Sun, 06 Apr 2025

Package silp updated to version 1.0.3 with previous version 1.0.2 dated 2025-04-02

Title: Conditional Process Analysis (CPA) via SEM Approach
Description: Utilizes the Reliability-Adjusted Product Indicator (RAPI) method to estimate effects among latent variables, thus allowing for more precise definition and analysis of mediation and moderation models. Our simulation studies reveal that while 'silp' may exhibit instability with smaller sample sizes and lower reliability scores (e.g., N = 100, 'omega' = 0.7), implementing nearest positive definite matrix correction and bootstrap confidence interval estimation can significantly ameliorate this volatility. When these adjustments are applied, 'silp' achieves estimations akin in quality to those derived from LMS. In conclusion, the 'silp' package is a valuable tool for researchers seeking to explore complex relational structures between variables without resorting to commercial software. Cheung et al.(2021)<doi:10.1007/s10869-020-09717-0> Hsiao et al.(2018)<doi:10.1177/0013164416679877>.
Author: Yi-Hsuan Tseng [aut, cre], Po-Hsien Huang [aut]
Maintainer: Yi-Hsuan Tseng <r12227115@g.ntu.edu.tw>

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Package bedr updated to version 1.1.3 with previous version 1.0.7 dated 2019-04-01

Title: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'
Description: Genomic regions processing using open-source command line tools such as 'BEDTools', 'BEDOPS' and 'Tabix'. These tools offer scalable and efficient utilities to perform genome arithmetic e.g indexing, formatting and merging. bedr API enhances access to these tools as well as offers additional utilities for genomic regions processing.
Author: Syed Haider [aut], Daryl Waggott [aut], Emilie Lalonde [ctb], Clement Fung [ctb], Helena Winata [ctb], Dan Knight [ctb], Michael Chirico [ctb], Melinda Luo [ctb], Paul C. Boutros [aut, cre, cph]
Maintainer: Paul C. Boutros <pboutros@mednet.ucla.edu>

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Package asremlPlus updated to version 4.4.48 with previous version 4.4.46 dated 2025-02-16

Title: Augments 'ASReml-R' in Fitting Mixed Models and Packages Generally in Exploring Prediction Differences
Description: Assists in automating the selection of terms to include in mixed models when 'asreml' is used to fit the models. Procedures are available for choosing models that conform to the hierarchy or marginality principle, for fitting and choosing between two-dimensional spatial models using correlation, natural cubic smoothing spline and P-spline models. A history of the fitting of a sequence of models is kept in a data frame. Also used to compute functions and contrasts of, to investigate differences between and to plot predictions obtained using any model fitting function. The content falls into the following natural groupings: (i) Data, (ii) Model modification functions, (iii) Model selection and description functions, (iv) Model diagnostics and simulation functions, (v) Prediction production and presentation functions, (vi) Response transformation functions, (vii) Object manipulation functions, and (viii) Miscellaneous functions (for further details see 'asremlPlus-package' in help). The [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>

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Package bsplus updated to version 0.1.5 with previous version 0.1.4 dated 2022-11-15

Title: Adds Functionality to the R Markdown + Shiny Bootstrap Framework
Description: The Bootstrap framework lets you add some JavaScript functionality to your web site by adding attributes to your HTML tags - Bootstrap takes care of the JavaScript <https://getbootstrap.com/docs/3.3/javascript/>. If you are using R Markdown or Shiny, you can use these functions to create collapsible sections, accordion panels, modals, tooltips, popovers, and an accordion sidebar framework (not described at Bootstrap site). Please note this package was designed for Bootstrap 3.3.
Author: Ian Lyttle [aut, cre] , Alex Shum [ctb], Emerson Berry [ctb]
Maintainer: Ian Lyttle <ijlyttle@me.com>

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Package ExclusionTable updated to version 1.2.0 with previous version 1.1.0 dated 2023-09-21

Title: Creating Tables of Excluded Observations
Description: Instead of counting observations before and after a subset() call, the ExclusionTable() function reports the number before and after each subset() call together with the number of observations that have been excluded. This is especially useful in observational studies for keeping track how many observations have been excluded for each in-/ or exclusion criteria. You just need to provide ExclusionTable() with a dataset and a list of logical filter statements.
Author: Joshua P. Entrop [aut, cre] , Simon Steiger [ctb]
Maintainer: Joshua P. Entrop <joshuaentrop@posteo.de>

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Package tidystats updated to version 0.6.3 with previous version 0.6.2 dated 2024-07-14

Title: Save Output of Statistical Tests
Description: Save the output of statistical tests in an organized file that can be shared with others or used to report statistics in scientific papers.
Author: Willem Sleegers [aut, cre]
Maintainer: Willem Sleegers <w.sleegers@me.com>

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Package bioinactivation updated to version 1.3.0 with previous version 1.2.3 dated 2019-08-01

Title: Mathematical Modelling of (Dynamic) Microbial Inactivation
Description: Functions for modelling microbial inactivation under isothermal or dynamic conditions. The calculations are based on several mathematical models broadly used by the scientific community and industry. Functions enable to make predictions for cases where the kinetic parameters are known. It also implements functions for parameter estimation for isothermal and dynamic conditions. The model fitting capabilities include an Adaptive Monte Carlo method for a Bayesian approach to parameter estimation.
Author: Alberto Garre [aut, cre], Pablo S. Fernandez [aut], Jose A. Egea [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>

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Package TrueSkillThroughTime updated to version 1.0.0 with previous version 0.1.1 dated 2023-04-26

Title: Skill Estimation Based on a Single Bayesian Network
Description: Most estimators implemented by the video game industry cannot obtain reliable initial estimates nor guarantee comparability between distant estimates. TrueSkill Through Time solves all these problems by modeling the entire history of activities using a single Bayesian network allowing the information to propagate correctly throughout the system. This algorithm requires only a few iterations to converge, allowing millions of observations to be analyzed using any low-end computer. Landfried G, Mocskos E (2025). "TrueSkill Through Time: Reliable Initial Skill Estimates and Historical Comparability with Julia, Python, and R." <doi:10.18637/jss.v112.i06>. The core ideas implemented in this project were developed by Dangauthier P, Herbrich R, Minka T, Graepel T (2007). "Trueskill through time: Revisiting the history of chess.".
Author: Gustavo Landfried [aut, cre]
Maintainer: Gustavo Landfried <gustavolandfried@gmail.com>

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Package spphpr updated to version 1.1.4 with previous version 1.0.0 dated 2025-01-08

Title: Spring Phenological Prediction
Description: Predicts the occurrence times (in day-of-year) of spring phenological events. Three methods, including the accumulated degree days (ADD) method, the accumulated days transferred to a standardized temperature (ADTS) method, and the accumulated developmental progress (ADP) method, were used. See Shi et al. (2017a) <doi:10.1016/j.agrformet.2017.04.001> and Shi et al. (2017b) <doi:10.1093/aesa/sax063> for details.
Author: Peijian Shi [aut, cre], Zhenghong Chen [aut], Jing Tan [aut], Brady K. Quinn [aut]
Maintainer: Peijian Shi <pjshi@njfu.edu.cn>

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Package fio updated to version 0.1.6 with previous version 0.1.5 dated 2025-04-02

Title: Friendly Input-Output Analysis
Description: Simplifies the process of importing and managing input-output matrices from 'Microsoft Excel' into R, and provides a suite of functions for analysis. It leverages the 'R6' class for clean, memory-efficient object-oriented programming. Furthermore, all linear algebra computations are implemented in 'Rust' to achieve highly optimized performance.
Author: Alberson da Silva Miranda [aut, cre, cph] , Celso Bissoli Sessa [dtc]
Maintainer: Alberson da Silva Miranda <albersonmiranda@hotmail.com>

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Package discord updated to version 1.2.3 with previous version 1.1.0 dated 2021-07-15

Title: Functions for Discordant Kinship Modeling
Description: Functions for discordant kinship modeling (and other sibling-based quasi-experimental designs). Contains data restructuring functions and functions for generating biometrically informed data for kin pairs. See [Garrison and Rodgers, 2016 <doi:10.1016/j.intell.2016.08.008>], [Sims, Trattner, and Garrison, 2024 <doi:10.3389/fpsyg.2024.1430978>] for empirical examples, and Garrison et al for theoretical work <https://osf.io/zpdwt/>.
Author: S. Mason Garrison [aut, cre, cph] , Jonathan Trattner [aut] , Yoo Ri Hwang [aut], Cermet Ream [ctb]
Maintainer: S. Mason Garrison <garrissm@wfu.edu>

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Package b64 updated to version 0.1.5 with previous version 0.1.4 dated 2025-03-31

Title: Fast and Vectorized Base 64 Engine
Description: Provides a fast, lightweight, and vectorized base 64 engine to encode and decode character and raw vectors as well as files stored on disk. Common base 64 alphabets are supported out of the box including the standard, URL-safe, bcrypt, crypt, 'BinHex', and IMAP-modified UTF-7 alphabets. Custom engines can be created to support unique base 64 encoding and decoding needs.
Author: Josiah Parry [aut, cre] , Etienne Bacher [ctb]
Maintainer: Josiah Parry <josiah.parry@gmail.com>

Diff between b64 versions 0.1.4 dated 2025-03-31 and 0.1.5 dated 2025-04-06

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Package AlgDesign updated to version 1.2.1.2 with previous version 1.2.1.1 dated 2024-09-21

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 [aut], Jerome Braun [cre]
Maintainer: Jerome Braun <jvbraun.statistics@gmail.com>

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Package ir updated to version 0.4.1 with previous version 0.2.1 dated 2022-05-02

Title: Functions to Handle and Preprocess Infrared Spectra
Description: Functions to import and handle infrared spectra (import from '.csv' and Thermo Galactic's '.spc', baseline correction, binning, clipping, interpolating, smoothing, averaging, adding, subtracting, dividing, multiplying, atmospheric correction, 'tidyverse' methods, plotting).
Author: Henning Teickner [aut, cre, cph]
Maintainer: Henning Teickner <henning.teickner@uni-muenster.de>

Diff between ir versions 0.2.1 dated 2022-05-02 and 0.4.1 dated 2025-04-06

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Sat, 05 Apr 2025

Package predhy updated to version 2.1.2 with previous version 2.1.1 dated 2024-05-23

Title: Genomic Prediction of Hybrid Performance
Description: Performs genomic prediction of hybrid performance using eight statistical methods including GBLUP, BayesB, RKHS, PLS, LASSO, EN, LightGBM and XGBoost along with additive and additive-dominance models. Users are able to incorporate parental phenotypic information in all methods based on their specific needs. (Xu S et al(2017) <doi:10.1534/g3.116.038059>; Xu Y et al (2021) <doi: 10.1111/pbi.13458>).
Author: Yang Xu [aut, cre], Guangning Yu [aut], Yanru Cui [aut], Shizhong Xu [aut], Chenwu Xu [aut]
Maintainer: Yang Xu <xuyang_89@126.com>

Diff between predhy versions 2.1.1 dated 2024-05-23 and 2.1.2 dated 2025-04-05

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Package hsphase updated to version 2.0.4 with previous version 2.0.3 dated 2024-02-16

Title: Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data
Description: Identification of recombination events, haplotype reconstruction, sire imputation and pedigree reconstruction using half-sib family SNP data.
Author: Mohammad Ferdosi [aut, cre], Cedric Gondro [aut]
Maintainer: Mohammad Ferdosi <mhferdosi@yahoo.com>

Diff between hsphase versions 2.0.3 dated 2024-02-16 and 2.0.4 dated 2025-04-05

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Package abms updated to version 0.2 with previous version 0.1 dated 2025-03-13

Title: Augmented Bayesian Model Selection for Regression Models
Description: Tools to perform model selection alongside estimation under Linear, Logistic, Negative binomial, Quantile, and Skew-Normal regression. Under the spike-and-slab method, a probability for each possible model is estimated with the posterior mean, credibility interval, and standard deviation of coefficients and parameters under the most probable model.
Author: Francisco Segovia [aut, cre], Luis Gutierres [aut], Ramses Mena [aut]
Maintainer: Francisco Segovia <fasegovia@uc.cl>

Diff between abms versions 0.1 dated 2025-03-13 and 0.2 dated 2025-04-05

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Package volker updated to version 3.1.0 with previous version 3.0.0 dated 2024-12-11

Title: High-Level Functions for Tabulating, Charting and Reporting Survey Data
Description: Craft polished tables and plots in Markdown reports. Simply choose whether to treat your data as counts or metrics, and the package will automatically generate well-designed default tables and plots for you. Boiled down to the basics, with labeling features and simple interactive reports. All functions are 'tidyverse' compatible.
Author: Jakob Juenger [aut, cre, cph] , Henrieke Kotthoff [aut, ctb], Chantal Gaertner [ctb]
Maintainer: Jakob Juenger <jakob.juenger@uni-muenster.de>

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Package abess updated to version 0.4.10 with previous version 0.4.9 dated 2024-09-09

Title: Fast Best Subset Selection
Description: Extremely efficient toolkit for solving the best subset selection problem <https://www.jmlr.org/papers/v23/21-1060.html>. This package is its R interface. The package implements and generalizes algorithms designed in <doi:10.1073/pnas.2014241117> that exploits a novel sequencing-and-splicing technique to guarantee exact support recovery and globally optimal solution in polynomial times for linear model. It also supports best subset selection for logistic regression, Poisson regression, Cox proportional hazard model, Gamma regression, multiple-response regression, multinomial logistic regression, ordinal regression, (sequential) principal component analysis, and robust principal component analysis. The other valuable features such as the best subset of group selection <doi:10.1287/ijoc.2022.1241> and sure independence screening <doi:10.1111/j.1467-9868.2008.00674.x> are also provided.
Author: Jin Zhu [aut, cre] , Zezhi Wang [aut], Liyuan Hu [aut], Junhao Huang [aut], Kangkang Jiang [aut], Yanhang Zhang [aut], Borui Tang [aut], Shiyun Lin [aut], Junxian Zhu [aut], Canhong Wen [aut], Heping Zhang [aut] , Xueqin Wang [aut] , spectra contribu [...truncated...]
Maintainer: Jin Zhu <zhuj37@mail2.sysu.edu.cn>

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Package tinycodet updated to version 0.5.6 with previous version 0.5.4 dated 2025-01-09

Title: Functions to Help in your Coding Etiquette
Description: Adds some functions to help in your coding etiquette. 'tinycodet' primarily focuses on 4 aspects. 1) Safer decimal (in)equality testing, standard-evaluated alternatives to with() and aes(), and other functions for safer coding. 2) A new package import system, that attempts to combine the benefits of using a package without attaching it, with the benefits of attaching a package. 3) Extending the string manipulation capabilities of the 'stringi' R package. 4) Reducing repetitive code. Besides linking to 'Rcpp', 'tinycodet' has only one other dependency, namely 'stringi'.
Author: Tony Wilkes [aut, cre, cph]
Maintainer: Tony Wilkes <tony_a_wilkes@outlook.com>

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Package reporttools updated to version 1.1.4 with previous version 1.1.3 dated 2021-10-12

Title: Generate "LaTeX"" Tables of Descriptive Statistics
Description: These functions are especially helpful when writing reports of data analysis using "Sweave".
Author: Kaspar Rufibach [aut, cre]
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>

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Package AIPW updated to version 0.6.9.2 with previous version 0.6.3.2 dated 2021-06-11

Title: Augmented Inverse Probability Weighting
Description: The 'AIPW' package implements the augmented inverse probability weighting, a doubly robust estimator, for average causal effect estimation with user-defined stacked machine learning algorithms. To cite the 'AIPW' package, please use: "Yongqi Zhong, Edward H. Kennedy, Lisa M. Bodnar, Ashley I. Naimi (2021). AIPW: An R Package for Augmented Inverse Probability Weighted Estimation of Average Causal Effects. American Journal of Epidemiology. <doi:10.1093/aje/kwab207>". Visit: <https://yqzhong7.github.io/AIPW/> for more information.
Author: Yongqi Zhong [aut, cre] , Ashley Naimi [aut] , Gabriel Conzuelo [ctb], Edward Kennedy [ctb]
Maintainer: Yongqi Zhong <yq.zhong7@gmail.com>

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Package RJSONIO updated to version 2.0.0 with previous version 1.3-1.11 dated 2025-03-26

Title: Serialize R Objects to JSON, JavaScript Object Notation
Description: This is a package that allows conversion to and from data in Javascript object notation (JSON) format. This allows R objects to be inserted into Javascript/ECMAScript/ActionScript code and allows R programmers to read and convert JSON content to R objects. This is an alternative to rjson package. Originally, that was too slow for converting large R objects to JSON and was not extensible. rjson's performance is now similar to this package, and perhaps slightly faster in some cases. This package uses methods and is readily extensible by defining methods for different classes, vectorized operations, and C code and callbacks to R functions for deserializing JSON objects to R. The two packages intentionally share the same basic interface. This package (RJSONIO) has many additional options to allow customizing the generation and processing of JSON content. This package uses libjson rather than implementing yet another JSON parser. The aim is to support other general projects by building on [...truncated...]
Author: Yaoxiang Li [aut, ctb, cre] , CRAN Team [aut], Duncan Temple Lang [aut] , Jonathan Wallace [aut]
Maintainer: Yaoxiang Li <liyaoxiang@outlook.com>

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Package smoothtail updated to version 2.0.6 with previous version 2.0.5 dated 2016-07-13

Title: Smooth Estimation of GPD Shape Parameter
Description: Given independent and identically distributed observations X(1), ..., X(n) from a Generalized Pareto distribution with shape parameter gamma in [-1,0], offers several estimates to compute estimates of gamma. The estimates are based on the principle of replacing the order statistics by quantiles of a distribution function based on a log--concave density function. This procedure is justified by the fact that the GPD density is log--concave for gamma in [-1,0].
Author: Kaspar Rufibach [aut, cre], Samuel Mueller [aut]
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>

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Package selectMeta updated to version 1.0.9 with previous version 1.0.8 dated 2015-07-03

Title: Estimation of Weight Functions in Meta Analysis
Description: Publication bias, the fact that studies identified for inclusion in a meta analysis do not represent all studies on the topic of interest, is commonly recognized as a threat to the validity of the results of a meta analysis. One way to explicitly model publication bias is via selection models or weighted probability distributions. In this package we provide implementations of several parametric and nonparametric weight functions. The novelty in Rufibach (2011) is the proposal of a non-increasing variant of the nonparametric weight function of Dear & Begg (1992). The new approach potentially offers more insight in the selection process than other methods, but is more flexible than parametric approaches. To maximize the log-likelihood function proposed by Dear & Begg (1992) under a monotonicity constraint we use a differential evolution algorithm proposed by Ardia et al (2010a, b) and implemented in Mullen et al (2009). In addition, we offer a method to compute a confidence inter [...truncated...]
Author: Kaspar Rufibach [aut, cre]
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>

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Package openalexR updated to version 2.0.0 with previous version 1.4.0 dated 2024-07-11

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

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More information about openalexR at CRAN
Permanent link

Package extrafrail updated to version 1.13 with previous version 1.12 dated 2024-09-22

Title: Estimation and Additional Tools for Alternative Shared Frailty Models
Description: Provide estimation and data generation tools for some new multivariate frailty models. This version includes the gamma, inverse Gaussian, weighted Lindley, Birnbaum-Saunders, truncated normal, mixture of inverse Gaussian, mixture of Birnbaum-Saunders and generalized exponential as the distribution for the frailty terms. For the basal model, it is considered a parametric approach based on the exponential, Weibull and the piecewise exponential distributions as well as a semiparametric approach. For details, see Gallardo and Bourguignon (2025) <doi:10.1002/bimj.70044> and Gallardo et al. (2024) <doi:10.1007/s11222-024-10458-w>.
Author: Diego Gallardo [aut, cre], Marcelo Bourguignon [aut], John Santibanez [ctb]
Maintainer: Diego Gallardo <dgallardo@ubiobio.cl>

Diff between extrafrail versions 1.12 dated 2024-09-22 and 1.13 dated 2025-04-05

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More information about extrafrail at CRAN
Permanent link

Package DataMetProcess updated to version 1.0.4 with previous version 1.0.3 dated 2024-10-03

Title: Meteorological Data Processing
Description: Set of tools aimed at processing meteorological data, converting hourly recorded data to daily, monthly and annual data.
Author: Wagner Martins dos Santos [aut, cre] , Hoi Leong Lee [aut], Edimir Xavier Leal Ferraz [aut] , Abelardo Antonio de Assuncao Montenegro [aut], Lady Daiane Costa de Sousa Martins [aut] , Alan Cezar Bezerra [aut], Ênio Farias de Franca e Silva [aut], Thi [...truncated...]
Maintainer: Wagner Martins dos Santos <wagnnerms97@gmail.com>

Diff between DataMetProcess versions 1.0.3 dated 2024-10-03 and 1.0.4 dated 2025-04-05

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More information about DataMetProcess at CRAN
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Package CopernicusMarine updated to version 0.2.5 with previous version 0.2.4 dated 2024-12-22

Title: Search Download and Handle Data from Copernicus Marine Service Information
Description: Subset and download data from EU Copernicus Marine Service Information: <https://data.marine.copernicus.eu>. Import data on the oceans physical and biogeochemical state from Copernicus into R without the need of external software.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>

Diff between CopernicusMarine versions 0.2.4 dated 2024-12-22 and 0.2.5 dated 2025-04-05

 DESCRIPTION                      |    6 +++---
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Permanent link

Package CDsampling updated to version 0.1.6 with previous version 0.1.5 dated 2025-03-30

Title: Constrained Sampling in Paid Research Studies
Description: In the context of paid research studies and clinical trials, budget considerations and patient sampling from available populations are subject to inherent constraints. We introduce the 'CDsampling' package, which integrates optimal design theories within the framework of constrained sampling. This package offers the possibility to find both D-optimal approximate and exact allocations for samplings with or without constraints. Additionally, it provides functions to find constrained uniform sampling as a robust sampling strategy with limited model information. Our package offers functions for the computation of the Fisher information matrix under generalized linear models (including regular linear regression model) and multinomial logistic models.To demonstrate the applications, we also provide a simulated dataset and a real dataset embedded in the package. Yifei Huang, Liping Tong, and Jie Yang (2025)<doi:10.5705/ss.202022.0414>.
Author: Yifei Huang [aut, cre], Liping Tong [aut], Jie Yang [aut]
Maintainer: Yifei Huang <yhuan39@uic.edu>

Diff between CDsampling versions 0.1.5 dated 2025-03-30 and 0.1.6 dated 2025-04-05

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More information about CDsampling at CRAN
Permanent link

Package gt updated to version 1.0.0 with previous version 0.11.1 dated 2024-10-04

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] , Ellis Hughes [aut] , Alexandra Lauer [aut] , JooYoung Seo [aut] , Ken Brevoort [aut] , Olivier Roy [aut], Posit Software, PBC [cph, fnd]
Maintainer: Richard Iannone <rich@posit.co>

Diff between gt versions 0.11.1 dated 2024-10-04 and 1.0.0 dated 2025-04-05

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More information about gt at CRAN
Permanent link

Package gghourglass updated to version 0.0.2 with previous version 0.0.1 dated 2025-03-25

Title: Plot Records per Time of Day
Description: Splits date and time of day components from continuous 'datetime' objects, then plots them using grammar of graphics ('ggplot2'). Plots can also be decorated with solar cycle information (e.g., sunset, sunrise, etc.). This is useful for visualising data that are associated with the solar cycle.
Author: Pepijn de Vries [aut, cre] , Sander Lagerveld [dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>

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Package biogas updated to version 1.64.0 with previous version 1.61 dated 2024-12-05

Title: Process Biogas Data and Predict Biogas Production
Description: Functions for calculating biochemical methane potential (BMP) from laboratory measurements and other types of data processing and prediction useful for biogas research. Raw laboratory measurements for diverse methods (volumetric, manometric, gravimetric, gas density) can be processed to calculate BMP. Theoretical maximum BMP or methane or biogas yield can be predicted from various measures of substrate composition. Molar mass and calculated oxygen demand (COD') can be determined from a chemical formula. Measured gas volume can be corrected for water vapor and to standard (or user-defined) temperature and pressure. Gas quantity can be converted between volume, mass, and moles. A function for planning BMP experiments can consider multiple constraints in suggesting substrate or inoculum quantities, and check for problems. Inoculum and substrate mass can be determined for planning BMP experiments. Finally, a set of first-order models can be fit to measured methane production rate or cumula [...truncated...]
Author: Sasha D. Hafner [aut, cre] , Charlotte Rennuit [aut], Camilla Justesen [aut], Nanna Lojborg [aut], Jacob Mortensen [aut], Jonas Ohlsson [aut], Sergi Astals [ctb], Konrad Koch [ctb], Soeren Weinrich [ctb], Jin Mi Triolo [ctb], Ali Heidarzadeh Vazifehk [...truncated...]
Maintainer: Sasha D. Hafner <sasha.hafner@bce.au.dk>

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Package TreeMineR updated to version 1.0.3 with previous version 1.0.2 dated 2024-08-27

Title: Tree-Based Scan Statistics
Description: Implementation of unconditional Bernoulli Scan Statistic developed by Kulldorff et al. (2003) <doi:10.1111/1541-0420.00039> for hierarchical tree structures. Tree-based Scan Statistics are an exploratory method to identify event clusters across the space of a hierarchical tree.
Author: Joshua P. Entrop [aut, cre, cph] , Viktor Wintzell [aut]
Maintainer: Joshua P. Entrop <joshuaentrop@posteo.de>

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Package rBiasCorrection updated to version 0.3.5 with previous version 0.3.4 dated 2022-06-20

Title: Correct Bias in DNA Methylation Analyses
Description: Implementation of the algorithms (with minor modifications) to correct bias in quantitative DNA methylation analyses as described by Moskalev et al. (2011) <doi:10.1093/nar/gkr213>. Publication: Kapsner et al. (2021) <doi:10.1002/ijc.33681>.
Author: Lorenz A. Kapsner [cre, aut, cph] , Evgeny A. Moskalev [aut]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>

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Package pillar updated to version 1.10.2 with previous version 1.10.1 dated 2025-01-07

Title: Coloured Formatting for Columns
Description: Provides 'pillar' and 'colonnade' generics designed for formatting columns of data using the full range of colours provided by modern terminals.
Author: Kirill Mueller [aut, cre] , Hadley Wickham [aut], RStudio [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>

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Package skewMLRM updated to version 1.7 with previous version 1.6 dated 2021-11-24

Title: Estimation for Scale-Shape Mixtures of Skew-Normal Distributions
Description: Provide data generation and estimation tools for the multivariate scale mixtures of normal presented in Lange and Sinsheimer (1993) <doi:10.2307/1390698>, the multivariate scale mixtures of skew-normal presented in Zeller, Lachos and Vilca (2011) <doi:10.1080/02664760903406504>, the multivariate skew scale mixtures of normal presented in Louredo, Zeller and Ferreira (2021) <doi:10.1007/s13571-021-00257-y> and the multivariate scale mixtures of skew-normal-Cauchy presented in Kahrari et al. (2020) <doi:10.1080/03610918.2020.1804582>.
Author: Clecio Ferreira [aut], Diego Gallardo [aut, cre], Camila Zeller [aut]
Maintainer: Diego Gallardo <dgallardo@ubiobio.cl>

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Package redatamx updated to version 1.1.2 with previous version 1.1.1 dated 2025-04-03

Title: R Interface to 'Redatam' Library
Description: Provides an API to work with 'Redatam' (see <https://redatam.org>) databases in both formats: 'RXDB' (new format) and 'DICX' (old format) and running 'Redatam' programs written in 'SPC' language. It's a wrapper around 'Redatam' core and provides functions to open/close a database (redatam_open()/redatam_close()), list entities and variables from the database (redatam_entities(), redatam_variables()) and execute a 'SPC' program and gets the results as data frames (redatam_query(), redatam_run()).
Author: Jaime Salvador [aut, cre] , CELADE [cph]
Maintainer: Jaime Salvador <jaime.salvador@ideasybits.com>

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Package orcamentoBR updated to version 1.0.4 with previous version 1.0.3 dated 2025-03-05

Title: Download Official Data on Brazil's Federal Budget
Description: Allows users to download and analyze official data on Brazil's federal budget through the 'SPARQL' endpoint provided by the Integrated Budget and Planning System ('SIOP'). This package enables access to detailed information on budget allocations and expenditures of the federal government, making it easier to analyze and visualize these data. Technical information on the Brazilian federal budget is available (Portuguese only) at <https://www1.siop.planejamento.gov.br/mto/>. The 'SIOP' endpoint is available at <https://www1.siop.planejamento.gov.br/sparql/>.
Author: Daniel Gersten Reiss [aut, cre] , Bernardo Borba de Andrade [ctb] , Gustavo Jose de Guimaraes e Souza [ctb] , Ministerio do Planejamento e Orcamento [cph, fnd]
Maintainer: Daniel Gersten Reiss <daniel.reiss@planejamento.gov.br>

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Package HTGM updated to version 1.1 with previous version 1.0 dated 2025-04-02

Title: High Throughput 'GoMiner'
Description: Two papers published in the early 2000's (Zeeberg, B.R., Feng, W., Wang, G. et al. (2003) <doi:10.1186/gb-2003-4-4-r28>) and (Zeeberg, B.R., Qin, H., Narashimhan, S., et al. (2005) <doi:10.1186/1471-2105-6-168>) implement 'GoMiner' and 'High Throughput GoMiner' ('HTGM') to map lists of genes to the Gene Ontology (GO) <https://geneontology.org>. Until recently, these were hosted on a server at The National Cancer Institute (NCI). In order to continue providing these services to the bio-medical community, I have developed stand-alone versions. The current package 'HTGM' builds upon my recent package 'GoMiner'. The output of 'GoMiner' is a heatmap showing the relationship of a single list of genes and the significant categories into which they map. 'High Throughput GoMiner' ('HTGM') integrates the results of the individual 'GoMiner' analyses. The output of 'HTGM' is a heatmap showing the relationship of the significant categories derived from each gene list. The heatmap [...truncated...]
Author: Barry Zeeberg [aut, cre]
Maintainer: Barry Zeeberg <barryz2013@gmail.com>

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Package gptr updated to version 0.7.0 with previous version 0.6.0 dated 2024-05-07

Title: A Convenient R Interface with the OpenAI 'ChatGPT' API
Description: A convenient interface with the OpenAI 'ChatGPT' API <https://openai.com/api>. 'gptr' allows you to interact with 'ChatGPT', a powerful language model, for various natural language processing tasks. The 'gptr' R package makes talking to 'ChatGPT' in R super easy. It helps researchers and data folks by simplifying the complicated stuff, like asking questions and getting answers. With 'gptr', you can use 'ChatGPT' in R without any hassle, making it simpler for everyone to do cool things with language!
Author: Wanjun Gu [aut, cre]
Maintainer: Wanjun Gu <wanjun.gu@ucsf.edu>

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Package ecochange updated to version 2.9.3.3 with previous version 2.9.3.2 dated 2024-06-11

Title: Integrating Ecosystem Remote Sensing Products to Derive EBV Indicators
Description: Essential Biodiversity Variables (EBV) are state variables with dimensions on time, space, and biological organization that document biodiversity change. Freely available ecosystem remote sensing products (ERSP) are downloaded and integrated with data for national or regional domains to derive indicators for EBV in the class ecosystem structure (Pereira et al., 2013) <doi:10.1126/science.1229931>, including horizontal ecosystem extents, fragmentation, and information-theory indices. To process ERSP, users must provide a polygon or geographic administrative data map. Downloadable ERSP include Global Surface Water (Peckel et al., 2016) <doi:10.1038/nature20584>, Forest Change (Hansen et al., 2013) <doi:10.1126/science.1244693>, and Continuous Tree Cover data (Sexton et al., 2013) <doi:10.1080/17538947.2013.786146>.
Author: Wilson Lara Henao [aut, cre] , Victor Gutierrez-Velez [aut] , Ivan Gonzalez [ctb] , Maria C. Londono [ctb]
Maintainer: Wilson Lara Henao <wilarhen@gmail.com>

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Package bioRad updated to version 0.9.1 with previous version 0.9.0 dated 2025-03-31

Title: Biological Analysis and Visualization of Weather Radar Data
Description: Extract, visualize and summarize aerial movements of birds and insects from weather radar data. See Dokter, A. M. et al. (2018) "bioRad: biological analysis and visualization of weather radar data" <doi:10.1111/ecog.04028> for a software paper describing package and methodologies.
Author: Adriaan M. Dokter [aut, cre] , Peter Desmet [aut] , Bart Kranstauber [aut] , Cecilia Nilsson [aut] , Stijn Van Hoey [aut] , Bart Hoekstra [ctb] , Pieter Huybrechts [ctb] , Hidde Leijnse [ctb] , Nicolas Noe [ctb] , Raphael Nussbaumer [ctb] , Jurriaan [...truncated...]
Maintainer: Adriaan M. Dokter <biorad@cornell.edu>

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Package sae.projection updated to version 0.1.3 with previous version 0.1.2 dated 2025-02-18

Title: Small Area Estimation Using Model-Assisted Projection Method
Description: Combines information from two independent surveys using a model-assisted projection method. Designed for survey sampling scenarios where a large sample collects only auxiliary information (Survey 1) and a smaller sample provides data on both variables of interest and auxiliary variables (Survey 2). Implements a working model to generate synthetic values of the variable of interest by fitting the model to Survey 2 data and predicting values for Survey 1 based on its auxiliary variables (Kim & Rao, 2012) <doi:10.1093/biomet/asr063>.
Author: Ridson Al Farizal P [aut, cre, cph] , Azka Ubaidillah [aut] , Silvi Ajeng Larasati [aut], Amelia Rahayu [aut]
Maintainer: Ridson Al Farizal P <ridsonalfarizal15@gmail.com>

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Package FAMoS updated to version 0.3.1 with previous version 0.3.0 dated 2020-04-14

Title: A Flexible Algorithm for Model Selection
Description: Given a set of parameters describing model dynamics and a corresponding cost function, FAMoS performs a dynamic forward-backward model selection on a specified selection criterion. It also applies a non-local swap search method. Works on any cost function. For detailed information see Gabel et al. (2019) <doi:10.1371/journal.pcbi.1007230>.
Author: Michael Gabel [aut, cre], Tobias Hohl [aut]
Maintainer: Michael Gabel <m_gabel@gmx.de>

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Package SoilTaxonomy updated to version 0.2.7 with previous version 0.2.4 dated 2023-11-16

Title: A System of Soil Classification for Making and Interpreting Soil Surveys
Description: Taxonomic dictionaries, formative element lists, and functions related to the maintenance, development and application of U.S. Soil Taxonomy. Data and functionality are based on official U.S. Department of Agriculture sources including the latest edition of the Keys to Soil Taxonomy. Descriptions and metadata are obtained from the National Soil Information System or Soil Survey Geographic databases. Other sources are referenced in the data documentation. Provides tools for understanding and interacting with concepts in the U.S. Soil Taxonomic System. Most of the current utilities are for working with taxonomic concepts at the "higher" taxonomic levels: Order, Suborder, Great Group, and Subgroup.
Author: Andrew Brown [aut, cre], Dylan Beaudette [aut]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>

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Package soilDB updated to version 2.8.9 with previous version 2.8.8 dated 2025-02-10

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 ijtiff updated to version 3.1.3 with previous version 3.1.1 dated 2025-03-21

Title: Comprehensive TIFF I/O with Full Support for 'ImageJ' TIFF Files
Description: General purpose TIFF file I/O for R users. Currently the only such package with read and write support for TIFF files with floating point (real-numbered) pixels, and the only package that can correctly import TIFF files that were saved from 'ImageJ' and write TIFF files than can be correctly read by 'ImageJ' <https://imagej.net/ij/>. Also supports text image I/O.
Author: Rory Nolan [aut, cre] , Kent Johnson [aut], Simon Urbanek [ctb], Sergi Padilla-Parra [ths] , Jeroen Ooms [rev, ctb] , Jon Clayden [rev]
Maintainer: Rory Nolan <rorynoolan@gmail.com>

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Fri, 04 Apr 2025

Package tpn updated to version 1.10 with previous version 1.9 dated 2024-11-17

Title: Truncated Positive Normal Model and Extensions
Description: Provide data generation and estimation tools for the truncated positive normal (tpn) model discussed in Gomez, Olmos, Varela and Bolfarine (2018) <doi:10.1007/s11766-018-3354-x>, the slash tpn distribution discussed in Gomez, Gallardo and Santoro (2021) <doi:10.3390/sym13112164>, the bimodal tpn distribution discussed in Gomez et al. (2022) <doi:10.3390/sym14040665> and the flexible tpn model.
Author: Diego Gallardo [aut, cre], Hector J. Gomez [aut], Yolanda M. Gomez [aut]
Maintainer: Diego Gallardo <dgallardo@ubiobio.cl>

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Package healthdb updated to version 0.4.1 with previous version 0.4.0 dated 2025-02-27

Title: Working with Healthcare Databases
Description: A system for identifying diseases or events from healthcare databases and preparing data for epidemiological studies. It includes capabilities not supported by 'SQL', such as matching strings by 'stringr' style regular expressions, and can compute comorbidity scores (Quan et al. (2005) <doi:10.1097/01.mlr.0000182534.19832.83>) directly on a database server. The implementation is based on 'dbplyr' with full 'tidyverse' compatibility.
Author: Kevin Hu [aut, cre, cph]
Maintainer: Kevin Hu <kevin.hu@bccdc.ca>

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Package FaaSr updated to version 1.4.4 with previous version 1.4.3 dated 2024-12-19

Title: FaaS (Function as a Service) Package
Description: Allows users to create and deploy the workflow with multiple functions in Function-as-a-Service (FaaS) cloud computing platforms. The 'FaaSr' package makes it simpler for R developers to use FaaS platforms by providing the following functionality: 1) Parsing and validating a JSON-based payload compliant to 'FaaSr' schema supporting multiple FaaS platforms 2) Invoking user functions written in R in a Docker container (derived from rocker), using a list generated from the parser as argument 3) Downloading/uploading of files from/to S3 buckets using simple primitives 4) Logging to files in S3 buckets 5) Triggering downstream actions supporting multiple FaaS platforms 6) Generating FaaS-specific API calls to simplify the registering of a user's workflow with a FaaS platform Supported FaaS platforms: Apache OpenWhisk <https://openwhisk.apache.org/> GitHub Actions <https://github.com/features/actions> Amazon Web Services (AWS) Lambda <https://aws.amazon.com/lambda/> Support [...truncated...]
Author: Figueiredo Renato [aut, cre, ths, cph] , Park Sungjae [aut] , Mu Nan [ctb], Ku Yun-Jung [ctb], Daneshmand Vahid [ctb], Thomas R. Quinn [aut], Carey Cayelan [ctb]
Maintainer: Figueiredo Renato <renato.figueiredo@oregonstate.edu>

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Package duckdbfs updated to version 0.1.0 with previous version 0.0.9 dated 2024-12-16

Title: High Performance Remote File System, Database and 'Geospatial' Access Using 'duckdb'
Description: Provides friendly wrappers for creating 'duckdb'-backed connections to tabular datasets ('csv', parquet, etc) on local or remote file systems. This mimics the behaviour of "open_dataset" in the 'arrow' package, but in addition to 'S3' file system also generalizes to any list of 'http' URLs.
Author: Carl Boettiger [aut, cre] , Michael D. Sumner [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>

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Package unsystation updated to version 0.2.1 with previous version 0.2.0 dated 2018-05-23

Title: Stationarity Test Based on Unsystematic Sub-Sampling
Description: Performs a test for second-order stationarity of time series based on unsystematic sub-samples.
Author: Haeran Cho [aut, cre]
Maintainer: Haeran Cho <haeran.cho@bristol.ac.uk>

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Package SSDforR updated to version 1.5.40 with previous version 1.5.39 dated 2025-03-25

Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre], Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>

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Package rbiom updated to version 2.2.0 with previous version 2.1.2 dated 2025-03-18

Title: Read/Write, Analyze, and Visualize 'BIOM' Data
Description: A toolkit for working with Biological Observation Matrix ('BIOM') files. Read/write all 'BIOM' formats. Compute rarefaction, alpha diversity, and beta diversity (including 'UniFrac'). Summarize counts by taxonomic level. Subset based on metadata. Generate visualizations and statistical analyses. CPU intensive operations are coded in C for speed.
Author: Daniel P. Smith [aut, cre] , Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>

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Package Pursuit updated to version 1.0.6 with previous version 1.0.5 dated 2024-06-21

Title: Projection Pursuit
Description: Projection pursuit (PP) with 17 methods and grand tour with 3 methods. Being that projection pursuit searches for low-dimensional linear projections in high-dimensional data structures, while grand tour is a technique used to explore multivariate statistical data through animation.
Author: Paulo Cesar Ossani [aut, cre] , Marcelo Angelo Cirillo [aut]
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>

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Package plotthis updated to version 0.6.0 with previous version 0.5.2 dated 2025-03-16

Title: High-Level Plotting Built Upon 'ggplot2' and Other Plotting Packages
Description: Provides high-level API and a wide range of options to create stunning, publication-quality plots effortlessly. It is built upon 'ggplot2' and other plotting packages, and is designed to be easy to use and to work seamlessly with 'ggplot2' objects. It is particularly useful for creating complex plots with multiple layers, facets, and annotations. It also provides a set of functions to create plots for specific types of data, such as Venn diagrams, alluvial diagrams, and phylogenetic trees. The package is designed to be flexible and customizable, and to work well with the 'ggplot2' ecosystem. The API can be found at <https://pwwang.github.io/plotthis/reference/index.html>.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>

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Package MVar.pt updated to version 2.2.6 with previous version 2.2.5 dated 2024-11-22

Title: Analise multivariada (brazilian portuguese)
Description: Analise multivariada, tendo funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de correlacao canonica (CCA), analise fatorial (FA), escalonamento multidimensional (MDS), analise discriminante linear (LDA) e quadratica (QDA), analise de cluster hierarquico e nao hierarquico, regressao linear simples e multipla, analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos, biplot, scatter plot, projection pursuit (PP), grant tour e outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani [aut, cre] , Marcelo Angelo Cirillo [aut]
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>

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Package MVar updated to version 2.2.6 with previous version 2.2.5 dated 2024-11-22

Title: Multivariate Analysis
Description: Multivariate analysis, having functions that perform simple correspondence analysis (CA) and multiple correspondence analysis (MCA), principal components analysis (PCA), canonical correlation analysis (CCA), factorial analysis (FA), multidimensional scaling (MDS), linear (LDA) and quadratic discriminant analysis (QDA), hierarchical and non-hierarchical cluster analysis, simple and multiple linear regression, multiple factor analysis (MFA) for quantitative, qualitative, frequency (MFACT) and mixed data, biplot, scatter plot, projection pursuit (PP), grant tour method and other useful functions for the multivariate analysis.
Author: Paulo Cesar Ossani [aut, cre] , Marcelo Angelo Cirillo [aut]
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>

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Package MFAg updated to version 2.1 with previous version 2.0 dated 2024-06-21

Title: Multiple Factor Analysis (MFA)
Description: Performs Multiple Factor Analysis method for quantitative, categorical, frequency and mixed data, in addition to generating a lot of graphics, also has other useful functions.
Author: Paulo Cesar Ossani [aut, cre] , Marcelo Angelo Cirillo [aut]
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>

Diff between MFAg versions 2.0 dated 2024-06-21 and 2.1 dated 2025-04-04

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Package ergMargins updated to version 1.5 with previous version 1.3 dated 2024-05-08

Title: Process Analysis for Exponential Random Graph Models
Description: Calculates marginal effects and conducts process analysis in exponential family random graph models (ERGM). Includes functions to conduct mediation and moderation analyses and to diagnose multicollinearity. URL: <https://github.com/sduxbury/ergMargins>. BugReports: <https://github.com/sduxbury/ergMargins/issues>. Duxbury, Scott W (2021) <doi:10.1177/0049124120986178>. Long, J. Scott, and Sarah Mustillo (2018) <doi:10.1177/0049124118799374>. Mize, Trenton D. (2019) <doi:10.15195/v6.a4>. Karlson, Kristian Bernt, Anders Holm, and Richard Breen (2012) <doi:10.1177/0081175012444861>. Duxbury, Scott W (2018) <doi:10.1177/0049124118782543>. Duxbury, Scott W, Jenna Wertsching (2023) <doi:10.1016/j.socnet.2023.02.003>. Huang, Peng, Carter Butts (2023) <doi:10.1016/j.socnet.2023.07.001>.
Author: Scott Duxbury [aut, cre, cph]
Maintainer: Scott Duxbury <duxbury@email.unc.edu>

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Package sommer updated to version 4.4.1 with previous version 4.3.7 dated 2025-02-03

Title: Solving Mixed Model Equations in R
Description: Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., heterogeneous and unstructured) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>; Jensen et al., 1997). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms for the problems r x r (r being the number of records) or using the Henderson-based average information algorithm for the problem c x c (c being the number of coefficients to estimate). Spatial models can also be fitted using the two-dimensional spline functionality available.
Author: Giovanny Covarrubias-Pazaran [aut, cre]
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>

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Package NLPwavelet updated to version 1.1 with previous version 1.0 dated 2025-02-13

Title: Bayesian Wavelet Analysis Using Non-Local Priors
Description: Performs Bayesian wavelet analysis using individual non-local priors as described in Sanyal & Ferreira (2017) <DOI:10.1007/s13571-016-0129-3> and non-local prior mixtures as described in Sanyal (2025) <DOI:10.48550/arXiv.2501.18134>.
Author: Nilotpal Sanyal [aut, cre]
Maintainer: Nilotpal Sanyal <nsanyal@utep.edu>

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Package campsis updated to version 1.7.0 with previous version 1.6.0 dated 2025-02-09

Title: Generic PK/PD Simulation Platform CAMPSIS
Description: A generic, easy-to-use and intuitive pharmacokinetic/pharmacodynamic (PK/PD) simulation platform based on R packages 'rxode2' and 'mrgsolve'. CAMPSIS provides an abstraction layer over the underlying processes of writing a PK/PD model, assembling a custom dataset and running a simulation. CAMPSIS has a strong dependency to the R package 'campsismod', which allows to read/write a model from/to files and adapt it further on the fly in the R environment. Package 'campsis' allows the user to assemble a dataset in an intuitive manner. Once the user’s dataset is ready, the package is in charge of preparing the simulation, calling 'rxode2' or 'mrgsolve' (at the user's choice) and returning the results, for the given model, dataset and desired simulation settings.
Author: Nicolas Luyckx [aut, cre]
Maintainer: Nicolas Luyckx <nicolas.luyckx@calvagone.com>

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Package lpl updated to version 0.12 with previous version 0.11 dated 2021-07-26

Title: Local Partial Likelihood Estimation and Simultaneous Confidence Band
Description: Local partial likelihood estimation by Fan, Lin and Zhou(2006)<doi:10.1214/009053605000000796> and simultaneous confidence band is a set of tools to test the covariates-biomarker interaction for survival data. Test for the covariates-biomarker interaction using the bootstrap method and the asymptotic method with simultaneous confidence band (Liu, Jiang and Chen (2015)<doi:10.1002/sim.6563>).
Author: Bingshu E. Chen [aut, cre], Yicong Liu [aut], Siwei Zhang [aut], Teng Wen [aut], Wenyu Jiang [aut]
Maintainer: Bingshu E. Chen <bingshu.chen@queensu.ca>

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Package symengine updated to version 0.2.10 with previous version 0.2.6 dated 2024-02-25

Title: Interface to the 'SymEngine' Library
Description: Provides an R interface to 'SymEngine' <https://github.com/symengine/>, a standalone 'C++' library for fast symbolic manipulation. The package has functionalities for symbolic computation like calculating exact mathematical expressions, solving systems of linear equations and code generation.
Author: Jialin Ma [cre, aut], Isuru Fernando [aut], Xin Chen [aut]
Maintainer: Jialin Ma <marlin@inventati.org>

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Package rms updated to version 8.0-0 with previous version 7.0-0 dated 2025-01-17

Title: Regression Modeling Strategies
Description: Regression modeling, testing, estimation, validation, graphics, prediction, and typesetting by storing enhanced model design attributes in the fit. 'rms' is a collection of functions that assist with and streamline modeling. It also contains functions for binary and ordinal logistic regression models, ordinal models for continuous Y with a variety of distribution families, and the Buckley-James multiple regression model for right-censored responses, and implements penalized maximum likelihood estimation for logistic and ordinary linear models. 'rms' works with almost any regression model, but it was especially written to work with binary or ordinal regression models, Cox regression, accelerated failure time models, ordinary linear models, the Buckley-James model, generalized least squares for serially or spatially correlated observations, generalized linear models, and quantile regression.
Author: Frank E Harrell Jr [aut, cre]
Maintainer: Frank E Harrell Jr <fh@fharrell.com>

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Package greybox updated to version 2.0.4 with previous version 2.0.3 dated 2024-12-09

Title: Toolbox for Model Building and Forecasting
Description: Implements functions and instruments for regression model building and its application to forecasting. The main scope of the package is in variables selection and models specification for cases of time series data. This includes promotional modelling, selection between different dynamic regressions with non-standard distributions of errors, selection based on cross validation, solutions to the fat regression model problem and more. Models developed in the package are tailored specifically for forecasting purposes. So as a results there are several methods that allow producing forecasts from these models and visualising them.
Author: Ivan Svetunkov [aut, cre] , Yves R. Sagaert [ctb]
Maintainer: Ivan Svetunkov <ivan@svetunkov.com>

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Package TreatmentPatterns updated to version 3.0.2 with previous version 3.0.1 dated 2025-03-10

Title: Analyzes Real-World Treatment Patterns of a Study Population of Interest
Description: Computes treatment patterns within a given cohort using the Observational Medical Outcomes Partnership (OMOP) common data model (CDM). As described in Markus, Verhamme, Kors, and Rijnbeek (2022) <doi:10.1016/j.cmpb.2022.107081>.
Author: Aniek Markus [aut] , Maarten van Kessel [cre]
Maintainer: Maarten van Kessel <m.l.vankessel@erasmusmc.nl>

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Package survivalsvm updated to version 0.0.6 with previous version 0.0.5 dated 2018-02-05

Title: Survival Support Vector Analysis
Description: Performs support vectors analysis for data sets with survival outcome. Three approaches are available in the package: The regression approach takes censoring into account when formulating the inequality constraints of the support vector problem. In the ranking approach, the inequality constraints set the objective to maximize the concordance index for comparable pairs of observations. The hybrid approach combines the regression and ranking constraints in the same model.
Author: Cesaire J. K. Fouodo [aut, cre]
Maintainer: Cesaire J. K. Fouodo <cesaire.kuetefouodo@uni-luebeck.de>

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Package sjtable2df updated to version 0.0.4 with previous version 0.0.3 dated 2023-04-13

Title: Convert 'sjPlot' HTML-Tables to R 'data.frame'
Description: A small set of helper functions to convert 'sjPlot' HTML-tables to R data.frame objects / knitr::kable-tables.
Author: Lorenz A. Kapsner [cre, aut, cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>

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Package plm updated to version 2.6-6 with previous version 2.6-5 dated 2025-01-17

Title: Linear Models for Panel Data
Description: A set of estimators for models and (robust) covariance matrices, and tests for panel data econometrics, including within/fixed effects, random effects, between, first-difference, nested random effects as well as instrumental-variable (IV) and Hausman-Taylor-style models, panel generalized method of moments (GMM) and general FGLS models, mean groups (MG), demeaned MG, and common correlated effects (CCEMG) and pooled (CCEP) estimators with common factors, variable coefficients and limited dependent variables models. Test functions include model specification, serial correlation, cross-sectional dependence, panel unit root and panel Granger (non-)causality. Typical references are general econometrics text books such as Baltagi (2021), Econometric Analysis of Panel Data (<doi:10.1007/978-3-030-53953-5>), Hsiao (2014), Analysis of Panel Data (<doi:10.1017/CBO9781139839327>), and Croissant and Millo (2018), Panel Data Econometrics with R (<doi:10.1002/9781119504641>).
Author: Yves Croissant [aut], Giovanni Millo [aut], Kevin Tappe [aut, cre], Ott Toomet [ctb], Christian Kleiber [ctb], Achim Zeileis [ctb], Arne Henningsen [ctb], Liviu Andronic [ctb], Nina Schoenfelder [ctb]
Maintainer: Kevin Tappe <kevin.tappe@bwi.uni-stuttgart.de>

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Package SimComp updated to version 3.6 with previous version 3.3 dated 2019-08-26

Title: Simultaneous Comparisons for Multiple Endpoints
Description: Simultaneous tests and confidence intervals are provided for one-way experimental designs with one or many normally distributed, primary response variables (endpoints). Differences (Hasler and Hothorn, 2011 <doi:10.2202/1557-4679.1258>) or ratios (Hasler and Hothorn, 2012 <doi:10.1080/19466315.2011.633868>) of means can be considered. Various contrasts can be chosen, unbalanced sample sizes are allowed as well as heterogeneous variances (Hasler and Hothorn, 2008 <doi:10.1002/bimj.200710466>) or covariance matrices (Hasler, 2014 <doi:10.1515/ijb-2012-0015>).
Author: Mario Hasler [aut, cre], Christof Kluss [aut]
Maintainer: Mario Hasler <hasler@email.uni-kiel.de>

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Package rJavaEnv updated to version 0.3.0 with previous version 0.2.2 dated 2024-09-13

Title: 'Java' Environments for R Projects
Description: Quickly install 'Java Development Kit (JDK)' without administrative privileges and set environment variables in current R session or project to solve common issues with 'Java' environment management in 'R'. Recommended to users of 'Java'/'rJava'-dependent 'R' packages such as 'r5r', 'opentripplanner', 'xlsx', 'openNLP', 'rWeka', 'RJDBC', 'tabulapdf', and many more. 'rJavaEnv' prevents common problems like 'Java' not found, 'Java' version conflicts, missing 'Java' installations, and the inability to install 'Java' due to lack of administrative privileges. 'rJavaEnv' automates the download, installation, and setup of the 'Java' on a per-project basis by setting the relevant 'JAVA_HOME' in the current 'R' session or the current working directory (via '.Rprofile', with the user's consent). Similar to what 'renv' does for 'R' packages, 'rJavaEnv' allows different 'Java' versions to be used across different projects, but can also be configured to allow multiple versions within the same proj [...truncated...]
Author: Egor Kotov [aut, cre, cph] , Chung-hong Chan [aut] , Mauricio Vargas [ctb] , Hadley Wickham [ctb] , Enrique Mondragon-Estrada [ctb] , Jonas Lieth [ctb]
Maintainer: Egor Kotov <kotov.egor@gmail.com>

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Package rintcal updated to version 1.1.3 with previous version 1.1.2 dated 2025-01-12

Title: Radiocarbon Calibration Curves
Description: The IntCal20 radiocarbon calibration curves (Reimer et al. 2020 <doi:10.1017/RDC.2020.68>) are provided as a data package, together with previous IntCal curves (IntCal13, IntCal09, IntCal04, IntCal98), other curves (e.g., NOTCal04 [van der Plicht et al. 2004], Arnold & Libby 1951) and postbomb curves. Also provided are functions to copy the curves into memory, and to read, query and plot the data underlying the IntCal20 curves.
Author: Maarten Blaauw [aut, cre]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>

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Package multilevelPSA updated to version 1.3.0 with previous version 1.2.5 dated 2018-03-22

Title: Multilevel Propensity Score Analysis
Description: Conducts and visualizes propensity score analysis for multilevel, or clustered data. Bryer & Pruzek (2011) <doi:10.1080/00273171.2011.636693>.
Author: Jason Bryer [aut, cre]
Maintainer: Jason Bryer <jason@bryer.org>

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Package cna updated to version 4.0.0 with previous version 3.6.2 dated 2024-07-05

Title: Causal Modeling with Coincidence Analysis
Description: Provides comprehensive functionalities for causal modeling with Coincidence Analysis (CNA), which is a configurational comparative method of causal data analysis that was first introduced in Baumgartner (2009) <doi:10.1177/0049124109339369>, and generalized in Baumgartner & Ambuehl (2020) <doi:10.1017/psrm.2018.45>. CNA is designed to recover INUS-causation from data, which is particularly relevant for analyzing processes featuring conjunctural causation (component causation) and equifinality (alternative causation). CNA is currently the only method for INUS-discovery that allows for multiple effects (outcomes/endogenous factors), meaning it can analyze common-cause and causal chain structures. Moreover, as of version 4.0, it is the only method of its kind that provides measures for model evaluation and selection that are custom-made for the problem of INUS-discovery.
Author: Mathias Ambuehl [aut, cre, cph], Michael Baumgartner [aut, cph], Ruedi Epple [ctb], Veli-Pekka Parkkinen [ctb], Alrik Thiem [ctb]
Maintainer: Mathias Ambuehl <mathias.ambuehl@consultag.ch>

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Package systemfonts updated to version 1.2.2 with previous version 1.2.1 dated 2025-01-20

Title: System Native Font Finding
Description: Provides system native access to the font catalogue. As font handling varies between systems it is difficult to correctly locate installed fonts across different operating systems. The 'systemfonts' package provides bindings to the native libraries on Windows, macOS and Linux for finding font files that can then be used further by e.g. graphic devices. The main use is intended to be from compiled code but 'systemfonts' also provides access from R.
Author: Thomas Lin Pedersen [aut, cre] , Jeroen Ooms [aut] , Devon Govett [aut] , Posit, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>

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Package cucumber updated to version 2.0.0 with previous version 1.2.1 dated 2025-03-20

Title: Behavior-Driven Development for R
Description: Write executable specifications in a natural language that describes how your code should behave. Write specifications in feature files using 'Gherkin' language and execute them using functions implemented in R. Use them as an extension to your 'testthat' tests to provide a high level description of how your code works.
Author: Jakub Sobolewski [aut, cre]
Maintainer: Jakub Sobolewski <jakupsob@gmail.com>

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Package Waypoint updated to version 1.1.1 with previous version 1.1.0 dated 2025-03-19

Title: Convert, Validate, Format and Print Geographic Coordinates and Waypoints
Description: Convert, validate, format and elegantly print geographic coordinates and waypoints (paired latitude and longitude values) in decimal degrees, degrees and minutes, and degrees, minutes and seconds using high performance C++ code to enable rapid conversion and formatting of large coordinate and waypoint datasets.
Author: Mark Eisler [aut, cre, cph]
Maintainer: Mark Eisler <mark.eisler@bristol.ac.uk>

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Package LikertMakeR updated to version 1.0.0 with previous version 0.4.0 dated 2024-11-19

Title: Synthesise and Correlate Likert Scale and Rating-Scale Data Based on Summary Statistics Only
Description: Generate and correlate synthetic Likert and rating-scale data with predefined means, standard deviations, _Cronbach's Alpha_, _Factor Loading table_, and other summary statistics.
Author: Hume Winzar [cre, aut]
Maintainer: Hume Winzar <winzar@gmail.com>

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Package analogue updated to version 0.18.0 with previous version 0.17-7 dated 2024-09-21

Title: Analogue and Weighted Averaging Methods for Palaeoecology
Description: Fits Modern Analogue Technique and Weighted Averaging transfer function models for prediction of environmental data from species data, and related methods used in palaeoecology.
Author: Gavin L. Simpson [aut, cre] , Jari Oksanen [aut], Martin Maechler [ctb]
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>

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Package WARDEN updated to version 0.99.3 with previous version 0.99.1 dated 2024-12-13

Title: Workflows for Health Technology Assessments in R using Discrete EveNts
Description: Toolkit to support and perform discrete event simulations without resource constraints in the context of health technology assessments (HTA). The package focuses on cost-effectiveness modelling and aims to be submission-ready to relevant HTA bodies in alignment with 'NICE TSD 15' <https://www.sheffield.ac.uk/nice-dsu/tsds/patient-level-simulation>. More details an examples can be found in the package website <https://jsanchezalv.github.io/WARDEN/>.
Author: Javier Sanchez Alvarez [aut, cre], Gabriel Lemyre [ctb], Valerie Aponte Ribero [ctb]
Maintainer: Javier Sanchez Alvarez <javiersanchezeco@gmail.com>

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Package cocorresp updated to version 0.4-6 with previous version 0.4-5 dated 2024-10-06

Title: Co-Correspondence Analysis Methods
Description: Fits predictive and symmetric co-correspondence analysis (CoCA) models to relate one data matrix to another data matrix. More specifically, CoCA maximises the weighted covariance between the weighted averaged species scores of one community and the weighted averaged species scores of another community. CoCA attempts to find patterns that are common to both communities.
Author: Gavin L. Simpson [aut, cre, trl] , Cajo J.F. ter Braak [aut] , Andre P Schaffers [aut] , Ron Wehrens [aut] ), Bjorn-Helge Mevik [aut] )
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>

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Package ARDECO updated to version 2.2.0 with previous version 2.1.0 dated 2024-11-21

Title: Annual Regional Database of the European Commission (ARDECO)
Description: A set of functions to access the 'ARDECO' (Annual Regional Database of the European Commission) data directly from the official ARDECO public repository through the exploitation of the 'ARDECO' APIs. The APIs are completely transparent to the user and the provided functions provide a direct access to the 'ARDECO' data. The 'ARDECO' database is a collection of variables related to demography, employment, labour market, domestic product, capital formation. Each variable can be exposed in one or more units of measure as well as refers to total values plus additional dimensions like economic sectors, gender, age classes. Data can be also aggregated at country level according to the tercet classes as defined by EUROSTAT. The description of the 'ARDECO' database can be found at the following URL <https://urban.jrc.ec.europa.eu/ardeco>.
Author: Carmelo Attardo [cre], Giuseppe Bucciarelli [aut], European Commission, JRC [cph]
Maintainer: Carmelo Attardo <carmelo.attardo@ec.europa.eu>

Diff between ARDECO versions 2.1.0 dated 2024-11-21 and 2.2.0 dated 2025-04-04

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Package jstable updated to version 1.3.11 with previous version 1.3.9 dated 2025-03-05

Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] , Zarathu [cph, fnd], Yoonkyoung Jeon [aut], Jaehun Shon [aut], Hyojong Myung [aut], Hyungwoo Jo [aut], Sungho Choi [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>

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Package airGRdatassim updated to version 0.1.4 with previous version 0.1.3 dated 2021-02-11

Title: Ensemble-Based Data Assimilation with GR Hydrological Models
Description: Add-on to the 'airGR' package which provides the tools to assimilate observed discharges in daily GR hydrological models. The package consists in two functions allowing to perform the assimilation of observed discharges via the Ensemble Kalman filter or the Particle filter as described in Piazzi et al. (2021) <doi:10.1029/2020WR028390>.
Author: Gaia Piazzi [aut] , Olivier Delaigue [aut, cre] , Guillaume Thirel [ctb] , Maxime Logez [ctb]
Maintainer: Olivier Delaigue <airGR@inrae.fr>

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Package kstIO updated to version 0.4-2 with previous version 0.4-1 dated 2025-01-20

Title: Knowledge Space Theory Input/Output
Description: Knowledge space theory by Doignon and Falmagne (1999) <doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical framework which proposes mathematical formalisms to operationalize knowledge structures in a particular domain. The 'kstIO' package provides basic functionalities to read and write KST data from/to files to be used together with the 'kst', 'kstMatrix', 'CDSS', 'pks', or 'DAKS' packages.
Author: Cord Hockemeyer [aut, cre]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>

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Package spaths updated to version 1.2.0 with previous version 1.1.3 dated 2024-07-11

Title: Shortest Paths Between Points in Grids
Description: Shortest paths between points in grids. Optional barriers and custom transition functions. Applications regarding planet Earth, as well as generally spheres and planes. Optimized for computational performance, customizability, and user friendliness. Graph-theoretical implementation tailored to gridded data. Currently focused on Dijkstra's (1959) <doi:10.1007/BF01386390> algorithm. Future updates broaden the scope to other least cost path algorithms and to centrality measures.
Author: Christian Dueben [aut, cre]
Maintainer: Christian Dueben <cdueben.ml+cran@proton.me>

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Package mgcv updated to version 1.9-3 with previous version 1.9-2 dated 2025-04-02

Title: Mixed GAM Computation Vehicle with Automatic Smoothness Estimation
Description: Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Generalized Cross Validation and similar, or using iterated nested Laplace approximation for fully Bayesian inference. See Wood (2017) <doi:10.1201/9781315370279> for an overview. Includes a gam() function, a wide variety of smoothers, 'JAGS' support and distributions beyond the exponential family.
Author: Simon Wood [aut, cre]
Maintainer: Simon Wood <simon.wood@r-project.org>

Diff between mgcv versions 1.9-2 dated 2025-04-02 and 1.9-3 dated 2025-04-04

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Package vapour updated to version 0.11.0 with previous version 0.10.0 dated 2024-06-14

Title: Lightweight Access to the 'Geospatial Data Abstraction Library' ('GDAL')
Description: Provides low-level access to 'GDAL' functionality. 'GDAL' is the 'Geospatial Data Abstraction Library' a translator for raster and vector geospatial data formats that presents a single raster abstract data model and single vector abstract data model to the calling application for all supported formats <https://gdal.org/>. This package is focussed on providing exactly and only what GDAL does, to enable developing further tools.
Author: Michael Sumner [aut, cre] , Simon Wotherspoon [ctb] , Mark Padgham [ctb] ), Edzer Pebesma [ctb] , Roger Bivand [ctb] , Jim Hester [ctb, cph] , Timothy Keitt [ctb] , Jeroen Ooms [ctb] , Dale Maschette [ctb] , Joseph Stachelek [ctb], Even Rouault [ctb] [...truncated...]
Maintainer: Michael Sumner <mdsumner@gmail.com>

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Thu, 03 Apr 2025

Package rdhte updated to version 0.0.2 with previous version 0.0.1 dated 2025-03-25

Title: Heterogeneous Treatment Effects in Regression Discontinuity Designs
Description: Understanding heterogeneous causal effects based on pretreatment covariates is a crucial step in modern empirical work in data science. Building on the recent developments in Calonico et al (2025) <https://rdpackages.github.io/references/Calonico-Cattaneo-Farrell-Palomba-Titiunik_2025_HTERD.pdf>, this package provides tools for estimation and inference of heterogeneous treatment effects in Regression Discontinuity (RD) Designs. The package includes two main commands: 'rdhte' to conduct estimation and robust bias-corrected inference for conditional RD treatment effects (given choice of bandwidth parameter); and 'rdbwhte', which implements automatic bandwidth selection methods.
Author: Sebastian Calonico [aut, cre], Matias D. Cattaneo [aut], Max H. Farrell [aut], Filippo Palomba [aut], Rocio Titiunik [aut]
Maintainer: Sebastian Calonico <scalonico@ucdavis.edu>

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Package lucid updated to version 1.9 with previous version 1.8 dated 2021-04-16

Title: Printing Floating Point Numbers in a Human-Friendly Format
Description: Print vectors (and data frames) of floating point numbers using a non-scientific format optimized for human readers. Vectors of numbers are rounded using significant digits, aligned at the decimal point, and all zeros trailing the decimal point are dropped. See: Wright (2016). Lucid: An R Package for Pretty-Printing Floating Point Numbers. In JSM Proceedings, Statistical Computing Section. Alexandria, VA: American Statistical Association. 2270-2279.
Author: Kevin Wright [aut, cre, cph]
Maintainer: Kevin Wright <kw.stat@gmail.com>

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Package logbin updated to version 2.0.6 with previous version 2.0.5 dated 2021-08-09

Title: Relative Risk Regression Using the Log-Binomial Model
Description: Methods for fitting log-link GLMs and GAMs to binomial data, including EM-type algorithms with more stable convergence properties than standard methods.
Author: Mark W. Donoghoe [aut, cre] , Ian C. Marschner [ths] , Alexandra C. Gillett [ctb] , The R Core Team [cph]
Maintainer: Mark W. Donoghoe <markdonoghoe@gmail.com>

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Package cAIC4 updated to version 1.1 with previous version 1.0 dated 2021-09-22

Title: Conditional Akaike Information Criterion for 'lme4' and 'nlme'
Description: Provides functions for the estimation of the conditional Akaike information in generalized mixed-effect models fitted with (g)lmer() from 'lme4', lme() from 'nlme' and gamm() from 'mgcv'. For a manual on how to use 'cAIC4', see Saefken et al. (2021) <doi:10.18637/jss.v099.i08>.
Author: Benjamin Saefken [aut], David Ruegamer [aut, cre], Philipp Baumann [aut], Rene-Marcel Kruse [aut], Sonja Greven [aut], Thomas Kneib [aut]
Maintainer: David Ruegamer <david.ruegamer@gmail.com>

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Package moderate.mediation updated to version 0.0.11 with previous version 0.0.10 dated 2024-05-23

Title: Causal Moderated Mediation Analysis
Description: Causal moderated mediation analysis using the methods proposed by Qin and Wang (2023) <doi:10.3758/s13428-023-02095-4>. Causal moderated mediation analysis is crucial for investigating how, for whom, and where a treatment is effective by assessing the heterogeneity of mediation mechanism across individuals and contexts. This package enables researchers to estimate and test the conditional and moderated mediation effects, assess their sensitivity to unmeasured pre-treatment confounding, and visualize the results. The package is built based on the quasi-Bayesian Monte Carlo method, because it has relatively better performance at small sample sizes, and its running speed is the fastest. The package is applicable to a treatment of any scale, a binary or continuous mediator, a binary or continuous outcome, and one or more moderators of any scale.
Author: Xu Qin [aut, cre, cph], Lijuan Wang [ctb]
Maintainer: Xu Qin <xuqin@pitt.edu>

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Package TriMatch updated to version 1.0.0 with previous version 0.9.9 dated 2017-12-05

Title: Propensity Score Matching of Non-Binary Treatments
Description: Propensity score matching for non-binary treatments.
Author: Jason Bryer [aut, cre]
Maintainer: Jason Bryer <jason@bryer.org>

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Package strata updated to version 1.4.5 with previous version 1.4.3 dated 2025-03-05

Title: Simple Framework for Simple Automation
Description: Build a project framework for users with access to only the most basic of automation tools.
Author: Alexander Senetcky [aut, cre, cph]
Maintainer: Alexander Senetcky <asenetcky@gmail.com>

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Package qicharts updated to version 0.5.10 with previous version 0.5.8 dated 2021-04-20

Title: Quality Improvement Charts
Description: Functions for making run charts [Anhoej, Olesen (2014) <doi:10.1371/journal.pone.0113825>] and basic Shewhart control charts [Mohammed, Worthington, Woodall (2008) <doi:10.1136/qshc.2004.012047>] for measure and count data. The main function, qic(), creates run and control charts and has a simple interface with a rich set of options to control data analysis and plotting, including options for automatic data aggregation by subgroups, easy analysis of before-and-after data, exclusion of one or more data points from analysis, and splitting charts into sequential time periods. Missing values and empty subgroups are handled gracefully.
Author: Jacob Anhoej [aut, cre], Timo Roeder [ctb]
Maintainer: Jacob Anhoej <jacob@anhoej.net>

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Package qrcm updated to version 3.2 with previous version 3.1 dated 2024-02-13

Title: Quantile Regression Coefficients Modeling
Description: Parametric modeling of quantile regression coefficient functions.
Author: Paolo Frumento [aut, cre]
Maintainer: Paolo Frumento <paolo.frumento@unipi.it>

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Package panelPomp updated to version 1.6.0.0 with previous version 1.5.0.0 dated 2024-12-08

Title: Inference for Panel Partially Observed Markov Processes
Description: Data analysis based on panel partially-observed Markov process (PanelPOMP) models. To implement such models, simulate them and fit them to panel data, 'panelPomp' extends some of the facilities provided for time series data by the 'pomp' package. Implemented methods include filtering (panel particle filtering) and maximum likelihood estimation (Panel Iterated Filtering) as proposed in Breto, Ionides and King (2020) "Panel Data Analysis via Mechanistic Models" <doi:10.1080/01621459.2019.1604367>.
Author: Carles Breto [aut] , Edward L. Ionides [aut] , Aaron A. King [aut] , Jesse Wheeler [aut, cre] , Aaron Abkemeier [ctb]
Maintainer: Jesse Wheeler <jeswheel@umich.edu>

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Package DiNAMIC.Duo updated to version 1.0.3 with previous version 1.0.2 dated 2023-03-02

Title: Finding Recurrent DNA Copy Number Alterations and Differences
Description: In tumor tissue, underlying genomic instability can lead to DNA copy number alterations, e.g., copy number gains or losses. Sporadic copy number alterations occur randomly throughout the genome, whereas recurrent alterations are observed in the same genomic region across multiple independent samples, perhaps because they provide a selective growth advantage. Here we use cyclic shift permutations to identify recurrent copy number alterations in a single cohort or recurrent copy number differences in two cohorts based on a common set of genomic markers. Additional functionality is provided to perform downstream analyses, including the creation of summary files and graphics. DiNAMIC.Duo builds upon the original DiNAMIC package of Walter et al. (2011) <doi:10.1093/bioinformatics/btq717> and leverages the theory developed in Walter et al. (2015) <doi:10.1093/biomet/asv046>. An article describing DiNAMIC.Duo by Walter et al. (2022) can be found at <doi: 10.1093/bioinformatics/ [...truncated...]
Author: Vonn Walter [aut, cre] , Hyo Young Choi [aut] , Xiaobei Zhao [aut] , Yan Gao [aut] , David Neil Hayes [aut]
Maintainer: Vonn Walter <vwalter1@pennstatehealth.psu.edu>

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Package capybara updated to version 0.9.3 with previous version 0.9.1 dated 2025-03-25

Title: Fast and Memory Efficient Fitting of Linear Models with High-Dimensional Fixed Effects
Description: Fast and user-friendly estimation of generalized linear models with multiple fixed effects and cluster the standard errors. The method to obtain the estimated fixed-effects coefficients is based on Stammann (2018) <doi:10.48550/arXiv.1707.01815> and Gaure (2013) <doi:10.1016/j.csda.2013.03.024>.
Author: Mauricio Vargas Sepulveda [aut, cre] , Yoto Yotov [ctb]
Maintainer: Mauricio Vargas Sepulveda <m.sepulveda@mail.utoronto.ca>

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Package speakeasyR updated to version 0.1.5 with previous version 0.1.4 dated 2024-09-24

Title: Fast and Robust Multi-Scale Graph Clustering
Description: A graph community detection algorithm that aims to be performant on large graphs and robust, returning consistent results across runs. SpeakEasy 2 (SE2), the underlying algorithm, is described in Chris Gaiteri, David R. Connell & Faraz A. Sultan et al. (2023) <doi:10.1186/s13059-023-03062-0>. The core algorithm is written in 'C', providing speed and keeping the memory requirements low. This implementation can take advantage of multiple computing cores without increasing memory usage. SE2 can detect community structure across scales, making it a good choice for biological data, which often has hierarchical structure. Graphs can be passed to the algorithm as adjacency matrices using base 'R' matrices, the 'Matrix' library, 'igraph' graphs, or any data that can be coerced into a matrix.
Author: David Connell [aut, cre, cph] , Chris Gaiteri [cph] , Gabor Csardi [cph, ctb] , Tamas Nepusz [cph, ctb] , Szabolcs Horvat [cph, ctb] , Vincent Traag [cph, ctb] , Fabio Zanini [cph, ctb] , Daniel Noom [cph, ctb] , The igraph development team [cph] , F [...truncated...]
Maintainer: David Connell <david32@dcon.addy.io>

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Package fgeo.tool updated to version 1.2.10 with previous version 1.2.9 dated 2024-01-27

Title: Import and Manipulate 'ForestGEO' Data
Description: To help you access, transform, analyze, and visualize 'ForestGEO' data, we developed a collection of R packages (<https://forestgeo.github.io/fgeo/>). This package, in particular, helps you to easily import, filter, and modify 'ForestGEO' data. To learn more about 'ForestGEO' visit <https://forestgeo.si.edu/>.
Author: Mauro Lepore [aut, ctr, cre] , Richard Condit [aut], Suzanne Lao [aut], Anudeep Singh [aut], CTFS-ForestGEO [cph, fnd]
Maintainer: Mauro Lepore <maurolepore@gmail.com>

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Package BIOdry updated to version 0.9.1 with previous version 0.9 dated 2022-05-02

Title: Multilevel Modeling of Dendroclimatical Fluctuations
Description: Multilevel ecological data series (MEDS) are sequences of observations ordered according to temporal/spatial hierarchies that are defined by sample designs, with sample variability confined to ecological factors. Dendroclimatic MEDS of tree rings and climate are modeled into normalized fluctuations of tree growth and aridity. Modeled fluctuations (model frames) are compared with Mantel correlograms on multiple levels defined by sample design. Package implementation can be understood by running examples in modelFrame(), and muleMan() functions.
Author: Wilson Lara [aut, cre] , Felipe Bravo [aut]
Maintainer: Wilson Lara <wilarhen@gmail.com>

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Package fgeo.analyze updated to version 1.1.15 with previous version 1.1.14 dated 2020-12-05

Title: Analyze ForestGEO Data
Description: To help you access, transform, analyze, and visualize ForestGEO data, we developed a collection of R packages (<https://forestgeo.github.io/fgeo/>). This package, in particular, helps you to implement analyses of plot species distributions, topography, demography, and biomass. It also includes a torus translation test to determine habitat associations of tree species as described by Zuleta et al. (2018) <doi:10.1007/s11104-018-3878-0>. To learn more about ForestGEO visit <https://forestgeo.si.edu/>.
Author: Mauro Lepore [aut, ctr, cre] , Gabriel Arellano [aut, rev], Richard Condit [aut], Matteo Detto [aut], Kyle Harms [aut], Suzanne Lao [aut, rev], KangMin Ngo [rev], Haley Overstreet [rev], Sabrina Russo [aut, rev], Daniel Zuleta [aut, rev], CTFS-Forest [...truncated...]
Maintainer: Mauro Lepore <maurolepore@gmail.com>

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Package dipsaus updated to version 0.3.1 with previous version 0.3.0 dated 2024-12-17

Title: A Dipping Sauce for Data Analysis and Visualizations
Description: Works as an "add-on" to packages like 'shiny', 'future', as well as 'rlang', and provides utility functions. Just like dipping sauce adding flavors to potato chips or pita bread, 'dipsaus' for data analysis and visualizations adds handy functions and enhancements to popular packages. The goal is to provide simple solutions that are frequently asked for online, such as how to synchronize 'shiny' inputs without freezing the app, or how to get memory size on 'Linux' or 'MacOS' system. The enhancements roughly fall into these four categories: 1. 'shiny' input widgets; 2. high-performance computing using the 'future' package; 3. modify R calls and convert among numbers, strings, and other objects. 4. utility functions to get system information such like CPU chip-set, memory limit, etc.
Author: Zhengjia Wang [aut, cre], John Magnotti [ctb] , Xiang Zhang [ctb]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>

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Package Cubist updated to version 0.5.0 with previous version 0.4.4 dated 2024-07-01

Title: Rule- And Instance-Based Regression Modeling
Description: Regression modeling using rules with added instance-based corrections.
Author: Max Kuhn [aut, cre], Steve Weston [ctb], Chris Keefer [ctb], Nathan Coulter [ctb], Ross Quinlan [aut] , Rulequest Research Pty Ltd. [cph]
Maintainer: Max Kuhn <mxkuhn@gmail.com>

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Package redatamx updated to version 1.1.1 with previous version 1.1.0 dated 2024-12-22

Title: R Interface to 'Redatam' Library
Description: Provides an API to work with 'Redatam' (see <https://redatam.org>) databases in both formats: 'RXDB' (new format) and 'DICX' (old format) and running 'Redatam' programs written in 'SPC' language. It's a wrapper around 'Redatam' core and provides functions to open/close a database (redatam_open()/redatam_close()), list entities and variables from the database (redatam_entities(), redatam_variables()) and execute a 'SPC' program and gets the results as data frames (redatam_query(), redatam_run()).
Author: Jaime Salvador [aut, cre] , CELADE [cph]
Maintainer: Jaime Salvador <jaime.salvador@ideasybits.com>

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Package r4ds.tutorials updated to version 0.3.1 with previous version 0.3.0 dated 2024-07-03

Title: Tutorials for "R for Data Science"
Description: When assigned "R for Data Science" (Wickham, Çetinkaya-Rundel, and Grolemund (2023, ISBN: 1492097402)), students should read the book and type in all the associated R commands themselves. Sadly, that never happens. These tutorials allow students to demonstrate (and their instructors to be sure) that all work has been completed. See Kane (2023) <https://ppbds.github.io/tutorial.helpers/articles/instructions.html> from the 'tutorial.helpers' package for a background discussion.
Author: David Kane [aut, cre, cph]
Maintainer: David Kane <dave.kane@gmail.com>

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Package rolldown updated to version 0.2 with previous version 0.1 dated 2019-07-14

Title: R Markdown Output Formats for Storytelling
Description: R Markdown output formats based on JavaScript libraries such as 'Scrollama' (<https://github.com/russellsamora/scrollama>) for storytelling.
Author: Yihui Xie [aut, cre] , Siqi Zhang [ctb], Russell Goldenberg [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

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Package kairos updated to version 2.2.1 with previous version 2.2.0 dated 2024-12-10

Title: Analysis of Chronological Patterns from Archaeological Count Data
Description: A toolkit for absolute and relative dating and analysis of chronological patterns. This package includes functions for chronological modeling and dating of archaeological assemblages from count data. It provides methods for matrix seriation. It also allows to compute time point estimates and density estimates of the occupation and duration of an archaeological site.
Author: Nicolas Frerebeau [aut, cre] , Brice Lebrun [art] , Ben Marwick [ctb] , Anne Philippe [ctb] , Universite Bordeaux Montaigne [fnd] , CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>

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Package bigD updated to version 0.3.1 with previous version 0.3.0 dated 2024-11-08

Title: Flexibly Format Dates and Times to a Given Locale
Description: Format dates and times flexibly and to whichever locales make sense. Parses dates, times, and date-times in various formats (including string-based ISO 8601 constructions). The formatting syntax gives the user many options for formatting the date and time output in a precise manner. Time zones in the input can be expressed in multiple ways and there are many options for formatting time zones in the output as well. Several of the provided helper functions allow for automatic generation of locale-aware formatting patterns based on date/time skeleton formats and standardized date/time formats with varying specificity.
Author: Richard Iannone [aut, cre] , Olivier Roy [ctb], Posit Software, PBC [cph, fnd]
Maintainer: Richard Iannone <rich@posit.co>

Diff between bigD versions 0.3.0 dated 2024-11-08 and 0.3.1 dated 2025-04-03

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Package oompaBase updated to version 3.2.10 with previous version 3.2.9 dated 2019-08-24

Title: Class Unions, Matrix Operations, and Color Schemes for OOMPA
Description: Provides the class unions that must be preloaded in order for the basic tools in the OOMPA (Object-Oriented Microarray and Proteomics Analysis) project to be defined and loaded. It also includes vectorized operations for row-by-row means, variances, and t-tests. Finally, it provides new color schemes. Details on the packages in the OOMPA project can be found at <http://oompa.r-forge.r-project.org/>.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>

Diff between oompaBase versions 3.2.9 dated 2019-08-24 and 3.2.10 dated 2025-04-03

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Package lazyWeave updated to version 3.0.3 with previous version 3.0.2 dated 2018-01-25

Title: LaTeX Wrappers for R Users
Description: Provides the functionality to write LaTeX code from within R without having to learn LaTeX. Functionality also exists to create HTML and Markdown code. While the functionality still exists to write complete documents with lazyWeave, it is generally easier to do so with with markdown and knitr. lazyWeave's main strength now is the ability to design custom and complex tables for reporting results.
Author: Benjamin Nutter [aut, cre]
Maintainer: Benjamin Nutter <benjamin.nutter@gmail.com>

Diff between lazyWeave versions 3.0.2 dated 2018-01-25 and 3.0.3 dated 2025-04-03

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Package arc updated to version 1.4.2 with previous version 1.4 dated 2023-08-17

Title: Association Rule Classification
Description: Implements the Classification-based on Association Rules (CBA) algorithm for association rule classification. The package, also described in Hahsler et al. (2019) <doi:10.32614/RJ-2019-048>, contains several convenience methods that allow to automatically set CBA parameters (minimum confidence, minimum support) and it also natively handles numeric attributes by integrating a pre-discretization step. The rule generation phase is handled by the 'arules' package. To further decrease the size of the CBA models produced by the 'arc' package, postprocessing by the 'qCBA' package is suggested.
Author: Tomas Kliegr [aut, cre]
Maintainer: Tomas Kliegr <kliegr@gmail.com>

Diff between arc versions 1.4 dated 2023-08-17 and 1.4.2 dated 2025-04-03

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Package SimBIID updated to version 0.2.2 with previous version 0.2.1 dated 2021-02-04

Title: Simulation-Based Inference Methods for Infectious Disease Models
Description: Provides some code to run simulations of state-space models, and then use these in the Approximate Bayesian Computation Sequential Monte Carlo (ABC-SMC) algorithm of Toni et al. (2009) <doi:10.1098/rsif.2008.0172> and a bootstrap particle filter based particle Markov chain Monte Carlo (PMCMC) algorithm (Andrieu et al., 2010 <doi:10.1111/j.1467-9868.2009.00736.x>). Also provides functions to plot and summarise the outputs.
Author: Trevelyan J. McKinley [aut, cre], Stefan Widgren [aut] , Pavol Bauer [cph] , Robin Eriksson [cph] , Stefan Engblom [cph]
Maintainer: Trevelyan J. McKinley <t.mckinley@exeter.ac.uk>

Diff between SimBIID versions 0.2.1 dated 2021-02-04 and 0.2.2 dated 2025-04-03

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Package revealjs updated to version 0.10.0 with previous version 0.9 dated 2017-03-13

Title: R Markdown Format for 'reveal.js' Presentations
Description: R Markdown format for 'reveal.js' presentations, a framework for easily creating beautiful presentations using HTML.
Author: Christophe Dervieux [cre], JJ Allaire [aut], Hakim El Hattab [aut, cph] , Asvin Goel [ctb, cph] , Greg Denehy [ctb, cph] , Posit Software, PBC [cph, fnd]
Maintainer: Christophe Dervieux <cderv@posit.co>

Diff between revealjs versions 0.9 dated 2017-03-13 and 0.10.0 dated 2025-04-03

 revealjs-0.10.0/revealjs/DESCRIPTION                                                           |   45 
 revealjs-0.10.0/revealjs/LICENSE                                                               |    4 
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 revealjs-0.10.0/revealjs/NAMESPACE                                                             |    8 
 revealjs-0.10.0/revealjs/NEWS.md                                                               |only
 revealjs-0.10.0/revealjs/R/revealjs.R                                                          |    6 
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 revealjs-0.9/revealjs/inst/COPYING                                                             |only
 revealjs-0.9/revealjs/inst/NEWS                                                                |only
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Package RARtrials updated to version 0.0.2 with previous version 0.0.1 dated 2024-06-04

Title: Response-Adaptive Randomization in Clinical Trials
Description: Some response-adaptive randomization methods commonly found in literature are included in this package. These methods include the randomized play-the-winner rule for binary endpoint (Wei and Durham (1978) <doi:10.2307/2286290>), the doubly adaptive biased coin design with minimal variance strategy for binary endpoint (Atkinson and Biswas (2013) <doi:10.1201/b16101>, Rosenberger and Lachin (2015) <doi:10.1002/9781118742112>) and maximal power strategy targeting Neyman allocation for binary endpoint (Tymofyeyev, Rosenberger, and Hu (2007) <doi:10.1198/016214506000000906>) and RSIHR allocation with each letter representing the first character of the names of the individuals who first proposed this rule (Youngsook and Hu (2010) <doi:10.1198/sbr.2009.0056>, Bello and Sabo (2016) <doi:10.1080/00949655.2015.1114116>), A-optimal Allocation for continuous endpoint (Sverdlov and Rosenberger (2013) <doi:10.1080/15598608.2013.783726>), Aa-optimal Allocatio [...truncated...]
Author: Chuyao Xu [aut, cre], Thomas Lumley [aut, ths], Alain Vandal [aut, ths], Sofia S. Villar [cph], Kyle J. Wathen [cph]
Maintainer: Chuyao Xu <cxu870@aucklanduni.ac.nz>

Diff between RARtrials versions 0.0.1 dated 2024-06-04 and 0.0.2 dated 2025-04-03

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Package qCBA updated to version 1.0.2 with previous version 1.0 dated 2024-08-28

Title: Postprocessing of Rule Classification Models Learnt on Quantized Data
Description: Implements the Quantitative Classification-based on Association Rules (QCBA) algorithm (<doi:10.1007/s10489-022-04370-x>). QCBA postprocesses rule classification models making them typically smaller and in some cases more accurate. Supported are 'CBA' implementations from 'rCBA', 'arulesCBA' and 'arc' packages, and 'CPAR', 'CMAR', 'FOIL2' and 'PRM' implementations from 'arulesCBA' package and 'SBRL' implementation from the 'sbrl' package. The result of the post-processing is an ordered CBA-like rule list.
Author: Tomas Kliegr [aut, cre]
Maintainer: Tomas Kliegr <kliegr@gmail.com>

Diff between qCBA versions 1.0 dated 2024-08-28 and 1.0.2 dated 2025-04-03

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Package abe updated to version 5.1.2 with previous version 3.0.1 dated 2017-10-30

Title: Augmented Backward Elimination
Description: Performs augmented backward elimination and checks the stability of the obtained model. Augmented backward elimination combines significance or information based criteria with the change in estimate to either select the optimal model for prediction purposes or to serve as a tool to obtain a practically sound, highly interpretable model. More details can be found in Dunkler et al. (2014) <doi:10.1371/journal.pone.0113677>.
Author: Rok Blagus [aut, cre], Sladana Babic [ctb], Daniela Dunkler [ctb], Georg Heinze [ctb], Gregor Steiner [ctb]
Maintainer: Rok Blagus <rok.blagus@mf.uni-lj.si>

Diff between abe versions 3.0.1 dated 2017-10-30 and 5.1.2 dated 2025-04-03

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More information about abe at CRAN
Permanent link

Package sentometrics updated to version 1.0.1 with previous version 1.0.0 dated 2021-08-18

Title: An Integrated Framework for Textual Sentiment Time Series Aggregation and Prediction
Description: Optimized prediction based on textual sentiment, accounting for the intrinsic challenge that sentiment can be computed and pooled across texts and time in various ways. See Ardia et al. (2021) <doi:10.18637/jss.v099.i02>.
Author: Samuel Borms [aut, cre] , David Ardia [aut] , Keven Bluteau [aut] , Kris Boudt [aut] , Jeroen Van Pelt [ctb], Andres Algaba [ctb]
Maintainer: Samuel Borms <borms_sam@hotmail.com>

Diff between sentometrics versions 1.0.0 dated 2021-08-18 and 1.0.1 dated 2025-04-03

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More information about sentometrics at CRAN
Permanent link

Package MLE updated to version 1.5 with previous version 1.4 dated 2025-02-17

Title: Maximum Likelihood Estimation of Various Univariate and Multivariate Distributions
Description: Several functions for maximum likelihood estimation of various univariate and multivariate distributions. The list includes more than 100 functions for univariate continuous and discrete distributions, distributions that lie on the real line, the positive line, interval restricted, circular distributions. Further, multivariate continuous and discrete distributions, distributions for compositional and directional data, etc. Some references include Johnson N. L., Kotz S. and Balakrishnan N. (1994). "Continuous Univariate Distributions, Volume 1" <ISBN:978-0-471-58495-7>, Johnson, Norman L. Kemp, Adrianne W. Kotz, Samuel (2005). "Univariate Discrete Distributions". <ISBN:978-0-471-71580-1> and Mardia, K. V. and Jupp, P. E. (2000). "Directional Statistics". <ISBN:978-0-471-95333-3>.
Author: Michail Tsagris [aut, cre], Sofia Piperaki [aut], Muhammad Imran [ctb], Rafail Vargiakakis [aut], Nikolaos Kontemeniotis [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>

Diff between MLE versions 1.4 dated 2025-02-17 and 1.5 dated 2025-04-03

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Package HDANOVA updated to version 0.8.3 with previous version 0.8.2 dated 2025-01-21

Title: High-Dimensional Analysis of Variance
Description: Functions and datasets to support Smilde, Marini, Westerhuis and Liland (2025, ISBN: 978-1-394-21121-0) "Analysis of Variance for High-Dimensional Data - Applications in Life, Food and Chemical Sciences". This implements and imports a collection of methods for HD-ANOVA data analysis with common interfaces, result- and plotting functions, multiple real data sets and four vignettes covering a range different applications.
Author: Kristian Hovde Liland [aut, cre]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>

Diff between HDANOVA versions 0.8.2 dated 2025-01-21 and 0.8.3 dated 2025-04-03

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Package toastui updated to version 0.4.0 with previous version 0.3.4 dated 2024-09-18

Title: Interactive Tables, Calendars and Charts for the Web
Description: Create interactive tables, calendars, charts and markdown WYSIWYG editor with 'TOAST UI' <https://ui.toast.com/> libraries to integrate in 'shiny' applications or 'rmarkdown' 'HTML' documents.
Author: Victor Perrier [aut, cre, cph], Fanny Meyer [aut], NHN FE Development Lab [cph]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

Diff between toastui versions 0.3.4 dated 2024-09-18 and 0.4.0 dated 2025-04-03

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Package ImportExport updated to version 1.3.1 with previous version 1.3 dated 2020-09-21

Title: Import and Export Data
Description: Import and export data from the most common statistical formats by using R functions that guarantee the least loss of the data information, giving special attention to the date variables and the labelled ones.
Author: Roger Pros [aut], Isaac Subirana [aut, cre], Joan Vila [ctb]
Maintainer: Isaac Subirana <isubirana@imim.es>

Diff between ImportExport versions 1.3 dated 2020-09-21 and 1.3.1 dated 2025-04-03

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Package GitStats updated to version 2.3.0 with previous version 2.2.2 dated 2025-02-11

Title: Standardized Git Repository Data
Description: Obtain standardized data from multiple 'Git' services, including 'GitHub' and 'GitLab'. Designed to be 'Git' service-agnostic, this package assists teams with activities spread across various 'Git' platforms by providing a unified way to access repository data.
Author: Maciej Banas [aut, cre], Kamil Koziej [aut], Karolina Marcinkowska [aut], Matt Secrest [aut]
Maintainer: Maciej Banas <banasmaciek@gmail.com>

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Package blastula updated to version 0.3.6 with previous version 0.3.5 dated 2024-02-24

Title: Easily Send HTML Email Messages
Description: Compose and send out responsive HTML email messages that render perfectly across a range of email clients and device sizes. Helper functions let the user insert embedded images, web link buttons, and 'ggplot2' plot objects into the message body. Messages can be sent through an 'SMTP' server, through the 'Posit Connect' service, or through the 'Mailgun' API service <https://www.mailgun.com/>.
Author: Richard Iannone [aut, cre] , Joe Cheng [aut], Jeroen Ooms [ctb] , Ted Goas [cph] , Posit Software, PBC [cph, fnd]
Maintainer: Richard Iannone <rich@posit.co>

Diff between blastula versions 0.3.5 dated 2024-02-24 and 0.3.6 dated 2025-04-03

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Package C50 updated to version 0.2.0 with previous version 0.1.8 dated 2023-02-08

Title: C5.0 Decision Trees and Rule-Based Models
Description: C5.0 decision trees and rule-based models for pattern recognition that extend the work of Quinlan (1993, ISBN:1-55860-238-0).
Author: Max Kuhn [aut, cre], Steve Weston [ctb], Mark Culp [ctb], Nathan Coulter [ctb], Ross Quinlan [aut] , RuleQuest Research [cph] , Rulequest Research Pty Ltd. [cph]
Maintainer: Max Kuhn <mxkuhn@gmail.com>

Diff between C50 versions 0.1.8 dated 2023-02-08 and 0.2.0 dated 2025-04-03

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Package amberr updated to version 1.2.0 with previous version 1.1.0 dated 2024-07-05

Title: 'Amber' Electronic Data Capture Client
Description: 'Amber' is a server application for capturing electronic data records. Rich forms are used to collect data. This 'Amber' client allows to perform data extraction for reporting or data transfer at persistent location purposes.
Author: Yannick Marcon [aut, cre] , OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>

Diff between amberr versions 1.1.0 dated 2024-07-05 and 1.2.0 dated 2025-04-03

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Package mclustAddons updated to version 0.9.2 with previous version 0.9.1 dated 2024-11-13

Title: Addons for the 'mclust' Package
Description: Extend the functionality of the 'mclust' package for Gaussian finite mixture modeling by including: density estimation for data with bounded support (Scrucca, 2019 <doi:10.1002/bimj.201800174>); modal clustering using MEM (Modal EM) algorithm for Gaussian mixtures (Scrucca, 2021 <doi:10.1002/sam.11527>); entropy estimation via Gaussian mixture modeling (Robin & Scrucca, 2023 <doi:10.1016/j.csda.2022.107582>); Gaussian mixtures modeling of financial log-returns (Scrucca, 2024 <doi:10.3390/e26110907>).
Author: Luca Scrucca [aut, cre, cph]
Maintainer: Luca Scrucca <luca.scrucca@unibo.it>

Diff between mclustAddons versions 0.9.1 dated 2024-11-13 and 0.9.2 dated 2025-04-03

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Package lazysf updated to version 0.2.0 with previous version 0.1.0 dated 2020-11-14

Title: Delayed Read for 'GDAL' Vector Data Sources
Description: Lazy read for drawings. A 'dplyr' back end for data sources supported by 'GDAL' vector drivers, that allows working with local or remote sources as if they are in-memory data frames. Basic features works with any drawing format ('GDAL vector data source') supported by the 'sf' package.
Author: Michael Sumner [aut, cre]
Maintainer: Michael Sumner <mdsumner@gmail.com>

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Package omnibus updated to version 1.2.15 with previous version 1.2.14 dated 2024-09-17

Title: Helper Tools for Managing Data, Dates, Missing Values, and Text
Description: An assortment of helper functions for managing data (e.g., rotating values in matrices by a user-defined angle, switching from row- to column-indexing), dates (e.g., intuiting year from messy date strings), handling missing values (e.g., removing elements/rows across multiple vectors or matrices if any have an NA), text (e.g., flushing reports to the console in real-time); and combining data frames with different schema (copying, filling, or concatenating columns or applying functions before combining).
Author: Adam B. Smith [cre, aut]
Maintainer: Adam B. Smith <adam.smith@mobot.org>

Diff between omnibus versions 1.2.14 dated 2024-09-17 and 1.2.15 dated 2025-04-03

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Wed, 02 Apr 2025

Package bsamGP updated to version 1.2.6 with previous version 1.2.5 dated 2024-03-18

Title: Bayesian Spectral Analysis Models using Gaussian Process Priors
Description: Contains functions to perform Bayesian inference using a spectral analysis of Gaussian process priors. Gaussian processes are represented with a Fourier series based on cosine basis functions. Currently the package includes parametric linear models, partial linear additive models with/without shape restrictions, generalized linear additive models with/without shape restrictions, and density estimation model. To maximize computational efficiency, the actual Markov chain Monte Carlo sampling for each model is done using codes written in FORTRAN 90. This software has been developed using funding supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (no. NRF-2016R1D1A1B03932178 and no. NRF-2017R1D1A3B03035235).
Author: Seongil Jo [aut], Taeryon Choi [aut], Beomjo Park [aut, cre], Peter J. Lenk [ctb]
Maintainer: Beomjo Park <beomjop@gmail.com>

Diff between bsamGP versions 1.2.5 dated 2024-03-18 and 1.2.6 dated 2025-04-02

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Package rbgm updated to version 0.2.0 with previous version 0.1.0 dated 2020-04-12

Title: Tools for 'Box Geometry Model' (BGM) Files and Topology for the Atlantis Ecosystem Model
Description: Facilities for working with Atlantis box-geometry model (BGM) files. Atlantis is a deterministic, biogeochemical, whole-of-ecosystem model. Functions are provided to read from BGM files directly, preserving their internal topology, as well as helper functions to generate spatial data from these mesh forms. This functionality aims to simplify the creation and modification of box and geometry as well as the ability to integrate with other data sources.
Author: Michael D. Sumner [aut, cre]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>

Diff between rbgm versions 0.1.0 dated 2020-04-12 and 0.2.0 dated 2025-04-02

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Package PROJ updated to version 0.6.0 with previous version 0.5.0 dated 2024-06-12

Title: Generic Coordinate System Transformations Using 'PROJ'
Description: A wrapper around the generic coordinate transformation software 'PROJ' that transforms coordinates from one coordinate reference system ('CRS') to another. This includes cartographic projections as well as geodetic transformations. The intention is for this package to be used by user-packages such as 'reproj', and that the older 'PROJ.4' and version 5 pathways be provided by the 'proj4' package.
Author: Michael D. Sumner [aut, cre] , Jeroen Ooms [ctb] , Simon Urbanek [cph, ctb] , Dewey Dunnington [ctb] , Anthony North [ctb]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>

Diff between PROJ versions 0.5.0 dated 2024-06-12 and 0.6.0 dated 2025-04-02

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Package growthPheno updated to version 3.1.11 with previous version 3.1.10 dated 2025-01-12

Title: Functional Analysis of Phenotypic Growth Data to Smooth and Extract Traits
Description: Assists in the plotting and functional smoothing of traits measured over time and the extraction of features from these traits, implementing the SET (Smoothing and Extraction of Traits) method described in Brien et al. (2020) Plant Methods, 16. Smoothing of growth trends for individual plants using natural cubic smoothing splines or P-splines is available for removing transient effects and segmented smoothing is available to deal with discontinuities in growth trends. There are graphical tools for assessing the adequacy of trait smoothing, both when using this and other packages, such as those that fit nonlinear growth models. A range of per-unit (plant, pot, plot) growth traits or features can be extracted from the data, including single time points, interval growth rates and other growth statistics, such as maximum growth or days to maximum growth. The package also has tools adapted to inputting data from high-throughput phenotyping facilities, such from a Lemna-Tec Scananalyzer 3D ( [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>

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Package faoutlier updated to version 0.7.7 with previous version 0.7.6 dated 2021-01-10

Title: Influential Case Detection Methods for Factor Analysis and Structural Equation Models
Description: Tools for detecting and summarize influential cases that can affect exploratory and confirmatory factor analysis models as well as structural equation models more generally (Chalmers, 2015, <doi:10.1177/0146621615597894>; Flora, D. B., LaBrish, C. & Chalmers, R. P., 2012, <doi:10.3389/fpsyg.2012.00055>).
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>

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Package glmmTMB updated to version 1.1.11 with previous version 1.1.10 dated 2024-09-26

Title: Generalized Linear Mixed Models using Template Model Builder
Description: Fit linear and generalized linear mixed models with various extensions, including zero-inflation. The models are fitted using maximum likelihood estimation via 'TMB' (Template Model Builder). Random effects are assumed to be Gaussian on the scale of the linear predictor and are integrated out using the Laplace approximation. Gradients are calculated using automatic differentiation.
Author: Mollie Brooks [aut, cre] , Ben Bolker [aut] , Kasper Kristensen [aut], Martin Maechler [aut] , Arni Magnusson [aut] , Maeve McGillycuddy [ctb], Hans Skaug [aut] , Anders Nielsen [aut] , Casper Berg [aut] , Koen van Bentham [aut], Nafis Sadat [ctb] , [...truncated...]
Maintainer: Mollie Brooks <mollieebrooks@gmail.com>

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Package scDECO updated to version 0.1.1 with previous version 0.1.0 dated 2024-06-04

Title: Estimating Dynamic Correlation
Description: Implementations for two different Bayesian models of differential co-expression. scdeco.cop() fits the bivariate Gaussian copula model from Zichen Ma, Shannon W. Davis, Yen-Yi Ho (2023) <doi:10.1111/biom.13701>, while scdeco.pg() fits the bivariate Poisson-Gamma model from Zhen Yang, Yen-Yi Ho (2022) <doi:10.1111/biom.13457>.
Author: Anderson Bussing [aut, cre], Yen-Yi Ho [aut, ths], Zichen Ma [aut], Zhen Yang [aut]
Maintainer: Anderson Bussing <abussing@email.sc.edu>

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Package BGmisc updated to version 1.3.5 with previous version 1.3.3 dated 2025-02-19

Title: An R Package for Extended Behavior Genetics Analysis
Description: Provides functions for behavior genetics analysis, including variance component model identification [Hunter et al. (2021) <doi:10.1007/s10519-021-10055-x>], calculation of relatedness coefficients using path-tracing methods [Wright (1922) <doi:10.1086/279872>; McArdle & McDonald (1984) <doi:10.1111/j.2044-8317.1984.tb00802.x>], inference of relatedness, pedigree conversion, and simulation of multi-generational family data [Lyu et al. (2024) <doi:10.1101/2024.12.19.629449>]. For a full overview, see Garrison et al. (2024) <doi:10.21105/joss.06203>.
Author: S. Mason Garrison [aut, cre] , Michael D. Hunter [aut] , Xuanyu Lyu [aut] , Rachel N. Good [ctb], Jonathan D. Trattner [aut] , S. Alexandra Burt [aut]
Maintainer: S. Mason Garrison <garrissm@wfu.edu>

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Package rsample updated to version 1.3.0 with previous version 1.2.1 dated 2024-03-25

Title: General Resampling Infrastructure
Description: Classes and functions to create and summarize different types of resampling objects (e.g. bootstrap, cross-validation).
Author: Hannah Frick [aut, cre] , Fanny Chow [aut], Max Kuhn [aut], Michael Mahoney [aut] , Julia Silge [aut] , Hadley Wickham [aut], Posit Software, PBC [cph, fnd]
Maintainer: Hannah Frick <hannah@posit.co>

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Package fio updated to version 0.1.5 with previous version 0.1.2 dated 2024-08-27

Title: Friendly Input-Output Analysis
Description: Simplifies the process of importing and managing input-output matrices from 'Microsoft Excel' into R, and provides a suite of functions for analysis. It leverages the 'R6' class for clean, memory-efficient object-oriented programming. Furthermore, all linear algebra computations are implemented in 'Rust' to achieve highly optimized performance.
Author: Alberson da Silva Miranda [aut, cre, cph] , Celso Bissoli Sessa [dtc]
Maintainer: Alberson da Silva Miranda <albersonmiranda@hotmail.com>

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Package AllelicSeries updated to version 0.1.1.5 with previous version 0.1.1.2 dated 2024-11-23

Title: Allelic Series Test
Description: Implementation of gene-level rare variant association tests targeting allelic series: genes where increasingly deleterious mutations have increasingly large phenotypic effects. The COding-variant Allelic Series Test (COAST) operates on the benign missense variants (BMVs), deleterious missense variants (DMVs), and protein truncating variants (PTVs) within a gene. COAST uses a set of adjustable weights that tailor the test towards rejecting the null hypothesis for genes where the average magnitude of effect increases monotonically from BMVs to DMVs to PTVs. See McCaw ZR, O’Dushlaine C, Somineni H, Bereket M, Klein C, Karaletsos T, Casale FP, Koller D, Soare TW. (2023) "An allelic series rare variant association test for candidate gene discovery" <doi:10.1016/j.ajhg.2023.07.001>.
Author: Zachary McCaw [aut, cre] , Christoph Klein [ctb] , Thomas Soare [ctb] , Jianhui Gao [ctb] , insitro [cph]
Maintainer: Zachary McCaw <zmccaw@alumni.harvard.edu>

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Package xfun updated to version 0.52 with previous version 0.51 dated 2025-02-19

Title: Supporting Functions for Packages Maintained by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] , Wush Wu [ctb], Daijiang Li [ctb], Xianying Tan [ctb], Salim Brueggemann [ctb] , Christophe Dervieux [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

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Package PSpower updated to version 0.1.1 with previous version 0.1.0 dated 2025-01-15

Title: Sample Size Calculation for Propensity Score Analysis
Description: Sample size calculations in causal inference with observational data are increasingly desired. This package is a tool to calculate sample size under prespecified power with minimal summary quantities needed.
Author: Bo Liu [aut, cre], Xiaoxiao Zhou [ctb], Fan Li [ctb]
Maintainer: Bo Liu <bl226@duke.edu>

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Package PAMscapes updated to version 0.11.3 with previous version 0.10.0 dated 2025-01-29

Title: Tools for Summarising and Analysing Soundscape Data
Description: A variety of tools relevant to the analysis of marine soundscape data. There are tools for downloading AIS (automatic identification system) data from Marine Cadastre <https://hub.marinecadastre.gov>, connecting AIS data to GPS coordinates, plotting summaries of various soundscape measurements, and downloading relevant environmental variables (wind, swell height) from the National Center for Atmospheric Research data server <https://rda.ucar.edu/datasets/ds084.1/>. Most tools were developed to work well with output from 'Triton' software, but can be adapted to work with any similar measurements.
Author: Taiki Sakai [aut, cre], Anne Simonis [ctb], Shannon Rankin [ctb], Megan McKenna [ctb], Kaitlin Palmer [ctb]
Maintainer: Taiki Sakai <taiki.sakai@noaa.gov>

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Package dsb updated to version 2.0.0 with previous version 1.0.4 dated 2024-06-15

Title: Normalize & Denoise Droplet Single Cell Protein Data (CITE-Seq)
Description: This lightweight R package provides a method for normalizing and denoising protein expression data from droplet based single cell experiments. Raw protein Unique Molecular Index (UMI) counts from sequencing DNA-conjugated antibody derived tags (ADT) in droplets (e.g. 'CITE-seq') have substantial measurement noise. Our experiments and computational modeling revealed two major components of this noise: 1) protein-specific noise originating from ambient, unbound antibody encapsulated in droplets that can be accurately inferred via the expected protein counts detected in empty droplets, and 2) droplet/cell-specific noise revealed via the shared variance component associated with isotype antibody controls and background protein counts in each cell. This package normalizes and removes both of these sources of noise from raw protein data derived from methods such as 'CITE-seq', 'REAP-seq', 'ASAP-seq', 'TEA-seq', 'proteogenomic' data from the Mission Bio platform, etc. See the vignette for tut [...truncated...]
Author: Matthew Mule [aut, cre] , Andrew Martins [aut] , John Tsang [pdr]
Maintainer: Matthew Mule <mattmule@gmail.com>

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Package pnd updated to version 0.0.10 with previous version 0.0.9 dated 2025-03-11

Title: Parallel Numerical Derivatives, Gradients, Jacobians, and Hessians of Arbitrary Accuracy Order
Description: Numerical derivatives through finite-difference approximations can be calculated using the 'pnd' package with parallel capabilities and optimal step-size selection to improve accuracy. These functions facilitate efficient computation of derivatives, gradients, Jacobians, and Hessians, allowing for more evaluations to reduce the mathematical and machine errors. Designed for compatibility with the 'numDeriv' package, which has not received updates in several years, it introduces advanced features such as computing derivatives of arbitrary order, improving the accuracy of Hessian approximations by avoiding repeated differencing, and parallelising slow functions on Windows, Mac, and Linux.
Author: Andrei Victorovitch Kostyrka [aut, cre]
Maintainer: Andrei Victorovitch Kostyrka <andrei.kostyrka@gmail.com>

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Package penetrance updated to version 0.1.1 with previous version 0.1.0 dated 2025-03-03

Title: Methods for Penetrance Estimation in Family-Based Studies
Description: Implements statistical methods for estimating disease penetrance in family-based studies. Penetrance refers to the probability of disease§ manifestation in individuals carrying specific genetic variants. The package provides tools for age-specific penetrance estimation, handling missing data, and accounting for ascertainment bias in family studies. Cite as: Kubista, N., Braun, D. & Parmigiani, G. (2024) <doi:10.48550/arXiv.2411.18816>.
Author: Nicolas Kubista [aut, cre], BayesMendel Lab [aut]
Maintainer: Nicolas Kubista <bmendel@jimmy.harvard.edu>

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Package pRecipe updated to version 3.0.3 with previous version 3.0.2 dated 2024-12-07

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

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Package MonotonicityTest updated to version 1.1 with previous version 1.0 dated 2025-01-17

Title: Nonparametric Bootstrap Test for Regression Monotonicity
Description: Implements nonparametric bootstrap tests for detecting monotonicity in regression functions from Hall, P. and Heckman, N. (2000) <doi:10.1214/aos/1016120363> Includes tools for visualizing results using Nadaraya-Watson kernel regression and supports efficient computation with 'C++'.
Author: Dylan Huynh [aut, cre]
Maintainer: Dylan Huynh <dylanhuynh@utexas.edu>

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Package GeneCycle updated to version 1.1.6 with previous version 1.1.5 dated 2021-01-05

Title: Identification of Periodically Expressed Genes
Description: The GeneCycle package implements the approaches of Wichert et al. (2004) <doi:10.1093/bioinformatics/btg364>, Ahdesmaki et al. (2005) <doi:10.1186/1471-2105-6-117> and Ahdesmaki et al. (2007) <DOI:10.1186/1471-2105-8-233> for detecting periodically expressed genes from gene expression time series data.
Author: Miika Ahdesmaki [aut, cre], Konstantinos Fokianos [aut], Korbinian Strimmer [aut]
Maintainer: Miika Ahdesmaki <miika.ahdesmaki@gmail.com>

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Package dbarts updated to version 0.9-32 with previous version 0.9-30 dated 2024-12-03

Title: Discrete Bayesian Additive Regression Trees Sampler
Description: Fits Bayesian additive regression trees (BART; Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>) while allowing the updating of predictors or response so that BART can be incorporated as a conditional model in a Gibbs/Metropolis-Hastings sampler. Also serves as a drop-in replacement for package 'BayesTree'.
Author: Vincent Dorie [aut, cre] , Hugh Chipman [aut], Robert McCulloch [aut], Armon Dadgar [ctb] , R Core Team [ctb] , Guido U Draheim [ctb] , Maarten Bosmans [ctb] , Christophe Tournayre [ctb] , Michael Petch [ctb] , Rafael de Lucena Valle [ctb] , Steven G [...truncated...]
Maintainer: Vincent Dorie <vdorie@gmail.com>

Diff between dbarts versions 0.9-30 dated 2024-12-03 and 0.9-32 dated 2025-04-02

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Package basifoR updated to version 0.4.1 with previous version 0.4 dated 2021-09-20

Title: Retrieval and Processing of the Spanish National Forest Inventory
Description: Data sets of the Spanish National Forest Inventory <https://www.miteco.gob.es/es/biodiversidad/servicios/banco-datos-naturaleza/informacion-disponible.html> are processed to compute tree metrics and statistics. Function metrics2Vol() controls most of the routines.
Author: Wilson Lara [aut, cre] , Cristobal Ordonez [aut] , Felipe Bravo [aut]
Maintainer: Wilson Lara <wilarhen@gmail.com>

Diff between basifoR versions 0.4 dated 2021-09-20 and 0.4.1 dated 2025-04-02

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Package PakNAcc updated to version 0.3.0 with previous version 0.1.0 dated 2024-11-11

Title: 'shiny' App for National Accounts
Description: Provides a comprehensive suite of tools for analyzing Pakistan's Quarterly National Accounts data. Users can gain detailed insights into Pakistan's economic performance, visualize quarterly trends, and detect patterns and anomalies in key economic indicators. Compare sector contributions—including agriculture, industry, and services—to understand their influence on economic growth or decline. Customize analyses by filtering and manipulating data to focus on specific areas of interest. Ideal for policymakers, researchers, and analysts aiming to make informed, data-driven decisions based on timely and detailed economic insights.
Author: Muhammad Yaseen [aut, cre, cph] , Zahid Asghar [ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>

Diff between PakNAcc versions 0.1.0 dated 2024-11-11 and 0.3.0 dated 2025-04-02

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Package LSAfun updated to version 0.8.1 with previous version 0.7.1 dated 2023-11-17

Title: Applied Latent Semantic Analysis (LSA) Functions
Description: Provides functions that allow for convenient working with vector space models of semantics/distributional semantic models/word embeddings. Originally built for LSA models (hence the name), but can be used for all such vector-based models. For actually building a vector semantic space, use the package 'lsa' or other specialized software. Downloadable semantic spaces can be found at <https://sites.google.com/site/fritzgntr/software-resources>.
Author: Fritz Guenther [aut, cre]
Maintainer: Fritz Guenther <fritz.guenther@uni-tuebingen.de>

Diff between LSAfun versions 0.7.1 dated 2023-11-17 and 0.8.1 dated 2025-04-02

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Package leidenbase updated to version 0.1.35 with previous version 0.1.32 dated 2025-02-05

Title: R and C/C++ Wrappers to Run the Leiden find_partition() Function
Description: An R to C/C++ interface that runs the Leiden community detection algorithm to find a basic partition (). It runs the equivalent of the 'leidenalg' find_partition() function, which is given in the 'leidenalg' distribution file 'leiden/src/functions.py'. This package includes the required source code files from the official 'leidenalg' distribution and functions from the R 'igraph' package. The 'leidenalg' distribution is available from <https://github.com/vtraag/leidenalg/> and the R 'igraph' package is available from <https://igraph.org/r/>. The Leiden algorithm is described in the article by Traag et al. (2019) <doi:10.1038/s41598-019-41695-z>. Leidenbase includes code from the packages: igraph version 0.9.8 with license GPL (>= 2), leidenalg version 0.8.10 with license GPL 3.
Author: Brent Ewing [aut, cre], Vincent Traag [ctb], Gabor Csardi [ctb], Tamas Nepusz [ctb], Szabolcs Horvat [ctb], Fabio Zanini [ctb]
Maintainer: Brent Ewing <bge@uw.edu>

Diff between leidenbase versions 0.1.32 dated 2025-02-05 and 0.1.35 dated 2025-04-02

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Package dndR updated to version 3.0.0 with previous version 2.0.0 dated 2024-04-26

Title: Dungeons & Dragons Functions for Players and Dungeon Masters
Description: The goal of 'dndR' is to provide a suite of Dungeons & Dragons related functions. This package is meant to be useful both to players and Dungeon Masters (DMs). Some functions apply to many tabletop role-playing games (e.g., dice rolling), but others are focused on Fifth Edition (a.k.a. "5e") and where possible both there 2014 and 2024 versions are supported.
Author: Nicholas Lyon [aut, cre, cph] , Tim Schatto-Eckrodt [aut] , Humberto Nappo [ctb]
Maintainer: Nicholas Lyon <njlyon@alumni.iastate.edu>

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Package smooth updated to version 4.2.0 with previous version 4.1.1 dated 2025-02-03

Title: Forecasting Using State Space Models
Description: Functions implementing Single Source of Error state space models for purposes of time series analysis and forecasting. The package includes ADAM (Svetunkov, 2023, <https://openforecast.org/adam/>), Exponential Smoothing (Hyndman et al., 2008, <doi: 10.1007/978-3-540-71918-2>), SARIMA (Svetunkov & Boylan, 2019 <doi: 10.1080/00207543.2019.1600764>), Complex Exponential Smoothing (Svetunkov & Kourentzes, 2018, <doi: 10.13140/RG.2.2.24986.29123>), Simple Moving Average (Svetunkov & Petropoulos, 2018 <doi: 10.1080/00207543.2017.1380326>) and several simulation functions. It also allows dealing with intermittent demand based on the iETS framework (Svetunkov & Boylan, 2019, <doi: 10.13140/RG.2.2.35897.06242>).
Author: Ivan Svetunkov [aut, cre]
Maintainer: Ivan Svetunkov <ivan@svetunkov.com>

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Package mlflow updated to version 2.21.2 with previous version 2.20.4 dated 2025-03-15

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>

Diff between mlflow versions 2.20.4 dated 2025-03-15 and 2.21.2 dated 2025-04-02

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Package yaConsensus updated to version 1.1 with previous version 1.0 dated 2021-07-01

Title: Consensus Clustering of Omic Data
Description: Procedures to perform consensus clustering starting from a dissimilarity matrix or a data matrix. It's allowed to select if the subsampling has to be by samples or features. In case of computational heavy load, the procedures can run in parallel.
Author: Stefano Maria Pagnotta [aut, cre, cph]
Maintainer: Stefano Maria Pagnotta <pagnotta@unisannio.it>

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Package twc updated to version 0.0.2 with previous version 0.0.1 dated 2024-12-02

Title: Terrestrial Water Cycle
Description: An open-access tool/framework that constitutes the core functions to analyze terrestrial water cycle data across various spatio-temporal scales.
Author: Mijael Rodrigo Vargas Godoy [aut, cre] , Yannis Markonis [aut]
Maintainer: Mijael Rodrigo Vargas Godoy <mirovago@gmail.com>

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Package tbrf updated to version 0.1.6 with previous version 0.1.5 dated 2020-04-09

Title: Time-Based Rolling Functions
Description: Provides rolling statistical functions based on date and time windows instead of n-lagged observations.
Author: Michael Schramm [aut, cre, cph] , Frank Harrell [ctb]
Maintainer: Michael Schramm <mpschramm@gmail.com>

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Package opendatatoronto updated to version 0.1.6 with previous version 0.1.5 dated 2022-04-13

Title: Access the City of Toronto Open Data Portal
Description: Access data from the "City of Toronto Open Data Portal" (<https://open.toronto.ca>) directly from R.
Author: Sharla Gelfand [aut, cre], City of Toronto [cph, fnd]
Maintainer: Sharla Gelfand <sharla.gelfand@gmail.com>

Diff between opendatatoronto versions 0.1.5 dated 2022-04-13 and 0.1.6 dated 2025-04-02

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Package lattice updated to version 0.22-7 with previous version 0.22-6 dated 2024-03-20

Title: Trellis Graphics for R
Description: A powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs, and is also flexible enough to handle most nonstandard requirements. See ?Lattice for an introduction.
Author: Deepayan Sarkar [aut, cre] , Felix Andrews [ctb], Kevin Wright [ctb] , Neil Klepeis [ctb], Johan Larsson [ctb] , Zhijian Wen [cph] , Paul Murrell [ctb], Stefan Eng [ctb] , Achim Zeileis [ctb] , Alexandre Courtiol [ctb]
Maintainer: Deepayan Sarkar <deepayan.sarkar@r-project.org>

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Package dimensio updated to version 0.13.0 with previous version 0.12.0 dated 2025-02-25

Title: Multivariate Data Analysis
Description: Simple Principal Components Analysis (PCA) and (Multiple) Correspondence Analysis (CA) based on the Singular Value Decomposition (SVD). This package provides S4 classes and methods to compute, extract, summarize and visualize results of multivariate data analysis. It also includes methods for partial bootstrap validation described in Greenacre (1984, ISBN: 978-0-12-299050-2) and Lebart et al. (2006, ISBN: 978-2-10-049616-7).
Author: Nicolas Frerebeau [aut, cre] , Jean-Baptiste Fourvel [ctb] , Camille Thabard [ctb] , Brice Lebrun [art] , Universite Bordeaux Montaigne [fnd] , CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>

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Package tame updated to version 0.2.0 with previous version 0.0.1 dated 2023-02-23

Title: Timing, Anatomical, Therapeutic and Chemical Based Medication Clustering
Description: Agglomerative hierarchical clustering with a bespoke distance measure based on medication similarities in the Anatomical Therapeutic Chemical Classification System, medication timing and medication amount or dosage. Tools for summarizing, illustrating and manipulating the cluster objects are also available.
Author: Anna Laksafoss [aut, cre]
Maintainer: Anna Laksafoss <adls@ssi.dk>

Diff between tame versions 0.0.1 dated 2023-02-23 and 0.2.0 dated 2025-04-02

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Package praatpicture updated to version 1.4.2 with previous version 1.4.0 dated 2025-01-14

Title: 'Praat Picture' Style Plots of Acoustic Data
Description: Quickly and easily generate plots of acoustic data aligned with transcriptions similar to those made in 'Praat' using either derived signals generated directly in R with 'wrassp' or imported derived signals from 'Praat'. Provides easy and fast out-of-the-box solutions but also a high extent of flexibility. Also provides options for embedding audio in figures and animating figures.
Author: Rasmus Puggaard-Rode [aut, cre, cph]
Maintainer: Rasmus Puggaard-Rode <r.puggaard@phonetik.uni-muenchen.de>

Diff between praatpicture versions 1.4.0 dated 2025-01-14 and 1.4.2 dated 2025-04-02

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Package mgcv updated to version 1.9-2 with previous version 1.9-1 dated 2023-12-20

Title: Mixed GAM Computation Vehicle with Automatic Smoothness Estimation
Description: Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Generalized Cross Validation and similar, or using iterated nested Laplace approximation for fully Bayesian inference. See Wood (2017) <doi:10.1201/9781315370279> for an overview. Includes a gam() function, a wide variety of smoothers, 'JAGS' support and distributions beyond the exponential family.
Author: Simon Wood [aut, cre]
Maintainer: Simon Wood <simon.wood@r-project.org>

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Package LNPar updated to version 1.1.1 with previous version 1.1.0 dated 2025-03-24

Title: Estimation and Testing for a Lognormal-Pareto Mixture
Description: Estimates a lognormal-Pareto mixture by means of the Expectation-Conditional-Maximization-Either algorithm and by maximizing the profile likelihood function. A likelihood ratio test for discriminating between lognormal and Pareto tail is also implemented. See Bee, M. (2022) <doi:10.1007/s11634-022-00497-4>.
Author: Marco Bee [aut, cre]
Maintainer: Marco Bee <marco.bee@unitn.it>

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Package bespatial updated to version 0.1.3 with previous version 0.1.2 dated 2024-06-07

Title: Boltzmann Entropy for Spatial Data
Description: Calculates several entropy metrics for spatial data inspired by Boltzmann's entropy formula. It includes metrics introduced by Cushman for landscape mosaics (Cushman (2015) <doi:10.1007/s10980-015-0305-2>), and landscape gradients and point patterns (Cushman (2021) <doi:10.3390/e23121616>); by Zhao and Zhang for landscape mosaics (Zhao and Zhang (2019) <doi:10.1007/s10980-019-00876-x>); and by Gao et al. for landscape gradients (Gao et al. (2018) <doi:10.1111/tgis.12315>; Gao and Li (2019) <doi:10.1007/s10980-019-00854-3>).
Author: Jakub Nowosad [aut, cre]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>

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Package RJSDMX updated to version 3.6-0 with previous version 3.5-0 dated 2024-11-07

Title: R Interface to SDMX Web Services
Description: Provides functions to retrieve data and metadata from providers that disseminate data by means of SDMX web services. SDMX (Statistical Data and Metadata eXchange) is a standard that has been developed with the aim of simplifying the exchange of statistical information. More about the SDMX standard and the SDMX Web Services can be found at: <https://sdmx.org>.
Author: Attilio Mattiocco [aut, cre]
Maintainer: Attilio Mattiocco <attilio.mattiocco@bancaditalia.it>

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Package CohortSurvival updated to version 1.0.1 with previous version 1.0.0 dated 2025-03-19

Title: Estimate Survival from Common Data Model Cohorts
Description: Estimate survival using data mapped to the Observational Medical Outcomes Partnership common data model. Survival can be estimated based on user-defined study cohorts.
Author: Kim Lopez-Gueell [aut, cre] , Edward Burn [aut] , Marti Catala [aut] , Xintong Li [aut] , Danielle Newby [aut] , Nuria Mercade-Besora [aut]
Maintainer: Kim Lopez-Gueell <kim.lopez@spc.ox.ac.uk>

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Package biotools updated to version 4.3 with previous version 4.2 dated 2021-08-07

Title: Tools for Biometry and Applied Statistics in Agricultural Science
Description: Tools designed to perform and evaluate cluster analysis (including Tocher's algorithm), discriminant analysis and path analysis (standard and under collinearity), as well as some useful miscellaneous tools for dealing with sample size and optimum plot size calculations. A test for seed sample heterogeneity is now available. Mantel's permutation test can be found in this package. A new approach for calculating its power is implemented. biotools also contains tests for genetic covariance components. Heuristic approaches for performing non-parametric spatial predictions of generic response variables and spatial gene diversity are implemented.
Author: Anderson Rodrigo da Silva [aut, cre]
Maintainer: Anderson Rodrigo da Silva <anderson.agro@hotmail.com>

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Package BigDataPE updated to version 0.0.96 with previous version 0.0.95 dated 2025-02-17

Title: Secure and Intuitive Access to 'BigDataPE' 'API' Datasets
Description: Designed to simplify the process of retrieving datasets from the 'Big Data PE' platform using secure token-based authentication. It provides functions for securely storing, retrieving, and managing tokens associated with specific datasets, as well as fetching and processing data using the 'httr2' package.
Author: Andre Leite [aut, cre], Hugo Vaconcelos [aut], Diogo Bezerra [aut]
Maintainer: Andre Leite <leite@castlab.org>

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Package simsem updated to version 0.5-17 with previous version 0.5-16 dated 2021-03-28

Title: SIMulated Structural Equation Modeling
Description: Provides an easy framework for Monte Carlo simulation in structural equation modeling, which can be used for various purposes, such as such as model fit evaluation, power analysis, or missing data handling and planning.
Author: Sunthud Pornprasertmanit [aut], Patrick Miller [aut], Alexander M. Schoemann [aut] , Terrence D. Jorgensen [aut, cre] , Corbin Quick [ctb]
Maintainer: Terrence D. Jorgensen <TJorgensen314@gmail.com>

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Package nanotime updated to version 0.3.12 with previous version 0.3.11 dated 2025-01-10

Title: Nanosecond-Resolution Time Support for R
Description: Full 64-bit resolution date and time functionality with nanosecond granularity is provided, with easy transition to and from the standard 'POSIXct' type. Three additional classes offer interval, period and duration functionality for nanosecond-resolution timestamps.
Author: Dirk Eddelbuettel [aut, cre] , Leonardo Silvestri [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package kstMatrix updated to version 1.2-0 with previous version 1.1-0 dated 2025-01-26

Title: Basic Functions in Knowledge Space Theory Using Matrix Representation
Description: Knowledge space theory by Doignon and Falmagne (1999) <doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical framework, which proposes mathematical formalisms to operationalize knowledge structures in a particular domain. The 'kstMatrix' package provides basic functionalities to generate, handle, and manipulate knowledge structures and knowledge spaces. Opposed to the 'kst' package, 'kstMatrix' uses matrix representations for knowledge structures. Furthermore, 'kstMatrix' contains several knowledge spaces developed by the research group around Cornelia Dowling through querying experts.
Author: Cord Hockemeyer [aut, cre], Wai Wong [ctb]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>

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Package gamCopula updated to version 0.0-8 with previous version 0.0-7 dated 2020-02-05

Title: Generalized Additive Models for Bivariate Conditional Dependence Structures and Vine Copulas
Description: Implementation of various inference and simulation tools to apply generalized additive models to bivariate dependence structures and non-simplified vine copulas.
Author: Thomas Nagler [aut], Thibault Vatter [aut, cre]
Maintainer: Thibault Vatter <thibault.vatter@gmail.com>

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Package TDAvec updated to version 0.1.41 with previous version 0.1.4 dated 2025-02-15

Title: Vector Summaries of Persistence Diagrams
Description: Provides tools for computing various vector summaries of persistence diagrams studied in Topological Data Analysis. For improved computational efficiency, all code for the vector summaries is written in 'C++' using the 'Rcpp' and 'RcppArmadillo' packages.
Author: Umar Islambekov [aut], Aleksei Luchinsky [aut, cre]
Maintainer: Aleksei Luchinsky <aluchi@bgsu.edu>

Diff between TDAvec versions 0.1.4 dated 2025-02-15 and 0.1.41 dated 2025-04-02

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Package tabula updated to version 3.2.1 with previous version 3.2.0 dated 2025-01-10

Title: Analysis and Visualization of Archaeological Count Data
Description: An easy way to examine archaeological count data. This package provides several tests and measures of diversity: heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.), richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), turnover and similarity (Brainerd-Robinson, etc.). It allows to easily visualize count data and statistical thresholds: rank vs abundance plots, heatmaps, Ford (1962) and Bertin (1977) diagrams, etc.
Author: Nicolas Frerebeau [aut, cre] , Brice Lebrun [art] , Matthew Peeples [ctb] , Ben Marwick [ctb] , Jean-Baptiste Fourvel [ctb] , Universite Bordeaux Montaigne [fnd] , CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>

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Package silp updated to version 1.0.2 with previous version 1.0.1 dated 2025-03-11

Title: Conditional Process Analysis (CPA) via SEM Approach
Description: Utilizes the Reliability-Adjusted Product Indicator (RAPI) method to estimate effects among latent variables, thus allowing for more precise definition and analysis of mediation and moderation models. Our simulation studies reveal that while 'silp' may exhibit instability with smaller sample sizes and lower reliability scores (e.g., N = 100, 'omega' = 0.7), implementing nearest positive definite matrix correction and bootstrap confidence interval estimation can significantly ameliorate this volatility. When these adjustments are applied, 'silp' achieves estimations akin in quality to those derived from LMS. In conclusion, the 'silp' package is a valuable tool for researchers seeking to explore complex relational structures between variables without resorting to commercial software. Cheung et al.(2021)<doi:10.1007/s10869-020-09717-0> Hsiao et al.(2018)<doi:10.1177/0013164416679877>.
Author: Yi-Hsuan Tseng [aut, cre], Po-Hsien Huang [aut]
Maintainer: Yi-Hsuan Tseng <r12227115@g.ntu.edu.tw>

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Package MortalityLaws updated to version 2.1.2 with previous version 2.1.0 dated 2024-01-15

Title: Parametric Mortality Models, Life Tables and HMD
Description: Fit the most popular human mortality 'laws', and construct full and abridge life tables given various input indices. A mortality law is a parametric function that describes the dying-out process of individuals in a population during a significant portion of their life spans. For a comprehensive review of the most important mortality laws see Tabeau (2001) <doi:10.1007/0-306-47562-6_1>. Practical functions for downloading data from various human mortality databases are provided as well.
Author: Marius D. Pascariu [aut, cre, cph] , Vladimir Canudas-Romo [ctb]
Maintainer: Marius D. Pascariu <mpascariu@outlook.com>

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Package clustvarsel updated to version 2.3.5 with previous version 2.3.4 dated 2020-12-16

Title: Variable Selection for Gaussian Model-Based Clustering
Description: Variable selection for Gaussian model-based clustering as implemented in the 'mclust' package. The methodology allows to find the (locally) optimal subset of variables in a data set that have group/cluster information. A greedy or headlong search can be used, either in a forward-backward or backward-forward direction, with or without sub-sampling at the hierarchical clustering stage for starting 'mclust' models. By default the algorithm uses a sequential search, but parallelisation is also available.
Author: Nema Dean [aut] , Adrian E. Raftery [aut], Luca Scrucca [aut, cre]
Maintainer: Luca Scrucca <luca.scrucca@unibo.it>

Diff between clustvarsel versions 2.3.4 dated 2020-12-16 and 2.3.5 dated 2025-04-02

 DESCRIPTION                |   14 
 MD5                        |   29 -
 NEWS.md                    |    5 
 R/clvarselgrbkw.R          |   12 
 R/clvarselgrfwd.R          |   42 +
 R/clvarselhlfwd.R          |   16 
 README.md                  |    4 
 build/vignette.rds         |binary
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 inst/doc/clustvarsel.R     |  422 +++++++++----------
 inst/doc/clustvarsel.Rmd   |    2 
 inst/doc/clustvarsel.html  |  959 +++++++++++++++++++++++++++++----------------
 man/clustvarsel.Rd         |    6 
 vignettes/clustvarsel.Rmd  |    2 
 vignettes/vignette.css     |   39 -
 vignettes/vignette_old.css |only
 16 files changed, 958 insertions(+), 628 deletions(-)

More information about clustvarsel at CRAN
Permanent link

Package terra updated to version 1.8-42 with previous version 1.8-29 dated 2025-02-26

Title: Spatial Data Analysis
Description: Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Author: Robert J. Hijmans [cre, aut] , Marcia Barbosa [ctb], Roger Bivand [ctb] , Andrew Brown [ctb], Michael Chirico [ctb], Emanuele Cordano [ctb] , Krzysztof Dyba [ctb] , Edzer Pebesma [ctb] , Barry Rowlingson [ctb], Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>

Diff between terra versions 1.8-29 dated 2025-02-26 and 1.8-42 dated 2025-04-02

 terra-1.8-29/terra/R/plot_legend.R                       |only
 terra-1.8-29/terra/src/Makevars.win                      |only
 terra-1.8-42/terra/DESCRIPTION                           |   10 
 terra-1.8-42/terra/MD5                                   |  891 ++---
 terra-1.8-42/terra/NAMESPACE                             |    2 
 terra-1.8-42/terra/NEWS.md                               |   44 
 terra-1.8-42/terra/R/Aclasses.R                          |  315 -
 terra-1.8-42/terra/R/Agenerics.R                         |    6 
 terra-1.8-42/terra/R/Arith_generics.R                    | 1534 ++++----
 terra-1.8-42/terra/R/RGB.R                               |  458 +-
 terra-1.8-42/terra/R/RcppExports.R                       |    4 
 terra-1.8-42/terra/R/SpatRasterDataset.R                 |  871 ++--
 terra-1.8-42/terra/R/SpatVectorCollection.R              |  336 -
 terra-1.8-42/terra/R/Zdeprecated.R                       |  138 
 terra-1.8-42/terra/R/aggregate.R                         |  654 +--
 terra-1.8-42/terra/R/animate.R                           |   64 
 terra-1.8-42/terra/R/app.R                               |  688 +--
 terra-1.8-42/terra/R/approximate.R                       |  126 
 terra-1.8-42/terra/R/arith.R                             |   74 
 terra-1.8-42/terra/R/autocor.R                           |  408 +-
 terra-1.8-42/terra/R/cells.R                             |  194 -
 terra-1.8-42/terra/R/clean.R                             |  140 
 terra-1.8-42/terra/R/click.R                             |  318 -
 terra-1.8-42/terra/R/clip.R                              |   84 
 terra-1.8-42/terra/R/coerce.R                            | 1529 ++++----
 terra-1.8-42/terra/R/colors.R                            |  194 -
 terra-1.8-42/terra/R/connect.R                           |  162 
 terra-1.8-42/terra/R/crosstab.R                          |  168 
 terra-1.8-42/terra/R/crs.R                               |  784 ++--
 terra-1.8-42/terra/R/dimensions.R                        |  414 +-
 terra-1.8-42/terra/R/distance.R                          |  607 +--
 terra-1.8-42/terra/R/draw.R                              |  176 -
 terra-1.8-42/terra/R/expand.R                            |  126 
 terra-1.8-42/terra/R/extent.R                            |  746 ++--
 terra-1.8-42/terra/R/extract.R                           | 1195 +++---
 terra-1.8-42/terra/R/extract_single.R                    |  612 +--
 terra-1.8-42/terra/R/focal.R                             | 1714 ++++-----
 terra-1.8-42/terra/R/focalMat.R                          |  148 
 terra-1.8-42/terra/R/gcp.R                               |   90 
 terra-1.8-42/terra/R/gdal.R                              |  362 +-
 terra-1.8-42/terra/R/generics.R                          | 2621 +++++++--------
 terra-1.8-42/terra/R/geocolors.R                         |   22 
 terra-1.8-42/terra/R/geom.R                              | 1625 ++++-----
 terra-1.8-42/terra/R/graticule.R                         |  452 +-
 terra-1.8-42/terra/R/hist.R                              |  212 -
 terra-1.8-42/terra/R/ifelse.R                            |  102 
 terra-1.8-42/terra/R/image.R                             |   54 
 terra-1.8-42/terra/R/init.R                              |   84 
 terra-1.8-42/terra/R/inset.R                             |  252 -
 terra-1.8-42/terra/R/interpolate.R                       |  154 
 terra-1.8-42/terra/R/k_means.R                           |  126 
 terra-1.8-42/terra/R/lapp.R                              |  650 +--
 terra-1.8-42/terra/R/layerCor.R                          |  396 +-
 terra-1.8-42/terra/R/levels.R                            | 1015 ++---
 terra-1.8-42/terra/R/lines.R                             |  322 -
 terra-1.8-42/terra/R/makeVRT.R                           |  244 -
 terra-1.8-42/terra/R/match.R                             |  126 
 terra-1.8-42/terra/R/math.R                              |  240 -
 terra-1.8-42/terra/R/merge.R                             |  154 
 terra-1.8-42/terra/R/mergeTime.R                         |  208 -
 terra-1.8-42/terra/R/messages.R                          |  156 
 terra-1.8-42/terra/R/names.R                             |  548 +--
 terra-1.8-42/terra/R/ncdf.R                              | 1214 +++---
 terra-1.8-42/terra/R/options.R                           |  433 +-
 terra-1.8-42/terra/R/panel.R                             |  222 -
 terra-1.8-42/terra/R/plotExtent.R                        |   76 
 terra-1.8-42/terra/R/plotRGB.R                           |  146 
 terra-1.8-42/terra/R/plot_2rasters.R                     |  404 +-
 terra-1.8-42/terra/R/plot_add.R                          |only
 terra-1.8-42/terra/R/plot_axes.R                         |  396 +-
 terra-1.8-42/terra/R/plot_cartogram.R                    |   44 
 terra-1.8-42/terra/R/plot_helper.R                       |only
 terra-1.8-42/terra/R/plot_legend_classes.R               |only
 terra-1.8-42/terra/R/plot_legend_continuous.R            |only
 terra-1.8-42/terra/R/plot_let.R                          |   16 
 terra-1.8-42/terra/R/plot_raster.R                       | 1907 ++++------
 terra-1.8-42/terra/R/plot_scale.R                        |  562 +--
 terra-1.8-42/terra/R/plot_vector.R                       | 1626 ++++-----
 terra-1.8-42/terra/R/predict.R                           |  541 +--
 terra-1.8-42/terra/R/princomp.R                          |   88 
 terra-1.8-42/terra/R/rapp.R                              |  152 
 terra-1.8-42/terra/R/rast.R                              | 1203 +++---
 terra-1.8-42/terra/R/rasterize.R                         |  731 ++--
 terra-1.8-42/terra/R/rasterizeWin.R                      |  734 ++--
 terra-1.8-42/terra/R/readsvg.R                           |  152 
 terra-1.8-42/terra/R/regress.R                           |  350 +-
 terra-1.8-42/terra/R/relate.R                            |  830 ++--
 terra-1.8-42/terra/R/replace.R                           |  606 +--
 terra-1.8-42/terra/R/replace_layer.R                     |  264 -
 terra-1.8-42/terra/R/replace_values.R                    |  732 ++--
 terra-1.8-42/terra/R/roll.R                              |  148 
 terra-1.8-42/terra/R/rowSums.R                           |  186 -
 terra-1.8-42/terra/R/sample.R                            | 2010 +++++------
 terra-1.8-42/terra/R/select.R                            |   92 
 terra-1.8-42/terra/R/selectHigh.R                        |   24 
 terra-1.8-42/terra/R/show.R                              |   29 
 terra-1.8-42/terra/R/spatDF.R                            |  194 -
 terra-1.8-42/terra/R/subset.R                            |  614 +--
 terra-1.8-42/terra/R/tags.R                              |  448 +-
 terra-1.8-42/terra/R/tapp.R                              |  380 +-
 terra-1.8-42/terra/R/tempfiles.R                         |  138 
 terra-1.8-42/terra/R/tiles.R                             |  282 -
 terra-1.8-42/terra/R/time.R                              |  774 ++--
 terra-1.8-42/terra/R/twoClasses.R                        |  152 
 terra-1.8-42/terra/R/update.R                            |   22 
 terra-1.8-42/terra/R/values.R                            | 1172 +++---
 terra-1.8-42/terra/R/vect.R                              | 1066 +++---
 terra-1.8-42/terra/R/watershed.R                         |   88 
 terra-1.8-42/terra/R/window.R                            |   68 
 terra-1.8-42/terra/R/wrap.R                              | 1038 ++---
 terra-1.8-42/terra/R/write.R                             |  378 +-
 terra-1.8-42/terra/R/xapp.R                              |  144 
 terra-1.8-42/terra/R/xyRowColCell.R                      |  468 +-
 terra-1.8-42/terra/R/zonal.R                             | 1150 +++---
 terra-1.8-42/terra/R/zoom.R                              |  100 
 terra-1.8-42/terra/R/zzz.R                               |  121 
 terra-1.8-42/terra/build/partial.rdb                     |binary
 terra-1.8-42/terra/configure                             |  693 ++-
 terra-1.8-42/terra/configure.ac                          |   80 
 terra-1.8-42/terra/inst/ex/test.grd                      |   52 
 terra-1.8-42/terra/inst/tinytest/test_aggregate.R        |   26 
 terra-1.8-42/terra/inst/tinytest/test_arith.R            |   14 
 terra-1.8-42/terra/inst/tinytest/test_cats.R             |  118 
 terra-1.8-42/terra/inst/tinytest/test_classify.R         |   48 
 terra-1.8-42/terra/inst/tinytest/test_crds.R             |   14 
 terra-1.8-42/terra/inst/tinytest/test_crop.R             |   58 
 terra-1.8-42/terra/inst/tinytest/test_equal.R            |   32 
 terra-1.8-42/terra/inst/tinytest/test_extent.R           |    6 
 terra-1.8-42/terra/inst/tinytest/test_extract.R          |  470 +-
 terra-1.8-42/terra/inst/tinytest/test_flowAccumulation.R |   68 
 terra-1.8-42/terra/inst/tinytest/test_focal.R            |  164 
 terra-1.8-42/terra/inst/tinytest/test_geom.R             |   44 
 terra-1.8-42/terra/inst/tinytest/test_global.R           |   22 
 terra-1.8-42/terra/inst/tinytest/test_matrix-input.R     |  102 
 terra-1.8-42/terra/inst/tinytest/test_merge.R            |   46 
 terra-1.8-42/terra/inst/tinytest/test_multivariate.R     |   24 
 terra-1.8-42/terra/inst/tinytest/test_patches.R          |   66 
 terra-1.8-42/terra/inst/tinytest/test_pitfinder.R        |  104 
 terra-1.8-42/terra/inst/tinytest/test_plot.R             |   10 
 terra-1.8-42/terra/inst/tinytest/test_raster-vector.R    |  124 
 terra-1.8-42/terra/inst/tinytest/test_rasterize.R        |   16 
 terra-1.8-42/terra/inst/tinytest/test_rds.R              |   18 
 terra-1.8-42/terra/inst/tinytest/test_replace.R          |   50 
 terra-1.8-42/terra/inst/tinytest/test_tags.R             |only
 terra-1.8-42/terra/inst/tinytest/test_time.R             |    8 
 terra-1.8-42/terra/inst/tinytest/test_vect-geom.R        |   28 
 terra-1.8-42/terra/inst/tinytest/test_vector-subset.R    |   34 
 terra-1.8-42/terra/inst/tinytest/test_weighted-mean.R    |   32 
 terra-1.8-42/terra/inst/tinytest/test_window.R           |   64 
 terra-1.8-42/terra/inst/tinytest/test_wkt_grd.R          |   34 
 terra-1.8-42/terra/inst/tinytest/test_zonal.R            |   48 
 terra-1.8-42/terra/inst/tinytest/tinytest.R              |    8 
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 terra-1.8-42/terra/man/NIPD.Rd                           |  196 -
 terra-1.8-42/terra/man/RGB.Rd                            |  168 
 terra-1.8-42/terra/man/SpatExtent-class.Rd               |   70 
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 terra-1.8-42/terra/man/animate.Rd                        |   88 
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 terra-1.8-42/terra/man/as.character.Rd                   |   78 
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 terra-1.8-42/terra/man/as.raster.Rd                      |   76 
 terra-1.8-42/terra/man/atan2.Rd                          |   84 
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 terra-1.8-42/terra/man/buffer.Rd                         |  134 
 terra-1.8-42/terra/man/c.Rd                              |  130 
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 terra-1.8-42/terra/man/clamp_ts.Rd                       |   96 
 terra-1.8-42/terra/man/classify.Rd                       |  196 -
 terra-1.8-42/terra/man/click.Rd                          |  120 
 terra-1.8-42/terra/man/coerce.Rd                         |  136 
 terra-1.8-42/terra/man/collapse.Rd                       |   78 
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 terra-1.8-42/terra/man/compare-generics.Rd               |  200 -
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 terra-1.8-42/terra/man/extractAlong.Rd                   |   88 
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 terra-1.8-42/terra/man/focal3D.Rd                        |  120 
 terra-1.8-42/terra/man/focalCpp.Rd                       |  202 -
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 terra-1.8-42/terra/man/global.Rd                         |  102 
 terra-1.8-42/terra/man/graticule.Rd                      |   90 
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 terra-1.8-42/terra/man/impose.Rd                         |   76 
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 terra-1.8-42/terra/man/lines.Rd                          |  172 
 terra-1.8-42/terra/man/makeTiles.Rd                      |  136 
 terra-1.8-42/terra/man/makeVRT.Rd                        |   94 
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Package gdverse updated to version 1.3-3 with previous version 1.3-2 dated 2025-02-17

Title: Analysis of Spatial Stratified Heterogeneity
Description: Detecting spatial associations via spatial stratified heterogeneity, accounting for spatial dependencies, interpretability, complex interactions, and robust stratification. In addition, it supports the spatial stratified heterogeneity family described in Lv et al. (2025)<doi:10.1111/tgis.70032>.
Author: Wenbo Lv [aut, cre, cph] , Yangyang Lei [aut] , Fangmei Liu [aut] , Jianwu Yan [aut] , Yongze Song [aut] , Wufan Zhao [aut]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>

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Package UComp updated to version 5.1 with previous version 5.0.6 dated 2025-02-28

Title: Automatic Univariate Time Series Modelling of many Kinds
Description: Comprehensive analysis and forecasting of univariate time series using automatic time series models of many kinds. Harvey AC (1989) <doi:10.1017/CBO9781107049994>. Pedregal DJ and Young PC (2002) <doi:10.1002/9780470996430>. Durbin J and Koopman SJ (2012) <doi:10.1093/acprof:oso/9780199641178.001.0001>. Hyndman RJ, Koehler AB, Ord JK, and Snyder RD (2008) <doi:10.1007/978-3-540-71918-2>. Gómez V, Maravall A (2000) <doi:10.1002/9781118032978>. Pedregal DJ, Trapero JR and Holgado E (2024) <doi:10.1016/j.ijforecast.2023.09.004>.
Author: Diego J. Pedregal [aut, cre]
Maintainer: Diego J. Pedregal <Diego.Pedregal@uclm.es>

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Package tican updated to version 1.0.2 with previous version 1.0.1 dated 2024-08-28

Title: Plot and Analyse Time-Intensity Data
Description: Plots and analyzes time-intensity curve data, such as data from (contrast-enhanced) ultrasound. Values such as peak intensity, time to peak and area under the curve are calculated.
Author: Samuel James Tingle [aut, cre]
Maintainer: Samuel James Tingle <samjamestingle@gmail.com>

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Package autoharp updated to version 0.0.12 with previous version 0.0.10 dated 2021-11-12

Title: Semi-Automatic Grading of R and Rmd Scripts
Description: A customisable set of tools for assessing and grading R or R-markdown scripts from students. It allows for checking correctness of code output, runtime statistics and static code analysis. The latter feature is made possible by representing R expressions using a tree structure.
Author: Vik Gopal [aut, cre], Samuel Seah [aut], Viknesh Jeya Kumar [aut], Gabriel Ang [aut], Ruofan Liu [ctb], National University of Singapore [cph]
Maintainer: Vik Gopal <vik.gopal@nus.edu.sg>

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Package rhino updated to version 1.11.0 with previous version 1.10.1 dated 2024-09-20

Title: A Framework for Enterprise Shiny Applications
Description: A framework that supports creating and extending enterprise Shiny applications using best practices.
Author: Kamil Zyla [aut, cre], Jakub Nowicki [aut], Leszek Sieminski [aut], Marek Rogala [aut], Recle Vibal [aut], Tymoteusz Makowski [aut], Rodrigo Basa [aut], Eduardo Almeida [ctb], Appsilon Sp. z o.o. [cph]
Maintainer: Kamil Zyla <opensource+kamil@appsilon.com>

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Package MortalityGaps updated to version 1.0.7 with previous version 1.0.0 dated 2018-07-20

Title: The Double-Gap Life Expectancy Forecasting Model
Description: Life expectancy is highly correlated over time among countries and between males and females. These associations can be used to improve forecasts. Here we have implemented a method for forecasting female life expectancy based on analysis of the gap between female life expectancy in a country compared with the record level of female life expectancy in the world. Second, to forecast male life expectancy, the gap between male life expectancy and female life expectancy in a country is analysed. We named this method the Double-Gap model. For a detailed description of the method see Pascariu et al. (2018). <doi:10.1016/j.insmatheco.2017.09.011>.
Author: Marius D. Pascariu [aut, cre]
Maintainer: Marius D. Pascariu <rpascariu@outlook.com>

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Package spqdep updated to version 0.1.3.6 with previous version 0.1.3.5 dated 2025-01-08

Title: Testing for Spatial Independence of Cross-Sectional Qualitative Data
Description: Testing for Spatial Dependence of Qualitative Data in Cross Section. The list of functions includes join-count tests, Q test, spatial scan test, similarity test and spatial runs test. The methodology of these models can be found in <doi:10.1007/s10109-009-0100-1> and <doi:10.1080/13658816.2011.586327>.
Author: Fernando Lopez [aut, cre] , Roman Minguez [aut] , Antonio Paez [aut] , Manuel Ruiz [aut]
Maintainer: Fernando Lopez <fernando.lopez@upct.es>

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Package doRNG updated to version 1.8.6.2 with previous version 1.8.6.1 dated 2025-01-13

Title: Generic Reproducible Parallel Backend for 'foreach' Loops
Description: Provides functions to perform reproducible parallel foreach loops, using independent random streams as generated by L'Ecuyer's combined multiple-recursive generator [L'Ecuyer (1999), <DOI:10.1287/opre.47.1.159>]. It enables to easily convert standard '%dopar%' loops into fully reproducible loops, independently of the number of workers, the task scheduling strategy, or the chosen parallel environment and associated foreach backend.
Author: Renaud Gaujoux [aut, cre]
Maintainer: Renaud Gaujoux <renozao@protonmail.com>

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Package rscopus updated to version 0.8.1 with previous version 0.6.6 dated 2019-09-17

Title: Scopus Database 'API' Interface
Description: Uses Elsevier 'Scopus' API <https://dev.elsevier.com/sc_apis.html> to download information about authors and their citations.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>

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Package quadprogXT updated to version 0.0.6 with previous version 0.0.5 dated 2020-01-15

Title: Quadratic Programming with Absolute Value Constraints
Description: Extends the quadprog package to solve quadratic programs with absolute value constraints and absolute values in the objective function.
Author: Bob Harlow [aut, cre], Brian Koch [ctb]
Maintainer: Bob Harlow <rharlow86@gmail.com>

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Package PerFit updated to version 1.4.7 with previous version 1.4.6 dated 2021-10-15

Title: Person Fit
Description: Several person-fit statistics (PFSs; Meijer and Sijtsma, 2001, <doi:10.1177/01466210122031957>) are offered. These statistics allow assessing whether individual response patterns to tests or questionnaires are (im)plausible given the other respondents in the sample or given a specified item response theory model. Some PFSs apply to dichotomous data, such as the likelihood-based PFSs (lz, lz*) and the group-based PFSs (personal biserial correlation, caution index, (normed) number of Guttman errors, agreement/disagreement/dependability statistics, U3, ZU3, NCI, Ht). PFSs suitable to polytomous data include extensions of lz, U3, and (normed) number of Guttman errors.
Author: Jorge N. Tendeiro [aut, cre]
Maintainer: Jorge N. Tendeiro <tendeiro@hiroshima-u.ac.jp>

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Tue, 01 Apr 2025

Package wrGraph updated to version 1.3.9 with previous version 1.3.8 dated 2024-11-21

Title: Graphics in the Context of Analyzing High-Throughput Data
Description: Additional options for making graphics in the context of analyzing high-throughput data are available here. This includes automatic segmenting of the current device (eg window) to accommodate multiple new plots, automatic checking for optimal location of legends in plots, small histograms to insert as legends, histograms re-transforming axis labels to linear when plotting log2-transformed data, a violin-plot <doi:10.1080/00031305.1998.10480559> function for a wide variety of input-formats, principal components analysis (PCA) <doi:10.1080/14786440109462720> with bag-plots <doi:10.1080/00031305.1999.10474494> to highlight and compare the center areas for groups of samples, generic MA-plots (differential- versus average-value plots) <doi:10.1093/nar/30.4.e15>, staggered count plots and generation of mouse-over interactive html pages.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>

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Package ctxR updated to version 1.1.1 with previous version 1.1.0 dated 2025-01-08

Title: Utilities for Interacting with the 'CTX' APIs
Description: Access chemical, hazard, bioactivity, and exposure data from the Computational Toxicology and Exposure ('CTX') APIs <https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis>. 'ctxR' was developed to streamline the process of accessing the information available through the 'CTX' APIs without requiring prior knowledge of how to use APIs. Most data is also available on the CompTox Chemical Dashboard ('CCD') <https://comptox.epa.gov/dashboard/> and other resources found at the EPA Computational Toxicology and Exposure Online Resources <https://www.epa.gov/comptox-tools>.
Author: Paul Kruse [aut] , Caroline Ring [aut] , Madison Feshuk [ctb] , Carter Thunes [ctb], Jason Brown [cre]
Maintainer: Jason Brown <brown.jason@epa.gov>

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