Thu, 19 Jan 2023

Package joineRML updated to version 0.4.6 with previous version 0.4.5 dated 2021-01-05

Title: Joint Modelling of Multivariate Longitudinal Data and Time-to-Event Outcomes
Description: Fits the joint model proposed by Henderson and colleagues (2000) <doi:10.1093/biostatistics/1.4.465>, but extended to the case of multiple continuous longitudinal measures. The time-to-event data is modelled using a Cox proportional hazards regression model with time-varying covariates. The multiple longitudinal outcomes are modelled using a multivariate version of the Laird and Ware linear mixed model. The association is captured by a multivariate latent Gaussian process. The model is estimated using a Monte Carlo Expectation Maximization algorithm. This project was funded by the Medical Research Council (Grant number MR/M013227/1).
Author: Graeme L. Hickey [cre, aut] , Pete Philipson [aut] , Andrea Jorgensen [ctb] , Ruwanthi Kolamunnage-Dona [aut] , Paula Williamson [ctb] , Dimitris Rizopoulos [ctb, dtc] , Alessandro Gasparini [aut] , Medical Research Council [fnd]
Maintainer: Graeme L. Hickey <graemeleehickey@gmail.com>

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Package genekitr updated to version 1.1.0 with previous version 1.0.8 dated 2022-11-23

Title: Gene Analysis Toolkit
Description: An analysis toolkit focused on genes. It mainly includes five features (search, convert, analysis, plot, and export). The user just needs to input feature id ('entrez', 'symbol', 'ensembl' or 'uniprot') to retrieve feature information and 'PubMed'<https://pubmed.ncbi.nlm.nih.gov/> records, to convert id types, to easily handle gene enrichment analysis and publication-level figures, to plot group interaction and export results as sheets in one 'excel' file to easily share and communicate with others.
Author: Yunze Liu [aut, cre]
Maintainer: Yunze Liu <jieandze1314@gmail.com>

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Package Allspice updated to version 1.0.7 with previous version 1.0.6 dated 2022-12-15

Title: RNA-Seq Profile Classifier
Description: We developed a lightweight machine learning tool for RNA profiling of acute lymphoblastic leukemia (ALL), however, it can be used for any problem where multiple classes need to be identified from multi-dimensional data. The methodology is described in Makinen V-P, Rehn J, Breen J, Yeung D, White DL (2022) Multi-cohort transcriptomic subtyping of B-cell acute lymphoblastic leukemia, International Journal of Molecular Sciences 23:4574, <doi:10.3390/ijms23094574>. The classifier contains optimized mean profiles of the classes (centroids) as observed in the training data, and new samples are matched to these centroids using the shortest Euclidean distance. Centroids derived from a dataset of 1,598 ALL patients are included, but users can train the models with their own data as well. The output includes both numerical and visual presentations of the classification results. Samples with mixed features from multiple classes or atypical values are also identified.
Author: Ville-Petteri Makinen [aut, cre]
Maintainer: Ville-Petteri Makinen <vpmakine@gmail.com>

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Package sp updated to version 1.6-0 with previous version 1.5-1 dated 2022-11-07

Title: Classes and Methods for Spatial Data
Description: Classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma [aut, cre], Roger Bivand [aut], Barry Rowlingson [ctb], Virgilio Gomez-Rubio [ctb], Robert Hijmans [ctb], Michael Sumner [ctb], Don MacQueen [ctb], Jim Lemon [ctb], Finn Lindgren [ctb], Josh O'Brien [ctb], Joseph O'Rourke [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

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Package rstac updated to version 0.9.2 with previous version 0.9.1-5 dated 2021-10-31

Title: Client Library for SpatioTemporal Asset Catalog
Description: Provides functions to access, search and download spacetime earth observation data via SpatioTemporal Asset Catalog (STAC). This package supports the version 1.0.0 (and older) of the STAC specification (<https://github.com/radiantearth/stac-spec>). For further details see Simoes et al. (2021) <doi:10.1109/IGARSS47720.2021.9553518>.
Author: Rolf Simoes [aut], Felipe Carvalho [aut, cre], Brazil Data Cube Team [aut], National Institute for Space Research [cph]
Maintainer: Felipe Carvalho <lipecaso@gmail.com>

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Package rmarkdown updated to version 2.20 with previous version 2.19 dated 2022-12-15

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

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New package rgudhi with initial version 0.1.0
Package: rgudhi
Title: An Interface to the GUDHI Library for Topological Data Analysis
Version: 0.1.0
Description: Provides an interface to the GUDHI library which is a generic open source C++ library, with a Python interface, for topological data analysis (TDA) and higher dimensional geometry understanding. The library offers state-of-the-art data structures and algorithms to construct simplicial complexes and compute persistent homology.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/LMJL-Alea/rgudhi, https://lmjl-alea.github.io/rgudhi/
BugReports: https://github.com/lmjl-alea/rgudhi/issues
Config/reticulate: list( packages = list( list(package = "scikit-learn", version = "1.2.0"), list(package = "gudhi", version = "3.7.1") ) )
Imports: cli, curl, dplyr, fs, ggplot2, purrr, R6, Rdpack (>= 2.4.0), reticulate, rlang, tibble, withr
Suggests: covr, testthat (>= 3.0.0), vdiffr
NeedsCompilation: no
Packaged: 2023-01-19 22:28:44 UTC; stamm-a
Author: Aymeric Stamm [aut, cre] , GUDHI Editorial Board [ctb]
Maintainer: Aymeric Stamm <aymeric.stamm@cnrs.fr>
Repository: CRAN
Date/Publication: 2023-01-19 23:30:08 UTC

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Package PublicationBias updated to version 2.3.0 with previous version 2.2.0 dated 2020-07-22

Title: Sensitivity Analysis for Publication Bias in Meta-Analyses
Description: Performs sensitivity analysis for publication bias in meta-analyses (per Mathur & VanderWeele, 2020 [<doi:10.31219/osf.io/s9dp6>]). These analyses enable statements such as: "For publication bias to shift the observed point estimate to the null, 'significant' results would need to be at least 30-fold more likely to be published than negative or 'nonsignificant' results." Comparable statements can be made regarding shifting to a chosen non-null value or shifting the confidence interval. Provides a worst-case meta-analytic point estimate under maximal publication bias obtained simply by conducting a standard meta-analysis of only the negative and "nonsignificant" studies.
Author: Mika Braginsky [aut, cre], Maya Mathur [aut], Tyler J. VanderWeele [aut]
Maintainer: Mika Braginsky <mika.br@gmail.com>

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Package OpenMx updated to version 2.21.1 with previous version 2.20.7 dated 2022-10-19

Title: Extended Structural Equation Modelling
Description: Create structural equation models that can be manipulated programmatically. Models may be specified with matrices or paths (LISREL or RAM) Example models include confirmatory factor, multiple group, mixture distribution, categorical threshold, modern test theory, differential Fit functions include full information maximum likelihood, maximum likelihood, and weighted least squares. equations, state space, and many others. Support and advanced package binaries available at <http://openmx.ssri.psu.edu>. The software is described in Neale, Hunter, Pritikin, Zahery, Brick, Kirkpatrick, Estabrook, Bates, Maes, & Boker (2016) <doi:10.1007/s11336-014-9435-8>.
Author: Steven M. Boker [aut], Michael C. Neale [aut], Hermine H. Maes [aut], Michael J. Wilde [ctb], Michael Spiegel [aut], Timothy R. Brick [aut], Ryne Estabrook [aut], Timothy C. Bates [aut], Paras Mehta [ctb], Timo von Oertzen [ctb], Ross J. Gore [aut], [...truncated...]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>

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Package kcpRS updated to version 1.1.0 with previous version 1.0.0 dated 2019-05-06

Title: Kernel Change Point Detection on the Running Statistics
Description: The running statistics of interest is first extracted using a time window which is slid across the time series, and in each window, the running statistics value is computed. KCP (Kernel Change Point) detection proposed by Arlot et al. (2012) <arXiv:1202.3878> is then implemented to flag the change points on the running statistics (Cabrieto et al., 2018, <doi:10.1016/j.ins.2018.03.010>). Change points are located by minimizing a variance criterion based on the pairwise similarities between running statistics which are computed via the Gaussian kernel. KCP can locate change points for a given k number of change points. To determine the optimal k, the KCP permutation test is first carried out by comparing the variance of the running statistics extracted from the original data to that of permuted data. If this test is significant, then there is sufficient evidence for at least one change point in the data. Model selection is then used to determine the optimal k>0.
Author: Jedelyn Cabrieto [aut], Kristof Meers [aut, cre], Evelien Schat [ctb], Janne Adolf [ctb], Peter Kuppens [ctb], Francis Tuerlinckx [ctb], Eva Ceulemans [ctb]
Maintainer: Kristof Meers <kristof.meers+cran@kuleuven.be>

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Package genepop updated to version 1.2.2 with previous version 1.1.7 dated 2020-02-23

Title: Population Genetic Data Analysis Using Genepop
Description: Makes the Genepop software available in R. This software implements a mixture of traditional population genetic methods and some more focused developments: it computes exact tests for Hardy-Weinberg equilibrium, for population differentiation and for genotypic disequilibrium among pairs of loci; it computes estimates of F-statistics, null allele frequencies, allele size-based statistics for microsatellites, etc.; and it performs analyses of isolation by distance from pairwise comparisons of individuals or population samples.
Author: Francois Rousset [aut, cre, cph] , Jimmy Lopez [ctb], Alexandre Genin [ctb], Khalid Belkhir [ctb]
Maintainer: Francois Rousset <francois.rousset@umontpellier.fr>

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Package markovchain updated to version 0.9.1 with previous version 0.9.0 dated 2022-07-01

Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov chains more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of their structural proprieties) analysis are provided. See Spedicato (2017) <doi:10.32614/RJ-2017-036>.
Author: Giorgio Alfredo Spedicato [aut, cre] , Tae Seung Kang [aut], Sai Bhargav Yalamanchi [aut], Mildenberger Thoralf [ctb] , Deepak Yadav [aut], Ignacio Cordon [aut] , Vandit Jain [ctb], Toni Giorgino [ctb] , Richel J.C. Bilderbeek [ctb] , Daniel Ebbert [ [...truncated...]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>

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Package CRE updated to version 0.2.0 with previous version 0.1.1 dated 2022-10-22

Title: Interpretable Subgroups Identification Through Ensemble Learning of Causal Rules
Description: Provides an interpretable identification of subgroups with heterogeneous causal effect. The heterogeneous subgroups are discovered through ensemble learning of causal rules. Causal rules are highly interpretable if-then statement that recursively partition the features space into heterogeneous subgroups. A small number of significant causal rules are selected through Stability Selection to control for family-wise error rate in the finite sample setting. It proposes various estimation methods for the conditional causal effects for each discovered causal rule. It is highly flexible and multiple causal estimands and imputation methods are implemented. Lee, K., Bargagli-Stoffi, F. J., & Dominici, F. (2020). Causal rule ensemble: Interpretable inference of heterogeneous treatment effects. arXiv preprint <arXiv:2009.09036>.
Author: Naeem Khoshnevis [aut, cre] , Daniela Maria Garcia [aut] , Riccardo Cadei [aut] , Kwonsang Lee [aut] , Falco Joannes Bargagli Stoffi [aut]
Maintainer: Naeem Khoshnevis <nkhoshnevis@g.harvard.edu>

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Package wdnet updated to version 1.0.0 with previous version 0.0.5 dated 2022-09-12

Title: Weighted and Directed Networks
Description: Implementations of network analysis including (1) assortativity coefficient of weighted and directed networks, Yuan, Yan and Zhang (2021) <doi:10.1093/comnet/cnab017>, (2) centrality measures for weighted and directed networks, Opsahl, Agneessens and Skvoretz (2010) <doi:10.1016/j.socnet.2010.03.006>, Zhang, Wang and Yan (2022) <doi:10.1016/j.physa.2021.126438>, (3) clustering coefficient of weighted and directed networks, Fagiolo (2007) <doi:10.1103/PhysRevE.76.026107> and Clemente and Grassi (2018) <doi:10.1016/j.chaos.2017.12.007>, (4) rewiring networks with given assortativity coefficients, Wang, Yan, Yuan and Zhang (2022) <doi:10.1007/s11222-022-10161-8>, (5) preferential attachment network generation.
Author: Yelie Yuan [aut, cre], Tiandong Wang [aut], Jun Yan [aut], Panpan Zhang [aut]
Maintainer: Yelie Yuan <yelie.yuan@uconn.edu>

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Package hisse updated to version 2.1.10 with previous version 2.1.9 dated 2022-06-15

Title: Hidden State Speciation and Extinction
Description: Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification. Beaulieu and O'Meara (2016) <doi:10.1093/sysbio/syw022>.
Author: Jeremy Beaulieu [aut, cre], Brian O'Meara [aut], Daniel Caetano [aut], James Boyko [aut], Thais Vasconcelos [aut]
Maintainer: Jeremy Beaulieu <jmbeauli@uark.edu>

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Package VineCopula updated to version 2.4.5 with previous version 2.4.4 dated 2022-05-24

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

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Package plot3Drgl updated to version 1.0.4 with previous version 1.0.3 dated 2022-06-21

Title: Plotting Multi-Dimensional Data - Using 'rgl'
Description: The 'rgl' implementation of plot3D functions.
Author: Karline Soetaert <karline.soetaert@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>

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Package zen4R updated to version 0.8 with previous version 0.7-1 dated 2023-01-09

Title: Interface to 'Zenodo' REST API
Description: Provides an Interface to 'Zenodo' (<https://zenodo.org>) REST API, including management of depositions, attribution of DOIs by 'Zenodo' and upload and download of files.
Author: Emmanuel Blondel [aut, cre] , Julien Barde [ctb] , Stephen Eglen [ctb] , Hans Van Calster [ctb] , Floris Vanderhaeghe [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>

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Package rSPDE updated to version 2.1.0 with previous version 1.2.0 dated 2022-09-16

Title: Rational Approximations of Fractional Stochastic Partial Differential Equations
Description: Functions that compute rational approximations of fractional elliptic stochastic partial differential equations. The package also contains functions for common statistical usage of these approximations.
Author: David Bolin [cre, aut], Alexandre Simas [aut], Finn Lindgren [ctb]
Maintainer: David Bolin <davidbolin@gmail.com>

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Package PNSIBGE updated to version 0.1.8 with previous version 0.1.7 dated 2022-03-25

Title: Downloading, Reading and Analyzing PNS Microdata
Description: Provides tools for downloading, reading and analyzing the PNS, a household survey from Brazilian Institute of Geography and Statistics - IBGE. The data must be downloaded from the official website <https://www.ibge.gov.br/>. Further analysis must be made using package 'survey'.
Author: Gabriel Assuncao [aut, cre], Luna Hidalgo [aut], Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>

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Package PNADcIBGE updated to version 0.7.2 with previous version 0.7.1 dated 2022-12-01

Title: Downloading, Reading and Analyzing PNADC Microdata
Description: Provides tools for downloading, reading and analyzing the PNADC, a household survey from Brazilian Institute of Geography and Statistics - IBGE. The data must be downloaded from the official website <https://www.ibge.gov.br/>. Further analysis must be made using package 'survey'.
Author: Douglas Braga [aut], Gabriel Assuncao [aut, cre], Luna Hidalgo [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>

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Package pbkrtest updated to version 0.5.2 with previous version 0.5.1 dated 2021-03-09

Title: Parametric Bootstrap, Kenward-Roger and Satterthwaite Based Methods for Test in Mixed Models
Description: Computes p-values based on (a) Satterthwaite or Kenward-Rogers degree of freedom methods and (b) parametric bootstrap for mixed effects models as implemented in the 'lme4' package. Implements parametric bootstrap test for generalized linear mixed models as implemented in 'lme4' and generalized linear models. The package is documented in the paper by Halekoh and Højsgaard, (2012, <doi:10.18637/jss.v059.i09>). Please see 'citation("pbkrtest")' for citation details.
Author: Ulrich Halekoh [aut, cph], Soeren Hoejsgaard [aut, cre, cph]
Maintainer: Soeren Hoejsgaard <sorenh@math.aau.dk>

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Package NADA2 updated to version 1.1.1 with previous version 1.1.0 dated 2022-09-05

Title: Data Analysis for Censored Environmental Data
Description: Contains methods described by Dennis Helsel in his book "Statistics for Censored Environmental Data using Minitab and R" (2011) and courses and videos at <https://practicalstats.com>. This package adds new functions to the `NADA` Package.
Author: Paul Julian [aut, cre], Dennis Helsel [aut, cph]
Maintainer: Paul Julian <pauljulianphd@gmail.com>

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Package libgeos updated to version 3.11.1-1 with previous version 3.11.0-2 dated 2022-10-08

Title: Open Source Geometry Engine ('GEOS') C API
Description: Provides the Open Source Geometry Engine ('GEOS') as a C API that can be used to write high-performance C and C++ geometry operations using R as an interface. Headers are provided to make linking to and using these functions from C++ code as easy and as safe as possible. This package contains an internal copy of the 'GEOS' library to guarantee the best possible consistency on multiple platforms.
Author: Dewey Dunnington [aut, cre] , GEOS authors [aut], Martin Davis [ctb, cph], Benjamin Campbell [ctb, cph], Tomasz Sowa [ctb, cph], Christian Kaiser [ctb, cph], David Skea [ctb, cph], Daniel Baston [ctb, cph], Sandro Santilli [ctb, cph], Mateusz Loskot [...truncated...]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>

Diff between libgeos versions 3.11.0-2 dated 2022-10-08 and 3.11.1-1 dated 2023-01-19

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 NEWS.md                                                          |    5 
 README.md                                                        |    4 
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Package COVIDIBGE updated to version 0.1.9 with previous version 0.1.8 dated 2021-11-30

Title: Downloading, Reading and Analyzing PNAD COVID19 Microdata
Description: Provides tools for downloading, reading and analyzing the PNAD COVID19, a household survey from Brazilian Institute of Geography and Statistics - IBGE. The data must be downloaded from the official website <https://www.ibge.gov.br/>. Further analysis must be made using package 'survey'.
Author: Gabriel Assuncao [aut, cre], Luna Hidalgo [aut], Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>

Diff between COVIDIBGE versions 0.1.8 dated 2021-11-30 and 0.1.9 dated 2023-01-19

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Package asbio updated to version 1.8-4 with previous version 1.8-3 dated 2022-11-18

Title: A Collection of Statistical Tools for Biologists
Description: Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.
Author: Ken Aho
Maintainer: Ken Aho <kenaho1@gmail.com>

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Package tiledb updated to version 0.18.0 with previous version 0.17.1 dated 2023-01-06

Title: Universal Storage Engine for Sparse and Dense Multidimensional Arrays
Description: The universal storage engine 'TileDB' introduces a powerful on-disk format for multi-dimensional arrays. It supports dense and sparse arrays, dataframes and key-values stores, cloud storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression, encryption and checksum filters, uses a fully multi-threaded implementation, supports parallel I/O, data versioning ('time travel'), metadata and groups. It is implemented as an embeddable cross-platform C++ library with APIs from several languages, and integrations.
Author: TileDB, Inc. [aut, cph], Dirk Eddelbuettel [cre]
Maintainer: Dirk Eddelbuettel <dirk@tiledb.com>

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Package PSPManalysis updated to version 0.3.9 with previous version 0.3.8 dated 2022-04-08

Title: Analysis of Physiologically Structured Population Models
Description: Performs demographic, bifurcation and evolutionary analysis of physiologically structured population models, which is a class of models that consistently translates continuous-time models of individual life history to the population level. A model of individual life history has to be implemented specifying the individual-level functions that determine the life history, such as development and mortality rates and fecundity. M.A. Kirkilionis, O. Diekmann, B. Lisser, M. Nool, B. Sommeijer & A.M. de Roos (2001) <doi:10.1142/S0218202501001264>. O.Diekmann, M.Gyllenberg & J.A.J.Metz (2003) <doi:10.1016/S0040-5809(02)00058-8>. A.M. de Roos (2008) <doi:10.1111/j.1461-0248.2007.01121.x>.
Author: Andre M. de Roos [aut, cre], Ernst Hairer [ctb], Gerhard Wanner [ctb]
Maintainer: Andre M. de Roos <A.M.deRoos@uva.nl>

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Package cops updated to version 1.3-1 with previous version 1.2-0 dated 2021-03-23

Title: Cluster Optimized Proximity Scaling
Description: Multidimensional scaling (MDS) methods that aim at pronouncing the clustered appearance of the configuration (Rusch, Mair & Hornik, 2021, <doi:10.1080/10618600.2020.1869027>). They achieve this by transforming proximities/distances with power functions and augment the fitting criterion with a clusteredness index, the OPTICS Cordillera (Rusch, Hornik & Mair, 2018, <doi:10.1080/10618600.2017.1349664>). There are two variants: One for finding the configuration directly (COPS-C) for ratio, power, interval and non-metric MDS (Borg & Groenen, 2005, ISBN:978-0-387-28981-6), and one for using the augmented fitting criterion to find optimal parameters (P-COPS). The package contains various functions, wrappers, methods and classes for fitting, plotting and displaying different MDS models in a COPS framework like ratio, interval and non-metric MDS for COPS-C and P-COPS with Torgerson scaling (Torgerson, 1958, ISBN:978-0471879459), scaling by majorizing a complex function ( [...truncated...]
Author: Thomas Rusch [aut, cre] , Jan de Leeuw [aut], Patrick Mair [aut]
Maintainer: Thomas Rusch <thomas.rusch@wu.ac.at>

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Package postdoc updated to version 1.2.0 with previous version 1.1.0 dated 2022-12-05

Title: Minimal and Uncluttered Package Documentation
Description: Generates simple and beautiful one-page HTML reference manuals with package documentation. Math rendering and syntax highlighting are done server-side in R such that no JavaScript libraries are needed in the browser, which makes the documentation portable and fast to load.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package RCzechia updated to version 1.10.1 with previous version 1.10.0 dated 2022-11-24

Title: Spatial Objects of the Czech Republic
Description: Administrative regions and other spatial objects of the Czech Republic.
Author: Jindra Lacko [aut, cre]
Maintainer: Jindra Lacko <jindra.lacko@gmail.com>

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Package ecmwfr updated to version 1.5.0 with previous version 1.4.0 dated 2022-08-17

Title: Interface to 'ECMWF' and 'CDS' Data Web Services
Description: Programmatic interface to the European Centre for Medium-Range Weather Forecasts dataset web services (ECMWF; <https://www.ecmwf.int/>) and Copernicus's Climate Data Store (CDS; <https://cds.climate.copernicus.eu>). Allows for easy downloads of weather forecasts and climate reanalysis data in R.
Author: Koen Hufkens [aut, cre] , Reto Stauffer [ctb] , Elio Campitelli [ctb] , BlueGreen Labs [cph, fnd]
Maintainer: Koen Hufkens <koen.hufkens@gmail.com>

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Package dracor updated to version 0.2.5 with previous version 0.2.4 dated 2020-10-27

Title: Decode Draco Format 3D Mesh Data
Description: Decodes meshes and point cloud data encoded by the Draco mesh compression library from Google. Note that this is only designed for basic decoding and not intended as a full scale wrapping of the Draco library.
Author: Gregory Jefferis [aut, cre] , Google Inc [aut, cph]
Maintainer: Gregory Jefferis <jefferis@gmail.com>

Diff between dracor versions 0.2.4 dated 2020-10-27 and 0.2.5 dated 2023-01-19

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Package gdalcubes updated to version 0.6.3 with previous version 0.6.2 dated 2022-10-10

Title: Earth Observation Data Cubes from Satellite Image Collections
Description: Processing collections of Earth observation images as on-demand multispectral, multitemporal raster data cubes. Users define cubes by spatiotemporal extent, resolution, and spatial reference system and let 'gdalcubes' automatically apply cropping, reprojection, and resampling using the 'Geospatial Data Abstraction Library' ('GDAL'). Implemented functions on data cubes include reduction over space and time, applying arithmetic expressions on pixel band values, moving window aggregates over time, filtering by space, time, bands, and predicates on pixel values, exporting data cubes as 'netCDF' or 'GeoTIFF' files, plotting, and extraction from spatial and or spatiotemporal features. All computational parts are implemented in C++, linking to the 'GDAL', 'netCDF', 'CURL', and 'SQLite' libraries. See Appel and Pebesma (2019) <doi:10.3390/data4030092> for further details.
Author: Marius Appel [aut, cre] , Edzer Pebesma [ctb] , Roger Bivand [ctb], Jeroen Ooms [ctb] , Lewis Van Winkle [cph], Ole Christian Eidheim [cph], Howard Hinnant [cph], Adrian Colomitchi [cph], Florian Dang [cph], Paul Thompson [cph], Tomasz Kaminski [cph] [...truncated...]
Maintainer: Marius Appel <marius.appel@uni-muenster.de>

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Package CalibrationCurves updated to version 1.0.0 with previous version 0.1.5 dated 2022-08-13

Title: Calibration Performance
Description: Plots calibration curves and computes statistics for assessing calibration performance. See Van Calster et al. (2016) <doi:10.1016/j.jclinepi.2015.12.005>.
Author: De Cock Bavo [aut, cre], Nieboer Daan [aut], Van Calster Ben [aut], Steyerberg Ewout [aut], Vergouwe Yvonne [aut]
Maintainer: De Cock Bavo <bavo.decock@kuleuven.be>

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Package stevedata updated to version 0.9.0 with previous version 0.8.0 dated 2022-11-18

Title: Steve's Toy Data for Teaching About a Variety of Methodological, Social, and Political Topics
Description: This is a collection of various kinds of data with broad uses for teaching. My students, and academics like me who teach the same topics I teach, should find this useful if their teaching workflow is also built around the R programming language. The applications are multiple but mostly cluster on topics of statistical methodology, international relations, and political economy.
Author: Steve Miller [aut, cre]
Maintainer: Steve Miller <steven.v.miller@gmail.com>

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Package LWFBrook90R updated to version 0.5.2 with previous version 0.5.0 dated 2022-06-13

Title: Simulate Evapotranspiration and Soil Moisture with the SVAT Model LWF-Brook90
Description: Provides a flexible and easy-to use interface for the soil vegetation atmosphere transport (SVAT) model LWF-BROOK90, written in Fortran. The model simulates daily transpiration, interception, soil and snow evaporation, streamflow and soil water fluxes through a soil profile covered with vegetation, as described in Hammel & Kennel (2001, ISBN:978-3-933506-16-0) and Federer et al. (2003) <doi:10.1175/1525-7541(2003)004%3C1276:SOAETS%3E2.0.CO;2>. A set of high-level functions for model set up, execution and parallelization provides easy access to plot-level SVAT simulations, as well as multi-run and large-scale applications.
Author: Paul Schmidt-Walter [aut, cre] , Volodymyr Trotsiuk [aut] , Klaus Hammel [aut], Martin Kennel [aut], Anthony Federer [aut], Robert Nuske [ctb] , Bavarian State Institute of Forestry [cph, fnd], Northwest German Forest Research Institute [cph, fnd]
Maintainer: Paul Schmidt-Walter <paulsw@posteo.de>

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Package klassR updated to version 0.2.0 with previous version 0.1.11 dated 2022-06-08

Title: Classifications and Codelists for Statistics Norway
Description: Functions to search, retrieve and apply classifications and codelists using Statistics Norway's API <https://www.ssb.no/klass> from the system 'KLASS'. Retrieves classifications by date with options to choose language, hierarchical level and formatting.
Author: Susie Jentoft, Lisa Li, Diana-Cristina Iancu
Maintainer: Susie Jentoft <susie.jentoft@ssb.no>

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Package gpboost updated to version 0.8.1 with previous version 0.8.0 dated 2022-12-01

Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2022, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre], Benoit Jacob [cph], Gael Guennebaud [cph], Nicolas Carre [cph], Pierre Zoppitelli [cph], Gauthier Brun [cph], Jean Ceccato [cph], Jitse Niesen [cph], Other authors of Eigen for the included version of Eigen [ctb, cph], Timot [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>

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 gpboost-0.8.1/gpboost/tests/testthat/test_GPModel_combined_GP_random_effects.R        |   18 
 gpboost-0.8.1/gpboost/tests/testthat/test_GPModel_gaussian_process.R                  |  724 ++--
 gpboost-0.8.1/gpboost/tests/testthat/test_GPModel_grouped_random_effects.R            |   63 
 gpboost-0.8.1/gpboost/tests/testthat/test_GPModel_non_Gaussian_data.R                 |  432 +-
 gpboost-0.8.1/gpboost/tests/testthat/test_z_GPBoost_algorithm.R                       |only
 gpboost-0.8.1/gpboost/tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data.R     |only
 49 files changed, 4309 insertions(+), 2893 deletions(-)

More information about gpboost at CRAN
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Package transfR (with last version 1.0.2) was removed from CRAN

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

2022-11-22 1.0.2
2022-11-08 1.0.1
2022-10-05 1.0.0
2022-05-11 0.1.2
2021-12-20 0.1.1
2021-09-08 0.1.0

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