Fri, 22 May 2020

Package carData updated to version 3.0-4 with previous version 3.0-3 dated 2019-11-16

Title: Companion to Applied Regression Data Sets
Description: Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Third Edition, Sage (2019).
Author: John Fox [aut, cre], Sanford Weisberg [aut], Brad Price [aut]
Maintainer: John Fox <jfox@mcmaster.ca>

Diff between carData versions 3.0-3 dated 2019-11-16 and 3.0-4 dated 2020-05-22

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Package suddengains updated to version 0.4.4 with previous version 0.4.3 dated 2020-03-14

Title: Identify Sudden Gains in Longitudinal Data
Description: Identify sudden gains based on the three criteria outlined by Tang and DeRubeis (1999) <doi:10.1037/0022-006X.67.6.894> to a selection of repeated measures. Sudden losses, defined as the opposite of sudden gains can also be identified. Two different datasets can be created, one including all sudden gains/losses and one including one selected sudden gain/loss for each case. It can extract scores around sudden gains/losses. It can plot the average change around sudden gains/losses and trajectories of individual cases.
Author: Milan Wiedemann [aut, cre] (<https://orcid.org/0000-0003-1991-282X>), Graham M Thew [ctb] (<https://orcid.org/0000-0003-2851-1315>), Richard Stott [ctb] (<https://orcid.org/0000-0003-2533-5504>), Anke Ehlers [ctb, ths] (<https://orcid.org/0000-0002-8742-0192>), Mental Health Research UK [fnd], Wellcome Trust [fnd]
Maintainer: Milan Wiedemann <milan.wiedemann@gmail.com>

Diff between suddengains versions 0.4.3 dated 2020-03-14 and 0.4.4 dated 2020-05-22

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Package lcc updated to version 1.1.0 with previous version 1.0.5 dated 2020-05-18

Title: Longitudinal Concordance Correlation
Description: Estimates the longitudinal concordance correlation to access the longitudinal agreement profile. The estimation approach implemented is variance components approach based on polynomial mixed effects regression model, as proposed by Oliveira, Hinde and Zocchi (2018) <doi:10.1007/s13253-018-0321-1>. In addition, non-parametric confidence intervals were implemented using percentile method or normal-approximation based on Fisher Z-transformation.
Author: Thiago de Paula Oliveira [aut, cre], Rafael de Andrade Moral [aut], Silvio Sandoval Zocchi [ctb], Clarice Garcia Borges Demetrio [ctb], John Hinde [aut]
Maintainer: Thiago de Paula Oliveira <thiago.paula.oliveira@usp.br>

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Package Immigrate updated to version 0.2.1 with previous version 0.1.1 dated 2020-05-18

Title: Iterative Max-Min Entropy Margin-Maximization with Interaction Terms for Feature Selection
Description: Based on large margin principle, this package performs feature selection methods: "IM4E"(Iterative Margin-Maximization under Max-Min Entropy Algorithm); "Immigrate"(Iterative Max-Min Entropy Margin-Maximization with Interaction Terms Algorithm); "BIM"(Boosted version of IMMIGRATE algorithm); "Simba"(Iterative Search Margin Based Algorithm); "LFE"(Local Feature Extraction Algorithm). This package also performs prediction for the above feature selection methods.
Author: Ruzhang Zhao, Pengyu Hong, Jun S. Liu
Maintainer: Ruzhang Zhao<ruzhangzhao@gmail.com>

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Package convey updated to version 0.2.2 with previous version 0.2.1 dated 2018-06-19

Title: Income Concentration Analysis with Complex Survey Samples
Description: Variance estimation on indicators of income concentration and poverty using complex sample survey designs. Wrapper around the 'survey' package.
Author: Djalma Pessoa [aut, cre], Anthony Damico [aut], Guilherme Jacob [aut]
Maintainer: Djalma Pessoa <pessoad@gmail.com>

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Package brinton updated to version 0.1.7 with previous version 0.1.6 dated 2020-04-15

Title: A Graphical EDA Tool
Description: An automated graphical exploratory data analysis (EDA) tool that introduces: a.) wideplot() graphics for exploring the structure of a dataset through a grid of variables and graphic types. b.) longplot() graphics, which present the entire catalog of available graphics for representing a particular variable using a grid of graphic types and variations on these types. c.) plotup() function, which presents a particular graphic for a specific variable of a dataset. The plotup() function also makes it possible to obtain the code used to generate the graphic, meaning that the user can adjust its properties as needed.
Author: Pere Millán-Martínez [aut, cre], Ramon Oller Piqué [ctb]
Maintainer: Pere Millán-Martínez <info@sciencegraph.org>

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Package edgar updated to version 2.0.3 with previous version 2.0.2 dated 2019-08-29

Title: Tool for the U.S. SEC EDGAR Retrieval and Parsing of Corporate Filings
Description: In the USA, companies file different forms with the U.S. Securities and Exchange Commission (SEC) through EDGAR (Electronic Data Gathering, Analysis, and Retrieval system). The EDGAR database automated system collects all the different necessary filings and makes it publicly available. This package facilitates retrieving, storing, searching, and parsing of all the available filings on the EDGAR server. It downloads filings from SEC server in bulk with a single query. Additionally, it provides various useful functions: extracts 8-K triggering events, extract "Business (Item 1)" and "Management's Discussion and Analysis(Item 7)" sections of annual statements, searches filings for desired keywords, provides sentiment measures, parses filing header information, and provides HTML view of SEC filings.
Author: Gunratan Lonare <lonare.gunratan@gmail.com>, Bharat Patil <bharatspatil@gmail.com>
Maintainer: Gunratan Lonare <lonare.gunratan@gmail.com>

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Package blogdown updated to version 0.19 with previous version 0.18 dated 2020-03-04

Title: Create Blogs and Websites with R Markdown
Description: Write blog posts and web pages in R Markdown. This package supports the static site generator 'Hugo' (<https://gohugo.io>) best, and it also supports 'Jekyll' (<http://jekyllrb.com>) and 'Hexo' (<https://hexo.io>).
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Beilei Bian [ctb], Forest Fang [ctb], Garrick Aden-Buie [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], JJ Allaire [ctb], Kevin Ushey [ctb], Leonardo Collado-Torres [ctb], Xianying Tan [ctb], Raniere Silva [ctb], Jozef Hajnala [ctb], RStudio, PBC [cph]
Maintainer: Yihui Xie <xie@yihui.name>

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Package tfhub updated to version 0.8.0 with previous version 0.7.0 dated 2019-12-18

Title: Interface to 'TensorFlow' Hub
Description: 'TensorFlow' Hub is a library for the publication, discovery, and consumption of reusable parts of machine learning models. A module is a self-contained piece of a 'TensorFlow' graph, along with its weights and assets, that can be reused across different tasks in a process known as transfer learning. Transfer learning train a model with a smaller dataset, improve generalization, and speed up training.
Author: Daniel Falbel [aut, cre], JJ Allaire [aut], RStudio [cph, fnd], Google Inc. [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>

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Package qualtRics updated to version 3.1.3 with previous version 3.1.2 dated 2020-02-24

Title: Download 'Qualtrics' Survey Data
Description: Provides functions to access survey results directly into R using the 'Qualtrics' API. 'Qualtrics' <https://www.qualtrics.com/about/> is an online survey and data collection software platform. See <https://api.qualtrics.com/> for more information about the 'Qualtrics' API. This package is community-maintained and is not officially supported by 'Qualtrics'.
Author: Jasper Ginn [aut], Jackson Curtis [ctb], Shaun Jackson [ctb], Samuel Kaminsky [ctb], Eric Knudsen [ctb], Joseph O'Brien [ctb], Daniel Seneca [ctb], Julia Silge [aut, cre] (<https://orcid.org/0000-0002-3671-836X>), Phoebe Wong [ctb]
Maintainer: Julia Silge <julia.silge@gmail.com>

Diff between qualtRics versions 3.1.2 dated 2020-02-24 and 3.1.3 dated 2020-05-22

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Package riverdist updated to version 0.15.1 with previous version 0.15.0 dated 2017-07-18

Title: River Network Distance Computation and Applications
Description: Reads river network shape files and computes network distances. Also included are a variety of computation and graphical tools designed for fisheries telemetry research, such as minimum home range, kernel density estimation, and clustering analysis using empirical k-functions with a bootstrap envelope. Tools are also provided for editing the river networks, meaning there is no reliance on external software.
Author: Matt Tyers [aut, cre]
Maintainer: Matt Tyers <matt.tyers@alaska.gov>

Diff between riverdist versions 0.15.0 dated 2017-07-18 and 0.15.1 dated 2020-05-22

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Package CINID updated to version 1.3-0 with previous version 1.2 dated 2014-10-07

Title: Curculionidae INstar IDentification
Description: Method for identifying the instar of Curculionid larvae from the observed distribution of the headcapsule size of mature larvae.
Author: Aurelie Siberchicot, Adrien Merville, Marie-Claude Bel-Venner and Samuel Venner
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>

Diff between CINID versions 1.2 dated 2014-10-07 and 1.3-0 dated 2020-05-22

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Package SP2000 updated to version 0.0.7 with previous version 0.0.6 dated 2020-05-14

Title: Catalogue of Life Toolkit
Description: A programmatic interface to <http://sp2000.org.cn>, re-written based on an accompanying 'Species 2000' API. Access tables describing catalogue of the Chinese known species of animals, plants, fungi, micro-organisms, and more. This package also supports access to catalogue of life global <http://catalogueoflife.org> and catalogue of life Taiwan <http://taibnet.sinica.edu.tw/home_eng.php?>. The development of 'SP2000' package were supported by Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China and Yunnan University's Research Innovation Fund for Graduate Students.
Author: Liuyong Ding [aut, cre], Minrui Huang [ctb], Ke Yang [ctb], Jun Wang [ctb], Juan Tao [ctb], Chengzhi Ding [ctb], Daming He [ctb]
Maintainer: Liuyong Ding <ly_ding@126.com>

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Package hsdar updated to version 1.0.2 with previous version 1.0.1 dated 2020-02-05

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 bnstruct updated to version 1.0.8 with previous version 1.0.7 dated 2020-05-09

Title: Bayesian Network Structure Learning from Data with Missing Values
Description: Bayesian Network Structure Learning from Data with Missing Values. The package implements the Silander-Myllymaki complete search, the Max-Min Parents-and-Children, the Hill-Climbing, the Max-Min Hill-climbing heuristic searches, and the Structural Expectation-Maximization algorithm. Available scoring functions are BDeu, AIC, BIC. The package also implements methods for generating and using bootstrap samples, imputed data, inference.
Author: Francesco Sambo [aut], Alberto Franzin [aut, cre]
Maintainer: Alberto Franzin <afranzin@ulb.ac.be>

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Package RolWinMulCor updated to version 0.4.0 with previous version 0.1.0 dated 2020-05-12

Title: Subroutines to Estimate Rolling Window Multiple Correlation
Description: Rolling Window Multiple Correlation ('RolWinMulCor') estimates the rolling (running) window correlation for the bi- and multi-variate cases between regular (sampled on identical time points) time series, with especial emphasis to environmental data (although this can be applied to other kinds of data sets). 'RolWinMulCor' is based on the concept of rolling or running window and is useful to evaluate the evolution of correlation through time and time-scales. 'RolWinMulCor' contains four functions: (1) the first two functions are focus on the bi-variate case, one of them produces a simple plot of correlation coefficients and p-values (<=0.05) for only one window-length (time-scale), and the other function produces a heat map for the statistically significant (p-values <=0.05) correlation coefficients taking into account all the possible window-lengths (which are determined by the number of elements of the time series under analysis) or for a band of window-lengths; (2) the second two functions are designed to analyse the multi-variate case and follow the bi-variate case to display visually the results although these two methods are different. The four functions contained in 'RolWinMulCor' are highly flexible since this contains a great number of parameters to control the estimation of correlation and the features of the plot output, e.g. to remove the (linear) trend contained in the time series under analysis, to choose different p-value correction methods (which are used to address the multiple comparison problem) or to personalise the plot output (e.g. this can be displayed in the screen or can be saved as PNG, JPEG, EPS or PDF formats). The 'RolWinMulCor' package also provides examples with synthetic and real environmental time series to exemplify its use. Methods derived from H. Abdi. (2007) <https://personal.utdallas.edu/~herve/Abdi-MCC2007-pretty.pdf>, J. M. Polanco-Martinez (2019) <doi:10.1007/s11071-019-04974-y>, and R. Telford (2013) <https://quantpalaeo.wordpress.com/2013/01/04/running-correlations-running-into-problems/>.
Author: Josue M. Polanco-Martinez [aut, cph, cre]
Maintainer: Josue M. Polanco-Martinez <josue.m.polanco@gmail.com>

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Package countrycode updated to version 1.2.0 with previous version 1.1.3 dated 2020-05-07

Title: Convert Country Names and Country Codes
Description: Standardize country names, convert them into one of 40 different coding schemes, convert between coding schemes, and assign region descriptors.
Author: Vincent Arel-Bundock [aut, cre] (<https://orcid.org/0000-0003-2042-7063>), CJ Yetman [ctb] (<https://orcid.org/0000-0001-5099-9500>), Nils Enevoldsen [ctb] (<https://orcid.org/0000-0001-7195-4117>)
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>

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Package Mondrian updated to version 1.1.0 with previous version 1.0-0 dated 2016-03-04

Title: A Simple Graphical Representation of the Relative Occurrence and Co-Occurrence of Events
Description: The unique function of this package allows representing in a single graph the relative occurrence and co-occurrence of events measured in a sample. As examples, the package was applied to describe the occurrence and co-occurrence of different species of bacterial or viral symbionts infecting arthropods at the individual level. The graphics allows determining the prevalence of each symbiont and the patterns of multiple infections (i.e. how different symbionts share or not the same individual hosts). We named the package after the famous painter as the graphical output recalls Mondrian’s paintings.
Author: Aurélie Siberchicot, Delphine Charif, Gabriel Terraz and Fabrice Vavre
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>

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Package dlnm updated to version 2.4.2 with previous version 2.4.1 dated 2020-05-13

Title: Distributed Lag Non-Linear Models
Description: Collection of functions for distributed lag linear and non-linear models.
Author: Antonio Gasparrini [aut, cre], Ben Armstrong [aut], Fabian Scheipl [ctb]
Maintainer: Antonio Gasparrini <antonio.gasparrini@lshtm.ac.uk>

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Package climatrends updated to version 0.1.7 with previous version 0.1.6 dated 2020-05-20

Title: Climate Variability Indices for Ecological Modelling
Description: Supports analysis of trends in climate change, ecological and crop modelling.
Author: Kauê de Sousa [aut, cre] (<https://orcid.org/0000-0002-7571-7845>), Jacob van Etten [ctb, ths] (<https://orcid.org/0000-0001-7554-2558>), Svein Ø. Solberg [ctb, ths] (<https://orcid.org/0000-0002-4491-4483>)
Maintainer: Kauê de Sousa <kaue.desousa@inn.no>

Diff between climatrends versions 0.1.6 dated 2020-05-20 and 0.1.7 dated 2020-05-22

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New package ergMargins with initial version 0.1.1
Package: ergMargins
Type: Package
Title: Process Analysis for Exponential Random Graph Models
Version: 0.1.1
Authors@R: c(person("Scott", "Duxbury",email="sduxburycpt@gmail.com", role=c("aut", "cre", "cph")), person("Bruce", "Desmarais",email="bdesmarais@psu.edu", role=c("ctb", "cph")), person("Philip","Leifeld",email="philip.leifeld@essex.ac.uk",role=c("ctb","cph")))
Maintainer: Scott Duxbury <sduxburycpt@gmail.com>
Description: Calculates marginal effects and conducts process analysis in exponential family random graph models (ERGM). Includes functions to conduct mediation and moderation analyses and to diagnose multicollinearity. URL: <http://github.com/sduxbury/ergMargins>. BugReports: <http://github.com/sduxbury/ergMargins/issues>. Duxbury, Scott W (2019) <doi:10.31235/osf.io/9bs4u>. Long, J. Scott, and Sarah Mustillo (2018) <doi:10.1177/0049124118799374>. Mize, Trenton D. (2019) <doi:10.15195/v6.a4>. Karlson, Kristian Bernt, Anders Holm, and Richard Breen (2012) <doi:10.1177/0081175012444861>. Duxbury, Scott W (2018) <doi:10.1177/0049124118782543>.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: numDeriv, statnet, stats, ergm, Matrix, network, btergm, methods, sna, xergm.common
Suggests: MASS, knitr, rmarkdown
NeedsCompilation: no
Packaged: 2020-05-22 14:01:17 UTC; 15179
Author: Scott Duxbury [aut, cre, cph], Bruce Desmarais [ctb, cph], Philip Leifeld [ctb, cph]
Repository: CRAN
Date/Publication: 2020-05-22 15:00:03 UTC

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Package MFAg updated to version 1.7 with previous version 1.6 dated 2020-03-24

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

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Package tmuxr updated to version 0.2.4 with previous version 0.2.3 dated 2020-05-07

Title: Manage 'tmux' Sessions, Windows, and Panes
Description: Create, control, and capture 'tmux' sessions, windows, and panes using a pipeable API.
Author: Jeroen Janssens [aut, cre] (<https://orcid.org/0000-0002-5878-8924>), Data Science Workshops [cph, fnd]
Maintainer: Jeroen Janssens <jeroen@datascienceworkshops.com>

Diff between tmuxr versions 0.2.3 dated 2020-05-07 and 0.2.4 dated 2020-05-22

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New package textrecipes with initial version 0.2.3
Package: textrecipes
Title: Extra 'Recipes' for Text Processing
Version: 0.2.3
Authors@R: person(given = "Emil", family = "Hvitfeldt", role = c("aut", "cre"), email = "emilhhvitfeldt@gmail.com", comment = c(ORCID = "0000-0002-0679-1945"))
Description: Converting text to numerical features requires specifically created procedures, which are implemented as steps according to the 'recipes' package. These steps allows for tokenization, filtering, counting (tf and tfidf) and feature hashing.
License: MIT + file LICENSE
URL: https://github.com/tidymodels/textrecipes, https://textrecipes.tidymodels.org
BugReports: https://github.com/tidymodels/textrecipes/issues
Depends: R (>= 2.10), recipes (>= 0.1.4)
Imports: generics, rlang, tokenizers, dplyr, tibble, tidyr, purrr, SnowballC, stopwords, magrittr, Matrix, stringr, vctrs, Rcpp
Suggests: covr, testthat (>= 2.1.0), knitr, text2vec, rmarkdown, textfeatures (>= 0.3.3), modeldata, spacyr
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0.9000
SystemRequirements: GNU make, C++11
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2020-05-20 22:38:21 UTC; emilhvitfeldthansen
Author: Emil Hvitfeldt [aut, cre] (<https://orcid.org/0000-0002-0679-1945>)
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Repository: CRAN
Date/Publication: 2020-05-22 11:40:06 UTC

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Package pdftools updated to version 2.3.1 with previous version 2.3 dated 2019-11-10

Title: Text Extraction, Rendering and Converting of PDF Documents
Description: Utilities based on 'libpoppler' for extracting text, fonts, attachments and metadata from a PDF file. Also supports high quality rendering of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for further processing in R.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between pdftools versions 2.3 dated 2019-11-10 and 2.3.1 dated 2020-05-22

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Package jomo updated to version 2.7-1 with previous version 2.7-0 dated 2020-05-13

Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package 'pan', 'jomo' is a package for multilevel joint modelling multiple imputation (Carpenter and Kenward, 2013) <doi: 10.1002/9781119942283>. Novel aspects of 'jomo' are the possibility of handling binary and categorical data through latent normal variables, the option to use cluster-specific covariance matrices and to impute compatibly with the substantive model.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <m.quartagno@ucl.ac.uk>

Diff between jomo versions 2.7-0 dated 2020-05-13 and 2.7-1 dated 2020-05-22

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Package LinkedMatrix updated to version 1.4.0 with previous version 1.3.1 dated 2018-08-06

Title: Column-Linked and Row-Linked Matrices
Description: A class that links matrix-like objects (nodes) by rows or by columns while behaving similarly to a base R matrix. Very large matrices are supported if the nodes are file-backed matrices.
Author: Gustavo de los Campos [aut], Alexander Grueneberg [aut, cre]
Maintainer: Alexander Grueneberg <cran@agrueneberg.info>

Diff between LinkedMatrix versions 1.3.1 dated 2018-08-06 and 1.4.0 dated 2020-05-22

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Package overlap updated to version 0.3.3 with previous version 0.3.2 dated 2018-05-03

Title: Estimates of Coefficient of Overlapping for Animal Activity Patterns
Description: Provides functions to fit kernel density functions to data on temporal activity patterns of animals; estimate coefficients of overlapping of densities for two species; and calculate bootstrap estimates of confidence intervals.
Author: Mike Meredith and Martin Ridout
Maintainer: Mike Meredith <mike@mmeredith.net>

Diff between overlap versions 0.3.2 dated 2018-05-03 and 0.3.3 dated 2020-05-22

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Package SWIM updated to version 0.2.1 with previous version 0.2.0 dated 2020-01-10

Title: Scenario Weights for Importance Measurement
Description: An efficient sensitivity analysis for stochastic models based on Monte Carlo samples. Provides weights on simulated scenarios from a stochastic model, such that stressed random variables fulfil given probabilistic constraints (e.g. specified values for risk measures), under the new scenario weights. Scenario weights are selected by constrained minimisation of the relative entropy to the baseline model. The 'SWIM' package is based on Pesenti S.M, Millossovich P., Tsanakas A. (2019) "Reverse Sensitivity Testing: What does it take to break the model", <openaccess.city.ac.uk/id/eprint/18896/>.
Author: Silvana M. Pesenti [aut, cre], Alberto Bettini [aut], Pietro Millossovich [aut], Andreas Tsanakas [aut]
Maintainer: Silvana M. Pesenti <swimpackage@gmail.com>

Diff between SWIM versions 0.2.0 dated 2020-01-10 and 0.2.1 dated 2020-05-22

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Package Rdimtools updated to version 1.0.3 with previous version 1.0.2 dated 2020-05-04

Title: Dimension Reduction and Estimation Methods
Description: We provide linear and nonlinear dimension reduction techniques. Intrinsic dimension estimation methods for exploratory analysis are also provided. For more details on dimensionality techniques, see the paper by Ma and Zhu (2013) <doi:10.1111/j.1751-5823.2012.00182.x> if you are interested in statistical approach, or Engel, Huttenberger, and Hamann (2012) <doi:10.4230/OASIcs.VLUDS.2011.135> for a broader multi-disciplinary overview.
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>), Changhee Suh [ctb]
Maintainer: Kisung You <kyoustat@gmail.com>

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Package periscope updated to version 0.4.10-1 with previous version 0.4.10 dated 2020-05-19

Title: Enterprise Streamlined 'Shiny' Application Framework
Description: An enterprise-targeted scalable and UI-standardized 'shiny' framework including a variety of developer convenience functions with the goal of both streamlining robust application development while assisting with creating a consistent user experience regardless of application or developer.
Author: Constance Brett [aut, cre], Isaac Neuhaus [aut] (canvasXpress JavaScript Library Maintainer), Ger Inberg [ctb], Bristol-Meyers Squibb (BMS) [cph]
Maintainer: Constance Brett <connie@aggregate-genius.com>

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New package outsider.base with initial version 0.1.1
Package: outsider.base
Type: Package
Title: Base Package for 'Outsider'
Version: 0.1.1
Authors@R: c( person("Dom", "Bennett", role = c("aut", "cre"), email = "dominic.john.bennett@gmail.com", comment = c(ORCID = "0000-0003-2722-1359")), person("Hannes", "Hettling", role = "ctb", comment = c(ORCID = "0000-0003-4144-2238")), person("Daniele", "Silvestro", role = "ctb", comment = c(ORCID = "0000-0003-0100-0961")), person("Rutger", "Vos", role = "ctb", comment = c(ORCID = "0000-0001-9254-7318")), person("Alexandre", "Antonelli", role = "ctb", comment = c(ORCID = "0000-0003-1842-9297")), person("Anna", "Krystalli", role = "rev", email = "annakrystalli@googlemail.com"))
Maintainer: Dom Bennett <dominic.john.bennett@gmail.com>
Description: Base package for 'outsider' <https://github.com/ropensci/outsider>. The 'outsider' package and its sister packages enable the installation and running of external, command-line software within R. This base package is a key dependency of the user-facing 'outsider' package as it provides the utilities for interfacing between 'Docker' <https://www.docker.com> and R. It is intended that end-users of 'outsider' do not directly work with this base package.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.0.2
SystemRequirements: docker (>=18.0.0)
URL: https://docs.ropensci.org/outsider.base, https://github.com/ropensci/outsider.base
BugReports: https://github.com/ropensci/outsider.base/issues
Language: en-GB
Depends: R (>= 3.3.0)
Imports: utils (>= 3.1), crayon, devtools (>= 1.1), jsonlite (>= 1.1), sys (>= 2.1), yaml (>= 2.0), callr (>= 3.0.0), withr (>= 2.0), tibble, cli, praise
Suggests: ssh, testthat (>= 2.0)
NeedsCompilation: no
Packaged: 2020-05-21 19:36:09 UTC; domben
Author: Dom Bennett [aut, cre] (<https://orcid.org/0000-0003-2722-1359>), Hannes Hettling [ctb] (<https://orcid.org/0000-0003-4144-2238>), Daniele Silvestro [ctb] (<https://orcid.org/0000-0003-0100-0961>), Rutger Vos [ctb] (<https://orcid.org/0000-0001-9254-7318>), Alexandre Antonelli [ctb] (<https://orcid.org/0000-0003-1842-9297>), Anna Krystalli [rev]
Repository: CRAN
Date/Publication: 2020-05-22 08:10:02 UTC

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Package nimble updated to version 0.9.1 with previous version 0.9.0 dated 2019-12-18

Title: MCMC, Particle Filtering, and Programmable Hierarchical Modeling
Description: A system for writing hierarchical statistical models largely compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models and do basic R-style math, and compiling both models and nimbleFunctions via custom- generated C++. 'NIMBLE' includes default methods for MCMC, particle filtering, Monte Carlo Expectation Maximization, and some other tools. The nimbleFunction system makes it easy to do things like implement new MCMC samplers from R, customize the assignment of samplers to different parts of a model from R, and compile the new samplers automatically via C++ alongside the samplers 'NIMBLE' provides. 'NIMBLE' extends the 'BUGS'/'JAGS' language by making it extensible: New distributions and functions can be added, including as calls to external compiled code. Although most people think of MCMC as the main goal of the 'BUGS'/'JAGS' language for writing models, one can use 'NIMBLE' for writing arbitrary other kinds of model-generic algorithms as well. A full User Manual is available at <https://r-nimble.org>.
Author: Perry de Valpine [aut], Christopher Paciorek [aut, cre], Daniel Turek [aut], Nick Michaud [aut], Cliff Anderson-Bergman [aut], Fritz Obermeyer [aut], Claudia Wehrhahn Cortes [aut] (Bayesian nonparametrics system), Abel Rodrìguez [aut] (Bayesian nonparametrics system), Duncan Temple Lang [aut] (packaging configuration), Sally Paganin [aut] (reversible jump MCMC), Jagadish Babu [ctb] (code for the compilation system for an early version of NIMBLE), Dao Nguyen [ctb] (contributions to the IF2 code), Lauren Ponisio [ctb] (contributions to the cross-validation code), Peter Sujan [ctb] (multivariate t distribution code)
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>

Diff between nimble versions 0.9.0 dated 2019-12-18 and 0.9.1 dated 2020-05-22

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 INSTALL                              |    6 -
 LICENSE                              |    2 
 MD5                                  |   78 +++++++++---------
 R/BNP_distributions.R                |    9 +-
 R/BUGS_BUGSdecl.R                    |    2 
 R/BUGS_model.R                       |    4 
 R/BUGS_modelDef.R                    |  144 ++++++++++++++++++++++++++---------
 R/BUGS_readBUGS.R                    |    2 
 R/BUGS_utils.R                       |    2 
 R/MCMC_autoBlock.R                   |   18 ++--
 R/MCMC_build.R                       |    4 
 R/MCMC_configuration.R               |   27 +++---
 R/MCMC_run.R                         |    2 
 R/MCMC_samplers.R                    |  138 ++++++++++++++++++---------------
 R/MCMC_utils.R                       |   10 +-
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New package llama with initial version 0.9.3
Package: llama
Type: Package
Title: Leveraging Learning to Automatically Manage Algorithms
Version: 0.9.3
Date: 2020-05-19
Author: Lars Kotthoff [aut,cre], Bernd Bischl [aut], Barry Hurley [ctb], Talal Rahwan [ctb]
Maintainer: Lars Kotthoff <larsko@uwyo.edu>
Description: Provides functionality to train and evaluate algorithm selection models for portfolios.
Depends: R (>= 4.0), mlr (>= 2.5)
Imports: rJava, parallelMap, ggplot2, checkmate, BBmisc, plyr
Suggests: testthat, ParamHelpers
License: BSD_3_clause + file LICENSE
URL: https://bitbucket.org/lkotthoff/llama
NeedsCompilation: no
Packaged: 2020-05-20 21:08:10 UTC; larsko
Repository: CRAN
Date/Publication: 2020-05-22 08:30:02 UTC

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New package eHOF with initial version 1.9
Package: eHOF
Version: 1.9
Encoding: UTF-8
Date: 2020-05-13
Title: Extended HOF (Huisman-Olff-Fresco) Models
Author: Florian Jansen, Jari Oksanen
Maintainer: Florian Jansen <florian.jansen@uni-rostock.de>
Depends: R (>= 2.5.0), mgcv, lattice
Suggests: vegdata, vegan, knitr, testthat
LazyData: yes
VignetteBuilder: knitr
Description: Extended and enhanced hierarchical logistic regression models (called Huisman-Olff-Fresco in biology, see Huisman et al. 1993 Journal of Vegetation Science <doi:10.1111/jvs.12050>) models. Response curves along one-dimensional gradients including no response, monotone, plateau, unimodal and bimodal models.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2020-05-20 21:45:20 UTC; jansen
Repository: CRAN
Date/Publication: 2020-05-22 08:30:06 UTC

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Package Blaunet updated to version 2.1.0 with previous version 2.0.9 dated 2020-05-10

Title: Calculate and Analyze Blau Status for (Covert) Organizations
Description: An integrated set of tools to calculate and analyze Blau statuses quantifying social distance between individuals belonging to (covert) organizations. Relational (network) data can be incorporated for additional analyses. This project is supported by Defense Threat Reduction Agency (DTRA) Grant HDTRA-10-1-0043.
Author: Cheng Wang*, Michael Genkin*, George Berry, Liyuan Chen, Matthew Brashears *Both authors contributed equally to this work and their names are randomly ordered
Maintainer: Cheng Wang <chengwang@wayne.edu>

Diff between Blaunet versions 2.0.9 dated 2020-05-10 and 2.1.0 dated 2020-05-22

 DESCRIPTION               |   12 ++++++------
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 inst/scripts/command.pdf  |binary
 inst/scripts/graphic.pdf  |binary
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New package RFmerge with initial version 0.1-10
Package: RFmerge
Type: Package
Title: Merging of Satellite Datasets with Ground Observations using Random Forests
Version: 0.1-10
Author: Mauricio Zambrano-Bigiarini [aut, cre, cph] (<https://orcid.org/0000-0002-9536-643X>), Oscar M. Baez-Villanueva [aut, cph], Juan Giraldo-Osorio [ctb]
Authors@R: c(person("Mauricio Zambrano-Bigiarini", email = "mzb.devel@gmail.com", role=c("aut", "cre", "cph"), comment=c(ORCID = "0000-0002-9536-643X")), person("Oscar M. Baez-Villanueva", email = "obaezvil@th-koeln.de", role=c("aut", "cph")), person("Juan Giraldo-Osorio", email = "j.giraldoo@javeriana.edu.co", role=c("ctb")) )
Maintainer: Mauricio Zambrano-Bigiarini <mzb.devel@gmail.com>
Description: S3 implementation of the Random Forest MErging Procedure (RF-MEP), which combines two or more satellite-based datasets (e.g., precipitation products, topography) with ground observations to produce a new dataset with improved spatio-temporal distribution of the target field. In particular, this package was developed to merge different Satellite-based Rainfall Estimates (SREs) with measurements from rain gauges, in order to obtain a new precipitation dataset where the time series in the rain gauges are used to correct different types of errors present in the SREs. However, this package might be used to merge other hydrological/environmental satellite fields with point observations. For details, see Baez-Villanueva et al. (2020) <doi:10.1016/j.rse.2019.111606>. Bugs / comments / questions / collaboration of any kind are very welcomed.
License: GPL (>= 3)
Depends: R (>= 3.5.0)
Imports: raster, sp, sf, randomForest, zoo, parallel, methods, stats, utils, pbapply
Suggests: knitr, rmarkdown, rgdal
VignetteBuilder: knitr
URL: https://github.com/hzambran/RFmerge
MailingList: https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
BugReports: https://github.com/hzambran/RFmerge/issues
LazyLoad: yes
NeedsCompilation: no
Repository: CRAN
Packaged: 2020-05-21 16:53:52 UTC; hzambran
Date/Publication: 2020-05-22 08:00:02 UTC

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New package DecisionAnalysis with initial version 1.1.0
Package: DecisionAnalysis
Type: Package
Title: Implementation of Multi Objective Decision Analysis
Version: 1.1.0
Authors@R: c( person("Josh", "Deehr", email = "josh.deehr@gmail.com", role = c("aut","cre")), person("Christopher", "Smith", email = "Cms3am@virginia.edu", role = c("aut")), person("Jason", "Freels", email = "auburngrads@live.com", role = c("aut")), person("Emily", "Meyer", email = "emily.meyer@theperducogroup.com", role = c("aut")) )
Maintainer: Josh Deehr <josh.deehr@gmail.com>
BugReports: https://github.com/AFIT-R/DecisionAnalysis
Date: 2020-5-21
Description: Aides in the multi objective decision analysis process by simplifying the creation of value hierarchy tree plots, calculating and plotting single and multi attribute value function scores, and conducting sensitivity analysis. Linear, exponential, and categorical single attribute value functions are supported. For details see Parnell (2013, ISBN:978-1-118-17313-8) Kirkwood (1997, ISBN:0-534-51692-0).
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: stats, ggplot2, tidyr, dplyr, graphics, data.tree, gridExtra, viridisLite, Cairo, methods, qpdf, DiagrammeR
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-05-22 01:11:38 UTC; ktdeehr
Author: Josh Deehr [aut, cre], Christopher Smith [aut], Jason Freels [aut], Emily Meyer [aut]
Repository: CRAN
Date/Publication: 2020-05-22 08:00:06 UTC

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Package chngpt updated to version 2020.5-21 with previous version 2020.5-13 dated 2020-05-13

Title: Estimation and Hypothesis Testing for Threshold Regression
Description: Threshold regression models are also called two-phase regression, broken-stick regression, split-point regression, structural change models, and regression kink models, with and without interaction terms. Methods for both continuous and discontinuous threshold models are included, but the support for the former is much greater. This package is described in Fong, Huang, Gilbert and Permar (2017) <DOI:10.1186/s12859-017-1863-x>.
Author: Youyi Fong [cre], Adam Elder [aut], Hyunju Son [aut], Zonglin He [aut], Tao Yang [aut]
Maintainer: Youyi Fong <youyifong@gmail.com>

Diff between chngpt versions 2020.5-13 dated 2020-05-13 and 2020.5-21 dated 2020-05-22

 ChangeLog                    |    3 +++
 DESCRIPTION                  |    8 ++++----
 MD5                          |   10 +++++-----
 R/double.hinge.R             |    6 +++++-
 inst/doc/chngpt-vignette.pdf |binary
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 6 files changed, 19 insertions(+), 11 deletions(-)

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Package phateR updated to version 1.0.4 with previous version 1.0.0 dated 2019-12-05

Title: PHATE - Potential of Heat-Diffusion for Affinity-Based Transition Embedding
Description: PHATE is a tool for visualizing high dimensional single-cell data with natural progressions or trajectories. PHATE uses a novel conceptual framework for learning and visualizing the manifold inherent to biological systems in which smooth transitions mark the progressions of cells from one state to another. To see how PHATE can be applied to single-cell RNA-seq datasets from hematopoietic stem cells, human embryonic stem cells, and bone marrow samples, check out our publication in Nature Biotechnology at <doi:10.1038/s41587-019-0336-3>.
Author: Krishnan Srinivasan [aut], Scott Gigante [cre] (<https://orcid.org/0000-0002-4544-2764>)
Maintainer: Scott Gigante <scott.gigante@yale.edu>

Diff between phateR versions 1.0.0 dated 2019-12-05 and 1.0.4 dated 2020-05-22

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 7 files changed, 32 insertions(+), 27 deletions(-)

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Package MVar.pt updated to version 2.1.3 with previous version 2.1.2 dated 2020-03-24

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

Diff between MVar.pt versions 2.1.2 dated 2020-03-24 and 2.1.3 dated 2020-05-22

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 11 files changed, 38 insertions(+), 22 deletions(-)

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Package MVar updated to version 2.1.3 with previous version 2.1.2 dated 2020-03-24

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

Diff between MVar versions 2.1.2 dated 2020-03-24 and 2.1.3 dated 2020-05-22

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 11 files changed, 40 insertions(+), 23 deletions(-)

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Package broman updated to version 0.70-4 with previous version 0.69-5 dated 2019-04-11

Title: Karl Broman's R Code
Description: Miscellaneous R functions, including functions related to graphics (mostly for base graphics), permutation tests, running mean/median, and general utilities.
Author: Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>), Aimee Teo Broman [ctb] (<https://orcid.org/0000-0003-3783-2807>)
Maintainer: Karl W Broman <broman@wisc.edu>

Diff between broman versions 0.69-5 dated 2019-04-11 and 0.70-4 dated 2020-05-22

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