Sat, 29 Mar 2025

Package fangs updated to version 0.2.18 with previous version 0.2.17 dated 2024-09-06

Title: Feature Allocation Neighborhood Greedy Search Algorithm
Description: A neighborhood-based, greedy search algorithm is performed to estimate a feature allocation by minimizing the expected loss based on posterior samples from the feature allocation distribution. The method is currently under peer review but an earlier draft is available in Dahl, Johnson, and Andros (2022+) <doi:10.48550/arXiv.2207.13824>.
Author: David B. Dahl [aut, cre] , R. Jacob Andros [aut] , Devin J. Johnson [aut] , Alex Crichton [ctb] , Andrii Dmytrenko [ctb] , Brendan Zabarauskas [ctb] , David B. Dahl [ctb] , David Tolnay [ctb] , Jim Turner [ctb] , Josh Stone [ctb] , Niko Matsakis [ctb [...truncated...]
Maintainer: David B. Dahl <dahl@stat.byu.edu>

Diff between fangs versions 0.2.17 dated 2024-09-06 and 0.2.18 dated 2025-03-29

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Package bfp updated to version 0.0-49 with previous version 0.0-48 dated 2024-03-14

Title: Bayesian Fractional Polynomials
Description: Implements the Bayesian paradigm for fractional polynomial models under the assumption of normally distributed error terms, see Sabanes Bove, D. and Held, L. (2011) <doi:10.1007/s11222-010-9170-7>.
Author: Daniel Sabanes Bove [aut, cre], Isaac Gravestock [aut], Robert Davies [cph], Stephen Moshier [cph], Gareth Ambler [cph], Axel Benner [cph]
Maintainer: Daniel Sabanes Bove <daniel.sabanesbove@gmx.net>

Diff between bfp versions 0.0-48 dated 2024-03-14 and 0.0-49 dated 2025-03-29

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Package simStateSpace updated to version 1.2.10 with previous version 1.2.9 dated 2025-02-14

Title: Simulate Data from State Space Models
Description: Provides a streamlined and user-friendly framework for simulating data in state space models, particularly when the number of subjects/units (n) exceeds one, a scenario commonly encountered in social and behavioral sciences. For an introduction to state space models in social and behavioral sciences, refer to Chow, Ho, Hamaker, and Dolan (2010) <doi:10.1080/10705511003661553>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>

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Package avesperu updated to version 0.0.4 with previous version 0.0.3 dated 2024-12-05

Title: Access to the List of Birds Species of Peru
Description: Allows access to the data found in the species list featured in the renowned 'List of the Birds of Peru' Plenge, M. A. (2023) <https://sites.google.com/site/boletinunop/checklist>. This publication stands as one of Peru's most comprehensive reviews of bird diversity. The dataset incorporates detailed species accounts and has been meticulously structured for effortless utilization within the R environment.
Author: Paul E. Santos Andrade [aut, cre]
Maintainer: Paul E. Santos Andrade <paulefrens@gmail.com>

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Package reportr updated to version 1.3.1 with previous version 1.3.0 dated 2018-10-26

Title: A General Message and Error Reporting System
Description: Provides a system for reporting messages, which provides certain useful features over the standard R system, such as the incorporation of output consolidation, message filtering, assertions, expression substitution, automatic generation of stack traces for debugging, and conditional reporting based on the current "output level".
Author: Jon Clayden [aut, cre]
Maintainer: Jon Clayden <code@clayden.org>

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Package DemographicTable updated to version 0.2.0 with previous version 0.1.11 dated 2025-03-15

Title: Create Demographic Table
Description: Functions for creating demographic table of simple summary statistics and comparison(s) over one or more groups.
Author: Tingting Zhan [aut, cre]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>

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

Title: Simple, Consistent Package Options
Description: Simple mechanisms for defining and interpreting package options. Provides helpers for interpreting environment variables, global options, defining default values and more.
Author: Doug Kelkhoff [aut, cre]
Maintainer: Doug Kelkhoff <doug.kelkhoff@gmail.com>

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Package EnsemblePenReg updated to version 0.8 with previous version 0.7 dated 2016-09-14

Title: Extensible Classes and Methods for Penalized-Regression-Based Integration of Base Learners
Description: Extending the base classes and methods of EnsembleBase package for Penalized-Regression-based (Ridge and Lasso) integration of base learners. Default implementation uses cross-validation error to choose the optimal lambda (shrinkage parameter) for the final predictor. The package takes advantage of the file method provided in EnsembleBase package for writing estimation objects to disk in order to circumvent RAM bottleneck. Special save and load methods are provided to allow estimation objects to be saved to permanent files on disk, and to be loaded again into temporary files in a later R session. Users and developers can extend the package by extending the generic methods and classes provided in EnsembleBase package as well as this package.
Author: Mansour T.A. Sharabiani [aut], Alireza S. Mahani [aut, cre]
Maintainer: Alireza S. Mahani <alireza.s.mahani@gmail.com>

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Package gie updated to version 0.1.3 with previous version 0.1.2 dated 2024-06-02

Title: API Wrapper for the Natural Gas Transparency Platforms of Gas Infrastructure Europe
Description: Providing access to the API for Gas Infrastructure Europe's natural gas transparency platforms <https://agsi.gie.eu/> and <https://alsi.gie.eu/>. Lets the user easily download metadata on companies and gas storage units covered by the API as well as the respective data on regional, country, company or facility level.
Author: Yannik Buhl [aut, cre]
Maintainer: Yannik Buhl <ybuhl@posteo.de>

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Package Rdistance updated to version 4.0.3 with previous version 3.1.4 dated 2025-03-11

Title: Density and Abundance from Distance-Sampling Surveys
Description: Distance-sampling (<doi:10.1007/978-3-319-19219-2>) estimates density and abundance of survey targets (e.g., animals) when detection probability declines with distance. Distance-sampling is popular in ecology, especially when survey targets are observed from aerial platforms (e.g., airplane or drone), surface vessels (e.g., boat or truck), or along walking transects. Distance-sampling includes line-transect studies that measure observation distances as the closest approach of the sample route (transect) to the target (i.e., perpendicular off-transect distance), and point-transect studies that measure observation distances from stationary observers to the target (i.e., radial distance). The routines included here fit smooth (parametric) curves to histograms of observation distances and use those functions to compute effective sampling distances, density of targets in the surveyed area, and abundance of targets in a surrounding study area. Curve shapes include the half-normal, haza [...truncated...]
Author: Trent McDonald [cre, aut], Jason Carlisle [aut], Aidan McDonald [aut] , Ryan Nielson [ctb] , Ben Augustine [ctb] , James Griswald [ctb] , Patrick McKann [ctb] , Lacey Jeroue [ctb] , Hoffman Abigail [ctb] , Kleinsausser Michael [ctb] , Joel Reynolds [ [...truncated...]
Maintainer: Trent McDonald <trent@mcdonalddatasciences.com>

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Package marginaleffects updated to version 0.25.1 with previous version 0.25.0 dated 2025-02-01

Title: Predictions, Comparisons, Slopes, Marginal Means, and Hypothesis Tests
Description: Compute and plot predictions, slopes, marginal means, and comparisons (contrasts, risk ratios, odds, etc.) for over 100 classes of statistical and machine learning models in R. Conduct linear and non-linear hypothesis tests, or equivalence tests. Calculate uncertainty estimates using the delta method, bootstrapping, or simulation-based inference. Details can be found in Arel-Bundock, Greifer, and Heiss (2024) <doi:10.18637/jss.v111.i09>.
Author: Vincent Arel-Bundock [aut, cre, cph] , Noah Greifer [ctb] , Etienne Bacher [ctb] , Grant McDermott [ctb] , Andrew Heiss [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>

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Package genset updated to version 0.1.1 with previous version 0.1.0 dated 2020-09-16

Title: Generates Multiple Data Sets
Description: Generate multiple data sets for educational purposes to demonstrate the importance of multiple regression. The genset function generates a data set from an initial data set to have the same summary statistics (mean, median, and standard deviation) but opposing regression results.
Author: Lori Murray [aut, cre]
Maintainer: Lori Murray <lori.murray@uwo.ca>

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Package EnsembleCV updated to version 0.9 with previous version 0.8 dated 2016-09-13

Title: Extensible Package for Cross-Validation-Based Integration of Base Learners
Description: Extends the base classes and methods of EnsembleBase package for cross-validation-based integration of base learners. Default implementation calculates average of repeated CV errors, and selects the base learner / configuration with minimum average error. The package takes advantage of the file method provided in EnsembleBase package for writing estimation objects to disk in order to circumvent RAM bottleneck. Special save and load methods are provided to allow estimation objects to be saved to permanent files on disk, and to be loaded again into temporary files in a later R session. The package can be extended, e.g. by adding variants of the current implementation.
Author: Mansour T.A. Sharabiani [aut], Alireza S. Mahani [aut, cre]
Maintainer: Alireza S. Mahani <alireza.s.mahani@gmail.com>

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Package polaroid updated to version 0.2.1 with previous version 0.1.0 dated 2023-11-18

Title: Create Hex Stickers with 'shiny'
Description: Create hexagonal shape sticker image. 'polaroid' can be used in user's web browser. 'polaroid' can be used in 'shinyapps.io'. In both way, user can download created 'hexSticker' as 'PNG' image. 'polaroid' is built based on 'argonDash', 'colourpicker' and 'hexSticker' R package.
Author: Jinhwan Kim [aut, cre, cph]
Maintainer: Jinhwan Kim <hwanistic@gmail.com>

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Package geneNR updated to version 2.0.1 with previous version 1.0.1 dated 2025-03-10

Title: Automated Gene Identification for Post-GWAS and QTL Analysis
Description: Facilitates the post-Genome Wide Association Studies (GWAS) and Quantitative Trait Loci (QTL) analysis of identifying candidate genes within user-defined search window, based on the identified Single Nucleotide Polymorphisms (SNPs) as given by Mazumder AK (2024) <doi:10.1038/s41598-024-66903-3>. It supports candidate gene analysis for wheat and rice. Just import your GWAS result as explained in the sample_data file and the function does all the manual search and retrieve candidate genes for you, while exporting the results into ready-to-use output.
Author: Rajamani Nirmalaruban [aut, cre, cph], R. Suvitha [aut], Rajbir Yadav [aut], Meda Alekya [aut], Amit Kumar Mazumder [aut], Subramani Sugumar [aut], Prashanth babu [aut], Manjeet Kumar [aut], Kiran B Gaikwad [aut], Naresh Kumar Bainsla [aut], S. Bhask [...truncated...]
Maintainer: Rajamani Nirmalaruban <nirmalaruban97@gmail.com>

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Package spNetwork updated to version 0.4.4.6 with previous version 0.4.4.5 dated 2025-01-20

Title: Spatial Analysis on Network
Description: Perform spatial analysis on network. Implement several methods for spatial analysis on network: Network Kernel Density estimation, building of spatial matrices based on network distance ('listw' objects from 'spdep' package), K functions estimation for point pattern analysis on network, k nearest neighbours on network, reachable area calculation, and graph generation References: Okabe et al (2019) <doi:10.1080/13658810802475491>; Okabe et al (2012, ISBN:978-0470770818);Baddeley et al (2015, ISBN:9781482210200).
Author: Jeremy Gelb [aut, cre] , Philippe Apparicio [ctb]
Maintainer: Jeremy Gelb <jeremy.gelb@ucs.inrs.ca>

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Package incgraph updated to version 1.0.3 with previous version 1.0.1 dated 2017-10-12

Title: Incremental Graphlet Counting for Network Optimisation
Description: An efficient and incremental approach for calculating the differences in orbit counts when performing single edge modifications in a network. Calculating the differences in orbit counts is much more efficient than recalculating all orbit counts from scratch for each time point.
Author: Robrecht Cannoodt [aut, cre]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>

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Package ggnormalviolin updated to version 0.2.1 with previous version 0.1.2 dated 2019-05-27

Title: A 'ggplot2' Extension to Make Normal Violin Plots
Description: Uses 'ggplot2' to create normally distributed violin plots with specified means and standard deviations. This function can be useful in showing hypothetically normal distributions and confidence intervals.
Author: W. Joel Schneider [aut, cre]
Maintainer: W. Joel Schneider <w.joel.schneider@gmail.com>

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Package DR.SC updated to version 3.5 with previous version 3.4 dated 2024-03-19

Title: Joint Dimension Reduction and Spatial Clustering
Description: Joint dimension reduction and spatial clustering is conducted for Single-cell RNA sequencing and spatial transcriptomics data, and more details can be referred to Wei Liu, Xu Liao, Yi Yang, Huazhen Lin, Joe Yeong, Xiang Zhou, Xingjie Shi and Jin Liu. (2022) <doi:10.1093/nar/gkac219>. It is not only computationally efficient and scalable to the sample size increment, but also is capable of choosing the smoothness parameter and the number of clusters as well.
Author: Wei Liu [aut, cre], Yi Yang [aut], Jin Liu [aut]
Maintainer: Wei Liu <liuweideng@gmail.com>

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Package corncob updated to version 0.4.2 with previous version 0.4.1 dated 2024-01-10

Title: Count Regression for Correlated Observations with the Beta-Binomial
Description: Statistical modeling for correlated count data using the beta-binomial distribution, described in Martin et al. (2020) <doi:10.1214/19-AOAS1283>. It allows for both mean and overdispersion covariates.
Author: Bryan D Martin [aut], Daniela Witten [aut], Sarah Teichman [ctb], Amy D Willis [aut, cre], Thomas W Yee [ctb] , Xiangjie Xue [ctb]
Maintainer: Amy D Willis <adwillis@uw.edu>

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Package tinythemes updated to version 0.0.3 with previous version 0.0.2 dated 2024-03-04

Title: Lightweight Repackaging of 'Themes' for 'ggplot2'
Description: Themes for 'ggplot2' are a convenient way to style plots. The 'hrbrthemes' package contains a particularly nice one, but brings along a significant tail of dependencies. So this (currently experimental) package brings along just the 'theme_ipsum_rc' theme using the 'Roboto' 'Condensed' font. Should the font not be installed on your system, see the help in the package 'hrbrthemes' on how to install 'Roboto Condensed'.
Author: Dirk Eddelbuettel [aut, cre] , Bob Rudis [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package SPREDA updated to version 1.2 with previous version 1.1 dated 2018-11-25

Title: Statistical Package for Reliability Data Analysis
Description: The Statistical Package for REliability Data Analysis (SPREDA) implements recently-developed statistical methods for the analysis of reliability data. Modern technological developments, such as sensors and smart chips, allow us to dynamically track product/system usage as well as other environmental variables, such as temperature and humidity. We refer to these variables as dynamic covariates. The package contains functions for the analysis of time-to-event data with dynamic covariates and degradation data with dynamic covariates. The package also contains functions that can be used for analyzing time-to-event data with right censoring, and with left truncation and right censoring. Financial support from NSF and DuPont are acknowledged.
Author: Yili Hong [aut, cre], Yimeng Xie [aut], Zhibing Xu [aut]
Maintainer: Yili Hong <yilihong@vt.edu>

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Package jiebaR updated to version 0.11.1 with previous version 0.11 dated 2019-12-13

Title: Chinese Text Segmentation
Description: Chinese text segmentation, keyword extraction and speech tagging For R.
Author: Qin Wenfeng, Wu Yanyi
Maintainer: ORPHANED

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Package guideR updated to version 0.3.0 with previous version 0.2.0 dated 2025-03-16

Title: Miscellaneous Statistical Functions Used in 'guide-R'
Description: Companion package for the manual 'guide-R : Guide pour l’analyse de données d’enquêtes avec R' available at <https://larmarange.github.io/guide-R/>. 'guideR' implements miscellaneous functions introduced in 'guide-R' to facilitate statistical analysis and manipulation of survey data.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>

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Package DATAstudio updated to version 1.2.1 with previous version 1.2 dated 2025-03-17

Title: The Research Data Warehouse of Miguel de Carvalho
Description: Pulls together a collection of datasets from Miguel de Carvalho research articles. Including, for example: - de Carvalho (2012) <doi:10.1016/j.jspi.2011.08.016>; - de Carvalho et al (2012) <doi:10.1080/03610926.2012.709905>; - de Carvalho et al (2012) <doi:10.1016/j.econlet.2011.09.007>); - de Carvalho and Davison (2014) <doi:10.1080/01621459.2013.872651>; - de Carvalho and Rua (2017) <doi:10.1016/j.ijforecast.2015.09.004>; - de Carvalho et al (2023) <doi:10.1002/sta4.560>; - de Carvalho et al (2022) <doi:10.1007/s13253-021-00469-9>; - Palacios et al (2024) <doi:10.1214/24-BA1420>.
Author: Miguel de Carvalho [aut, cre]
Maintainer: Miguel de Carvalho <Miguel.deCarvalho@ed.ac.uk>

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Package blit updated to version 0.2.0 with previous version 0.1.0 dated 2025-02-27

Title: Bioinformatics Library for Integrated Tools
Description: An all-encompassing R toolkit designed to streamline the process of calling various bioinformatics software and then performing data analysis and visualization in R. With 'blit', users can easily integrate a wide array of bioinformatics command line tools into their workflows, leveraging the power of R for sophisticated data manipulation and graphical representation.
Author: Yun Peng [aut, cre] , Shixiang Wang [aut] , Jennifer Lu [cph] , Li Song [cph] , X. Shirley Liu [cph]
Maintainer: Yun Peng <yunyunp96@163.com>

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Package swephR updated to version 0.3.2 with previous version 0.3.1 dated 2023-05-08

Title: High Precision Swiss Ephemeris
Description: The Swiss Ephemeris (version 2.10.03) is a high precision ephemeris based upon the DE431 ephemerides from NASA's JPL. It covers the time range 13201 BCE to 17191 CE. This package uses the semi-analytic theory by Steve Moshier. For faster and more accurate calculations, the compressed Swiss Ephemeris data is available in the 'swephRdata' package. To access this data package, run 'install.packages("swephRdata", repos = "https://rstub.r-universe.dev", type = "source")'. The size of the 'swephRdata' package is approximately 115 MB. The user can also use the original JPL DE431 data.
Author: Ralf Stubner [aut, cre], Victor Reijs [aut], Authors and copyright holder of the Swiss Ephemeris [aut, cph]
Maintainer: Ralf Stubner <ralf.stubner@gmail.com>

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Package git2r updated to version 0.36.2 with previous version 0.35.0 dated 2024-10-20

Title: Provides Access to Git Repositories
Description: Interface to the 'libgit2' library, which is a pure C implementation of the 'Git' core methods. Provides access to 'Git' repositories to extract data and running some basic 'Git' commands.
Author: Stefan Widgren [aut, cre] , Gabor Csardi [ctb], Gregory Jefferis [ctb], Jennifer Bryan [ctb], Jeroen Ooms [ctb], Jim Hester [ctb], John Blischak [ctb], Karthik Ram [ctb], Peter Carbonetto [ctb], Scott Chamberlain [ctb], Thomas Rosendal [ctb]
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>

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Package GeneralizedHyperbolic updated to version 0.8-7 with previous version 0.8-6 dated 2023-11-26

Title: The Generalized Hyperbolic Distribution
Description: Functions for the hyperbolic and related distributions. Density, distribution and quantile functions and random number generation are provided for the hyperbolic distribution, the generalized hyperbolic distribution, the generalized inverse Gaussian distribution and the skew-Laplace distribution. Additional functionality is provided for the hyperbolic distribution, normal inverse Gaussian distribution and generalized inverse Gaussian distribution, including fitting of these distributions to data. Linear models with hyperbolic errors may be fitted using hyperblmFit.
Author: David Scott [aut, cre]
Maintainer: David Scott <d.scott@auckland.ac.nz>

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Package gemini.R updated to version 0.11.0 with previous version 0.10.1 dated 2025-03-19

Title: Interface for 'Google Gemini' API
Description: Provides a comprehensive interface for Google Gemini API, enabling users to access and utilize Gemini Large Language Model (LLM) functionalities directly from R. This package facilitates seamless integration with Google Gemini, allowing for advanced language processing, text generation, and other AI-driven capabilities within the R environment. For more information, please visit <https://ai.google.dev/docs/gemini_api_overview>.
Author: Jinhwan Kim [aut, cre, cph] , Maciej Nasinski [ctb]
Maintainer: Jinhwan Kim <hwanistic@gmail.com>

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Package vein updated to version 1.3.0 with previous version 1.1.3 dated 2024-05-01

Title: Vehicular Emissions Inventories
Description: Elaboration of vehicular emissions inventories, consisting in four stages, pre-processing activity data, preparing emissions factors, estimating the emissions and post-processing of emissions in maps and databases. More details in Ibarra-Espinosa et al (2018) <doi:10.5194/gmd-11-2209-2018>. Before using VEIN you need to know the vehicular composition of your study area, in other words, the combination of of type of vehicles, size and fuel of the fleet. Then, it is recommended to start with the project to download a template to create a structure of directories and scripts.
Author: Sergio Ibarra-Espinosa [aut, cre] , Daniel Schuch [ctb] , Joao Bazzo [ctb] , Mario Gavidia-Calderon [ctb] , Karl Ropkins [ctb]
Maintainer: Sergio Ibarra-Espinosa <zergioibarra@gmail.com>

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More information about vein at CRAN
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Package enmSdmX updated to version 1.2.12 with previous version 1.2.10 dated 2024-12-11

Title: Species Distribution Modeling and Ecological Niche Modeling
Description: Implements species distribution modeling and ecological niche modeling, including: bias correction, spatial cross-validation, model evaluation, raster interpolation, biotic "velocity" (speed and direction of movement of a "mass" represented by a raster), interpolating across a time series of rasters, and use of spatially imprecise records. The heart of the package is a set of "training" functions which automatically optimize model complexity based number of available occurrences. These algorithms include MaxEnt, MaxNet, boosted regression trees/gradient boosting machines, generalized additive models, generalized linear models, natural splines, and random forests. To enhance interoperability with other modeling packages, no new classes are created. The package works with 'PROJ6' geodetic objects and coordinate reference systems.
Author: Adam B. Smith [cre, aut]
Maintainer: Adam B. Smith <adam.smith@mobot.org>

Diff between enmSdmX versions 1.2.10 dated 2024-12-11 and 1.2.12 dated 2025-03-29

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 enmSdmX-1.2.12/enmSdmX/NEWS.md                                   |   12 
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 43 files changed, 507 insertions(+), 208 deletions(-)

More information about enmSdmX at CRAN
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