Sat, 28 Nov 2020

New package SeleMix with initial version 1.0.2
Package: SeleMix
Type: Package
Title: Selective Editing via Mixture Models
Version: 1.0.2
Date: 2020-10-30
Author: Ugo Guarnera [aut], Teresa Buglielli [aut, cre]
Maintainer: Teresa Buglielli <bugliell@istat.it>
Description: Detection of outliers and influential errors using a latent variable model.
Imports: mvtnorm, graphics
Suggests: Ecdat, xtable
License: EUPL
LazyData: yes
NeedsCompilation: no
Packaged: 2020-11-28 22:16:43 UTC; Teresa
Repository: CRAN
Date/Publication: 2020-11-29 01:30:03 UTC

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Package LAGOSNE updated to version 2.0.2 with previous version 2.0.1 dated 2019-07-29

Title: Interface to the Lake Multi-Scaled Geospatial and Temporal Database
Description: Client for programmatic access to the Lake Multi-scaled Geospatial and Temporal database <https://lagoslakes.org>, with functions for accessing lake water quality and ecological context data for the US.
Author: Joseph Stachelek [aut, cre] (<https://orcid.org/0000-0002-5924-2464>), Samantha Oliver [aut] (<https://orcid.org/0000-0001-5668-1165>), Farzan Masrour [aut]
Maintainer: Joseph Stachelek <stachel2@msu.edu>

Diff between LAGOSNE versions 2.0.1 dated 2019-07-29 and 2.0.2 dated 2020-11-28

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Package dscore updated to version 1.4.0 with previous version 1.3.0 dated 2020-05-12

Title: D-Score for Child Development
Description: The D-score is a quantitative measure of child development. The D-score follows the Rasch model. See Jacobusse, van Buuren and Verkerk (2006) <doi:10.1002/sim.2351>. The user can convert milestone scores from 19 assessment instruments into the D-score and the DAZ (D-score adjusted for age). Several tools assist in mapping milestone names into the 9-position Global Scale of Early Development (GSED) convention. Supports calculation of the D-score using 'dutch' <doi:10.1177/0962280212473300>, 'gcdg' <doi:10.1136/bmjgh-2019-001724> and 'gsed' conversion keys. The user can calculate DAZ using 'dutch' and 'gcdg' age-conditional references.
Author: Stef van Buuren [cre, aut], Iris Eekhout [aut], Arjan Huizing [aut]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>

Diff between dscore versions 1.3.0 dated 2020-05-12 and 1.4.0 dated 2020-11-28

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Package CNVScope updated to version 3.3.7 with previous version 3.1.8 dated 2020-07-03

Title: A Versatile Toolkit for Copy Number Variation Relationship Data Analysis and Visualization
Description: Provides the ability to create interaction maps, discover CNV map domains (edges), gene annotate interactions, and create interactive visualizations of these CNV interaction maps.
Author: James Dalgeish, Yonghong Wang, Jack Zhu, Paul Meltzer
Maintainer: James Dalgleish <james.dalgleish@nih.gov>

Diff between CNVScope versions 3.1.8 dated 2020-07-03 and 3.3.7 dated 2020-11-28

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Package microplot updated to version 1.0-44 with previous version 1.0-42 dated 2018-08-19

Title: Microplots (Sparklines) in 'LaTeX', 'Word', 'HTML', 'Excel'
Description: The microplot function writes a set of R graphics files to be used as microplots (sparklines) in tables in either 'LaTeX', 'HTML', 'Word', or 'Excel' files. For 'LaTeX', we provide methods for the Hmisc::latex() generic function to construct 'latex' tabular environments which include the graphs. These can be used directly with the operating system 'pdflatex' or 'latex' command, or by using one of 'Sweave', 'knitr', 'rmarkdown', or 'Emacs org-mode' as an intermediary. For 'MS Word', the msWord() function uses the 'flextable' package to construct 'Word' tables which include the graphs. There are several distinct approaches for constructing HTML files. The simplest is to use the msWord() function with argument filetype="html". Alternatively, use either 'Emacs org-mode' or the htmlTable::htmlTable() function to construct an 'HTML' file containing tables which include the graphs. See the documentation for our as.htmlimg() function. For 'Excel' use on 'Windows', the file examples/irisExcel.xls includes 'VBA' code which brings the individual panels into individual cells in the spreadsheet. Examples in the examples and demo subdirectories are shown with 'lattice' graphics, 'ggplot2' graphics, and 'base' graphics. Examples for 'LaTeX' include 'Sweave' (both 'LaTeX'-style and 'Noweb'-style), 'knitr', 'emacs org-mode', and 'rmarkdown' input files and their 'pdf' output files. Examples for 'HTML' include 'org-mode' and 'Rmd' input files and their webarchive 'HTML' output files. In addition, the as.orgtable() function can display a data.frame in an 'org-mode' document. The examples for 'MS Word' (with either filetype="docx" or filetype="html") work with all operating systems. The package does not require the installation of 'LaTeX' or 'MS Word' to be able to write '.tex' or '.docx' files.
Author: Richard M. Heiberger, with contributions from Karen Byron and Nooreen Dabbish.
Maintainer: Richard M. Heiberger <rmh@temple.edu>

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Package SpatialKDE updated to version 0.6.2 with previous version 0.6.1 dated 2020-04-16

Title: Kernel Density Estimation for Spatial Data
Description: Calculate Kernel Density Estimation (KDE) for spatial data. The algorithm is inspired by the tool 'Heatmap' from 'QGIS'. The method is described by: Hart, T., Zandbergen, P. (2014) <doi:10.1108/PIJPSM-04-2013-0039>, Nelson, T. A., Boots, B. (2008) <doi:10.1111/j.0906-7590.2008.05548.x>, Chainey, S., Tompson, L., Uhlig, S.(2008) <doi:10.1057/palgrave.sj.8350066>.
Author: Jan Caha [aut, cre] (<https://orcid.org/0000-0003-0165-0606>)
Maintainer: Jan Caha <jan.caha@outlook.com>

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Package zenplots updated to version 1.0.3 with previous version 1.0.2 dated 2020-10-03

Title: Zigzag Expanded Navigation Plots
Description: Graphical tools for visualizing high-dimensional data along a path of alternating one- and two-dimensional plots. Note that this includes interactive graphics plots based on 'loon' in turn based on 'tcltk' (included as part of the standard R distribution). It also requires 'graph' from Bioconductor. For more detail on use and algorithms, see <doi:10.18637/jss.v095.i04>.
Author: Marius Hofert [aut], Wayne Oldford [aut, cre]
Maintainer: Wayne Oldford <rwoldford@uwaterloo.ca>

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Package assert updated to version 1.0.1 with previous version 1.0.0 dated 2020-10-24

Title: Validate Function Arguments
Description: Lightweight validation tool for checking function arguments and validating data analysis scripts. This is an alternative to stopifnot() from the 'base' package and to assert_that() from the 'assertthat' package. It provides more informative error messages and facilitates debugging.
Author: Olivier Binette [aut, cre, cph]
Maintainer: Olivier Binette <olivier.binette@gmail.com>

Diff between assert versions 1.0.0 dated 2020-10-24 and 1.0.1 dated 2020-11-28

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Package asciiSetupReader updated to version 2.3.2 with previous version 2.3.1 dated 2020-03-21

Title: Reads Fixed-Width ASCII Data Files (.txt or .dat) that Have Accompanying Setup Files (.sps or .sas)
Description: Lets you open a fixed-width ASCII file (.txt or .dat) that has an accompanying setup file (.sps or .sas). These file combinations are sometimes referred to as .txt+.sps, .txt+.sas, .dat+.sps, or .dat+.sas. This will only run in a txt-sps or txt-sas pair in which the setup file contains instructions to open that text file. It will NOT open other text files, .sav, .sas, or .por data files. Fixed-width ASCII files with setup files are common in older (pre-2000) government data.
Author: Jacob Kaplan [aut, cre] (<https://orcid.org/0000-0002-0601-0387>)
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>

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Package vegan updated to version 2.5-7 with previous version 2.5-6 dated 2019-09-01

Title: Community Ecology Package
Description: Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
Author: Jari Oksanen, F. Guillaume Blanchet, Michael Friendly, Roeland Kindt, Pierre Legendre, Dan McGlinn, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Eduard Szoecs, Helene Wagner
Maintainer: Jari Oksanen <jhoksane@gmail.com>

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New package stpm with initial version 1.7.9
Package: stpm
Type: Package
Title: Stochastic Process Model for Analysis of Longitudinal and Time-to-Event Outcomes
Version: 1.7.9
Date: 2020-11-27
Author: I. Y. Zhbannikov, Liang He, K. G. Arbeev, I. Akushevich, A. I. Yashin.
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>
Description: Utilities to estimate parameters of the models with survival functions induced by stochastic covariates. Miscellaneous functions for data preparation and simulation are also provided. For more information, see: (i)"Stochastic model for analysis of longitudinal data on aging and mortality" by Yashin A. et al. (2007), Mathematical Biosciences, 208(2), 538-551, <DOI:10.1016/j.mbs.2006.11.006>; (ii) "Health decline, aging and mortality: how are they related?" by Yashin A. et al. (2007), Biogerontology 8(3), 291(302), <DOI:10.1007/s10522-006-9073-3>.
License: GPL
Imports: sas7bdat,stats,nloptr,survival,tools,MASS
LinkingTo: Rcpp,RcppArmadillo
Depends: R (>= 2.10), Rcpp (>= 0.11.1)
VignetteBuilder: knitr
Suggests: knitr (>= 1.11), rmarkdown (>= 1.9)
RoxygenNote: 7.1.1
NeedsCompilation: yes
Packaged: 2020-11-28 08:10:41 UTC; iz12
Repository: CRAN
Date/Publication: 2020-11-28 15:20:02 UTC

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New package occCite with initial version 0.4.5
Package: occCite
Type: Package
Title: Querying and Managing Large Biodiversity Occurrence Datasets
Version: 0.4.5
Authors@R: c( person(given = "Hannah L.", family = "Owens", ,"hannah.owens@gmail.com", role=c("aut","cre"), comment = c(ORCID = "0000-0003-0071-1745")), person(given = "Cory", family = "Merow",,,role="aut", comment = c(ORCID = "0000-0003-0561-053X")), person(given = "Brian", family = "Maitner", ,,,role="aut", comment = c(ORCID = "0000-0002-2118-9880")), person(given = "Jamie M.", family = "Kass", ,,,role="aut", comment = c(ORCID = "0000-0002-9432-895X")), person(given = "Vijay", family = "Barve",,"vijay.barve@gmail.com ",role="aut", comment = c(ORCID = "0000-0002-4852-2567")), person(given = "Robert P.", family = "Guralnick",,,role="aut", comment = c(ORCID = "0000-0001-6682-1504")) )
Author: Hannah L. Owens [aut, cre] (<https://orcid.org/0000-0003-0071-1745>), Cory Merow [aut] (<https://orcid.org/0000-0003-0561-053X>), Brian Maitner [aut] (<https://orcid.org/0000-0002-2118-9880>), Jamie M. Kass [aut] (<https://orcid.org/0000-0002-9432-895X>), Vijay Barve [aut] (<https://orcid.org/0000-0002-4852-2567>), Robert P. Guralnick [aut] (<https://orcid.org/0000-0001-6682-1504>)
Maintainer: Hannah L. Owens <hannah.owens@gmail.com>
Description: Facilitates the gathering of biodiversity occurrence data from disparate sources. Metadata is managed throughout the process to facilitate reporting and enhanced ability to repeat analyses.
License: GPL-3
URL: https://github.com/hannahlowens/occCite
BugReports: https://github.com/hannahlowens/occCite/issues
Encoding: UTF-8
LazyData: true
Language: en-US
Depends: R (>= 3.5.0)
Suggests: rmarkdown, RColorBrewer, viridis, remotes, RefManageR, testthat
Imports: bib2df, BIEN, bit64, dplyr, ape, lubridate, methods, rgbif (>= 3.1), taxize, stringr, knitr, stats, leaflet, htmltools, ggplot2, rlang, magrittr, tidyr, RPostgreSQL, DBI, waffle
VignetteBuilder: knitr
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-11-27 08:42:17 UTC; Hannah
Repository: CRAN
Date/Publication: 2020-11-28 15:20:06 UTC

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Package fda updated to version 5.1.7 with previous version 5.1.5.1 dated 2020-08-02

Title: Functional Data Analysis
Description: These functions were developed to support functional data analysis as described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data Analysis. New York: Springer and in Ramsay, J. O., Hooker, Giles, and Graves, Spencer (2009). Functional Data Analysis with R and Matlab (Springer). The package includes data sets and script files working many examples including all but one of the 76 figures in this latter book. Matlab versions are available by ftp from <http://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/>.
Author: J. O. Ramsay <ramsay@psych.mcgill.ca> [aut,cre], Spencer Graves <spencer.graves@effectivedefense.org> [ctb], Giles Hooker <gjh27@cornell.edu> [ctb]
Maintainer: J. O. Ramsay <ramsay@psych.mcgill.ca>

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Package BatchGetSymbols updated to version 2.6.1 with previous version 2.6 dated 2020-11-22

Title: Downloads and Organizes Financial Data for Multiple Tickers
Description: Makes it easy to download financial data from Yahoo Finance <https://finance.yahoo.com/>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>

Diff between BatchGetSymbols versions 2.6 dated 2020-11-22 and 2.6.1 dated 2020-11-28

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Package MLGL updated to version 0.6.5 with previous version 0.6.1 dated 2020-01-16

Title: Multi-Layer Group-Lasso
Description: It implements a new procedure of variable selection in the context of redundancy between explanatory variables, which holds true with high dimensional data (Grimonprez et al. (2018) <https://hal.inria.fr/hal-01857242>).
Author: Quentin Grimonprez [aut, cre], Samuel Blanck [ctb], Alain Celisse [ths], Guillemette Marot [ths], Yi Yang [ctb], Hui Zou [ctb]
Maintainer: Quentin Grimonprez <quentingrim@yahoo.fr>

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Package MKpower updated to version 0.5 with previous version 0.4 dated 2020-02-02

Title: Power Analysis and Sample Size Calculation
Description: Power analysis and sample size calculation for Welch and Hsu (Hedderich and Sachs (2018), ISBN:978-3-662-56657-2) t-tests including Monte-Carlo simulations of empirical power and type-I-error. Power and sample size calculation for Wilcoxon rank sum and signed rank tests via Monte-Carlo simulations. Power and sample size required for the evaluation of a diagnostic test(-system) (Flahault et al. (2005), <doi:10.1016/j.jclinepi.2004.12.009>; Dobbin and Simon (2007), <doi:10.1093/biostatistics/kxj036>) as well as for a single proportion (Fleiss et al. (2003), ISBN:978-0-471-52629-2; Piegorsch (2004), <doi:10.1016/j.csda.2003.10.002>; Thulin (2014), <doi:10.1214/14-ejs909>) and comparing two negative binomial rates (Zhu and Lakkis (2014), <doi:10.1002/sim.5947>).
Author: Matthias Kohl [aut, cre] (<https://orcid.org/0000-0001-9514-8910>)
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>

Diff between MKpower versions 0.4 dated 2020-02-02 and 0.5 dated 2020-11-28

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Package fdaoutlier updated to version 0.1.1 with previous version 0.1.0 dated 2020-11-26

Title: Outlier Detection Tools for Functional Data Analysis
Description: A collection of functions for outlier detection in functional data analysis. Methods implemented include directional outlyingness, MS-plot, total variation depth, and sequential transformations among others.
Author: Oluwasegun Taiwo Ojo [aut, cre, cph] (<https://orcid.org/0000-0001-9629-6990>), Rosa Elvira Lillo [aut], Antonio Fernandez Anta [aut, fnd]
Maintainer: Oluwasegun Taiwo Ojo <seguntaiwoojo@gmail.com>

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Package GWpcor updated to version 0.1.5 with previous version 0.1.4 dated 2020-11-14

Title: Geographically Weighted Partial Correlation Coefficient
Description: Implements a geographically weighted partial correlation which is an extension from gwss() function in the 'GWmodel' package (Percival and Tsutsumida (2017) <doi:10.1553/giscience2017_01_s36>).
Author: Narumasa Tsutsumida [aut, cre] (<https://orcid.org/0000-0002-6333-0301>), Joseph Percival [aut]
Maintainer: Narumasa Tsutsumida <rsnaru.jp@gmail.com>

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Package gplots updated to version 3.1.1 with previous version 3.1.0 dated 2020-09-18

Title: Various R Programming Tools for Plotting Data
Description: Various R programming tools for plotting data, including: - calculating and plotting locally smoothed summary function as ('bandplot', 'wapply'), - enhanced versions of standard plots ('barplot2', 'boxplot2', 'heatmap.2', 'smartlegend'), - manipulating colors ('col2hex', 'colorpanel', 'redgreen', 'greenred', 'bluered', 'redblue', 'rich.colors'), - calculating and plotting two-dimensional data summaries ('ci2d', 'hist2d'), - enhanced regression diagnostic plots ('lmplot2', 'residplot'), - formula-enabled interface to 'stats::lowess' function ('lowess'), - displaying textual data in plots ('textplot', 'sinkplot'), - plotting a matrix where each cell contains a dot whose size reflects the relative magnitude of the elements ('balloonplot'), - plotting "Venn" diagrams ('venn'), - displaying Open-Office style plots ('ooplot'), - plotting multiple data on same region, with separate axes ('overplot'), - plotting means and confidence intervals ('plotCI', 'plotmeans'), - spacing points in an x-y plot so they don't overlap ('space').
Author: Gregory R. Warnes [aut], Ben Bolker [aut], Lodewijk Bonebakker [aut], Robert Gentleman [aut], Wolfgang Huber [aut], Andy Liaw [aut], Thomas Lumley [aut], Martin Maechler [aut], Arni Magnusson [aut], Steffen Moeller [aut], Marc Schwartz [aut], Bill Venables [aut], Tal Galili [ctb, cre]
Maintainer: Tal Galili <tal.galili@gmail.com>

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Package gaussplotR updated to version 0.2.0 with previous version 0.1.6 dated 2020-11-03

Title: Fit, Predict and Plot 2D Gaussians
Description: Functions to fit two-dimensional Gaussian functions, predict values from fits, and produce plots of predicted data via either 'ggplot2' or base R plotting.
Author: Vikram B. Baliga [aut, cre, cph] (<https://orcid.org/0000-0002-9367-8974>)
Maintainer: Vikram B. Baliga <vbaliga87@gmail.com>

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Package sensitivity updated to version 1.23.0 with previous version 1.22.2 dated 2020-10-25

Title: Global Sensitivity Analysis of Model Outputs
Description: A collection of functions for factor screening, global sensitivity analysis and robustness analysis. Most of the functions have to be applied on model with scalar output, but several functions support multi-dimensional outputs.
Author: Bertrand Iooss, Sebastien Da Veiga, Alexandre Janon and Gilles Pujol, with contributions from Baptiste Broto, Khalid Boumhaout, Thibault Delage, Reda El Amri, Jana Fruth, Laurent Gilquin, Joseph Guillaume, Loic Le Gratiet, Paul Lemaitre, Amandine Marrel, Anouar Meynaoui, Barry L. Nelson, Filippo Monari, Roelof Oomen, Oldrich Rakovec, Bernardo Ramos, Olivier Roustant, Eunhye Song, Jeremy Staum, Roman Sueur, Taieb Touati, Frank Weber
Maintainer: Bertrand Iooss <biooss@yahoo.fr>

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Package HH updated to version 3.1-43 with previous version 3.1-42 dated 2020-09-07

Title: Statistical Analysis and Data Display: Heiberger and Holland
Description: Support software for Statistical Analysis and Data Display (Second Edition, Springer, ISBN 978-1-4939-2121-8, 2015) and (First Edition, Springer, ISBN 0-387-40270-5, 2004) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
Author: Richard M. Heiberger
Maintainer: Richard M. Heiberger <rmh@temple.edu>

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