Wed, 19 Sep 2018

Package NetworkToolbox updated to version 1.2.1 with previous version 1.2.0 dated 2018-07-25

Title: Methods and Measures for Brain, Cognitive, and Psychometric Network Analysis
Description: Implements network analysis and graph theory measures used in neuroscience, cognitive science, and psychology. Methods include various filtering methods and approaches such as threshold, dependency (Kenett, Tumminello, Madi, Gur-Gershogoren, Mantegna, & Ben-Jacob, 2010 <doi:10.1371/journal.pone.0015032>), Information Filtering Networks (Barfuss, Massara, Di Matteo, & Aste, 2016 <doi:10.1103/PhysRevE.94.062306>), and Efficiency-Cost Optimization (Fallani, Latora, & Chavez, 2017 <doi:10.1371/journal.pcbi.1005305>). Brain methods include the recently developed Connectome Predictive Modeling (see references in package). Also implements several network measures including local network characteristics (e.g., centrality), community-level network characteristics (e.g., community centrality), global network characteristics (e.g., clustering coefficient), and various other measures associated with the reliability and reproducibility of network analysis.
Author: Alexander Christensen
Maintainer: Alexander Christensen <alexpaulchristensen@gmail.com>

Diff between NetworkToolbox versions 1.2.0 dated 2018-07-25 and 1.2.1 dated 2018-09-19

 DESCRIPTION            |   10 +++++-----
 MD5                    |   48 +++++++++++++++++++++++++-----------------------
 NAMESPACE              |    1 +
 NEWS                   |   10 ++++++++++
 R/LoGo.R               |    7 ++++++-
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 R/net.coverage.R       |   14 ++++++++++++--
 R/resp.rep.R           |only
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 man/net.coverage.Rd    |   12 +++++++++++-
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 man/resp.rep.Rd        |only
 man/smallworldness.Rd  |    4 ++--
 man/stable.Rd          |    4 ++--
 man/threshold.Rd       |    8 ++------
 26 files changed, 137 insertions(+), 105 deletions(-)

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Package Gmisc updated to version 1.6.4 with previous version 1.6.2 dated 2018-06-20

Title: Descriptive Statistics, Transition Plots, and More
Description: Tools for making the descriptive "Table 1" used in medical articles, a transition plot for showing changes between categories, flow charts by extending the grid package, a method for variable selection based on the SVD, Bézier lines with arrows complementing the ones in the 'grid' package, and more.
Author: Max Gordon <max@gforge.se>
Maintainer: Max Gordon <max@gforge.se>

Diff between Gmisc versions 1.6.2 dated 2018-06-20 and 1.6.4 dated 2018-09-19

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 41 files changed, 328 insertions(+), 304 deletions(-)

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Package data.table updated to version 1.11.6 with previous version 1.11.4 dated 2018-05-27

Title: Extension of `data.frame`
Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
Author: Matt Dowle [aut, cre], Arun Srinivasan [aut], Jan Gorecki [ctb], Michael Chirico [ctb], Pasha Stetsenko [ctb], Tom Short [ctb], Steve Lianoglou [ctb], Eduard Antonyan [ctb], Markus Bonsch [ctb], Hugh Parsonage [ctb]
Maintainer: Matt Dowle <mattjdowle@gmail.com>

Diff between data.table versions 1.11.4 dated 2018-05-27 and 1.11.6 dated 2018-09-19

 DESCRIPTION                                                 |    6 
 MD5                                                         |  142 
 NAMESPACE                                                   |    3 
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 R/IDateTime.R                                               |   91 
 R/as.data.table.R                                           |    6 
 R/between.R                                                 |   15 
 R/bmerge.R                                                  |   10 
 R/cedta.R                                                   |   19 
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 R/fcast.R                                                   |    4 
 R/foverlaps.R                                               |    2 
 R/fread.R                                                   |   80 
 R/fwrite.R                                                  |   19 
 R/onAttach.R                                                |    2 
 R/onLoad.R                                                  |    4 
 R/setkey.R                                                  |   73 
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 man/assign.Rd                                               |    2 
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 src/assign.c                                                |   42 
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 src/fmelt.c                                                 |   47 
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 src/rbindlist.c                                             |   27 
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 72 files changed, 6278 insertions(+), 4305 deletions(-)

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New package binb with initial version 0.0.1
Package: binb
Type: Package
Title: 'binb' is not 'Beamer'
Version: 0.0.1
Date: 2018-09-19
Author: Dirk Eddelbuettel and Ista Zahn
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Description: A collection of 'LaTeX' styles using 'Beamer' customization for pdf-based presentation slides in 'RMarkdown'. At present it contains 'RMarkdown' adaptations of the LaTeX themes 'Metropolis' (formerly 'mtheme') theme by Matthias Vogelgesang and others (now included in 'TeXLive'), and the 'IQSS' by Ista Zahn (which is included here). Additional (free) fonts may be needed: 'Metropolis' prefers 'Fira', and 'IQSS' requires 'Libertinus'.
URL: https://github.com/eddelbuettel/binb
BugReports: https://github.com/eddelbuettel/binb/issues
Imports: rmarkdown, knitr
VignetteBuilder: knitr
License: GPL (>= 2)
Encoding: UTF-8
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-09-19 12:26:29.858568 UTC; edd
Repository: CRAN
Date/Publication: 2018-09-19 22:30:03 UTC

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New package bcf with initial version 1.2.1
Package: bcf
Type: Package
Title: Causal Inference for a Binary Treatment and Continuous Outcome using Bayesian Causal Forests
Version: 1.2.1
Date: 2018-09-19
Author: P. Richard Hahn, Jared S. Murray, and Carlos Carvalho
Maintainer: Jared S. Murray <jared.murray@mccombs.utexas.edu>
Description: Causal inference for a binary treatment and continuous outcome using Bayesian Causal Forests. See Hahn, Murray and Carvalho (2017) <arXiv:1706.09523> for additional information. This implementation relies on code originally accompanying Pratola et. al. (2013) <arXiv:1309.1906>.
License: GPL-3
Depends: Rcpp (>= 0.10.4)
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
RoxygenNote: 6.0.1
Packaged: 2018-09-19 21:17:11 UTC; jared
Repository: CRAN
Date/Publication: 2018-09-19 22:20:02 UTC

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Package pssmooth updated to version 1.0.1 with previous version 1.0.0 dated 2018-07-29

Title: Flexible and Efficient Evaluation of Principal Surrogates/Treatment Effect Modifiers
Description: Implements estimation and testing procedures for evaluating an intermediate biomarker response as a principal surrogate of a clinical response to treatment (i.e., principal stratification effect modification analysis), as described in Juraska M, Huang Y, and Gilbert PB, Inference on treatment effect modification by biomarker response in a three-phase sampling design (under review). The methods avoid the restrictive 'placebo structural risk' modeling assumption common to past methods and further improve robustness by the use of nonparametric kernel smoothing for biomarker density estimation. A randomized controlled two-group clinical efficacy trial is assumed with an ordered categorical or continuous univariate biomarker response measured at a fixed timepoint post-randomization and with a univariate baseline surrogate measure allowed to be observed in only a subset of trial participants with an observed biomarker response (see the flexible three-phase sampling design in the paper for details). Bootstrap-based procedures are available for pointwise and simultaneous confidence intervals and testing of four relevant hypotheses. Summary and plotting functions are provided for estimation results.
Author: Michal Juraska [aut, cre]
Maintainer: Michal Juraska <mjuraska@fredhutch.org>

Diff between pssmooth versions 1.0.0 dated 2018-07-29 and 1.0.1 dated 2018-09-19

 DESCRIPTION              |   11 +-
 MD5                      |   18 ++--
 NEWS                     |binary
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 10 files changed, 160 insertions(+), 107 deletions(-)

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Package droptest updated to version 0.1.3 with previous version 0.1.2 dated 2018-08-18

Title: Simulates LOX Drop Testing
Description: Generates simulated data representing the LOX drop testing process (also known as impact testing). A simulated process allows for accelerated study of test behavior. Functions are provided to simulate trials, test series, and groups of test series. Functions for creating plots specific to this process are also included. Test attributes and criteria can be set arbitrarily. This work is not endorsed by or affiliated with NASA. See "ASTM G86-17, Standard Test Method for Determining Ignition Sensitivity of Materials to Mechanical Impact in Ambient Liquid Oxygen and Pressurized Liquid and Gaseous Oxygen Environments" <doi:10.1520/G0086-17>.
Author: Chad Ross [aut, cre]
Maintainer: Chad Ross <chad.ross@gmail.com>

Diff between droptest versions 0.1.2 dated 2018-08-18 and 0.1.3 dated 2018-09-19

 DESCRIPTION |    6 +++---
 MD5         |    6 +++---
 NEWS.md     |    3 +++
 R/dtrials.R |    2 +-
 4 files changed, 10 insertions(+), 7 deletions(-)

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New package taipan with initial version 0.1.1
Package: taipan
Version: 0.1.1
Title: Tool for Annotating Images in Preparation for Analysis
Authors@R: c(person("Stephanie", "Kobakian", email = "stephanie.kobakian@gmail.com", role = c("aut", "cre")), person("Mitchell", "O'Hara-Wild", email = "mail@mitchelloharawild.com", role = c("aut")))
Description: A tool to help create shiny apps for selecting and annotating elements of images. Users must supply images, questions, and answer choices. The user interface is a dynamic shiny app, that displays the images and questions and answer choices. The data generated can be saved to a file that can be used for subsequent analysis. The original purpose was to annotate still images from tennis video for face recognition and emotion detection purposes.
Depends: R (>= 3.2.0)
Imports: shiny, utils
Suggests: testthat, knitr, rmarkdown, tidyverse
URL: https://github.com/srkob1/taipan
BugReports: https://github.com/srkob1/taipan/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
ByteCompile: true
RoxygenNote: 6.1.0
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-09-12 03:11:56 UTC; steff
Author: Stephanie Kobakian [aut, cre], Mitchell O'Hara-Wild [aut]
Maintainer: Stephanie Kobakian <stephanie.kobakian@gmail.com>
Repository: CRAN
Date/Publication: 2018-09-19 15:10:03 UTC

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Package RTest updated to version 1.1.9.0 with previous version 1.1.8.0 dated 2018-08-24

Title: A XML-Based Testing Framework for Automated Component Tests of R Packages
Description: This provides a framework for R packages developed for a regulatory environment. It is based on the 'testthat' unit testing system and provides the adapter functionalities for XML-based test case definition as well as for standardized reporting of the test results.
Author: Sebastian Wolf [aut, cre], Matthias Pfeifer [aut, ctb], Sergej Potapov [ctb], Roche [cph, fnd]
Maintainer: Sebastian Wolf <sebastian.wolf.sw1@roche.com>

Diff between RTest versions 1.1.8.0 dated 2018-08-24 and 1.1.9.0 dated 2018-09-19

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 man/package_md5.Rd                                       |   58 +--
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 man/xmlWriteTest_variable.Rd                             |   58 +--
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 87 files changed, 3002 insertions(+), 3058 deletions(-)

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Package kst updated to version 0.5-0 with previous version 0.4-0 dated 2018-04-13

Title: Knowledge Space Theory
Description: Knowledge space theory by Doignon and Falmagne (1999) <doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical framework, which proposes mathematical formalisms to operationalize knowledge structures in a particular domain. The 'kst' package provides basic functionalities to generate, handle, and manipulate knowledge structures and knowledge spaces.
Author: Christina Stahl [aut], David Meyer [aut], Cord Hockemeyer [aut, cre]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>

Diff between kst versions 0.4-0 dated 2018-04-13 and 0.5-0 dated 2018-09-19

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 vignettes/kst-classes.png |only
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 33 files changed, 332 insertions(+), 132 deletions(-)

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Package EffectTreat updated to version 0.4 with previous version 0.3 dated 2017-01-27

Title: Prediction of Therapeutic Success
Description: In personalized medicine, one wants to know, for a given patient and his or her outcome for a predictor (pre-treatment variable), how likely it is that a treatment will be more beneficial than an alternative treatment. This package allows for the quantification of the predictive causal association (i.e., the association between the predictor variable and the individual causal effect of the treatment) and related metrics. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>

Diff between EffectTreat versions 0.3 dated 2017-01-27 and 0.4 dated 2018-09-19

 DESCRIPTION              |    8 ++++----
 MD5                      |   13 ++++++++-----
 NAMESPACE                |    3 +++
 NEWS                     |    2 ++
 R/Min.Max.Multivar.PCA.R |   28 ++++++++++++++--------------
 R/Min.R2.delta.R         |only
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 9 files changed, 52 insertions(+), 42 deletions(-)

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New package distdichoR with initial version 0.1-0
Package: distdichoR
Type: Package
Title: Distributional Method for the Dichotomisation of Continuous Outcomes
Version: 0.1-0
Author: Odile Sauzet
Maintainer: Odile Sauzet <odile.sauzet@uni-bielefeld.de>
Description: Contains a range of functions covering the present development of the distributional method for the dichotomisation of continuous outcomes. The method provides estimates with standard error of a comparison of proportions (difference, odds ratio and risk ratio) derived, with similar precision, from a comparison of means. See the URL below or <arXiv:1809.03279> for more information.
URL: https://arxiv.org/abs/1809.03279
Encoding: UTF-8
LazyData: true
License: MIT + file LICENSE
Depends: R (>= 2.10)
Imports: boot, sn, lsmeans, stats, nlme
Suggests: knitr, rmarkdown
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-09-13 16:07:40 UTC; janne
Repository: CRAN
Date/Publication: 2018-09-19 15:20:06 UTC

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New package ddsPLS with initial version 1.0.0
Package: ddsPLS
Version: 1.0.0
Title: Multi-Data-Driven Sparse PLS Robust to Missing Samples
Description: Allows to build Multi-Data-Driven Sparse PLS models. Multi-blocks with high-dimensional settings are particularly sensible to this.
Authors@R: person("Hadrien","Lorenzo", role = c("aut", "cre"), email = "hadrien.lorenzo.2015@gmail.com")
Maintainer: Hadrien Lorenzo <hadrien.lorenzo.2015@gmail.com>
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
ByteCompile: true
RoxygenNote: 6.1.0
Imports: RColorBrewer,MASS,graphics,stats,utils,Rdpack,doParallel,foreach,parallel,iterators
RdMacros: Rdpack
Suggests: knitr,rmarkdown
Depends: R (>= 2.10)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-09-12 15:34:16 UTC; hl1
Author: Hadrien Lorenzo [aut, cre]
Repository: CRAN
Date/Publication: 2018-09-19 15:10:06 UTC

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Package zoo updated to version 1.8-4 with previous version 1.8-3 dated 2018-07-16

Title: S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)
Description: An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with ts and base R by providing methods to extend standard generics.
Author: Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>), Gabor Grothendieck [aut], Jeffrey A. Ryan [aut], Joshua M. Ulrich [ctb], Felix Andrews [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>

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Package rcmdcheck updated to version 1.3.0 with previous version 1.2.1 dated 2016-09-28

Title: Run 'R CMD check' from 'R' and Capture Results
Description: Run 'R CMD check' from 'R' programmatically, and capture the results of the individual checks.
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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Package MXM updated to version 1.4.0 with previous version 1.3.9 dated 2018-08-27

Title: Feature Selection (Including Multiple Solutions) and Bayesian Networks
Description: Many feature selection methods for a wide range of response variables, including minimal, statistically-equivalent and equally-predictive feature subsets. Bayesian network algorithms and related functions are also included. The package name 'MXM' stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin. Reference: Feature Selection with the R Package MXM: Discovering Statistically Equivalent Feature Subsets, Lagani, V. and Athineou, G. and Farcomeni, A. and Tsagris, M. and Tsamardinos, I. (2017). Journal of Statistical Software, 80(7). <doi:10.18637/jss.v080.i07>.
Author: Michail Tsagris [aut, cre], Ioannis Tsamardinos [aut, cph], Vincenzo Lagani [aut, cph], Giorgos Athineou [aut], Giorgos Borboudakis [ctb], Anna Roumpelaki [ctb]
Maintainer: Michail Tsagris <mtsagris@csd.uoc.gr>

Diff between MXM versions 1.3.9 dated 2018-08-27 and 1.4.0 dated 2018-09-19

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Package maptools updated to version 0.9-4 with previous version 0.9-3 dated 2018-07-31

Title: Tools for Handling Spatial Objects
Description: Set of tools for manipulating geographic data. It includes binary access to 'GSHHG' shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as 'PBSmapping', 'spatstat', 'maps', 'RArcInfo', 'Stata tmap', 'WinBUGS', 'Mondrian', and others.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>), Nicholas Lewin-Koh [aut], Edzer Pebesma [ctb], Eric Archer [ctb], Adrian Baddeley [ctb], Nick Bearman [ctb], Hans-Jörg Bibiko [ctb], Steven Brey [ctb], Jonathan Callahan [ctb], German Carrillo [ctb], Stéphane Dray [ctb], David Forrest [ctb], Michael Friendly [ctb], Patrick Giraudoux [ctb], Duncan Golicher [ctb], Virgilio Gómez Rubio [ctb], Patrick Hausmann [ctb], Karl Ove Hufthammer [ctb], Thomas Jagger [ctb], Kent Johnson [ctb], Sebastian Luque [ctb], Don MacQueen [ctb], Andrew Niccolai [ctb], Edzer Pebesma [ctb], Oscar Perpiñán Lamigueiro [ctb], Tom Short [ctb], Greg Snow [ctb], Ben Stabler [ctb], Murray Stokely [ctb], Rolf Turner [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

Diff between maptools versions 0.9-3 dated 2018-07-31 and 0.9-4 dated 2018-09-19

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Package KFAS updated to version 1.3.3 with previous version 1.3.2 dated 2018-05-21

Title: Kalman Filter and Smoother for Exponential Family State Space Models
Description: State space modelling is an efficient and flexible framework for statistical inference of a broad class of time series and other data. KFAS includes computationally efficient functions for Kalman filtering, smoothing, forecasting, and simulation of multivariate exponential family state space models, with observations from Gaussian, Poisson, binomial, negative binomial, and gamma distributions. See the paper by Helske (2017) <doi:10.18637/jss.v078.i10> for details.
Author: Jouni Helske <jouni.helske@iki.fi>
Maintainer: Jouni Helske <jouni.helske@iki.fi>

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Package CIAAWconsensus updated to version 1.3 with previous version 1.2 dated 2017-08-18

Title: Isotope Ratio Meta-Analysis
Description: Calculation of consensus values for atomic weights, isotope amount ratios, and isotopic abundances with the associated uncertainties using multivariate meta-regression approach for consensus building.
Author: Juris Meija and Antonio Possolo
Maintainer: Juris Meija <juris.meija@nrc-cnrc.gc.ca>

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Package wilson updated to version 2.0.2 with previous version 2.0.1 dated 2018-07-20

Title: Web-Based Interactive Omics Visualization
Description: Tool-set of modules for creating web-based applications that use plot based strategies to visualize and analyze multi-omics data. This package utilizes the 'shiny' and 'plotly' frameworks to provide a user friendly dashboard for interactive plotting.
Author: Hendrik Schultheis [aut, cre], Jens Preussner [aut], Looso Mario [aut]
Maintainer: Hendrik Schultheis <hendrik.schultheis@mpi-bn.mpg.de>

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New package SplitSoftening with initial version 1.0-0
Package: SplitSoftening
Version: 1.0-0
Title: Softening Splits in Decision Trees
Author: Jakub Dvorak
Maintainer: Jakub Dvorak <JakubDvorak@email.cz>
Depends: R (>= 3.0.0)
Enhances: tree
Suggests: gsl
Description: Allows to produce and use classification trees with probability (soft) splits.
License: GPL (>= 2)
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2018-09-12 09:48:49 UTC; jdv01
Repository: CRAN
Date/Publication: 2018-09-19 10:00:06 UTC

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Package BayLum updated to version 0.1.3 with previous version 0.1.2 dated 2018-06-22

Title: Chronological Bayesian Models Integrating Optically Stimulated Luminescence and Radiocarbon Age Dating
Description: Bayesian analysis of luminescence data and C-14 age estimates. Bayesian models are based on the following publications: Combes, B. & Philippe, A. (2017) <doi:10.1016/j.quageo.2017.02.003> and Combes et al (2015) <doi:10.1016/j.quageo.2015.04.001>. This includes, amongst others, data import, export, application of age models and palaeodose model.
Author: Claire Christophe [aut], Anne Philippe [aut, cre], Sebastian Kreutzer [aut] (<https://orcid.org/0000-0002-0734-2199>), Guillaume Guerin [aut] (<https://orcid.org/0000-0001-6298-5579>)
Maintainer: Anne Philippe <anne.philippe@univ-nantes.fr>

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New package bayesdfa with initial version 0.1.0
Package: bayesdfa
Type: Package
Title: Bayesian Dynamic Factor Analysis (DFA) with 'Stan'
Version: 0.1.0
Authors@R: c( person(c("Eric", "J."), "Ward", role = c("aut", "cre"), email = "eric.ward@noaa.gov"), person(c("Sean", "C."), "Anderson", role = "aut"), person(c("Luis", "A."), "Damiano", role = "aut"), person(c("Mary", "E."), "Hunsicker,", role = "ctb"), person(c("Mike", "A."), "Litzow", role = "ctb"), person("Trustees of", "Columbia University", role = "cph"))
Description: Implements Bayesian dynamic factor analysis with 'Stan'. Dynamic factor analysis is a dimension reduction tool for multivariate time series. 'bayesdfa' extends conventional dynamic factor models in several ways. First, extreme events may be estimated in the latent trend by modeling process error with a student-t distribution. Second, autoregressive and moving average components can be optionally included. Third, the estimated dynamic factors can be analyzed with hidden Markov models to evaluate support for latent regimes.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.4.0), Rcpp (>= 0.12.0)
Imports: rstan (>= 2.16.0), ggplot2 (>= 2.2.0), loo, dplyr (>= 0.7.0), methods, rlang, reshape2
LinkingTo: StanHeaders (>= 2.16.0), rstan (>= 2.16.0), BH (>= 1.62.0), Rcpp (>= 0.12.0), RcppEigen
Suggests: testthat, parallel, knitr, rmarkdown, MARSS
URL: https://github.com/fate-ewi/bayesdfa
BugReports: https://github.com/fate-ewi/bayesdfa/issues
RoxygenNote: 6.1.0
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-09-10 12:15:54 UTC; eric.ward
Author: Eric J. Ward [aut, cre], Sean C. Anderson [aut], Luis A. Damiano [aut], Mary E. Hunsicker, [ctb], Mike A. Litzow [ctb], Trustees of Columbia University [cph]
Maintainer: Eric J. Ward <eric.ward@noaa.gov>
Repository: CRAN
Date/Publication: 2018-09-19 10:00:02 UTC

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Package auditor updated to version 0.3.1 with previous version 0.3.0 dated 2018-08-27

Title: Model Audit - Verification, Validation, and Error Analysis
Description: Provides an easy to use unified interface for creating validation plots for any model. The 'auditor' helps to avoid repetitive work consisting of writing code needed to create residual plots. This visualizations allow to asses and compare the goodness of fit, performance, and similarity of models.
Author: Alicja Gosiewska [aut, cre], Przemyslaw Biecek [aut, ths]
Maintainer: Alicja Gosiewska <alicjagosiewska@gmail.com>

Diff between auditor versions 0.3.0 dated 2018-08-27 and 0.3.1 dated 2018-09-19

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More information about auditor at CRAN
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Package dataCompareR updated to version 0.1.2 with previous version 0.1.1 dated 2017-11-14

Title: Compare Two Data Frames and Summarise the Difference
Description: Easy comparison of two tabular data objects in R. Specifically designed to show differences between two sets of data in a useful way that should make it easier to understand the differences, and if necessary, help you work out how to remedy them. Aims to offer a more useful output than all.equal() when your two data sets do not match, but isn't intended to replace all.equal() as a way to test for equality.
Author: Rob Noble-Eddy [aut, cre], Sarah Johnston [aut], Sarah Pollicott [aut], Merlijn van Horssen [aut], Lukas Drapal [ctb], Nikolaos Perrakis [ctb], Nikhil Thomas Joy [ctb], Shahriar Asta [ctb], Karandeep Lidher [ctb], Dan Kellett [ctb], Kevin Chisholm [ctb], Laura Joy [ctb], Fergus Wadsley [ctb], Heather Hackett [ctb], David Robinson [ctb], Cheryl Renton [ctb], Matt Triggs [ctb], Krishan Bhasin [ctb], Carola Deppe [ctb], Ruijing Li [ctb], John Swift [ctb]
Maintainer: Rob Noble-Eddy <opensource@capitalone.com>

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Package personalized updated to version 0.2.1 with previous version 0.2.0 dated 2018-09-18

Title: Estimation and Validation Methods for Subgroup Identification and Personalized Medicine
Description: Provides functions for fitting and validation of models for subgroup identification and personalized medicine / precision medicine under the general subgroup identification framework of Chen et al. (2017) <doi:10.1111/biom.12676>. This package is intended for use for both randomized controlled trials and observational studies.
Author: Jared Huling [aut, cre], Aaron Potvien [ctb], Alexandros Karatzoglou [cph], Alex Smola [cph]
Maintainer: Jared Huling <jaredhuling@gmail.com>

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Package PAFit updated to version 1.0.0.7 with previous version 1.0.0.6 dated 2018-08-28

Title: Generative Mechanism Estimation in Temporal Complex Networks
Description: Statistical methods for estimating preferential attachment and node fitness generative mechanisms in temporal complex networks are provided. Thong Pham et al. (2015) <doi:10.1371/journal.pone.0137796>. Thong Pham et al.(2016) <doi:10.1038/srep32558>.
Author: Thong Pham, Paul Sheridan, Hidetoshi Shimodaira
Maintainer: Thong Pham <thongpham@thongpham.net>

Diff between PAFit versions 1.0.0.6 dated 2018-08-28 and 1.0.0.7 dated 2018-09-19

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Package furniture updated to version 1.8.0 with previous version 1.7.9 dated 2018-06-01

Title: Tables for Quantitative Scientists
Description: Contains three main functions (i.e., three pieces of furniture): table1() which produces a well-formatted table of descriptives common as Table 1 in research articles, tableC() which produces a well-formatted table of correlations, tableF() which provides frequency counts, and washer() which is helpful in cleaning up the data. These furniture-themed functions are designed to simplify common tasks in quantitative analysis. Other data summary and cleaning tools are also available.
Author: Tyson S. Barrett [aut, cre] (<https://orcid.org/0000-0002-2137-1391>), Emily Brignone [aut], Daniel J. Laxman [aut]
Maintainer: Tyson S. Barrett <t.barrett@aggiemail.usu.edu>

Diff between furniture versions 1.7.9 dated 2018-06-01 and 1.8.0 dated 2018-09-19

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Package cglasso updated to version 1.1.0 with previous version 1.0.0 dated 2018-09-14

Title: L1-Penalized Censored Gaussian Graphical Models
Description: The l1-penalized censored Gaussian graphical model is an extension of the graphical lasso estimator developed to handle datasets with censored observations. An EM-like algorithm is implemented to estimate the parameters of the censored Gaussian graphical models.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro <luigi.augugliaro@unipa.it>

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Package seminr updated to version 0.5.2 with previous version 0.5.1 dated 2018-09-10

Title: Domain-Specific Language for Building PLS Structural Equation Models
Description: A powerful, easy to write and easy to modify syntax for specifying and estimating Partial Least Squares (PLS) path models allowing for the latest estimation methods for Consistent PLS as per Dijkstra & Henseler (2015, MISQ 39(2): 297-316), adjusted interactions as per Henseler & Chin (2010) <doi:10.1080/10705510903439003> and bootstrapping utilizing parallel processing as per Hair et al. (2017, ISBN:978-1483377445).
Author: Soumya Ray [aut, ths], Nicholas Danks [aut, cre], Juan Manuel Velasquez Estrada [aut]
Maintainer: Nicholas Danks <nicholasdanks@hotmail.com>

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 tests/fixtures/pvalues.csv                               |    6 
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 tests/testthat/test-bootstrap.R                          |  129 ++-------------
 tests/testthat/test-consistent.R                         |   10 -
 tests/testthat/test-inner_weighting.R                    |   12 -
 tests/testthat/test-metric.R                             |    2 
 tests/testthat/test-output.r                             |   12 -
 tests/testthat/test-summary.R                            |   60 +-----
 tests/testthat/test_validity.R                           |    6 
 23 files changed, 166 insertions(+), 279 deletions(-)

More information about seminr at CRAN
Permanent link

Package replyr updated to version 0.9.8 with previous version 0.9.7 dated 2018-07-20

Title: Patches to Use 'dplyr' on Remote Data Sources
Description: Patches to use 'dplyr' on remote data sources ('SQL' databases, 'Spark' 2.0.0 and above) in a reliable "generic" fashion (generic meaning user code works similarly on all such sources, without needing per-source adaption). Due to the fluctuating nature of 'dplyr'/'dbplyr'/'rlang' 'APIs' this package is going into maintenance mode. Most of the 'replyr' functions are already done better by one of the non-monolithic replacement packages: 'wrapr', 'seplyr', 'rquery', or 'cdata'.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

Diff between replyr versions 0.9.7 dated 2018-07-20 and 0.9.8 dated 2018-09-19

 DESCRIPTION                     |   14 +++++++-------
 MD5                             |   36 ++++++++++++++++++------------------
 NEWS.md                         |    4 ++++
 R/addIds.R                      |    3 ++-
 README.md                       |    6 +++---
 inst/doc/DependencySorting.html |   22 +++++++++++-----------
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 inst/doc/coalesce.html          |    8 ++++----
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 inst/doc/letExample.html        |    8 ++++----
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 man/inspectDescrAndJoinPlan.Rd  |    3 ++-
 man/replyr_add_ids.Rd           |    5 +++--
 man/replyr_check_ranks.Rd       |    4 ++--
 man/replyr_coalesce.Rd          |    3 ++-
 man/replyr_copy_to.Rd           |    4 ++--
 man/replyr_inTest.Rd            |    3 ++-
 man/replyr_summary.Rd           |    4 ++--
 19 files changed, 88 insertions(+), 79 deletions(-)

More information about replyr at CRAN
Permanent link

Package IRISSeismic updated to version 1.4.9 with previous version 1.4.8 dated 2018-05-07

Title: Classes and Methods for Seismic Data Analysis
Description: Provides classes and methods for seismic data analysis. The base classes and methods are inspired by the python code found in the 'ObsPy' python toolbox <https://github.com/obsypy/obspy>. Additional classes and methods support data returned by web services provided by the 'IRIS DMC' <http://service.iris.edu/>.
Author: Jonathan Callahan [aut], Rob Casey [aut], Gillian Sharer [aut, cre], Mary Templeton [aut], Chad Trabant [ctb]
Maintainer: Gillian Sharer <gillian@iris.washington.edu>

Diff between IRISSeismic versions 1.4.8 dated 2018-05-07 and 1.4.9 dated 2018-09-19

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 136 files changed, 678 insertions(+), 537 deletions(-)

More information about IRISSeismic at CRAN
Permanent link

Package augSIMEX updated to version 3.0 with previous version 2.2 dated 2018-07-23

Title: Analysis of Data with Mixed Measurement Error and Misclassification in Covariates
Description: Implementation of the augmented Simulation-Extrapolation (SIMEX) algorithm proposed by Yi et al. (2015) <doi:10.1080/01621459.2014.922777> for analyzing the data with mixed measurement error and misclassification. The main function provides a similar summary output as that of glm() function. Both parametric and empirical SIMEX are considered in the package.
Author: Qihuang Zhang <qihuang.zhang@uwaterloo.ca>, Grace Y. Yi <yyi@uwaterloo.ca>
Maintainer: Qihuang Zhang <qihuang.zhang@uwaterloo.ca>

Diff between augSIMEX versions 2.2 dated 2018-07-23 and 3.0 dated 2018-09-19

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 31 files changed, 198 insertions(+), 125 deletions(-)

More information about augSIMEX at CRAN
Permanent link


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