Wed, 06 Jul 2016

Package sodium updated to version 0.4 with previous version 0.2 dated 2015-10-18

Title: A Modern and Easy-to-Use Crypto Library
Description: Bindings to libsodium: a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. Sodium uses curve25519, a state-of-the-art Diffie-Hellman function by Daniel Bernstein, which has become very popular after it was discovered that the NSA had backdoored Dual EC DRBG.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

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Package roahd updated to version 1.2 with previous version 1.1 dated 2016-05-12

Title: Robust Analysis of High Dimensional Data
Description: A collection of methods for the robust analysis of univariate and multivariate functional data, possibly in high-dimensional cases, and hence with attention to computational efficiency and simplicity of use.
Author: Nicholas Tarabelloni [aut, cre], Ana Arribas-Gil [aut], Francesca Ieva [aut], Anna Maria Paganoni [aut], Juan Romo [aut]
Maintainer: Nicholas Tarabelloni <nicholas.tarabelloni@polimi.it>

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Package permPATH updated to version 0.7 with previous version 0.6 dated 2016-05-18

Title: Permutation Based Gene Expression Pathway Analysis
Description: Can be used to carry out permutation based gene expression pathway analysis. This work was supported by a National Institute of Allergy and Infectious Disease/National Institutes of Health contract (No. HHSN272200900059C).
Author: Ivo D. Shterev [aut, cre], Kouros Owzar [aut], Gregory D. Sempowski [aut], Kenneth Wilder [ctb, cph] (wrote original version of ranker.h)
Maintainer: Ivo D. Shterev <i.shterev@duke.edu>

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Package multipanelfigure updated to version 0.8.3 with previous version 0.8.2 dated 2016-06-13

Title: Infrastructure to Assemble Multi-Panel Figures (from Grobs)
Description: Tools to create a layout for figures made of multiple panels, and to fill the panels with base, lattice and ggplot2 plots, grobs, and PNG, JPEG, and TIFF images.
Author: Johannes Graumann [cre, aut], Richard Cotton [ctb]
Maintainer: Johannes Graumann <jog2030@qatar-med.cornell.edu>

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Package beanz updated to version 1.5 with previous version 1.0 dated 2016-05-04

Title: Bayesian Analysis of Heterogeneous Treatment Effect
Description: It is vital to assess the heterogeneity of treatment effects (HTE) when making health care decisions for an individual patient or a group of patients. Nevertheless, it remains challenging to evaluate HTE based on information collected from clinical studies that are often designed and conducted to evaluate the efficacy of a treatment for the overall population. The Bayesian framework offers a principled and flexible approach to estimate and compare treatment effects across subgroups of patients defined by their characteristics. This package allows users to explore a wide range of Bayesian HTE analysis models, and produce posterior inferences about HTE.
Author: Chenguang Wang [aut, cre], Ravi Varadhan [aut], Trustees of Columbia University [cph] (tools/make_cpp.R, R/stanmodels.R)
Maintainer: Chenguang Wang <cwang68@jhmi.edu>

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Package rsvg updated to version 0.6 with previous version 0.5 dated 2016-03-02

Title: Render SVG Images into PDF, PNG, PostScript, or Bitmap Arrays
Description: Renders vector-based svg images into high-quality custom-size bitmap arrays using 'librsvg2'. The resulting bitmap can be written to e.g. png, jpeg or webp format. In addition, the package can convert images directly to various formats such as pdf or postscript.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

Diff between rsvg versions 0.5 dated 2016-03-02 and 0.6 dated 2016-07-06

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New package RSmartlyIO with initial version 0.1.0
Package: RSmartlyIO
Type: Package
Title: Loading Facebook and Instagram Advertising Data from Smartly.io
Description: Aims at loading Facebook and Instagram advertising data from Smartly.io into R. Smartly.io is an online advertising service that enables advertisers to display commercial ads on social media networks. The package offers an interface to query the Smartly.io API and loads data directly into R for further data processing and data analysis.
Version: 0.1.0
Author: Johannes Burkhardt <johannes.burkhardt@gmail.com>
Maintainer: Johannes Burkhardt <johannes.burkhardt@gmail.com>
Depends: R (>= 3.0.0)
Imports: RCurl
License: MIT + file LICENSE
URL: https://github.com/rstats-lab/RSmartlyIO, https://app.smartly.io
BugReports: https://github.com/rstats-lab/RSmartlyIO/issues
Date: 2016-05-25
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-06 14:02:03 UTC; jburkhardt
Repository: CRAN
Date/Publication: 2016-07-06 17:35:03

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Package meta4diag updated to version 2.0.5 with previous version 2.0.4 dated 2016-07-03

Title: Meta-Analysis for Diagnostic Test Studies
Description: Bayesian inference analysis for bivariate meta-analysis of diagnostic test studies using integrated nested Laplace approximation with INLA. A purpose built graphic user interface is available. The installation of R package INLA is compulsory for successful usage. The INLA package can be obtained from <http://www.r-inla.org>. We recommend the testing version, which can be downloaded by running: install.packages("INLA", repos="http://www.math.ntnu.no/inla/R/testing").
Author: Jingyi Guo <jingyi.guo@math.ntnu.no> and Andrea Riebler <andrea.riebler@math.ntnu.no>
Maintainer: Jingyi Guo <jingyi.guo@math.ntnu.no>

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Package excursions updated to version 2.2.1 with previous version 2.1.1 dated 2016-03-10

Title: Excursion Sets and Contour Credibility Regions for Random Fields
Description: Functions that compute probabilistic excursion sets, contour credibility regions, contour avoiding regions, and simultaneous confidence bands for latent Gaussian random processes and fields. The package also contains functions that calculate these quantities for models estimated with the INLA package.
Author: David Bolin <davidbolin@gmail.com> and Finn Lindgren <finn.lindgren@gmail.com>
Maintainer: David Bolin <davidbolin@gmail.com>

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Package eggCounts updated to version 1.1 with previous version 1.0 dated 2016-04-16

Title: Hierarchical Modelling of Faecal Egg Counts
Description: An implementation of hierarchical models for faecal egg count data to assess anthelmintic efficacy. Bayesian inference is done via MCMC sampling using Stan.
Author: Craig Wang [cre, aut], Michaela Paul [aut], Reinhard Furrer [ctb], Trustees of Columbia University [cph] (rstanarm)
Maintainer: Craig Wang <craig.wang@uzh.ch>

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Package Rvcg updated to version 0.14 with previous version 0.13.1.2 dated 2016-01-21

Title: Manipulations of Triangular Meshes Based on the 'VCGLIB' API
Description: Operations on triangular meshes based on 'VCGLIB'. This package integrates nicely with the R-package 'rgl' to render the meshes processed by 'Rvcg'. The Visualization and Computer Graphics Library (VCG for short) is an open source portable C++ templated library for manipulation, processing and displaying with OpenGL of triangle and tetrahedral meshes. The library, composed by more than 100k lines of code, is released under the GPL license, and it is the base of most of the software tools of the Visual Computing Lab of the Italian National Research Council Institute ISTI (http://vcg.isti.cnr.it), like 'metro' and 'MeshLab'. The 'VCGLIB' source is pulled from trunk (svn:// svn.code.sf.net/p/vcg/code/trunk/vcglib) and patched to work with options determined by the configure script as well as to work with the header files included by 'RcppEigen'.
Author: Stefan Schlager [aut, cre, cph], Girinon Francois [ctb]
Maintainer: Stefan Schlager <zarquon42@gmail.com>

Diff between Rvcg versions 0.13.1.2 dated 2016-01-21 and 0.14 dated 2016-07-06

 Rvcg-0.13.1.2/Rvcg/configure                                                                    |only
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 Rvcg-0.14/Rvcg/DESCRIPTION                                                                      |   22 
 Rvcg-0.14/Rvcg/MD5                                                                              |  299 -
 Rvcg-0.14/Rvcg/NAMESPACE                                                                        |   11 
 Rvcg-0.14/Rvcg/R/Rvcg-package.R                                                                 |   21 
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 Rvcg-0.14/Rvcg/R/vcgImport.r                                                                    |    5 
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 Rvcg-0.14/Rvcg/R/vcgIsosurface.r                                                                |   20 
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 Rvcg-0.14/Rvcg/R/vcgPlyWrite.r                                                                  |    5 
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 Rvcg-0.14/Rvcg/R/vcgSample.r                                                                    |   25 
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 Rvcg-0.14/Rvcg/cleanup                                                                          |    2 
 Rvcg-0.14/Rvcg/data/dummyhead.rda                                                               |binary
 Rvcg-0.14/Rvcg/inst/COPYRIGHTS                                                                  |    5 
 Rvcg-0.14/Rvcg/inst/NEWS.Rd                                                                     |   32 
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 Rvcg-0.14/Rvcg/man/Rvcg-package.Rd                                                              |    4 
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 Rvcg-0.14/Rvcg/man/vcgIsosurface.Rd                                                             |    9 
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 Rvcg-0.14/Rvcg/man/vcgQEdecim.Rd                                                                |    6 
 Rvcg-0.14/Rvcg/man/vcgSample.Rd                                                                 |    6 
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 Rvcg-0.14/Rvcg/src/Makevars                                                                     |only
 Rvcg-0.14/Rvcg/src/ROneRing.cpp                                                                 |    2 
 Rvcg-0.14/Rvcg/src/RQEdecim.cpp                                                                 |   41 
 Rvcg-0.14/Rvcg/src/RVFadj.cpp                                                                   |    2 
 Rvcg-0.14/Rvcg/src/RallRead.cpp                                                                 |    2 
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 Rvcg-0.14/Rvcg/src/Rballpivot.cpp                                                               |only
 Rvcg-0.14/Rvcg/src/Rclean.cpp                                                                   |    2 
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 Rvcg-0.14/Rvcg/src/Rcurvature.cpp                                                               |    2 
 Rvcg-0.14/Rvcg/src/Rexport.cpp                                                                  |    2 
 Rvcg-0.14/Rvcg/src/RgetEdge.cpp                                                                 |    2 
 Rvcg-0.14/Rvcg/src/Rintersect.cpp                                                               |    2 
 Rvcg-0.14/Rvcg/src/Risolated.cpp                                                                |   50 
 Rvcg-0.14/Rvcg/src/Rkdtree.cpp                                                                  |  138 
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 Rvcg-0.14/Rvcg/src/Rmarch.cpp                                                                   |    2 
 Rvcg-0.14/Rvcg/src/Rmeshres.cpp                                                                 |    2 
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 Rvcg-0.14/Rvcg/src/Rplatonic.cpp                                                                |    2 
 Rvcg-0.14/Rvcg/src/Rsample.cpp                                                                  |    6 
 Rvcg-0.14/Rvcg/src/Rsmooth.cpp                                                                  |    2 
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 Rvcg-0.14/Rvcg/src/Runiform_resample.cpp                                                        |    2 
 Rvcg-0.14/Rvcg/src/RupdateNormals.cpp                                                           |    2 
 Rvcg-0.14/Rvcg/src/RvcgIO.h                                                                     |  108 
 Rvcg-0.14/Rvcg/src/RvcgKD.h                                                                     |  163 
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 Rvcg-0.14/Rvcg/src/checkListNames.h                                                             |    2 
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 Rvcg-0.14/Rvcg/src/vcglib/vcg/complex/algorithms/stat.h                                         |   52 
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Package protolite updated to version 1.3 with previous version 1.2 dated 2016-05-08

Title: Fast and Simple Object Serialization to Protocol Buffers
Description: An optimized, permissively licensed C++ implementation for serializing R objects to protocol-buffers. This lightweight package is complementary to the much larger 'RProtoBuf' package which provides a full featured toolkit for working with protocol-buffers in R.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

Diff between protolite versions 1.2 dated 2016-05-08 and 1.3 dated 2016-07-06

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Package MANOVA.RM updated to version 0.0.3 with previous version 0.0.2 dated 2016-06-30

Title: Analysis of Multivariate Data and Repeated Measures Designs
Description: Implemented are various tests for semi-parametric repeated measures and general MANOVA designs that do neither assume multivariate normality nor covariance homogeneity, i.e., the procedures are applicable for a wide range of general multivariate factorial designs.
Author: Sarah Friedrich, Frank Konietschke, Markus Pauly
Maintainer: Sarah Friedrich <sarah.friedrich@uni-ulm.de>

Diff between MANOVA.RM versions 0.0.2 dated 2016-06-30 and 0.0.3 dated 2016-07-06

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New package forestinventory with initial version 0.1.0
Package: forestinventory
Type: Package
Title: Design-Based Global and Small-Area Estimations for Multiphase Forest Inventories
Version: 0.1.0
Date: 2016-07-06
Authors@R: c(person(given = c("Andreas"), family = "Hill", email = "forestinventory@gmx.ch", role = c("aut","cre")), person(given = c("Alexander"), family = "Massey", email = "forestinventory@gmx.ch", role = c("aut")), person(given = c("Daniel"), family = "Mandallaz", role = c("ctb")) )
Maintainer: Andreas Hill <forestinventory@gmx.ch>
Description: Extensive global and small-area estimation procedures for multiphase forest inventories under the design-based Monte-Carlo approach are provided. The implementation includes estimators for simple and cluster sampling published by Daniel Mandallaz in 2007 (<DOI:10.1201/9781584889779>), 2013 (<DOI:10.1139/cjfr-2012-0381>, <DOI:10.1139/cjfr-2013-0181>, <DOI:10.1139/cjfr-2013-0449>, <DOI:10.3929/ethz-a-009990020>) and 2016 (<DOI:10.3929/ethz-a-010579388>). It provides point estimates, their external- and design-based variances as well as confidence intervals. The procedures have also been optimized for the use of remote sensing data as auxiliary information.
License: GPL (>= 2)
LazyData: TRUE
Imports: plyr (>= 1.8.3), stats, utils
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-06 13:01:28 UTC; hilla
Author: Andreas Hill [aut, cre], Alexander Massey [aut], Daniel Mandallaz [ctb]
Repository: CRAN
Date/Publication: 2016-07-06 16:04:39

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Package shapes updated to version 1.1-13 with previous version 1.1-11 dated 2015-08-18

Title: Statistical Shape Analysis
Description: Routines for the statistical analysis of landmark shapes, including Procrustes analysis, graphical displays, principal components analysis, permutation and bootstrap tests, thin-plate spline transformation grids and comparing covariance matrices.
Author: Ian L. Dryden
Maintainer: Ian Dryden <ian.dryden@nottingham.ac.uk>

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Package lcopula updated to version 0.206 with previous version 0.205 dated 2015-08-26

Title: Liouville Copulas
Description: Collections of functions allowing random number generations and estimation of Liouville copulas.
Author: Leo Belzile [aut, cre], Christian Genest [aut, ctb], Alexander J. McNeil [ctb], Johanna G. Neslehova [ctb]
Maintainer: Leo Belzile <leo.belzile@epfl.ch>

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Package warbleR updated to version 1.1.2 with previous version 1.1.1 dated 2016-04-19

Title: Streamline Bioacoustic Analysis
Description: Offers three overarching categories of functions to obtain bird vocalization recordings from the web, manage sound files, and facilitate (bio)acoustic analysis in R.
Author: Marcelo Araya-Salas & Grace Smith Vidaurre
Maintainer: Marcelo Araya-Salas <araya-salas@cornell.edu>

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Package tigris updated to version 0.3.3 with previous version 0.3 dated 2016-05-17

Title: Load Census TIGER/Line Shapefiles into R
Description: Download TIGER/Line shapefiles from the United States Census Bureau and load into R as 'SpatialDataFrame' objects.
Author: Kyle Walker [aut, cre], Bob Rudis [ctb]
Maintainer: Kyle Walker <kyle.walker@tcu.edu>

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Package sparsevar updated to version 0.0.7 with previous version 0.0.5 dated 2016-06-13

Title: A Package for Sparse VAR/VECM Estimation
Description: A wrapper for sparse VAR/VECM time series models estimation using penalties like ENET, SCAD and MCP.
Author: Simone Vazzoler [aut, cre], Lorenzo Frattarolo [aut], Monica Billio [aut]
Maintainer: Simone Vazzoler <svazzole@gmail.com>

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Package som updated to version 0.3-5.1 with previous version 0.3-5 dated 2010-04-07

Title: Self-Organizing Map
Description: Self-Organizing Map (with application in gene clustering).
Author: Jun Yan <jyan@stat.uconn.edu>
Maintainer: Jun Yan <jyan@stat.uconn.edu>

Diff between som versions 0.3-5 dated 2010-04-07 and 0.3-5.1 dated 2016-07-06

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 6 files changed, 13 insertions(+), 8 deletions(-)

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Package RAdwords updated to version 0.1.10 with previous version 0.1.6 dated 2015-08-07

Title: Loading Google Adwords Data into R
Description: Aims at loading Google Adwords data into R. Adwords is an online advertising service that enables advertisers to display advertising copy to web users. Therefore the package implements three main features. First, the package provides an authentication process for R with the Google Adwords API via OAUTH2. Second, the package offers an interface to apply the Adwords query language in R and query the Adwords API with ad-hoc reports. Third, the received data are transformed into suitable data formats for further data processing and data analysis.
Author: Johannes Burkhardt <johannes.burkhardt@gmail.com>, Matthias Bannert <matthias.bannert@gmail.com>
Maintainer: Johannes Burkhardt <johannes.burkhardt@gmail.com>

Diff between RAdwords versions 0.1.6 dated 2015-08-07 and 0.1.10 dated 2016-07-06

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New package propr with initial version 1.1.0
Package: propr
Title: Calculating Proportionality Between Vectors of Compositional Data
Version: 1.1.0
URL: http://github.com/tpq/propr
BugReports: http://github.com/tpq/propr/issues
Authors@R: c( person("Thomas", "Quinn", email = "contacttomquinn@gmail.com", role = c("aut", "cre")), person("David", "Lovell", email = "david.lovell@qut.edu.au", role = "aut") )
Description: The bioinformatic evaluation of gene co-expression often begins with correlation-based analyses. However, this approach lacks statistical validity when applied to relative data, including those biological count data produced by microarray assays or high-throughput RNA-sequencing. As an alternative, Lovell et al propose a proportionality metric, phi, derived from compositional data analysis, a branch of math dealing specifically with relative data. In a subsequent publication, Erb and Nicodemus expounded these efforts by elaborating on another proportionality metric, rho. This package introduces a programmatic framework for the calculation of feature dependence using proportionality and other compositional data methods discussed in the cited publications.
License: GPL-2
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 5.0.1
Depends: R (>= 3.2.2)
Imports: methods
Suggests: compositions, dendextend, ggplot2, ggthemes, knitr, rmarkdown, testthat
NeedsCompilation: no
Packaged: 2016-07-06 00:08:59 UTC; thom
Author: Thomas Quinn [aut, cre], David Lovell [aut]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
Repository: CRAN
Date/Publication: 2016-07-06 09:44:00

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New package pbmcapply with initial version 1.0.0
Package: pbmcapply
Type: Package
Title: Tracking the Progress of Mc*pply with Progress Bar
Version: 1.0.0
Author: Kevin Kuang
Maintainer: Kevin kuang <kvn.kuang@mail.utoronto.ca>
Description: A light-weight package helps you track and visualize the progress of parallel version of vectorized R functions (mc*apply).
Depends: utils, parallel
BugReports: https://github.com/kvnkuang/pbmcapply
License: MIT + file LICENSE
LazyData: TRUE
NeedsCompilation: no
Packaged: 2016-07-05 14:28:11 UTC; kevinkuang
Repository: CRAN
Date/Publication: 2016-07-06 09:43:59

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New package MLPUGS with initial version 0.2.0
Package: MLPUGS
Type: Package
Title: Multi-Label Prediction Using Gibbs Sampling (and Classifier Chains)
Version: 0.2.0
Date: 2016-07-05
Authors@R: person("Mikhail", "Popov", email = "mikhail@mpopov.com", role = c("aut", "cre"), comment = "@bearloga on Twitter")
Maintainer: Mikhail Popov <mikhail@mpopov.com>
Description: An implementation of classifier chains (CC's) for multi-label prediction. Users can employ an external package (e.g. 'randomForest', 'C50'), or supply their own. The package can train a single set of CC's or train an ensemble of CC's -- in parallel if running in a multi-core environment. New observations are classified using a Gibbs sampler since each unobserved label is conditioned on the others. The package includes methods for evaluating the predictions for accuracy and aggregating across iterations and models to produce binary or probabilistic classifications.
URL: https://github.com/bearloga/MLPUGS
BugReports: https://github.com/bearloga/MLPUGS/issues
Depends: R (>= 3.1.2)
Suggests: knitr, progress, C50, randomForest
VignetteBuilder: knitr
LazyData: true
License: MIT + file LICENSE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-06 00:24:49 UTC; mpopov
Author: Mikhail Popov [aut, cre] (@bearloga on Twitter)
Repository: CRAN
Date/Publication: 2016-07-06 09:43:54

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Package linear.tools updated to version 1.3.0 with previous version 1.2.0 dated 2016-05-22

Title: Manipulate Formulas and Evaluate Marginal Effects
Description: Provides tools to manipulate formulas, such as getting x, y or contrasts from the model/formula, and functions to evaluate and check the marginal effects of a linear model.
Author: Fan Yang
Maintainer: Fan Yang <yfno1@msn.com>

Diff between linear.tools versions 1.2.0 dated 2016-05-22 and 1.3.0 dated 2016-07-06

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 10 files changed, 458 insertions(+), 494 deletions(-)

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Package ggsn updated to version 0.3.1 with previous version 0.3.0 dated 2016-01-14

Title: North Symbols and Scale Bars for Maps Created with 'ggplot2' or 'ggmap'
Description: Adds north symbols (18 options) and scale bars in kilometers to maps in geographic or metric coordinates created with 'ggplot2' or 'ggmap'.
Author: Oswaldo Santos Baquero [aut, cre]
Maintainer: Oswaldo Santos Baquero <oswaldosant@gmail.com>

Diff between ggsn versions 0.3.0 dated 2016-01-14 and 0.3.1 dated 2016-07-06

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 13 files changed, 101 insertions(+), 87 deletions(-)

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New package gwdegree with initial version 0.1.0
Package: gwdegree
Title: A Shiny App to Aid Interpretation of Geometrically-Weighted Degree Estimates in Exponential Random Graph Models
Version: 0.1.0
Authors@R: person("Michael", "Levy", email = "malevy@ucdavis.edu", role = c("aut", "cre"))
License: MIT + file LICENSE
Description: This is a Shiny application intended to provide better understanding of how geometrically-weighted degree terms function in exponential random graph models of networks.
Depends: R (>= 3.2.3), ergm, ggplot2, shiny, shinydashboard
Imports: dplyr, gtools, magrittr, network, scales, sna, tidyr
Suggests: testthat
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-06 06:32:48 UTC; malevy
Author: Michael Levy [aut, cre]
Maintainer: Michael Levy <malevy@ucdavis.edu>
Repository: CRAN
Date/Publication: 2016-07-06 09:50:45

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Package BayesTree updated to version 0.3-1.4 with previous version 0.3-1.3 dated 2016-02-23

Title: Bayesian Additive Regression Trees
Description: This is an implementation of BART:Bayesian Additive Regression Trees, by Chipman, George, McCulloch (2010).
Author: Hugh Chipman <hugh.chipman@gmail.com>, Robert McCulloch <robert.e.mcculloch@gmail.com>
Maintainer: Robert McCulloch <robert.e.mcculloch@gmail.com>

Diff between BayesTree versions 0.3-1.3 dated 2016-02-23 and 0.3-1.4 dated 2016-07-06

 DESCRIPTION  |    6 +++---
 MD5          |    4 ++--
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 3 files changed, 7 insertions(+), 7 deletions(-)

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