Sun, 19 Mar 2023

Package hmcdm updated to version 2.1.1 with previous version 2.1.0 dated 2023-01-25

Title: Hidden Markov Cognitive Diagnosis Models for Learning
Description: Fitting hidden Markov models of learning under the cognitive diagnosis framework. The estimation of the hidden Markov diagnostic classification model, the first order hidden Markov model, the reduced-reparameterized unified learning model, and the joint learning model for responses and response times.
Author: Susu Zhang [aut], Shiyu Wang [aut], Yinghan Chen [aut], Sunbeom Kwon [aut, cre]
Maintainer: Sunbeom Kwon <sunbeom2@illinois.edu>

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Package ggfortify updated to version 0.4.16 with previous version 0.4.15 dated 2022-11-11

Title: Data Visualization Tools for Statistical Analysis Results
Description: Unified plotting tools for statistics commonly used, such as GLM, time series, PCA families, clustering and survival analysis. The package offers a single plotting interface for these analysis results and plots in a unified style using 'ggplot2'.
Author: Masaaki Horikoshi [aut], Yuan Tang [aut, cre] , Austin Dickey [ctb], Matthias Grenie [ctb], Ryan Thompson [ctb], Luciano Selzer [ctb], Dario Strbenac [ctb], Kirill Voronin [ctb], Damir Pulatov [ctb]
Maintainer: Yuan Tang <terrytangyuan@gmail.com>

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Package sf updated to version 1.0-12 with previous version 1.0-11 dated 2023-03-15

Title: Simple Features for R
Description: Support for simple features, a standardized way to encode spatial vector data. Binds to 'GDAL' for reading and writing data, to 'GEOS' for geometrical operations, and to 'PROJ' for projection conversions and datum transformations. Uses by default the 's2' package for spherical geometry operations on ellipsoidal (long/lat) coordinates.
Author: Edzer Pebesma [aut, cre] , Roger Bivand [ctb] , Etienne Racine [ctb], Michael Sumner [ctb], Ian Cook [ctb], Tim Keitt [ctb], Robin Lovelace [ctb], Hadley Wickham [ctb], Jeroen Ooms [ctb] , Kirill Mueller [ctb], Thomas Lin Pedersen [ctb], Dan Baston [c [...truncated...]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

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Package waywiser updated to version 0.3.0 with previous version 0.2.0 dated 2022-10-22

Title: Ergonomic Methods for Assessing Spatial Models
Description: Assessing predictive models of spatial data can be challenging, both because these models are typically built for extrapolating outside the original region represented by training data and due to potential spatially structured errors, with "hot spots" of higher than expected error clustered geographically due to spatial structure in the underlying data. Methods are provided for assessing models fit to spatial data, including approaches for measuring the spatial structure of model errors, assessing model predictions at multiple spatial scales, and evaluating where predictions can be made safely. Methods are particularly useful for models fit using the 'tidymodels' framework. Methods include Moran's I ('Moran' (1950) <doi:10.2307/2332142>), Geary's C ('Geary' (1954) <doi:10.2307/2986645>), Getis-Ord's G ('Ord' and 'Getis' (1995) <doi:10.1111/j.1538-4632.1995.tb00912.x>), agreement coefficients from 'Ji' and Gallo (2006) (<doi: 10.14358/PERS.72.7.823>), agreement m [...truncated...]
Author: Michael Mahoney [aut, cre] , Lucas Johnson [ctb] , Virgilio Gomez-Rubio [rev] for rOpenSci, see <https://github.com/ropensci/software-review/issues/571>), Jakub Nowosad [rev] for rOpenSci, see <https://github.com/ropensci/software-review/issues/571 [...truncated...]
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>

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Package survHE updated to version 2.0.1 with previous version 1.1.2 dated 2021-02-08

Title: Survival Analysis in Health Economic Evaluation
Description: Contains a suite of functions for survival analysis in health economics. These can be used to run survival models under a frequentist (based on maximum likelihood) or a Bayesian approach (both based on Integrated Nested Laplace Approximation or Hamiltonian Monte Carlo). To run the Bayesian models, the user needs to install additional modules (packages), i.e. 'survHEinla' and 'survHEhmc'. These can be installed using 'remotes::install_github' from their GitHub repositories: (<https://github.com/giabaio/survHEhmc> and <https://github.com/giabaio/survHEinla/> respectively). 'survHEinla' is based on the package INLA, which is available for download at <https://inla.r-inla-download.org/R/stable/>. The user can specify a set of parametric models using a common notation and select the preferred mode of inference. The results can also be post-processed to produce probabilistic sensitivity analysis and can be used to export the output to an Excel file (e.g. for a Markov model, [...truncated...]
Author: Gianluca Baio [aut, cre], Andrea Berardi [ctb], Philip Cooney [ctb], Andrew Jones [ctb], Nathan Green [ctb]
Maintainer: Gianluca Baio <g.baio@ucl.ac.uk>

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More information about survHE at CRAN
Permanent link

Package randomizeR updated to version 3.0.1 with previous version 3.0.0 dated 2023-03-14

Title: Randomization for Clinical Trials
Description: This tool enables the user to choose a randomization procedure based on sound scientific criteria. It comprises the generation of randomization sequences as well the assessment of randomization procedures based on carefully selected criteria. Furthermore, 'randomizeR' provides a function for the comparison of randomization procedures.
Author: David Schindler [aut], Diane Uschner [aut], Denis Razsolkov [ctb], Dimitar Mihaylov [ctb], Marcia Viviane Rueckbeil [ctb], Martin Manolov [ctb], Thi Mui Pham [ctb], Michael Martini [ctb], Ralf-Dieter Hilgers [aut, ths, cre], Nicole Heussen [aut, ths]
Maintainer: Ralf-Dieter Hilgers <rhilgers@ukaachen.de>

Diff between randomizeR versions 3.0.0 dated 2023-03-14 and 3.0.1 dated 2023-03-19

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New package PPMiss with initial version 0.1.0
Package: PPMiss
Date: 2023-03-17
Title: Copula-Based Estimator for Long-Range Dependent Processes under Missing Data
Version: 0.1.0
Depends: R (>= 4.0.0)
Imports: copula, pracma, stats, zoo
Description: Implements the copula-based estimator for univariate long-range dependent processes, introduced in Pumi et al. (2023) <doi:10.1007/s00362-023-01418-z>. Notably, this estimator is capable of handling missing data and has been shown to perform exceptionally well, even when up to 70% of data is missing (as reported in <arXiv:2303.04754>) and has been found to outperform several other commonly applied estimators.
License: GPL (>= 3)
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2023-03-17 18:45:55 UTC; Taiane
Author: Taiane Schaedler Prass [aut, cre, com] , Guilherme Pumi [aut, ctb]
Maintainer: Taiane Schaedler Prass <taianeprass@gmail.com>
Repository: CRAN
Date/Publication: 2023-03-19 22:20:15 UTC

More information about PPMiss at CRAN
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Package mvp updated to version 1.0-14 with previous version 1.0-12 dated 2022-01-12

Title: Fast Symbolic Multivariate Polynomials
Description: Fast manipulation of symbolic multivariate polynomials using the 'Map' class of the Standard Template Library. The package uses print and coercion methods from the 'mpoly' package (Kahle 2013, "Multivariate polynomials in R", The R Journal, 5(1):162), but offers speed improvements. It is comparable in speed to the 'spray' package for sparse arrays, but retains the symbolic benefits of 'mpoly'. To cite the package in publications, use Hankin 2022 <doi:10.48550/ARXIV.2210.15991>. Uses 'disordR' discipline.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

Diff between mvp versions 1.0-12 dated 2022-01-12 and 1.0-14 dated 2023-03-19

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More information about mvp at CRAN
Permanent link

Package glmmTMB updated to version 1.1.6 with previous version 1.1.5 dated 2022-11-16

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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More information about glmmTMB at CRAN
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Package partykit updated to version 1.2-19 with previous version 1.2-18 dated 2023-03-09

Title: A Toolkit for Recursive Partytioning
Description: A toolkit with infrastructure for representing, summarizing, and visualizing tree-structured regression and classification models. This unified infrastructure can be used for reading/coercing tree models from different sources ('rpart', 'RWeka', 'PMML') yielding objects that share functionality for print()/plot()/predict() methods. Furthermore, new and improved reimplementations of conditional inference trees (ctree()) and model-based recursive partitioning (mob()) from the 'party' package are provided based on the new infrastructure. A description of this package was published by Hothorn and Zeileis (2015) <https://jmlr.org/papers/v16/hothorn15a.html>.
Author: Torsten Hothorn [aut, cre] , Heidi Seibold [ctb] , Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between partykit versions 1.2-18 dated 2023-03-09 and 1.2-19 dated 2023-03-19

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More information about partykit at CRAN
Permanent link

Package metafor updated to version 4.0-0 with previous version 3.8-1 dated 2022-08-26

Title: Meta-Analysis Package for R
Description: A comprehensive collection of functions for conducting meta-analyses in R. The package includes functions to calculate various effect sizes or outcome measures, fit equal-, fixed-, random-, and mixed-effects models to such data, carry out moderator and meta-regression analyses, and create various types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe, Baujat, bubble, and GOSH plots). For meta-analyses of binomial and person-time data, the package also provides functions that implement specialized methods, including the Mantel-Haenszel method, Peto's method, and a variety of suitable generalized linear (mixed-effects) models (i.e., mixed-effects logistic and Poisson regression models). Finally, the package provides functionality for fitting meta-analytic multivariate/multilevel models that account for non-independent sampling errors and/or true effects (e.g., due to the inclusion of multiple treatment studies, multiple endpoints, or other forms of clustering). Network meta [...truncated...]
Author: Wolfgang Viechtbauer [aut, cre]
Maintainer: Wolfgang Viechtbauer <wvb@metafor-project.org>

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More information about metafor at CRAN
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Package fungible updated to version 2.3 with previous version 2.2.1 dated 2022-06-10

Title: Psychometric Functions from the Waller Lab
Description: Computes fungible coefficients and Monte Carlo data. Underlying theory for these functions is described in the following publications: Waller, N. (2008). Fungible Weights in Multiple Regression. Psychometrika, 73(4), 691-703, <DOI:10.1007/s11336-008-9066-z>. Waller, N. & Jones, J. (2009). Locating the Extrema of Fungible Regression Weights. Psychometrika, 74(4), 589-602, <DOI:10.1007/s11336-008-9087-7>. Waller, N. G. (2016). Fungible Correlation Matrices: A Method for Generating Nonsingular, Singular, and Improper Correlation Matrices for Monte Carlo Research. Multivariate Behavioral Research, 51(4), 554-568, <DOI:10.1080/00273171.2016.1178566>. Jones, J. A. & Waller, N. G. (2015). The normal-theory and asymptotic distribution-free (ADF) covariance matrix of standardized regression coefficients: theoretical extensions and finite sample behavior. Psychometrika, 80, 365-378, <DOI:10.1007/s11336-013-9380-y>. Waller, N. G. (2018). Direct Schmid-Leiman tran [...truncated...]
Author: Niels Waller [aut, cre], Jeff Jones [ctb], Casey Giordano [ctb], Hoang V. Nguyen [ctb]
Maintainer: Niels Waller <nwaller@umn.edu>

Diff between fungible versions 2.2.1 dated 2022-06-10 and 2.3 dated 2023-03-19

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Permanent link

Package rswipl updated to version 9.1.7 with previous version 9.1.6 dated 2023-02-20

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

Diff between rswipl versions 9.1.6 dated 2023-02-20 and 9.1.7 dated 2023-03-19

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Package sensitivity updated to version 1.28.1 with previous version 1.28.0 dated 2022-09-29

Title: Global Sensitivity Analysis of Model Outputs
Description: A collection of functions for sensitivity analysis of model outputs (factor screening, global sensitivity analysis and robustness analysis), as well as for interpretability of machine learning models. Most of the functions have to be applied on scalar output, but several functions support multi-dimensional outputs.
Author: Bertrand Iooss, Sebastien Da Veiga, Alexandre Janon and Gilles Pujol, with contributions from Baptiste Broto, Khalid Boumhaout, Thibault Delage, Reda El Amri, Jana Fruth, Laurent Gilquin, Joseph Guillaume, Margot Herin, Marouane Il Idrissi, Loic Le G [...truncated...]
Maintainer: Bertrand Iooss <biooss@yahoo.fr>

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Package jskm updated to version 0.5 with previous version 0.4.4 dated 2023-01-06

Title: Kaplan-Meier Plot with 'ggplot2'
Description: The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator.
Author: Jinseob Kim [aut, cre] , Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>

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Package oddsapiR updated to version 0.0.3 with previous version 0.0.2 dated 2023-01-05

Title: Access Live Sports Odds from the Odds API
Description: A utility to quickly obtain clean and tidy sports odds from The Odds API <https://the-odds-api.com>.
Author: Saiem Gilani [aut, cre]
Maintainer: Saiem Gilani <saiem.gilani@gmail.com>

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Package logconcens updated to version 0.17-2 with previous version 0.17-1 dated 2022-10-17

Title: Maximum Likelihood Estimation of a Log-Concave Density Based on Censored Data
Description: Based on right or interval censored data, compute the maximum likelihood estimator of a (sub)probability density under the assumption that it is log-concave. For further information see Duembgen, Rufibach and Schuhmacher (2014) <doi:10.1214/14-EJS930>.
Author: Dominic Schuhmacher <dominic.schuhmacher@mathematik.uni-goettingen.de>, Kaspar Rufibach <kaspar.rufibach@gmail.com>, Lutz Duembgen <duembgen@stat.unibe.ch>
Maintainer: Dominic Schuhmacher <dominic.schuhmacher@mathematik.uni-goettingen.de>

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Package samplingR updated to version 0.1.2 with previous version 0.1.1 dated 2023-03-09

Title: Sampling and Estimation Methods
Description: Functions to take samples of data, sample size estimation and getting useful estimators such as total, mean, proportion about its population using simple random sampling and stratified sampling.
Author: Javier Estevez [aut, cre, cph]
Maintainer: Javier Estevez <javier.estase@gmail.com>

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Package bdrc updated to version 1.1.0 with previous version 1.0.0 dated 2021-07-28

Title: Bayesian Discharge Rating Curves
Description: Fits a discharge rating curve based on the power-law and the generalized power-law from data on paired stage and discharge measurements in a given river using a Bayesian hierarchical model as described in Hrafnkelsson et al. (2020) <arXiv:2010.04769>.
Author: Birgir Hrafnkelsson [aut, cph] , Solvi Rognvaldsson [aut, cre] , Axel Orn Jansson [aut], Rafael Vias [aut]
Maintainer: Solvi Rognvaldsson <solviro@gmail.com>

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Package starter updated to version 0.1.13 with previous version 0.1.12 dated 2022-10-31

Title: Starter Kit for New Projects
Description: Get started with new projects by dropping a skeleton of a new project into a new or existing directory, initialise git repositories, and create reproducible environments with the 'renv' package. The package allows for dynamically named files, folders, file content, as well as the functionality to drop individual template files into existing projects.
Author: Daniel D. Sjoberg [aut, cre] , Emily Vertosick [ctb]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>

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Package PracTools updated to version 1.3 with previous version 1.2.8 dated 2022-08-17

Title: Tools for Designing and Weighting Survey Samples
Description: Functions and datasets to support Valliant, Dever, and Kreuter, Practical Tools for Designing and Weighting Survey Samples (2nd edition, 2018). Contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs, and single-stage audit sample designs. Functions are included that will group geographic units accounting for distances apart and measures of size. Other functions compute variance components for multistage designs and sample sizes in two-phase designs. A number of example data sets are included.
Author: Richard Valliant, Jill A. Dever, Frauke Kreuter, George Zipf
Maintainer: Richard Valliant <valliant@umich.edu>

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Package ExactMed updated to version 0.2.0 with previous version 0.1.0 dated 2022-03-09

Title: Exact Mediation Analysis for Binary Outcomes
Description: A tool for conducting exact parametric regression-based causal mediation analysis of binary outcomes as described in Samoilenko, Blais and Lefebvre (2018) <doi:10.1353/obs.2018.0013>; Samoilenko, Lefebvre (2021) <doi:10.1093/aje/kwab055>; and Samoilenko, Lefebvre (2022) <doi:10.1002/sim.9621>.
Author: Miguel Caubet [aut, cre], Mariia Samoilenko [aut], Genevieve Lefebvre [aut]
Maintainer: Miguel Caubet <caubet_fernandez.miguel@uqam.ca>

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Package XML updated to version 3.99-0.14 with previous version 3.99-0.13 dated 2022-12-04

Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an 'XPath' "interpreter".
Author: CRAN Team [ctb, cre] , Duncan Temple Lang [aut] , Tomas Kalibera [ctb]
Maintainer: CRAN Team <CRAN@r-project.org>

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Package rxode2parse updated to version 2.0.15 with previous version 2.0.14 dated 2023-03-17

Title: Parsing and Code Generation Functions for 'rxode2'
Description: Provides the parsing needed for 'rxode2' (Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>). It also provides the 'stan' based advan linear compartment model solutions with gradients (Carpenter et al (2015), <arXiv:1509.07164>) needed in 'nlmixr2' (Fidler et al (2019) <doi:10.1002/psp4.12445>). This split will reduce computational burden of recompiling 'rxode2'.
Author: Matthew L. Fidler [aut, cre] , Wenping Wang [aut], Richard Upton [ctb], Gabriel Staples [ctb], Goro Fuji [ctb], Morwenn [ctb], Igor Kushnir [ctb], Kevin Ushey [ctb], David Cooley [ctb]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>

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Package redist updated to version 4.1.0 with previous version 4.0.1 dated 2022-06-16

Title: Simulation Methods for Legislative Redistricting
Description: Enables researchers to sample redistricting plans from a pre-specified target distribution using Sequential Monte Carlo and Markov Chain Monte Carlo algorithms. The package allows for the implementation of various constraints in the redistricting process such as geographic compactness and population parity requirements. Tools for analysis such as computation of various summary statistics and plotting functionality are also included. The package implements the SMC algorithm of McCartan and Imai (2020) <arXiv:2008.06131>, the enumeration algorithm of Fifield, Imai, Kawahara, and Kenny (2020) <doi:10.1080/2330443X.2020.1791773>, the Flip MCMC algorithm of Fifield, Higgins, Imai and Tarr (2020) <doi:10.1080/10618600.2020.1739532>, the Merge-split/Recombination algorithms of Carter et al. (2019) <arXiv:1911.01503> and DeFord et al. (2021) <doi:10.1162/99608f92.eb30390f>, and the Short-burst optimization algorithm of Cannon et al. (2020) <arXiv:2011.02288> [...truncated...]
Author: Christopher T. Kenny [aut, cre], Cory McCartan [aut], Ben Fifield [aut], Kosuke Imai [aut], Jun Kawahara [ctb], Alexander Tarr [ctb], Michael Higgins [ctb]
Maintainer: Christopher T. Kenny <christopherkenny@fas.harvard.edu>

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More information about redist at CRAN
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Package coronavirus updated to version 0.4.1 with previous version 0.4.0 dated 2023-02-13

Title: The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Dataset
Description: Provides a daily summary of the Coronavirus (COVID-19) cases by state/province. Data source: Johns Hopkins University Center for Systems Science and Engineering (JHU CCSE) Coronavirus <https://systems.jhu.edu/research/public-health/ncov/>.
Author: Rami Krispin [aut, cre], Jarrett Byrnes [aut]
Maintainer: Rami Krispin <rami.krispin@gmail.com>

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Package agriutilities updated to version 1.1.0 with previous version 1.0.0 dated 2023-02-16

Title: Utilities for Data Analysis in Agriculture
Description: Utilities designed to make the analysis of field trials easier and more accessible for everyone working in plant breeding. It provides a simple and intuitive interface for conducting single and multi-environmental trial analysis, with minimal coding required. Whether you're a beginner or an experienced user, 'agriutilities' will help you quickly and easily carry out complex analyses with confidence. With built-in functions for fitting Linear Mixed Models, 'agriutilities' is the ideal choice for anyone who wants to save time and focus on interpreting their results. Some of the functions require the R package 'asreml' for the 'ASReml' software, this can be obtained upon purchase from 'VSN' international (<https://vsni.co.uk/software/asreml-r>).
Author: Johan Aparicio [aut, cre], Alexia Bornhorst [aut], The Alliance of Bioversity International and CIAT [cph]
Maintainer: Johan Aparicio <johanstevenapa@gmail.com>

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More information about agriutilities at CRAN
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