Thu, 21 Dec 2017

Package rmpw updated to version 0.0.2 with previous version 0.0.1 dated 2017-02-27

Title: Causal Mediation Analysis Using Weighting Approach
Description: We implement causal mediation analysis using the methods proposed by Hong (2010) and Hong, Deutsch & Hill (2015) <doi:10.3102/1076998615583902>. It allows the estimation and hypothesis testing of causal mediation effects through ratio of mediator probability weights (RMPW). This strategy conveniently relaxes the assumption of no treatment-by-mediator interaction while greatly simplifying the outcome model specification without invoking strong distributional assumptions. We also implement a sensitivity analysis by extending the RMPW method to assess potential bias in the presence of omitted pretreatment or posttreatment covariates. The sensitivity strategy was proposed by Hong, Qin, and Yang (2018) <doi:10.3102/1076998615583902>.
Author: Xu Qin, Guanglei Hong, and Fan Yang
Maintainer: Xu Qin <xuqin@uchicago.edu>

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Package rlang updated to version 0.1.6 with previous version 0.1.4 dated 2017-11-05

Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.
Author: Lionel Henry [aut, cre], Hadley Wickham [aut], RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>

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Package RBesT updated to version 1.3-1 with previous version 1.2-3 dated 2017-08-21

Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis. This includes meta-analysis, (robust) prior derivation from historical data, operating characteristics and analysis (1 and 2 sample cases).
Author: Novartis Pharma AG [cph], Sebastian Weber [aut, cre], Beat Neuenschwander [ctb], Heinz Schmidli [ctb], Baldur Magnusson [ctb], Yue Li [ctb], Satrajit Roychoudhury [ctb], Trustees of Columbia University [cph] (src/init.cpp, tools/make_cpp.R, R/stanmodels.R)
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>

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Package lme4 updated to version 1.1-15 with previous version 1.1-14 dated 2017-09-27

Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut], Martin Maechler [aut], Ben Bolker [aut, cre], Steven Walker [aut], Rune Haubo Bojesen Christensen [ctb], Henrik Singmann [ctb], Bin Dai [ctb], Fabian Scheipl [ctb], Gabor Grothendieck [ctb], Peter Green [ctb]
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>

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Package fdcov updated to version 1.1.0 with previous version 1.0.0 dated 2016-06-16

Title: Analysis of Covariance Operators
Description: Provides a variety of tools for the analysis of covariance operators including k-sample tests for equality and classification and clustering methods found in the works of Cabassi et al (2017) <doi:10.1214/17-EJS1347>, Kashlak et al (2017) <arXiv:1604.06310>, Pigoli et al (2014) <doi:10.1093/biomet/asu008>, and Panaretos et al (2010) <doi:10.1198/jasa.2010.tm09239>.
Author: Alessandra Cabassi [aut], Adam B Kashlak [aut, cre], Davide Pigoli [ctb]
Maintainer: Adam B Kashlak <kashlak@ualberta.ca>

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Package EValue updated to version 1.1.1 with previous version 1.1.0 dated 2017-11-29

Title: Sensitivity Analyses for Unmeasured Confounding in Observational Studies and Meta-Analyses
Description: Conducts sensitivity analyses for unmeasured confounding for either an observational study or a meta-analysis of observational studies. For a single observational study, the package reports E-values, defined as the minimum strength of association on the risk ratio scale that an unmeasured confounder would need to have with both the treatment and the outcome to fully explain away a specific treatment-outcome association, conditional on the measured covariates. One can use one of the evalues.XX() functions to compute E-values for the relevant outcome types. Outcome types include risk ratios, odds ratio with common or rare outcomes, hazard ratios with common or rare outcomes, and standardized differences in outcomes. Optionally, one can use the bias_plot() function to plot the bias factor as a function of two sensitivity parameters. (See VanderWeele & Ding, 2017 [<http://annals.org/aim/article/2643434>] for details.) For a meta-analysis, use the function confounded_meta to compute point estimates and inference for: (1) the proportion of studies with true causal effect sizes more extreme than a specified threshold of scientific importance; and (2) the minimum bias factor and confounding strength required to reduce to less than a specified threshold the proportion of studies with true effect sizes of scientifically significant size. The functions sens_plot() and sens_table() create plots and tables for visualizing these meta-analysis metrics across a range of bias values, and scrape_meta helps scrape study-level data from a published forest plot or summary table to obtain the needed estimates when these are not reported. (See Mathur & VanderWeele [<https://osf.io/jkhfg/>] for details.) Most of the analyses available in this package can also be conducted using web-based graphical interfaces (for a single observational study: <https://mmathur.shinyapps.io/evalue/>; for a meta-analysis: <https://mmathur.shinyapps.io/meta_gui_2/>).
Author: Maya B. Mathur, Peng Ding, Tyler J. VanderWeele
Maintainer: Maya B. Mathur <mmathur@stanford.edu>

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Package brms updated to version 2.0.1 with previous version 2.0.0 dated 2017-12-15

Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized (non-)linear multivariate multilevel models using Stan for full Bayesian inference. A wide range of distributions and link functions are supported, allowing users to fit -- among others -- linear, robust linear, count data, survival, response times, ordinal, zero-inflated, hurdle, and even self-defined mixture models all in a multilevel context. Further modeling options include non-linear and smooth terms, auto-correlation structures, censored data, meta-analytic standard errors, and quite a few more. In addition, all parameters of the response distribution can be predicted in order to perform distributional regression. Prior specifications are flexible and explicitly encourage users to apply prior distributions that actually reflect their beliefs. Model fit can easily be assessed and compared with posterior predictive checks and leave-one-out cross-validation.
Author: Paul-Christian Bürkner [aut, cre]
Maintainer: Paul-Christian Bürkner <paul.buerkner@gmail.com>

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Package bdsmatrix updated to version 1.3-3 with previous version 1.3-2 dated 2014-08-22

Title: Routines for Block Diagonal Symmetric Matrices
Description: This is a special case of sparse matrices, used by coxme.
Author: Terry Therneau
Maintainer: Terry Therneau <therneau@mayo.edu>

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Package slam updated to version 0.1-42 with previous version 0.1-40 dated 2016-12-01

Title: Sparse Lightweight Arrays and Matrices
Description: Data structures and algorithms for sparse arrays and matrices, based on index arrays and simple triplet representations, respectively.
Author: Kurt Hornik [aut, cre] (0000-0003-4198-9911), David Meyer [aut], Christian Buchta [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

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Package praznik updated to version 2.0.0 with previous version 1.0.0 dated 2017-11-20

Title: Collection of Information-Based Feature Selection Filters
Description: A collection of feature selection filters performing greedy optimisation of mutual information-based usefulness criteria, inspired by the overview by Brown, Pocock, Zhao and Lujan (2012) <http://www.jmlr.org/papers/v13/brown12a.html>. Implements, among other, minimum redundancy maximal relevancy ('mRMR') method by Peng, Long and Ding (2005) <doi:10.1109/TPAMI.2005.159>; joint mutual information ('JMI') method by Yang and Moody (1999) <http://papers.nips.cc/paper/1779-data-visualization-and-feature-selection-new-algorithms-for-nongaussian-data>; double input symmetrical relevance ('DISR') method by Meyer and Bontempi (2006) <doi:10.1007/11732242_9> as well as joint mutual information maximisation ('JMIM') method by Bennasar, Hicks and Setchi (2015) <doi:10.1016/j.eswa.2015.07.007>.
Author: Miron B. Kursa
Maintainer: Miron B. Kursa <M.Kursa@icm.edu.pl>

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Package boxcoxmix updated to version 0.15 with previous version 0.14 dated 2017-10-09

Title: Response Transformations for Random Effect and Variance Component Models
Description: Response transformations for overdispersed generalized linear models and variance component models using nonparametric profile maximum likelihood estimation. The main function is optim.boxcox().
Author: Amani Almohaimeed and Jochen Einbeck
Maintainer: Amani Almohaimeed <amani.almohaimeed@gmail.com>

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Package spam64 updated to version 2.1-2 with previous version 2.1-1 dated 2017-07-02

Title: 64-Bit Extension of the SPArse Matrix R Package 'spam'
Description: Provides the Fortran code of the R package 'spam' with 64-bit integers. Loading this package together with the R package 'spam' enables the sparse matrix class "spam" to handle huge sparse matrices with more than 2^31-1 non-zero elements.
Author: Reinhard Furrer [aut, cre], Florian Gerber [ctb], Daniel Gerber [ctb], Kaspar Moesinger [ctb], Youcef Saad [ctb] (SPARSEKIT http://www-users.cs.umn.edu/~saad/software/SPARSKIT/), Esmond G. Ng [ctb] (Fortran Cholesky routines), Barry W. Peyton [ctb] (Fortran Cholesky routines), Joseph W.H. Liu [ctb] (Fortran Cholesky routines), Alan D. George [ctb] (Fortran Cholesky routines)
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>

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Package rstantools updated to version 1.4.0 with previous version 1.3.0 dated 2017-08-02

Title: Tools for Developing R Packages Interfacing with 'Stan'
Description: Provides various tools for developers of R packages interfacing with 'Stan' <http://mc-stan.org>, including functions to set up the required package structure, S3 generics and default methods to unify function naming across 'Stan'-based R packages, and a vignette with recommendations for developers.
Author: Jonah Gabry [aut, cre], Ben Goodrich [aut], Trustees of Columbia University [cph]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>

Diff between rstantools versions 1.3.0 dated 2017-08-02 and 1.4.0 dated 2017-12-21

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Package rstanarm updated to version 2.17.2 with previous version 2.15.3 dated 2017-04-29

Title: Bayesian Applied Regression Modeling via Stan
Description: Estimates previously compiled regression models using the 'rstan' package, which provides the R interface to the Stan C++ library for Bayesian estimation. Users specify models via the customary R syntax with a formula and data.frame plus some additional arguments for priors.
Author: Jonah Gabry [aut], Imad Ali [ctb], Sam Brilleman [ctb], Trustees of Columbia University [cph], Simon Wood [cph] (R/stan_gamm4.R), R Core Deveopment Team [cph] (R/stan_aov.R), Douglas Bates [cph] (R/pp_data.R), Martin Maechler [cph] (R/pp_data.R), Ben Bolker [cph] (R/pp_data.R), Steve Walker [cph] (R/pp_data.R), Brian Ripley [cph] (R/stan_aov.R, R/stan_polr.R), William Venables [cph] (R/stan_polr.R), Ben Goodrich [cre, aut]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>

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Package MetaLandSim updated to version 1.0 with previous version 0.5.6 dated 2017-07-08

Title: Landscape and Range Expansion Simulation
Description: Tools to generate random landscape graphs, evaluate species occurrence in dynamic landscapes, simulate future landscape occupation and evaluate range expansion when new empty patches are available (e.g. as a result of climate change).
Author: Frederico Mestre, Fernando Canovas, Benjamin Risk, Ricardo Pita, Antonio Mira, Pedro Beja.
Maintainer: Frederico Mestre <mestre.frederico@gmail.com>

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Package canvasXpress updated to version 1.18.1 with previous version 1.17.9 dated 2017-11-28

Title: Visualization Package for CanvasXpress in R
Description: Enables creation of visualizations using the CanvasXpress framework in R. CanvasXpress is a standalone JavaScript library for reproducible research with complete tracking of data and end-user modifications stored in a single PNG image that can be played back. See <http://canvasxpress.org> for more information.
Author: Isaac Neuhaus [aut, cre], Connie Brett [ctb]
Maintainer: Connie Brett <connie@aggregate-genius.com>

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Package wikitaxa updated to version 0.2.0 with previous version 0.1.4 dated 2017-05-05

Title: Taxonomic Information from 'Wikipedia'
Description: 'Taxonomic' information from 'Wikipedia', 'Wikicommons', 'Wikispecies', and 'Wikidata'. Functions included for getting taxonomic information from each of the sources just listed, as well performing taxonomic search.
Author: Scott Chamberlain [aut, cre], Ethan Welty [aut]
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>

Diff between wikitaxa versions 0.1.4 dated 2017-05-05 and 0.2.0 dated 2017-12-21

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Package Ternary updated to version 1.0.0 with previous version 0.1.1 dated 2017-11-23

Title: A Package to Generate Ternary Plots
Description: Plots ternary diagrams using the standard graphics functions. An alternative to 'ggtern', which uses the 'ggplot2' family of plotting functions.
Author: Martin R. Smith [aut, cre, cph] (0000-0001-5660-1727)
Maintainer: Martin R. Smith <martins@gmail.com>

Diff between Ternary versions 0.1.1 dated 2017-11-23 and 1.0.0 dated 2017-12-21

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New package swatches with initial version 0.5.0
Package: swatches
Type: Package
Title: Read, Inspect, and Manipulate Color Swatch Files
Version: 0.5.0
Date: 2017-12-20
Authors@R: c( person("Bob", "Rudis", email = "bob@rud.is", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5670-2640")) )
Maintainer: Bob Rudis <bob@rud.is>
Description: There are numerous places to create and download color palettes. These are usually shared in 'Adobe' swatch file formats of some kind. There is also often the need to use standard palettes developed within an organization to ensure that aesthetics are carried over into all projects and output. Now there is a way to read these swatch files in R and avoid transcribing or converting color values by hand or or with other programs. This package provides functions to read and inspect 'Adobe Color' ('ACO'), 'Adobe Swatch Exchange' ('ASE'), 'GIMP Palette' ('GPL'), 'OpenOffice' palette ('SOC') files and 'KDE Palette' ('colors') files. Detailed descriptions of 'Adobe Color' and 'Swatch Exchange' file formats as well as other swatch file formats can be found at <http://www.selapa.net/swatches/colors/fileformats.php>.
URL: https://github.com/hrbrmstr/swatches
BugReports: https://github.com/hrbrmstr/swatches/issues
License: MIT + file LICENSE
Encoding: UTF-8
NeedsCompilation: yes
Imports: httr, pack, stringr, xml2, tools, colorspace, grDevices, graphics, methods, stats
Suggests: testthat, covr
Depends: R (>= 3.2.0)
RoxygenNote: 6.0.1.9000
Packaged: 2017-12-21 15:27:58 UTC; hrbrmstr
Author: Bob Rudis [aut, cre] (0000-0001-5670-2640)
Repository: CRAN
Date/Publication: 2017-12-21 15:43:03 UTC

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Package simmer.plot updated to version 0.1.12 with previous version 0.1.11 dated 2017-10-24

Title: Plotting Methods for 'simmer'
Description: A set of plotting methods for 'simmer' trajectories and simulations.
Author: Iñaki Ucar [aut, cph, cre] (0000-0001-6403-5550), Bart Smeets [aut, cph]
Maintainer: Iñaki Ucar <i.ucar86@gmail.com>

Diff between simmer.plot versions 0.1.11 dated 2017-10-24 and 0.1.12 dated 2017-12-21

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New package samplesizeCMH with initial version 0.0.0
Package: samplesizeCMH
Title: Power and Sample Size Calculation for the Cochran-Mantel-Haenszel Test
Date: 2017-12-13
Version: 0.0.0
Authors@R: c( person("Paul", "Egeler", email = "paul.egeler@spectrumhealth.org", role = c("aut", "cre")), person("Spectrum Health, Grand Rapids, MI", role = "cph"))
Copyright: Spectrum Health, Grand Rapids, MI
Description: Calculates the power and sample size for Cochran-Mantel-Haenszel tests. There are also several helper functions for working with probability, odds, relative risk, and odds ratio values.
Depends: R (>= 3.4.0)
Imports: stats
License: GPL-2 | GPL-3
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown, DescTools, datasets, testthat
VignetteBuilder: knitr
RoxygenNote: 6.0.1
URL: https://github.com/pegeler/samplesizeCMH
BugReports: https://github.com/pegeler/samplesizeCMH/issues
NeedsCompilation: no
Packaged: 2017-12-21 14:19:57 UTC; pau64307
Author: Paul Egeler [aut, cre], Spectrum Health, Grand Rapids, MI [cph]
Maintainer: Paul Egeler <paul.egeler@spectrumhealth.org>
Repository: CRAN
Date/Publication: 2017-12-21 15:15:57 UTC

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New package labelVector with initial version 0.0.1
Package: labelVector
Title: Label Attributes for Atomic Vectors
Version: 0.0.1
Authors@R: person("Benjamin", "Nutter", , "benjamin.nutter@gmail.com", role = c("aut", "cre"))
Description: Labels are a common construct in statistical software providing a human readable description of a variable. While variable names are succinct, quick to type, and follow a language's naming conventions, labels may be more illustrative and may use plain text and spaces. R does not provide native support for labels. Some packages, however, have made this feature available. Most notably, the 'Hmisc' package provides labelling methods for a number of different object. Due to design decisions, these methods are not all exported, and so are unavailable for use in package development. The 'labelVector' package supports labels for atomic vectors in a light-weight design that is suitable for use in other packages.
Depends: R (>= 2.0.0)
Suggests: Hmisc, knitr, testthat
License: MIT + file LICENSE
LazyData: true
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-12-21 14:50:54 UTC; benjamin
Author: Benjamin Nutter [aut, cre]
Maintainer: Benjamin Nutter <benjamin.nutter@gmail.com>
Repository: CRAN
Date/Publication: 2017-12-21 15:23:41 UTC

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New package alphashape3d with initial version 1.3
Package: alphashape3d
Version: 1.3
Date: 2017-12-14
Title: Implementation of the 3D Alpha-Shape for the Reconstruction of 3D Sets from a Point Cloud
Author: Thomas Lafarge, Beatriz Pateiro-Lopez
Maintainer: Beatriz Pateiro-Lopez <beatriz.pateiro@usc.es>
Depends: geometry, rgl
Suggests: alphahull
Description: Implementation in R of the alpha-shape of a finite set of points in the three-dimensional space. The alpha-shape generalizes the convex hull and allows to recover the shape of non-convex and even non-connected sets in 3D, given a random sample of points taken into it. Besides the computation of the alpha-shape, this package provides users with functions to compute the volume of the alpha-shape, identify the connected components and facilitate the three-dimensional graphical visualization of the estimated set.
License: GPL-2
LazyLoad: yes
NeedsCompilation: yes
RoxygenNote: 6.0.1
Packaged: 2017-12-21 12:37:08 UTC; beatriz
Repository: CRAN
Date/Publication: 2017-12-21 16:04:36

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Package propagate updated to version 1.0-5 with previous version 1.0-4 dated 2014-09-27

Title: Propagation of Uncertainty
Description: Propagation of uncertainty using higher-order Taylor expansion and Monte Carlo simulation.
Author: Andrej-Nikolai Spiess <a.spiess@uke.uni-hamburg.de>
Maintainer: Andrej-Nikolai Spiess <a.spiess@uke.uni-hamburg.de>

Diff between propagate versions 1.0-4 dated 2014-09-27 and 1.0-5 dated 2017-12-21

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Package PBIBD updated to version 1.3 with previous version 1.2 dated 2017-01-20

Title: Partially Balanced Incomplete Block Designs
Description: The PBIB designs are important type of incomplete block designs having wide area of their applications for example in agricultural experiments, in plant breeding, in sample surveys etc. This package constructs various series of PBIB designs and assists in checking all the necessary conditions of PBIB designs and the association scheme on which these designs are based on. It also assists in calculating the efficiencies of PBIB designs with any number of associate classes. The package also constructs Youden-m square designs which are Row-Column designs for the two-way elimination of heterogeneity. The incomplete columns of these Youden-m square designs constitute PBIB designs. With the present functionality, the package will be of immense importance for the researchers as it will help them to construct PBIB designs, to check if their PBIB designs and association scheme satisfy various necessary conditions for the existence, to calculate the efficiencies of PBIB designs based on any association scheme and to construct Youden-m square designs for the two-way elimination of heterogeneity. R. C. Bose and K. R. Nair (1939) <http://www.jstor.org/stable/40383923>.
Author: Parneet Kaur <parneet.nonu93@gmail.com>, Kush Sharma <kush.vashishtha@gmail.com>, Davinder Kumar Garg <dkgarg_stat@yahoo.co.in>
Maintainer: Kush Sharma <kush.vashishtha@gmail.com>

Diff between PBIBD versions 1.2 dated 2017-01-20 and 1.3 dated 2017-12-21

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Package PairedData updated to version 1.1.0 with previous version 1.0.1 dated 2013-04-19

Title: Paired Data Analysis
Description: Many datasets and a set of graphics (based on ggplot2), statistics, effect sizes and hypothesis tests are provided for analysing paired data with S4 class.
Author: Stephane Champely <champely@univ-lyon1.fr>
Maintainer: Stephane Champely <champely@univ-lyon1.fr>

Diff between PairedData versions 1.0.1 dated 2013-04-19 and 1.1.0 dated 2017-12-21

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Package fractal updated to version 2.0-4 with previous version 2.0-1 dated 2016-05-20

Title: A Fractal Time Series Modeling and Analysis Package
Description: Stochastic fractal and deterministic chaotic time series analysis.
Author: William Constantine [cre, aut], Donald Percival [aut]
Maintainer: William Constantine <wlbconstan@gmail.com>

Diff between fractal versions 2.0-1 dated 2016-05-20 and 2.0-4 dated 2017-12-21

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New package BioCircos with initial version 0.2.2
Package: BioCircos
Title: Interactive Circular Visualization of Genomic Data using 'htmlwidgets' and 'BioCircos.js'
Version: 0.2.2
Authors@R: c(person("Loan", "Vulliard", email = "lvulliard@cemm.at", role = c("trl", "cre")), person("Xiaowei", "Chen", email = "chenxiaowei@moon.ibp.ac.cn", role = c("aut")), person("Ya", "Cui", email = "cui_ya@163.com", role = c("aut")))
Description: Implement in 'R' interactive Circos-like visualizations of genomic data, to map information such as genetic variants, genomic fusions and aberrations to a circular genome, as proposed by the 'JavaScript' library 'BioCircos.js', based on the 'JQuery' and 'D3' technologies.
Depends: R (>= 3.1.0)
License: GPL-2 | file LICENSE
Encoding: UTF-8
URL: https://github.com/lvulliard/BioCircos.R
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Imports: RColorBrewer, htmlwidgets, jsonlite, plyr, grDevices
NeedsCompilation: no
Packaged: 2017-12-20 15:58:48 UTC; lvulliard
Author: Loan Vulliard [trl, cre], Xiaowei Chen [aut], Ya Cui [aut]
Maintainer: Loan Vulliard <lvulliard@cemm.at>
Repository: CRAN
Date/Publication: 2017-12-21 14:07:41 UTC

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New package wtss with initial version 1.0.0
Package: wtss
Title: An R Client for a Web Time-Series Service
Version: 1.0.0
Date: 2017-12-14
Authors@R: c(person("Victor", "Maus", role = c("aut"), email ="vwmaus1@gmail.com"), person("Pedro", "Andrade", role = c("aut"), email ="pedro.andrade@inpe.br"), person("Alber", "Sanchez", role = c("aut"),email ="alber.ipia@inpe.br"), person("Luiz Fernando", "Assis", role = c("aut"), email ="luizffga@dpi.inpe.br"), person("Gilberto", "Ribeiro", role = c("aut"), email ="gilberto.queiroz@inpe.br"), person("Gilberto", "Camara", role = c("aut", "cre"), email = "gilberto.camara@inpe.br"))
Maintainer: Gilberto Camara <gilberto.camara@inpe.br>
Description: An R client that provides remote access to satellite image time series. The client allows Earth observation users to obtain time series from data sets available in a Web Time Series Server. The functions include: (a) listing the data sets available in the server; (b) describing the contents of a data set; (c) retrieving a time series based on spatial location and temporal filters.
Depends: R (>= 3.0.0)
License: GPL-3
Imports: methods, roxygen2, RCurl, jsonlite, lubridate, zoo
RoxygenNote: 6.0.1
URL: https://github.com/e-sensing/wtss
BugReports: https://github.com/e-sensing/wtss/issues
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-12-21 10:41:32 UTC; gilberto
Author: Victor Maus [aut], Pedro Andrade [aut], Alber Sanchez [aut], Luiz Fernando Assis [aut], Gilberto Ribeiro [aut], Gilberto Camara [aut, cre]
Repository: CRAN
Date/Publication: 2017-12-21 13:30:45 UTC

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New package skimr with initial version 1.0
Package: skimr
Title: Compact and Flexible Summaries of Data
Version: 1.0
Authors@R: c( person("Amelia", "McNamara", email="amcnamara@smith.edu", role = "aut"), person("Eduardo", "Arino de la Rubia", email="earino@gmail.com", role = "aut"), person("Hao", "Zhu", email="haozhu233@gmail.com", role = "aut"), person("Julia", "Lowndes", email="lowndes@nceas.ucsb.edu", role = 'ctb'), person("Shannon", "Ellis", email="sellis18@jhmi.edu", role = "aut"), person("Elin", "Waring", email="elin.waring@gmail.com", role = "cre"), person("Michael", "Quinn", email="msquinn2@illinois.edu", role = "aut"), person("Hope", "McLeod", email="hmgit2@gmail.com", role = 'ctb'), person("Hadley", "Wickham", email="hadley@rstudio.com", role = 'ctb'), person("Kirill", "Müller", email="krlmlr+r@mailbox.org", role = 'ctb'), person(family = "RStudio, Inc.", role = "cph", comment = "Spark functions"), person("Connor", "Kirkpatrick", email="hello@connorkirkpatrick.com", role = 'ctb'), person("Scott","Brenstuhl", email="brenstsr@miamioh.edu", role = 'ctb') )
Maintainer: Elin Waring <elin.waring@gmail.com>
Description: A simple to use summary function that can be used with pipes and displays nicely in the console. The default summary statistics may be modified by the user as can the default formatting. Support for data frames and vectors is included, and users can implement their own skim methods for specific object types as described in a vignette. Default summaries include support for inline spark graphs. Instructions for managing these on specific operating systems are given in the "Using skimr" vignette and the README.
Depends: R (>= 3.1.2)
Imports: dplyr (>= 0.7), magrittr, pander, purrr, rlang, stats, stringr, knitr, tibble (>= 0.6), tidyr (>= 0.7), tidyselect
Suggests: extrafont, rmarkdown, testthat, withr
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/ropenscilabs/skimr
BugReports: https://github.com/ropenscilabs/skimr/issues
VignetteBuilder: knitr
RoxygenNote: 6.0.1
Collate: 'skimr-package.R' 'formats.R' 'stats.R' 'functions.R' 'options.R' 'skim.R' 'skim_print.R' 'skim_v.R' 'summary.R'
NeedsCompilation: no
Packaged: 2017-12-21 09:57:47 UTC; elinwaring
Author: Amelia McNamara [aut], Eduardo Arino de la Rubia [aut], Hao Zhu [aut], Julia Lowndes [ctb], Shannon Ellis [aut], Elin Waring [cre], Michael Quinn [aut], Hope McLeod [ctb], Hadley Wickham [ctb], Kirill Müller [ctb], RStudio, Inc. [cph] (Spark functions), Connor Kirkpatrick [ctb], Scott Brenstuhl [ctb]
Repository: CRAN
Date/Publication: 2017-12-21 13:16:25 UTC

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New package simtimer with initial version 3.0.0
Package: simtimer
Type: Package
Title: Datetimes as Integers for Discrete-Event Simulations
Version: 3.0.0
Date: 2017-12-21
Author: Adrian Staempfli, Christoph Strauss, Michael Schmid
Maintainer: Adrian Staempfli <adrian.staempfli@fhsg.ch>
Description: Handles datetimes as integers for the usage inside Discrete-Event Simulations (DES). The conversion is made using the internally generic function as.numeric() of the base package. DES is described in Simulation Modeling and Analysis by Averill Law and David Kelton (1999) <doi:10.2307/2288169>.
License: GPL-3
LazyData: TRUE
Suggests: testthat, knitr, rmarkdown, microbenchmark, lubridate
URL: http://github.com/ims-fhs/simtimer
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-12-21 10:46:31 UTC; SCN
Repository: CRAN
Date/Publication: 2017-12-21 13:33:14 UTC

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New package seaaroundus with initial version 1.2.0
Package: seaaroundus
Title: Sea Around Us API Wrapper
Description: Access Sea Around Us (<http://www.seaaroundus.org/>) fish catch data, including tools for visualizing the data.
Version: 1.2.0
Authors@R: c( person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus+r@gmail.com"), person("Robert Scott", "Reis", email = "reis.robert.s@gmail.com", role="aut") )
Depends: R (>= 3.2.2)
License: Apache License 2.0
LazyData: true
Imports: crul (>= 0.4.0), jsonlite, ggplot2, grid, scales, sp, rgdal, maps, wicket (>= 0.4.0)
Suggests: roxygen2 (>= 6.0.1), testthat
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-12-21 05:30:59 UTC; sckott
Author: Scott Chamberlain [aut, cre], Robert Scott Reis [aut]
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>
Repository: CRAN
Date/Publication: 2017-12-21 13:03:11 UTC

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New package robis with initial version 1.0.0
Package: robis
Title: Ocean Biogeographic Information System (OBIS) Client
Description: Client for the Ocean Biogeographic Information System (<http://iobis.org>). Includes functions for each of the API methods, including searching for occurrences, creating a checklist, searching for datasets and for visualizing the results.
Version: 1.0.0
Date: 2017-12-20
Authors@R: c( person("Pieter", "Provoost", , "pieterprovoost@gmail.com", role = "aut"), person("Samuel", "Bosch", , "mail@samuelbosch.com", role = "aut"), person("Ward", "Appeltans", role = "ctb"), person(, "OBIS", , "support@iobis.org", role = c("cre","cph")) )
URL: https://github.com/iobis/robis
BugReports: https://github.com/iobis/robis/issues
Depends: R (>= 3.1.3)
Imports: httr, dplyr, jsonlite, leaflet
License: MIT + file LICENSE
Suggests: testthat
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-12-21 10:43:07 UTC; samuel
Author: Pieter Provoost [aut], Samuel Bosch [aut], Ward Appeltans [ctb], OBIS [cre, cph]
Maintainer: OBIS <support@iobis.org>
Repository: CRAN
Date/Publication: 2017-12-21 13:20:38 UTC

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New package grapherator with initial version 1.0.0
Package: grapherator
Title: A Modular Multi-Step Graph Generator
Description: Set of functions for step-wise generation of (weighted) graphs. Aimed for research in the field of single- and multi-objective combinatorial optimization. Graphs are generated adding nodes, edges and weights. Each step may be repeated multiple times with different predefined and custom generators resulting in high flexibility regarding the graph topology and structure of edge weights.
Version: 1.0.0
Encoding: UTF-8
Date: 2017-12-20
Authors@R: c(person("Jakob", "Bossek", email = "j.bossek@gmail.com", role = c("aut", "cre")))
Maintainer: Jakob Bossek <j.bossek@gmail.com>
License: BSD_2_clause + file LICENSE
URL: https://github.com/jakobbossek/grapherator
BugReports: https://github.com/jakobbossek/grapherator/issues
Imports: BBmisc (>= 1.6), checkmate (>= 1.1), reshape2 (>= 1.4.1), vegan, ggplot2 (>= 1.0.0), lhs, deldir, grDevices
Suggests: testthat (>= 0.9.1), knitr, rmarkdown, gridExtra, magrittr
ByteCompile: yes
LazyData: yes
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-12-20 16:53:57 UTC; jboss
Author: Jakob Bossek [aut, cre]
Repository: CRAN
Date/Publication: 2017-12-21 13:19:38 UTC

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New package ePCR with initial version 0.9.9-4
Package: ePCR
Type: Package
Title: Ensemble Penalized Cox Regression for Survival Prediction
Version: 0.9.9-4
Date: 2017-12-21
Author: Teemu Daniel Laajala <teelaa@utu.fi> [aut, cre], Mika Murtojärvi <mianmu2@hotmail.com> [ctb]
Maintainer: Teemu Daniel Laajala <teelaa@utu.fi>
Depends: R (>= 3.0.0)
Imports: grDevices, graphics, stats, utils, Matrix, MASS, glmnet, hamlet, survival, ROCR, timeROC, pracma, Bolstad2, impute, c060, methods
Description: The top-performing ensemble-based Penalized Cox Regression (ePCR) framework developed during the DREAM 9.5 mCRPC Prostate Cancer Challenge <https://www.synapse.org/ProstateCancerChallenge> presented in Guinney J, Wang T, Laajala TD, et al. (2017) <doi:10.1016/S1470-2045(16)30560-5> is provided here-in, together with the corresponding follow-up work. While initially aimed at modeling the most advanced stage of prostate cancer, metastatic Castration-Resistant Prostate Cancer (mCRPC), the modeling framework has subsequently been extended to cover also the non-metastatic form of advanced prostate cancer (CRPC). Readily fitted ensemble-based model S4-objects are provided, and a simulated example dataset based on a real-life cohort is provided from the Turku University Hospital, to illustrate the use of the package. Functionality of the ePCR methodology relies on constructing ensembles of strata in patient cohorts and averaging over them, with each ensemble member consisting of a highly optimized penalized/regularized Cox regression model. Various cross-validation and other modeling schema are provided for constructing novel model objects.
License: GPL (>= 2)
Encoding: UTF-8
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-12-21 12:11:42 UTC; teelaa
Repository: CRAN
Date/Publication: 2017-12-21 13:41:43 UTC

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Package archiDART updated to version 3.0 with previous version 2.0 dated 2017-05-11

Title: Plant Root System Architecture Analysis Using DART and RSML Files
Description: Analysis of complex plant root system architectures (RSA) using the output files created by Data Analysis of Root Tracings (DART), an open-access software dedicated to the study of plant root architecture and development across time series (Le Bot et al (2010) "DART: a software to analyse root system architecture and development from captured images", Plant and Soil, <DOI:10.1007/s11104-009-0005-2>), and RSA data encoded with the Root System Markup Language (RSML) (Lobet et al (2015) "Root System Markup Language: toward a unified root architecture description language", Plant Physiology, <DOI:10.1104/pp.114.253625>). More information can be found in Delory et al (2016) "archiDART: an R package for the automated computation of plant root architectural traits", Plant and Soil, <DOI:10.1007/s11104-015-2673-4>.
Author: Benjamin M Delory, Caroline Baudson, Yves Brostaux, Guillaume Lobet, Patrick du Jardin, Loic Pages, Pierre Delaplace
Maintainer: Benjamin M Delory <Benjamin.Delory@leuphana.de>

Diff between archiDART versions 2.0 dated 2017-05-11 and 3.0 dated 2017-12-21

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 archiDART-3.0/archiDART/R/archidraw.R                     |  250 ++++-
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Package BullsEyeR updated to version 0.2.0 with previous version 0.1.0 dated 2017-12-11

Title: Topic Modelling
Description: Helps in initial processing like converting text to lower case, removing punctuation, numbers, stop words, stemming, sparsity control and term frequency inverse document frequency processing. Helps in recognizing domain or corpus specific stop words. Makes use of 'ldatunig' output to pick optimal number of topics for topic modelling. Helps in topic modelling the content.
Author: Krishna Harsha
Maintainer: Krishna Harsha <khkrishnaharsha123@gmail.com>

Diff between BullsEyeR versions 0.1.0 dated 2017-12-11 and 0.2.0 dated 2017-12-21

 DESCRIPTION      |    8 +--
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 5 files changed, 19 insertions(+), 133 deletions(-)

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New package OptSig with initial version 1.0
Package: OptSig
Type: Package
Title: Optimal Level of Significance for Regression and Other Statistical Tests
Version: 1.0
Imports: pwr
Date: 2017-12-18
Author: Jae H. Kim <J.Kim@latrobe.edu.au>
Maintainer: Jae H. Kim <J.Kim@latrobe.edu.au>
Description: Calculates the optimal level of significance based on a decision-theoretic approach. The optimal level is chosen so that the expected loss from hypothesis testing is minimized. A range of statistical tests are covered, including the test for the population mean, population proportion, and a linear restriction in a multiple regression model. The details are covered in Kim, Jae H. and Choi, In, Choosing the Level of Significance: A Decision-Theoretic Approach (December 18, 2017), available at SSRN: <https://ssrn.com/abstract=2652773> or <doi:10.2139/ssrn.2652773>. See also Kim and Ji (2015) <doi:10.1016/j.jempfin.2015.08.006>.
License: GPL-2
NeedsCompilation: no
Packaged: 2017-12-20 19:54:59 UTC; JKim
Repository: CRAN
Date/Publication: 2017-12-21 10:26:39 UTC

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New package TrioSGL with initial version 1.1.0
Package: TrioSGL
Type: Package
Encoding: UTF-8
Title: Trio Model with a Combination of Lasso and Group Lasso Regularization
Version: 1.1.0
Date: 2017-12-18
Author: Timo Stöcker, Noah Simon, Jerome Friedman, Trevor Hastie, and Rob Tibshirani
Maintainer: Timo Stöcker <timo.stoecker@hhu.de>
Description: Fit a trio model via penalized maximum likelihood. The model is fit for a path of values of the penalty parameter. This package is based on Noah Simon, et al. (2011) <doi:10.1080/10618600.2012.681250>.
NeedsCompilation: yes
License: GPL
Packaged: 2017-12-20 16:59:28 UTC; stoecker
Repository: CRAN
Date/Publication: 2017-12-21 09:40:55 UTC

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New package SimRVPedigree with initial version 0.1.0
Package: SimRVPedigree
Type: Package
Title: Simulate Pedigrees Ascertained for a Rare Disease
Version: 0.1.0
Authors@R: c(person("Christina", "Nieuwoudt", role = c("aut", "cre"), email = "cnieuwou@sfu.ca"), person("Jinko", "Graham", role = "aut"))
Description: Routines to simulate and manipulate pedigrees ascertained to contain multiple family members affected by a rare disease. Christina Nieuwoudt, Samantha J Jones, Angela Brooks-Wilson, and Jinko Graham (2017) <doi:10.1101/234153>.
Depends: R (>= 3.4.0)
Imports: kinship2 (>= 1.6.4), dplyr (>= 0.7.4), stats (>= 3.4.0)
Suggests: doParallel (>= 1.0.11), doRNG (>= 1.6.6), graphics (>= 3.4.0), knitr (>= 1.17), rmarkdown (>= 1.8), roxygen2 (>= 6.0.1), testthat (>= 2.0.0)
License: GNU General Public License
LazyData: TRUE
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-12-20 15:43:09 UTC; cnieuwoudt
Author: Christina Nieuwoudt [aut, cre], Jinko Graham [aut]
Maintainer: Christina Nieuwoudt <cnieuwou@sfu.ca>
Repository: CRAN
Date/Publication: 2017-12-21 09:43:13 UTC

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New package RSocrata with initial version 1.7.4-7
Package: RSocrata
Type: Package
Title: Download or Upload 'Socrata' Data Sets
Description: Provides easier interaction with 'Socrata' open data portals <http://dev.socrata.com>. Users can provide a 'Socrata' data set resource URL, or a 'Socrata' Open Data API (SoDA) web query, or a 'Socrata' "human-friendly" URL, returns an R data frame. Converts dates to 'POSIX' format and manages throttling by 'Socrata'. Users can upload data to 'Socrata' portals directly from R.
Version: 1.7.4-7
Date: 2017-12-20
Author: Hugh Devlin, Ph. D., Tom Schenk, Jr., Gene Leynes, Nick Lucius, John Malc, Mark Silverberg, and Peter Schmeideskamp
Maintainer: "Tom Schenk Jr." <developers@cityofchicago.org>
Depends: R (>= 3.3.0)
Imports: httr (>= 1.0.0), jsonlite (>= 0.9.16), mime (>= 0.3), plyr (>= 1.8.4)
Suggests: testthat (>= 0.10.0), roxygen2 (>= 4.1.0), readr (>= 0.2.2)
License: MIT + file LICENSE
URL: https://github.com/Chicago/RSocrata
BugReports: https://github.com/Chicago/RSocrata/issues
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-12-20 15:59:21 UTC; appveyor
Repository: CRAN
Date/Publication: 2017-12-21 09:34:43 UTC

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Package ggspectra updated to version 0.2.3 with previous version 0.2.2 dated 2017-08-31

Title: Extensions to 'ggplot2' for Radiation Spectra
Description: Additional annotations, and stats for plotting "light" spectra with 'ggplot2', together with specializations of ggplot() and plot() methods for spectral data stored in objects of the classes defined in package 'photobiology' and a plot() method for objects of class "waveband", also defined in package 'photobiology'.
Author: Pedro J. Aphalo [aut, cre], Titta K. Kotilainen [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

Diff between ggspectra versions 0.2.2 dated 2017-08-31 and 0.2.3 dated 2017-12-21

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 vignettes/userguide1-grammar.Rmd       |   21 ++--
 vignettes/userguide2-plot-methods.Rmd  |   31 +++++-
 86 files changed, 575 insertions(+), 298 deletions(-)

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