Thu, 06 Feb 2020

Package vcfR updated to version 1.10.0 with previous version 1.9.0 dated 2020-01-10

Title: Manipulate and Visualize VCF Data
Description: Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.
Author: Brian J. Knaus [cre, aut] (<https://orcid.org/0000-0003-1665-4343>), Niklaus J. Grunwald [aut] (<https://orcid.org/0000-0003-1656-7602>), Eric C. Anderson [ctb], David J. Winter [ctb], Zhian N. Kamvar [ctb] (<https://orcid.org/0000-0003-1458-7108>), Javier F. Tabima [ctb] (<https://orcid.org/0000-0002-3603-2691>)
Maintainer: Brian J. Knaus <briank.lists@gmail.com>

Diff between vcfR versions 1.9.0 dated 2020-01-10 and 1.10.0 dated 2020-02-06

 DESCRIPTION                    |    6 -
 MD5                            |   36 ++++-----
 R/chromR_functions.R           |    2 
 R/io_vcfR.R                    |    2 
 R/proc_chromR.R                |    4 -
 R/ranking.R                    |    2 
 R/summary_tables.R             |    2 
 R/vcfR_conversion.R            |    2 
 R/vcfR_to_tidy_functions.R     |  153 +++++++++++++++++++++++++----------------
 R/windowing.R                  |    2 
 inst/doc/converting_data.R     |   26 +++---
 inst/doc/converting_data.html  |   14 +--
 inst/doc/intro_to_vcfR.R       |   20 ++---
 inst/doc/intro_to_vcfR.html    |   26 +++---
 inst/doc/vcf_data.R            |   16 ++--
 inst/doc/vcf_data.html         |   94 +++++++++++--------------
 inst/doc/workflow.html         |   12 +--
 man/proc_chromR.Rd             |    2 
 tests/testthat/test_vcfRtidy.R |    3 
 19 files changed, 223 insertions(+), 201 deletions(-)

More information about vcfR at CRAN
Permanent link

Package umx updated to version 3.0.6 with previous version 3.0.5 dated 2019-12-06

Title: Structural Equation and Twin Modeling in R
Description: Quickly create, run, and report structural equation and twin models. See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS.
Author: Timothy C. Bates [aut, cre] (<https://orcid.org/0000-0002-1153-9007>), Joshua N. Pritikin [ctb], Michael C. Neale [ctb], Hermine Maes [ctb]
Maintainer: Timothy C. Bates <timothy.c.bates@gmail.com>

Diff between umx versions 3.0.5 dated 2019-12-06 and 3.0.6 dated 2020-02-06

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More information about umx at CRAN
Permanent link

Package nlme updated to version 3.1-144 with previous version 3.1-143 dated 2019-12-10

Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version), Douglas Bates [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), Siem Heisterkamp [ctb] (Author fixed sigma), Bert Van Willigen [ctb] (Programmer fixed sigma), R-core [aut, cre]
Maintainer: R-core <R-core@R-project.org>

Diff between nlme versions 3.1-143 dated 2019-12-10 and 3.1-144 dated 2020-02-06

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More information about nlme at CRAN
Permanent link

Package LaplacesDemon updated to version 16.1.4 with previous version 16.1.1 dated 2018-06-30

Title: Complete Environment for Bayesian Inference
Description: Provides a complete environment for Bayesian inference using a variety of different samplers (see ?LaplacesDemon for an overview). The README describes the history of the package development process.
Author: Byron Hall [aut], Martina Hall [aut], Statisticat, LLC [aut], Eric Brown [ctb], Richard Hermanson [ctb], Emmanuel Charpentier [ctb], Daniel Heck [ctb], Stephane Laurent [ctb], Quentin F. Gronau [ctb], Henrik Singmann [cre]
Maintainer: Henrik Singmann <singmann+LaplacesDemon@gmail.com>

Diff between LaplacesDemon versions 16.1.1 dated 2018-06-30 and 16.1.4 dated 2020-02-06

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Package hypergate updated to version 0.8.3 with previous version 0.8.1 dated 2019-04-17

Title: Machine Learning of Hyperrectangular Gating Strategies for High-Dimensional Cytometry
Description: Given a high-dimensional dataset that typically represents a cytometry dataset, and a subset of the datapoints, this algorithm outputs an hyperrectangle so that datapoints within the hyperrectangle best correspond to the specified subset. In essence, this allows the conversion of clustering algorithms' outputs to gating strategies outputs.
Author: Etienne Becht [cre, aut], Samuel Granjeaud [ctb]
Maintainer: Etienne Becht <etienne.becht@protonmail.com>

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Package errorlocate updated to version 0.3.0 with previous version 0.2.0 dated 2019-07-01

Title: Locate Errors with Validation Rules
Description: Errors in data can be located and removed using validation rules from package 'validate'.
Author: Edwin de Jonge [aut, cre] (<https://orcid.org/0000-0002-6580-4718>), Mark van der Loo [aut]
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>

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Package emba updated to version 0.1.2 with previous version 0.1.1 dated 2019-10-21

Title: Ensemble Boolean Model Biomarker Analysis
Description: Analysis and visualization of an ensemble of boolean models for biomarker discovery in cancer cell networks. The package allows to easily import the data results of a software pipeline that predicts synergistic drug combinations in cancer cell lines, developed by the DrugLogics research group in NTNU. It has generic functions that can be used to split a boolean model dataset to model groups with regards to the models predictive performance (number of true positive predictions or Matthews correlation coefficient score) or synergy prediction based on a given set of observed synergies and find the average activity difference per network node between all group pairs. Thus, given user-specific thresholds, important nodes (biomarkers) can be accessed in the sense that they make the models predict specific synergies (synergy biomarkers) or have better performance in general (performance biomarkers). Lastly, if the boolean models have a specific equation form and differ only in their link operator, link operator biomarkers can also be assessed.
Author: John Zobolas [aut, cph, cre] (<https://orcid.org/0000-0002-3609-8674>)
Maintainer: John Zobolas <bblodfon@gmail.com>

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Package PKconverter updated to version 1.5 with previous version 1.3 dated 2018-12-03

Title: The Parameter Converter of the Pharmacokinetic Models
Description: Pharmacokinetics is the study of drug absorption, distribution, metabolism, and excretion. The pharmacokinetics model explains that how the drug concentration change as the drug moves through the different compartments of the body. For pharmacokinetic modeling and analysis, it is essential to understand the basic pharmacokinetic parameters. All parameters are considered, but only some of parameters are used in the model. Therefore, we need to convert the estimated parameters to the other parameters after fitting the specific pharmacokinetic model. This package is developed to help this converting work. For more detailed explanation of pharmacokinetic parameters, see "Gabrielsson and Weiner" (2007), "ISBN-10: 9197651001"; "Benet and Zia-Amirhosseini" (1995) <DOI: 10.1177/019262339502300203>; "Mould and Upton" (2012) <DOI: 10.1038/psp.2012.4>; "Mould and Upton" (2013) <DOI: 10.1038/psp.2013.14>.
Author: Eun-Kyung Lee, Hye-sun Cho
Maintainer: Eun-Kyung Lee <lee.eunk@gmail.com>

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Package spBayes updated to version 0.4-3 with previous version 0.4-2 dated 2019-03-07

Title: Univariate and Multivariate Spatial-Temporal Modeling
Description: Fits univariate and multivariate spatio-temporal random effects models for point-referenced data using Markov chain Monte Carlo (MCMC). Details are given in Finley, Banerjee, and Gelfand (2015) <doi:10.18637/jss.v063.i13> and Finley, Banerjee, and Cook (2014) <doi:10.1111/2041-210X.12189>.
Author: Andrew Finley [aut, cre], Sudipto Banerjee [aut]
Maintainer: Andrew Finley <finleya@msu.edu>

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Package shazam updated to version 0.2.3 with previous version 0.2.2 dated 2019-12-16

Title: Immunoglobulin Somatic Hypermutation Analysis
Description: Provides a computational framework for analyzing mutations in immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of antigen-driven selection pressure, mutational load quantification, building of somatic hypermutation (SHM) models, and model-dependent distance calculations. Also includes empirically derived models of SHM for both mice and humans. Citations: Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>, Yaari, et al (2012) <doi:10.1093/nar/gks457>, Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>, Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.
Author: Mohamed Uduman [aut], Gur Yaari [aut], Namita Gupta [aut], Jason Vander Heiden [aut, cre], Ang Cui [ctb], Susanna Marquez [ctb], Julian Zhou [ctb], Nima Nouri [ctb], Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@yale.edu>

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Package RandomFields updated to version 3.3.8 with previous version 3.3.7 dated 2019-12-12

Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields. Main geostatistical parts are based on the books by Christian Lantuejoul <doi:10.1007/978-3-662-04808-5>, Jean-Paul Chiles and Pierre Delfiner <doi:10.1002/9781118136188> and Noel A. Cressie <doi:10.1002/9781119115151>. For the extreme value random fields see Oesting, Schlather, Schillings (2019) <doi.org/10.1002/sta4.228> and Schlather (2002) <doi.org/10.1023/A:1020977924878>.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Jonas Auel[ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Paulo Ribeiro [ctb], Brian D. Ripley [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>

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Package mvSLOUCH updated to version 2.3 with previous version 2.2 dated 2020-01-12

Title: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history. See K. Bartoszek, J, Pienaar, P. Mostad, S. Andersson, T. F.Hansen (2012) <doi:10.1016/j.jtbi.2012.08.005>. The suggested PCMBaseCpp package (which significantly speeds up the likelihood calculations) can be obtained from <https://github.com/venelin/PCMBaseCpp/>.
Author: Krzysztof Bartoszek <krzbar@protonmail.ch>
Maintainer: Krzysztof Bartoszek <krzbar@protonmail.ch>

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Package longmemo updated to version 1.1-2 with previous version 1.1-1 dated 2018-09-14

Title: Statistics for Long-Memory Processes (Book Jan Beran), and Related Functionality
Description: Datasets and Functionality from 'Jan Beran' (1994). Statistics for Long-Memory Processes; Chapman & Hall. Estimation of Hurst (and more) parameters for fractional Gaussian noise, 'fARIMA' and 'FEXP' models.
Author: S scripts originally by Jan Beran <jan.beran@uni-konstanz.de>; Datasets via Brandon Whitcher <brandon@stat.washington.edu>. Toplevel R functions and much more by Martin Maechler.
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>

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Package copula updated to version 0.999-20 with previous version 0.999-19.1 dated 2019-04-22

Title: Multivariate Dependence with Copulas
Description: Classes (S4) of commonly used elliptical, Archimedean, extreme-value and other copula families, as well as their rotations, mixtures and asymmetrizations. Nested Archimedean copulas, related tools and special functions. Methods for density, distribution, random number generation, bivariate dependence measures, Rosenblatt transform, Kendall distribution function, perspective and contour plots. Fitting of copula models with potentially partly fixed parameters, including standard errors. Serial independence tests, copula specification tests (independence, exchangeability, radial symmetry, extreme-value dependence, goodness-of-fit) and model selection based on cross-validation. Empirical copula, smoothed versions, and non-parametric estimators of the Pickands dependence function.
Author: Marius Hofert [aut] (<https://orcid.org/0000-0001-8009-4665>), Ivan Kojadinovic [aut] (<https://orcid.org/0000-0002-2903-1543>), Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>), Jun Yan [aut] (<https://orcid.org/0000-0003-4401-7296>), Johanna G. Nešlehová [ctb] (evTestK(), <https://orcid.org/0000-0001-9634-4796>)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>

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Package analogue updated to version 0.17-4 with previous version 0.17-3 dated 2019-05-11

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] (<https://orcid.org/0000-0002-9084-8413>), Jari Oksanen [aut]
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>

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Package AER updated to version 1.2-9 with previous version 1.2-8 dated 2019-11-08

Title: Applied Econometrics with R
Description: Functions, data sets, examples, demos, and vignettes for the book Christian Kleiber and Achim Zeileis (2008), Applied Econometrics with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2. (See the vignette "AER" for a package overview.)
Author: Christian Kleiber [aut] (<https://orcid.org/0000-0002-6781-4733>), Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>

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Package rorcid updated to version 0.6.4 with previous version 0.6.0 dated 2020-01-28

Title: Interface to the 'Orcid.org' API
Description: Client for the 'Orcid.org' API (<https://orcid.org/>). Functions included for searching for people, searching by 'DOI', and searching by 'Orcid' 'ID'.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), rOpenSci [fnd] (https://ropensci.org/)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package rDEA updated to version 1.2-6 with previous version 1.2-5 dated 2016-11-25

Title: Robust Data Envelopment Analysis (DEA) for R
Description: Data Envelopment Analysis for R, estimating robust DEA scores without and with environmental variables and doing returns-to-scale tests.
Author: Jaak Simm [aut, cre], Galina Besstremyannaya [aut]
Maintainer: Jaak Simm <jaak.simm@gmail.com>

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Package NetworkChange updated to version 0.6 with previous version 0.5 dated 2019-05-08

Title: Bayesian Package for Network Changepoint Analysis
Description: Network changepoint analysis for undirected network data. The package implements a hidden Markov network change point model (Park and Sohn 2019). Functions for break number detection using the approximate marginal likelihood and WAIC are also provided.
Author: Jong Hee Park [aut,cre], Yunkyu Sohn [aut]
Maintainer: Jong Hee Park <jongheepark@snu.ac.kr>

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Package l0ara updated to version 0.1.6 with previous version 0.1.5 dated 2017-07-23

Title: Sparse Generalized Linear Model with L0 Approximation for Feature Selection
Description: An efficient procedure for feature selection for generalized linear models with L0 penalty, including linear, logistic, Poisson, gamma, inverse Gaussian regression. Adaptive ridge algorithms are used to fit the models.
Author: Wenchuan Guo, Shujie Ma, Zhenqiu Liu
Maintainer: Wenchuan Guo <wguo007@ucr.edu>

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Wed, 05 Feb 2020

Package TestDesign updated to version 1.0.2 with previous version 1.0.1 dated 2020-01-24

Title: Optimal Test Design Approach to Fixed and Adaptive Test Construction
Description: Use the optimal test design approach by Birnbaum (1968, ISBN:9781593119348) and van der Linden (2018) <doi:10.1201/9781315117430> in constructing fixed and adaptive tests. Supports the following mixed-integer programming (MIP) solver packages: 'lpsymphony', 'Rsymphony', 'gurobi', 'lpSolve', and 'Rglpk'. The 'gurobi' package is not available from CRAN; see <https://www.gurobi.com/downloads>. See vignette for installing 'Rsymphony' package on Mac systems.
Author: Seung W. Choi [aut, cre] (<https://orcid.org/0000-0003-4777-5420>), Sangdon Lim [aut] (<https://orcid.org/0000-0002-2988-014X>)
Maintainer: Seung W. Choi <schoi@austin.utexas.edu>

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Package stockR updated to version 1.0.73 with previous version 1.0.68 dated 2018-06-14

Title: Identifying Stocks in Genetic Data
Description: Provides a mixture model for clustering individuals (or sampling groups) into stocks based on their genetic profile. Here, sampling groups are individuals that are sure to come from the same stock (e.g. breeding adults or larvae). The mixture (log-)likelihood is maximised using the EM-algorithm after find good starting values via a K-means clustering of the genetic data. Details can be found in Foster, Feutry, Grewe, Berry, Hui, Davies (2019) Reliably Discriminating Stock Structure with Genetic Markers: Mixture Models with Robust and Fast Computation. Molecular Ecology Resources.
Author: Scott D. Foster [aut, cre]
Maintainer: Scott D. Foster <scott.foster@data61.csiro.au>

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Package prioritizr updated to version 4.1.5 with previous version 4.1.4 dated 2019-10-03

Title: Systematic Conservation Prioritization in R
Description: Conservation prioritization using integer programming techniques. To solve large-scale problems, users should install the 'gurobi' optimizer (available from <http://www.gurobi.com/>).
Author: Jeffrey O Hanson [aut], Richard Schuster [aut, cre], Nina Morrell [aut], Matthew Strimas-Mackey [aut], Matthew E Watts [aut], Peter Arcese [aut], Joseph Bennett [aut], Hugh P Possingham [aut]
Maintainer: Richard Schuster <richard.schuster@glel.carleton.ca>

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Package gaselect updated to version 1.0.9 with previous version 1.0.7 dated 2019-03-13

Title: Genetic Algorithm (GA) for Variable Selection from High-Dimensional Data
Description: Provides a genetic algorithm for finding variable subsets in high dimensional data with high prediction performance. The genetic algorithm can use ordinary least squares (OLS) regression models or partial least squares (PLS) regression models to evaluate the prediction power of variable subsets. By supporting different cross-validation schemes, the user can fine-tune the tradeoff between speed and quality of the solution.
Author: David Kepplinger
Maintainer: David Kepplinger <david.kepplinger@gmail.com>

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Package DMMF updated to version 0.5.1.1 with previous version 0.5.0.2 dated 2018-08-17

Title: Daily Based Morgan-Morgan-Finney (DMMF) Soil Erosion Model
Description: Implements the daily based Morgan-Morgan-Finney (DMMF) soil erosion model (Choi et al., 2017 <doi:10.3390/w9040278>) for estimating surface runoff and sediment budgets from a field or a catchment on a daily basis.
Author: Kwanghun Choi [aut, cre], Sebastian Arnhold [dtc, ctb], Bjoern Reineking [ths, ctb]
Maintainer: Kwanghun Choi <kwanghun.choi@yahoo.com>

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Package checkmate updated to version 2.0.0 with previous version 1.9.4 dated 2019-07-04

Title: Fast and Versatile Argument Checks
Description: Tests and assertions to perform frequent argument checks. A substantial part of the package was written in C to minimize any worries about execution time overhead.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>), Bernd Bischl [ctb]
Maintainer: Michel Lang <michellang@gmail.com>

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Package bisque updated to version 1.0.2 with previous version 1.0.1 dated 2019-04-26

Title: Approximate Bayesian Inference via Sparse Grid Quadrature Evaluation (BISQuE) for Hierarchical Models
Description: Implementation of the 'bisque' strategy for approximate Bayesian posterior inference. See Hewitt and Hoeting (2019) <arXiv:1904.07270> for complete details. 'bisque' combines conditioning with sparse grid quadrature rules to approximate marginal posterior quantities of hierarchical Bayesian models. The resulting approximations are computationally efficient for many hierarchical Bayesian models. The 'bisque' package allows approximate posterior inference for custom models; users only need to specify the conditional densities required for the approximation.
Author: Joshua Hewitt
Maintainer: Joshua Hewitt <joshua.hewitt@duke.edu>

Diff between bisque versions 1.0.1 dated 2019-04-26 and 1.0.2 dated 2020-02-05

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Package azuremlsdk updated to version 0.6.85 with previous version 0.5.7 dated 2019-11-15

Title: Interface to the 'Azure Machine Learning' 'SDK'
Description: Interface to the 'Azure Machine Learning' Software Development Kit ('SDK'). Data scientists can use the 'SDK' to train, deploy, automate, and manage machine learning models on the 'Azure Machine Learning' service. To learn more about 'Azure Machine Learning' visit the website: <https://docs.microsoft.com/en-us/azure/machine-learning/service/overview-what-is-azure-ml>.
Author: Heemanshu Suri [cre, aut], Billy Hu [aut], Diondra Peck [aut], Minna Xiao [aut], Himanshu Chandola [ctb], Abe Omorogbe [ctb], Microsoft [cph, fnd], Google Inc. [cph] (Examples and Tutorials), The TensorFlow Authors [cph] (Examples and Tutorials), RStudio Inc. [cph] (Examples and Tutorials)
Maintainer: Heemanshu Suri <Heemanshu.Suri@microsoft.com>

Diff between azuremlsdk versions 0.5.7 dated 2019-11-15 and 0.6.85 dated 2020-02-05

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Package assertr updated to version 2.7 with previous version 2.6 dated 2019-01-22

Title: Assertive Programming for R Analysis Pipelines
Description: Provides functionality to assert conditions that have to be met so that errors in data used in analysis pipelines can fail quickly. Similar to 'stopifnot()' but more powerful, friendly, and easier for use in pipelines.
Author: Tony Fischetti [aut, cre]
Maintainer: Tony Fischetti <tony.fischetti@gmail.com>

Diff between assertr versions 2.6 dated 2019-01-22 and 2.7 dated 2020-02-05

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Package stringb updated to version 0.1.14 with previous version 0.1.13 dated 2016-11-01

Title: Convenient Base R String Handling
Description: Base R already ships with string handling capabilities 'out- of-the-box' but lacks streamlined function names and workflow. The 'stringi' ('stringr') package on the other hand has well named functions, extensive Unicode support and allows for a streamlined workflow. On the other hand it adds dependencies and regular expression interpretation between base R functions and 'stringi' functions might differ. This packages aims at providing a solution to the use case of unwanted dependencies on the one hand but the need for streamlined text processing on the other. The packages' functions are solely based on wrapping base R functions into 'stringr'/'stringi' like function names. Along the way it adds one or two extra functions and last but not least provides all functions as generics, therefore allowing for adding methods for other text structures besides plain character vectors.
Author: Peter Meissner [aut, cre]
Maintainer: Peter Meissner <retep.meissner@gmail.com>

Diff between stringb versions 0.1.13 dated 2016-11-01 and 0.1.14 dated 2020-02-05

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Package rsf updated to version 0.2.1 with previous version 0.2.0 dated 2019-10-05

Title: Report of Statistical Findings in 'bookdown'
Description: A report of statistical findings (RSF) project template is generated using a 'bookdown' format. 'YAML' fields can be further customized. Additional helper functions provide extra features to the RSF.
Author: Derek Chiu [aut, cre]
Maintainer: Derek Chiu <dchiu@bccrc.ca>

Diff between rsf versions 0.2.0 dated 2019-10-05 and 0.2.1 dated 2020-02-05

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Package GenEst updated to version 1.4.0.2 with previous version 1.4.0.1 dated 2019-11-22

Title: Generalized Mortality Estimator
Description: Command-line and 'shiny' GUI implementation of the GenEst models for estimating bird and bat mortality at wind and solar power facilities, following Dalthorp, et al. (2018) <doi:10.3133/tm7A2>.
Author: Daniel Dalthorp [aut, cre], Juniper Simonis [aut], Lisa Madsen [aut], Manuela Huso [aut], Paul Rabie [aut], Jeffrey Mintz [aut], Robert Wolpert [aut], Jared Studyvin [aut], Franzi Korner-Nievergelt [aut]
Maintainer: Daniel Dalthorp <ddalthorp@usgs.gov>

Diff between GenEst versions 1.4.0.1 dated 2019-11-22 and 1.4.0.2 dated 2020-02-05

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Package RODBCext updated to version 0.3.2 with previous version 0.3.1 dated 2017-07-31

Title: Parameterized Queries Extension for RODBC
Description: An extension for RODBC package adding support for parameterized queries.
Author: Mateusz Zoltak [aut, cre], Brian Ripley [aut], Michael Lapsley [aut], Will Beasley [ctb], Juergen Altfeld [ctb]
Maintainer: Mateusz Zoltak <zozlak@zozlak.org>

Diff between RODBCext versions 0.3.1 dated 2017-07-31 and 0.3.2 dated 2020-02-05

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Package SplitReg updated to version 1.0.2 with previous version 1.0.1 dated 2020-01-16

Title: Split Regularized Regression
Description: Functions for computing split regularized estimators defined in Christidis, Lakshmanan, Smucler and Zamar (2019) <arXiv:1712.03561>. The approach fits linear regression models that split the set of covariates into groups. The optimal split of the variables into groups and the regularized estimation of the regression coefficients are performed by minimizing an objective function that encourages sparsity within each group and diversity among them. The estimated coefficients are then pooled together to form the final fit.
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>, Ezequiel Smucler <ezequiels.90@gmail.com>, Ruben Zamar <ruben@stat.ubc.ca>
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>

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Package simTargetCov updated to version 1.0.1 with previous version 1.0 dated 2019-10-10

Title: Data Transformation or Simulation with Empirical Covariance Matrix
Description: Transforms or simulates data with a target empirical covariance matrix supplied by the user. The method to obtain the data with the target empirical covariance matrix is described in Section 5.1 of Christidis, Van Aelst and Zamar (2019) <arXiv:1812.05678>.
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>, Stefan Van Aelst <stefan.vanaelst@kuleuven.be>, Ruben Zamar <ruben@stat.ubc.ca>
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>

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Package rdbnomics updated to version 0.5.2 with previous version 0.5.1 dated 2020-01-07

Title: Download DBnomics Data
Description: R access to hundreds of millions data series from DBnomics API (<https://db.nomics.world/>).
Author: Sebastien Galais [cre, ctb], Thomas Brand [aut]
Maintainer: Sebastien Galais <s915.stem@gmail.com>

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Package yuima updated to version 1.9.6 with previous version 1.8.1 dated 2018-05-21

Title: The YUIMA Project Package for SDEs
Description: Simulation and Inference for SDEs and Other Stochastic Processes.
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus <stefano.iacus@unimi.it>

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Package pksensi updated to version 1.1.5 with previous version 1.1.4 dated 2019-09-19

Title: Global Sensitivity Analysis in Physiologically Based Kinetic Modeling
Description: Applying the global sensitivity analysis workflow to investigate the parameter uncertainty and sensitivity in physiologically based kinetic (PK) models, especially the physiologically based pharmacokinetic/toxicokinetic model with multivariate outputs. The package also provides some functions to check the convergence and sensitivity of model parameters.
Author: Nan-Hung Hsieh [aut, cre] (<https://orcid.org/0000-0003-0163-2766>), Brad Reisfeld [aut], Weihsueh A. Chiu [aut] (<https://orcid.org/0000-0002-7575-2368>)
Maintainer: Nan-Hung Hsieh <nhsieh@cvm.tamu.edu>

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Package mlr3db updated to version 0.1.4 with previous version 0.1.3 dated 2019-10-29

Title: Data Base Backend for 'mlr3'
Description: Extends the 'mlr3' package with a backend to transparently work with data bases. Internally relies on the abstraction of package 'dbplyr' to interact with one of the many supported data base management systems (DBMS).
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>)
Maintainer: Michel Lang <michellang@gmail.com>

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Package manymodelr updated to version 0.2.3 with previous version 0.2.2 dated 2019-07-08

Title: Build and Tune Several Models
Description: Frequently one needs a convenient way to build and tune several models in one go.The goal is to provide a number of convenience functions useful in machine learning applications. It provides the ability to build, tune and obtain predictions of several models in one function. The models are built using 'caret' functions with easier to read syntax. Kuhn(2014) <arXiv:1405.6974v14>. Kuhn(2008) <doi10.18637/jss.v028.i05>. Chambers,J.M.(1992) <doi:10.1007/978-3-642-50096-1_48>. Wilkinson,G.N. and Rogers, C. E. (1973) <doi:10.2307/2346786>.
Author: Nelson Gonzabato [aut, cre]
Maintainer: Nelson Gonzabato <gonzabato@hotmail.com>

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Package FactoMineR updated to version 2.2 with previous version 2.1 dated 2020-01-17

Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis. F. Husson, S. Le and J. Pages (2017).
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson <francois.husson@agrocampus-ouest.fr>

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Package date updated to version 1.2-39 with previous version 1.2-38 dated 2018-01-06

Title: Functions for Handling Dates
Description: Functions for handling dates.
Author: Terry Therneau [aut], Thomas Lumley [trl] (R port), Kjetil Halvorsen [trl] (R port), Kurt Hornik [trl, ctb, cre] (<https://orcid.org/0000-0003-4198-9911>, R port), R Core Team [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

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Package chk updated to version 0.3.1 with previous version 0.3.0 dated 2020-01-15

Title: Check User-Supplied Function Arguments
Description: For developers to check user-supplied function arguments. It is designed to be simple, fast and customizable. Error messages follow the tidyverse style guide.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>), Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>), Ayla Pearson [ctb] (<https://orcid.org/0000-0001-7388-1222>), Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

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Package VIM updated to version 5.1.0 with previous version 4.8.0 dated 2019-02-11

Title: Visualization and Imputation of Missing Values
Description: New tools for the visualization of missing and/or imputed values are introduced, which can be used for exploring the data and the structure of the missing and/or imputed values. Depending on this structure of the missing values, the corresponding methods may help to identify the mechanism generating the missing values and allows to explore the data including missing values. In addition, the quality of imputation can be visually explored using various univariate, bivariate, multiple and multivariate plot methods (<doi:10.1007/s11634-011-0102-y>). A graphical user interface available in the separate package VIMGUI allows an easy handling of the implemented plot methods. Fast imputation methods such as k-nearest neighbor imputation (<doi:10.18637/jss.v074.i07>) and imputation using robust methods are provided (<doi:10.1016/j.csda.2011.04.012>).
Author: Matthias Templ [aut, cre] (<https://orcid.org/0000-0002-8638-5276>), Alexander Kowarik [aut] (<https://orcid.org/0000-0001-8598-4130>), Andreas Alfons [aut], Bernd Prantner [ctb]
Maintainer: Matthias Templ <matthias.templ@gmail.com>

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Package symmoments updated to version 1.2.1 with previous version 1.2 dated 2014-08-04

Title: Symbolic Central and Noncentral Moments of the Multivariate Normal Distribution
Description: Symbolic central and non-central moments of the multivariate normal distribution. Computes a standard representation, LateX code, and values at specified mean and covariance matrices.
Author: Kem Phillips
Maintainer: Kem Phillips <kemphillips@comcast.net>

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Package PAFway updated to version 0.1.3 with previous version 0.1.2 dated 2019-12-16

Title: Pairwise Association of Functional Annotations
Description: Finds pairs of functional annotations or gene ontology (GO) terms that are enriched within a directed network (such as a gene regulatory network). This works with or without edge weights and includes visualizations (both as a network where the functions are nodes and as a heatmap). PAFway is an acronym for Pairwise Associations of Functional annotations in biological networks and pathWAYs.
Author: Daphne Ezer [aut, cre], Mahair Mahjoub [aut]
Maintainer: Daphne Ezer <daphne.ezer@york.ac.uk>

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Package hsdar updated to version 1.0.1 with previous version 1.0.0 dated 2019-05-25

Title: Manage, Analyse and Simulate Hyperspectral Data
Description: Transformation of reflectance spectra, calculation of vegetation indices and red edge parameters, spectral resampling for hyperspectral remote sensing, simulation of reflectance and transmittance using the leaf reflectance model PROSPECT and the canopy reflectance model PROSAIL.
Author: Lukas W. Lehnert [cre, aut] (<https://orcid.org/0000-0002-5229-2282>), Hanna Meyer [ctb], Joerg Bendix [ctb]
Maintainer: Lukas W. Lehnert <lukaslehnert@googlemail.com>

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Package GLDEX updated to version 2.0.0.7 with previous version 2.0.0.6 dated 2019-08-23

Title: Fitting Single and Mixture of Generalised Lambda Distributions (RS and FMKL) using Various Methods
Description: The fitting algorithms considered in this package have two major objectives. One is to provide a smoothing device to fit distributions to data using the weight and unweighted discretised approach based on the bin width of the histogram. The other is to provide a definitive fit to the data set using the maximum likelihood and quantile matching estimation. Other methods such as moment matching, starship method, L moment matching are also provided. Diagnostics on goodness of fit can be done via qqplots, KS-resample tests and comparing mean, variance, skewness and kurtosis of the data with the fitted distribution.
Author: Steve Su, with contributions from: Diethelm Wuertz, Martin Maechler and Rmetrics core team members for low discrepancy algorithm, Juha Karvanen for L moments codes, Robert King for gld C codes and starship codes, Benjamin Dean for corrections and input in ks.gof code and R core team for histsu function.
Maintainer: Steve Su <allegro.su@gmail.com>

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Package gamCopula updated to version 0.0-7 with previous version 0.0-6 dated 2019-12-04

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 beadplexr updated to version 0.3.0 with previous version 0.2.0 dated 2018-12-07

Title: Analysis of Multiplex Cytometric Bead Assays
Description: Reproducible and automated analysis of multiplex bead assays such as CBA (Morgan et al. 2004; <doi: 10.1016/j.clim.2003.11.017>), LEGENDplex (Yu et al. 2015; <doi: 10.1084/jem.20142318>), and MACSPlex (Miltenyi Biotec 2014; Application note: Data acquisition and analysis without the MACSQuant analyzer; <https://www.miltenyibiotec.com/upload/assets/IM0021608.PDF>). The package provides functions for streamlined reading of fcs files, and identification of bead clusters and analyte expression. The package eases the calculation of standard curves and the subsequent calculation of the analyte concentration.
Author: Ulrik Stervbo [aut, cre] (<https://orcid.org/0000-0002-2831-8868>)
Maintainer: Ulrik Stervbo <ulrik.stervbo@gmail.com>

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 R/panel_information.R                                                               |   28 
 R/read_fcs.R                                                                        |    2 
 README.md                                                                           |    4 
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 man/as_data_frame_analyte.Rd                                                        |    7 
 man/assign_analyte_id.Rd                                                            |    9 
 man/calc_analyte_mfi.Rd                                                             |    8 
 man/calc_std_conc.Rd                                                                |    3 
 man/calculate_concentration.Rd                                                      |    8 
 man/cluster_events.Rd                                                               |   29 
 man/do_find_turning_points.Rd                                                       |    3 
 man/facs_plot.Rd                                                                    |   18 
 man/fit_standard_curve.Rd                                                           |    9 
 man/ident_bead_pop.Rd                                                               |    9 
 man/identify_analyte.Rd                                                             |   15 
 man/identify_assay_analyte.Rd                                                       |   18 
 man/load_panel.Rd                                                                   |   12 
 man/plot_concentrations.Rd                                                          |   27 
 man/read_fcs.Rd                                                                     |   13 
 man/trim_population.Rd                                                              |    3 
 man/turning_point.Rd                                                                |   23 
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Package SGB updated to version 1.0.1 with previous version 1.0 dated 2019-05-13

Title: Simplicial Generalized Beta Regression
Description: Main properties and regression procedures using a generalization of the Dirichlet distribution called Simplicial Generalized Beta distribution. It is a new distribution on the simplex (i.e. on the space of compositions or positive vectors with sum of components equal to 1). The Dirichlet distribution can be constructed from a random vector of independent Gamma variables divided by their sum. The SGB follows the same construction with generalized Gamma instead of Gamma variables. The Dirichlet exponents are supplemented by an overall shape parameter and a vector of scales. The scale vector is itself a composition and can be modeled with auxiliary variables through a log-ratio transformation. Graf, M. (2017, ISBN: 978-84-947240-0-8). See also the vignette enclosed in the package.
Author: Monique Graf
Maintainer: Monique Graf <monique.p.n.graf@bluewin.ch>

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Package PoissonBinomial updated to version 1.0.1 with previous version 1.0.0 dated 2020-01-22

Title: Exact and Approximate Implementations of the Poisson Binomial Distribution
Description: Implementations of multiple exact and approximate methods as described in Hong (2013) <doi:10.1016/j.csda.2012.10.006> and Biscarri et al. (2018) <doi:10.1016/j.csda.2018.01.007> for computing the probability mass, cumulative distribution and quantile functions, as well as generating random numbers for the Poisson binomial distribution.
Author: Florian Junge [aut, cre]
Maintainer: Florian Junge <florian.junge@h-da.de>

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Package NeuralSens updated to version 0.1.4 with previous version 0.1.3 dated 2020-01-11

Title: Sensitivity Analysis of Neural Networks
Description: Analysis functions to quantify inputs importance in neural network models. Functions are available for calculating and plotting the inputs importance and obtaining the activation function of each neuron layer and its derivatives. The importance of a given input is defined as the distribution of the derivatives of the output with respect to that input in each training data point.
Author: José Portela González [aut], Antonio Muñoz San Roque [aut], Jaime Pizarroso Gonzalo [ctb, cre]
Maintainer: Jaime Pizarroso Gonzalo <jpizarroso@comillas.edu>

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Package fuzzyforest updated to version 1.0.7 with previous version 1.0.6 dated 2019-10-26

Title: Fuzzy Forests
Description: Fuzzy forests, a new algorithm based on random forests, is designed to reduce the bias seen in random forest feature selection caused by the presence of correlated features. Fuzzy forests uses recursive feature elimination random forests to select features from separate blocks of correlated features where the correlation within each block of features is high and the correlation between blocks of features is low. One final random forest is fit using the surviving features. This package fits random forests using the 'randomForest' package and allows for easy use of 'WGCNA' to split features into distinct blocks. See D. Conn, Ngun, T., C. Ramirez, and G. Li (2019) <doi:10.18637/jss.v091.i09> for further details.
Author: Daniel Conn [aut, cre], Tuck Ngun [aut], Christina M. Ramirez [aut]
Maintainer: Daniel Conn <djconn17@gmail.com>

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Package Factoshiny updated to version 2.2 with previous version 2.1 dated 2020-01-17

Title: Perform Factorial Analysis from 'FactoMineR' with a Shiny Application
Description: Perform factorial analysis with a menu and draw graphs interactively thanks to 'FactoMineR' and a Shiny application.
Author: Pauline Vaissie, Astrid Monge, Francois Husson
Maintainer: Francois Husson <husson@agrocampus-ouest.fr>

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Package surveysd updated to version 1.2.0 with previous version 1.1.0 dated 2019-07-15

Title: Survey Standard Error Estimation for Cumulated Estimates and their Differences in Complex Panel Designs
Description: Calculate point estimates and their standard errors in complex household surveys using bootstrap replicates. Bootstrapping considers survey design with a rotating panel. A comprehensive description of the methodology can be found under <https://statistikat.github.io/surveysd/articles/methodology.html>.
Author: Johannes Gussenbauer [aut, cre], Alexander Kowarik [aut] (<https://orcid.org/0000-0001-8598-4130>), Gregor de Cillia [aut], Matthias Till [ctb]
Maintainer: Johannes Gussenbauer <Johannes.Gussenbauer@statistik.gv.at>

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Package season updated to version 0.3.9 with previous version 0.3.8 dated 2018-09-10

Title: Seasonal Analysis of Health Data
Description: Routines for the seasonal analysis of health data, including regression models, time-stratified case-crossover, plotting functions and residual checks, see Barnett and Dobson (2010) ISBN 978-3-642-10748-1. Thanks to Yuming Guo for checking the case-crossover code.
Author: Adrian Barnett and Peter Baker
Maintainer: Adrian Barnett <a.barnett@qut.edu.au>

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Package rticles updated to version 0.14 with previous version 0.13 dated 2019-12-19

Title: Article Formats for R Markdown
Description: A suite of custom R Markdown formats and templates for authoring journal articles and conference submissions.
Author: JJ Allaire [aut], Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), R Foundation [aut, cph], Hadley Wickham [aut], Journal of Statistical Software [aut, cph], RStudio [cph], Ramnath Vaidyanathan [aut, cph], Association for Computing Machinery [aut, cph], Carl Boettiger [aut, cph], Elsevier [aut, cph], Karl Broman [aut, cph], Kirill Mueller [aut, cph], Bastiaan Quast [aut, cph], Randall Pruim [aut, cph], Ben Marwick [aut, cph], Charlotte Wickham [aut, cph], Oliver Keyes [aut, cph], Miao Yu [aut, cph], Daniel Emaasit [aut, cph], Thierry Onkelinx [aut, cph], Alessandro Gasparini [aut, cph] (<https://orcid.org/0000-0002-8319-7624>), Marc-Andre Desautels [aut, cph], Dominik Leutnant [aut, cph] (<https://orcid.org/0000-0003-3293-2315>), MDPI [aut, cph], Taylor and Francis [aut, cph], Oğuzhan Öğreden [aut] (<https://orcid.org/0000-0002-9949-3348>), Dalton Hance [aut], Daniel Nüst [aut, cph] (<https://orcid.org/0000-0002-0024-5046>), Petter Uvesten [aut, cph], Elio Campitelli [aut, cph] (<https://orcid.org/0000-0002-7742-9230>), John Muschelli [aut, cph] (<https://orcid.org/0000-0001-6469-1750>), Zhian N. Kamvar [aut, cph] (<https://orcid.org/0000-0003-1458-7108>), Noam Ross [aut, cph] (<https://orcid.org/0000-0002-2136-0000>), Robrecht Cannoodt [aut, cph] (<https://orcid.org/0000-0003-3641-729X>, rcannood), Duncan Luguern [aut], David M. Kaplan [aut, ctb] (<https://orcid.org/0000-0001-6087-359X>, dmkaplan2000)
Maintainer: Yihui Xie <xie@yihui.name>

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Package mcompanion updated to version 0.5-2 with previous version 0.5-1 dated 2019-12-18

Title: Objects and Methods for Multi-Companion Matrices
Description: Provides a class for multi-companion matrices with methods for arithmetic and factorization. A method for generation of multi-companion matrices with prespecified spectral properties is provided, as well as some utilities for periodically correlated and multivariate time series models. See Boshnakov (2002) <doi:10.1016/S0024-3795(01)00475-X> and Boshnakov & Iqelan (2009) <doi:10.1111/j.1467-9892.2009.00617.x>.
Author: Georgi N. Boshnakov [aut, cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>

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Package laeken updated to version 0.5.1 with previous version 0.5.0 dated 2019-01-10

Title: Estimation of Indicators on Social Exclusion and Poverty
Description: Estimation of indicators on social exclusion and poverty, as well as Pareto tail modeling for empirical income distributions.
Author: Andreas Alfons [aut, cre], Josef Holzer [aut], Matthias Templ [aut], Alexander Haider [ctb]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>

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Package kergp updated to version 0.5.1 with previous version 0.5.0 dated 2019-09-30

Title: Gaussian Process Laboratory
Description: Gaussian process regression with an emphasis on kernels. Quantitative and qualitative inputs are accepted. Some pre-defined kernels are available, such as radial or tensor-sum for quantitative inputs, and compound symmetry, low rank, group kernel for qualitative inputs. The user can define new kernels and composite kernels through a formula mechanism. Useful methods include parameter estimation by maximum likelihood, simulation, prediction and leave-one-out validation.
Author: Yves Deville, David Ginsbourger, Olivier Roustant. Contributors: Nicolas Durrande.
Maintainer: Olivier Roustant <roustant@insa-toulouse.fr>

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Package DT updated to version 0.12 with previous version 0.11 dated 2019-12-19

Title: A Wrapper of the JavaScript Library 'DataTables'
Description: Data objects in R can be rendered as HTML tables using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' library has been included in this R package. The package name 'DT' is an abbreviation of 'DataTables'.
Author: Yihui Xie [aut, cre], Joe Cheng [aut], Xianying Tan [aut], JJ Allaire [ctb], Maximilian Girlich [ctb], Greg Freedman Ellis [ctb], Johannes Rauh [ctb], jQuery contributors [ctb, cph] (jQuery in htmlwidgets/lib), SpryMedia Limited [ctb, cph] (DataTables in htmlwidgets/lib), Brian Reavis [ctb, cph] (selectize.js in htmlwidgets/lib), Leon Gersen [ctb, cph] (noUiSlider in htmlwidgets/lib), Bartek Szopka [ctb, cph] (jquery.highlight.js in htmlwidgets/lib), RStudio Inc [cph]
Maintainer: Yihui Xie <xie@yihui.name>

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Package tolerance updated to version 2.0.0 with previous version 1.3.0 dated 2017-02-04

Title: Statistical Tolerance Intervals and Regions
Description: Statistical tolerance limits provide the limits between which we can expect to find a specified proportion of a sampled population with a given level of confidence. This package provides functions for estimating tolerance limits (intervals) for various univariate distributions (binomial, Cauchy, discrete Pareto, exponential, two-parameter exponential, extreme value, hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric, normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot), Bayesian normal tolerance limits, multivariate normal tolerance regions, nonparametric tolerance intervals, tolerance bands for regression settings (linear regression, nonlinear regression, nonparametric regression, and multivariate regression), and analysis of variance tolerance intervals. Visualizations are also available for most of these settings.
Author: Derek S. Young [aut, cre]
Maintainer: Derek S. Young <derek.young@uky.edu>

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Package pomp updated to version 2.6 with previous version 2.5 dated 2020-01-28

Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Author: Aaron A. King [aut, cre], Edward L. Ionides [aut], Carles Breto [aut], Stephen P. Ellner [ctb], Matthew J. Ferrari [ctb], Bruce E. Kendall [ctb], Michael Lavine [ctb], Dao Nguyen [ctb], Daniel C. Reuman [ctb], Helen Wearing [ctb], Simon N. Wood [ctb], Sebastian Funk [ctb], Steven G. Johnson [ctb], Eamon O'Dea [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>

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Package jmvcore updated to version 1.2.5 with previous version 1.0.8 dated 2019-10-21

Title: Dependencies for the 'jamovi' Framework
Description: A framework for creating rich interactive analyses for the jamovi platform (see <https://www.jamovi.org> for more information).
Author: Jonathon Love
Maintainer: Jonathon Love <jon@thon.cc>

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Package hierNet updated to version 1.9 with previous version 1.8 dated 2019-12-08

Title: A Lasso for Hierarchical Interactions
Description: Fits sparse interaction models for continuous and binary responses subject to the strong (or weak) hierarchy restriction that an interaction between two variables only be included if both (or at least one of) the variables is included as a main effect. For more details, see Bien, J., Taylor, J., Tibshirani, R., (2013) "A Lasso for Hierarchical Interactions." Annals of Statistics. 41(3). 1111-1141.
Author: Jacob Bien and Rob Tibshirani
Maintainer: Jacob Bien <jbien@usc.edu>

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Package emld updated to version 0.4.0 with previous version 0.3.0 dated 2019-10-11

Title: Ecological Metadata as Linked Data
Description: This is a utility for transforming Ecological Metadata Language ('EML') files into 'JSON-LD' and back into 'EML.' Doing so creates a list-based representation of 'EML' in R, so that 'EML' data can easily be manipulated using standard 'R' tools. This makes this package an effective backend for other 'R'-based tools working with 'EML.' By abstracting away the complexity of 'XML' Schema, developers can build around native 'R' list objects and not have to worry about satisfying many of the additional constraints of set by the schema (such as element ordering, which is handled automatically). Additionally, the 'JSON-LD' representation enables the use of developer-friendly 'JSON' parsing and serialization that may facilitate the use of 'EML' in contexts outside of 'R,' as well as the informatics-friendly serializations such as 'RDF' and 'SPARQL' queries.
Author: Carl Boettiger [aut, cre, cph] (<https://orcid.org/0000-0002-1642-628X>), Matthew B. Jones [aut, cph] (<https://orcid.org/0000-0003-0077-4738>), Bryce Mecum [aut, cph] (<https://orcid.org/0000-0002-0381-3766>)
Maintainer: Carl Boettiger <cboettig@gmail.com>

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Package BAwiR updated to version 1.2.1 with previous version 1.2 dated 2019-02-17

Title: Analysis of Basketball Data
Description: Collection of tools to work with basketball data. Functions available are related to friendly web scraping and visualization. Data were obtained from <http://www.euroleague.net/>, <http://www.eurocupbasketball.com/> and <http://www.acb.com>, following the instructions of their respectives robots.txt files, when available. Tools for visualization include a population pyramid, 2D plots, circular plots of players' percentiles, plots of players' monthly/yearly stats, team heatmaps, team shooting plots, team four factors plots, cross-tables with the results of regular season games and maps of nationalities. Please see Vinue (2020) <doi:10.1089/big.2018.0124>.
Author: Guillermo Vinue
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>

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Package serrsBayes updated to version 0.4-1 with previous version 0.4-0 dated 2019-04-29

Title: Bayesian Modelling of Raman Spectroscopy
Description: Sequential Monte Carlo (SMC) algorithms for fitting a generalised additive mixed model (GAMM) to surface-enhanced resonance Raman spectroscopy (SERRS), using the method of Moores et al. (2016) <arXiv:1604.07299>. Multivariate observations of SERRS are highly collinear and lend themselves to a reduced-rank representation. The GAMM separates the SERRS signal into three components: a sequence of Lorentzian, Gaussian, or pseudo-Voigt peaks; a smoothly-varying baseline; and additive white noise. The parameters of each component of the model are estimated iteratively using SMC. The posterior distributions of the parameters given the observed spectra are represented as a population of weighted particles.
Author: Matt Moores [aut, cre] (<https://orcid.org/0000-0003-4531-3572>), Jake Carson [aut] (<https://orcid.org/0000-0002-7896-0971>), Benjamin Moskowitz [ctb], Kirsten Gracie [dtc], Karen Faulds [dtc] (<https://orcid.org/0000-0002-5567-7399>), Mark Girolami [aut], Engineering and Physical Sciences Research Council [fnd] (EPSRC programme grant ref: EP/L014165/1), University of Warwick [cph]
Maintainer: Matt Moores <mmoores@gmail.com>

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Package FSSF updated to version 0.1.1 with previous version 0.1.0 dated 2020-01-31

Title: Generate Fully-Sequential Space-Filling Designs Inside a Unit Hypercube
Description: Provides three methods proposed by Shang and Apley (2019) <doi:10.1080/00224065.2019.1705207> to generate fully-sequential space-filling designs inside a unit hypercube. A 'fully-sequential space-filling design' means a sequence of nested designs (as the design size varies from one point up to some maximum number of points) with the design points added one at a time and such that the design at each size has good space-filling properties. Two methods target the minimum pairwise distance criterion and generate maximin designs, among which one method is more efficient when design size is large. One method targets the maximum hole size criterion and uses a heuristic to generate what is closer to a minimax design.
Author: Boyang Shang and Daniel W. Apley
Maintainer: Boyang Shang <boyangshang2015@u.northwestern.edu>

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Package gdm updated to version 1.4 with previous version 1.3.11 dated 2018-06-05

Title: Generalized Dissimilarity Modeling
Description: A toolkit with functions to fit, plot, summarize, and apply Generalized Dissimilarity Models.
Author: Matthew C. Fitzpatrick, Karel Mokany, Glenn Manion, Matthew Lisk, Simon Ferrier, Diego Nieto-Lugilde
Maintainer: Matthew C. Fitzpatrick <mfitzpatrick@umces.edu>

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Package dttr2 updated to version 0.0.2 with previous version 0.0.1 dated 2019-06-28

Title: Manipulate Dates, DateTimes and Times
Description: Manipulates date (Date), datetime (POSIXct) and time (hms) vectors. Date/times are considered discrete and are floored whenever encountered. Times are wrapped and time zones are maintained unless explicitly altered by the user.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>)
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

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Package TRES updated to version 1.1.1 with previous version 1.1.0 dated 2019-11-17

Title: Tensor Regression with Envelope Structure and Three Generic Envelope Estimation Approaches
Description: Provides three estimators for tensor response regression (TRR) and tensor predictor regression (TPR) models with tensor envelope structure. The three types of estimation approaches are generic and can be applied to any envelope estimation problems. The full Grassmannian (FG) optimization is often associated with likelihood-based estimation but requires heavy computation and good initialization; the one-directional optimization approaches (1D and ECD algorithms) are faster, stable and does not require carefully chosen initial values; the SIMPLS-type is motivated by the partial least squares regression and is computationally the least expensive. For details of TRR, see Li L, Zhang X (2017) <doi:10.1080/01621459.2016.1193022>. For details of TPR, see Zhang X, Li L (2017) <doi:10.1080/00401706.2016.1272495>. For details of 1D algorithm, see Cook RD, Zhang X (2016) <doi:10.1080/10618600.2015.1029577>. For details of ECD algorithm, see Cook RD, Zhang X (2018) <doi:10.5705/ss.202016.0037>.
Author: Wenjing Wang [aut], Jing Zeng [aut, cre], Xin Zhang [aut]
Maintainer: Jing Zeng <jing.zeng@stat.fsu.edu>

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Package Numero updated to version 1.4.1 with previous version 1.4.0 dated 2019-12-14

Title: Statistical Framework to Define Subgroups in Complex Datasets
Description: High-dimensional datasets that do not exhibit a clear intrinsic clustered structure pose a challenge to conventional clustering algorithms. For this reason, we developed an unsupervised framework that helps scientists to better subgroup their datasets based on visual cues, please see Gao S, Mutter S, Casey A, Makinen V-P (2019) Numero: a statistical framework to define multivariable subgroups in complex population-based datasets, Int J Epidemiology, 48:369-37, <doi:10.1093/ije/dyy113>. The framework includes the necessary functions to construct a self-organizing map of the data, to evaluate the statistical significance of the observed data patterns, and to visualize the results.
Author: Song Gao [aut], Stefan Mutter [aut], Aaron E. Casey [aut], Ville-Petteri Makinen [aut, cre]
Maintainer: Ville-Petteri Makinen <vpmakine@gmail.com>

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Tue, 04 Feb 2020

Package xpose updated to version 0.4.7 with previous version 0.4.6 dated 2020-01-12

Title: Diagnostics for Pharmacometric Models
Description: Diagnostics for non-linear mixed-effects (population) models from 'NONMEM' <http://www.iconplc.com/innovation/nonmem/>. 'xpose' facilitates data import, creation of numerical run summary and provide 'ggplot2'-based graphics for data exploration and model diagnostics.
Author: Benjamin Guiastrennec [aut, cre, cph], Andrew C. Hooker [aut, cph], Sebastian Ueckert [aut, cph], Mike K. Smith [ctb], Mats O. Karlsson [aut, cph]
Maintainer: Benjamin Guiastrennec <guiastrennec@gmail.com>

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Package RCSF updated to version 1.0.2 with previous version 1.0.1 dated 2018-11-14

Title: Airborne LiDAR Filtering Method Based on Cloth Simulation
Description: Cloth Simulation Filter (CSF) is an airborne LiDAR (Light Detection and Ranging) ground points filtering algorithm which is based on cloth simulation. It tries to simulate the interactions between the cloth nodes and the corresponding LiDAR points, the locations of the cloth nodes can be determined to generate an approximation of the ground surface <https://www.mdpi.com/2072-4292/8/6/501/htm>.
Author: Jean-Romain Roussel [aut, cre, cph], Jianbo Qi [aut, cph], Wuming Zhang [cph], Peng Wan [cph], Hongtao Wang [cph], State Key Laboratory of Remote Sensing Science, Institute of Remote Sensing Science and Engineering, Beijing Normal University [cph]
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>

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Package bpnreg updated to version 1.0.3 with previous version 1.0.2 dated 2019-12-08

Title: Bayesian Projected Normal Regression Models for Circular Data
Description: Fitting Bayesian multiple and mixed-effect regression models for circular data based on the projected normal distribution. Both continuous and categorical predictors can be included. Sampling from the posterior is performed via an MCMC algorithm. Posterior descriptives of all parameters, model fit statistics and Bayes factors for hypothesis tests for inequality constrained hypotheses are provided. See Cremers, Mulder & Klugkist (2018) <doi:10.1111/bmsp.12108> and Nuñez-Antonio & Guttiérez-Peña (2014) <doi:10.1016/j.csda.2012.07.025>.
Author: Jolien Cremers [aut, cre]
Maintainer: Jolien Cremers <joliencremers@gmail.com>

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Package warbleR updated to version 1.1.21 with previous version 1.1.20 dated 2020-01-11

Title: Streamline Bioacoustic Analysis
Description: Functions aiming to facilitate the analysis of the structure of animal acoustic signals in 'R'. Users can collect open-access avian recordings or enter their own data into a workflow that facilitates spectrographic visualization and measurement of acoustic parameters. 'warbleR' makes use of the basic sound analysis tools from the package 'seewave', and offers new tools for acoustic structure analysis. The main features of the package are the use of loops to apply tasks through acoustic signals referenced in a selection (annotation) table and the production of spectrograms in image files that allow to organize data and verify acoustic analyzes. The package offers functions to explore, organize and manipulate multiple sound files, explore and download 'Xeno-Canto' recordings, detect signals automatically, create spectrograms of complete recordings or individual signals, run different measures of acoustic signal structure, evaluate the performance of measurement methods, catalog signals, characterize different structural levels in acoustic signals, run statistical analysis of duet coordination and consolidate databases and annotation tables, among others.
Author: Marcelo Araya-Salas [aut, cre] (<https://orcid.org/0000-0003-3594-619X>), Grace Smith-Vidaurre [aut]
Maintainer: Marcelo Araya-Salas <marceloa27@gmail.com>

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Package pagedown updated to version 0.8 with previous version 0.7 dated 2019-12-19

Title: Paginate the HTML Output of R Markdown with CSS for Print
Description: Use the paged media properties in CSS and the JavaScript library 'paged.js' to split the content of an HTML document into discrete pages. Each page can have its page size, page numbers, margin boxes, and running headers, etc. Applications of this package include books, letters, reports, papers, business cards, resumes, and posters.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Romain Lesur [aut, cph] (<https://orcid.org/0000-0002-0721-5595>), Brent Thorne [aut] (<https://orcid.org/0000-0002-1099-3857>), Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>), Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>), RStudio, Inc. [cph], Adam Hyde [ctb] (paged.js in resources/js/), Min-Zhong Lu [ctb] (resume.css in resources/css/), Zulko [ctb] (poster-relaxed.css in resources/css/)
Maintainer: Yihui Xie <xie@yihui.name>

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Package mime updated to version 0.9 with previous version 0.8 dated 2019-12-19

Title: Map Filenames to MIME Types
Description: Guesses the MIME type from a filename extension using the data derived from /etc/mime.types in UNIX-type systems.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Jeffrey Horner [ctb], Beilei Bian [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

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Package eq5d updated to version 0.6.0 with previous version 0.5.0 dated 2019-12-15

Title: Methods for Calculating 'EQ-5D' Utility Index Scores
Description: EQ-5D is a popular health related quality of life instrument used in the clinical and economic evaluation of health care. Developed by the EuroQol group <https://www.euroqol.org>, the instrument consists of two components: health state description and evaluation. For the description component a subject self-rates their health in terms of five dimensions; mobility, self-care, usual activities, pain/discomfort, and anxiety/depression using either a three-level (EQ-5D-3L, <https://www.euroqol.org/eq-5d-instruments/eq-5d-3l-about>) or a five-level (EQ-5D-5L, <https://www.euroqol.org/eq-5d-instruments/eq-5d-5l-about>) scale. Frequently the scores on these five dimensions are converted to a single utility index using country specific value sets, which can be used in the clinical and economic evaluation of health care as well as in population health surveys. The eq5d package provides methods to calculate index scores from a subject's dimension scores. 25 TTO and 11 VAS EQ-5D-3L value sets including those for countries in Szende et al (2007) <doi:10.1007/1-4020-5511-0> and Szende et al (2014) <doi:10.1007/978-94-007-7596-1>, 20 EQ-5D-5L EQ-VT value sets from the EuroQol website, and the EQ-5D-5L crosswalk value sets developed by van Hout et al. (2012) <doi:10.1016/j.jval.2012.02.008> are included. Additionally, a shiny web tool is included to enable the calculation, visualisation and automated statistical analysis of EQ-5D index values via a web browser using EQ-5D dimension scores stored in CSV or Excel files.
Author: Fraser Morton [aut, cre], Jagtar Singh Nijjar [aut]
Maintainer: Fraser Morton <fraser.morton@glasgow.ac.uk>

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Package biclust updated to version 2.0.2 with previous version 2.0.1 dated 2018-06-09

Title: BiCluster Algorithms
Description: The main function biclust() provides several algorithms to find biclusters in two-dimensional data: Cheng and Church (2000, ISBN:1-57735-115-0), spectral (2003) <doi:10.1101/gr.648603>, plaid model (2005) <doi:10.1016/j.csda.2004.02.003>, xmotifs (2003) <doi:10.1142/9789812776303_0008> and bimax (2006) <doi:10.1093/bioinformatics/btl060>. In addition, the package provides methods for data preprocessing (normalization and discretisation), visualisation, and validation of bicluster solutions.
Author: Sebastian Kaiser, Rodrigo Santamaria, Tatsiana Khamiakova, Martin Sill, Roberto Theron, Luis Quintales, Friedrich Leisch and Ewoud De Troyer.
Maintainer: Sebastian Kaiser <dr.sebastian.kaiser@gmail.com>

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Package surveydata updated to version 0.2.4 with previous version 0.2.3 dated 2019-01-23

Title: Tools to Work with Survey Data
Description: Data obtained from surveys contains information not only about the survey responses, but also the survey metadata, e.g. the original survey questions and the answer options. The 'surveydata' package makes it easy to keep track of this metadata, and to easily extract columns with specific questions.
Author: Andrie de Vries [aut, cre, cph], Evan Odell [ctb]
Maintainer: Andrie de Vries <apdevries@gmail.com>

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Package RclusTool updated to version 0.91.3 with previous version 0.91.2 dated 2020-01-09

Title: Graphical Toolbox for Clustering and Classification of Data Frames
Description: Graphical toolbox for clustering and classification of data frames. It proposes a graphical interface to process clustering and classification methods on features data-frames, and to view initial data as well as resulted cluster or classes. According to the level of available labels, different approaches are proposed: unsupervised clustering, semi-supervised clustering and supervised classification. To assess the processed clusters or classes, the toolbox can import and show some supplementary data formats: either profile/time series, or images. These added information can help the expert to label clusters (clustering), or to constrain data frame rows (semi-supervised clustering), using Constrained spectral embedding algorithm by Wacquet et al. (2013) <doi:10.1016/j.patrec.2013.02.003> and the methodology provided by Wacquet et al. (2013) <doi:10.1007/978-3-642-35638-4_21>.
Author: Guillaume Wacquet [aut], Pierre-Alexandre Hebert [aut, cre], Emilie Poisson [aut], Pierre Talon [aut]
Maintainer: Pierre-Alexandre Hebert <hebert@univ-littoral.fr>

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Package fpc updated to version 2.2-5 with previous version 2.2-4 dated 2020-01-17

Title: Flexible Procedures for Clustering
Description: Various methods for clustering and cluster validation. Fixed point clustering. Linear regression clustering. Clustering by merging Gaussian mixture components. Symmetric and asymmetric discriminant projections for visualisation of the separation of groupings. Cluster validation statistics for distance based clustering including corrected Rand index. Standardisation of cluster validation statistics by random clusterings and comparison between many clustering methods and numbers of clusters based on this. Cluster-wise cluster stability assessment. Methods for estimation of the number of clusters: Calinski-Harabasz, Tibshirani and Walther's prediction strength, Fang and Wang's bootstrap stability. Gaussian/multinomial mixture fitting for mixed continuous/categorical variables. Variable-wise statistics for cluster interpretation. DBSCAN clustering. Interface functions for many clustering methods implemented in R, including estimating the number of clusters with kmeans, pam and clara. Modality diagnosis for Gaussian mixtures. For an overview see package?fpc.
Author: Christian Hennig <christian.hennig@unibo.it>
Maintainer: Christian Hennig <christian.hennig@unibo.it>

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Package fields updated to version 10.3 with previous version 10.2 dated 2020-02-02

Title: Tools for Spatial Data
Description: For curve, surface and function fitting with an emphasis on splines, spatial data, geostatistics, and spatial statistics. The major methods include cubic, and thin plate splines, Kriging, and compactly supported covariance functions for large data sets. The splines and Kriging methods are supported by functions that can determine the smoothing parameter (nugget and sill variance) and other covariance function parameters by cross validation and also by restricted maximum likelihood. For Kriging there is an easy to use function that also estimates the correlation scale (range parameter). A major feature is that any covariance function implemented in R and following a simple format can be used for spatial prediction. There are also many useful functions for plotting and working with spatial data as images. This package also contains an implementation of sparse matrix methods for large spatial data sets and currently requires the sparse matrix (spam) package. Use help(fields) to get started and for an overview. The fields source code is deliberately commented and provides useful explanations of numerical details as a companion to the manual pages. The commented source code can be viewed by expanding source code version and looking in the R subdirectory. The reference for fields can be generated by the citation function in R and has DOI <doi:10.5065/D6W957CT>. Development of this package was supported in part by the National Science Foundation Grant 1417857 and the National Center for Atmospheric Research. See the Fields URL for a vignette on using this package and some background on spatial statistics.
Author: Douglas Nychka [aut, cre], Reinhard Furrer [aut], John Paige [aut], Stephan Sain [aut], Florian Gerber [aut], Matthew Iverson [aut], University Corporation for Atmospheric Research [cph]
Maintainer: Douglas Nychka <douglasnychka@gmail.com>

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Package FactoInvestigate updated to version 1.6 with previous version 1.5 dated 2019-11-16

Title: Automatic Description of Factorial Analysis
Description: Brings a set of tools to help and automatically realise the description of principal component analyses (from 'FactoMineR' functions). Detection of existing outliers, identification of the informative components, graphical views and dimensions description are performed threw dedicated functions. The Investigate() function performs all these functions in one, and returns the result as a report document (Word, PDF or HTML).
Author: Simon Thuleau, Francois Husson
Maintainer: Francois Husson <husson@agrocampus-ouest.fr>

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Package arrayhelpers updated to version 1.1-0 with previous version 1.0-20160527 dated 2016-05-27

Title: Convenience Functions for Arrays
Description: Some convenient functions to work with arrays.
Author: C. Beleites <claudia.beleites@chemometrix.eu>
Maintainer: C. Beleites <claudia.beleites@chemometrix.eu>

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Package apcf updated to version 0.1.4 with previous version 0.1.3 dated 2019-06-13

Title: Adapted Pair Correlation Function
Description: The adapted pair correlation function transfers the concept of the pair correlation function from point patterns to patterns of objects of finite size and irregular shape (e.g. lakes within a country). This is a reimplementation of the method suggested by Nuske et al. (2009) <doi:10.1016/j.foreco.2009.09.050> using the libraries 'GEOS' and 'GDAL' directly instead of through 'PostGIS'.
Author: Robert Nuske [aut, cre] (<https://orcid.org/0000-0001-9773-2061>)
Maintainer: Robert Nuske <robert.nuske@mailbox.org>

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Package tigris updated to version 0.9.2 with previous version 0.9.1 dated 2020-01-13

Title: Load Census TIGER/Line Shapefiles
Description: Download TIGER/Line shapefiles from the United States Census Bureau (<https://www.census.gov/geo/maps-data/data/tiger-line.html>) and load into R as 'SpatialDataFrame' or 'sf' objects.
Author: Kyle Walker [aut, cre], Bob Rudis [ctb]
Maintainer: Kyle Walker <kyle.walker@tcu.edu>

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Package rrtable updated to version 0.1.7 with previous version 0.1.6 dated 2020-01-29

Title: Reproducible Research with a Table of R Codes
Description: Makes documents containing plots and tables from a table of R codes. Can make "HTML", "pdf('LaTex')", "docx('MS Word')" and "pptx('MS Powerpoint')" documents with or without R code. In the package, modularized 'shiny' app codes are provided. These modules are intended for reuse across applications.
Author: Keon-Woong Moon [aut, cre]
Maintainer: Keon-Woong Moon <cardiomoon@gmail.com>

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Package rlas updated to version 1.3.5 with previous version 1.3.4 dated 2019-09-19

Title: Read and Write 'las' and 'laz' Binary File Formats Used for Remote Sensing Data
Description: Read and write 'las' and 'laz' binary file formats. The LAS file format is a public file format for the interchange of 3-dimensional point cloud data between data users. The LAS specifications are approved by the American Society for Photogrammetry and Remote Sensing <https://www.asprs.org/divisions-committees/lidar-division/laser-las-file-format-exchange-activities>. The LAZ file format is an open and lossless compression scheme for binary LAS format versions 1.0 to 1.3 <https://laszip.org/>.
Author: Jean-Romain Roussel [aut, cre, cph], Florian De Boissieu [aut, ctb] (Enable the support of .lax file and extra byte attributes), Martin Isenburg [cph] (Is the author of the LASlib and LASzip libraries), David Auty [ctb] (Reviewed the documentation), Pierrick Marie [ctb] (Helped to compile LASlib code in R), Tiago de Conto [ctb] (Implemented the -thin_with_voxel filter method)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>

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Package importinegi updated to version 1.1.0 with previous version 1.0.0 dated 2019-08-05

Title: Download and Manage Open Data from INEGI
Description: Download and manage data sets of statistical projects and geographic data created by Instituto Nacional de Estadistica y Geografia (INEGI). See <https://www.inegi.org.mx/>.
Author: Cesar Renteria [aut, cre]
Maintainer: Cesar Renteria <crenteria@albany.edu>

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Package aroma.core updated to version 3.2.1 with previous version 3.2.0 dated 2019-06-17

Title: Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
Description: Core methods and classes used by higher-level 'aroma.*' packages part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'.
Author: Henrik Bengtsson [aut, cre, cph], Mark Robinson [ctb], Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

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Package fuzzySim updated to version 3.0 with previous version 2.0 dated 2018-12-18

Title: Fuzzy Similarity in Species Distributions
Description: Functions to calculate fuzzy versions of species' occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis and prevalence-independent favourability GLM), and pair-wise fuzzy similarity (based on fuzzy versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model comparison (overlap and fuzzy similarity, loss or gain), and for data preparation, such as obtaining unique abbreviations of species names, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, assessing the false discovery rate, or analysing and dealing with multicollinearity among variables. Includes also sample datasets for providing practical examples.
Author: Barbosa A.M.
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>

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Package filling updated to version 0.2.1 with previous version 0.2.0 dated 2018-09-16

Title: Matrix Completion, Imputation, and Inpainting Methods
Description: Filling in the missing entries of a partially observed data is one of fundamental problems in various disciplines of mathematical science. For many cases, data at our interests have canonical form of matrix in that the problem is posed upon a matrix with missing values to fill in the entries under preset assumptions and models. We provide a collection of methods from multiple disciplines under Matrix Completion, Imputation, and Inpainting. See Davenport and Romberg (2016) <doi:10.1109/JSTSP.2016.2539100> for an overview of the topic.
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyoustat@gmail.com>

Diff between filling versions 0.2.0 dated 2018-09-16 and 0.2.1 dated 2020-02-04

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Package FAOSTAT updated to version 2.1.1 with previous version 2.0 dated 2015-06-01

Title: Download Data from the FAOSTAT Database of the Food and Agricultural Organization (FAO) of the United Nations
Description: A list of functions to download statistics from FAOSTAT (database of the Food and Agricultural Organization of the United Nations) and WDI (database of the World Bank), and to perform some harmonization operations.
Author: Michael C. J. Kao <michael.kao@fao.org>, Markus Gesmann, Filippo Gheri
Maintainer: Paul Rougieux <paul.rougieux@gmail.com>

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Package cgraph updated to version 6.0.0 with previous version 5.0.1 dated 2019-11-26

Title: Computational Graphs
Description: Allows to create, evaluate, and differentiate computational graphs in R. A computational graph is a graph representation of a multivariate function decomposed by its (elementary) operations. Nodes in the graph represent arrays while edges represent dependencies among the arrays. An advantage of expressing a function as a computational graph is that this enables to differentiate the function by automatic differentiation. The 'cgraph' package supports various operations including basic arithmetic, trigonometry operations, and linear algebra operations. It differentiates computational graphs by reverse automatic differentiation. The flexible architecture of the package makes it applicable to solve a variety of problems including local sensitivity analysis, gradient-based optimization, and machine learning.
Author: Ron Triepels
Maintainer: Ron Triepels <dev@cgraph.org>

Diff between cgraph versions 5.0.1 dated 2019-11-26 and 6.0.0 dated 2020-02-04

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Package CAISEr updated to version 1.0.16 with previous version 1.0.15 dated 2019-08-19

Title: Comparison of Algorithms with Iterative Sample Size Estimation
Description: Functions for performing experimental comparisons of algorithms using adequate sample sizes for power and accuracy. Implements the methodology originally presented in Campelo and Takahashi (2019) <doi:10.1007/s10732-018-9396-7> for the comparison of two algorithms, and later generalised in Campelo and Wanner (Submitted, 2019) <arxiv:1908.01720>.
Author: Felipe Campelo [aut, cre], Fernanda Takahashi [ctb], Elizabeth Wanner [ctb]
Maintainer: Felipe Campelo <f.campelo@aston.ac.uk>

Diff between CAISEr versions 1.0.15 dated 2019-08-19 and 1.0.16 dated 2020-02-04

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Package pyMTurkR updated to version 1.1.4 with previous version 1.1 dated 2019-09-05

Title: A Client for the 'MTurk' Requester API
Description: Provides access to the latest 'Amazon Mechanical Turk' ('MTurk') <https://www.mturk.com> Requester API (version '2017–01–17'), replacing the now deprecated 'MTurkR' package.
Author: Tyler Burleigh [aut, cre] (https://twitter.com/tylerburleigh), Thomas J. Leeper [aut] (<https://orcid.org/0000-0003-4097-6326>), Solomon Messing [ctb], Sean Murphy [ctb], Jonathan Chang [ctb], Andrew Brown [ctb]
Maintainer: Tyler Burleigh <tylerburleigh@gmail.com>

Diff between pyMTurkR versions 1.1 dated 2019-09-05 and 1.1.4 dated 2020-02-04

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Package ifaTools updated to version 0.21 with previous version 0.20 dated 2019-12-12

Title: Toolkit for Item Factor Analysis with 'OpenMx'
Description: Tools, tutorials, and demos of Item Factor Analysis using 'OpenMx'.
Author: Joshua N. Pritikin [cre, aut]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>

Diff between ifaTools versions 0.20 dated 2019-12-12 and 0.21 dated 2020-02-04

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Package signnet updated to version 0.5.1 with previous version 0.5.0 dated 2020-01-24

Title: Methods to Analyse Signed Networks
Description: Methods for the analysis of signed networks. This includes several measures for structural balance as introduced by Cartwright and Harary (1956) <doi:10.1037/h0046049>, blockmodeling algorithms from Doreian (2008) <doi:10.1016/j.socnet.2008.03.005>, various centrality indices, and projections of signed two-mode networks introduced by Schoch (2020) <doi:10.1080/0022250X.2019.1711376>.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david.schoch@manchester.ac.uk>

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Package PolynomF updated to version 2.0-3 with previous version 2.0-2 dated 2019-06-18

Title: Polynomials in R
Description: Implements univariate polynomial operations in R, including polynomial arithmetic, finding zeros, plotting, and some operations on lists of polynomials.
Author: Bill Venables, with contribution by Kurt Hornik and Georgi Boshnakov
Maintainer: Bill Venables <Bill.Venables@gmail.com>

Diff between PolynomF versions 2.0-2 dated 2019-06-18 and 2.0-3 dated 2020-02-04

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Package set6 updated to version 0.1.1 with previous version 0.1.0 dated 2019-12-23

Title: R6 Mathematical Sets Interface
Description: An object-oriented package for mathematical sets, upgrading the current gold-standard {sets}. Many forms of mathematical sets are implemented, including (countably finite) sets, tuples, intervals (countably infinite or uncountable), and fuzzy variants. Wrappers extend functionality by allowing symbolic representations of complex operations on sets, including unions, (cartesian) products, exponentiation, and differences (asymmetric and symmetric).
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>), Franz Kiraly [aut]
Maintainer: Raphael Sonabend <raphael.sonabend.15@ucl.ac.uk>

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Package indicspecies updated to version 1.7.9 with previous version 1.7.8 dated 2019-11-05

Title: Relationship Between Species and Groups of Sites
Description: Functions to assess the strength and statistical significance of the relationship between species occurrence/abundance and groups of sites [De Caceres & Legendre (2009) <doi:10.1890/08-1823.1>]. Also includes functions to measure species niche breadth using resource categories [De Caceres et al. (2011) <doi:10.1111/J.1600-0706.2011.19679.x>].
Author: Miquel De Cáceres [aut, cre], Florian Jansen [aut], Noah Dell [aut]
Maintainer: Miquel De Cáceres <miquelcaceres@gmail.com>

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Package tsDyn updated to version 10-1.2 with previous version 10-1.1 dated 2020-01-10

Title: Nonlinear Time Series Models with Regime Switching
Description: Implements nonlinear autoregressive (AR) time series models. For univariate series, a non-parametric approach is available through additive nonlinear AR. Parametric modeling and testing for regime switching dynamics is available when the transition is either direct (TAR: threshold AR) or smooth (STAR: smooth transition AR, LSTAR). For multivariate series, one can estimate a range of TVAR or threshold cointegration TVECM models with two or three regimes. Tests can be conducted for TVAR as well as for TVECM (Hansen and Seo 2002 and Seo 2006).
Author: Antonio Fabio Di Narzo [aut], Jose Luis Aznarte [ctb], Matthieu Stigler [aut], Ho Tsung-wu [cre]
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>

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Package RSSL updated to version 0.9.1 with previous version 0.8 dated 2019-03-08

Title: Implementations of Semi-Supervised Learning Approaches for Classification
Description: A collection of implementations of semi-supervised classifiers and methods to evaluate their performance. The package includes implementations of, among others, Implicitly Constrained Learning, Moment Constrained Learning, the Transductive SVM, Manifold regularization, Maximum Contrastive Pessimistic Likelihood estimation, S4VM and WellSVM.
Author: Jesse Krijthe [aut, cre]
Maintainer: Jesse Krijthe <jkrijthe@gmail.com>

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Package mistr updated to version 0.0.3 with previous version 0.0.2 dated 2019-07-25

Title: Mixture and Composite Distributions
Description: A flexible computational framework for mixture distributions with the focus on the composite models.
Author: Lukas Sablica [aut, cre] (<https://orcid.org/0000-0001-9166-4563>), Kurt Hornik [aut] (<https://orcid.org/0000-0003-4198-9911>)
Maintainer: Lukas Sablica <lsablica@wu.ac.at>

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Package GMSE updated to version 0.4.0.13 with previous version 0.4.0.11 dated 2019-03-18

Title: Generalised Management Strategy Evaluation Simulator
Description: Integrates game theory and ecological theory to construct social-ecological models that simulate the management of populations and stakeholder actions. These models build off of a previously developed management strategy evaluation (MSE) framework to simulate all aspects of management: population dynamics, manager observation of populations, manager decision making, and stakeholder responses to management decisions. The newly developed generalised management strategy evaluation (GMSE) framework uses genetic algorithms to mimic the decision-making process of managers and stakeholders under conditions of change, uncertainty, and conflict. Simulations can be run using gmse(), gmse_apply(), and gmse_gui() functions.
Author: A. Bradley Duthie [aut, cre] (<https://orcid.org/0000-0001-8343-4995>), Nils Bunnefeld [ctb, fnd] (<https://orcid.org/0000-0002-1349-4463>), Jeremy Cusack [ctb] (<https://orcid.org/0000-0003-3004-1586>), Isabel Jones [ctb] (<https://orcid.org/0000-0002-8361-1370>), Jeroen Minderman [ctb] (<https://orcid.org/0000-0002-8451-5540>), Erlend Nilsen [ctb] (<https://orcid.org/0000-0002-5119-8331>), Rocio Pozo [ctb] (<https://orcid.org/0000-0002-7546-8076>), Sarobidy Rakotonarivo [ctb] (<https://orcid.org/0000-0002-8032-1431>), Bram Van Moorter [ctb] (<https://orcid.org/0000-0002-3196-1993>)
Maintainer: A. Bradley Duthie <brad.duthie@gmail.com>

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Package rtmpt updated to version 0.1-18 with previous version 0.1-17 dated 2019-10-14

Title: Fitting RT-MPT Models
Description: Fit response-time extended multinomial processing tree (RT-MPT) models by Klauer and Kellen (2018) <doi:10.1016/j.jmp.2017.12.003>. The RT-MPT class not only incorporate frequencies like traditional multinomial processing tree (MPT) models, but also latencies. This enables it to estimate process completion times and encoding plus motor execution times next to the process probabilities of traditional MPTs. 'rtmpt' is a Bayesian framework and posterior samples are sampled using a Metropolis-Gibbs sampler like the one described in the Klauer and Kellen (2018), but with some modifications. Other than in the original C++ program we use the free and open source GNU Scientific Library (GSL). There is also the possibility to suppress single process completion times.
Author: Raphael Hartmann [aut, cre], Karl C. Klauer [cph, aut, ctb, ths], Henrik Singmann [aut, ctb, cph], Jean Marie Linhart [cph]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>

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Package Radviz updated to version 0.8.2 with previous version 0.8.1 dated 2020-01-10

Title: Project Multidimensional Data in 2D Space
Description: An implementation of the radviz projection in R. It enables the visualization of multidimensional data while maintaining the relation to the original dimensions. This package provides functions to create and plot radviz projections, and a number of summary plots that enable comparison and analysis. For reference see Ankerst *et al.* (1996) (<http://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.68.1811>) for original implementation, see Di Caro *et al* 2012 (<http://link.springer.com/chapter/10.1007/978-3-642-13672-6_13>) for the original method for dimensional anchor arrangements.
Author: Yann Abraham [aut, cre]
Maintainer: Yann Abraham <yann.abraham@gmail.com>

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Package pairwise updated to version 0.4.4-7 with previous version 0.4.4-5.1 dated 2019-01-31

Title: Rasch Model Parameters by Pairwise Algorithm
Description: Performs the explicit calculation -- not estimation! -- of the Rasch item parameters for dichotomous and polytomous item responses, using a pairwise comparison approach. Person parameters (WLE) are calculated according to Warm's weighted likelihood approach.
Author: Joerg-Henrik Heine <jhheine@googlemail.com>
Maintainer: Joerg-Henrik Heine <jhheine@googlemail.com>

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Package sen2r updated to version 1.3.0 with previous version 1.2.1 dated 2019-11-12

Title: Find, Download and Process Sentinel-2 Data
Description: Functions to download Sentinel-2 optical images and perform preliminary processing operations. 'sen2r' provides the instruments required to easily perform (and eventually automate) the steps necessary to build a complete Sentinel-2 processing chain. A Graphical User Interface to facilitate data processing is also provided.
Author: Luigi Ranghetti [aut, cre] (<https://orcid.org/0000-0001-6207-5188>), Lorenzo Busetto [aut] (<https://orcid.org/0000-0001-9634-6038>)
Maintainer: Luigi Ranghetti <luigi@ranghetti.info>

Diff between sen2r versions 1.2.1 dated 2019-11-12 and 1.3.0 dated 2020-02-04

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Package rbin updated to version 0.1.2 with previous version 0.1.1 dated 2019-01-04

Title: Tools for Binning Data
Description: Manually bin data using weight of evidence and information value. Includes other binning methods such as equal length, quantile and winsorized. Options for combining levels of categorical data are also available. Dummy variables can be generated based on the bins created using any of the available binning methods. References: Siddiqi, N. (2006) <doi:10.1002/9781119201731.biblio>.
Author: Aravind Hebbali [aut, cre]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>

Diff between rbin versions 0.1.1 dated 2019-01-04 and 0.1.2 dated 2020-02-04

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Package bssm updated to version 0.1.10 with previous version 0.1.9 dated 2020-01-28

Title: Bayesian Inference of Non-Linear and Non-Gaussian State Space Models
Description: Efficient methods for Bayesian inference of state space models via particle Markov chain Monte Carlo and parallel importance sampling type weighted Markov chain Monte Carlo (Vihola, Helske, and Franks, 2017, <arXiv:1609.02541>). Gaussian, Poisson, binomial, or negative binomial observation densities and basic stochastic volatility models with Gaussian state dynamics, as well as general non-linear Gaussian models and discretised diffusion models are supported.
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>), Matti Vihola [aut] (<https://orcid.org/0000-0002-8041-7222>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>

Diff between bssm versions 0.1.9 dated 2020-01-28 and 0.1.10 dated 2020-02-04

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Package tidygapminder updated to version 0.1.1 with previous version 0.1.0 dated 2019-12-06

Title: Easily Tidy Gapminder Datasets
Description: A toolset that allows you to easily import and tidy data sheets retrieved from Gapminder data web tools. It will therefore contribute to reduce the time used in data cleaning of Gapminder indicator data sheets as they are very messy.
Author: Anicet Ebou [aut, cre] (<https://orcid.org/0000-0003-4005-177X>)
Maintainer: Anicet Ebou <anicet.ebou@gmail.com>

Diff between tidygapminder versions 0.1.0 dated 2019-12-06 and 0.1.1 dated 2020-02-04

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Package Runuran updated to version 0.28 with previous version 0.27 dated 2019-03-14

Title: R Interface to the 'UNU.RAN' Random Variate Generators
Description: Interface to the 'UNU.RAN' library for Universal Non-Uniform RANdom variate generators. Thus it allows to build non-uniform random number generators from quite arbitrary distributions. In particular, it provides an algorithm for fast numerical inversion for distribution with given density function. In addition, the package contains densities, distribution functions and quantiles from a couple of distributions.
Author: Josef Leydold [aut, cre], Wolfgang H"ormann [aut]
Maintainer: Josef Leydold <josef.leydold@wu.ac.at>

Diff between Runuran versions 0.27 dated 2019-03-14 and 0.28 dated 2020-02-04

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Package qqplotr updated to version 0.0.4 with previous version 0.0.3 dated 2018-07-18

Title: Quantile-Quantile Plot Extensions for 'ggplot2'
Description: Extensions of 'ggplot2' Q-Q plot functionalities.
Author: Alexandre Almeida [aut], Adam Loy [aut, cre], Heike Hofmann [aut]
Maintainer: Adam Loy <loyad01@gmail.com>

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Package leiden updated to version 0.3.3 with previous version 0.3.2 dated 2020-01-18

Title: R Implementation of Leiden Clustering Algorithm
Description: Implements the 'Python leidenalg' module to be called in R. Enables clustering using the leiden algorithm for partition a graph into communities. See the 'Python' repository for more details: <https://github.com/vtraag/leidenalg> Traag et al (2018) From Louvain to Leiden: guaranteeing well-connected communities. <arXiv:1810.08473>.
Author: S. Thomas Kelly [aut, cre, trl], Vincent A. Traag [com]
Maintainer: S. Thomas Kelly <tom.kelly@riken.jp>

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Package emIRT updated to version 0.0.11 with previous version 0.0.9 dated 2019-12-13

Title: EM Algorithms for Estimating Item Response Theory Models
Description: Various Expectation-Maximization (EM) algorithms are implemented for item response theory (IRT) models. The current implementation includes IRT models for binary and ordinal responses, along with dynamic and hierarchical IRT models with binary responses. The latter two models are derived and implemented using variational EM. Subsequent edits also include variational network and text scaling models.
Author: Kosuke Imai <kimai@princeton.edu>, James Lo <lojames@usc.edu>, Jonathan Olmsted <jpolmsted@gmail.com>
Maintainer: James Lo <lojames@usc.edu>

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Package MARSS updated to version 3.10.12 with previous version 3.10.10 dated 2018-11-02

Title: Multivariate Autoregressive State-Space Modeling
Description: The MARSS package provides maximum-likelihood parameter estimation for constrained and unconstrained linear multivariate autoregressive state-space (MARSS) models fit to multivariate time-series data. Fitting is primarily via an Expectation-Maximization (EM) algorithm, although fitting via the BFGS algorithm (using the optim function) is also provided. MARSS models are a class of dynamic linear model (DLM) and vector autoregressive model (VAR) model. Functions are provided for parametric and innovations bootstrapping, Kalman filtering and smoothing, bootstrap model selection criteria (AICb), confidences intervals via the Hessian approximation and via bootstrapping and calculation of auxiliary residuals for detecting outliers and shocks. The user guide shows examples of using MARSS for parameter estimation for a variety of applications, model selection, dynamic factor analysis, outlier and shock detection, and addition of covariates. Type RShowDoc("UserGuide", package="MARSS") at the R command line to open the MARSS user guide. Online workshops (lectures and computer labs) at <https://nwfsc-timeseries.github.io/> See the NEWS file for update information.
Author: Eli Holmes, Eric Ward, Mark Scheuerell, and Kellie Wills, NOAA, Seattle, USA
Maintainer: Elizabeth Holmes - NOAA Federal <eli.holmes@noaa.gov>

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More information about MARSS at CRAN
Permanent link

Mon, 03 Feb 2020

Package OpenMx updated to version 2.16.0 with previous version 2.15.5 dated 2019-12-09

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], Michael D. Hunter [aut], Daniel C. Hackett [ctb], Julian Karch [ctb], Andreas M. Brandmaier [ctb], Joshua N. Pritikin [aut, cre], Mahsa Zahery [aut], Robert M. Kirkpatrick [aut], Yang Wang [ctb], Ben Goodrich [ctb], Charles Driver [ctb], Massachusetts Institute of Technology [cph], S. G. Johnson [cph], Association for Computing Machinery [cph], Dieter Kraft [cph], Stefan Wilhelm [cph], Sarah Medland [cph], Carl F. Falk [cph], Matt Keller [cph], Manjunath B G [cph], The Regents of the University of California [cph], Lester Ingber [cph], Wong Shao Voon [cph], Juan Palacios [cph], Jiang Yang [cph], Gael Guennebaud [cph], Jitse Niesen [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>

Diff between OpenMx versions 2.15.5 dated 2019-12-09 and 2.16.0 dated 2020-02-03

 DESCRIPTION                                                            |   10 
 MD5                                                                    |  399 +++----
 NAMESPACE                                                              |    4 
 NEWS.md                                                                |    1 
 R/MxAlgebra.R                                                          |    2 
 R/MxAlgebraConvert.R                                                   |    2 
 R/MxAlgebraObjective.R                                                 |    2 
 R/MxApply.R                                                            |    2 
 R/MxBaseNamed.R                                                        |    2 
 R/MxCommunication.R                                                    |    2 
 R/MxCompare.R                                                          |    4 
 R/MxConstraint.R                                                       |    2 
 R/MxCycleDetection.R                                                   |   11 
 R/MxData.R                                                             |   16 
 R/MxDependencies.R                                                     |    2 
 R/MxDetectCores.R                                                      |    2 
 R/MxErrorHandling.R                                                    |    2 
 R/MxExpectationGREML.R                                                 |    2 
 R/MxExpectationLISREL.R                                                |   30 
 R/MxExpectationNormal.R                                                |   88 +
 R/MxExpectationRAM.R                                                   |   25 
 R/MxFitFunctionAlgebra.R                                               |    2 
 R/MxLISRELModel.R                                                      |   27 
 R/MxMI.R                                                               |    2 
 R/MxMLObjective.R                                                      |    2 
 R/MxModel.R                                                            |   47 
 R/MxPath.R                                                             |    5 
 R/MxRAMModel.R                                                         |    2 
 R/MxRAMtoML.R                                                          |    2 
 R/MxRename.R                                                           |    1 
 R/MxRestore.R                                                          |    2 
 R/MxRowObjective.R                                                     |    2 
 R/MxRunHelperFunctions.R                                               |    2 
 R/MxSummary.R                                                          |   59 -
 R/MxSwift.R                                                            |    2 
 R/MxUnitTesting.R                                                      |    2 
 R/MxVersion.R                                                          |    2 
 R/OriginalMx.R                                                         |    2 
 R/omxGetNPSOL.R                                                        |    2 
 demo/UnivariateTwinAnalysis_MatrixRaw.R                                |    2 
 inst/CITATION                                                          |    4 
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 inst/models/passing/IntroSEM-OneFactorRaw.R                            |    2 
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 inst/models/passing/MxPath.R                                           |    5 
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 inst/models/passing/SummaryCheck.R                                     |    2 
 inst/models/passing/cycle.R                                            |    4 
 inst/models/passing/defvaralgebra.R                                    |    2 
 inst/models/passing/dependentConstraintTest.R                          |    2 
 inst/models/passing/derivFilter.R                                      |    2 
 inst/models/passing/ifa-lmp.R                                          |    4 
 inst/models/passing/lmer-1.R                                           |    2 
 inst/models/passing/redundantConstraintTest.R                          |    2 
 inst/models/passing/rfitfunc.R                                         |    2 
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 inst/models/passing/testNumericDerivWithConstraintWarning.R            |    2 
 inst/tools/testModels.R                                                |    2 
 inst/tools/updateCopyright.sh                                          |    2 
 man/MxModel-class.Rd                                                   |   24 
 man/OpenMx.Rd                                                          |    1 
 man/genericFitDependencies-MxBaseFitFunction-method.Rd                 |    4 
 man/imxCreateMatrix.Rd                                                 |   17 
 man/imxGenericModelBuilder.Rd                                          |   12 
 man/imxGetSlotDisplayNames.Rd                                          |    9 
 man/imxModelBuilder.Rd                                                 |   12 
 man/imxPPML.Test.Battery.Rd                                            |   12 
 man/imxPPML.Test.Test.Rd                                               |    9 
 man/mxAlgebra.Rd                                                       |    2 
 man/mxBootstrapEval.Rd                                                 |    2 
 man/mxCheckIdentification.Rd                                           |    2 
 man/mxComputeCheckpoint.Rd                                             |   25 
 man/mxComputeConfidenceInterval.Rd                                     |   13 
 man/mxComputeEM.Rd                                                     |   20 
 man/mxComputeGradientDescent.Rd                                        |   19 
 man/mxComputeIterate.Rd                                                |   12 
 man/mxComputeLoadContext.Rd                                            |   12 
 man/mxComputeLoadData.Rd                                               |   23 
 man/mxComputeLoop.Rd                                                   |   13 
 man/mxComputeNewtonRaphson.Rd                                          |   11 
 man/mxComputeNumericDeriv.Rd                                           |   17 
 man/mxComputeOnce.Rd                                                   |   11 
 man/mxComputeSequence.Rd                                               |    8 
 man/mxComputeStandardError.Rd                                          |    3 
 man/mxComputeTryHard.Rd                                                |   11 
 man/mxData.Rd                                                          |   26 
 man/mxDataWLS.Rd                                                       |    7 
 man/mxDescribeDataWLS.Rd                                               |    7 
 man/mxEval.Rd                                                          |    2 
 man/mxExpectationBA81.Rd                                               |   17 
 man/mxExpectationLISREL.Rd                                             |    8 
 man/mxExpectationRAM.Rd                                                |   15 
 man/mxFitFunctionML.Rd                                                 |    2 
 man/mxFitFunctionMultigroup.Rd                                         |    2 
 man/mxMatrix.Rd                                                        |    2 
 man/mxRestore.Rd                                                       |   15 
 man/mxSE.Rd                                                            |   13 
 man/mxSave.Rd                                                          |    5 
 man/omxAugmentDataWithWLSSummary.Rd                                    |   14 
 man/omxCheckEquals.Rd                                                  |    2 
 man/omxCheckIdentical.Rd                                               |    2 
 man/omxCheckSetEquals.Rd                                               |    2 
 man/omxCheckTrue.Rd                                                    |    2 
 man/omxCheckWithinPercentError.Rd                                      |    2 
 man/omxManifestModelByParameterJacobian.Rd                             |    3 
 man/omxSetParameters.Rd                                                |    2 
 src/AlgebraFunctions.h                                                 |   66 -
 src/Compute.cpp                                                        |  265 ++--
 src/Compute.h                                                          |    6 
 src/ComputeGD.cpp                                                      |   46 
 src/ComputeNM.cpp                                                      |   32 
 src/ComputeNM.h                                                        |    2 
 src/ComputeNR.cpp                                                      |    6 
 src/Connectedness.h                                                    |    6 
 src/FellnerFitFunction.cpp                                             |   10 
 src/LoadDataAPI.h                                                      |   11 
 src/MarkovExpectation.cpp                                              |    2 
 src/MarkovFF.cpp                                                       |   12 
 src/RAMInternal.h                                                      |    7 
 src/asubnp.cpp                                                         |    8 
 src/ba81quad.cpp                                                       |  467 ++------
 src/ba81quad.h                                                         |  505 ++++++--
 src/dmvnorm.cpp                                                        |   30 
 src/finiteDifferences.h                                                |    8 
 src/fitMultigroup.cpp                                                  |   10 
 src/glue.cpp                                                           |   36 
 src/matrix.cpp                                                         |   20 
 src/matrix.h                                                           |   24 
 src/omxAlgebra.cpp                                                     |   73 -
 src/omxAlgebra.h                                                       |   10 
 src/omxAlgebraFitFunction.cpp                                          |   14 
 src/omxData.cpp                                                        |  562 ++++++----
 src/omxData.h                                                          |   81 -
 src/omxDefines.h                                                       |   24 
 src/omxExpectation.cpp                                                 |   34 
 src/omxExpectation.h                                                   |    8 
 src/omxExpectationBA81.cpp                                             |   50 
 src/omxExpectationBA81.h                                               |    7 
 src/omxFIMLFitFunction.cpp                                             |   20 
 src/omxFIMLFitFunction.h                                               |    2 
 src/omxFitFunction.cpp                                                 |   35 
 src/omxFitFunction.h                                                   |    2 
 src/omxFitFunctionBA81.cpp                                             |   29 
 src/omxGREMLExpectation.cpp                                            |   18 
 src/omxGREMLExpectation.h                                              |    6 
 src/omxGREMLfitfunction.cpp                                            |   22 
 src/omxHessianCalculation.cpp                                          |    8 
 src/omxImportFrontendState.cpp                                         |   10 
 src/omxLISRELExpectation.cpp                                           |   22 
 src/omxLISRELExpectation.h                                             |    2 
 src/omxMLFitFunction.cpp                                               |   28 
 src/omxMatrix.cpp                                                      |   47 
 src/omxMatrix.h                                                        |   21 
 src/omxNLopt.cpp                                                       |    6 
 src/omxNLopt.h                                                         |    2 
 src/omxNPSOLSpecific.cpp                                               |    4 
 src/omxRAMExpectation.cpp                                              |  152 +-
 src/omxRowFitFunction.cpp                                              |   41 
 src/omxSadmvnWrapper.h                                                 |   10 
 src/omxState.cpp                                                       |   35 
 src/omxState.h                                                         |   10 
 src/omxStateSpaceExpectation.cpp                                       |    2 
 src/omxWLSFitFunction.cpp                                              |   11 
 src/path.h                                                             |   15 
 src/polynomial.h                                                       |    8 
 src/povRAM.cpp                                                         |   20 
 src/ssMLFit.cpp                                                        |   11 
 tests/testthat/test-ACELRTCI20160808.R                                 |    2 
 tests/testthat/test-ConstantSubst.R                                    |    2 
 tests/testthat/test-DataErrorDetection.R                               |    2 
 tests/testthat/test-GREML_Error_Detection.R                            |    2 
 tests/testthat/test-MatrixErrorDetection.R                             |    2 
 tests/testthat/test-ModelIdentification.R                              |    2 
 tests/testthat/test-cor.R                                              |only
 tests/testthat/test-defvar.R                                           |    2 
 tests/testthat/test-dmvnorm.R                                          |    2 
 tests/testthat/test-ifa-drm1.R                                         |    3 
 tests/testthat/test-mxBounds.R                                         |    2 
 tests/testthat/test-mxsave.R                                           |    2 
 tests/testthat/test-naAction.R                                         |only
 tests/testthat/test-simplestCI.R                                       |    2 
 tests/testthat/test-wls-binary.R                                       |only
 tools/ifa-regression                                                   |   46 
 202 files changed, 2578 insertions(+), 1869 deletions(-)

More information about OpenMx at CRAN
Permanent link

Package opusminer updated to version 0.1-1 with previous version 0.1-0 dated 2017-02-16

Title: OPUS Miner Algorithm for Filtered Top-k Association Discovery
Description: Provides a simple R interface to the OPUS Miner algorithm (implemented in C++) for finding the top-k productive, non-redundant itemsets from transaction data. The OPUS Miner algorithm uses the OPUS search algorithm to efficiently discover the key associations in transaction data, in the form of self-sufficient itemsets, using either leverage or lift. See <http://i.giwebb.com/index.php/research/association-discovery/> for more information in relation to the OPUS Miner algorithm.
Author: Geoffrey I Webb [aut, cph] (OPUS Miner algorithm and C++ implementation, http://i.giwebb.com/index.php/research/association-discovery/), Christoph Bergmeir [ctb, cre], Angus Dempster [ctb, cph] (R interface)
Maintainer: Christoph Bergmeir <christoph.bergmeir@monash.edu>

Diff between opusminer versions 0.1-0 dated 2017-02-16 and 0.1-1 dated 2020-02-03

 DESCRIPTION        |    6 +++---
 MD5                |    4 ++--
 src/opus_miner.cpp |    2 +-
 3 files changed, 6 insertions(+), 6 deletions(-)

More information about opusminer at CRAN
Permanent link

Package netCoin updated to version 1.1.24 with previous version 1.1.23 dated 2019-11-09

Title: Interactive Analytic Networks
Description: Create interactive analytic networks. It joins the data analysis power of R to obtain coincidences, co-occurrences and correlations, and the visualization libraries of 'JavaScript' in one package.
Author: Modesto Escobar <modesto@usal.es>, David Barrios <metal@usal.es>, Carlos Prieto <cprietos@usal.es>, Luis Martinez-Uribe <lmartinez@usal.es>.
Maintainer: Modesto Escobar <modesto@usal.es>

Diff between netCoin versions 1.1.23 dated 2019-11-09 and 1.1.24 dated 2020-02-03

 DESCRIPTION           |    8 
 MD5                   |   18 
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 R/netcoin.R           |   76 +--
 build/vignette.rds    |binary
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 10 files changed, 1220 insertions(+), 1216 deletions(-)

More information about netCoin at CRAN
Permanent link

Package ymlthis updated to version 0.1.2 with previous version 0.1.1 dated 2019-11-18

Title: Write 'YAML' for 'R Markdown', 'bookdown', 'blogdown', and More
Description: Write 'YAML' front matter for R Markdown and related documents. yml_*() functions write 'YAML' and use_*() functions let you write the resulting 'YAML' to your clipboard or to .yml files related to your project.
Author: Malcolm Barrett [aut, cre] (<https://orcid.org/0000-0003-0299-5825>), Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>), RStudio [cph, fnd]
Maintainer: Malcolm Barrett <malcolmbarrett@gmail.com>

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Package rstream updated to version 1.3.6 with previous version 1.3.5 dated 2017-06-21

Title: Streams of Random Numbers
Description: Unified object oriented interface for multiple independent streams of random numbers from different sources.
Author: Josef Leydold <josef.leydold@wu.ac.at>
Maintainer: Josef Leydold <josef.leydold@wu.ac.at>

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Package pubh updated to version 1.1.5 with previous version 1.1.3 dated 2019-12-10

Title: A Toolbox for Public Health and Epidemiology
Description: A toolbox for making R functions and capabilities more accessible to students and professionals from Epidemiology and Public Health related disciplines. Includes a function to report coefficients and confidence intervals from models using robust standard errors (when available), functions that expand 'ggplot2' plots and functions relevant for introductory papers in Epidemiology or Public Health. Please note that use of the provided data sets is for educational purposes only.
Author: Josie Athens [aut, cre], Frank Harell [ctb], John Fox [ctb], R-Core [ctb]
Maintainer: Josie Athens <josie.athens@otago.ac.nz>

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Package enviGCMS updated to version 0.6.0 with previous version 0.5.7 dated 2019-08-22

Title: GC/LC-MS Data Analysis for Environmental Science
Description: Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data Analysis for Environmental Science. This package covered topics such molecular isotope ratio, matrix effects and Short-Chain Chlorinated Paraffins analysis etc. in environmental analysis.
Author: Miao YU [aut, cre] (<https://orcid.org/0000-0002-2804-6014>), Thanh Wang [ctb] (<https://orcid.org/0000-0002-5729-1908>)
Maintainer: Miao YU <yufreecas@gmail.com>

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Package shinySIR updated to version 0.1.1 with previous version 0.1.0 dated 2020-01-20

Title: Interactive Plotting for Mathematical Models of Infectious Disease Spread
Description: Provides interactive plotting for mathematical models of infectious disease spread. Users can choose from a variety of common built-in ordinary differential equation (ODE) models (such as the SIR, SIRS, and SIS models), or create their own. This latter flexibility allows 'shinySIR' to be applied to simple ODEs from any discipline. The package is a useful teaching tool as students can visualize how changing different parameters can impact model dynamics, with minimal knowledge of coding in R. The built-in models are inspired by those featured in Keeling and Rohani (2008) <doi:10.2307/j.ctvcm4gk0> and Bjornstad (2018) <doi:10.1007/978-3-319-97487-3>.
Author: Sinead E. Morris [aut, cre] (<https://orcid.org/0000-0001-8626-1698>), Ottar N. Bjornstad [ctb]
Maintainer: Sinead E. Morris <sinead.morris@columbia.edu>

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Package rivernet updated to version 1.2.1 with previous version 1.2 dated 2019-03-08

Title: Read, Analyze and Plot River Networks
Description: Functions for reading, analysing and plotting river networks. For this package, river networks consist of sections and nodes with associated attributes, e.g. to characterise their morphological, chemical and biological state. The package provides functions to read this data from text files, to analyse the network structure and network paths and regions consisting of sections and nodes that fulfill prescribed criteria, and to plot the river network and associated properties.
Author: Peter Reichert
Maintainer: Peter Reichert <peter.reichert@eawag.ch>

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Package plsVarSel updated to version 0.9.5 with previous version 0.9.4 dated 2017-12-15

Title: Variable Selection in Partial Least Squares
Description: Interfaces and methods for variable selection in Partial Least Squares. The methods include filter methods, wrapper methods and embedded methods. Both regression and classification is supported.
Author: Kristian Hovde Liland, Tahir Mehmood, Solve Sæbø
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>

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Package glmmTMB updated to version 1.0.0 with previous version 0.2.3 dated 2019-01-11

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: Arni Magnusson [aut] (<https://orcid.org/0000-0003-2769-6741>), Hans Skaug [aut], Anders Nielsen [aut] (<https://orcid.org/0000-0001-9683-9262>), Casper Berg [aut] (<https://orcid.org/0000-0002-3812-5269>), Kasper Kristensen [aut], Martin Maechler [aut] (<https://orcid.org/0000-0002-8685-9910>), Koen van Bentham [aut], Ben Bolker [aut] (<https://orcid.org/0000-0002-2127-0443>), Nafis Sadat [ctb] (<https://orcid.org/0000-0001-5715-616X>), Daniel Lüdecke [ctb] (<https://orcid.org/0000-0002-8895-3206>), Russ Lenth [ctb], Mollie Brooks [aut, cre] (<https://orcid.org/0000-0001-6963-8326>)
Maintainer: Mollie Brooks <mollieebrooks@gmail.com>

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Package ghyp updated to version 1.5.9 with previous version 1.5.8 dated 2020-01-23

Title: Generalized Hyperbolic Distribution and Its Special Cases
Description: Detailed functionality for working with the univariate and multivariate Generalized Hyperbolic distribution and its special cases (Hyperbolic (hyp), Normal Inverse Gaussian (NIG), Variance Gamma (VG), skewed Student-t and Gaussian distribution). Especially, it contains fitting procedures, an AIC-based model selection routine, and functions for the computation of density, quantile, probability, random variates, expected shortfall and some portfolio optimization and plotting routines as well as the likelihood ratio test. In addition, it contains the Generalized Inverse Gaussian distribution. See Chapter 3 of A. J. McNeil, R. Frey, and P. Embrechts. Quantitative risk management: Concepts, techniques and tools. Princeton University Press, Princeton (2005).
Author: David Luethi, Wolfgang Breymann
Maintainer: Damien Challet <damien.challet@gmail.com>

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Package FSA updated to version 0.8.27 with previous version 0.8.26 dated 2019-11-22

Title: Simple Fisheries Stock Assessment Methods
Description: A variety of simple fish stock assessment methods. Detailed vignettes are available on the fishR website <http://derekogle.com/fishR/>.
Author: Derek Ogle [aut, cre] (<https://orcid.org/0000-0002-0370-9299>), Powell Wheeler [aut], Alexis Dinno [aut] (Provided base functionality of dunnTest())
Maintainer: Derek Ogle <derek@derekogle.com>

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Package entrymodels updated to version 0.2.0 with previous version 0.1.0 dated 2019-11-25

Title: Estimate Entry Models
Description: Tools for measuring empirically the effects of entry in concentrated markets, based in Bresnahan and Reiss (1991) <https://www.jstor.org/stable/2937655>.
Author: Guilherme Jardim [aut, cre], Arthur Bragança [ctb], Pedro Fernandes [ctb]
Maintainer: Guilherme Jardim <gnjardim1@gmail.com>

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Package Ecfun updated to version 0.2-2 with previous version 0.2-0 dated 2019-02-25

Title: Functions for Ecdat
Description: Functions to update data sets in Ecdat and to create, manipulate, plot, and analyze those and similar data sets.
Author: Spencer Graves <spencer.graves@effectivedefense.org>
Maintainer: Spencer Graves <spencer.graves@effectivedefense.org>

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Package doBy updated to version 4.6-4.1 with previous version 4.6-3 dated 2019-10-23

Title: Groupwise Statistics, LSmeans, Linear Contrasts, Utilities
Description: Contains: 1) Facilities for working with grouped data: 'do' something to data stratified 'by' some variables. 2) LSmeans (least-squares means), general linear contrasts. 3) Miscellaneous other utilities.
Author: Søren Højsgaard <sorenh@math.aau.dk> and Ulrich Halekoh <uhalekoh@health.sdu.dk>
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>

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Package DAMisc updated to version 1.5.1 with previous version 1.5 dated 2019-06-25

Title: Dave Armstrong's Miscellaneous Functions
Description: Miscellaneous set of functions I use in my teaching either at the University of Western Ontario or the Inter-university Consortium for Political and Social Research (ICPSR) Summer Program in Quantitative Methods. Broadly, the functions help with presentation and interpretation of LMs and GLMs, but also implement some new tools like Alternating Least Squares Optimal Scaling for dependent variables, a Bayesian analog to the ALSOS algorithm. There are also tools to help understand interactions in both LMs and binary GLMs.
Author: Dave Armstrong [aut, cre]
Maintainer: Dave Armstrong <dave@quantoid.net>

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Package baseline updated to version 1.2-3 with previous version 1.2-2 dated 2019-11-05

Title: Baseline Correction of Spectra
Description: Collection of baseline correction algorithms, along with a framework and a GUI for optimising baseline algorithm parameters. Typical use of the package is for removing background effects from spectra originating from various types of spectroscopy and spectrometry, possibly optimizing this with regard to regression or classification results. Correction methods include polynomial fitting, weighted local smoothers and many more.
Author: Kristian Hovde Liland [aut, cre], Bjørn-Helge Mevik [aut], Roberto Canteri [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>

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Package telefit updated to version 1.0.3 with previous version 1.0.2 dated 2019-12-17

Title: Estimation and Prediction for Remote Effects Spatial Process Models
Description: Implementation of the remote effects spatial process (RESP) model for teleconnection. The RESP model is a geostatistical model that allows a spatially-referenced variable (like average precipitation) to be influenced by covariates defined on a remote domain (like sea surface temperatures). The RESP model is introduced in Hewitt et al. (2018) <doi:10.1002/env.2523>. Sample code for working with the RESP model is available at <https://jmhewitt.github.io/research/resp_example>. This material is based upon work supported by the National Science Foundation under grant number AGS 1419558. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.
Author: Joshua Hewitt
Maintainer: Joshua Hewitt <joshua.hewitt@duke.edu>

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Package protViz updated to version 0.6.0 with previous version 0.5.1 dated 2019-11-18

Title: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics
Description: Helps with quality checks, visualizations and analysis of mass spectrometry data, coming from proteomics experiments. The package is developed, tested and used at the Functional Genomics Center Zurich <https://fgcz.ch>. We use this package mainly for prototyping, teaching, and having fun with proteomics data. But it can also be used to do data analysis for small scale data sets.
Author: Christian Panse [aut, cre] (<https://orcid.org/0000-0003-1975-3064>), Jonas Grossmann [aut] (<https://orcid.org/0000-0002-6899-9020>), Simon Barkow-Oesterreicher [ctb]
Maintainer: Christian Panse <cp@fgcz.ethz.ch>

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Package moko updated to version 1.0.2 with previous version 1.0.1 dated 2017-07-08

Title: Multi-Objective Kriging Optimization
Description: Multi-Objective optimization based on the Kriging metamodel. Important functions: mkm() (builder for the multiobjective models), MVPF() (sequential minimizator using variance reduction), MEGO() (generalization of ParEgo) and HEGO() (minimizator using the expected hypervolume improvement). References are Passos and Luersen (2018) <doi:10.1590/1679-78254324>.
Author: Adriano Passos [aut, cre], Marco Luersen [ctb]
Maintainer: Adriano Passos <adriano.utfpr@gmail.com>

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Package LS2Wstat updated to version 2.1-2 with previous version 2.1-1 dated 2018-07-18

Title: A Multiscale Test of Spatial Stationarity for LS2W Processes
Description: Wavelet-based methods for testing stationarity and quadtree segmenting of images, see Taylor et al (2014) <doi:10.1080/00401706.2013.823890>.
Author: Sarah Taylor [aut], Matt Nunes [aut, cre], Idris Eckley [ctb, ths]
Maintainer: Matt Nunes <nunesrpackages@gmail.com>

Diff between LS2Wstat versions 2.1-1 dated 2018-07-18 and 2.1-2 dated 2020-02-03

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Package xnet updated to version 0.1.11 with previous version 0.1.10 dated 2020-01-09

Title: Two-Step Kernel Ridge Regression for Network Predictions
Description: Fit a two-step kernel ridge regression model for predicting edges in networks, and carry out cross-validation using shortcuts for swift and accurate performance assessment (Stock et al, 2018 <doi:10.1093/bib/bby095> ).
Author: Joris Meys [cre, aut], Michiel Stock [aut]
Maintainer: Joris Meys <Joris.Meys@UGent.be>

Diff between xnet versions 0.1.10 dated 2020-01-09 and 0.1.11 dated 2020-02-03

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Package qgam updated to version 1.3.2 with previous version 1.3.1 dated 2020-02-01

Title: Smooth Additive Quantile Regression Models
Description: Smooth additive quantile regression models, fitted using the methods of Fasiolo et al. (2017) <arXiv:1707.03307>. Differently from 'quantreg', the smoothing parameters are estimated automatically by marginal loss minimization, while the regression coefficients are estimated using either PIRLS or Newton algorithm. The learning rate is determined so that the Bayesian credible intervals of the estimated effects have approximately the correct coverage. The main function is qgam() which is similar to gam() in 'mgcv', but fits non-parametric quantile regression models.
Author: Matteo Fasiolo [aut, cre], Simon N. Wood [ctb], Margaux Zaffran [ctb], Yannig Goude [ctb], Raphael Nedellec [ctb]
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>

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Package LCMCR updated to version 0.4.11 with previous version 0.4.3 dated 2017-07-08

Title: Bayesian Non-Parametric Latent-Class Capture-Recapture
Description: Bayesian population size estimation using non parametric latent-class models.
Author: Daniel Manrique-Vallier
Maintainer: Daniel Manrique-Vallier <dmanriqu@indiana.edu>

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Package gambin updated to version 2.4.3 with previous version 2.4.1 dated 2019-03-03

Title: Fit the Gambin Model to Species Abundance Distributions
Description: Fits unimodal and multimodal gambin distributions to species-abundance distributions from ecological data, as in in Matthews et al. (2014) <DOI:10.1111/ecog.00861>. 'gambin' is short for 'gamma-binomial'. The main function is fit_abundances(), which estimates the 'alpha' parameter(s) of the gambin distribution using maximum likelihood. Functions are also provided to generate the gambin distribution and for calculating likelihood statistics.
Author: Thomas Matthews [aut, cre], Michael Krabbe Borregaard [aut], Karl Ugland [aut], Colin Gillespie [aut]
Maintainer: Thomas Matthews <txm676@gmail.com>

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Package DGLMExtPois updated to version 0.1.1 with previous version 0.1.0 dated 2019-08-01

Title: Double Generalized Linear Models Extending Poisson Regression
Description: Model estimation, dispersion testing and diagnosis of hyper-Poisson Saez-Castillo, A.J. and Conde-Sanchez, A. (2013) <doi:10.1016/j.csda.2012.12.009> and Conway-Maxwell-Poisson Huang, A. (2017) <doi:10.1177/1471082X17697749> regression models.
Author: Antonio Jose Saez-Castillo [aut], Antonio Conde-Sanchez [aut], Francisco Martinez [aut, cre]
Maintainer: Francisco Martinez <fmartin@ujaen.es>

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Package coil updated to version 1.2.1 with previous version 1.1.0 dated 2019-12-05

Title: Contextualization and Evaluation of COI-5P Barcode Data
Description: Designed for the cleaning, contextualization and assessment of cytochrome c oxidase I DNA barcode data (COI-5P, or the five prime portion of COI). It contains functions for placing COI-5P barcode sequences into a common reading frame, translating DNA sequences to amino acids and for assessing the likelihood that a given barcode sequence includes an insertion or deletion error. The error assessment relies on the comparison of input sequences against nucleotide and amino acid profile hidden Markov models (PHMMs) (for details see Durbin et al. 1998, ISBN: 9780521629713) trained on a taxonomically diverse set of reference sequences. The functions are provided as a complete pipeline and are also available individually for efficient and targeted analysis of barcode data.
Author: Cameron M. Nugent
Maintainer: Cameron M. Nugent <nugentc@uoguelph.ca>

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Package adehabitatHR updated to version 0.4.18 with previous version 0.4.16 dated 2019-04-07

Title: Home Range Estimation
Description: A collection of tools for the estimation of animals home range.
Author: Clement Calenge, contributions from Scott Fortmann-Roe
Maintainer: Clement Calenge <clement.calenge@ofb.gouv.fr>

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Package rv updated to version 2.3.4 with previous version 2.3.3 dated 2019-01-08

Title: Simulation-Based Random Variable Objects
Description: Implements a simulation-based random variable class and a suite of methods for extracting parts of random vectors, calculating extremes of random vectors, and generating random vectors under a variety of distributions following Kerman and Gelman (2007) <doi:10.1007/s11222-007-9020-4>.
Author: Jouni Kerman [aut], Joseph Stachelek [ctb, cre]
Maintainer: Joseph Stachelek <stachel2@msu.edu>

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Package labelled updated to version 2.2.2 with previous version 2.2.1 dated 2019-05-26

Title: Manipulating Labelled Data
Description: Work with labelled data imported from 'SPSS' or 'Stata' with 'haven' or 'foreign'. This package provides useful functions to deal with "haven_labelled" and "haven_labelled_spss" classes introduced by 'haven' package.
Author: Joseph Larmarange [aut, cre] (<https://orcid.org/0000-0001-7097-700X>), Daniel Ludecke [ctb], Hadley Wickham [ctb], Michal Bojanowski [ctb], François Briatte [ctb]
Maintainer: Joseph Larmarange <joseph@larmarange.net>

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Package Umpire updated to version 1.3.9 with previous version 1.3.8 dated 2020-01-07

Title: Simulating Realistic Gene Expression Data
Description: The Ultimate Microrray Prediction, Reality and Inference Engine (UMPIRE) is a package to facilitate the simulation of realistic microarray data sets with link to associate outcomes. See Zhang and Coombes (2012) <doi:10.1186/1471-2105-13-S13-S1>.
Author: Kevin R. Coombes, Jiexin Zhang
Maintainer: Kevin R. Coombes <krc@silicovore.com>

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Package survPen updated to version 1.3.0 with previous version 1.2.0 dated 2019-08-29

Title: Multidimensional Penalized Splines for Survival and Net Survival Models
Description: Fits hazard and excess hazard models with multidimensional penalized splines allowing for time-dependent effects, non-linear effects and interactions between several continuous covariates. In survival and net survival analysis, in addition to modelling the effect of time (via the baseline hazard), one has often to deal with several continuous covariates and model their functional forms, their time-dependent effects, and their interactions. Model specification becomes therefore a complex problem and penalized regression splines represent an appealing solution to that problem as splines offer the required flexibility while penalization limits overfitting issues. Current implementations of penalized survival models can be slow or unstable and sometimes lack some key features like taking into account expected mortality to provide net survival and excess hazard estimates. In contrast, survPen provides an automated, fast, and stable implementation (thanks to explicit calculation of the derivatives of the likelihood) and offers a unified framework for multidimensional penalized hazard and excess hazard models. survPen may be of interest to those who 1) analyse any kind of time-to-event data: mortality, disease relapse, machinery breakdown, unemployment, etc 2) wish to describe the associated hazard and to understand which predictors impact its dynamics. See Fauvernier et al. (2019a) <doi:10.21105/joss.01434> for an overview of the package and Fauvernier et al. (2019b) <doi:10.1111/rssc.12368> for the method.
Author: Mathieu Fauvernier [aut, cre], Laurent Roche [aut], Laurent Remontet [aut], Zoe Uhry [ctb], Nadine Bossard [ctb]
Maintainer: Mathieu Fauvernier <mathieu.fauvernier@gmail.com>

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Package PMA updated to version 1.2.1 with previous version 1.2 dated 2020-01-16

Title: Penalized Multivariate Analysis
Description: Performs Penalized Multivariate Analysis: a penalized matrix decomposition, sparse principal components analysis, and sparse canonical correlation analysis, described in Witten, Tibshirani and Hastie (2009) <doi:10.1093/biostatistics/kxp008> and Witten and Tibshirani (2009) Extensions of sparse canonical correlation analysis, with applications to genomic data <doi:10.2202/1544-6115.1470>.
Author: Daniela Witten and Rob Tibshirani
Maintainer: Rob Tibshirani <tibs@stanford.edu>

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Package pim updated to version 2.0.2 with previous version 2.0.1 dated 2017-04-29

Title: Fit Probabilistic Index Models
Description: Fit a probabilistic index model as described in Thas et al, 2012: <doi:10.1111/j.1467-9868.2011.01020.x>. The interface to the modeling function has changed in this new version. The old version is still available at R-Forge.
Author: Joris Meys [aut, cre], Jan De Neve [aut], Nick Sabbe [aut], Gustavo Guimaraes de Castro Amorim [aut]
Maintainer: Joris Meys <Joris.Meys@UGent.be>

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Package MatchLinReg updated to version 0.7.3 with previous version 0.7.0 dated 2015-07-12

Title: Combining Matching and Linear Regression for Causal Inference
Description: Core functions as well as diagnostic and calibration tools for combining matching and linear regression for causal inference in observational studies.
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani <alireza.s.mahani@gmail.com>

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Package gamlss.add updated to version 5.1-6 with previous version 5.1-5 dated 2020-01-19

Title: Extra Additive Terms for Generalized Additive Models for Location Scale and Shape
Description: Interface for extra smooth functions including tensor products, neural networks and decision trees.
Author: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>, Bob Rigby, Vlasios Voudouris, Daniil Kiose
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>

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Package DivE updated to version 1.2 with previous version 1.1 dated 2019-09-19

Title: Diversity Estimator
Description: Contains functions for the 'DivE' estimator <doi:10.1371/journal.pcbi.1003646>. The 'DivE' estimator is a heuristic approach to estimate the number of classes or the number of species (species richness) in a population.
Author: Daniel J. Laydon, Aaron Sim, Charles R.M. Bangham, Becca Asquith
Maintainer: Daniel Laydon <d.laydon@imperial.ac.uk>

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Package dispRity updated to version 1.3.5 with previous version 1.3.3 dated 2019-12-06

Title: Measuring Disparity
Description: A modular package for measuring disparity from multidimensional matrices. Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics (Guillerme (2018) <doi:10.1111/2041-210X.13022>). The package also provides functions for looking at disparity in a serial way (e.g. disparity through time - Guillerme and Cooper (2018) <doi:10.1111/pala.12364>) or per groups as well as visualising the results. Finally, this package provides several basic statistical tests for disparity analysis.
Author: Thomas Guillerme [aut, cre, cph], Mark N Puttick [aut, cph]
Maintainer: Thomas Guillerme <guillert@tcd.ie>

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Package subgroup.discovery updated to version 0.3.0 with previous version 0.2.1 dated 2019-06-21

Title: Subgroup Discovery and Bump Hunting
Description: Developed to assist in discovering interesting subgroups in high-dimensional data. The PRIM implementation is based on the 1998 paper "Bump hunting in high-dimensional data" by Jerome H. Friedman and Nicholas I. Fisher <doi:10.1023/A:1008894516817>. PRIM involves finding a set of "rules" which combined imply unusually large values of some other target variable. Specifically one tries to find a set of sub regions in which the target variable is substantially larger than overall mean. The objective of bump hunting in general is to find regions in the input (attribute/feature) space with relatively high values for the target variable. The regions are described by simple rules of the type if: condition-1 and ... and condition-n then: estimated target value. Given the data (or a subset of the data), the goal is to produce a box B within which the target mean is as large as possible.
Author: Jurian Baas [aut, cre, cph], Ad Feelders [ctb]
Maintainer: Jurian Baas <j.baas@uu.nl>

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Package RMySQL updated to version 0.10.19 with previous version 0.10.18 dated 2019-12-14

Title: Database Interface and 'MySQL' Driver for R
Description: Legacy 'DBI' interface to 'MySQL' / 'MariaDB' based on old code ported from S-PLUS. A modern 'MySQL' client based on 'Rcpp' is available from the 'RMariaDB' package.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>), David James [aut], Saikat DebRoy [aut], Hadley Wickham [aut], Jeffrey Horner [aut], RStudio [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package Polychrome updated to version 1.2.4 with previous version 1.2.3 dated 2019-08-01

Title: Qualitative Palettes with Many Colors
Description: Tools for creating, viewing, and assessing qualitative palettes with many (20-30 or more) colors. See Coombes and colleagues (2019) <doi:10.18637/jss.v090.c01>.
Author: Kevin R. Coombes, Guy Brock
Maintainer: Kevin R. Coombes <krc@silicovore.com>

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Package multicolor updated to version 0.1.4 with previous version 0.1.3 dated 2019-04-13

Title: Add Multiple Colors to your Console & RMarkdown Output
Description: Add multiple colors to text that is printed to the console.
Author: Amanda Dobbyn [aut, cre], Hernando Cortina [aut] (<https://orcid.org/0000-0001-6790-4870>)
Maintainer: Amanda Dobbyn <amanda.e.dobbyn@gmail.com>

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Package hexbin updated to version 1.28.1 with previous version 1.28.0 dated 2019-11-11

Title: Hexagonal Binning Routines
Description: Binning and plotting functions for hexagonal bins.
Author: Dan Carr <dcarr@voxel.galaxy.gmu.edu>, ported by Nicholas Lewin-Koh and Martin Maechler <maechler@stat.math.ethz.ch>, contains copies of lattice functions written by Deepayan Sarkar <deepayan.sarkar@r-project.org>
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

Diff between hexbin versions 1.28.0 dated 2019-11-11 and 1.28.1 dated 2020-02-03

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Package desctable updated to version 0.1.7 with previous version 0.1.6 dated 2019-04-01

Title: Produce Descriptive and Comparative Tables Easily
Description: Easily create descriptive and comparative tables. It makes use and integrates directly with the tidyverse family of packages, and pipes. Tables are produced as data frames/lists of data frames for easy manipulation after creation, and ready to be saved as csv, or piped to DT::datatable() or pander::pander() to integrate into reports.
Author: Maxime Wack [aut, cre], Adrien Boukobza [aut]
Maintainer: Maxime Wack <maximewack@free.fr>

Diff between desctable versions 0.1.6 dated 2019-04-01 and 0.1.7 dated 2020-02-03

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Package vamc updated to version 0.2.0 with previous version 0.1.1 dated 2020-01-20

Title: A Monte Carlo Valuation Framework for Variable Annuities
Description: Implementation of a Monte Carlo simulation engine for valuing synthetic portfolios of variable annuities, which reflect realistic features of common annuity contracts in practice. It aims to facilitate the development and dissemination of research related to the efficient valuation of a portfolio of large variable annuities. The main valuation methodology was proposed by Gan (2017) <doi:10.1515/demo-2017-0021>.
Author: Hengxin Li [aut, cph], Ben Feng [aut, cph], Mingyi Jiang [aut, cph, cre], GuoJun Gan [ctb]
Maintainer: Mingyi Jiang <m64jiang@uwaterloo.ca>

Diff between vamc versions 0.1.1 dated 2020-01-20 and 0.2.0 dated 2020-02-03

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Package shinyjqui updated to version 0.3.3 with previous version 0.3.2 dated 2018-07-25

Title: 'jQuery UI' Interactions and Effects for Shiny
Description: An extension to shiny that brings interactions and animation effects from 'jQuery UI' library.
Author: Yang Tang [aut, cre]
Maintainer: Yang Tang <tang_yang@outlook.com>

Diff between shinyjqui versions 0.3.2 dated 2018-07-25 and 0.3.3 dated 2020-02-03

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Package sdm updated to version 1.0-82 with previous version 1.0-81 dated 2020-01-17

Title: Species Distribution Modelling
Description: An extensible framework for developing species distribution models using individual and community-based approaches, generate ensembles of models, evaluate the models, and predict species potential distributions in space and time. For more information, please check the following paper: Naimi, B., Araujo, M.B. (2016) <doi:10.1111/ecog.01881>.
Author: Babak Naimi, Miguel B. Araujo
Maintainer: Babak Naimi <naimi.b@gmail.com>

Diff between sdm versions 1.0-81 dated 2020-01-17 and 1.0-82 dated 2020-02-03

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Package ribd updated to version 1.0.1 with previous version 1.0.0 dated 2019-11-01

Title: Pedigree-based Relatedness Coefficients
Description: Recursive algorithms for computing various relatedness coefficients, including pairwise kinship, kappa and identity coefficients. Both autosomal and X-linked coefficients are computed. Founders are allowed to be inbred. In addition to the standard pairwise coefficients, ribd also computes a range of lesser-known coefficients, including generalised kinship coefficients (Karigl (1981) <doi:10.1111/j.1469-1809.1981.tb00341.x>; Weeks and Lange (1988) <https:www.ncbi.nlm.nih.gov/pmc/articles/PMC1715269>), two-locus coefficients (Thompson (1988) <doi:10.1093/imammb/5.4.261>) and multi-person coefficients. This package is part of the ped suite, a collection of packages for pedigree analysis with 'pedtools' as the core package for creating and handling pedigree objects.
Author: Magnus Dehli Vigeland [aut, cre] (<https://orcid.org/0000-0002-9134-4962>)
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>

Diff between ribd versions 1.0.0 dated 2019-11-01 and 1.0.1 dated 2020-02-03

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Package ProTrackR updated to version 0.3.7 with previous version 0.3.6 dated 2019-02-06

Title: Manipulate and Play 'ProTracker' Modules
Description: 'ProTracker' is a popular music tracker to sequence music on a Commodore Amiga machine. This package offers the opportunity to import, export, manipulate and play 'ProTracker' module files. Even though the file format could be considered archaic, it still remains popular to this date. This package intends to contribute to this popularity and therewith keeping the legacy of 'ProTracker' and the Commodore Amiga alive.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>

Diff between ProTrackR versions 0.3.6 dated 2019-02-06 and 0.3.7 dated 2020-02-03

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Permanent link

Package pedtools updated to version 0.9.2 with previous version 0.9.1 dated 2019-12-02

Title: Creating and Working with Pedigrees and Marker Data
Description: A lightweight, but comprehensive collection of tools for creating, manipulating and visualising pedigrees and genetic marker data. Pedigrees can be read from text files or created on the fly with built-in functions. A range of utilities enable modifications like adding or removing individuals, breaking loops, and merging pedigrees. Pedigree plots are produced by wrapping the plotting functionality of the 'kinship2' package.
Author: Magnus Dehli Vigeland [aut, cre] (<https://orcid.org/0000-0002-9134-4962>)
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>

Diff between pedtools versions 0.9.1 dated 2019-12-02 and 0.9.2 dated 2020-02-03

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Package gamlss.dist updated to version 5.1-6 with previous version 5.1-5 dated 2019-10-04

Title: Distributions for Generalized Additive Models for Location Scale and Shape
Description: A set of distributions which can be used for modelling the response variables in Generalized Additive Models for Location Scale and Shape, Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The distributions can be continuous, discrete or mixed distributions. Extra distributions can be created, by transforming, any continuous distribution defined on the real line, to a distribution defined on ranges 0 to infinity or 0 to 1, by using a ''log'' or a ''logit' transformation respectively.
Author: Mikis Stasinopoulos [aut, cre, cph], Robert Rigby [aut], Calliope Akantziliotou [ctb], Vlasios Voudouris [ctb], Gillian Heller [ctb], Fernanda De Bastiani [ctb], Raydonal Ospina [ctb], Nicoletta Motpan [ctb], Fiona McElduff [ctb], Majid Djennad [ctb], Marco Enea [ctb], Alexios Ghalanos [ctb], Christos Argyropoulos [ctb], Almond Stocker [ctb], Jens Lichter [ctb], Stanislaus Stadlmann [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>

Diff between gamlss.dist versions 5.1-5 dated 2019-10-04 and 5.1-6 dated 2020-02-03

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Package gamlss updated to version 5.1-6 with previous version 5.1-5 dated 2019-10-06

Title: Generalised Additive Models for Location Scale and Shape
Description: Functions for fitting the Generalized Additive Models for Location Scale and Shape introduced by Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The models use a distributional regression approach where all the parameters of the conditional distribution of the response variable are modelled using explanatory variables.
Author: Mikis Stasinopoulos [aut, cre, cph], Bob Rigby [aut], Vlasios Voudouris [ctb], Calliope Akantziliotou [ctb], Marco Enea [ctb], Daniil Kiose [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>

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Package gnm updated to version 1.1-1 with previous version 1.1-0 dated 2018-06-21

Title: Generalized Nonlinear Models
Description: Functions to specify and fit generalized nonlinear models, including models with multiplicative interaction terms such as the UNIDIFF model from sociology and the AMMI model from crop science, and many others. Over-parameterized representations of models are used throughout; functions are provided for inference on estimable parameter combinations, as well as standard methods for diagnostics etc.
Author: Heather Turner [aut, cre] (<https://orcid.org/0000-0002-1256-3375>), David Firth [aut] (<https://orcid.org/0000-0003-0302-2312>), Brian Ripley [ctb], Bill Venables [ctb], Douglas M. Bates [ctb], Martin Maechler [ctb] (<https://orcid.org/0000-0002-8685-9910>)
Maintainer: Heather Turner <ht@heatherturner.net>

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Package DatabionicSwarm updated to version 1.1.3 with previous version 1.1.2 dated 2019-12-11

Title: Swarm Intelligence for Self-Organized Clustering
Description: Algorithms implementing populations of agents that interact with one another and sense their environment may exhibit emergent behavior such as self-organization and swarm intelligence. Here, a swarm system called Databionic swarm (DBS) is introduced which was published in Thrun, M.C., Ultsch A.: "Swarm Intelligence for Self-Organized Clustering" (2020), Artificial Intelligence, <DOI:10.1016/j.artint.2020.103237>. DBS is able to adapt itself to structures of high-dimensional data such as natural clusters characterized by distance and/or density based structures in the data space. The first module is the parameter-free projection method called Pswarm (Pswarm()), which exploits the concepts of self-organization and emergence, game theory, swarm intelligence and symmetry considerations. The second module is the parameter-free high-dimensional data visualization technique, which generates projected points on the topographic map with hypsometric tints defined by the generalized U-matrix (GeneratePswarmVisualization()). The third module is the clustering method itself with non-critical parameters (DBSclustering()). Clustering can be verified by the visualization and vice versa. The term DBS refers to the method as a whole. It enables even a non-professional in the field of data mining to apply its algorithms for visualization and/or clustering to data sets with completely different structures drawn from diverse research fields. The comparison to common projection methods can be found in the book of Thrun, M.C.: "Projection Based Clustering through Self-Organization and Swarm Intelligence" (2018) <DOI:10.1007/978-3-658-20540-9>. A comparison to 26 common clustering algorithms on 15 datasets is presented on the website.
Author: Michael Thrun [aut, cre, cph]
Maintainer: Michael Thrun <m.thrun@gmx.net>

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Package BradleyTerry2 updated to version 1.1-2 with previous version 1.1-0 dated 2019-05-11

Title: Bradley-Terry Models
Description: Specify and fit the Bradley-Terry model, including structured versions in which the parameters are related to explanatory variables through a linear predictor and versions with contest-specific effects, such as a home advantage.
Author: Heather Turner [aut, cre], David Firth [aut]
Maintainer: Heather Turner <ht@heatherturner.net>

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Package EDR updated to version 0.6-7 with previous version 0.6-6 dated 2016-09-14

Title: Estimation of the Effective Dimension Reduction ('EDR') Space
Description: The library contains R-functions to estimate the effective dimension reduction space in 'multi-index' regression models.
Author: Joerg Polzehl <joerg.polzehl@wias-berlin.de>
Maintainer: Joerg Polzehl <joerg.polzehl@wias-berlin.de>

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Package ProjectionBasedClustering updated to version 1.1.0 with previous version 1.0.7 dated 2018-05-06

Title: Projection Based Clustering
Description: A clustering approach applicable to every projection method is proposed here. The two-dimensional scatter plot of any projection method can construct a topographic map which displays unapparent data structures by using distance and density information of the data. The generalized U*-matrix renders this visualization in the form of a topographic map, which can be used to automatically define the clusters of high-dimensional data. The whole system is the generalization of on an idea from the book "Projection-Based Clustering through Self-Organization and Swarm Intelligence" <DOI:10.1007/978-3-658-20540-9>. Selecting the correct projection method will result in a visualization in which mountains surround each cluster. The number of clusters can be determined by counting valleys on the topographic map. Most projection methods are wrappers for already available methods in R. By contrast, the neighbor retrieval visualizer (NeRV) is based on C++ source code of the 'dredviz' software package, and the Curvilinear Component Analysis (CCA) is translated from 'MATLAB' ('SOM Toolbox' 2.0) to R.
Author: Michael Thrun [aut, cre, cph], Florian Lerch [aut], Felix Pape [aut], Tim Schreier [aut], Luis Winckelmann [aut], Kristian Nybo [cph], Jarkko Venna [cph]
Maintainer: Michael Thrun <m.thrun@gmx.net>

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Package blorr updated to version 0.2.2 with previous version 0.2.1 dated 2019-03-12

Title: Tools for Developing Binary Logistic Regression Models
Description: Tools designed to make it easier for beginner and intermediate users to build and validate binary logistic regression models. Includes bivariate analysis, comprehensive regression output, model fit statistics, variable selection procedures, model validation techniques and a 'shiny' app for interactive model building.
Author: Aravind Hebbali [aut, cre] (<https://orcid.org/0000-0001-9220-9669>)
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>

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Package bbmle updated to version 1.0.23.1 with previous version 1.0.22 dated 2019-12-19

Title: Tools for General Maximum Likelihood Estimation
Description: Methods and functions for fitting maximum likelihood models in R.
Author: Ben Bolker [aut, cre], R Development Core Team [aut], Iago Giné-Vázquez [ctb]
Maintainer: Ben Bolker <bolker@mcmaster.ca>

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Package mapproj updated to version 1.2.7 with previous version 1.2.6 dated 2018-03-29

Title: Map Projections
Description: Converts latitude/longitude into projected coordinates.
Author: Doug McIlroy. Packaged for R by Ray Brownrigg and Thomas P Minka, transition to Plan 9 codebase by Roger Bivand.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>

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Package GMMBoost updated to version 1.1.3 with previous version 1.1.2 dated 2013-11-22

Title: Likelihood-Based Boosting for Generalized Mixed Models
Description: Likelihood-based boosting approaches for generalized mixed models are provided.
Author: Andreas Groll
Maintainer: Andreas Groll <groll@mathematik.uni-muenchen.de>

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Package ConnMatTools updated to version 0.3.5 with previous version 0.3.3 dated 2016-11-02

Title: Tools for Working with Connectivity Data
Description: Collects several different methods for analyzing and working with connectivity data in R. Though primarily oriented towards marine larval dispersal, many of the methods are general and useful for terrestrial systems as well.
Author: David M. Kaplan <dmkaplan2000@gmail.com> [cre,aut], Marco Andrello <marco.andrello@gmail.com> [ctb]
Maintainer: David M. Kaplan <dmkaplan2000@gmail.com>

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More information about ConnMatTools at CRAN
Permanent link

Package vote updated to version 1.2-1 with previous version 1.2-0 dated 2020-01-30

Title: Election Vote Counting
Description: Counting election votes and determining election results by different methods, including the single transferable vote (ranked choice), approval, score and plurality methods.
Author: Hana Sevcikova, Bernard Silverman, Adrian Raftery
Maintainer: Hana Sevcikova<hanas@uw.edu>

Diff between vote versions 1.2-0 dated 2020-01-30 and 1.2-1 dated 2020-02-03

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More information about vote at CRAN
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Package vampyr updated to version 1.0.6 with previous version 1.0.5 dated 2020-01-20

Title: Factor Analysis Controlling the Effects of Response Bias
Description: Vampirize the response biases from a dataset! Performs factor analysis controlling the effects of social desirability and acquiescence using the method described in Ferrando, Lorenzo-Seva & Chico (2009) <doi:10.1080/10705510902751374>.
Author: David Navarro-Gonzalez, Andreu Vigil-Colet, Pere J. Ferrando, Urbano Lorenzo-Seva, Jorge N. Tendeiro
Maintainer: David Navarro-Gonzalez <david.navarro@urv.cat>

Diff between vampyr versions 1.0.5 dated 2020-01-20 and 1.0.6 dated 2020-02-03

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More information about vampyr at CRAN
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Package shadow updated to version 0.6.4 with previous version 0.6.3 dated 2019-11-11

Title: Geometric Shadow Calculations
Description: Functions for calculating: (1) shadow height, (2) logical shadow flag, (3) shadow footprint, (4) Sky View Factor and (5) radiation load. Basic required inputs include a polygonal layer of obstacle outlines along with their heights (i.e. "extruded polygons"), sun azimuth and sun elevation. The package also provides functions for related preliminary calculations: breaking polygons into line segments, determining azimuth of line segments, shifting segments by azimuth and distance, constructing the footprint of a line-of-sight between an observer and the sun, and creating a 3D grid covering the surface area of extruded polygons.
Author: Michael Dorman [aut, cre], Evyatar Erell [ctb], Itai Kloog [ctb], Adi Vulkan [ctb]
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>

Diff between shadow versions 0.6.3 dated 2019-11-11 and 0.6.4 dated 2020-02-03

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More information about shadow at CRAN
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Package QuantumOps updated to version 3.0.1 with previous version 3.0.0 dated 2019-12-14

Title: Performs Common Linear Algebra Operations Used in Quantum Computing and Implements Quantum Algorithms
Description: Contains basic structures and operations used frequently in quantum computing. Intended to be a convenient tool to help learn quantum mechanics and algorithms. Can create arbitrarily sized kets and bras and implements quantum gates, inner products, and tensor products. Creates arbitrarily controlled versions of all gates and can simulate complete or partial measurements of kets. Has functionality to convert functions into equivalent quantum gates and model quantum noise. Includes larger applications, such as Steane error correction <DOI:10.1103/physrevlett.77.793>, Quantum Fourier Transform and Shor's algorithm (Shor 1999), Grover's algorithm (1996), Quantum Approximation Optimization Algorithm (QAOA) (Farhi, Goldstone, and Gutmann 2014) <arXiv:1411.4028>, and a variational quantum classifier (Schuld 2018) <arXiv:1804.00633>. Can be used with the gridsynth algorithm <arXiv:1212.6253> to perform decomposition into the Clifford+T set.
Author: Salonik Resch
Maintainer: Salonik Resch <resc0059@umn.edu>

Diff between QuantumOps versions 3.0.0 dated 2019-12-14 and 3.0.1 dated 2020-02-03

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More information about QuantumOps at CRAN
Permanent link

Package pivottabler updated to version 1.3.0 with previous version 1.2.3 dated 2019-11-01

Title: Create Pivot Tables
Description: Create regular pivot tables with just a few lines of R. More complex pivot tables can also be created, e.g. pivot tables with irregular layouts, multiple calculations and/or derived calculations based on multiple data frames. Pivot tables are constructed using R only and can be written to a range of output formats (plain text, 'HTML', 'Latex' and 'Excel'), including with styling/formatting.
Author: Christopher Bailiss [aut, cre]
Maintainer: Christopher Bailiss <cbailiss@gmail.com>

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Package nngeo updated to version 0.3.4 with previous version 0.3.0 dated 2019-12-03

Title: k-Nearest Neighbor Join for Spatial Data
Description: K-nearest neighbor search for projected and non-projected 'sf' spatial layers. Nearest neighbor search uses (1) C code from 'GeographicLib' for lon-lat point layers, (2) function nn2() from package 'RANN' for projected point layers, or (3) function st_distance() from package 'sf' for line or polygon layers. The package also includes several other utility functions for spatial analysis.
Author: Michael Dorman [aut, cre], Johnathan Rush [ctb], Ian Hough [ctb], Dominic Russel [ctb], Charles F.F Karney [ctb, cph] (Author of included C code from 'GeographicLib' for geodesic distance)
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>

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Package mnormt updated to version 1.5-6 with previous version 1.5-5 dated 2016-10-15

Title: The Multivariate Normal and t Distributions
Description: Functions are provided for computing the density and the distribution function of multivariate normal and "t" random variables, and for generating random vectors sampled from these distributions. Probabilities are computed via non-Monte Carlo methods; different routines are used in the case d=1, d=2, d>2, if d denotes the number of dimensions.
Author: Fortran code by Alan Genz and other people referred to in the code, R code by Adelchi Azzalini
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>

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Package ImpactEffectsize updated to version 0.3.2 with previous version 0.3.1 dated 2020-01-29

Title: Calculation and Visualization of the Impact Effect Size Measure
Description: A non-parametric effect size measure capturing changes in central tendency or shape of data distributions. The package provides the necessary functions to calculate and plot the Impact effect size measure between two groups.
Author: Jorn Lotsch[aut,cre], Alfred Ultsch[aut]
Maintainer: Jorn Lotsch <j.loetsch@em.uni-frankfurt.de>

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Package flextable updated to version 0.5.7 with previous version 0.5.6 dated 2019-11-12

Title: Functions for Tabular Reporting
Description: Create pretty tables for 'HTML', 'Microsoft Word' and 'Microsoft PowerPoint' documents. Functions are provided to let users create tables, modify and format their content. It extends package 'officer' that does not contain any feature for customized tabular reporting and can be used within R markdown documents.
Author: David Gohel [aut, cre], Quentin Fazilleau [ctb], Maxim Nazarov [ctb] (rmarkdown for docx output), Titouan Robert [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>

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Package episensr updated to version 0.9.5 with previous version 0.9.4 dated 2019-09-02

Title: Basic Sensitivity Analysis of Epidemiological Results
Description: Basic sensitivity analysis of the observed relative risks adjusting for unmeasured confounding and misclassification of the exposure/outcome, or both. It follows the bias analysis methods and examples from the book by Lash T.L, Fox M.P, and Fink A.K. "Applying Quantitative Bias Analysis to Epidemiologic Data", ('Springer', 2009).
Author: Denis Haine [aut, cre] (<https://orcid.org/0000-0002-6691-7335>)
Maintainer: Denis Haine <denis.haine@gmail.com>

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Package deldir updated to version 0.1-25 with previous version 0.1-23 dated 2019-07-31

Title: Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
Description: Calculates the Delaunay triangulation and the Dirichlet or Voronoi tessellation (with respect to the entire plane) of a planar point set. Plots triangulations and tessellations in various ways. Clips tessellations to sub-windows. Calculates perimeters of tessellations. Summarises information about the tiles of the tessellation.
Author: Rolf Turner
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>

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Package betareg updated to version 3.1-3 with previous version 3.1-2 dated 2019-05-16

Title: Beta Regression
Description: Beta regression for modeling beta-distributed dependent variables, e.g., rates and proportions. In addition to maximum likelihood regression (for both mean and precision of a beta-distributed response), bias-corrected and bias-reduced estimation as well as finite mixture models and recursive partitioning for beta regressions are provided.
Author: Achim Zeileis [aut, cre], Francisco Cribari-Neto [aut], Bettina Gruen [aut], Ioannis Kosmidis [aut], Alexandre B. Simas [ctb] (earlier version by), Andrea V. Rocha [ctb] (earlier version by)
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>

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Package AdaptGauss updated to version 1.5.6 with previous version 1.5.4 dated 2019-11-18

Title: Gaussian Mixture Models (GMM)
Description: Multimodal distributions can be modelled as a mixture of components. The model is derived using the Pareto Density Estimation (PDE) for an estimation of the pdf. PDE has been designed in particular to identify groups/classes in a dataset. Precise limits for the classes can be calculated using the theorem of Bayes. Verification of the model is possible by QQ plot, Chi-squared test and Kolmogorov-Smirnov test. The package is based on the publication of Ultsch, A., Thrun, M.C., Hansen-Goos, O., Lotsch, J. (2015) <DOI:10.3390/ijms161025897>.
Author: Michael Thrun [aut, cre] (<https://orcid.org/0000-0001-9542-5543>), Onno Hansen-Goos [aut, rev], Rabea Griese [ctr, ctb], Catharina Lippmann [ctr], Florian Lerch [ctb, rev], Jorn Lotsch [dtc, rev, fnd, ctb], Alfred Ultsch [aut, cph, ths]
Maintainer: Michael Thrun <m.thrun@gmx.net>

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Package RcmdrPlugin.FactoMineR updated to version 1.7 with previous version 1.6-0 dated 2016-01-06

Title: Graphical User Interface for FactoMineR
Description: Rcmdr Plugin for the 'FactoMineR' package.
Author: Francois Husson, Julie Josse, Sebastien Le
Maintainer: Francois Husson <francois.husson@agrocampus-ouest.fr>

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Package psfmi updated to version 0.2.0 with previous version 0.1.0 dated 2019-05-16

Title: Prediction Model Selection and Performance Evaluation in Multiple Imputed Datasets
Description: Provides functions to apply pooling or backward selection of logistic, Cox regression and Multilevel (mixed models) prediction models in multiply imputed datasets. Backward selection can be done from the pooled model using Rubin's Rules (RR), the D1, D2, D3 and promising median p-values method. The model can contain continuous, dichotomous, categorical predictors and interaction terms between all these type of predictors. Continuous predictors can also be introduced as restricted cubic spline coefficients. It is also possible to force (spline) predictors or interaction terms in the model during predictor selection. The package includes a function to evaluate the stability of the models using bootstrapping and cluster bootstrapping. The package further contains functions to generate pooled model performance measures in multiply imputed datasets as ROC/AUC, R-squares, Brier score, fit test values and calibration plots for logistic regression models. A function to apply Bootstrap internal validation is also available where two methods can be used to combine bootstrapping and multiple imputation. One method, boot_MI, first draws bootstrap samples and subsequently performs multiple imputation and with the other method, MI_boot, first bootstrap samples are drawn from each imputed dataset before results are combined. The adjusted intercept after shrinkage of the pooled regression coefficients can be subsequently obtained. Backward selection as part of internal validation is also an option. Also a function to externally validate logistic prediction models in multiple imputed datasets is available. Eekhout (2017) <doi:10.1186/s12874-017-0404-7>. Wiel (2009) <doi:10.1093/biostatistics/kxp011>. Marshall (2009) <doi:10.1186/1471-2288-9-57>.
Author: Martijn Heymans [cre, aut], Iris Eekhout [ctb]
Maintainer: Martijn Heymans <mw.heymans@amsterdamumc.nl>

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Package ggstatsplot updated to version 0.2.0 with previous version 0.1.4 dated 2019-12-18

Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates graphics with details from statistical tests included in the plots themselves. It is targeted primarily at behavioral sciences community to provide a one-line code to generate information-rich plots for statistical analysis of continuous (violin plots, scatterplots, histograms, dot plots, dot-and-whisker plots) or categorical (pie and bar charts) data. Currently, it supports only the most common types of statistical tests: parametric, nonparametric, robust, and bayesian versions of t-test/anova, correlation analyses, contingency table analysis, and regression analyses.
Author: Indrajeet Patil [cre, aut, ctb] (<https://orcid.org/0000-0003-1995-6531>), Chuck Powell [ctb] (<https://orcid.org/0000-0002-3606-2188>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

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