Mon, 04 Nov 2024

Package spatstat.univar updated to version 3.1-1 with previous version 3.0-1 dated 2024-09-05

Title: One-Dimensional Probability Distribution Support for the 'spatstat' Family
Description: Estimation of one-dimensional probability distributions including kernel density estimation, weighted empirical cumulative distribution functions, Kaplan-Meier and reduced-sample estimators for right-censored data, heat kernels, kernel properties, quantiles and integration.
Author: Adrian Baddeley [aut, cre, cph] , Tilman M. Davies [aut, ctb, cph] , Martin L. Hazelton [aut, ctb, cph] , Ege Rubak [aut, cph] , Rolf Turner [aut, cph] , Greg McSwiggan [ctb, cph]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

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Package glmertree updated to version 0.2-6 with previous version 0.2-5 dated 2024-06-28

Title: Generalized Linear Mixed Model Trees
Description: Recursive partitioning based on (generalized) linear mixed models (GLMMs) combining lmer()/glmer() from 'lme4' and lmtree()/glmtree() from 'partykit'. The fitting algorithm is described in more detail in Fokkema, Smits, Zeileis, Hothorn & Kelderman (2018; <DOI:10.3758/s13428-017-0971-x>). For detecting and modeling subgroups in growth curves with GLMM trees see Fokkema & Zeileis (2024; <DOI:10.3758/s13428-024-02389-1>).
Author: Marjolein Fokkema [aut, cre] , Achim Zeileis [aut]
Maintainer: Marjolein Fokkema <M.Fokkema@fsw.leidenuniv.nl>

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Package soilDB updated to version 2.8.5 with previous version 2.8.4 dated 2024-08-17

Title: Soil Database Interface
Description: A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.
Author: Dylan Beaudette [aut], Jay Skovlin [aut], Stephen Roecker [aut], Andrew Brown [aut, cre]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>

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Package isotracer updated to version 1.1.7 with previous version 1.1.6 dated 2024-05-15

Title: Isotopic Tracer Analysis Using MCMC
Description: Implements Bayesian models to analyze data from tracer addition experiments. The implemented method was originally described in the article "A New Method to Reconstruct Quantitative Food Webs and Nutrient Flows from Isotope Tracer Addition Experiments" by López-Sepulcre et al. (2020) <doi:10.1086/708546>.
Author: Andres Lopez-Sepulcre [aut] , Matthieu Bruneaux [aut, cre]
Maintainer: Matthieu Bruneaux <matthieu.bruneaux@gmail.com>

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Package fable updated to version 0.4.1 with previous version 0.4.0 dated 2024-09-24

Title: Forecasting Models for Tidy Time Series
Description: Provides a collection of commonly used univariate and multivariate time series forecasting models including automatically selected exponential smoothing (ETS) and autoregressive integrated moving average (ARIMA) models. These models work within the 'fable' framework provided by the 'fabletools' package, which provides the tools to evaluate, visualise, and combine models in a workflow consistent with the tidyverse.
Author: Mitchell O'Hara-Wild [aut, cre], Rob Hyndman [aut], Earo Wang [aut], Gabriel Caceres [ctb] , Christoph Bergmeir [ctb] , Tim-Gunnar Hensel [ctb], Timothy Hyndman [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>

Diff between fable versions 0.4.0 dated 2024-09-24 and 0.4.1 dated 2024-11-04

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Package csvread updated to version 1.2.3 with previous version 1.2.2 dated 2023-12-11

Title: Fast Specialized CSV File Loader
Description: Functions for loading large (10M+ lines) CSV and other delimited files, similar to read.csv, but typically faster and using less memory than the standard R loader. While not entirely general, it covers many common use cases when the types of columns in the CSV file are known in advance. In addition, the package provides a class 'int64', which represents 64-bit integers exactly when reading from a file. The latter is useful when working with 64-bit integer identifiers exported from databases. The CSV file loader supports common column types including 'integer', 'double', 'string', and 'int64', leaving further type transformations to the user.
Author: Sergei Izrailev [aut, cre]
Maintainer: Sergei Izrailev <sizrailev@jabiruventures.com>

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Package WeightedTreemaps updated to version 0.1.3 with previous version 0.1.2 dated 2024-01-09

Title: Generate and Plot Voronoi or Sunburst Treemaps from Hierarchical Data
Description: Treemaps are a visually appealing graphical representation of numerical data using a space-filling approach. A plane or 'map' is subdivided into smaller areas called cells. The cells in the map are scaled according to an underlying metric which allows to grasp the hierarchical organization and relative importance of many objects at once. This package contains two different implementations of treemaps, Voronoi treemaps and Sunburst treemaps. The Voronoi treemap function subdivides the plot area in polygonal cells according to the highest hierarchical level, then continues to subdivide those parental cells on the next lower hierarchical level, and so on. The Sunburst treemap is a computationally less demanding treemap that does not require iterative refinement, but simply generates circle sectors that are sized according to predefined weights. The Voronoi tesselation is based on functions from Paul Murrell (2012) <https://www.stat.auckland.ac.nz/~paul/Reports/VoronoiTreemap/voronoi [...truncated...]
Author: Michael Jahn [aut, cre] , David Leslie [aut], Ahmadou Dicko [aut] , Paul Murrell [aut, cph]
Maintainer: Michael Jahn <jahn@mpusp.mpg.de>

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Package OpenSpecy updated to version 1.4.0 with previous version 1.2.0 dated 2024-09-13

Title: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra
Description: Raman and (FT)IR spectral analysis tool for plastic particles and other environmental samples (Cowger et al. 2021, <doi:10.1021/acs.analchem.1c00123>). With read_any(), Open Specy provides a single function for reading individual, batch, or map spectral data files like .asp, .csv, .jdx, .spc, .spa, .0, and .zip. process_spec() simplifies processing spectra, including smoothing, baseline correction, range restriction and flattening, intensity conversions, wavenumber alignment, and min-max normalization. Spectra can be identified in batch using an onboard reference library (Cowger et al. 2020, <doi:10.1177/0003702820929064>) using match_spec(). A Shiny app is available via run_app() or online at <https://openanalysis.org/openspecy/>.
Author: Win Cowger [cre, aut, dtc] , Zacharias Steinmetz [aut] , Hazel Vaquero [aut] , Nick Leong [aut] , Andrea Faltynkova [aut, dtc] , Hannah Sherrod [aut] , Andrew B Gray [ctb] , Hannah Hapich [ctb] , Jennifer Lynch [ctb, dtc] , Hannah De Frond [ctb, dtc] [...truncated...]
Maintainer: Win Cowger <wincowger@gmail.com>

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Package CORElearn updated to version 1.57.3.1 with previous version 1.57.3 dated 2022-11-18

Title: Classification, Regression and Feature Evaluation
Description: A suite of machine learning algorithms written in C++ with the R interface contains several learning techniques for classification and regression. Predictive models include e.g., classification and regression trees with optional constructive induction and models in the leaves, random forests, kNN, naive Bayes, and locally weighted regression. All predictions obtained with these models can be explained and visualized with the 'ExplainPrediction' package. This package is especially strong in feature evaluation where it contains several variants of Relief algorithm and many impurity based attribute evaluation functions, e.g., Gini, information gain, MDL, and DKM. These methods can be used for feature selection or discretization of numeric attributes. The OrdEval algorithm and its visualization is used for evaluation of data sets with ordinal features and class, enabling analysis according to the Kano model of customer satisfaction. Several algorithms support parallel multithreaded executi [...truncated...]
Author: Marko Robnik-Sikonja [aut, cre], Petr Savicky [aut]
Maintainer: Marko Robnik-Sikonja <marko.robnik@fri.uni-lj.si>

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Package AdverseEvents updated to version 0.0.3 with previous version 0.0.2 dated 2024-10-28

Title: 'shiny' Application for Adverse Event Analysis of 'OnCore' Data
Description: An application for analysis of Adverse Events, as described in Chen, et al., (2023) <doi:10.3390/cancers15092521>. The required data for the application includes demographics, follow up, adverse event, drug administration and optional tumor measurement data. The app can produce swimmers plots of adverse events, Kaplan-Meier plots and Cox Proportional Hazards model results for the association of adverse event biomarkers and overall survival and progression free survival. The adverse event biomarkers include occurrence of grade 3, low grade (1-2), and treatment related adverse events. Plots and tables of results are downloadable.
Author: Z Thompson [aut, cre], A Obermayer [aut], DT Chen [aut]
Maintainer: Z Thompson <zachary.thompson@moffitt.org>

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Package rBeta2009 updated to version 1.0.1 with previous version 1.0 dated 2012-03-01

Title: The Beta Random Number and Dirichlet Random Vector Generating Functions
Description: Contains functions to generate random numbers from the beta distribution and random vectors from the Dirichlet distribution.
Author: Ching-Wei Cheng [aut, cre], Ying-Chao Hung [aut], Narayanaswamy Balakrishnan [aut]
Maintainer: Ching-Wei Cheng <aks43725@gmail.com>

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Package StepReg updated to version 1.5.5 with previous version 1.5.4 dated 2024-10-12

Title: Stepwise Regression Analysis
Description: The stepwise regression analysis is a statistical technique used to identify a subset of predictor variables essential for constructing predictive models. This package performs stepwise regression analysis across various regression models such as linear, logistic, Cox proportional hazards, Poisson, Gamma, and negative binomial regression. It incorporates diverse stepwise regression algorithms like forward selection, backward elimination, and bidirectional elimination alongside the best subset method. Additionally, it offers a wide range of selection criteria, including Akaike Information Criterion (AIC), Sawa Bayesian Information Criterion (BIC), and Significance Levels (SL). We validated the output accuracy of StepReg using public datasets within the SAS software environment. To facilitate efficient model comparison and selection, StepReg allows for multiple strategies and selection metrics to be executed in a single function call. Moreover, StepReg integrates a Shiny application for [...truncated...]
Author: Junhui Li [cre] , Junhui Li [aut], Kai Hu [aut], Xiaohuan Lu [aut], Kun Cheng [ctb], Sushmita N Nayak [ctb], Cesar Bautista Sotelo [ctb], Michael A Lodato [ctb], Robert H Brown [ctb], Wenxin Liu [aut], Lihua Julie Zhu [aut]
Maintainer: Junhui Li <junhui.li11@umassmed.edu>

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Package redatam updated to version 2.0.2 with previous version 2.0.0 dated 2024-10-21

Title: Import 'REDATAM' Files
Description: Read 'REDATAM' microdata exported into R native format (RDS). This is based on the Open Redatam initiative that provides a set of tools to read 'REDATAM' files and convert them into open formats.
Author: Mauricio Vargas Sepulveda [aut, cre] , Lital Barkai [aut]
Maintainer: Mauricio Vargas Sepulveda <m.sepulveda@mail.utoronto.ca>

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Package Keng updated to version 2024.11.02 with previous version 2024.10.16 dated 2024-10-17

Title: Knock Errors Off Nice Guesses
Description: Miscellaneous functions and data used in Qingyao's psychological research and teaching. Keng currently could test the significance and compute the cut-off values of Pearson's r without raw data. Keng could also compare lm()'s fitted outputs using R-squared and PRE (Proportional Reduction in Error, also called partial R-squared or partial Eta-squared).
Author: Qingyao Zhang [aut, cre]
Maintainer: Qingyao Zhang <qingyaozhang@outlook.com>

Diff between Keng versions 2024.10.16 dated 2024-10-17 and 2024.11.02 dated 2024-11-04

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Package salad updated to version 1.1 with previous version 1.0 dated 2024-06-24

Title: Simple Automatic Differentiation
Description: Handles both vector and matrices, using a flexible S4 class for automatic differentiation. The method used is forward automatic differentiation. Many functions and methods have been defined, so that in most cases, functions written without automatic differentiation in mind can be used without change.
Author: Herve Perdry [aut, cre]
Maintainer: Herve Perdry <herve.perdry@universite-paris-saclay.fr>

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Package mvtnorm updated to version 1.3-2 with previous version 1.3-1 dated 2024-09-03

Title: Multivariate Normal and t Distributions
Description: Computes multivariate normal and t probabilities, quantiles, random deviates, and densities. Log-likelihoods for multivariate Gaussian models and Gaussian copulae parameterised by Cholesky factors of covariance or precision matrices are implemented for interval-censored and exact data, or a mix thereof. Score functions for these log-likelihoods are available. A class representing multiple lower triangular matrices and corresponding methods are part of this package.
Author: Alan Genz [aut], Frank Bretz [aut], Tetsuhisa Miwa [aut], Xuefei Mi [aut], Friedrich Leisch [ctb], Fabian Scheipl [ctb], Bjoern Bornkamp [ctb] , Martin Maechler [ctb] , Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

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Package wbs updated to version 1.4.1 with previous version 1.4 dated 2019-05-14

Title: Wild Binary Segmentation for Multiple Change-Point Detection
Description: Provides efficient implementation of the Wild Binary Segmentation and Binary Segmentation algorithms for estimation of the number and locations of multiple change-points in the piecewise constant function plus Gaussian noise model.
Author: Rafal Baranowski [aut, cre], Piotr Fryzlewicz [aut]
Maintainer: Rafal Baranowski <package_maintenance@rbaranowski.com>

Diff between wbs versions 1.4 dated 2019-05-14 and 1.4.1 dated 2024-11-04

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Package simctest updated to version 2.6.1 with previous version 2.6 dated 2019-11-04

Title: Safe Implementation of Monte Carlo Tests
Description: Algorithms for the implementation and evaluation of Monte Carlo tests, as well as for their use in multiple testing procedures.
Author: Axel Gandy [aut, cre], Patrick Rubin-Delanchy [ctb], Georg Hahn [ctb], Dong Ding [ctb]
Maintainer: Axel Gandy <a.gandy@imperial.ac.uk>

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Package RRF updated to version 1.9.4.1 with previous version 1.9.4 dated 2022-05-30

Title: Regularized Random Forest
Description: Feature Selection with Regularized Random Forest. This package is based on the 'randomForest' package by Andy Liaw. The key difference is the RRF() function that builds a regularized random forest. Fortran original by Leo Breiman and Adele Cutler, R port by Andy Liaw and Matthew Wiener, Regularized random forest for classification by Houtao Deng, Regularized random forest for regression by Xin Guan. Reference: Houtao Deng (2013) <doi:10.48550/arXiv.1306.0237>.
Author: Houtao Deng [aut, cre], Xin Guan [aut], Andy Liaw [aut], Leo Breiman [aut], Adele Cutler [aut]
Maintainer: Houtao Deng <softwaredeng@gmail.com>

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Package poilog updated to version 0.4.2.1 with previous version 0.4.2 dated 2022-10-13

Title: Poisson Lognormal and Bivariate Poisson Lognormal Distribution
Description: Functions for obtaining the density, random deviates and maximum likelihood estimates of the Poisson lognormal distribution and the bivariate Poisson lognormal distribution.
Author: Vidar Grotan [aut, cre], Steinar Engen [aut]
Maintainer: Vidar Grotan <vidar.grotan@ntnu.no>

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Package gremlin updated to version 1.1.0 with previous version 1.0.1 dated 2020-06-25

Title: Mixed-Effects REML Incorporating Generalized Inverses
Description: Fit linear mixed-effects models using restricted (or residual) maximum likelihood (REML) and with generalized inverse matrices to specify covariance structures for random effects. In particular, the package is suited to fit quantitative genetic mixed models, often referred to as 'animal models'. Implements the average information algorithm as the main tool to maximize the restricted log-likelihood, but with other algorithms available.
Author: Matthew Wolak [cre, aut]
Maintainer: Matthew Wolak <matthewwolak@gmail.com>

Diff between gremlin versions 1.0.1 dated 2020-06-25 and 1.1.0 dated 2024-11-04

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Package flare updated to version 1.7.0.2 with previous version 1.7.0.1 dated 2022-05-23

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 [aut, cre], Tuo Zhao [aut], Lie Wang [aut], Xiaoming Yuan [aut], Han Liu [aut]
Maintainer: Xingguo Li <xingguo.leo@gmail.com>

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Package barrks updated to version 1.0.1 with previous version 1.0.0 dated 2024-08-26

Title: Calculate Bark Beetle Phenology Using Different Models
Description: Calculate the bark beetle phenology based on raster data or point-related data. There are multiple models implemented for two bark beetle species. The models can be customized and their submodels (onset of infestation, beetle development, diapause initiation, mortality) can be combined. The following models are available in the package: PHENIPS-Clim (first-time release in this package), PHENIPS (Baier et al. 2007) <doi:10.1016/j.foreco.2007.05.020>, RITY (Ogris et al. 2019) <doi:10.1016/j.ecolmodel.2019.108775>, CHAPY (Ogris et al. 2020) <doi:10.1016/j.ecolmodel.2020.109137>, BSO (Jakoby et al. 2019) <doi:10.1111/gcb.14766>, Lange et al. (2008) <doi:10.1007/978-3-540-85081-6_32>, Jönsson et al. (2011) <doi:10.1007/s10584-011-0038-4>. The package may be expanded by models for other bark beetle species in the future.
Author: Jakob Jentschke [aut, cre], FVA BW, Abt. Waldschutz [cph, fnd]
Maintainer: Jakob Jentschke <jakob.jentschke@forst.bwl.de>

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Package ahaz updated to version 1.15.1 with previous version 1.15 dated 2022-05-13

Title: Regularization for Semiparametric Additive Hazards Regression
Description: Computationally efficient procedures for regularized estimation with the semiparametric additive hazards regression model.
Author: Anders Gorst-Rasmussen [aut, cre]
Maintainer: Anders Gorst-Rasmussen <agorstras@gmail.com>

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Package WeibullR.learnr updated to version 0.2 with previous version 0.1.3 dated 2024-07-09

Title: An Interactive Introduction to Life Data Analysis
Description: An interactive introduction to Life Data Analysis that depends on 'WeibullR' by David Silkworth and Jurgen Symynck (2022) <https://CRAN.R-project.org/package=WeibullR>, a R package for Weibull Analysis, and 'learnr' by Garrick Aden-Buie et al. (2023) <https://CRAN.R-project.org/package=learnr>, a framework for building interactive learning modules in R.
Author: Paul Govan [aut, cre, cph]
Maintainer: Paul Govan <paul.govan2@gmail.com>

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Package waveband updated to version 4.7.4 with previous version 4.7.3 dated 2024-05-20

Title: Computes Credible Intervals for Bayesian Wavelet Shrinkage
Description: Computes Bayesian wavelet shrinkage credible intervals for nonparametric regression. The method uses cumulants to derive Bayesian credible intervals for wavelet regression estimates. The first four cumulants of the posterior distribution of the estimates are expressed in terms of the observed data and integer powers of the mother wavelet functions. These powers are closely approximated by linear combinations of wavelet scaling functions at an appropriate finer scale. Hence, a suitable modification of the discrete wavelet transform allows the posterior cumulants to be found efficiently for any data set. Johnson transformations then yield the credible intervals themselves. Barber, S., Nason, G.P. and Silverman, B.W. (2002) <doi:10.1111/1467-9868.00332>.
Author: Stuart Barber [aut], Guy Nason [cre, ctb]
Maintainer: Guy Nason <g.nason@imperial.ac.uk>

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Package bayesRecon updated to version 0.3.2 with previous version 0.3.1 dated 2024-08-28

Title: Probabilistic Reconciliation via Conditioning
Description: Provides methods for probabilistic reconciliation of hierarchical forecasts of time series. The available methods include analytical Gaussian reconciliation (Corani et al., 2021) <doi:10.1007/978-3-030-67664-3_13>, MCMC reconciliation of count time series (Corani et al., 2024) <doi:10.1016/j.ijforecast.2023.04.003>, Bottom-Up Importance Sampling (Zambon et al., 2024) <doi:10.1007/s11222-023-10343-y>, methods for the reconciliation of mixed hierarchies (Mix-Cond and TD-cond) (Zambon et al., 2024. The 40th Conference on Uncertainty in Artificial Intelligence, accepted).
Author: Dario Azzimonti [aut, cre] , Nicolo Rubattu [aut] , Lorenzo Zambon [aut] , Giorgio Corani [aut]
Maintainer: Dario Azzimonti <dario.azzimonti@gmail.com>

Diff between bayesRecon versions 0.3.1 dated 2024-08-28 and 0.3.2 dated 2024-11-04

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 bayesRecon-0.3.2/bayesRecon/NEWS.md                                                                          |    8 
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Package waldo updated to version 0.6.0 with previous version 0.5.3 dated 2024-08-23

Title: Find Differences Between R Objects
Description: Compare complex R objects and reveal the key differences. Designed particularly for use in testing packages where being able to quickly isolate key differences makes understanding test failures much easier.
Author: Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>

Diff between waldo versions 0.5.3 dated 2024-08-23 and 0.6.0 dated 2024-11-04

 DESCRIPTION                                 |   13 +-
 MD5                                         |   36 +++----
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 man/compare.Rd                              |    2 
 tests/testthat/_snaps/compare-data-frame.md |    5 
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 21 files changed, 380 insertions(+), 135 deletions(-)

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Package NSM3 updated to version 1.19 with previous version 1.18 dated 2023-09-04

Title: Functions and Datasets to Accompany Hollander, Wolfe, and Chicken - Nonparametric Statistical Methods, Third Edition
Description: Designed to replace the tables which were in the back of the first two editions of Hollander and Wolfe - Nonparametric Statistical Methods. Exact procedures are performed when computationally possible. Monte Carlo and Asymptotic procedures are performed otherwise. For those procedures included in the base packages, our code simply provides a wrapper to standardize the output with the other procedures in the package.
Author: Grant Schneider [aut, cre], Eric Chicken [aut], Rachel Becvarik [aut]
Maintainer: Grant Schneider <gschneidz@gmail.com>

Diff between NSM3 versions 1.18 dated 2023-09-04 and 1.19 dated 2024-11-04

 DESCRIPTION   |   25 ++++++++--
 MD5           |    6 +-
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 4 files changed, 68 insertions(+), 104 deletions(-)

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Package hydroTSM updated to version 0.7-0.1 with previous version 0.7-0 dated 2024-01-18

Title: Time Series Management and Analysis for Hydrological Modelling
Description: S3 functions for management, analysis, interpolation and plotting of time series used in hydrology and related environmental sciences. In particular, this package is highly oriented to hydrological modelling tasks. The focus of this package has been put in providing a collection of tools useful for the daily work of hydrologists (although an effort was made to optimise each function as much as possible, functionality has had priority over speed). Bugs / comments / questions / collaboration of any kind are very welcomed, and in particular, datasets that can be included in this package for academic purposes.
Author: Mauricio Zambrano-Bigiarini [aut, cre, cph]
Maintainer: Mauricio Zambrano-Bigiarini <mzb.devel@gmail.com>

Diff between hydroTSM versions 0.7-0 dated 2024-01-18 and 0.7-0.1 dated 2024-11-04

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Package hydroGOF updated to version 0.6-0.1 with previous version 0.6-0 dated 2024-05-08

Title: Goodness-of-Fit Functions for Comparison of Simulated and Observed Hydrological Time Series
Description: S3 functions implementing both statistical and graphical goodness-of-fit measures between observed and simulated values, mainly oriented to be used during the calibration, validation, and application of hydrological models. Missing values in observed and/or simulated values can be removed before computations. Comments / questions / collaboration of any kind are very welcomed.
Author: Mauricio Zambrano-Bigiarini [aut, cre, cph]
Maintainer: Mauricio Zambrano-Bigiarini <mzb.devel@gmail.com>

Diff between hydroGOF versions 0.6-0 dated 2024-05-08 and 0.6-0.1 dated 2024-11-04

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Package httr2 updated to version 1.0.6 with previous version 1.0.5 dated 2024-09-26

Title: Perform HTTP Requests and Process the Responses
Description: Tools for creating and modifying HTTP requests, then performing them and processing the results. 'httr2' is a modern re-imagining of 'httr' that uses a pipe-based interface and solves more of the problems that API wrapping packages face.
Author: Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd], Maximilian Girlich [ctb]
Maintainer: Hadley Wickham <hadley@posit.co>

Diff between httr2 versions 1.0.5 dated 2024-09-26 and 1.0.6 dated 2024-11-04

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

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2020-04-03 1.0.4

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Package physiology (with last version 1.2.1) was removed from CRAN

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

2018-11-28 1.2.1
2018-07-16 1.0.1
2015-01-06 0.2.2

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Package orcutt (with last version 2.3) was removed from CRAN

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2018-09-27 2.3
2017-10-23 2.2
2017-04-09 2.1
2017-01-28 2.0
2012-10-15 1.1
2012-09-15 1.0

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Package maraca (with last version 0.7) was removed from CRAN

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2024-03-18 0.7
2023-10-24 0.6
2023-09-06 0.5.1

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Package neuronorm (with last version 1.0.2) was removed from CRAN

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2022-09-23 1.0.2

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Package SecDim (with last version 3.2) was removed from CRAN

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2023-05-20 3.2
2022-05-25 2.2
2022-05-02 1.3

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Package Thermistor (with last version 1.1.0) was removed from CRAN

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2024-04-05 1.1.0

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Package cbioportalR (with last version 1.1.0) was removed from CRAN

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2023-10-05 1.1.0
2022-08-29 1.0.1
2022-08-10 1.0.0

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Package clusterCons (with last version 1.2) was removed from CRAN

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2022-02-22 1.2

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Package hansard (with last version 0.8.0) was removed from CRAN

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2019-11-13 0.8.0
2019-09-08 0.7.1
2019-05-21 0.7.0
2019-01-10 0.6.3
2018-03-02 0.6.0
2017-10-09 0.5.5
2017-08-13 0.5.2
2017-07-10 0.5.0
2017-06-05 0.4.6
2017-03-24 0.4.0
2016-12-13 0.3.4
2016-11-12 0.2.5

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Package idmodelr (with last version 0.4.0) was removed from CRAN

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2022-09-02 0.4.0
2020-06-11 0.3.2
2019-09-10 0.3.1
2019-08-01 0.3.0

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Package card (with last version 0.1.0) was removed from CRAN

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2020-09-03 0.1.0

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2023-02-08 0.3.0

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Package PRISMAstatement (with last version 1.1.1) was removed from CRAN

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2019-05-08 1.1.1
2018-08-08 1.0.4
2018-08-04 1.0.3
2018-07-19 1.0.2
2016-10-11 1.0.1

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Package pmlbr updated to version 0.2.2 with previous version 0.2.1 dated 2023-09-28

Title: Interface to the Penn Machine Learning Benchmarks Data Repository
Description: Check available classification and regression data sets from the PMLB repository and download them. The PMLB repository (<https://github.com/EpistasisLab/pmlbr>) contains a curated collection of data sets for evaluating and comparing machine learning algorithms. These data sets cover a range of applications, and include binary/multi-class classification problems and regression problems, as well as combinations of categorical, ordinal, and continuous features. There are currently over 150 datasets included in the PMLB repository.
Author: Trang Le [aut, cre] , makeyourownmaker [aut] , Jason Moore [aut] , University of Pennsylvania [cph]
Maintainer: Trang Le <grixor@gmail.com>

Diff between pmlbr versions 0.2.1 dated 2023-09-28 and 0.2.2 dated 2024-11-04

 DESCRIPTION |    8 +++---
 MD5         |    6 ++--
 NEWS.md     |    3 ++
 R/pmlb.R    |   73 +++++++++++++++++++++++++++++++++++++++++++++++-------------
 4 files changed, 68 insertions(+), 22 deletions(-)

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New package sicure with initial version 0.1.0
Package: sicure
Title: Single-Index Mixture Cure Models
Version: 0.1.0
Description: Single-index mixture cure models allow estimating the probability of cure and the latency depending on a vector (or functional) covariate, avoiding the curse of dimensionality. The vector of parameters that defines the model can be estimated by maximum likelihood. A nonparametric estimator for the conditional density of the susceptible population is provided. For more details, see Piñeiro-Lamas (2024) (<https://ruc.udc.es/dspace/handle/2183/37035>).
License: GPL (>= 2)
Encoding: UTF-8
Imports: caTools, doBy, fda, npcure, StatMatch, stats
NeedsCompilation: no
Packaged: 2024-10-31 14:11:41 UTC; Bea
Author: Beatriz Pineiro-Lamas [aut, cre] , Ana Lopez-Cheda [aut], Ricardo Cao [aut]
Maintainer: Beatriz Pineiro-Lamas <b.pineiro.lamas@udc.es>
Repository: CRAN
Date/Publication: 2024-11-04 12:30:03 UTC

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Package rmarkdown updated to version 2.29 with previous version 2.28 dated 2024-08-17

Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut], Yihui Xie [aut, cre] , Christophe Dervieux [aut] , Jonathan McPherson [aut], Javier Luraschi [aut], Kevin Ushey [aut], Aron Atkins [aut], Hadley Wickham [aut], Joe Cheng [aut], Winston Chang [aut], Richard Iannone [aut] , Andrew Dun [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between rmarkdown versions 2.28 dated 2024-08-17 and 2.29 dated 2024-11-04

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 15 files changed, 162 insertions(+), 36 deletions(-)

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New package pk.unit.trans with initial version 0.1.0
Package: pk.unit.trans
Title: Achieve Numerical Conversion Between Units Commonly Used in Pharmacokinetics
Version: 0.1.0
Author: Fu Yongchao [aut, cre, cph]
Maintainer: Fu Yongchao <3212418315@qq.com>
Description: Achieve internal conversions of mass units, molar units, and volume units commonly used in pharmacokinetics, as well as conversions between mass units and molar units.
Imports: stringi(>= 1.8.4), maditr (>= 0.8.4)
License: MIT + file LICENSE
Depends: R (>= 4.1.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-10-31 18:43:03 UTC; admin
Repository: CRAN
Date/Publication: 2024-11-04 12:40:02 UTC

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New package ip2whois with initial version 1.0.0
Package: ip2whois
Title: Lookup 'WHOIS' Information for a Particular Domain
Version: 1.0.0
Maintainer: IP2WHOIS <support@ip2whois.com>
Description: Easily implement the checking of 'WHOIS' information for a particular domain. 'IP2WHOIS' supports the query for 1113 Top-level Domains(TLDs) and 634 Country Code Top-level Domains(ccTLDs). To get started with a free API key, you may sign up at here <https://www.ip2whois.com/register>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: reticulate (>= 1.13), jsonlite (>= 1.6)
SystemRequirements: IP2WHOIS Python library <https://github.com/ip2whois/ip2whois-python>
NeedsCompilation: no
Packaged: 2024-10-31 23:24:58 UTC; ooi18
Author: IP2WHOIS [aut, cre]
Repository: CRAN
Date/Publication: 2024-11-04 12:40:06 UTC

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New package ETRep with initial version 0.1.0
Package: ETRep
Title: Analysis of Elliptical Tubes Under the Relative Curvature Condition
Version: 0.1.0
Maintainer: Mohsen Taheri <MohsenTaheriShalmani@gmail.com>
Description: Analysis of elliptical tubes with applications in biological modeling. The package is based on the references: Taheri, M., Pizer, S. M., & Schulz, J. (2024) "The Mean Shape under the Relative Curvature Condition." arXiv <doi:10.48550/arXiv.2404.01043>. Mohsen Taheri Shalmani (2024) "Shape Statistics via Skeletal Structures", PhD Thesis, University of Stavanger, Norway <doi:10.13140/RG.2.2.34500.23685>. Key features include constructing discrete elliptical tubes, calculating transformations, validating structures under the Relative Curvature Condition, computing means, and generating simulations. Supports intrinsic and non-intrinsic mean calculations and transformations, size estimation, plotting, and random sample generation based on a reference tube.
License: MIT + file LICENSE
URL: https://github.com/MohsenTaheriShalmani/Elliptical_Tubes
Depends: R (>= 4.0.0)
Author: Mohsen Taheri [aut, cre]
Encoding: UTF-8
LazyData: true
Imports: rgl, shapes, Morpho, matlib, RiemBase, RSpincalc, rotations, SphericalCubature, Rvcg, fields, Matrix, pracma, truncnorm, ggplot2, reshape2, dplyr, ptinpoly
NeedsCompilation: no
Packaged: 2024-10-31 14:48:12 UTC; mohsentaheri
Repository: CRAN
Date/Publication: 2024-11-04 12:40:13 UTC

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New package dpkg with initial version 0.6.0
Package: dpkg
Title: Create, Stow, and Read Data Packages
Version: 0.6.0
Description: Data frame, tibble, or tbl objects are converted to data package objects using specific metadata labels (name, version, title, homepage, description). A data package object ('dpkg') can be written to disk as a 'parquet' file or released to a 'GitHub' repository. Data package objects can be read into R from online repositories and downloaded files are cached locally across R sessions.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: dplyr, geoarrow, gert, gh, sf, testthat (>= 3.0.0), usethis, withr
URL: https://github.com/cole-brokamp/dpkg, https://cole-brokamp.github.io/dpkg/
BugReports: https://github.com/cole-brokamp/dpkg/issues
Imports: arrow, cli, fs, glue, httr2, rlang, tibble
NeedsCompilation: no
Packaged: 2024-10-31 21:35:51 UTC; cole
Author: Cole Brokamp [aut, cre, cph]
Maintainer: Cole Brokamp <cole@colebrokamp.com>
Repository: CRAN
Date/Publication: 2024-11-04 12:40:09 UTC

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Package CompExpDes updated to version 1.0.5 with previous version 1.0.4 dated 2024-09-26

Title: Computer Experiment Designs
Description: In computer experiments space-filling designs are having great impact. Most popularly used space-filling designs are Uniform designs (UDs), Latin hypercube designs (LHDs) etc. For further references one can see Mckay (1979) <DOI:10.1080/00401706.1979.10489755> and Fang (1980) <https://cir.nii.ac.jp/crid/1570291225616774784>. In this package, we have provided algorithms for generate efficient LHDs and UDs. Here, generated LHDs are efficient as they possess lower value of Maxpro measure, Phi_p value and Maximum Absolute Correlation (MAC) value based on the weightage given to each criterion. On the other hand, the produced UDs are having good space-filling property as they always attain the lower bound of Discrete Discrepancy measure. Further, some useful functions added in this package for adding more value to this package.
Author: Ashutosh Dalal [aut, cre], Cini Varghese [aut, ctb], Rajender Parsad [aut, ctb], Mohd Harun [aut, ctb]
Maintainer: Ashutosh Dalal <ashutosh.dalal97@gmail.com>

Diff between CompExpDes versions 1.0.4 dated 2024-09-26 and 1.0.5 dated 2024-11-04

 DESCRIPTION                 |    6 -
 MD5                         |   36 ++++++-----
 NAMESPACE                   |    5 +
 R/Best_Model.R              |only
 R/LHDs_I.R                  |   12 +--
 R/LHDs_II.R                 |    9 +-
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 R/UDesigns_II.R             |   43 ++++----------
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 man/UDesigns_II.Rd          |   12 +--
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 20 files changed, 187 insertions(+), 198 deletions(-)

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New package NPFD with initial version 1.0.0
Package: NPFD
Title: N-Power Fourier Deconvolution
Version: 1.0.0
Description: Provides tools for non-parametric Fourier deconvolution using the N-Power Fourier Deconvolution (NPFD) method. This package includes methods for density estimation (densprf()) and sample generation (createSample()), enabling users to perform statistical analyses on mixed or replicated data sets.
Depends: R (>= 3.5.0)
Imports: siggenes, KernSmooth, splines, stats, graphics, VGAM
License: GPL-3
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-10-31 09:31:12 UTC; Akin
Author: Akin Anarat [aut, cre]
Maintainer: Akin Anarat <akin.anarat@hhu.de>
Repository: CRAN
Date/Publication: 2024-11-04 11:10:04 UTC

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Package cNORM updated to version 3.4.0 with previous version 3.3.1 dated 2024-10-16

Title: Continuous Norming
Description: A comprehensive toolkit for generating continuous test norms in psychometrics and biometrics, and analyzing model fit. The package offers both distribution-free modeling using Taylor polynomials and parametric modeling using the beta-binomial distribution. Originally developed for achievement tests, it is applicable to a wide range of mental, physical, or other test scores dependent on continuous or discrete explanatory variables. The package provides several advantages: It minimizes deviations from representativeness in subsamples, interpolates between discrete levels of explanatory variables, and significantly reduces the required sample size compared to conventional norming per age group. cNORM enables graphical and analytical evaluation of model fit, accommodates a wide range of scales including those with negative and descending values, and even supports conventional norming. It generates norm tables including confidence intervals. It also includes methods for addressing represent [...truncated...]
Author: Alexandra Lenhard [aut] , Wolfgang Lenhard [cre, aut] , Sebastian Gary [aut], WPS publisher [fnd]
Maintainer: Wolfgang Lenhard <wolfgang.lenhard@uni-wuerzburg.de>

Diff between cNORM versions 3.3.1 dated 2024-10-16 and 3.4.0 dated 2024-11-04

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New package rnnmf with initial version 0.3.0
Package: rnnmf
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Version: 0.3.0
Date: 2024-10-30
License: LGPL-3
Title: Regularized Non-Negative Matrix Factorization
BugReports: https://github.com/shabbychef/rnnmf/issues
Description: A proof of concept implementation of regularized non-negative matrix factorization optimization. A non-negative matrix factorization factors non-negative matrix Y approximately as L R, for non-negative matrices L and R of reduced rank. This package supports such factorizations with weighted objective and regularization penalties. Allowable regularization penalties include L1 and L2 penalties on L and R, as well as non-orthogonality penalties. This package provides multiplicative update algorithms, which are a modification of the algorithm of Lee and Seung (2001) <http://papers.nips.cc/paper/1861-algorithms-for-non-negative-matrix-factorization.pdf>, as well as an additive update derived from that multiplicative update. See also Pav (2004) <doi:10.48550/arXiv.2410.22698>.
Depends: R (>= 3.0.2)
Imports: Matrix
Suggests: testthat, dplyr, ggplot2, scales, viridis, knitr
URL: https://github.com/shabbychef/rnnmf
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-10-31 03:07:08 UTC; spav
Author: Steven E. Pav [aut, cre]
Repository: CRAN
Date/Publication: 2024-11-04 10:40:02 UTC

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New package mcmapper with initial version 0.0.11
Package: mcmapper
Title: Mapping First Moment and C-Statistic to the Parameters of Distributions for Risk
Version: 0.0.11
Description: Provides a series of numerical methods for extracting parameters of distributions for risks based on knowing the expected value and c-statistics (e.g., from a published report on the performance of a risk prediction model). This package implements the methodology described in Sadatsafavi et al (2024) <doi:10.48550/arXiv.2409.09178>. The core of the package is mcmap(), which takes a pair of (mean, c-statistic) and the distribution type requested. This function provides a generic interface to more customized functions (mcmap_beta(), mcmap_logitnorm(), mcmap_probitnorm()) for specific distributions.
License: MIT + file LICENSE
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-10-31 04:23:02 UTC; msafavi
Author: Mohsen Sadatsafavi [aut, cre]
Maintainer: Mohsen Sadatsafavi <mohsen.sadatsafavi@ubc.ca>
Repository: CRAN
Date/Publication: 2024-11-04 10:40:06 UTC

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Package gdtools updated to version 0.4.1 with previous version 0.4.0 dated 2024-08-28

Title: Utilities for Graphical Rendering and Fonts Management
Description: Tools are provided to compute metrics of formatted strings and to check the availability of a font. Another set of functions is provided to support the collection of fonts from 'Google Fonts' in a cache. Their use is simple within 'R Markdown' documents and 'shiny' applications but also with graphic productions generated with the 'ggiraph', 'ragg' and 'svglite' packages or with tabular productions from the 'flextable' package.
Author: David Gohel [aut, cre], Hadley Wickham [aut], Lionel Henry [aut], Jeroen Ooms [aut] , Yixuan Qiu [ctb], R Core Team [cph] , ArData [cph], RStudio [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>

Diff between gdtools versions 0.4.0 dated 2024-08-28 and 0.4.1 dated 2024-11-04

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Package APIS updated to version 2.0.8 with previous version 2.0.7 dated 2024-10-02

Title: Auto-Adaptive Parentage Inference Software Tolerant to Missing Parents
Description: Parentage assignment package. Parentage assignment is performed based on observed average Mendelian transmission probability distributions or Exclusion. The main functions of this package are the function APIS_2n(), APIS_3n() and launch_APIShiny(), which perform parentage assignment.
Author: Julien Roche [aut, cre], Ronan Griot [aut], Mathieu Besson [aut], Francois Allal [aut], Marc Vandeputte [aut], Jonathan D'Ambrosio [aut], Romain Morvezen [aut], Florence Phocas [aut], Sophie Brard-Fudulea [aut], Pierrick Haffray [aut]
Maintainer: Julien Roche <julien.roche@inrae.fr>

Diff between APIS versions 2.0.7 dated 2024-10-02 and 2.0.8 dated 2024-11-04

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Package enrichR (with last version 3.2) was removed from CRAN

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

2023-04-14 3.2
2022-08-10 3.1
2021-02-01 3.0
2019-08-29 2.1
2019-07-25 2.0
2017-04-02 1.0

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Package blockTools (with last version 0.6.5) was removed from CRAN

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

2024-10-19 0.6.5
2023-02-06 0.6.4

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Package autoGO (with last version 0.9.1) was removed from CRAN

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

2023-02-13 0.9.1
2023-01-16 0.9

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Package datagovsgR (with last version 1.0.1) was removed from CRAN

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

2024-06-27 1.0.1
2023-01-15 1.0.0
2022-12-22 0.3.3

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Package secr updated to version 5.1.0 with previous version 5.0.0 dated 2024-10-02

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

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Package fastdid updated to version 1.0.3 with previous version 1.0.2 dated 2024-10-28

Title: Fast Staggered Difference-in-Difference Estimators
Description: A fast and flexible implementation of Callaway and Sant'Anna's (2021)<doi:10.1016/j.jeconom.2020.12.001> staggered Difference-in-Differences (DiD) estimators, 'fastdid' reduces the computation time from hours to seconds, and incorporates extensions such as time-varying covariates and multiple events.
Author: Lin-Tung Tsai [aut, cre, cph], Maxwell Kellogg [ctb], Kuan-Ju Tseng [ctb]
Maintainer: Lin-Tung Tsai <tsaidondon@gmail.com>

Diff between fastdid versions 1.0.2 dated 2024-10-28 and 1.0.3 dated 2024-11-04

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Package EIEntropy updated to version 0.0.1.3 with previous version 0.0.1.2 dated 2024-11-02

Title: Ecological Inference Applying Entropy
Description: Implements two estimations related to the foundations of info metrics applied to ecological inference. These methodologies assess the lack of disaggregated data and provide an approach to obtaining disaggregated territorial-level data. For more details, see the following references: Fernández-Vázquez, E., Díaz-Dapena, A., Rubiera-Morollón, F. et al. (2020) "Spatial Disaggregation of Social Indicators: An Info-Metrics Approach." <doi:10.1007/s11205-020-02455-z>. Díaz-Dapena, A., Fernández-Vázquez, E., Rubiera-Morollón, F., & Vinuela, A. (2021) "Mapping poverty at the local level in Europe: A consistent spatial disaggregation of the AROPE indicator for France, Spain, Portugal and the United Kingdom." <doi:10.1111/rsp3.12379>.
Author: Alberto Diaz-Dapena [aut, cph], Esteban Fernandez-Vazquez [aut, cph], Silvia Maria Franco Anaya [aut, cre, cph]
Maintainer: Silvia Maria Franco Anaya <sfrana@unileon.es>

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Package dhis2r updated to version 0.2.1 with previous version 0.2.0 dated 2024-10-29

Title: Client for the 'DHIS2' Web API
Description: Connect and pull data from a 'DHIS2 (District Health Information Software 2)' instance into R.
Author: Robinson Amanyiraho [cre, aut, cph]
Maintainer: Robinson Amanyiraho <amanyiraho@gmail.com>

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Package changepoint updated to version 2.3 with previous version 2.2.4 dated 2022-11-03

Title: Methods for Changepoint Detection
Description: Implements various mainstream and specialised changepoint methods for finding single and multiple changepoints within data. Many popular non-parametric and frequentist methods are included. The cpt.mean(), cpt.var(), cpt.meanvar() functions should be your first point of call.
Author: Rebecca Killick [aut, cre], Kaylea Haynes [ctb], Harjit Hullait [ctb], Idris Eckley [ths], Paul Fearnhead [ctb, ths], Robin Long [ctb], Jamie Lee [ctr]
Maintainer: Rebecca Killick <r.killick@lancs.ac.uk>

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Package BioPred updated to version 1.0.2 with previous version 1.0.1 dated 2024-06-06

Title: An R Package for Biomarkers Analysis in Precision Medicine
Description: Provides functions for training extreme gradient boosting model using propensity score A-learning and weight-learning methods. For further details, see Liu et al. (2024) <doi:10.1093/bioinformatics/btae592>.
Author: Zihuan Liu [aut, cre], Yan Sun [aut], Xin Huang [aut]
Maintainer: Zihuan Liu <zihuan.liu@abbvie.com>

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