressive approach, we can construct display tables with a cohesive set of table parts. Table values can be formatted using any of the included formatting functions. Footnotes and cell styles can be precisely added through a location targeting system. The way in which 'gt' handles things for you means that you don't often have to worry about the fine details.
Author: Richard Iannone [aut, cre] , Joe Cheng [aut], Barret Schloerke [aut] , RStudio [cph, fnd]
Maintainer: Richard Iannone <rich@rstudio.com>

Diff between gt versions 0.5.0 dated 2022-04-21 and 0.6.0 dated 2022-05-24

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Package AntibodyTiters updated to version 0.1.24 with previous version 0.1.18 dated 2021-10-28

Title: Antibody Titer Analysis of Vaccinated Patients
Description: Visualization of antibody titer scores is valuable for examination of vaccination effects. 'AntibodyTiters' visualizes antibody titers of all or selected patients. This package also produces empty excel files in a specified format, in which users can fill in experimental data for visualization. Excel files with toy data can also be produced, so that users can see how it is visualized before obtaining real data. The data should contain titer scores at pre-vaccination, after-1st shot, after-2nd shot, and at least one additional sampling points. Patients with missing values can be included. The first two sampling points (pre-vaccination and after-1st shot) will be plotted discretely, whereas those following will be plotted on a continuous time scale that starts from the day of second shot. Half-life of titer can also be calculated for each pair of sampling points.
Author: Yuuki Mizumoto [aut], Hiroaki Kato [aut, cre] , Takeshi Urano [ctb]
Maintainer: Hiroaki Kato <hkato@med.shimane-u.ac.jp>

Diff between AntibodyTiters versions 0.1.18 dated 2021-10-28 and 0.1.24 dated 2022-05-24

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Mon, 23 May 2022

Package support.BWS2 updated to version 0.4-0 with previous version 0.3-1 dated 2021-11-23

Title: Tools for Case 2 Best-Worst Scaling
Description: Provides three basic functions that support an implementation of Case 2 (profile case) best-worst scaling. The first is to convert an orthogonal main-effect design into questions, the second is to create a dataset suitable for analysis, and the third is to calculate count-based scores. For details, see Aizaki and Fogarty (2019) <doi:10.1016/j.jocm.2019.100171>.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>

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Package CNprep updated to version 2.2 with previous version 2.0 dated 2014-12-31

Title: Pre-Process DNA Copy Number (CN) Data for Detection of CN Events
Description: DNA copy number data evaluation using both their initial form (copy number as a noisy function of genomic position) and their approximation by a piecewise-constant function (segmentation), for the purpose of identifying genomic regions where the copy number differs from the norm.
Author: Alex Krasnitz, Guoli Sun
Maintainer: Guoli Sun <guolisun87@gmail.com>

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Package mlflow updated to version 1.26.0 with previous version 1.25.1 dated 2022-04-20

Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for the complete machine learning life cycle, see <https://mlflow.org/>. This package supports installing 'MLflow', tracking experiments, creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre], Javier Luraschi [aut], Kevin Kuo [aut] , RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>

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Package CORE updated to version 3.2 with previous version 3.0 dated 2014-12-29

Title: Cores of Recurrent Events
Description: Given a collection of intervals with integer start and end positions, find recurrently targeted regions and estimate the significance of finding. Randomization is implemented by parallel methods, either using local host machines, or submitting grid engine jobs.
Author: Alex Krasnitz, Guoli Sun
Maintainer: Guoli Sun <guolisun87@gmail.com>

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Package CMplot updated to version 4.1.0 with previous version 4.0.0 dated 2022-01-13

Title: Circle Manhattan Plot
Description: Manhattan plot, a type of scatter plot, was widely used to display the association results. However, it is usually time-consuming and laborious for a non-specialist user to write scripts and adjust parameters of an elaborate plot. Moreover, the ever-growing traits measured have necessitated the integration of results from different Genome-wide association study researches. Circle Manhattan Plot is the first open R package that can lay out. Genome-wide association study P-value results in both traditional rectangular patterns, QQ-plot and novel circular ones. United in only one bull's eye style plot, association results from multiple traits can be compared interactively, thereby to reveal both similarities and differences between signals. Additional functions include: highlight signals, a group of SNPs, chromosome visualization and candidate genes around SNPs.
Author: LiLin-Yin
Maintainer: LiLin-Yin <ylilin@163.com>

Diff between CMplot versions 4.0.0 dated 2022-01-13 and 4.1.0 dated 2022-05-23

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Package disordR updated to version 0.0-9-1 with previous version 0.0-9 dated 2021-12-09

Title: Non-Ordered Vectors
Description: Functionality for manipulating values of associative maps. Ordinary R vectors are unsuitable for working with values of associative maps because elements of an R vector may be accessed by reference to their location in the vector, but associative maps are stored in arbitrary order. However, when associating keys with values one needs both parts to be in 1-1 correspondence, so one cannot dispense with the order entirely. The 'disordR' package includes a single S4 class, disord. This class allows one to perform only those operations appropriate for manipulating values of associative maps and prevents any other operation (such as accessing an element at a particular location). A useful heuristic is that one is only allowed to access or modify a disord object using a python list comprehension. The idea is to prevent ill-defined operations on values (or keys) of associative maps, whose order is undefined or at best implementation-specific, while allowing and facilitating sensible operations.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

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Package superml updated to version 0.5.5 with previous version 0.5.4 dated 2022-05-12

Title: Build Machine Learning Models Like Using Python's Scikit-Learn Library in R
Description: The idea is to provide a standard interface to users who use both R and Python for building machine learning models. This package provides a scikit-learn's fit, predict interface to train machine learning models in R.
Author: Manish Saraswat [aut, cre]
Maintainer: Manish Saraswat <manish06saraswat@gmail.com>

Diff between superml versions 0.5.4 dated 2022-05-12 and 0.5.5 dated 2022-05-23

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Package santaR updated to version 1.2.3 with previous version 1.2.2 dated 2022-05-23

Title: Short Asynchronous Time-Series Analysis
Description: A graphical and automated pipeline for the analysis of short time-series in R ('santaR'). This approach is designed to accommodate asynchronous time sampling (i.e. different time points for different individuals), inter-individual variability, noisy measurements and large numbers of variables. Based on a smoothing splines functional model, 'santaR' is able to detect variables highlighting significantly different temporal trajectories between study groups. Designed initially for metabolic phenotyping, 'santaR' is also suited for other Systems Biology disciplines. Command line and graphical analysis (via a 'shiny' application) enable fast and parallel automated analysis and reporting, intuitive visualisation and comprehensive plotting options for non-specialist users.
Author: Arnaud Wolfer [aut, cre] , Timothy Ebbels [ctb], Joe Cheng [ctb]
Maintainer: Arnaud Wolfer <adwolfer@gmail.com>

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Package randtoolbox updated to version 2.0.0 with previous version 1.31.1 dated 2021-10-30

Title: Toolbox for Pseudo and Quasi Random Number Generation and Random Generator Tests
Description: Provides (1) pseudo random generators - general linear congruential generators, multiple recursive generators and generalized feedback shift register (SF-Mersenne Twister algorithm and WELL generators); (2) quasi random generators - the Torus algorithm, the Sobol sequence, the Halton sequence (including the Van der Corput sequence) and (3) some generator tests - the gap test, the serial test, the poker test. See e.g. Gentle (2003) <doi:10.1007/b97336>. The package can be provided without the rngWELL dependency on demand. Take a look at the Distribution task view of types and tests of random number generators. Package in Memoriam of Diethelm and Barbara Wuertz.
Author: R port by Yohan Chalabi, Christophe Dutang, Petr Savicky and Diethelm Wuertz with some underlying C codes of the SFMT algorithm from M. Matsumoto and M. Saito, the Knuth-TAOCP RNG from D. Knuth.
Maintainer: Christophe Dutang <dutangc@gmail.com>

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Package oscar updated to version 1.0.4 with previous version 1.0.3 dated 2022-05-20

Title: Optimal Subset Cardinality Regression (OSCAR) Models Using the L0-Pseudonorm
Description: Optimal Subset Cardinality Regression (OSCAR) models offer regularized linear regression using the L0-pseudonorm, conventionally known as the number of non-zero coefficients. The package estimates an optimal subset of features using the L0-penalization via cross-validation, bootstrapping and visual diagnostics. Effective Fortran implementations are offered along the package for finding optima for the DC-decomposition, which is used for transforming the discrete L0-regularized optimization problem into a continuous non-convex optimization task. These optimization modules include DBDC ('Double Bundle method for nonsmooth DC optimization' as described in Joki et al. (2018) <doi:10.1137/16M1115733>) and LMBM ('Limited Memory Bundle Method for large-scale nonsmooth optimization' as in Haarala et al. (2004) <doi:10.1080/10556780410001689225>). Multiple regression model families are supported: Cox, logistic, and Gaussian.
Author: Teemu Daniel Laajala [aut, cre] , Kaisa Joki [aut], Anni Halkola [aut]
Maintainer: Teemu Daniel Laajala <teelaa@utu.fi>

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Package shazam updated to version 1.1.1 with previous version 1.1.0 dated 2021-07-08

Title: Immunoglobulin Somatic Hypermutation Analysis
Description: Provides a computational framework for analyzing mutations in immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of antigen-driven selection pressure, mutational load quantification, building of somatic hypermutation (SHM) models, and model-dependent distance calculations. Also includes empirically derived models of SHM for both mice and humans. Citations: Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>, Yaari, et al (2012) <doi:10.1093/nar/gks457>, Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>, Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.
Author: Mohamed Uduman [aut], Namita Gupta [aut], Susanna Marquez [aut], Julian Zhou [aut], Nima Nouri [aut], Ang Cui [ctb], Jason Vander Heiden [aut, cre], Gur Yaari [aut], Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@gmail.com>

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Package condGEE updated to version 0.2.0 with previous version 0.1-4 dated 2013-08-17

Title: Parameter Estimation in Conditional GEE for Recurrent Event Gap Times
Description: Solves for the mean parameters, the variance parameter, and their asymptotic variance in a conditional GEE for recurrent event gap times, as described by Clement and Strawderman (2009) in the journal Biostatistics. Makes a parametric assumption for the length of the censored gap time.
Author: David Clement
Maintainer: David Clement <dyc24@cornell.edu>

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Package ramchoice updated to version 2.1 with previous version 2.0 dated 2021-10-22

Title: Revealed Preference and Attention Analysis in Random Limited Attention Models
Description: It is widely documented in psychology, economics and other disciplines that socio-economic agent may not pay full attention to all available alternatives, rendering standard revealed preference theory invalid. This package implements the estimation and inference procedures of Cattaneo, Ma, Masatlioglu and Suleymanov (2020) <arXiv:1712.03448> and Cattaneo, Cheung, Ma, and Masatlioglu (2022) <arXiv:2110.10650>, which utilizes standard choice data to partially identify and estimate a decision maker's preference and attention. For inference, several simulation-based critical values are provided.
Author: Matias D. Cattaneo, Paul Cheung, Xinwei Ma, Yusufcan Masatlioglu, Elchin Suleymanov
Maintainer: Xinwei Ma <x1ma@ucsd.edu>

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Package miRtest updated to version 2.0 with previous version 1.8 dated 2014-11-26

Title: Combined miRNA- And mRNA-Testing
Description: Package for combined miRNA- and mRNA-testing.
Author: Stephan Artmann, Klaus Jung, Tim Beissbarth
Maintainer: Stephan Artmann <stephanartmann@gmx.net>

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Package robmed updated to version 0.11.0 with previous version 0.10.1 dated 2022-03-17

Title: (Robust) Mediation Analysis
Description: Perform mediation analysis via a (fast and robust) bootstrap test.
Author: Andreas Alfons [aut, cre] , Nufer Y. Ates [ctb]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>

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Package jenga updated to version 1.2.0 with previous version 1.1.0 dated 2022-04-16

Title: Fast Extrapolation of Time Features using K-Nearest Neighbors
Description: Fast extrapolation of univariate and multivariate time features using K-Nearest Neighbors. The compact set of hyper-parameters is tuned via grid or random search.
Author: Giancarlo Vercellino
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>

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Package text2map updated to version 0.1.5 with previous version 0.1.4 dated 2022-04-12

Title: R Tools for Text Matrices, Embeddings, and Networks
Description: This is a collection of functions optimized for working with with various kinds of text matrices. Focusing on the text matrix as the primary object - represented either as a base R dense matrix or a 'Matrix' package sparse matrix - allows for a consistent and intuitive interface that stays close to the underlying mathematical foundation of computational text analysis. In particular, the package includes functions for working with word embeddings, text networks, and document-term matrices. Methods developed in Stoltz and Taylor (2019) <doi:10.1007/s42001-019-00048-6>, Taylor and Stoltz (2020) <doi:10.1007/s42001-020-00075-8>, Taylor and Stoltz (2020) <doi:10.15195/v7.a23>, and Stoltz and Taylor (2021) <doi:10.1016/j.poetic.2021.101567>.
Author: Dustin Stoltz [aut, cre] , Marshall Taylor [aut]
Maintainer: Dustin Stoltz <maintainers@textmapping.com>

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Package stuart updated to version 0.10.0 with previous version 0.9.1 dated 2020-08-26

Title: Subtests Using Algorithmic Rummaging Techniques
Description: Construct subtests from a pool of items by using ant-colony-optimization, genetic algorithms, brute force, or random sampling. Schultze (2017) <doi:10.17169/refubium-622>.
Author: Martin Schultze [aut, cre], Johanna Schueller [ctb]
Maintainer: Martin Schultze <schultze@psych.uni-frankfurt.de>

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Package orthogonalsplinebasis updated to version 0.1.7 with previous version 0.1.6 dated 2015-03-31

Title: Orthogonal B-Spline Basis Functions
Description: Represents the basis functions for B-splines in a simple matrix formulation that facilitates, taking integrals, derivatives, and making orthogonal the basis functions.
Author: Andrew Redd
Maintainer: Andrew Redd <andrew.redd@hsc.utah.edu>

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Package MHCtools updated to version 1.4.2 with previous version 1.4.1 dated 2021-10-11

Title: Analysis of MHC Data in Non-Model Species
Description: Twelve tools for bioinformatical processing and analysis of major histocompatibility complex (MHC) data. The functions are tailored for amplicon data sets that have been filtered using the 'dada2' method (for more information on 'dada2', visit <https://benjjneb.github.io/dada2/> ), but even other types of data sets can be analyzed. The DistCalc() function calculates Grantham, Sandberg, or p-distances from pairwise comparisons of all sequences in a data set, and mean distances of all pairwise comparisons within each sample in a data set. The function additionally outputs five tables with physico-chemical z-descriptor values (based on Sandberg et al. 1998) for each amino acid position in all sequences in the data set. These tables may be useful for further downstream analyses, such as estimation of MHC supertypes. The BootKmeans() function is a wrapper for the kmeans() function of the 'stats' package, which allows for bootstrapping. Bootstrapping k-estimates may be desirable in data sets, where e.g. BIC- vs. k-values do not produce clear inflection points ("elbows"). BootKmeans() performs multiple runs of kmeans() and estimates optimal k-values based on a user-defined threshold of BIC reduction. The method is an automated and bootstrapped version of visually inspecting elbow plots of BIC- vs. k-values. The ClusterMatch() function is a tool for evaluating whether different k-means() clustering models identify similar clusters, and summarize bootstrap model stats as means for different estimated values of k. It is designed to take files produced by the BootKmeans() function as input, but other data can be analysed if the descriptions of the required data formats are observed carefully. The HpltFind() function infers putative haplotypes from families in the data set. The GetHpltTable() and GetHpltStats() functions evaluate the accuracy of the haplotype inference. The PapaDiv() function compares parent pairs in the data set and calculate their joint MHC diversity, taking into account sequence variants that occur in both parents. The ReplMatch() function matches replicates in data sets in order to evaluate genotyping success. The GetReplTable() and GetReplStats() functions perform such an evaluation. The CreateFas() function creates a fasta file with all the sequences in the data set. The CreateSamplesFas() function creates individual fasta files for each sample in the data set.
Author: Jacob Roved [aut, cre]
Maintainer: Jacob Roved <jacob.roved@biol.lu.se>

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Package lidaRtRee updated to version 4.0.1 with previous version 3.1.2 dated 2021-12-09

Title: Forest Analysis with Airborne Laser Scanning (LiDAR) Data
Description: Provides functions for forest analysis using airborne laser scanning (LiDAR remote sensing) data: tree detection (method 1 in Eysn et al. (2015) <doi:10.3390/f6051721>) and segmentation; forest parameters estimation and mapping with the area-based approach. It includes complementary steps for forest mapping: co-registration of field plots with LiDAR data (Monnet and Mermin (2014) <doi:10.3390/f5092307>); extraction of both physical (gaps, edges, trees) and statistical features from LiDAR data useful for e.g. habitat suitability modeling (Glad et al. (2020) <doi:10.1002/rse2.117>); model calibration with ground reference, and maps export.
Author: Jean-Matthieu Monnet [aut, cre] , Pascal Obstetar [ctb]
Maintainer: Jean-Matthieu Monnet <jean-matthieu.monnet@inrae.fr>

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Package KoboconnectR updated to version 1.1.1 with previous version 1.1.0 dated 2022-05-16

Title: Download Data from Kobotoolbox to R
Description: Wrapper for 'Kobotoolbox' APIs ver 2 mentioned at <https://support.kobotoolbox.org/api.html>, to download data from 'Kobotoolbox' to R. Small and simple package that adds immense convenience for the data professionals using 'Kobotoolbox'.
Author: Asitav Sen [aut, cre, cph]
Maintainer: Asitav Sen <hello@asitavsen.com>

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Package import updated to version 1.3.0 with previous version 1.2.0 dated 2020-09-24

Title: An Import Mechanism for R
Description: Alternative mechanism for importing objects from packages and R modules. The syntax allows for importing multiple objects with a single command in an expressive way. The import package bridges some of the gap between using library (or require) and direct (single-object) imports. Furthermore the imported objects are not placed in the current environment.
Author: Stefan Milton Bache [aut], Magnus Thor Torfason [aut, cre]
Maintainer: Magnus Thor Torfason <m@zulutime.net>

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Package gjam updated to version 2.6.2 with previous version 2.6 dated 2022-04-15

Title: Generalized Joint Attribute Modeling
Description: Analyzes joint attribute data (e.g., species abundance) that are combinations of continuous and discrete data with Gibbs sampling. Full model and computation details are described in Clark et al. (2018) <doi:10.1002/ecm.1241>.
Author: James S. Clark, Daniel Taylor-Rodriquez
Maintainer: James S. Clark <jimclark@duke.edu>

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Package GGIR updated to version 2.7-0 with previous version 2.6-0 dated 2022-02-02

Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from 'GENEActiv' <https://www.activinsights.com/> and GENEA devices (not for sale), .csv-export data from 'Actigraph' <https://actigraphcorp.com> devices, and .cwa and .wav-format data from 'Axivity' <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format and has either no header or a two column header. Also the package allows for external function embedding.
Author: Vincent T van Hees [aut, cre], Jairo H Migueles [aut], Severine Sabia [ctb], Matthew R Patterson [ctb], Zhou Fang [ctb], Jing Hua Zhao [ctb], Joe Heywood [ctb], Evgeny Mirkes [ctb], Joan Capdevila Pujol [ctb], Dan Jackson [ctb], Lena Kushleyeva [ctb] [...truncated...]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>

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Package nombre updated to version 0.4.1 with previous version 0.4.0 dated 2021-10-25

Title: Number Names
Description: Converts numeric vectors to character vectors of English number names. Provides conversion to cardinals, ordinals, numerators, and denominators. Supports negative and non-integer numbers.
Author: Alexander Rossell Hayes [aut, cre, cph] , Eli Pousson [ctb]
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>

Diff between nombre versions 0.4.0 dated 2021-10-25 and 0.4.1 dated 2022-05-23

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Package gtrendsR updated to version 1.5.1 with previous version 1.5.0 dated 2021-10-24

Title: Perform and Display Google Trends Queries
Description: An interface for retrieving and displaying the information returned online by Google Trends is provided. Trends (number of hits) over the time as well as geographic representation of the results can be displayed.
Author: Philippe Massicotte [aut, cre], Dirk Eddelbuettel [aut]
Maintainer: Philippe Massicotte <pmassicotte@hotmail.com>

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Package fastglm updated to version 0.0.3 with previous version 0.0.2 dated 2022-04-24

Title: Fast and Stable Fitting of Generalized Linear Models using 'RcppEigen'
Description: Fits generalized linear models efficiently using 'RcppEigen'. The iteratively reweighted least squares implementation utilizes the step-halving approach of Marschner (2011) <doi:10.32614/RJ-2011-012> to help safeguard against convergence issues.
Author: Jared Huling [aut, cre], Douglas Bates [cph], Dirk Eddelbuettel [cph], Romain Francois [cph], Yixuan Qiu [cph]
Maintainer: Jared Huling <jaredhuling@gmail.com>

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Package keras updated to version 2.9.0 with previous version 2.8.0 dated 2022-02-09

Title: R Interface to 'Keras'
Description: Interface to 'Keras' <https://keras.io>, a high-level neural networks 'API'. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both 'CPU' and 'GPU' devices.
Author: Tomasz Kalinowski [ctb, cph, cre], Daniel Falbel [ctb, cph], JJ Allaire [aut, cph], Francois Chollet [aut, cph], RStudio [ctb, cph, fnd], Google [ctb, cph, fnd], Yuan Tang [ctb, cph] , Wouter Van Der Bijl [ctb, cph], Martin Studer [ctb, cph], Sigrid [...truncated...]
Maintainer: Tomasz Kalinowski <tomasz.kalinowski@rstudio.com>

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Package harmonizer updated to version 0.3.0 with previous version 0.2.1 dated 2022-03-07

Title: Harmonizing CN8 and PC8 Product Codes
Description: Several functions are provided to harmonize CN8 (Combined Nomenclature 8 digits) and PC8 (Production Communautaire 8 digits) product codes over time and the classification systems HS6 and BEC. Harmonization of CN8 codes are possible by default from 1995 to 2022 and of PC8 from 2001 to 2021, respectively.
Author: Christoph Baumgartner [cre, aut] , Stjepan Srhoj [aut] , Janette Walde [aut]
Maintainer: Christoph Baumgartner <Christoph.Baumgartner@uibk.ac.at>

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Package corto updated to version 1.1.11 with previous version 1.1.10 dated 2021-10-22

Title: Inference of Gene Regulatory Networks
Description: We present 'corto' (Correlation Tool), a simple package to infer gene regulatory networks and visualize master regulators from gene expression data using DPI (Data Processing Inequality) and bootstrapping to recover edges. An initial step is performed to calculate all significant edges between a list of source nodes (centroids) and target genes. Then all triplets containing two centroids and one target are tested in a DPI step which removes edges. A bootstrapping process then calculates the robustness of the network, eventually re-adding edges previously removed by DPI. The algorithm has been optimized to run outside a computing cluster, using a fast correlation implementation. The package finally provides functions to calculate network enrichment analysis from RNA-Seq and ATAC-Seq signatures as described in the article by Giorgi lab (2020) <doi:10.1093/bioinformatics/btaa223>.
Author: Federico M. Giorgi [aut, cre], Daniele Mercatelli [ctb], Gonzalo Lopez-Garcia [ctb]
Maintainer: Federico M. Giorgi <federico.giorgi@gmail.com>

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Package cata updated to version 0.0.10.9 with previous version 0.0.10.8 dated 2022-03-05

Title: Analysis of Check-All-that-Apply (CATA) Data
Description: Functions for analyzing check-all-that-apply (CATA) data from consumer and sensory tests. Cochran's Q test, McNemar's test, and Penalty-Lift analysis provided, as described in for CATA data analysis by Meyners, Castura & Carr (2013) <doi:10.1016/j.foodqual.2013.06.010>. Cluster analysis can be performed using b-cluster analysis. The quality of cluster analysis solutions can be evaluated using various measures. The methods related to b-cluster analysis are described in a manuscript by Castura, Meyners, Varela & Naes (2022) <doi:10.1016/j.foodqual.2022.104564>.
Author: J.C. Castura [aut, cre, ctb]
Maintainer: J.C. Castura <jcastura@compusense.com>

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Package rfacebookstat updated to version 2.6.2 with previous version 2.5.0 dated 2021-12-16

Title: Load Data from Facebook API Marketing
Description: Load data by campaigns, ads, ad sets and insights, ad account and business manager from Facebook Marketing API into R. For more details see official documents by Facebook Marketing API <https://developers.facebook.com/docs/marketing-apis/>.
Author: Alexey Seleznev [aut, cre]
Maintainer: Alexey Seleznev <selesnow@gmail.com>

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Package RcmdrPlugin.BiclustGUI updated to version 1.1.3.1 with previous version 1.1.3 dated 2020-07-13

Title: 'Rcmdr' Plug-in GUI for Biclustering
Description: A plug-in for R Commander ('Rcmdr'). The package is a Graphical User Interface (GUI) in which several biclustering methods can be executed, followed by diagnostics and plots of the results. Further, the GUI also has the possibility to connect the methods to more general diagnostic packages for biclustering. Biclustering methods from 'biclust', 'fabia', 's4vd', 'iBBiG', 'isa2', 'BiBitR', 'rqubic' and 'BicARE' are implemented. Additionally, 'superbiclust' and 'BcDiag' are also implemented to be able to further investigate results. The GUI also provides a couple of extra utilities to export, save, search through and plot the results. 'RcmdrPlugin.BiclustGUI' also provides a very specific framework for biclustering in which new methods, diagnostics and plots can be added. Scripts were prepared so that R-package developers can freely design their own dialogs in the GUI which can then be added by the maintainer of 'RcmdrPlugin.BiclustGUI'. These scripts do not required any knowledge of 'tcltk' and 'Rcmdr' and are easy to fill in. (Note: rqubic currently requires manual installation through BiocManager::install('rqubic').)
Author: De Troyer Ewoud, Otava Martin
Maintainer: De Troyer Ewoud <ewoud.detroyer@uhasselt.be>

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Package outbreaker2 updated to version 1.1.3 with previous version 1.1.2 dated 2021-02-09

Title: Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data
Description: Bayesian reconstruction of disease outbreaks using epidemiological and genetic information. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C and Ferguson N. 2014. <doi:10.1371/journal.pcbi.1003457>. Campbell, F, Cori A, Ferguson N, Jombart T. 2019. <doi:10.1371/journal.pcbi.1006930>.
Author: Thibaut Jombart [aut], Finlay Campbell [aut, cre], Rich Fitzjohn [aut], Gerry Tonkin-Hill [ctb], Kristjan Eldjarn [ctb], Alexis Robert [ctb]
Maintainer: Finlay Campbell <finlaycampbell93@gmail.com>

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Package nlmixr2est updated to version 2.0.7 with previous version 2.0.6 dated 2022-05-12

Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation Routines
Description: Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] , Yuan Xiong [aut], Rik Schoemaker [aut] , Justin Wilkins [aut] , Wenping Wang [aut], Robert Leary [ctb], Mason McComb [ctb] , Vipul Mann [aut], Mirjam Trame [ctb], Mahmoud Abdelwahab [ctb], Teun Post [ctb], Richard Hooijmai [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>

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Package RadioSonde updated to version 4.2 with previous version 1.4 dated 2014-09-17

Title: Tools for Plotting Skew-T Diagrams and Wind Profiles
Description: A collection of programs for plotting SKEW-T,log p diagrams and wind profiles for data collected by radiosondes (the typical weather balloon-borne instrument). The format of this plot with companion lines to assess atmospheric stability are both standard in meteorology and difficult to create from basic graphics functions. Hence this package. One novel feature is being able add several profiles to the same plot for comparison. Use "help(ExampleSonde)" for an explanation of the variables needed and how they should be named in a data frame. See <https://github.com/dnychka/Radiosonde> for the package home page.
Author: Doug Nychka, Eric Gilleland, Liangying Zhang, Tim Hoar, Kate Young
Maintainer: Doug Nychka <nychka@mines.edu>

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Package MiMIR updated to version 1.4 with previous version 1.3 dated 2022-05-18

Title: Metabolomics-Based Models for Imputing Risk
Description: Provides an intuitive framework for ad-hoc statistical analysis of 1H-NMR metabolomics by Nightingale Health. It allows to easily explore new metabolomics measurements assayed by Nightingale Health, comparing the distributions with a large Consortium (BBMRI-nl); project previously published metabolic scores [<doi:10.1016/j.ebiom.2021.103764>, <doi:10.1161/CIRCGEN.119.002610>, <doi:10.1038/s41467-019-11311-9>, <doi:10.7554/eLife.63033>, <doi:10.1161/CIRCULATIONAHA.114.013116>, <doi:10.1007/s00125-019-05001-w>]; and calibrate the metabolic surrogate values to a desired dataset.
Author: Daniele Bizzarri [aut, cre] , Marcel Reinders [aut, ths] , Marian Beekman [aut] , Pieternella Eline Slagboom [aut, ths] , Erik van den Akker [aut, ths]
Maintainer: Daniele Bizzarri <d.bizzarri@lumc.nl>

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Package GNE updated to version 0.99-4 with previous version 0.99-3.1 dated 2022-05-23

Title: Computation of Generalized Nash Equilibria
Description: Provide functions to compute standard and generalized Nash Equilibria. Optimization methods are available nonsmooth reformulation, fixed-point formulation, minimization problem and constrained-equation reformulation. See e.g. Kanzow and Facchinei (2010), <doi:10.1007/s10479-009-0653-x>.
Author: Christophe Dutang
Maintainer: Christophe Dutang <dutangc@gmail.com>

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Package speaq updated to version 2.7.0 with previous version 2.6.1 dated 2019-12-10

Title: Tools for Nuclear Magnetic Resonance (NMR) Spectra Alignment, Peak Based Processing, Quantitative Analysis and Visualizations
Description: Makes Nuclear Magnetic Resonance spectroscopy (NMR spectroscopy) data analysis as easy as possible by only requiring a small set of functions to perform an entire analysis. 'speaq' offers the possibility of raw spectra alignment and quantitation but also an analysis based on features whereby the spectra are converted to peaks which are then grouped and turned into features. These features can be processed with any number of statistical tools either included in 'speaq' or available elsewhere on CRAN. More details can be found in Vu et al. (2011) <doi:10.1186/1471-2105-12-405> and Beirnaert et al. (2018) <doi:10.1371/journal.pcbi.1006018>.
Author: Charlie Beirnaert, Trung Nghia Vu, Pieter Meysman, Kris Laukens and Dirk Valkenborg
Maintainer: Charlie Beirnaert <charlie_beirnaert@icloud.com>

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Package R2HTML updated to version 2.3.3 with previous version 2.3.2 dated 2016-06-23

Title: HTML Exportation for R Objects
Description: Includes HTML function and methods to write in an HTML file. Thus, making HTML reports is easy. Includes a function that allows redirection on the fly, which appears to be very useful for teaching purpose, as the student can keep a copy of the produced output to keep all that he did during the course. Package comes with a vignette describing how to write HTML reports for statistical analysis. Finally, a driver for 'Sweave' allows to parse HTML flat files containing R code and to automatically write the corresponding outputs (tables and graphs).
Author: Eric Lecoutre [aut], Milan Bouchet-Valat [cre, ctb], Thomas Friedrichsmeier [ctb]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>

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Package nsga2R updated to version 1.1 with previous version 1.0 dated 2013-06-16

Title: Elitist Non-Dominated Sorting Genetic Algorithm
Description: Box-constrained multiobjective optimization using the elitist non-dominated sorting genetic algorithm - NSGA-II. Fast non-dominated sorting, crowding distance, tournament selection, simulated binary crossover, and polynomial mutation are called in the main program. The methods are described in Deb et al. (2002) <doi:10.1109/4235.996017>.
Author: Ching-Shih Tsou <cstsou@mail.ntcb.edu.tw>
Maintainer: Ming-Chang (Alan) Lee <alan9956@ydu.edu.tw>

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Package SVMMaj updated to version 0.2.9.1 with previous version 0.2.9 dated 2019-01-26

Title: Implementation of the SVM-Maj Algorithm
Description: Implements the SVM-Maj algorithm to train data with support vector machine as described in Groenen et al. (2008) <doi:10.1007/s11634-008-0020-9>. This algorithm uses two efficient updates, one for linear kernel and one for the nonlinear kernel.
Author: Hoksan Yip, Patrick J.F. Groenen, Georgi Nalbantov
Maintainer: Hok San Yip <hoksan@gmail.com>

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Package randomForest updated to version 4.7-1.1 with previous version 4.7-1 dated 2022-02-03

Title: Breiman and Cutler's Random Forests for Classification and Regression
Description: Classification and regression based on a forest of trees using random inputs, based on Breiman (2001) <DOI:10.1023/A:1010933404324>.
Author: Fortran original by Leo Breiman and Adele Cutler, R port by Andy Liaw and Matthew Wiener.
Maintainer: Andy Liaw <andy_liaw@merck.com>

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Package pcSteiner updated to version 1.0.0.1 with previous version 1.0.0 dated 2020-08-31

Title: Convenient Tool for Solving the Prize-Collecting Steiner Tree Problem
Description: The Prize-Collecting Steiner Tree problem asks to find a subgraph connecting a given set of vertices with the most expensive nodes and least expensive edges. Since it is proven to be NP-hard, exact and efficient algorithm does not exist. This package provides convenient functionality for obtaining an approximate solution to this problem using loopy belief propagation algorithm.
Author: Aleksei Krasikov <krasikov.as@phystech.edu>
Maintainer: Aleksei Krasikov <krasikov.as@phystech.edu>

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Package ML2Pvae updated to version 1.0.0.1 with previous version 1.0.0 dated 2020-11-16

Title: Variational Autoencoder Models for IRT Parameter Estimation
Description: Based on the work of Curi, Converse, Hajewski, and Oliveira (2019) <doi:10.1109/IJCNN.2019.8852333>. This package provides easy-to-use functions which create a variational autoencoder (VAE) to be used for parameter estimation in Item Response Theory (IRT) - namely the Multidimensional Logistic 2-Parameter (ML2P) model. To use a neural network as such, nontrivial modifications to the architecture must be made, such as restricting the nonzero weights in the decoder according to some binary matrix Q. The functions in this package allow for straight-forward construction, training, and evaluation so that minimal knowledge of 'tensorflow' or 'keras' is required.
Author: Geoffrey Converse [aut, cre, cph], Suely Oliveira [ctb, ths], Mariana Curi [ctb]
Maintainer: Geoffrey Converse <converseg@gmail.com>

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Package lbfgs updated to version 1.2.1.1 with previous version 1.2.1 dated 2014-08-31

Title: Limited-memory BFGS Optimization
Description: A wrapper built around the libLBFGS optimization library by Naoaki Okazaki. The lbfgs package implements both the Limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) and the Orthant-Wise Quasi-Newton Limited-Memory (OWL-QN) optimization algorithms. The L-BFGS algorithm solves the problem of minimizing an objective, given its gradient, by iteratively computing approximations of the inverse Hessian matrix. The OWL-QN algorithm finds the optimum of an objective plus the L1-norm of the problem's parameters. The package offers a fast and memory-efficient implementation of these optimization routines, which is particularly suited for high-dimensional problems.
Author: Antonio Coppola [aut, cre, cph], Brandon Stewart [aut, cph], Naoaki Okazaki [aut, cph], David Ardia [ctb, cph], Dirk Eddelbuettel [ctb, cph], Katharine Mullen [ctb, cph], Jorge Nocedal [ctb, cph]
Maintainer: Antonio Coppola <acoppola@college.harvard.edu>

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Package gtools updated to version 3.9.2.1 with previous version 3.9.2 dated 2021-06-06

Title: Various R Programming Tools
Description: Functions to assist in R programming, including: - assist in developing, updating, and maintaining R and R packages ('ask', 'checkRVersion', 'getDependencies', 'keywords', 'scat'), - calculate the logit and inverse logit transformations ('logit', 'inv.logit'), - test if a value is missing, empty or contains only NA and NULL values ('invalid'), - manipulate R's .Last function ('addLast'), - define macros ('defmacro'), - detect odd and even integers ('odd', 'even'), - convert strings containing non-ASCII characters (like single quotes) to plain ASCII ('ASCIIfy'), - perform a binary search ('binsearch'), - sort strings containing both numeric and character components ('mixedsort'), - create a factor variable from the quantiles of a continuous variable ('quantcut'), - enumerate permutations and combinations ('combinations', 'permutation'), - calculate and convert between fold-change and log-ratio ('foldchange', 'logratio2foldchange', 'foldchange2logratio'), - calculate probabilities and generate random numbers from Dirichlet distributions ('rdirichlet', 'ddirichlet'), - apply a function over adjacent subsets of a vector ('running'), - modify the TCP\_NODELAY ('de-Nagle') flag for socket objects, - efficient 'rbind' of data frames, even if the column names don't match ('smartbind'), - generate significance stars from p-values ('stars.pval'), - convert characters to/from ASCII codes ('asc', 'chr'), - convert character vector to ASCII representation ('ASCIIfy'), - apply title capitalization rules to a character vector ('capwords').
Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
Maintainer: Gregory R. Warnes <greg@warnes.net>

Diff between gtools versions 3.9.2 dated 2021-06-06 and 3.9.2.1 dated 2022-05-23

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Package GNE updated to version 0.99-3.1 with previous version 0.99-3 dated 2020-01-08

Title: Computation of Generalized Nash Equilibria
Description: Provide functions to compute standard and generalized Nash Equilibria. Optimization methods are available nonsmooth reformulation, fixed-point formulation, minimization problem and constrained-equation reformulation. See e.g. Kanzow and Facchinei (2010), <doi:10.1007/s10479-009-0653-x>.
Author: Christophe Dutang
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>

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Package FNN updated to version 1.1.3.1 with previous version 1.1.3 dated 2019-02-15

Title: Fast Nearest Neighbor Search Algorithms and Applications
Description: Cover-tree and kd-tree fast k-nearest neighbor search algorithms and related applications including KNN classification, regression and information measures are implemented.
Author: Alina Beygelzimer, Sham Kakadet and John Langford , Sunil Arya and David Mount , Shengqiao Li
Maintainer: Shengqiao Li <lishengqiao@yahoo.com>

Diff between FNN versions 1.1.3 dated 2019-02-15 and 1.1.3.1 dated 2022-05-23

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Package flare updated to version 1.7.0.1 with previous version 1.7.0 dated 2020-11-30

Title: Family of Lasso Regression
Description: Provide the implementation of a family of Lasso variants including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating high dimensional sparse linear model. We adopt the alternating direction method of multipliers and convert the original optimization problem into a sequential L1 penalized least square minimization problem, which can be efficiently solved by linearization algorithm. A multi-stage screening approach is adopted for further acceleration. Besides the sparse linear model estimation, we also provide the extension of these Lasso variants to sparse Gaussian graphical model estimation including TIGER and CLIME using either L1 or adaptive penalty. Missing values can be tolerated for Dantzig selector and CLIME. The computation is memory-optimized using the sparse matrix output. For more information, please refer to <https://www.jmlr.org/papers/volume16/li15a/li15a.pdf>.
Author: Xingguo Li, Tuo Zhao, Lie Wang, Xiaoming Yuan, and Han Liu
Maintainer: Xingguo Li <xingguo.leo@gmail.com>

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Package bruceR updated to version 0.8.7 with previous version 0.8.6 dated 2022-04-13

Title: Broadly Useful Convenient and Efficient R Functions
Description: Broadly useful convenient and efficient R functions that bring users concise and elegant R data analyses. This package includes easy-to-use functions for (1) basic R programming (e.g., set working directory to the path of currently opened file; import/export data from/to files in any format; print tables to Microsoft Word); (2) multivariate computation (e.g., compute scale sums/means/... with reverse scoring); (3) reliability analyses and factor analyses; (4) descriptive statistics and correlation analyses; (5) t-test, multi-factor analysis of variance (ANOVA), simple-effect analysis, and post-hoc multiple comparison; (6) tidy report of statistical models (to R Console and Microsoft Word); (7) mediation and moderation analyses (PROCESS); and (8) additional toolbox for statistics and graphics.
Author: Han-Wu-Shuang Bao [aut, cre]
Maintainer: Han-Wu-Shuang Bao <baohws@foxmail.com>

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Package rQCC updated to version 2.22.5 with previous version 2.22.1 dated 2022-01-25

Title: Robust Quality Control Chart
Description: Constructs various robust quality control charts based on the median or Hodges-Lehmann estimator (location) and the median absolute deviation (MAD) or Shamos estimator (scale). The estimators used for the robust control charts are all unbiased with a sample of finite size. For more details, see Park, Kim and Wang (2022) <doi:10.1080/03610918.2019.1699114>. In addition, using this R package, the conventional quality control charts such as X-bar, S, R, p, np, u, c, g and h charts are also easily constructed. This work was partially supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (NRF-2017R1A2B4004169).
Author: Chanseok Park [aut, cre] , Min Wang [ctb]
Maintainer: Chanseok Park <statpnu@gmail.com>

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Package ichimoku updated to version 1.3.1 with previous version 1.3.0 dated 2022-02-21

Title: Visualization and Tools for Ichimoku Kinko Hyo Strategies
Description: An implementation of 'Ichimoku Kinko Hyo', also commonly known as 'cloud charts'. Static and interactive visualizations with tools for creating, backtesting and development of quantitative 'ichimoku' strategies. As described in Sasaki (1996, ISBN:4925152009), the technique is a refinement on candlestick charting, originating from Japan and now in widespread use in technical analysis worldwide. Translating as 'one-glance equilibrium chart', it allows the price action and market structure of financial securities to be determined 'at-a-glance'. Incorporates an interface with the OANDA fxTrade API <https://developer.oanda.com/> for retrieving historical and live streaming price data for major currencies, metals, commodities, government bonds and stock indices.
Author: Charlie Gao [aut, cre]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>

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Package spOccupancy updated to version 0.3.2 with previous version 0.3.1 dated 2022-04-13

Title: Single-Species, Multi-Species, and Integrated Spatial Occupancy Models
Description: Fits single-species, multi-species, and integrated non-spatial and spatial occupancy models using Markov Chain Monte Carlo (MCMC). Models are fit using Polya-Gamma data augmentation detailed in Polson, Scott, and Windle (2013) <doi:10.1080/01621459.2013.829001>. Spatial models are fit using either Gaussian processes or Nearest Neighbor Gaussian Processes (NNGP) for large spatial datasets. Details on NNGP models are given in Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091> and Finley, Datta, and Banerjee (2020) <arXiv:2001.09111>. Provides functionality for data integration of multiple single-species occupancy data sets using a joint likelihood framework. Details on data integration are given in Miller, Pacifici, Sanderlin, and Reich (2019) <doi:10.1111/2041-210X.13110>. Details on single-species and multi-species models are found in MacKenzie, Nichols, Lachman, Droege, Royle, and Langtimm (2002) <doi:10.1890/0012-9658(2002)083[2248:ESORWD]2.0.CO;2> and Dorazio and Royle <doi:10.1198/016214505000000015>, respectively.
Author: Jeffrey Doser [aut, cre], Andrew Finley [aut]
Maintainer: Jeffrey Doser <doserjef@msu.edu>

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Package santaR updated to version 1.2.2 with previous version 1.2.0 dated 2022-04-09

Title: Short Asynchronous Time-Series Analysis
Description: A graphical and automated pipeline for the analysis of short time-series in R ('santaR'). This approach is designed to accommodate asynchronous time sampling (i.e. different time points for different individuals), inter-individual variability, noisy measurements and large numbers of variables. Based on a smoothing splines functional model, 'santaR' is able to detect variables highlighting significantly different temporal trajectories between study groups. Designed initially for metabolic phenotyping, 'santaR' is also suited for other Systems Biology disciplines. Command line and graphical analysis (via a 'shiny' application) enable fast and parallel automated analysis and reporting, intuitive visualisation and comprehensive plotting options for non-specialist users.
Author: Arnaud Wolfer [aut, cre] , Timothy Ebbels [ctb], Joe Cheng [ctb]
Maintainer: Arnaud Wolfer <adwolfer@gmail.com>

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Package pedmod updated to version 0.2.1 with previous version 0.2.0 dated 2022-04-28

Title: Pedigree Models
Description: Provides functions to estimate mixed probit models using, for instance, pedigree data like in <doi:10.1002/sim.1603>. The models are also commonly called liability threshold models. The approximation is based on direct log marginal likelihood approximations like the randomized Quasi-Monte Carlo suggested by <doi:10.1198/106186002394> with a similar procedure to approximate the derivatives. The minimax tilting method suggested by <doi:10.1111/rssb.12162> is also supported. Graph-based methods are also provided that can be used to simplify pedigrees.
Author: Benjamin Christoffersen [cre, aut] , Alan Genz [cph], Frank Bretz [cph], Bjoern Bornkamp [cph], Torsten Hothorn [cph], Christophe Dutang [cph], Diethelm Wuertz [cph], R-core [cph], Leo Belzile [cph], Zdravko Botev [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>

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Package pdfetch updated to version 0.2.7 with previous version 0.2.6 dated 2022-02-25

Title: Fetch Economic and Financial Time Series Data from Public Sources
Description: Download economic and financial time series from public sources, including the St Louis Fed's FRED system, Yahoo Finance, the US Bureau of Labor Statistics, the US Energy Information Administration, the World Bank, Eurostat, the European Central Bank, the Bank of England, the UK's Office of National Statistics, Deutsche Bundesbank, and INSEE.
Author: Abiel Reinhart <abielr@gmail.com>
Maintainer: Abiel Reinhart <abielr@gmail.com>

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Package hetu updated to version 1.0.7 with previous version 1.0.1 dated 2020-10-24

Title: Structural Handling of Finnish Personal Identity Codes
Description: Structural handling of Finnish identity codes (natural persons and organizations); extract information, check ID validity and diagnostics.
Author: Pyry Kantanen [aut, cre] , Mans Magnusson [aut], Jussi Paananen [aut], Juho Kopra [ctb], Oskari Luomala [ctb], Tuomo Nieminen [ctb], Leo Lahti [aut]
Maintainer: Pyry Kantanen <pyry.kantanen@gmail.com>

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Package fossilbrush updated to version 1.0.2 with previous version 1.0.1 dated 2022-05-19

Title: Automated Cleaning of Fossil Occurrence Data
Description: Functions to automate the detection and resolution of taxonomic and stratigraphic errors in fossil occurrence datasets. Functions were developed using data from the Paleobiology Database.
Author: Joe Flannery-Sutherland [aut, cre] , Nussaïbah Raja-Schoob [aut, ctb], Ádam Kocsis [aut, ctb], Wolfgang Kiessling [aut]
Maintainer: Joe Flannery-Sutherland <jf15558@bristol.ac.uk>

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Package enetLTS updated to version 1.1.0 with previous version 0.1.0 dated 2018-01-22

Title: Robust and Sparse Methods for High Dimensional Linear and Binary and Multinomial Regression
Description: Fully robust versions of the elastic net estimator are introduced for linear and binary and multinomial regression, in particular high dimensional data. The algorithm searches for outlier free subsets on which the classical elastic net estimators can be applied. A reweighting step is added to improve the statistical efficiency of the proposed estimators. Selecting appropriate tuning parameters for elastic net penalties are done via cross-validation.
Author: Fatma Sevinc Kurnaz and Irene Hoffmann and Peter Filzmoser
Maintainer: Fatma Sevinc Kurnaz <fatmasevinckurnaz@gmail.com>

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Package csurvey updated to version 1.3 with previous version 1.2 dated 2021-08-12

Title: Constrained Regression for Survey Data
Description: Domain mean estimation with monotonicity or block monotone constraints. See Xu X, Meyer MC and Opsomer JD (2021)<doi:10.1016/j.jspi.2021.02.004> for more details.
Author: Xiyue Liao
Maintainer: Xiyue Liao <xiyue.liao@csulb.edu>

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Package BayesOrdDesign updated to version 0.1.1 with previous version 0.1.0 dated 2021-09-21

Title: Bayesian Group Sequential Design for Ordinal Data
Description: The proposed group-sequential trial design is based on Bayesian methods for ordinal endpoints, including three methods, the proportional-odds-model (PO)-based, non-proportional-odds-model (NPO)-based, and PO/NPO switch-model-based designs, which makes our proposed methods generic to be able to deal with various scenarios. Richard J. Barker, William A. Link (2013) <doi:10.1080/00031305.2013.791644>. Thomas A. Murray, Ying Yuan, Peter F. Thall, Joan H. Elizondo, Wayne L.Hofstetter (2018) <doi:10.1111/biom.12842>. Chengxue Zhong, Haitao Pan, Hongyu Miao (2021) <arXiv:2108.06568>.
Author: Chengxue Zhong [aut, cre], Haitao Pan [aut], Hongyu Miao [aut]
Maintainer: Chengxue Zhong <chengxue.zhong@uth.tmc.edu>

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Sat, 21 May 2022

Package plotmo updated to version 3.6.2 with previous version 3.6.1 dated 2021-07-17

Title: Plot a Model's Residuals, Response, and Partial Dependence Plots
Description: Plot model surfaces for a wide variety of models using partial dependence plots and other techniques. Also plot model residuals and other information on the model.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>

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Package jmvReadWrite updated to version 0.3.2 with previous version 0.3.1 dated 2022-02-28

Title: Read and Write 'jamovi' Files ('.omv')
Description: The free and open a statistical spreadsheet 'jamovi' (www.jamovi.org) aims to make statistical analyses easy and intuitive. 'jamovi' produces syntax that can directly be used in R (in connection with the R-package 'jmv'). Having import / export routines for the data files 'jamovi' produces ('.omv') permits an easy transfer of analyses between 'jamovi' and R.
Author: Sebastian Jentschke [aut, cre]
Maintainer: Sebastian Jentschke <sebastian.jentschke@uib.no>

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Package WebPower updated to version 0.7 with previous version 0.6 dated 2021-05-18

Title: Basic and Advanced Statistical Power Analysis
Description: This is a collection of tools for conducting both basic and advanced statistical power analysis including correlation, proportion, t-test, one-way ANOVA, two-way ANOVA, linear regression, logistic regression, Poisson regression, mediation analysis, longitudinal data analysis, structural equation modeling and multilevel modeling. It also serves as the engine for conducting power analysis online at <https://webpower.psychstat.org>.
Author: Zhiyong Zhang [aut, cre], Yujiao Mai [aut], Miao Yang [ctb]
Maintainer: Zhiyong Zhang <johnnyzhz@gmail.com>

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Package IsoplotRgui updated to version 4.4 with previous version 4.3 dated 2022-03-07

Title: Web Interface to 'IsoplotR'
Description: Provides a graphical user interface to the 'IsoplotR' package for radiometric geochronology. The GUI runs in an internet browser and can either be used offline, or hosted on a server to provide online access to the 'IsoplotR' toolbox.
Author: Pieter Vermeesch [aut, cre], Tim Band [ctb]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>

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More information about IsoplotRgui at CRAN
Permanent link

Package IsoplotR updated to version 4.4 with previous version 4.3 dated 2022-03-06

Title: Statistical Toolbox for Radiometric Geochronology
Description: Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington' and 'Ludwig' approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Constructs total Pb-U, Pb-Pb, Th-Pb, K-Ca, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isochrons as well as 230Th-U evolution plots.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>

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More information about IsoplotR at CRAN
Permanent link

Package ggstatsplot updated to version 0.9.2 with previous version 0.9.1 dated 2022-01-14

Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates graphics with details from statistical tests included in the plots themselves. It provides an easier syntax to generate information-rich plots for statistical analysis of continuous (violin plots, scatterplots, histograms, dot plots, dot-and-whisker plots) or categorical (pie and bar charts) data. Currently, it supports the most common types of statistical approaches and tests: parametric, nonparametric, robust, and Bayesian versions of t-test/ANOVA, correlation analyses, contingency table analysis, meta-analysis, and regression analyses.
Author: Indrajeet Patil [cre, aut, cph]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

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Package DataVisualizations updated to version 1.2.3 with previous version 1.2.2 dated 2021-01-12

Title: Visualizations of High-Dimensional Data
Description: Gives access to data visualisation methods that are relevant from the data scientist's point of view. The flagship idea of 'DataVisualizations' is the mirrored density plot (MD-plot) for either classified or non-classified multivariate data published in Thrun, M.C. et al.: "Analyzing the Fine Structure of Distributions" (2020), PLoS ONE, <DOI:10.1371/journal.pone.0238835>. The MD-plot outperforms the box-and-whisker diagram (box plot), violin plot and bean plot and geom_violin plot of ggplot2. Furthermore, a collection of various visualization methods for univariate data is provided. In the case of exploratory data analysis, 'DataVisualizations' makes it possible to inspect the distribution of each feature of a dataset visually through a combination of four methods. One of these methods is the Pareto density estimation (PDE) of the probability density function (pdf). Additionally, visualizations of the distribution of distances using PDE, the scatter-density plot using PDE for two variables as well as the Shepard density plot and the Bland-Altman plot are presented here. Pertaining to classified high-dimensional data, a number of visualizations are described, such as f.ex. the heat map and silhouette plot. A political map of the world or Germany can be visualized with the additional information defined by a classification of countries or regions. By extending the political map further, an uncomplicated function for a Choropleth map can be used which is useful for measurements across a geographic area. For categorical features, the Pie charts, slope charts and fan plots, improved by the ABC analysis, become usable. More detailed explanations are found in the book by Thrun, M.C.: "Projection-Based Clustering through Self-Organization and Swarm Intelligence" (2018) <DOI:10.1007/978-3-658-20540-9>.
Author: Michael Thrun [aut, cre, cph] , Felix Pape [aut, rev], Onno Hansen-Goos [ctr, ctb], Hamza Tayyab [ctr, ctb], Dirk Eddelbuettel [ctr], Craig Varrichio [ctr], Alfred Ultsch [dtc, ctb, ctr]
Maintainer: Michael Thrun <m.thrun@gmx.net>

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Package DALEX updated to version 2.4.1 with previous version 2.4.0 dated 2022-02-21

Title: moDel Agnostic Language for Exploration and eXplanation
Description: Any unverified black box model is the path to failure. Opaqueness leads to distrust. Distrust leads to ignoration. Ignoration leads to rejection. DALEX package xrays any model and helps to explore and explain its behaviour. Machine Learning (ML) models are widely used and have various applications in classification or regression. Models created with boosting, bagging, stacking or similar techniques are often used due to their high performance. But such black-box models usually lack direct interpretability. DALEX package contains various methods that help to understand the link between input variables and model output. Implemented methods help to explore the model on the level of a single instance as well as a level of the whole dataset. All model explainers are model agnostic and can be compared across different models. DALEX package is the cornerstone for 'DrWhy.AI' universe of packages for visual model exploration. Find more details in (Biecek 2018) <arXiv:1806.08915>.
Author: Przemyslaw Biecek [aut, cre] , Szymon Maksymiuk [aut] , Hubert Baniecki [aut]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>

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Package tensorflow updated to version 2.9.0 with previous version 2.8.0 dated 2022-02-09

Title: R Interface to 'TensorFlow'
Description: Interface to 'TensorFlow' <https://www.tensorflow.org/>, an open source software library for numerical computation using data flow graphs. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them. The flexible architecture allows you to deploy computation to one or more 'CPUs' or 'GPUs' in a desktop, server, or mobile device with a single 'API'. 'TensorFlow' was originally developed by researchers and engineers working on the Google Brain Team within Google's Machine Intelligence research organization for the purposes of conducting machine learning and deep neural networks research, but the system is general enough to be applicable in a wide variety of other domains as well.
Author: Daniel Falbel [ctb, cph], JJ Allaire [aut, cph], RStudio [cph, fnd], Yuan Tang [aut, cph] , Dirk Eddelbuettel [ctb, cph], Nick Golding [ctb, cph], Tomasz Kalinowski [ctb, cph, cre], Google Inc. [ctb, cph]
Maintainer: Tomasz Kalinowski <tomasz.kalinowski@rstudio.com>

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Package rpart.plot updated to version 3.1.1 with previous version 3.1.0 dated 2021-07-24

Title: Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'
Description: Plot 'rpart' models. Extends plot.rpart() and text.rpart() in the 'rpart' package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>

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Package network updated to version 1.17.2 with previous version 1.17.1 dated 2021-06-14

Title: Classes for Relational Data
Description: Tools to create and modify network objects. The network class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.
Author: Carter T. Butts [aut, cre], David Hunter [ctb], Mark Handcock [ctb], Skye Bender-deMoll [ctb], Jeffrey Horner [ctb], Li Wang [ctb], Pavel N. Krivitsky [ctb] , Brendan Knapp [ctb] , Michal Bojanowski [ctb], Chad Klumb [ctb]
Maintainer: Carter T. Butts <buttsc@uci.edu>

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Package fracture updated to version 0.2.1 with previous version 0.2.0 dated 2021-10-25

Title: Convert Decimals to Fractions
Description: Provides functions for converting decimals to a matrix of numerators and denominators or a character vector of fractions. Supports mixed or improper fractions, finding common denominators for vectors of fractions, limiting denominators to powers of ten, and limiting denominators to a maximum value. Also includes helper functions for finding the least common multiple and greatest common divisor for a vector of integers. Implemented using C++ for maximum speed.
Author: Alexander Rossell Hayes [aut, cre, cph]
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>

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Package rtables updated to version 0.5.1 with previous version 0.5.0 dated 2022-03-31

Title: Reporting Tables
Description: Reporting tables often have structure that goes beyond simple rectangular data. The 'rtables' package provides a framework for declaring complex multi-level tabulations and then applying them to data. This framework models both tabulation and the resulting tables as hierarchical, tree-like objects which support sibling sub-tables, arbitrary splitting or grouping of data in row and column dimensions, cells containing multiple values, and the concept of contextual summary computations. A convenient pipe-able interface is provided for declaring table layouts and the corresponding computations, and then applying them to data.
Author: Gabriel Becker [aut, cre], Adrian Waddell [aut], Daniel Sabanes Bove [ctb], Maximilian Mordig [ctb]
Maintainer: Gabriel Becker <gabembecker@gmail.com>

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Package RSQL updated to version 0.2.1 with previous version 0.2.0 dated 2022-04-14

Title: Database Agnostic Package to Generate and Process 'SQL' Queries in R
Description: Allows the user to generate and execute select, insert, update and delete 'SQL' queries the underlying database without having to explicitly write 'SQL' code.
Author: Alejandro Baranek [cre, aut], Leonardo Belen [aut]
Maintainer: Alejandro Baranek <abaranek@dc.uba.ar>

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Package lmtp updated to version 1.3.0 with previous version 1.0.0 dated 2021-09-29

Title: Non-Parametric Causal Effects of Feasible Interventions Based on Modified Treatment Policies
Description: Non-parametric estimators for casual effects based on longitudinal modified treatment policies as described in Diaz, Williams, Hoffman, and Schenck <doi:10.1080/01621459.2021.1955691>, traditional point treatment, and traditional longitudinal effects. Continuous, binary, and categorical treatments are allowed as well are censored outcomes. The treatment mechanism is estimated via a density ratio classification procedure irrespective of treatment variable type. For both continuous and binary outcomes, additive treatment effects can be calculated and relative risks and odds ratios may be calculated for binary outcomes.
Author: Nicholas Williams [aut, cre, cph] , Ivan Diaz [aut, cph]
Maintainer: Nicholas Williams <ntwilliams.personal@gmail.com>

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Fri, 20 May 2022

Package formatters updated to version 0.3.1 with previous version 0.2.0 dated 2022-03-29

Title: ASCII Formatting for Values and Tables
Description: We provide a framework for rendering complex tables to ASCII, and a set of formatters for transforming values or sets of values into ASCII-ready display strings.
Author: Gabriel Becker [aut, cre], Adrian Waddell [aut], F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Gabriel Becker <gabembecker@gmail.com>

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Package elfgen updated to version 2.3.0 with previous version 2.2.8 dated 2022-03-29

Title: Ecological Limit Function Model Generation, Analysis, and Visualization using 'ggplot2' and Statistical Methods
Description: A toolset for generating Ecological Limit Function (ELF) models and evaluating potential species loss resulting from flow change, based on the "elfgen" framework. ELFs describe the relation between aquatic species richness (fish or benthic macroinvertebrates) and stream size characteristics (streamflow or drainage area). Journal publications are available outlining framework methodology (Kleiner et al. (2020) <doi:10.1111/1752-1688.12876>) and application (Rapp et al. (2020) <doi:10.1111/1752-1688.12877>).
Author: Joseph Kleiner [aut, cre]
Maintainer: Joseph Kleiner <joseph.d.kleiner@gmail.com>

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Package CSCDRNA updated to version 1.0.2 with previous version 1.0.1 dated 2022-05-17

Title: Covariance Based Single-Cell Decomposition of Bulk Expression Data
Description: Provides accurate cell type proportion estimation by incorporating covariance structure in both single-cell and bulk RNA-seq datasets into the analysis. For more detail, see Karimnezhad, A. (2022) <doi:10.1101/2022.05.13.491858>.
Author: Ali Karimnezhad [aut, cre, ctb]
Maintainer: Ali Karimnezhad <ali.karimnezhad@gmail.com>

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Package seismic updated to version 1.1 with previous version 1.0 dated 2015-06-05

Title: Predict Information Cascade by Self-Exciting Point Process
Description: An implementation of self-exciting point process model for information cascades, which occurs when many people engage in the same acts after observing the actions of others (e.g. post resharings on Facebook or Twitter). It provides functions to estimate the infectiousness of an information cascade and predict its popularity given the observed history. See <http://snap.stanford.edu/seismic/> for more information and datasets.
Author: Hera He, Murat Erdogdu, Qingyuan Zhao
Maintainer: Qingyuan Zhao <qingyzhao@gmail.com>

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Package DanielBiostatistics10th updated to version 0.1.3 with previous version 0.1.2 dated 2022-05-13

Title: Functions for Wayne W. Daniel's Biostatistics, Tenth Edition
Description: Functions to accompany Wayne W. Daniel's Biostatistics: A Foundation for Analysis in the Health Sciences, Tenth Edition.
Author: Tingting Zhan [aut, cre, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>

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Package correlation updated to version 0.8.1 with previous version 0.8.0 dated 2022-02-14

Title: Methods for Correlation Analysis
Description: Lightweight package for computing different kinds of correlations, such as partial correlations, Bayesian correlations, multilevel correlations, polychoric correlations, biweight correlations, distance correlations and more. Part of the 'easystats' ecosystem.
Author: Dominique Makowski [aut, inv] , Brenton M. Wiernik [aut, cre] , Indrajeet Patil [aut] , Daniel Luedecke [aut] , Mattan S. Ben-Shachar [aut] , Mark White [rev], Maximilian M. Rabe [rev]
Maintainer: Brenton M. Wiernik <brenton@wiernik.org>

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Package statsExpressions updated to version 1.3.2 with previous version 1.3.1 dated 2022-03-29

Title: Tidy Dataframes and Expressions with Statistical Details
Description: Utilities for producing dataframes with rich details for the most common types of statistical approaches and tests: parametric, nonparametric, robust, and Bayesian t-test, one-way ANOVA, correlation analyses, contingency table analyses, and meta-analyses. The functions are pipe-friendly and provide a consistent syntax to work with tidy data. These dataframes additionally contain expressions with statistical details, and can be used in graphing packages. This package also forms the statistical processing backend for 'ggstatsplot'.
Author: Indrajeet Patil [cre, aut, cph]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

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Package LocalControl updated to version 1.1.3 with previous version 1.1.2.2 dated 2020-11-26

Title: Nonparametric Methods for Generating High Quality Comparative Effectiveness Evidence
Description: Implements novel nonparametric approaches to address biases and confounding when comparing treatments or exposures in observational studies of outcomes. While designed and appropriate for use in studies involving medicine and the life sciences, the package can be used in other situations involving outcomes with multiple confounders. The package implements a family of methods for non-parametric bias correction when comparing treatments in observational studies, including survival analysis settings, where competing risks and/or censoring may be present. The approach extends to bias-corrected personalized predictions of treatment outcome differences, and analysis of heterogeneity of treatment effect-sizes across patient subgroups. For further details, please see: Lauve NR, Nelson SJ, Young SS, Obenchain RL, Lambert CG. LocalControl: An R Package for Comparative Safety and Effectiveness Research. Journal of Statistical Software. 2020. p. 1–32. Available from <doi:10.18637/jss.v096.i04>.
Author: Nicolas R. Lauve [aut] , Stuart J. Nelson [aut] , S. Stanley Young [aut] , Robert L. Obenchain [aut] , Melania Pintilie [ctb], Martin Kutz [ctb], Christophe G. Lambert [aut, cre]
Maintainer: Christophe G. Lambert <cglambert@unm.edu>

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Package conf updated to version 1.7.1 with previous version 1.7.0 dated 2020-08-24

Title: Visualization and Analysis of Statistical Measures of Confidence
Description: Enables: (1) plotting two-dimensional confidence regions, (2) coverage analysis of confidence region simulations and (3) calculating confidence intervals and the associated actual coverage for binomial proportions. Each is given in greater detail next. (1) Plots the two-dimensional confidence region for probability distribution parameters (supported distribution suffixes: cauchy, gamma, invgauss, logis, llogis, lnorm, norm, unif, weibull) corresponding to a user-given complete or right-censored dataset and level of significance. The crplot() algorithm plots more points in areas of greater curvature to ensure a smooth appearance throughout the confidence region boundary. An alternative heuristic plots a specified number of points at roughly uniform intervals along its boundary. Both heuristics build upon the radial profile log-likelihood ratio technique for plotting confidence regions given by Jaeger (2016) <doi:10.1080/00031305.2016.1182946>, and are detailed in a publication by Weld (2019) <doi:10.1080/00031305.2018.1564696>. (2) Performs confidence region coverage simulations for a random sample drawn from a user- specified parametric population distribution, or for a user-specified dataset and point of interest with coversim(). (3) Calculates confidence interval bounds for a binomial proportion with binomTest(), calculates the actual coverage with binomTestCoverage(), and plots the actual coverage with binomTestCoveragePlot(). Calculates confidence interval bounds for the binomial proportion using an ensemble of constituent confidence intervals with binomTestEnsemble(). Calculates confidence interval bounds for the binomial proportion using a complete enumeration of all possible transitions from one actual coverage acceptance curve to another which minimizes the root mean square error for n <= 15 and follows the transitions for well-known confidence intervals for n > 15 using binomTestMSE().
Author: Christopher Weld [aut, cre] , Hayeon Park [aut], Kexin Feng [aut], Heather Sasinowska [aut], Lawrence Leemis [aut], Andrew Loh [ctb], Yuan Chang [ctb], Brock Crook [ctb], Xin Zhang [ctb]
Maintainer: Christopher Weld <ceweld@email.wm.edu>

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Package meifly updated to version 0.3.1 with previous version 0.3 dated 2014-04-23

Title: Interactive Model Exploration using 'GGobi'
Description: Exploratory model analysis with <http://ggobi.org>. Fit and graphical explore ensembles of linear models.
Author: Hadley Wickham <h.wickham@gmail.com>
Maintainer: Hadley Wickham <h.wickham@gmail.com>

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Package FCPS updated to version 1.3.1 with previous version 1.3.0 dated 2021-07-07

Title: Fundamental Clustering Problems Suite
Description: Over sixty clustering algorithms are provided in this package with consistent input and output, which enables the user to try out algorithms swiftly. Additionally, 26 statistical approaches for the estimation of the number of clusters as well as the mirrored density plot (MD-plot) of clusterability are implemented. The packages is published in Thrun, M.C., Stier Q.: "Fundamental Clustering Algorithms Suite" (2021), SoftwareX, <DOI:10.1016/j.softx.2020.100642>. Moreover, the fundamental clustering problems suite (FCPS) offers a variety of clustering challenges any algorithm should handle when facing real world data, see Thrun, M.C., Ultsch A.: "Clustering Benchmark Datasets Exploiting the Fundamental Clustering Problems" (2020), Data in Brief, <DOI:10.1016/j.dib.2020.105501>.
Author: Michael Thrun [aut, cre, cph] , Peter Nahrgang [ctr, ctb], Felix Pape [ctr, ctb], Vasyl Pihur [ctb], Guy Brock [ctb], Susmita Datta [ctb], Somnath Datta [ctb], Luis Winckelmann [com], Alfred Ultsch [dtc, ctb], Quirin Stier [ctb, rev]
Maintainer: Michael Thrun <m.thrun@gmx.net>

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Package praznik updated to version 11.0.0 with previous version 10.0.0 dated 2021-11-09

Title: Tools for Information-Based Feature Selection and Scoring
Description: A toolbox of fast, native and parallel implementations of various information-based importance criteria estimators and feature selection filters based on them, inspired by the overview by Brown, Pocock, Zhao and Lujan (2012) <https://www.jmlr.org/papers/v13/brown12a.html>. Contains, among other, minimum redundancy maximal relevancy ('mRMR') method by Peng, Long and Ding (2005) <doi:10.1109/TPAMI.2005.159>; joint mutual information ('JMI') method by Yang and Moody (1999) <https://papers.nips.cc/paper/1779-data-visualization-and-feature-selection-new-algorithms-for-nongaussian-data>; double input symmetrical relevance ('DISR') method by Meyer and Bontempi (2006) <doi:10.1007/11732242_9> as well as joint mutual information maximisation ('JMIM') method by Bennasar, Hicks and Setchi (2015) <doi:10.1016/j.eswa.2015.07.007>.
Author: Miron B. Kursa [aut, cre]
Maintainer: Miron B. Kursa <m@mbq.me>

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Package mikropml updated to version 1.3.0 with previous version 1.2.2 dated 2022-02-03

Title: User-Friendly R Package for Supervised Machine Learning Pipelines
Description: An interface to build machine learning models for classification and regression problems. 'mikropml' implements the ML pipeline described by Topçuoğlu et al. (2020) <doi:10.1128/mBio.00434-20> with reasonable default options for data preprocessing, hyperparameter tuning, cross-validation, testing, model evaluation, and interpretation steps. See the website <https://www.schlosslab.org/mikropml/> for more information, documentation, and examples.
Author: Beguem Topcuoğlu [aut] , Zena Lapp [aut] , Kelly Sovacool [aut, cre] , Evan Snitkin [aut] , Jenna Wiens [aut] , Patrick Schloss [aut] , Nick Lesniak [ctb] , Courtney Armour [ctb] , Sarah Lucas [ctb]
Maintainer: Kelly Sovacool <sovacool@umich.edu>

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Package invGauss updated to version 1.2 with previous version 1.1 dated 2014-03-28

Title: Threshold Regression that Fits the (Randomized Drift) Inverse Gaussian Distribution to Survival Data
Description: Fits the (randomized drift) inverse Gaussian distribution to survival data. The model is described in Aalen OO, Borgan O, Gjessing HK. Survival and Event History Analysis. A Process Point of View. Springer, 2008. It is based on describing time to event as the barrier hitting time of a Wiener process, where drift towards the barrier has been randomized with a Gaussian distribution. The model allows covariates to influence starting values of the Wiener process and/or average drift towards a barrier, with a user-defined choice of link functions.
Author: Hakon K. Gjessing
Maintainer: Hakon K. Gjessing <hakon.gjessing@uib.no>

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Package fritools updated to version 3.5.0 with previous version 3.4.0 dated 2022-04-26

Title: Utilities for the Forest Research Institute of the State Baden-Wuerttemberg
Description: Miscellaneous utilities, tools and helper functions for finding and searching files on disk, searching for and removing R objects from the workspace. These are utilities for packages <https://CRAN.R-project.org/package=cleanr>, <https://CRAN.R-project.org/package=document>, <https://CRAN.R-project.org/package=fakemake>, <https://CRAN.R-project.org/package=packager> and <https://CRAN.R-project.org/package=rasciidoc>. Does not import or depend on any third party package, but on core R only (i.e. it may depend on packages with priority 'base').
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>

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Package UWHAM updated to version 1.1 with previous version 1.0 dated 2013-01-26

Title: Unbinned Weighted Histogram Analysis Method (UWHAM)
Description: A method for estimating log-normalizing constants (or free energies) and expectations from multiple distributions (such as multiple generalized ensembles).
Author: Zhiqiang Tan and Emilio Gallicchio
Maintainer: Zhiqiang Tan <ztan@stat.rutgers.edu>

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Package RAthena updated to version 2.6.0 with previous version 2.5.1 dated 2022-01-26

Title: Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Description: Designed to be compatible with the R package 'DBI' (Database Interface) when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>. To do this 'Python' 'Boto3' Software Development Kit ('SDK') <https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>

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Package porridge updated to version 0.3.1 with previous version 0.3.0 dated 2022-01-08

Title: Ridge-Type Penalized Estimation of a Potpourri of Models
Description: The name of the package is derived from the French, 'pour' ridge, and provides functionality for ridge-type estimation of a potpourri of models. Currently, this estimation concerns that of various Gaussian graphical models from different study designs. Among others it considers the regular Gaussian graphical model and a mixture of such models. The porridge-package implements the estimation of the former either from i) data with replicated observations by penalized loglikelihood maximization using the regular ridge penalty on the parameters (van Wieringen, Chen, 2021) or ii) from non-replicated data by means of either a ridge estimator with multiple shrinkage targets (as presented in van Wieringen et al. 2020, <doi:10.1016/j.jmva.2020.104621>) or the generalized ridge estimator that allows for both the inclusion of quantitative and qualitative prior information on the precision matrix via element-wise penalization and shrinkage (van Wieringen, 2019, <doi:10.1080/10618600.2019.1604374>). Additionally, the porridge-package facilitates the ridge penalized estimation of a mixture of Gaussian graphical models (Aflakparast et al., 2018). On another note, the package also includes functionality for ridge-type estimation of the generalized linear model (as presented in van Wieringen, Binder, 2022, <doi:10.1080/10618600.2022.2035231>).
Author: Wessel N. van Wieringen [aut, cre] , Mehran Aflakparast [ctb]
Maintainer: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>

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Package iWeigReg updated to version 1.1 with previous version 1.0 dated 2013-02-25

Title: Improved Methods for Causal Inference and Missing Data Problems
Description: Improved methods based on inverse probability weighting and outcome regression for causal inference and missing data problems.
Author: Zhiqiang Tan and Heng Shu
Maintainer: Zhiqiang Tan <ztan@stat.rutgers.edu>

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Package frscore updated to version 0.2.0 with previous version 0.1.1 dated 2022-01-09

Title: Functions for Calculating Fit-Robustness of CNA-Solutions
Description: Functions for automatically performing a reanalysis series on a data set using CNA, and for calculating the fit-robustness of the resulting models, as described in Parkkinen and Baumgartner (2021) <doi:10.1177/0049124120986200>.
Author: Veli-Pekka Parkkinen [aut, cre, cph], Michael Baumgartner [aut, cph], Mathias Ambuehl [ctb]
Maintainer: Veli-Pekka Parkkinen <parkkinenv@gmail.com>

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Package tidyseurat updated to version 0.5.3 with previous version 0.5.1 dated 2022-02-03

Title: Brings Seurat to the Tidyverse
Description: It creates an invisible layer that allow to see the 'Seurat' object as tibble and interact seamlessly with the tidyverse.
Author: Stefano Mangiola [aut, cre], Maria Doyle [ctb]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>

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Package tidyquant updated to version 1.0.4 with previous version 1.0.3 dated 2021-03-05

Title: Tidy Quantitative Financial Analysis
Description: Bringing business and financial analysis to the 'tidyverse'. The 'tidyquant' package provides a convenient wrapper to various 'xts', 'zoo', 'quantmod', 'TTR' and 'PerformanceAnalytics' package functions and returns the objects in the tidy 'tibble' format. The main advantage is being able to use quantitative functions with the 'tidyverse' functions including 'purrr', 'dplyr', 'tidyr', 'ggplot2', 'lubridate', etc. See the 'tidyquant' website for more information, documentation and examples.
Author: Matt Dancho [aut, cre], Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>

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Package noctua updated to version 2.6.0 with previous version 2.5.1 dated 2022-01-26

Title: Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI' Interface)
Description: Designed to be compatible with the 'R' package 'DBI' (Database Interface) when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>. To do this the 'R' 'AWS' Software Development Kit ('SDK') 'paws' <https://github.com/paws-r/paws> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>

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Package micEconAids updated to version 0.6-20 with previous version 0.6-18 dated 2017-03-16

Title: Demand Analysis with the Almost Ideal Demand System (AIDS)
Description: Functions and tools for analysing consumer demand with the Almost Ideal Demand System (AIDS) suggested by Deaton and Muellbauer (1980).
Author: Arne Henningsen
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>

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Package mapbayr updated to version 0.7.0 with previous version 0.6.0 dated 2022-02-18

Title: MAP-Bayesian Estimation of PK Parameters
Description: Performs maximum a posteriori Bayesian estimation of individual pharmacokinetic parameters from a model defined in `mrgsolve`, typically for model-based therapeutic drug monitoring. Internally computes an objective function value from model and data, performs optimization and returns predictions in a convenient format.
Author: Felicien Le Louedec [aut, cre] , Kyle T Baron [ctb]
Maintainer: Felicien Le Louedec <lelouedec.felicien@iuct-oncopole.fr>

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Package EpiInvert updated to version 0.1.1 with previous version 0.1.0 dated 2022-05-18

Title: Estimation of Time Varying Reproduction Numbers and Restored Incidence Curves Using Variational Techniques
Description: Estimation, by inverting a renewal equation, of time-varying reproduction numbers and restored incidence curves with festive days and weekly biases corrected as described in Alvarez et al. (2021) <doi:10.1073/pnas.2105112118> and Alvarez et al. (2022) <doi:10.3390/biology11040540>.
Author: Luis Alvarez [aut, cre] , Jean-David Morel [ctb] , Jean-Michel Morel [ctb]
Maintainer: Luis Alvarez <lalvarez@ulpgc.es>

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Package adiv updated to version 2.1.2 with previous version 2.1.1 dated 2021-09-27

Title: Analysis of Diversity
Description: Functions, data sets and examples for the calculation of various indices of biodiversity including species, functional and phylogenetic diversity. Part of the indices are expressed in terms of equivalent numbers of species. The package also provides ways to partition biodiversity across spatial or temporal scales (alpha, beta, gamma diversities). In addition to the quantification of biodiversity, ordination approaches are available which rely on diversity indices and allow the detailed identification of species, functional or phylogenetic differences between communities.
Author: Sandrine Pavoine
Maintainer: Sandrine Pavoine <sandrine.pavoine@mnhn.fr>

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Package tidytransit updated to version 1.3.1 with previous version 1.3.0 dated 2022-01-31

Title: Read, Validate, Analyze, and Map GTFS Feeds
Description: Read General Transit Feed Specification (GTFS) zipfiles into a list of R dataframes. Perform validation of the data structure against the specification. Analyze the headways and frequencies at routes and stops. Create maps and perform spatial analysis on the routes and stops. Please see the GTFS documentation here for more detail: <https://gtfs.org/>.
Author: Flavio Poletti [aut, cre], Daniel Herszenhut [aut] , Mark Padgham [aut], Tom Buckley [aut], Danton Noriega-Goodwin [aut], Angela Li [ctb], Elaine McVey [ctb], Charles Hans Thompson [ctb], Michael Sumner [ctb], Patrick Hausmann [ctb], Bob Rudis [ctb], [...truncated...]
Maintainer: Flavio Poletti <flavio.poletti@hotmail.ch>

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Package permutes updated to version 2.4 with previous version 2.3.2 dated 2021-12-16

Title: Permutation Tests for Time Series Data
Description: Helps you determine the analysis window to use when analyzing densely-sampled time-series data, such as EEG data, using permutation testing (Maris & Oostenveld, 2007) <doi:10.1016/j.jneumeth.2007.03.024>. These permutation tests can help identify the timepoints where significance of an effect begins and ends, and the results can be plotted in various types of heatmap for reporting. Mixed-effects models are supported using an implementation of the approach by Lee & Braun (2012) <doi:10.1111/j.1541-0420.2011.01675.x>.
Author: Cesko C. Voeten [aut, cre]
Maintainer: Cesko C. Voeten <cvoeten@gmail.com>

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Package Haplin updated to version 7.3.0 with previous version 7.2.3 dated 2020-09-07

Title: Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes
Description: Performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. 'Haplin' estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. 'Haplin' also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. 'Haplin' allows special models, like X-inactivation, to be fitted on the X-chromosome. A GxE analysis allows testing interactions between environment and all estimated genetic effects. The models were originally described in "Gjessing HK and Lie RT. Case-parent triads: Estimating single- and double-dose effects of fetal and maternal disease gene haplotypes. Annals of Human Genetics (2006) 70, pp. 382-396".
Author: Hakon K. Gjessing [aut, cre], Miriam Gjerdevik [ctb] , Julia Romanowska [ctb] , Oivind Skare [ctb]
Maintainer: Hakon K. Gjessing <hakon.gjessing@uib.no>

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