Thu, 31 Dec 2015

New package hdr with initial version 0.1
Package: hdr
Title: Interface to the UNDR Human Development Report API
Version: 0.1
Authors@R: person("Eric", "Persson", email = "expersso5@gmail.com", role = c("aut", "cre"))
Description: Provides a complete interface to the United Nations Development Programme Human Development Report API (<http://hdr.undp.org>). The API includes a large amount of human development data, including all the series used to compute the Human Development Index (HDI), as well as the HDI itself.
Depends: R (>= 3.2.3)
License: CC0
LazyData: true
BugReports: https://github.com/expersso/hdr
URL: http://hdr.undp.org ; https://github.com/expersso/hdr
RoxygenNote: 5.0.1
Imports: httr
Suggests: ggplot2, dplyr, tidyr, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-12-31 15:45:07 UTC; quad
Author: Eric Persson [aut, cre]
Maintainer: Eric Persson <expersso5@gmail.com>
Repository: CRAN
Date/Publication: 2015-12-31 23:31:44

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Package FCNN4R updated to version 0.6.0 with previous version 0.5.0 dated 2015-10-12

Title: Fast Compressed Neural Networks for R
Description: Provides an interface to kernel routines from the FCNN C++ library. FCNN is based on a completely new Artificial Neural Network representation that offers unmatched efficiency, modularity, and extensibility. FCNN4R provides standard teaching (backpropagation, Rprop, simulated annealing, stochastic gradient) and pruning algorithms (minimum magnitude, Optimal Brain Surgeon), but it is first and foremost an efficient computational engine. Users can easily implement their algorithms by taking advantage of fast gradient computing routines, as well as network reconstruction functionality (removing weights and redundant neurons, reordering inputs, merging networks). Networks can be exported to C functions in order to integrate them into virtually any software solution.
Author: Grzegorz Klima <gklima@users.sourceforge.net>
Maintainer: Grzegorz Klima <gklima@users.sourceforge.net>

Diff between FCNN4R versions 0.5.0 dated 2015-10-12 and 0.6.0 dated 2015-12-31

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New package BMRV with initial version 1.31
Package: BMRV
Type: Package
Title: Bayesian Models for Rare Variant Association Analysis
Version: 1.31
Date: 2015-12-06
Author: Liang He
Maintainer: Liang He <liang.he@duke.edu>
Description: Provides two Bayesian models for detecting the association between rare variants and traits that can be continuous, ordinal or binary. Bayesian latent variable collapsing model (BLVCM) detects interaction effect and is dedicated to twin design while it can also be applied to independent samples. Hierarchical Bayesian multiple regression model (HBMR) incorporates genotype uncertainty information and can be applied to either independent or family samples. Furthermore, it deals with continuous, binary and ordinal traits.
License: GPL (>= 2)
Depends: R (>= 3.1.1), stats
Encoding: latin1
LinkingTo: BH
Repository: CRAN
Repository/R-Forge/Project: bmrv
Repository/R-Forge/Revision: 7
Repository/R-Forge/DateTimeStamp: 2015-12-31 02:33:47
Date/Publication: 2015-12-31 23:22:59
NeedsCompilation: yes
Packaged: 2015-12-31 03:25:48 UTC; rforge

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Package textmineR updated to version 1.5.1 with previous version 1.5.0 dated 2015-12-30

Title: Functions for Text Mining and Topic Modeling
Description: An aid for text mining in R, with a syntax that is more familiar to experienced R users. Also, implements various functions related to topic modeling. It works well with with the "lda" package by J. Chang.
Author: "Thomas W. Jones <jones.thos.w@gmail.com>"
Maintainer: Thomas W. Jones <jones.thos.w@gmail.com>

Diff between textmineR versions 1.5.0 dated 2015-12-30 and 1.5.1 dated 2015-12-31

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Package rsunlight updated to version 0.4.2 with previous version 0.4.0 dated 2015-07-01

Title: Interface to 'Sunlight' Foundation 'APIs'
Description: Interface to three 'Sunlight' Foundation 'APIs' (http:// sunlightfoundation.com/api/) for government data, including the Congress 'API' 'v3', the Capitol Words 'API', and the Open States 'API'. 'Sunlight' Foundation is a 'nonpartison' 'nonprofit' that collects and provides data on government activities, and those that influence government. Functions are provided to interact with each of the three 'APIs'.
Author: Scott Chamberlain [aut, cre], Thomas J. Leeper [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package eva updated to version 0.1.2 with previous version 0.1.1 dated 2015-12-29

Title: Extreme Value Analysis with Goodness-of-Fit Testing
Description: Goodness-of-fit tests for selection of r in the r-largest order statistics (GEVr) model. Goodness-of-fit tests for threshold selection in the peaks-over-threshold approach. Random number generation and density functions for the GEVr distribution. Profile likelihood for return level estimation using the GEVr and generalized pareto distributions. P-value adjustments for sequential, multiple testing error control.
Author: Brian Bader [aut, cre], Jun Yan [aut]
Maintainer: Brian Bader <brianbader@mail.com>

Diff between eva versions 0.1.1 dated 2015-12-29 and 0.1.2 dated 2015-12-31

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Package DTR updated to version 1.7 with previous version 1.6 dated 2015-05-06

Title: Estimation and Comparison of Dynamic Treatment Regimes
Description: Estimation and comparison of survival distributions of dynamic treatment regimes (DTRs) from sequentially randomized clinical trials.
Author: Xinyu Tang [aut, cre], Maria Melguizo [aut]
Maintainer: Xinyu Tang <xtang@uams.edu>

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Package rmarkdown updated to version 0.9.1 with previous version 0.9 dated 2015-12-22

Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre], Joe Cheng [aut], Yihui Xie [aut], Jonathan McPherson [aut], Winston Chang [aut], Jeff Allen [aut], Hadley Wickham [aut], Aron Atkins [aut], Rob Hyndman [aut], RStudio, Inc. [cph], jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/rmd/h/jquery-AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. [ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library)
Maintainer: JJ Allaire <jj@rstudio.com>

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Package optiRum updated to version 0.37.3 with previous version 0.37.1 dated 2015-11-07

Title: Financial Functions & More
Description: This fills the gaps credit analysts and loan modellers at Optimum Credit identify in the existing R code body. It allows for the production of documentation with less coding, replicates a number of Microsoft Excel functions useful for modelling loans (without rounding), and other helpful functions for producing charts and tables. It also has some additional scales for use, including a GBP scale.
Author: Stephanie Locke [aut, cre]
Maintainer: Stephanie Locke <stephanie.g.locke@gmail.com>

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Package viridis updated to version 0.3.2 with previous version 0.3.1 dated 2015-10-11

Title: Default Color Maps from 'matplotlib'
Description: Port of the new 'matplotlib' color maps ('viridis' - the default -, 'magma', 'plasma' and 'inferno') to 'R'. 'matplotlib' <http://matplotlib.org/ > is a popular plotting library for 'python'. These color maps are designed in such a way that they will analytically be perfectly perceptually-uniform, both in regular form and also when converted to black-and-white. They are also designed to be perceived by readers with the most common form of color blindness.
Author: Simon Garnier [aut, cre], Noam Ross [ctb, cph] (Continuous scale), Bob Rudis [ctb, cph] (Combined scales)
Maintainer: Simon Garnier <garnier@njit.edu>

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More information about viridis at CRAN
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Package Rvcg updated to version 0.13.1.1 with previous version 0.13.1 dated 2015-12-22

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; the authors of VCGLIB for the included version of the code
Maintainer: Stefan Schlager <zarquon42@gmail.com>

Diff between Rvcg versions 0.13.1 dated 2015-12-22 and 0.13.1.1 dated 2015-12-31

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Package networkD3 updated to version 0.2.8 with previous version 0.2.6 dated 2015-10-11

Title: D3 JavaScript Network Graphs from R
Description: Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey graphs from 'R'.
Author: Christopher Gandrud [aut, cre], J.J. Allaire [aut], Kenton Russell [aut], B.W. Lewis [ctb], Kevin Kuo [ctb], Charles Sese [ctb], Peter Ellis [ctb], Jonathan Owen [ctb], Jennifer Rogers [ctb]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>

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Package viridisLite updated to version 0.1.1 with previous version 0.1 dated 2015-11-13

Title: Default Color Maps from 'matplotlib' (Lite Version)
Description: Port of the new 'matplotlib' color maps ('viridis' - the default -, 'magma', 'plasma' and 'inferno') to 'R'. 'matplotlib' <http://matplotlib.org/ > is a popular plotting library for 'python'. These color maps are designed in such a way that they will analytically be perfectly perceptually-uniform, both in regular form and also when converted to black-and-white. They are also designed to be perceived by readers with the most common form of color blindness. This is the 'lite' version of the more complete 'viridis' package that can be found at <https://cran.r-project.org/package=viridis>.
Author: Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph]
Maintainer: Simon Garnier <garnier@njit.edu>

Diff between viridisLite versions 0.1 dated 2015-11-13 and 0.1.1 dated 2015-12-31

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Package Sim.DiffProc updated to version 3.1 with previous version 3.0 dated 2015-10-29

Title: Simulation of Diffusion Processes
Description: Provides the functions for simulation and modeling of stochastic differential equations (SDE's) the type Ito and Stratonovich. This package contains many objects, the numerical methods to find the solutions to SDE's (1, 2 and 3-dim), with a possibility for simulates a flows trajectories,with good accuracy. Many theoretical problems on the SDE's have become the object of practical research, as statistical analysis and simulation of solution of SDE's, enabled many searchers in different domains to use these equations to modeling and to analyse practical problems, in financial and actuarial modeling and other areas of application, for example modelling and simulate of dispersion in shallow water using the attractive center (Boukhetala K, 1996). We hope that the package presented here and the updated survey on the subject might be of help for practitioners, postgraduate and PhD students, and researchers in the field who might want to implement new methods.
Author: Arsalane Chouaib Guidoum, Kamal Boukhetala
Maintainer: Arsalane Chouaib Guidoum <acguidoum@usthb.dz>

Diff between Sim.DiffProc versions 3.0 dated 2015-10-29 and 3.1 dated 2015-12-31

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Package ParallelPC updated to version 1.2 with previous version 1.1 dated 2015-10-02

Title: Paralellised Versions of Constraint Based Causal Discovery Algorithms
Description: Parallelise constraint based causality discovery and causal inference methods. The parallelised algorithms in the package will generate the same results as that of the 'pcalg' package but will be much more efficient.
Author: Thuc Duy Le, Tao Hoang, Shu Hu, and Liang Zhang
Maintainer: Thuc Duy Le <Thuc.Le@unisa.edu.au>

Diff between ParallelPC versions 1.1 dated 2015-10-02 and 1.2 dated 2015-12-31

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Package mpoly updated to version 1.0.0 with previous version 0.1.0 dated 2015-05-01

Title: Symbolic Computation and More with Multivariate Polynomials
Description: Symbolic computing with multivariate polynomials in R.
Author: David Kahle [aut, cre]
Maintainer: David Kahle <david.kahle@gmail.com>

Diff between mpoly versions 0.1.0 dated 2015-05-01 and 1.0.0 dated 2015-12-31

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Package markophylo updated to version 1.0.4 with previous version 1.0.3 dated 2015-11-05

Title: Markov Chain Models for Phylogenetic Trees
Description: Allows for fitting of maximum likelihood models using Markov chains on phylogenetic trees for analysis of discrete character data. Examples of such discrete character data include restriction sites, gene family presence/absence, intron presence/absence, and gene family size data. Hypothesis-driven user- specified substitution rate matrices can be estimated. Allows for biologically realistic models combining constrained substitution rate matrices, site rate variation, site partitioning, branch-specific rates, allowing for non-stationary prior root probabilities, correcting for sampling bias, etc.
Author: Utkarsh J. Dang and G. Brian Golding
Maintainer: Utkarsh J. Dang <udang@mcmaster.ca>

Diff between markophylo versions 1.0.3 dated 2015-11-05 and 1.0.4 dated 2015-12-31

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Package arfima updated to version 1.3-4 with previous version 1.3-3 dated 2015-12-28

Title: Fractional ARIMA (and Other Long Memory) Time Series Modeling
Description: Simulates, fits, and predicts long-memory and anti-persistent time series, possibly mixed with ARMA, regression, transfer-function components. Exact methods (MLE, forecasting, simulation) are used.
Author: Justin Q. Veenstra [aut, cre], A.I. McLeod [aut]
Maintainer: Justin Q. Veenstra <justin.veenstra@gmail.com>

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Wed, 30 Dec 2015

New package webp with initial version 0.2
Package: webp
Type: Package
Title: A New Format for Lossless and Lossy Image Compression
Version: 0.2
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Description: Lossless webp images are 26% smaller in size compared to PNG. Lossy webp images are 25-34% smaller in size compared to JPEG. This package reads and writes webp images into a 3 (rgb) or 4 (rgba) channel bitmap array using conventions from the 'jpeg' and 'png' packages.
License: MIT + file LICENSE
URL: https://github.com/jeroenooms/webp https://developers.google.com/speed/webp
BugReports: https://github.com/jeroenooms/webp/issues
LazyData: TRUE
Suggests: jpeg, png
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2015-12-30 17:52:33 UTC; jeroen
Repository: CRAN
Date/Publication: 2015-12-30 23:19:29

More information about webp at CRAN
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Package statar updated to version 0.4.0 with previous version 0.3.0 dated 2015-06-07

Title: Tools Inspired by Stata to Manipulate Tabular Data
Description: A set of tools inspired by Stata to explore data.frames (summarize, tabulate, xtile, pctile, binscatter, elapsed quarters/month, lead/lag).
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez <mattg@princeton.edu>

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Package soundecology updated to version 1.3.1 with previous version 1.3 dated 2015-05-02

Title: Soundscape Ecology
Description: Functions to calculate indices for soundscape ecology and other ecology research that uses audio recordings.
Author: Luis J. Villanueva-Rivera and Bryan C. Pijanowski
Maintainer: Luis J. Villanueva-Rivera <ljvillanueva@coquipr.com>

Diff between soundecology versions 1.3 dated 2015-05-02 and 1.3.1 dated 2015-12-30

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Permanent link

Package RNeXML updated to version 2.0.5 with previous version 2.0.4 dated 2015-10-14

Title: Semantically Rich I/O for the 'NeXML' Format
Description: Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.
Author: Carl Boettiger [cre, aut], Scott Chamberlain [aut], Hilmar Lapp [aut], Kseniia Shumelchyk [aut], Rutger Vos [aut]
Maintainer: Carl Boettiger <cboettig@gmail.com>

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Package nat updated to version 1.8.1 with previous version 1.7.0 dated 2015-07-01

Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Description: NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D biological image data, especially traced neurons. Reads and writes 3D images in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf format. Traced neurons can be imported from and written to SWC and 'Amira' LineSet and SkeletonGraph formats. These data can then be visualised in 3D via 'rgl', manipulated including applying calculated registrations, e.g. using the 'CMTK' registration suite, and analysed. There is also a simple representation for neurons that have been subjected to 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the 'nat.nblast' extension package).
Author: Greg Jefferis and James Manton
Maintainer: Greg Jefferis <jefferis@gmail.com>

Diff between nat versions 1.7.0 dated 2015-07-01 and 1.8.1 dated 2015-12-30

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More information about nat at CRAN
Permanent link

Package GGally updated to version 1.0.0 with previous version 0.5.0 dated 2014-12-01

Title: Extension to ggplot2
Description: The R package \href{http://docs.ggplot2.org/current/}{ggplot2} is a plotting system based on the grammar of graphics. \href{https:// ggobi.github.io/ggally}{GGally} extends ggplot2 by adding several functions to reduce the complexity of combining geoms with transformed data. Some of these functions include a pairwise plot matrix, a scatterplot plot matrix, a parallel coordinates plot, a survival plot, and several functions to plot networks.
Author: Barret Schloerke [aut, cre] (author for ggpairs and ggally_*. contributor for all functions.), Jason Crowley [aut] (ggparcoord), Di Cook [aut, ths] (ggscatmat, gglyph), Heike Hofmann [ths], Hadley Wickham [ths], Francois Briatte [aut] (ggcorr, ggnet, ggnet2), Moritz Marbach [aut] (ggnet, ggnet2), Edwin Thoen [aut] (ggsurv), Amos Elberg [aut] (ggnetworkmap)
Maintainer: Barret Schloerke <schloerke@gmail.com>

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Package gapminder updated to version 0.2.0 with previous version 0.1.0 dated 2015-03-17

Title: Data from Gapminder
Description: An excerpt of the data available at Gapminder.org. For each of 142 countries, the package provides values for life expectancy, GDP per capita, and population, every five years, from 1952 to 2007.
Author: Jennifer Bryan [aut, cre]
Maintainer: Jennifer Bryan <jenny@stat.ubc.ca>

Diff between gapminder versions 0.1.0 dated 2015-03-17 and 0.2.0 dated 2015-12-30

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More information about gapminder at CRAN
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New package geomnet with initial version 0.0.1
Package: geomnet
Type: Package
Title: Network Visualization in the 'ggplot2' Framework
Version: 0.0.1
Date: 2015-12-30
Author: Samantha Tyner, Heike Hofmann
Maintainer: Samantha Tyner <sctyner@iastate.edu>
Description: Network visualization in the 'ggplot2' framework. Network functionality is provided in a single 'ggplot2' layer by calling the geom 'net'. Layouts are calculated using the 'sna' package, example networks are included.
License: GPL (>= 2)
LazyData: TRUE
Depends: R (>= 2.14), ggplot2 (>= 1.0.1.9003)
Imports: sna, network
Suggests: dplyr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-30 18:00:56 UTC; samanthatyner
Repository: CRAN
Date/Publication: 2015-12-31 00:02:33

More information about geomnet at CRAN
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Package future updated to version 0.10.0 with previous version 0.9.0 dated 2015-12-12

Title: A Future API for R
Description: A Future API for R is provided. In programming, a future is an abstraction for a value that may be available at some point in the future. The state of a future can either be unresolved or resolved. As soon as it is resolved, the value is available. Futures are useful constructs in for instance concurrent evaluation, e.g. multicore parallel processing and distributed processing on compute clusters. The purpose of this package is to provide a lightweight interface for using futures in R. Functions 'future()' and 'value()' exist for creating futures and requesting their values. An infix assignment operator '%<=%' exists for creating futures whose values are accessible by the assigned variables (as promises). This package implements the synchronous "lazy" and "eager" futures, and the asynchronous "multicore" future (not on Windows). Additional types of futures are provided by other packages enhancing this package.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

Diff between future versions 0.9.0 dated 2015-12-12 and 0.10.0 dated 2015-12-30

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Package choroplethrAdmin1 updated to version 1.1.0 with previous version 1.0.0 dated 2014-12-02

Title: Contains an Administrative-Level-1 Map of the World
Description: Contains an administrative-level-1 map of the world. Administrative-level-1 is the generic term for the largest sub-national subdivision of a country. This package was created for use with the choroplethr package.
Author: Ari Lamstein <arilamstein@gmail.com>
Maintainer: Ari Lamstein <arilamstein@gmail.com>

Diff between choroplethrAdmin1 versions 1.0.0 dated 2014-12-02 and 1.1.0 dated 2015-12-30

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Package bc3net updated to version 1.0.3 with previous version 1.0.2 dated 2013-04-07

Title: Gene Regulatory Network Inference with Bc3net
Description: Implementation of the BC3NET algorithm for gene regulatory network inference (de Matos Simoes and Frank Emmert-Streib, Bagging Statistical Network Inference from Large-Scale Gene Expression Data, PLoS ONE 7(3): e33624).
Author: Ricardo de Matos Simoes [aut, cre], Frank Emmert-Streib [aut]
Maintainer: Ricardo de Matos Simoes <ricardo_dematossimoes@dfci.harvard.edu>

Diff between bc3net versions 1.0.2 dated 2013-04-07 and 1.0.3 dated 2015-12-30

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Package acc updated to version 1.2.4 with previous version 1.2.3 dated 2015-12-30

Title: Functions for Processing and Analyzing Accelerometer Data
Description: Processes accelerometer data from uni-axial and tri-axial devices, and generates data summaries. Also includes functions to plot, analyze, and simulate accelerometer data.
Author: Jaejoon Song, Matthew G. Cox
Maintainer: Jaejoon Song <jjsong2@mdanderson.org>

Diff between acc versions 1.2.3 dated 2015-12-30 and 1.2.4 dated 2015-12-30

 DESCRIPTION        |    8 ++++----
 MD5                |   12 ++++++------
 NAMESPACE          |    5 +++++
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 R/aeefit.R         |    2 ++
 R/internal.R       |    1 +
 R/summary.aeefit.R |    2 +-
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More information about acc at CRAN
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Package RcmdrPlugin.KMggplot2 updated to version 0.2-3 with previous version 0.2-2 dated 2015-12-22

Title: An Rcmdr Plug-in for Kaplan-Meier Plots and Other Plots by Using the ggplot2 Package
Description: A GUI front-end for ggplot2 allows Kaplan-Meier plot, histogram, Q-Q plot, box plot, errorbar plot, scatter plot, line chart, pie chart, bar chart, contour plot, and distribution plot.
Author: Triad sou. and Kengo NAGASHIMA
Maintainer: Triad sou. <triadsou@gmail.com>

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Package sdmvspecies updated to version 0.3.2 with previous version 0.3.1 dated 2014-09-19

Title: Create Virtual Species for Species Distribution Modelling
Description: A software package help user to create virtual species for species distribution modelling. It includes several methods to help user to create virtual species distribution map. Those maps can be used for Species Distribution Modelling (SDM) study. SDM use environmental data for sites of occurrence of a species to predict all the sites where the environmental conditions are suitable for the species to persist, and may be expected to occur.
Author: Xiaoquan Kong [aut, cre, cph], Renyan Duan [ths], Minyi Huang [ths]
Maintainer: Xiaoquan Kong <u1mail2me@gmail.com>

Diff between sdmvspecies versions 0.3.1 dated 2014-09-19 and 0.3.2 dated 2015-12-30

 DESCRIPTION                                         |   43 ++++++----
 MD5                                                 |   64 +++++++--------
 NAMESPACE                                           |    9 --
 R/artificial_bell_response.R                        |   19 +---
 R/auto_PCA.R                                        |    4 
 R/config_stack.R                                    |   12 +-
 R/niche_synthese.R                                  |   45 +++++-----
 R/pick_mean.R                                       |   19 ++--
 R/pick_median.R                                     |   19 ++--
 R/rescale.R                                         |   17 +---
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Package plspm.formula updated to version 1.0.1 with previous version 1.0 dated 2015-12-19

Title: Formula Based PLS Path Modeling
Description: The main objective is to make easy the PLS Path Modeling with R using the package 'plspm'. It compute automatically the inner matrix and the outer list the 'plspm' function need simply by specify the model using formulas.
Author: ACHIEPO Odilon Yapo M. [aut, cre]
Maintainer: ACHIEPO Odilon Yapo M. <kingodilon@gmail.com>

Diff between plspm.formula versions 1.0 dated 2015-12-19 and 1.0.1 dated 2015-12-30

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New package geoelectrics with initial version 0.1.5
Package: geoelectrics
Title: 3D-Visualization of Geoelectric Resistivity Measurement Profiles
Version: 0.1.5
Author: Anja Kleebaum <anja.kleebaum@stmail.uni-bayreuth.de>
Maintainer: Anja Kleebaum <anja.kleebaum@stmail.uni-bayreuth.de>
Description: Visualizes two-dimensional geoelectric resistivity measurement profiles in three dimensions.
Depends: R (>= 2.10), lattice, rgl, fields
Imports: methods
License: GPL
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-30 13:30:44 UTC; anja
Repository: CRAN
Date/Publication: 2015-12-30 16:54:37

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New package textmineR with initial version 1.5.0
Package: textmineR
Title: Functions for Text Mining and Topic Modeling
Version: 1.5.0
Date: 2015-12-28
Author: "Thomas W. Jones <jones.thos.w@gmail.com>"
Maintainer: Thomas W. Jones <jones.thos.w@gmail.com>
Description: An aid for text mining in R, with a syntax that is more familiar to experienced R users. Also, implements various functions related to topic modeling. It works well with with the "lda" package by J. Chang.
Depends: R (>= 3.0.2), Matrix
Imports: lda, parallel, tm, RWeka, Rcpp, RcppProgress
License: GPL (>= 3)
LazyData: true
LinkingTo: Rcpp, RcppArmadillo, RcppProgress
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2015-12-30 04:04:06 UTC; tommy
Repository: CRAN
Date/Publication: 2015-12-30 11:54:12

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Package spdynmod updated to version 1.1.3 with previous version 1.1.2 dated 2015-11-06

Title: Spatio-Dynamic Wetland Plant Communities Model
Description: A spatio-dynamic modelling package that focuses on three characteristic wetland plant communities in a semiarid Mediterranean wetland in response to hydrological pressures from the catchment. The package includes the data on watershed hydrological pressure and the initial raster maps of plant communities but also allows for random initial distribution of plant communities. Ongoing developments of the package focus on offering easy to use tools for creating other spatio-dynamic models.
Author: Javier Martinez-Lopez <javi.martinez.lopez@gmail.com>, Babak Naimi <naimi.b@gmail.com>, Julia Martinez-Fernandez <juliamf@um.es>
Maintainer: Javier Martinez-Lopez <javi.martinez.lopez@gmail.com>

Diff between spdynmod versions 1.1.2 dated 2015-11-06 and 1.1.3 dated 2015-12-30

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 NAMESPACE                 |    2 +-
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Package shinyjs updated to version 0.3.0 with previous version 0.2.3 dated 2015-11-08

Title: Perform Common JavaScript Operations in Shiny Apps using Plain R Code
Description: Perform common JavaScript operations in Shiny applications without having to know any JavaScript. Examples include: hiding an element, disabling an input, resetting an input back to its original value, delaying code execution by a few seconds, and many more useful functions. 'shinyjs' can also be used to easily run your own custom JavaScript functions from R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>

Diff between shinyjs versions 0.2.3 dated 2015-11-08 and 0.3.0 dated 2015-12-30

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Package seqHMM updated to version 1.0.3-1 with previous version 1.0.3 dated 2015-12-23

Title: Hidden Markov Models for Life Sequences and Other Multivariate, Multichannel Categorical Time Series
Description: Designed for fitting hidden (latent) Markov models and mixture hidden Markov models for social sequence data and other categorical time series. Also some more restricted versions of these type of models are available: Markov models, mixture Markov models, and latent class models. The package supports models for one or multiple subjects with one or multiple parallel sequences (channels). External covariates can be added to explain cluster membership in mixture models. The package provides functions for evaluating and comparing models, as well as functions for easy plotting of multichannel sequence data and hidden Markov models. Models are estimated using maximum likelihood via the EM algorithm and/or direct numerical maximization with analytical gradients. All main algorithms are written in C++ with support for parallel computation.
Author: Jouni Helske, Satu Helske
Maintainer: Jouni Helske <jouni.helske@jyu.fi>

Diff between seqHMM versions 1.0.3 dated 2015-12-23 and 1.0.3-1 dated 2015-12-30

 DESCRIPTION         |    8 +++---
 MD5                 |   22 +++++++++----------
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 R/mhmm_biofam.R     |    6 ++---
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New package pseval with initial version 1.0.0
Package: pseval
Type: Package
Title: Methods for Evaluating Principal Surrogates of Treatment Response
Version: 1.0.0
Date: 2015-12-28
Author: Michael C Sachs
Maintainer: Michael C Sachs <sachsmc@gmail.com>
Description: Contains the core methods for the evaluation of principal surrogates in a single clinical trial. Provides a flexible interface for defining models for the risk given treatment and the surrogate, the models for integration over the missing counterfactual surrogate responses, and the estimation methods. Estimated maximum likelihood and pseudo-score can be used for estimation, and the bootstrap for inference. A variety of post-estimation summary methods are provided, including print, summary, plot, and testing.
License: MIT + file LICENSE
LazyData: TRUE
Suggests: ggplot2, testthat, knitr, printr
Imports: survival
VignetteBuilder: knitr
RoxygenNote: 5.0.1
Additional_repositories: http://yihui.name/xran
NeedsCompilation: no
Packaged: 2015-12-29 22:51:11 UTC; sachsmc
Repository: CRAN
Date/Publication: 2015-12-30 11:46:39

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Package ifctools updated to version 0.3.2 with previous version 0.3.1 dated 2015-05-27

Title: Italian Fiscal Code ('Codice Fiscale') Utilities
Description: Provides utility functions to deal with Italian fiscal code ('codice fiscale').
Author: Luca Braglia [aut, cre]
Maintainer: Luca Braglia <lbraglia@gmail.com>

Diff between ifctools versions 0.3.1 dated 2015-05-27 and 0.3.2 dated 2015-12-30

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 MD5                  |   18 +++++++++---------
 NAMESPACE            |    3 ++-
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Package GSE updated to version 3.2.3 with previous version 3.2.2 dated 2015-09-24

Title: Robust Estimation in the Presence of Cellwise and Casewise Contamination and Missing Data
Description: Robust Estimation of Multivariate Location and Scatter in the Presence of Cellwise and Casewise Contamination and Missing Data.
Author: Andy Leung, Mike Danilov, Victor Yohai, Ruben Zamar
Maintainer: Andy Leung <andy.leung@stat.ubc.ca>

Diff between GSE versions 3.2.2 dated 2015-09-24 and 3.2.3 dated 2015-12-30

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 R/TSGS.R                |    4 ++
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Package gRain updated to version 1.2-5 with previous version 1.2-4 dated 2015-09-10

Title: Graphical Independence Networks
Description: Probability propagation in graphical independence networks, also known as Bayesian networks or probabilistic expert systems.
Author: Søren Højsgaard
Maintainer: Søren Højsgaard

Diff between gRain versions 1.2-4 dated 2015-09-10 and 1.2-5 dated 2015-12-30

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 DESCRIPTION              |    8 
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New package BIOdry with initial version 0.2
Package: BIOdry
Type: Package
Title: Multilevel Modeling of Dendroclimatical Fluctuations
Version: 0.2
Author: Wilson Lara <wilarhen@gmail.com>, Felipe Bravo <fbravo@pvs.uva.es>
Date: 2015-12-27
Maintainer: Wilson Lara <wilarhen@gmail.com>
Description: Multilevel data frames of tree rings and climate are modeled into normalized fluctuations of tree growth and aridity. Modeled fluctuations (model frames) are compared with Mantel correlograms on multiple levels defined by sample design. Package implementation can be understood by running examples in functions modelFrame and ringApply.
License: GPL-3
Depends: nlme, ecodist
LazyData: TRUE
NeedsCompilation: no
Packaged: 2015-12-29 16:57:29 UTC; wilar
Repository: CRAN
Date/Publication: 2015-12-30 11:52:21

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Package acc updated to version 1.2.3 with previous version 1.1.7 dated 2015-07-17

Title: Functions for Processing and Analyzing Accelerometer Data
Description: Processes accelerometer data from uni-axial and tri-axial devices, and generates data summaries. Also includes functions to plot, analyze, and simulate accelerometer data.
Author: Jaejoon Song, Matthew G. Cox
Maintainer: Jaejoon Song <jjsong2@mdanderson.org>

Diff between acc versions 1.1.7 dated 2015-07-17 and 1.2.3 dated 2015-12-30

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Package TransferEntropy updated to version 1.1 with previous version 1.0 dated 2015-12-26

Title: The Transfer Entropy Package
Description: Estimates the transfer entropy from one time series to another, where each time series consists of continuous random variables. The transfer entropy is an extension of mutual information which takes into account the direction of information flow, under the assumption that the underlying processes can be described by a Markov model. Two estimation methods are provided. The first calculates transfer entropy as the difference of mutual information. Mutual information is estimated using the Kraskov method, which builds on a nearest-neighbor framework (see package references). The second estimation method estimate transfer entropy via the a generalized correlation sum.
Author: Ghazaleh Haratinezhad Torbati [aut, cre], Glenn Lawyer [aut]
Maintainer: Ghazaleh Haratinezhad Torbati <ghazaleh@mpi-inf.mpg.de>

Diff between TransferEntropy versions 1.0 dated 2015-12-26 and 1.1 dated 2015-12-30

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 7 files changed, 54 insertions(+), 17 deletions(-)

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Package rvalues updated to version 0.6 with previous version 0.3 dated 2015-01-28

Title: R-Values for Ranking in High-Dimensional Settings
Description: A collection of functions for computing "r-values" from various kinds of user input such as MCMC output or a list of effect size estimates and associated standard errors. Given a large collection of measurement units, the r-value, r, of a particular unit is a reported percentile that may be interpreted as the smallest percentile at which the unit should be placed in the top r-fraction of units.
Author: Nicholas Henderson [cre], Michael Newton [aut]
Maintainer: Nicholas Henderson <nhenders@stat.wisc.edu>

Diff between rvalues versions 0.3 dated 2015-01-28 and 0.6 dated 2015-12-30

 DESCRIPTION           |   22 +++++++----
 MD5                   |   57 +++++++++++++++-------------
 NAMESPACE             |   23 ++++-------
 R/HyperEstimate.R     |    3 +
 R/NPagrid.R           |   99 +++++++++++++++++++++++++++++---------------------
 R/NPestBinomial.R     |   44 +++++++++++++++-------
 R/NPestNormal.R       |   50 ++++++++++++++++---------
 R/NPestPoisson.R      |   43 ++++++++++++++-------
 R/NPestT.R            |   72 +++++++++++++++++++++---------------
 R/PostPercentile.R    |    1 
 R/ThetaQuantiles.R    |    3 -
 R/Valpha.R            |   11 ++---
 R/agrid_fns.R         |    8 ++--
 R/npml.R              |   15 ++++++-
 R/rvalueBoot.R        |    2 -
 R/rvalueGuts.R        |   27 ++++++++-----
 R/rvalues.R           |   47 +++++++++++++----------
 R/rvaluesMCMC.R       |    8 ++--
 README.md             |only
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 man/PostPercentile.Rd |    2 -
 man/Valpha.Rd         |    4 +-
 man/mroot.Rd          |    2 -
 man/rvalueBoot.Rd     |    2 -
 man/rvalues.Rd        |    6 +--
 man/rvaluesMCMC.Rd    |    4 +-
 src/Vcut.c            |   32 +++++++++++++---
 src/zeroin.c          |    2 -
 31 files changed, 357 insertions(+), 235 deletions(-)

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New package robreg3S with initial version 0.3
Package: robreg3S
Type: Package
Title: Three-Step Regression and Inference for Cellwise and Casewise Contamination
Version: 0.3
Date: 2015-12-28
Author: Andy Leung, Hongyang Zhang, Ruben Zamar
Maintainer: Andy Leung <andy.leung@stat.ubc.ca>
Description: Three-step regression and inference for cellwise and casewise contamination.
Depends: GSE, MASS
Imports: robustbase
License: GPL (>= 2)
Packaged: 2015-12-30 02:02:57 UTC; Andy
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-12-30 08:36:45

More information about robreg3S at CRAN
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Package nhanesA updated to version 0.6.2.1 with previous version 0.6.2 dated 2015-12-28

Title: NHANES Data Retrieval
Description: Utility to retrieve data from the National Health and Nutrition Examination Survey (NHANES).
Author: Christopher Endres
Maintainer: Christopher Endres <cjendres1@gmail.com>

Diff between nhanesA versions 0.6.2 dated 2015-12-28 and 0.6.2.1 dated 2015-12-30

 DESCRIPTION                       |    8 ++++----
 MD5                               |    8 ++++----
 R/nhanes.R                        |   10 +++++-----
 inst/doc/Introducing_nhanesA.html |    4 ++--
 man/browseNHANES.Rd               |   10 +++++-----
 5 files changed, 20 insertions(+), 20 deletions(-)

More information about nhanesA at CRAN
Permanent link

Package FinCal updated to version 0.6.2 with previous version 0.6 dated 2014-02-24

Title: Time Value of Money, Time Series Analysis and Computational Finance
Description: Package for time value of money calculation, time series analysis and computational finance.
Author: Felix Yanhui Fan <nolanfyh@gmail.com>
Maintainer: Felix Yanhui Fan <nolanfyh@gmail.com>

Diff between FinCal versions 0.6 dated 2014-02-24 and 0.6.2 dated 2015-12-30

 FinCal-0.6.2/FinCal/DESCRIPTION                  |   18 -
 FinCal-0.6.2/FinCal/MD5                          |  253 +++++++++++------------
 FinCal-0.6.2/FinCal/NAMESPACE                    |  145 +++++++------
 FinCal-0.6.2/FinCal/NEWS                         |  239 +++++++++++----------
 FinCal-0.6.2/FinCal/R/EIR.R                      |   80 +++----
 FinCal-0.6.2/FinCal/R/EPS.R                      |   26 +-
 FinCal-0.6.2/FinCal/R/SFRatio.R                  |   24 +-
 FinCal-0.6.2/FinCal/R/Sharpe.ratio.R             |   26 +-
 FinCal-0.6.2/FinCal/R/bdy.R                      |   26 +-
 FinCal-0.6.2/FinCal/R/bdy2mmy.R                  |   24 +-
 FinCal-0.6.2/FinCal/R/candlestickChart.R         |   84 +++----
 FinCal-0.6.2/FinCal/R/cash.ratio.R               |   26 +-
 FinCal-0.6.2/FinCal/R/coefficient.variation.R    |   22 +-
 FinCal-0.6.2/FinCal/R/cogs.R                     |  202 +++++++++---------
 FinCal-0.6.2/FinCal/R/current.ratio.R            |   24 +-
 FinCal-0.6.2/FinCal/R/ddb.R                      |   62 ++---
 FinCal-0.6.2/FinCal/R/debt.ratio.R               |   26 +-
 FinCal-0.6.2/FinCal/R/diluted.EPS.R              |   62 ++---
 FinCal-0.6.2/FinCal/R/discount.rate.R            |   64 +----
 FinCal-0.6.2/FinCal/R/ear.R                      |   34 +--
 FinCal-0.6.2/FinCal/R/ear.continuous.R           |   28 +-
 FinCal-0.6.2/FinCal/R/ear2bey.R                  |   22 +-
 FinCal-0.6.2/FinCal/R/ear2hpr.R                  |   28 +-
 FinCal-0.6.2/FinCal/R/financial.leverage.R       |   26 +-
 FinCal-0.6.2/FinCal/R/fv.R                       |   48 ++--
 FinCal-0.6.2/FinCal/R/fv.annuity.R               |   42 +--
 FinCal-0.6.2/FinCal/R/fv.simple.R                |   30 +-
 FinCal-0.6.2/FinCal/R/fv.uneven.R                |   36 +--
 FinCal-0.6.2/FinCal/R/geometric.mean.R           |   20 -
 FinCal-0.6.2/FinCal/R/get.ohlc.google.R          |   90 ++++----
 FinCal-0.6.2/FinCal/R/get.ohlc.yahoo.R           |   85 +++----
 FinCal-0.6.2/FinCal/R/get.ohlcs.google.R         |  100 ++++-----
 FinCal-0.6.2/FinCal/R/get.ohlcs.yahoo.R          |  103 ++++-----
 FinCal-0.6.2/FinCal/R/gpm.R                      |   22 +-
 FinCal-0.6.2/FinCal/R/harmonic.mean.R            |   16 -
 FinCal-0.6.2/FinCal/R/hpr.R                      |   30 +-
 FinCal-0.6.2/FinCal/R/hpr2bey.R                  |   24 +-
 FinCal-0.6.2/FinCal/R/hpr2ear.R                  |   28 +-
 FinCal-0.6.2/FinCal/R/hpr2mmy.R                  |   26 +-
 FinCal-0.6.2/FinCal/R/irr.R                      |   36 +--
 FinCal-0.6.2/FinCal/R/iss.R                      |   32 +-
 FinCal-0.6.2/FinCal/R/lineChart.R                |   71 +++---
 FinCal-0.6.2/FinCal/R/lineChartMult.R            |   88 ++++----
 FinCal-0.6.2/FinCal/R/lt.d2e.R                   |   26 +-
 FinCal-0.6.2/FinCal/R/mmy2hpr.R                  |   28 +-
 FinCal-0.6.2/FinCal/R/n.period.R                 |   50 ++--
 FinCal-0.6.2/FinCal/R/npm.R                      |   22 +-
 FinCal-0.6.2/FinCal/R/npv.R                      |   32 +-
 FinCal-0.6.2/FinCal/R/pmt.R                      |   52 ++--
 FinCal-0.6.2/FinCal/R/pv.R                       |   54 ++--
 FinCal-0.6.2/FinCal/R/pv.annuity.R               |   40 +--
 FinCal-0.6.2/FinCal/R/pv.perpetuity.R            |   54 ++--
 FinCal-0.6.2/FinCal/R/pv.simple.R                |   30 +-
 FinCal-0.6.2/FinCal/R/pv.uneven.R                |   36 +--
 FinCal-0.6.2/FinCal/R/quick.ratio.R              |   28 +-
 FinCal-0.6.2/FinCal/R/r.continuous.R             |   24 +-
 FinCal-0.6.2/FinCal/R/r.norminal.R               |   30 +-
 FinCal-0.6.2/FinCal/R/r.perpetuity.R             |   24 +-
 FinCal-0.6.2/FinCal/R/sampling.error.R           |   22 +-
 FinCal-0.6.2/FinCal/R/slde.R                     |   24 +-
 FinCal-0.6.2/FinCal/R/total.d2e.R                |   26 +-
 FinCal-0.6.2/FinCal/R/twrr.R                     |   48 ++--
 FinCal-0.6.2/FinCal/R/volumeChart.R              |   43 +--
 FinCal-0.6.2/FinCal/R/was.R                      |   50 ++--
 FinCal-0.6.2/FinCal/R/wpr.R                      |   30 +-
 FinCal-0.6.2/FinCal/README.md                    |only
 FinCal-0.6.2/FinCal/man/EIR.Rd                   |   93 ++++----
 FinCal-0.6.2/FinCal/man/EPS.Rd                   |   53 ++--
 FinCal-0.6.2/FinCal/man/SFRatio.Rd               |   48 ++--
 FinCal-0.6.2/FinCal/man/Sharpe.ratio.Rd          |   52 ++--
 FinCal-0.6.2/FinCal/man/bdy.Rd                   |   50 ++--
 FinCal-0.6.2/FinCal/man/bdy2mmy.Rd               |   44 ++--
 FinCal-0.6.2/FinCal/man/candlestickChart.Rd      |   67 ++----
 FinCal-0.6.2/FinCal/man/cash.ratio.Rd            |   53 ++--
 FinCal-0.6.2/FinCal/man/coefficient.variation.Rd |   44 ++--
 FinCal-0.6.2/FinCal/man/cogs.Rd                  |   68 ++----
 FinCal-0.6.2/FinCal/man/current.ratio.Rd         |   50 ++--
 FinCal-0.6.2/FinCal/man/ddb.Rd                   |   58 ++---
 FinCal-0.6.2/FinCal/man/debt.ratio.Rd            |   53 ++--
 FinCal-0.6.2/FinCal/man/diluted.EPS.Rd           |   96 ++++----
 FinCal-0.6.2/FinCal/man/discount.rate.Rd         |   78 +++----
 FinCal-0.6.2/FinCal/man/ear.Rd                   |   60 ++---
 FinCal-0.6.2/FinCal/man/ear.continuous.Rd        |   49 ++--
 FinCal-0.6.2/FinCal/man/ear2bey.Rd               |   41 +--
 FinCal-0.6.2/FinCal/man/ear2hpr.Rd               |   52 ++--
 FinCal-0.6.2/FinCal/man/financial.leverage.Rd    |   53 ++--
 FinCal-0.6.2/FinCal/man/fv.Rd                    |   79 +++----
 FinCal-0.6.2/FinCal/man/fv.annuity.Rd            |   59 ++---
 FinCal-0.6.2/FinCal/man/fv.simple.Rd             |   53 ++--
 FinCal-0.6.2/FinCal/man/fv.uneven.Rd             |   44 ++--
 FinCal-0.6.2/FinCal/man/geometric.mean.Rd        |   34 +--
 FinCal-0.6.2/FinCal/man/get.ohlc.google.Rd       |   57 ++---
 FinCal-0.6.2/FinCal/man/get.ohlc.yahoo.Rd        |   62 ++---
 FinCal-0.6.2/FinCal/man/get.ohlcs.google.Rd      |   57 ++---
 FinCal-0.6.2/FinCal/man/get.ohlcs.yahoo.Rd       |   60 ++---
 FinCal-0.6.2/FinCal/man/gpm.Rd                   |   46 ++--
 FinCal-0.6.2/FinCal/man/harmonic.mean.Rd         |   34 +--
 FinCal-0.6.2/FinCal/man/hpr.Rd                   |   56 ++---
 FinCal-0.6.2/FinCal/man/hpr2bey.Rd               |   45 ++--
 FinCal-0.6.2/FinCal/man/hpr2ear.Rd               |   52 ++--
 FinCal-0.6.2/FinCal/man/hpr2mmy.Rd               |   48 ++--
 FinCal-0.6.2/FinCal/man/irr.Rd                   |   45 ++--
 FinCal-0.6.2/FinCal/man/iss.Rd                   |   50 ++--
 FinCal-0.6.2/FinCal/man/lineChart.Rd             |   61 ++---
 FinCal-0.6.2/FinCal/man/lineChartMult.Rd         |   69 +++---
 FinCal-0.6.2/FinCal/man/lt.d2e.Rd                |   53 ++--
 FinCal-0.6.2/FinCal/man/mmy2hpr.Rd               |   52 ++--
 FinCal-0.6.2/FinCal/man/n.period.Rd              |   75 +++---
 FinCal-0.6.2/FinCal/man/npm.Rd                   |   45 ++--
 FinCal-0.6.2/FinCal/man/npv.Rd                   |   55 ++---
 FinCal-0.6.2/FinCal/man/pmt.Rd                   |   75 +++---
 FinCal-0.6.2/FinCal/man/pv.Rd                    |   83 +++----
 FinCal-0.6.2/FinCal/man/pv.annuity.Rd            |   59 ++---
 FinCal-0.6.2/FinCal/man/pv.perpetuity.Rd         |   63 ++---
 FinCal-0.6.2/FinCal/man/pv.simple.Rd             |   53 ++--
 FinCal-0.6.2/FinCal/man/pv.uneven.Rd             |   49 ++--
 FinCal-0.6.2/FinCal/man/quick.ratio.Rd           |   57 ++---
 FinCal-0.6.2/FinCal/man/r.continuous.Rd          |   45 ++--
 FinCal-0.6.2/FinCal/man/r.norminal.Rd            |   53 ++--
 FinCal-0.6.2/FinCal/man/r.perpetuity.Rd          |   44 ++--
 FinCal-0.6.2/FinCal/man/sampling.error.Rd        |   38 +--
 FinCal-0.6.2/FinCal/man/slde.Rd                  |   51 ++--
 FinCal-0.6.2/FinCal/man/total.d2e.Rd             |   53 ++--
 FinCal-0.6.2/FinCal/man/twrr.Rd                  |   48 ++--
 FinCal-0.6.2/FinCal/man/volumeChart.Rd           |   60 ++---
 FinCal-0.6.2/FinCal/man/was.Rd                   |   54 ++--
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 129 files changed, 3331 insertions(+), 3318 deletions(-)

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New package cricketr with initial version 0.0.11
Package: cricketr
Type: Package
Title: Analyze Cricketers Based on ESPN Cricinfo Statsguru
Description: Tools for analyzing performances of cricketers based on stats in ESPN Cricinfo Statsguru. The toolset can be used for analysis of Tests,ODIs and Twenty20 matches of both batsmen and bowlers.
Version: 0.0.11
Date: 2015-12-26
Author: Tinniam V Ganesh
Maintainer: Tinniam V Ganesh <tvganesh.85@gmail.com>
License: MIT + file LICENSE
Depends: R (>= 3.1.2)
Imports: dplyr, plotrix, ggplot2, scatterplot3d, forecast, lubridate, XML, graphics, grDevices, stats, utils
URL: https://github.com/tvganesh/cricketr
BugReports: https://github.com/tvganesh/cricketr/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-30 04:09:31 UTC; Ganesh
Repository: CRAN
Date/Publication: 2015-12-30 08:45:30

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Tue, 29 Dec 2015

Package seroincidence updated to version 1.0.5 with previous version 1.0.4 dated 2015-05-22

Title: Estimating Infection Rates from Serological Data
Description: Translates antibody levels measured in a (cross-sectional) population sample into an estimate of the frequency with which seroconversions (infections) occur in the sampled population.
Author: Peter Teunis [aut] (Author of the method and original code), Daniel Lewandowski [com, ctb] (Creator of the R package), Chantal Quinten [ctb, cre] (Project manager and the package maintainer)
Maintainer: Chantal Quinten <seroincidence@ecdc.europa.eu>

Diff between seroincidence versions 1.0.4 dated 2015-05-22 and 1.0.5 dated 2015-12-29

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 NAMESPACE                               |    2 -
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 R/estimateSeroincidence.R               |    7 +--
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 R/rinvgamma.R                           |    2 -
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 man/summary.seroincidence.Rd            |    4 +-
 vignettes/methodology.Rmd               |    1 
 31 files changed, 105 insertions(+), 88 deletions(-)

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Package xtal updated to version 1.15 with previous version 1.0 dated 2014-11-05

Title: Crystallization Toolset
Description: This is the tool set for crystallographer to design and analyze crystallization experiments, especially for ribosome from Mycobacterium tuberculosis.
Author: Qingan Sun, Xiaojun Li
Maintainer: Qingan Sun <quinsun@gmail.com>

Diff between xtal versions 1.0 dated 2014-11-05 and 1.15 dated 2015-12-29

 DESCRIPTION         |   10 +++++-----
 MD5                 |    6 +++---
 R/Design8Vertex.R   |    2 +-
 man/xtal-package.Rd |    4 ++--
 4 files changed, 11 insertions(+), 11 deletions(-)

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Package TOC updated to version 0.0-4 with previous version 0.0-3 dated 2015-08-05

Title: Total Operating Characteristic Curve and ROC Curve
Description: Construction of the Total Operating Characteristic (TOC) Curve and the Receiver (aka Relative) Operating Characteristic (ROC) Curve for spatial and non-spatial data. The TOC method is a modification of the ROC method which measures the ability of an index variable to diagnose either presence or absence of a characteristic. The diagnosis depends on whether the value of an index variable is above a threshold. Each threshold generates a two-by-two contingency table, which contains four entries: hits (H), misses (M), false alarms (FA), and correct rejections (CR). While ROC shows for each threshold only two ratios, H/(H + M) and FA/(FA + CR), TOC reveals the size of every entry in the contingency table for each threshold (Pontius Jr., R.G., Si, K. 2014. The total operating characteristic to measure diagnostic ability for multiple thresholds. Int. J. Geogr. Inf. Sci. 28 (3), 570-583).
Author: Robert G. Pontius , Alí Santacruz, Amin Tayyebi, Benoit Parmentier, Kangping Si
Maintainer: Alí Santacruz

Diff between TOC versions 0.0-3 dated 2015-08-05 and 0.0-4 dated 2015-12-29

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 MD5                |   12 ++++++------
 NAMESPACE          |    2 +-
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 R/plotTOC.R        |    4 ++--
 man/TOC-package.Rd |    4 ++--
 7 files changed, 19 insertions(+), 17 deletions(-)

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Package telegram updated to version 0.3.0 with previous version 0.1 dated 2015-12-24

Title: R Wrapper Around the Telegram Bot API
Description: R wrapper around the Telegram Bot API (http://core.telegram.org/bots/api) to access Telegram's messaging facilities with ease (e.g. you send messages, images, files from R to your smartphone).
Author: Luca Braglia [aut, cre]
Maintainer: Luca Braglia <lbraglia@gmail.com>

Diff between telegram versions 0.1 dated 2015-12-24 and 0.3.0 dated 2015-12-29

 DESCRIPTION          |    8 
 MD5                  |   16 +
 NAMESPACE            |    2 
 R/TGBot.R            |  507 ++++++++++++++++++++++++++++++++++-----------------
 R/telegram-package.r |    1 
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 inst                 |only
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 man/bot_token.Rd     |only
 9 files changed, 467 insertions(+), 233 deletions(-)

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Package spatstat updated to version 1.44-1 with previous version 1.44-0 dated 2015-12-23

Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing spatial data, mainly Spatial Point Patterns, including multi-type/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, and point patterns on a linear network. Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference. Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks. Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported. Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods. A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above. Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>, Rolf Turner <r.turner@auckland.ac.nz> and Ege Rubak <rubak@math.aau.dk>, with substantial contributions of code by Kasper Klitgaard Berthelsen; Ute Hahn; Abdollah Jalilian; Marie-Colette van Lieshout; Tuomas Rajala; Dominic Schuhmacher; and Rasmus Waagepetersen. Additional contributions by Q.W. Ang; S. Azaele; M. Baddeley; C. Beale; M. Bell; R. Bernhardt; T. Bendtsen; A. Bevan; B. Biggerstaff; A. Bilgrau; L. Bischof; C. Biscio; R. Bivand; J.M. Blanco Moreno; F. Bonneu; J. Burgos; S. Byers; Y.M. Chang; J.B. Chen; I. Chernayavsky; Y.C. Chin; B. Christensen; J.-F. Coeurjolly; R. Corria Ainslie; M. de la Cruz; P. Dalgaard; S. Das; P.J. Diggle; P. Donnelly; I. Dryden; S. Eglen; A. El-Gabbas; B. Fandohan; O. Flores; E.D. Ford; P. Forbes; S. Frank; J. Franklin; N. Funwi-Gabga; O. Garcia; A. Gault; J. Geldmann; M. Genton; S. Ghalandarayeshi; J. Gilbey; J. Goldstick; P. Grabarnik; C. Graf; U. Hahn; A. Hardegen; M.B. Hansen; M. Hazelton; J. Heikkinen; M. Hering; M. Herrmann; K. Hingee; K. Hornik; P. Hunziker; J. Hywood; R. Ihaka; A. Jammalamadaka; R. John-Chandran; D. Johnson; M. Khanmohammadi; R. Klaver; P. Kovesi; M. Kuhn; J. Laake; F. Lavancier; T. Lawrence; R.A. Lamb; J. Lee; G.P. Leser; H.T. Li; G. Limitsios; A. Lister; B. Madin; M. Maechler; J. Marcus; K. Marchikanti; R. Mark; J. Mateu; P. McCullagh; U. Mehlig; S. Meyer; X.C. Mi; L. De Middeleer; R.K. Milne; E. Miranda; J. Moller; E. Mudrak; G.M. Nair; N. Nava; L.S. Nielsen; F. Nunes; J.R. Nyengaard; J. Oehlschlaegel; T. Onkelinx; S. O'Riordan; E. Parilov; J. Picka; N. Picard; M. Porter; S. Protsiv; A. Raftery; S. Rakshit; B. Ramage; P. Ramon; X. Raynaud, M. Reiter; I. Renner; T.O. Richardson; B.D. Ripley; E. Rosenbaum; B. Rowlingson; J. Rudokas; J. Rudge; C. Ryan; F. Safavimanesh; A. Sarkka; C. Schank; K. Schladitz; S. Schutte; B.T. Scott; O. Semboli; F. Semecurbe; V. Shcherbakov; G.C. Shen; P. Shi; H.-J. Ship; I.-M. Sintorn; Y. Song; M. Spiess; M. Stevenson; K. Stucki; M. Sumner; P. Surovy; B. Taylor; T. Thorarinsdottir; B. Turlach; T. Tvedebrink; K. Ummer; M. Uppala; A. van Burgel; T. Verbeke; M. Vihtakari; A. Villers; F. Vinatier; S. Voss; H. Wang; H. Wendrock; J. Wild; C. Witthoft; S. Wong; M. Woringer; M.E. Zamboni and A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

Diff between spatstat versions 1.44-0 dated 2015-12-23 and 1.44-1 dated 2015-12-29

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More information about spatstat at CRAN
Permanent link

New package RImagePalette with initial version 0.1.0
Package: RImagePalette
Type: Package
Title: Extract the Colors from Images
Version: 0.1.0
Date: 2015-12-29
Author: Joel Carlson
Maintainer: Joel Carlson <jnkcarlson@gmail.com>
Description: A pure R implementation of the median cut algorithm. Extracts the dominant colors from an image, and turns them into a scale for use in plots or for fun!
License: MIT + file LICENSE
LazyData: TRUE
Depends: R (>= 2.1.0)
Imports: ggplot2
Suggests: testthat, scales, jpeg, png
NeedsCompilation: no
Packaged: 2015-12-29 10:53:14 UTC; joel
Repository: CRAN
Date/Publication: 2015-12-29 22:01:51

More information about RImagePalette at CRAN
Permanent link

Package RDS updated to version 0.7-4 with previous version 0.7-3 dated 2015-09-20

Title: Respondent-Driven Sampling
Description: Provides functionality for carrying out estimation with data collected using Respondent-Driven Sampling. This includes Heckathorn's RDS-I and RDS-II estimators as well as Gile's Sequential Sampling estimator. The package is part of the "RDS Analyst" suite of packages for the analysis of respondent-driven sampling data.
Author: Mark S. Handcock [aut, cre], Krista J. Gile [aut], Ian E. Fellows [aut], W. Whipple Neely [aut]
Maintainer: Mark S. Handcock <handcock@stat.ucla.edu>

Diff between RDS versions 0.7-3 dated 2015-09-20 and 0.7-4 dated 2015-12-29

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More information about RDS at CRAN
Permanent link

Package protr updated to version 1.1-1 with previous version 1.0-1 dated 2015-11-27

Title: Generating Various Numerical Representation Schemes of Protein Sequence
Description: Comprehensive toolkit for generating various numerical representation schemes of protein sequence. The descriptors and similarity scores included are extensively used in bioinformatics and chemogenomics. For full functionality, the software 'ncbi-blast+' is needed, see <http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download> for more information.
Author: Nan Xiao <road2stat@gmail.com>, Qingsong Xu <dasongxu@gmail.com>, Dongsheng Cao <oriental-cds@163.com>
Maintainer: Nan Xiao <road2stat@gmail.com>

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More information about protr at CRAN
Permanent link

Package PopED updated to version 0.3.0 with previous version 0.2.0 dated 2015-03-20

Title: Population (and Individual) Optimal Experimental Design
Description: Optimal experimental designs for both population and individual studies based on nonlinear mixed-effect models. Often this is based on a computation of the Fisher Information Matrix (FIM). This package was developed for pharmacometric problems, and examples and predefined models are available for these types of systems.
Author: Andrew C. Hooker [aut, cre, trl, cph], Sebastian Ueckert [aut] (MATLAB version), Marco Foracchia [aut] (O-Matrix version), Joakim Nyberg [aut] (MATLAB version), Eric Stroemberg [ctb] (MATLAB version)
Maintainer: Andrew C. Hooker <andrew.hooker@farmbio.uu.se>

Diff between PopED versions 0.2.0 dated 2015-03-20 and 0.3.0 dated 2015-12-29

 PopED-0.2.0/PopED/R/PopED-package.R                                                    |only
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 PopED-0.2.0/PopED/man/PopED-package.Rd                                                 |only
 PopED-0.2.0/PopED/tests/test-all.R                                                     |only
 PopED-0.3.0/PopED/DESCRIPTION                                                          |   20 
 PopED-0.3.0/PopED/MD5                                                                  |  459 +++++-----
 PopED-0.3.0/PopED/NAMESPACE                                                            |  110 ++
 PopED-0.3.0/PopED/NEWS                                                                 |   14 
 PopED-0.3.0/PopED/R/Doptim.R                                                           |   90 +
 PopED-0.3.0/PopED/R/Dtrace.R                                                           |    4 
 PopED-0.3.0/PopED/R/LEDoptim.R                                                         |    3 
 PopED-0.3.0/PopED/R/LinMatrixH.R                                                       |    5 
 PopED-0.3.0/PopED/R/LinMatrixL.R                                                       |    2 
 PopED-0.3.0/PopED/R/LinMatrixLH.R                                                      |    2 
 PopED-0.3.0/PopED/R/LinMatrixL_occ.R                                                   |    2 
 PopED-0.3.0/PopED/R/PopED.R                                                            |only
 PopED-0.3.0/PopED/R/RS_opt.R                                                           |    2 
 PopED-0.3.0/PopED/R/RS_opt_gen.R                                                       |    2 
 PopED-0.3.0/PopED/R/a_line_search.R                                                    |    1 
 PopED-0.3.0/PopED/R/bfgsb_min.R                                                        |    4 
 PopED-0.3.0/PopED/R/blockexp.R                                                         |    6 
 PopED-0.3.0/PopED/R/blockfinal.R                                                       |   47 -
 PopED-0.3.0/PopED/R/blockheader.R                                                      |   64 -
 PopED-0.3.0/PopED/R/blockopt.R                                                         |    3 
 PopED-0.3.0/PopED/R/build_sfg.R                                                        |   25 
 PopED-0.3.0/PopED/R/calc_ofv_and_fim.R                                                 |    1 
 PopED-0.3.0/PopED/R/cell.R                                                             |    3 
 PopED-0.3.0/PopED/R/convert_variables.R                                                |    3 
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 PopED-0.3.0/PopED/R/create_design.R                                                    |    2 
 PopED-0.3.0/PopED/R/create_design_space.R                                              |   11 
 PopED-0.3.0/PopED/R/diag_matlab.R                                                      |    2 
 PopED-0.3.0/PopED/R/downsizing_general_design.R                                        |    4 
 PopED-0.3.0/PopED/R/ed_laplace_ofv.R                                                   |    7 
 PopED-0.3.0/PopED/R/ed_mftot.R                                                         |    4 
 PopED-0.3.0/PopED/R/evaluate.e.ofv.fim.R                                               |    1 
 PopED-0.3.0/PopED/R/evaluate.fim.R                                                     |    7 
 PopED-0.3.0/PopED/R/feval.R                                                            |    4 
 PopED-0.3.0/PopED/R/fileparts.R                                                        |    3 
 PopED-0.3.0/PopED/R/find.largest.index.R                                               |only
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 PopED-0.3.0/PopED/R/get_all_params.R                                                   |    2 
 PopED-0.3.0/PopED/R/get_cv.R                                                           |    2 
 PopED-0.3.0/PopED/R/get_unfixed_params.R                                               |   80 -
 PopED-0.3.0/PopED/R/get_vector_str.R                                                   |    6 
 PopED-0.3.0/PopED/R/getfulld.R                                                         |    5 
 PopED-0.3.0/PopED/R/inv.R                                                              |   10 
 PopED-0.3.0/PopED/R/isempty.R                                                          |    3 
 PopED-0.3.0/PopED/R/isfield.R                                                          |    3 
 PopED-0.3.0/PopED/R/log_prior_pdf.R                                                    |    3 
 PopED-0.3.0/PopED/R/mf.R                                                               |    2 
 PopED-0.3.0/PopED/R/mf3.R                                                              |   26 
 PopED-0.3.0/PopED/R/mf5.R                                                              |    2 
 PopED-0.3.0/PopED/R/mf6.R                                                              |    2 
 PopED-0.3.0/PopED/R/mf7.R                                                              |    2 
 PopED-0.3.0/PopED/R/mf8.R                                                              |    2 
 PopED-0.3.0/PopED/R/mfea.R                                                             |    2 
 PopED-0.3.0/PopED/R/mftot.R                                                            |    3 
 PopED-0.3.0/PopED/R/mftot0.R                                                           |    3 
 PopED-0.3.0/PopED/R/mftot1.R                                                           |    3 
 PopED-0.3.0/PopED/R/mftot2.R                                                           |    3 
 PopED-0.3.0/PopED/R/mftot3.R                                                           |    3 
 PopED-0.3.0/PopED/R/mftot4.R                                                           |    3 
 PopED-0.3.0/PopED/R/mftot5.R                                                           |    2 
 PopED-0.3.0/PopED/R/mftot6.R                                                           |    3 
 PopED-0.3.0/PopED/R/mftot7.R                                                           |    2 
 PopED-0.3.0/PopED/R/model_prediction.R                                                 |    9 
 PopED-0.3.0/PopED/R/models.R                                                           |   13 
 PopED-0.3.0/PopED/R/ofv_criterion.R                                                    |    1 
 PopED-0.3.0/PopED/R/ofv_fim.R                                                          |    6 
 PopED-0.3.0/PopED/R/ones.R                                                             |    2 
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 PopED-0.3.0/PopED/R/optim_LS.R                                                         |only
 PopED-0.3.0/PopED/R/pargen.R                                                           |   30 
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 PopED-0.3.0/PopED/R/poped_optim.R                                                      |only
 PopED-0.3.0/PopED/R/poped_optimize.R                                                   |    2 
 PopED-0.3.0/PopED/R/rand.R                                                             |    3 
 PopED-0.3.0/PopED/R/randn.R                                                            |    3 
 PopED-0.3.0/PopED/R/randperm.R                                                         |    3 
 PopED-0.3.0/PopED/R/size.R                                                             |    2 
 PopED-0.3.0/PopED/R/start_parallel.R                                                   |only
 PopED-0.3.0/PopED/R/test_for_max.R                                                     |    3 
 PopED-0.3.0/PopED/R/test_for_min.R                                                     |    3 
 PopED-0.3.0/PopED/R/test_for_zeros.R                                                   |    3 
 PopED-0.3.0/PopED/R/test_mat_size.R                                                    |    3 
 PopED-0.3.0/PopED/R/tic.R                                                              |    2 
 PopED-0.3.0/PopED/R/toc.R                                                              |    7 
 PopED-0.3.0/PopED/R/zeros.R                                                            |    2 
 PopED-0.3.0/PopED/README.md                                                            |    6 
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 PopED-0.3.0/PopED/inst/shinyapp/server.R                                               |   13 
 PopED-0.3.0/PopED/inst/shinyapp/ui.R                                                   |   20 
 PopED-0.3.0/PopED/man/Doptim.Rd                                                        |  119 +-
 PopED-0.3.0/PopED/man/Dtrace.Rd                                                        |   21 
 PopED-0.3.0/PopED/man/LEDoptim.Rd                                                      |   79 +
 PopED-0.3.0/PopED/man/LinMatrixH.Rd                                                    |   50 -
 PopED-0.3.0/PopED/man/LinMatrixL.Rd                                                    |   26 
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 PopED-0.3.0/PopED/man/PopED.Rd                                                         |only
 PopED-0.3.0/PopED/man/RS_opt.Rd                                                        |   72 -
 PopED-0.3.0/PopED/man/RS_opt_gen.Rd                                                    |   78 +
 PopED-0.3.0/PopED/man/a_line_search.Rd                                                 |   42 
 PopED-0.3.0/PopED/man/bfgsb_min.Rd                                                     |   38 
 PopED-0.3.0/PopED/man/blockexp.Rd                                                      |   26 
 PopED-0.3.0/PopED/man/blockfinal.Rd                                                    |   38 
 PopED-0.3.0/PopED/man/blockheader.Rd                                                   |   59 -
 PopED-0.3.0/PopED/man/blockopt.Rd                                                      |   26 
 PopED-0.3.0/PopED/man/calc_autofocus.Rd                                                |   43 
 PopED-0.3.0/PopED/man/calc_ofv_and_fim.Rd                                              |   88 +
 PopED-0.3.0/PopED/man/calc_ofv_and_grad.Rd                                             |   43 
 PopED-0.3.0/PopED/man/cell.Rd                                                          |   16 
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 PopED-0.3.0/PopED/man/create.poped.database.Rd                                         |   92 +-
 PopED-0.3.0/PopED/man/create_design.Rd                                                 |   20 
 PopED-0.3.0/PopED/man/create_design_space.Rd                                           |   24 
 PopED-0.3.0/PopED/man/diag_matlab.Rd                                                   |   21 
 PopED-0.3.0/PopED/man/downsizing_general_design.Rd                                     |   32 
 PopED-0.3.0/PopED/man/ed_laplace_ofv.Rd                                                |   56 -
 PopED-0.3.0/PopED/man/ed_mftot.Rd                                                      |   79 +
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 PopED-0.3.0/PopED/man/evaluate.fim.Rd                                                  |   70 -
 PopED-0.3.0/PopED/man/feps.add.Rd                                                      |   30 
 PopED-0.3.0/PopED/man/feps.add.prop.Rd                                                 |   30 
 PopED-0.3.0/PopED/man/feps.prop.Rd                                                     |   45 
 PopED-0.3.0/PopED/man/feval.Rd                                                         |   15 
 PopED-0.3.0/PopED/man/ff.PK.1.comp.oral.md.CL.Rd                                       |   28 
 PopED-0.3.0/PopED/man/ff.PK.1.comp.oral.md.KE.Rd                                       |   28 
 PopED-0.3.0/PopED/man/ff.PK.1.comp.oral.sd.CL.Rd                                       |   43 
 PopED-0.3.0/PopED/man/ff.PK.1.comp.oral.sd.KE.Rd                                       |   28 
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 PopED-0.3.0/PopED/man/ff.PKPD.1.comp.sd.CL.emax.Rd                                     |   26 
 PopED-0.3.0/PopED/man/fileparts.Rd                                                     |   15 
 PopED-0.3.0/PopED/man/getTruncatedNormal.Rd                                            |    5 
 PopED-0.3.0/PopED/man/get_all_params.Rd                                                |   19 
 PopED-0.3.0/PopED/man/get_rse.Rd                                                       |   21 
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 PopED-0.3.0/PopED/man/getfulld.Rd                                                      |    5 
 PopED-0.3.0/PopED/man/gradf_eps.Rd                                                     |   48 -
 PopED-0.3.0/PopED/man/inv.Rd                                                           |only
 PopED-0.3.0/PopED/man/isempty.Rd                                                       |   15 
 PopED-0.3.0/PopED/man/isfield.Rd                                                       |   15 
 PopED-0.3.0/PopED/man/log_prior_pdf.Rd                                                 |   38 
 PopED-0.3.0/PopED/man/mf.Rd                                                            |   47 -
 PopED-0.3.0/PopED/man/mf3.Rd                                                           |   49 -
 PopED-0.3.0/PopED/man/mf5.Rd                                                           |   57 -
 PopED-0.3.0/PopED/man/mf6.Rd                                                           |   49 -
 PopED-0.3.0/PopED/man/mf7.Rd                                                           |   47 -
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Package jackstraw updated to version 1.1 with previous version 1.0 dated 2014-01-31

Title: Statistical Inference of Variables Driving Systematic Variation
Description: Significance test for association between variables and their estimated latent variables. Latent variables may be estimated by principal component analysis (PCA), logistic factor analysis (LFA), and other techniques.
Author: Neo Christopher Chung <nchchung@gmail.com>, Wei Hao <whao@princeton.edu>, John D. Storey <jstorey@princeton.edu>
Maintainer: Neo Christopher Chung <nchchung@gmail.com>

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New package eva with initial version 0.1.1
Package: eva
Title: Extreme Value Analysis with Goodness-of-Fit Testing
Date: 2015-12-28
Version: 0.1.1
Authors@R: c(person(given = "Brian", family = "Bader", role = c("aut", "cre"), email = "brianbader@mail.com"), person(given = "Jun", family = "Yan", role = "aut"))
Description: Goodness-of-fit tests for selection of r in the r-largest order statistics (GEVr) model. Goodness-of-fit tests for threshold selection in the peaks-over-threshold approach. Random number generation and density functions for the GEVr distribution. Profile likelihood for return level estimation using the GEVr and generalized pareto distributions. P-value adjustments for sequential, multiple testing error control.
Imports: parallel, stats, graphics
Depends: R(>= 2.10.0)
Suggests: knitr, ggplot2
License: GPL (>= 2)
Repository: CRAN
VignetteBuilder: knitr
URL: https://github.com/geekman1/eva_package
BugReports: https://github.com/geekman1/eva_package/issues
LazyData: true
RoxygenNote: 5.0.1
Packaged: 2015-12-29 14:45:06 UTC; Beatrice
Author: Brian Bader [aut, cre], Jun Yan [aut]
Maintainer: Brian Bader <brianbader@mail.com>
NeedsCompilation: no
Date/Publication: 2015-12-29 22:02:48

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Package doBy updated to version 4.5-14 with previous version 4.5-13 dated 2014-12-11

Title: Groupwise Statistics, LSmeans, Linear Contrasts, Utilities
Description: The facilities can roughly be grouped as: 1) Facilities for groupwise computations of summary statistics and other facilities for working with grouped data: 'do' something to data stratified 'by' some variables. 2) LSmeans (least-squares means), general linear contrasts. 3) Miscellaneous other utilities.
Author: Søren Højsgaard and Ulrich Halekoh
Maintainer: Søren Højsgaard

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Package diffeR updated to version 0.0-4 with previous version 0.0-3 dated 2015-07-07

Title: Metrics of Difference for Comparing Pairs of Maps
Description: Metrics of difference for comparing pairs of maps representing real or categorical variables at original and multiple resolutions.
Author: Robert Gilmore Pontius Jr. , Alí Santacruz
Maintainer: Alí Santacruz

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Package Deducer updated to version 0.7-9 with previous version 0.7-7 dated 2014-04-30

Title: A Data Analysis GUI for R
Description: An intuitive, cross-platform graphical data analysis system. It uses menus and dialogs to guide the user efficiently through the data manipulation and analysis process, and has an excel like spreadsheet for easy data frame visualization and editing. Deducer works best when used with the Java based R GUI JGR, but the dialogs can be called from the command line. Dialogs have also been integrated into the Windows Rgui.
Author: Ian Fellows with contributions from others (see documentation).
Maintainer: Ian Fellows <ian@fellstat.com>

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Package dc3net updated to version 1.0.1 with previous version 1.0 dated 2015-10-01

Title: Inferring Disease Networks via Differential Network Inference
Description: Performs differential network analysis to infer disease specific gene networks.
Author: Gokmen Altay
Maintainer: Gokmen Altay <altayscience@gmail.com>

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Package WGCNA updated to version 1.49 with previous version 1.48 dated 2015-10-29

Title: Weighted Correlation Network Analysis
Description: Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Author: Peter Langfelder <Peter.Langfelder@gmail.com> and Steve Horvath <SHorvath@mednet.ucla.edu> with contributions by Chaochao Cai, Jun Dong, Jeremy Miller, Lin Song, Andy Yip, and Bin Zhang
Maintainer: Peter Langfelder <Peter.Langfelder@gmail.com>

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Package profileR updated to version 0.3-2 with previous version 0.3-1 dated 2015-10-19

Title: Profile Analysis of Multivariate Data in R
Description: Fit profile analytic models. This includes the multivariate methods and data visualization tools to implement profile analysis and cross-validation techniques described in Davison & Davenport (2002) and Bulut (2013).
Author: Okan Bulut <okanbulut84@gmail.com>, Christopher David Desjardins <cddesjardins@gmail.com>
Maintainer: Christopher David Desjardins <cddesjardins@gmail.com>

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Package htmltools updated to version 0.3 with previous version 0.2.6 dated 2014-09-08

Title: Tools for HTML
Description: Tools for HTML generation and output.
Author: RStudio, Inc.
Maintainer: Joe Cheng <joe@rstudio.com>

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Package GiANT updated to version 1.2 with previous version 1.1 dated 2015-09-08

Title: Gene Set Uncertainty in Enrichment Analysis
Description: Toolbox for various enrichment analysis methods and quantification of uncertainty of gene sets.
Author: Florian Schmid, Christoph Müssel, Johann M. Kraus, Hans A. Kestler
Maintainer: Hans Kestler <hans.kestler@uni-ulm.de>

Diff between GiANT versions 1.1 dated 2015-09-08 and 1.2 dated 2015-12-29

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More information about GiANT at CRAN
Permanent link

Package cIRT updated to version 1.1.0 with previous version 1.0.0 dated 2015-12-06

Title: Choice Item Response Theory
Description: Jointly model the accuracy of cognitive responses and item choices within a bayesian hierarchical framework as described by Culpepper and Balamuta (2015) <doi:10.1007/s11336-015-9484-7>. In addition, the package contains the datasets used within the analysis of the paper.
Author: Steve Culpepper [aut, cph], James Balamuta [aut, cre, ctb, com, cph]
Maintainer: James Balamuta <balamut2@illinois.edu>

Diff between cIRT versions 1.0.0 dated 2015-12-06 and 1.1.0 dated 2015-12-29

 DESCRIPTION                       |   10 
 MD5                               |   54 +--
 NAMESPACE                         |   10 
 R/RcppExports.R                   |  612 +++++++++++++++++++-------------------
 R/cIRT-package.R                  |   54 +--
 R/choice_matrix.R                 |   32 +
 R/payout_matrix.R                 |   26 -
 R/survey_data.R                   |   34 +-
 R/trial_matrix.R                  |   80 ++--
 data/choice_matrix.rda            |binary
 inst/CITATION                     |   40 +-
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 man/Total_Tabulate.Rd             |   50 +--
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 man/cIRT.Rd                       |  236 +++++++-------
 man/cIRT_package.Rd               |   70 ++--
 man/center_matrix.Rd              |   70 ++--
 man/choice_matrix.Rd              |   56 +--
 man/direct_sum.Rd                 |   72 ++--
 man/payout_matrix.Rd              |   50 +--
 man/probitHLM.Rd                  |  150 ++++-----
 man/riwishart.Rd                  |   60 +--
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 man/rwishart.Rd                   |   88 ++---
 man/survey_data.Rd                |   58 +--
 man/trial_matrix.Rd               |  104 +++---
 vignettes/parse_results.R         |  254 +++++++--------
 vignettes/simulation_CIRT_beta2.R |  192 +++++------
 28 files changed, 1381 insertions(+), 1381 deletions(-)

More information about cIRT at CRAN
Permanent link

Mon, 28 Dec 2015

Package rrepast updated to version 0.3 with previous version 0.2 dated 2015-12-05

Title: Invoke 'Repast Simphony' Simulation Models
Description: An R and Repast integration tool for running individual-based (IbM) simulation models developed using 'Repast Simphony' Agent-Based framework directly from R code. This package integrates 'Repast Simphony' models within R environment, making easier the tasks of running and analyzing model output data for automated parameter calibration and for carrying out uncertainty and sensitivity analysis using the power of R environment.
Author: Antonio Prestes Garcia [aut, cre], Alfonso Rodriguez-Paton [aut, ths]
Maintainer: Antonio Prestes Garcia <antonio.pgarcia@alumnos.upm.es>

Diff between rrepast versions 0.2 dated 2015-12-05 and 0.3 dated 2015-12-28

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More information about rrepast at CRAN
Permanent link

Package rglwidget updated to version 0.1.1434 with previous version 0.1.1431 dated 2015-12-07

Title: 'rgl' in 'htmlwidgets' Framework
Description: Provides an 'htmlwidgets' framework for the 'rgl' package.
Author: Duncan Murdoch
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>

Diff between rglwidget versions 0.1.1431 dated 2015-12-07 and 0.1.1434 dated 2015-12-28

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More information about rglwidget at CRAN
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Package rgl updated to version 0.95.1435 with previous version 0.95.1429 dated 2015-12-07

Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Daniel Adler <dadler@uni-goettingen.de>, Duncan Murdoch <murdoch@stats.uwo.ca>, and others (see README)
Maintainer: Duncan Murdoch <murdoch@stats.uwo.ca>

Diff between rgl versions 0.95.1429 dated 2015-12-07 and 0.95.1435 dated 2015-12-28

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More information about rgl at CRAN
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Package nhanesA updated to version 0.6.2 with previous version 0.6.1 dated 2015-10-08

Title: NHANES Data Retrieval
Description: Utility to retrieve data from the National Health and Nutrition Examination Survey (NHANES).
Author: Christopher Endres
Maintainer: Christopher Endres <cjendres1@gmail.com>

Diff between nhanesA versions 0.6.1 dated 2015-10-08 and 0.6.2 dated 2015-12-28

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 nhanesA-0.6.2/nhanesA/inst/doc/Introducing_nhanesA.Rmd  |   20 ++
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More information about nhanesA at CRAN
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Package multilevelPSA updated to version 1.2.4 with previous version 1.2.3 dated 2015-11-05

Title: Multilevel Propensity Score Analysis
Description: Functions to estimate and visualize propensity score analysis for multilevel, or clustered, data.
Author: Jason Bryer <jason@bryer.org>
Maintainer: Jason Bryer <jason@bryer.org>

Diff between multilevelPSA versions 1.2.3 dated 2015-11-05 and 1.2.4 dated 2015-12-28

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 multilevelPSA-1.2.4/multilevelPSA/NAMESPACE                 |   19 ++++++++-
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 multilevelPSA-1.2.4/multilevelPSA/R/multilevelPSA-package.R |    7 ++-
 multilevelPSA-1.2.4/multilevelPSA/R/plot.difftable.R        |    6 +--
 multilevelPSA-1.2.4/multilevelPSA/R/plot.missing.R          |    4 +-
 multilevelPSA-1.2.4/multilevelPSA/R/plot.mlpsa.circ.R       |   22 ++++++-----
 multilevelPSA-1.2.4/multilevelPSA/R/plot.mlpsa.difference.R |    7 ++-
 multilevelPSA-1.2.4/multilevelPSA/man/missing.plot.Rd       |    6 +--
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 14 files changed, 73 insertions(+), 53 deletions(-)

More information about multilevelPSA at CRAN
Permanent link

Package GMDH updated to version 1.2 with previous version 1.1 dated 2015-07-20

Title: Short Term Forecasting via GMDH-Type Neural Network Algorithms
Description: Group method of data handling (GMDH) - type neural network algorithm is the heuristic self-organization method for modelling the complex systems. In this package, GMDH-type neural network algorithms are applied to make short term forecasting for a univariate time series.
Author: Osman Dag, Ceylan Yozgatligil
Maintainer: Osman Dag <osman.dag@hacettepe.edu.tr>

Diff between GMDH versions 1.1 dated 2015-07-20 and 1.2 dated 2015-12-28

 DESCRIPTION  |   13 ++++++-------
 MD5          |    6 +++---
 man/GMDH.Rd  |    8 ++++----
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 4 files changed, 18 insertions(+), 19 deletions(-)

More information about GMDH at CRAN
Permanent link

Package arfima updated to version 1.3-3 with previous version 1.2-7 dated 2014-11-21

Title: Fractional ARIMA (and Other Long Memory) Time Series Modeling
Description: Simulates, fits, and predicts long-memory and anti-persistent time series, possibly mixed with ARMA, regression, transfer-function components. Exact methods (MLE, forecasting, simulation) are used.
Author: Justin Q. Veenstra [aut, cre], A.I. McLeod [aut]
Maintainer: Justin Q. Veenstra <justin.veenstra@gmail.com>

Diff between arfima versions 1.2-7 dated 2014-11-21 and 1.3-3 dated 2015-12-28

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 src/Makevars          |    2 
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More information about arfima at CRAN
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Package vdmR updated to version 0.2.1 with previous version 0.2.0 dated 2015-11-18

Title: Visual Data Mining Tools for R
Description: This provides web-based visual data-mining tools by adding interactive functions to 'ggplot2' graphics. Brushing and linking between the multiple plots is one of the main feature of this package. Currently scatter plots, histograms, parallel coordinate plots and choropleth maps are supported.
Author: Tomokazu Fujino
Maintainer: Tomokazu Fujino <fujino@fwu.ac.jp>

Diff between vdmR versions 0.2.0 dated 2015-11-18 and 0.2.1 dated 2015-12-28

 DESCRIPTION        |   20 ++++++++---------
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Package tweet2r updated to version 0.3 with previous version 0.2 dated 2015-11-01

Title: Twitter Collector and Export to 'postGIS'
Description: This is an improved implementation of the package 'StreamR' to capture tweets and store it into a 'postGIS' data base. The package simplifies the configuration task to capture tweets and facilitates its store into a 'PostGIS' database.
Author: Pau Aragó
Maintainer: Pau Aragó <parago@uji.es>

Diff between tweet2r versions 0.2 dated 2015-11-01 and 0.3 dated 2015-12-28

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New package markmyassignment with initial version 0.3.0
Package: markmyassignment
Type: Package
Title: Automatic Marking of R Assignments
Version: 0.3.0
Date: 2015-12-28
Author: Mans Magnusson, Oscar Pettersson
Maintainer: Mans Magnusson <mons.magnusson@gmail.com>
Description: Automatic marking of R assignments for students and teachers based on testthat test suites.
License: BSD_2_clause + file LICENSE
Depends: R (>= 3.1.0), methods, yaml, testthat (>= 0.11.0), httr
Imports: codetools
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-28 11:30:00 UTC; manma97
Repository: CRAN
Date/Publication: 2015-12-28 14:07:13

More information about markmyassignment at CRAN
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Package BH updated to version 1.60.0-1 with previous version 1.58.0-1 dated 2015-05-21

Title: Boost C++ Header Files
Description: Boost provides free peer-reviewed portable C++ source libraries. A large part of Boost is provided as C++ template code which is resolved entirely at compile-time without linking. This package aims to provide the most useful subset of Boost libraries for template use among CRAN package. By placing these libraries in this package, we offer a more efficient distribution system for CRAN as replication of this code in the sources of other packages is avoided. As of release 1.60, the following Boost libraries are included: algorithm any bind circular_buffer concept config container date_time detail dynamic_bitset exception filesystem foreach functional fusion geometry graph heap integer interprocess intrusive io iostreams iterator math move mpl multiprcecision numeric pending phoenix preprocessor random range smart_ptr spirit tuple type_trains typeof unordered utility uuid.
Author: Dirk Eddelbuettel, John W. Emerson and Michael J. Kane
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between BH versions 1.58.0-1 dated 2015-05-21 and 1.60.0-1 dated 2015-12-28

 ChangeLog                                                                                    |   13 
 DESCRIPTION                                                                                  |   18 
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 README.md                                                                                    |   14 
 inst/NEWS.Rd                                                                                 |   40 
 inst/include/boost/align/align.hpp                                                           |   10 
 inst/include/boost/align/detail/address.hpp                                                  |   26 
 inst/include/boost/align/detail/align.hpp                                                    |   46 
 inst/include/boost/align/detail/align_cxx11.hpp                                              |   20 
 inst/include/boost/align/detail/is_alignment.hpp                                             |   30 
 inst/include/boost/aligned_storage.hpp                                                       |  127 
 inst/include/boost/archive/archive_exception.hpp                                             |   25 
 inst/include/boost/archive/basic_archive.hpp                                                 |    4 
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 inst/include/boost/asio                                                                      |only
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 inst/include/boost/atomic/detail/ops_windows.hpp                                             |    1 
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 inst/include/boost/bind.hpp                                                                  |   19 
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 inst/include/boost/bind/bind_mf_cc.hpp                                                       |   54 
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 inst/include/boost/chrono/detail/inlined/mac/process_cpu_clocks.hpp                          |    2 
 inst/include/boost/chrono/detail/inlined/posix/process_cpu_clocks.hpp                        |    2 
 inst/include/boost/chrono/duration.hpp                                                       |    3 
 inst/include/boost/chrono/io/time_point_units.hpp                                            |   15 
 inst/include/boost/concept/detail/general.hpp                                                |   11 
 inst/include/boost/concept_check.hpp                                                         |   17 
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 inst/include/boost/config/select_compiler_config.hpp                                         |   10 
 inst/include/boost/config/select_platform_config.hpp                                         |    4 
 inst/include/boost/config/stdlib/dinkumware.hpp                                              |   28 
 inst/include/boost/config/stdlib/libcomo.hpp                                                 |   12 
 inst/include/boost/config/stdlib/libcpp.hpp                                                  |   10 
 inst/include/boost/config/stdlib/libstdcpp3.hpp                                              |   29 
 inst/include/boost/config/stdlib/modena.hpp                                                  |   10 
 inst/include/boost/config/stdlib/msl.hpp                                                     |   19 
 inst/include/boost/config/stdlib/roguewave.hpp                                               |    9 
 inst/include/boost/config/stdlib/sgi.hpp                                                     |   13 
 inst/include/boost/config/stdlib/stlport.hpp                                                 |   18 
 inst/include/boost/config/stdlib/vacpp.hpp                                                   |   13 
 inst/include/boost/config/suffix.hpp                                                         |   20 
 inst/include/boost/container/adaptive_pool.hpp                                               |   40 
 inst/include/boost/container/allocator.hpp                                                   |   43 
 inst/include/boost/container/allocator_traits.hpp                                            |   75 
 inst/include/boost/container/container_fwd.hpp                                               |   40 
 inst/include/boost/container/deque.hpp                                                       |  119 
 inst/include/boost/container/detail/adaptive_node_pool.hpp                                   |    1 
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 inst/include/boost/container/detail/node_alloc_holder.hpp                                    |  108 
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 inst/include/boost/container/detail/pool_common_alloc.hpp                                    |   12 
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 inst/include/boost/container/detail/variadic_templates_tools.hpp                             |    2 
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 inst/include/boost/container/flat_set.hpp                                                    |    6 
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 inst/include/boost/container/map.hpp                                                         |    6 
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 inst/include/boost/container/scoped_allocator_fwd.hpp                                        |   31 
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 inst/include/boost/core/demangle.hpp                                                         |   11 
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 inst/include/boost/date_time/int_adapter.hpp                                                 |    4 
 inst/include/boost/date_time/posix_time/posix_time_duration.hpp                              |    6 
 inst/include/boost/date_time/time_system_counted.hpp                                         |    2 
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 inst/include/boost/detail/winapi/GetCurrentProcess.hpp                                       |   15 
 inst/include/boost/detail/winapi/GetCurrentThread.hpp                                        |   22 
 inst/include/boost/detail/winapi/GetLastError.hpp                                            |   14 
 inst/include/boost/detail/winapi/GetProcessTimes.hpp                                         |   51 
 inst/include/boost/detail/winapi/GetThreadTimes.hpp                                          |   42 
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 inst/include/boost/format/parsing.hpp                                                        |    2 
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 inst/include/boost/function_types/is_member_pointer.hpp                                      |    2 
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 inst/include/boost/function_types/result_type.hpp                                            |    2 
 inst/include/boost/functional/hash/hash.hpp                                                  |    2 
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 inst/include/boost/fusion/container/vector/vector_fwd.hpp                                    |   73 
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 inst/include/boost/geometry/algorithms/detail/overlay/check_enrich.hpp                       |    4 
 inst/include/boost/geometry/algorithms/detail/overlay/clip_linestring.hpp                    |   22 
 inst/include/boost/geometry/algorithms/detail/overlay/copy_segment_point.hpp                 |   14 
 inst/include/boost/geometry/algorithms/detail/overlay/copy_segments.hpp                      |   47 
 inst/include/boost/geometry/algorithms/detail/overlay/enrich_intersection_points.hpp         |   37 
 inst/include/boost/geometry/algorithms/detail/overlay/enrichment_info.hpp                    |    6 
 inst/include/boost/geometry/algorithms/detail/overlay/follow.hpp                             |   14 
 inst/include/boost/geometry/algorithms/detail/overlay/follow_linear_linear.hpp               |   41 
 inst/include/boost/geometry/algorithms/detail/overlay/get_intersection_points.hpp            |    3 
 inst/include/boost/geometry/algorithms/detail/overlay/get_ring.hpp                           |    6 
 inst/include/boost/geometry/algorithms/detail/overlay/get_turn_info.hpp                      |   34 
 inst/include/boost/geometry/algorithms/detail/overlay/get_turn_info_for_endpoint.hpp         |   25 
 inst/include/boost/geometry/algorithms/detail/overlay/get_turn_info_helpers.hpp              |   99 
 inst/include/boost/geometry/algorithms/detail/overlay/get_turn_info_la.hpp                   |    6 
 inst/include/boost/geometry/algorithms/detail/overlay/get_turn_info_ll.hpp                   |    8 
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 inst/include/boost/geometry/algorithms/detail/overlay/intersection_insert.hpp                |  258 
 inst/include/boost/geometry/algorithms/detail/overlay/linear_linear.hpp                      |   30 
 inst/include/boost/geometry/algorithms/detail/overlay/overlay.hpp                            |   46 
 inst/include/boost/geometry/algorithms/detail/overlay/pointlike_linear.hpp                   |only
 inst/include/boost/geometry/algorithms/detail/overlay/pointlike_pointlike.hpp                |    8 
 inst/include/boost/geometry/algorithms/detail/overlay/ring_properties.hpp                    |    7 
 inst/include/boost/geometry/algorithms/detail/overlay/segment_identifier.hpp                 |   18 
 inst/include/boost/geometry/algorithms/detail/overlay/self_turn_points.hpp                   |    1 
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 inst/include/boost/geometry/algorithms/detail/overlay/traverse.hpp                           |   33 
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 inst/include/boost/geometry/algorithms/detail/point_is_spike_or_equal.hpp                    |   46 
 inst/include/boost/geometry/algorithms/detail/recalculate.hpp                                |    1 
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 inst/include/boost/geometry/algorithms/detail/relate/boundary_checker.hpp                    |   42 
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 inst/include/boost/geometry/algorithms/detail/relate/topology_check.hpp                      |   36 
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 inst/include/boost/geometry/algorithms/detail/sections/sectionalize.hpp                      |   54 
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 inst/include/boost/geometry/algorithms/detail/single_geometry.hpp                            |   12 
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 inst/include/boost/geometry/algorithms/detail/turns/compare_turns.hpp                        |   16 
 inst/include/boost/geometry/algorithms/detail/turns/print_turns.hpp                          |    4 
 inst/include/boost/geometry/algorithms/detail/vincenty_direct.hpp                            |  121 
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 inst/include/boost/geometry/algorithms/touches.hpp                                           |   48 
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 inst/include/boost/geometry/algorithms/validity_failure_type.hpp                             |    5 
 inst/include/boost/geometry/algorithms/within.hpp                                            |   30 
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 inst/include/boost/geometry/arithmetic/determinant.hpp                                       |    2 
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 inst/include/boost/geometry/core/radian_access.hpp                                           |   16 
 inst/include/boost/geometry/geometries/box.hpp                                               |   89 
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 inst/include/boost/geometry/geometries/multi_linestring.hpp                                  |   11 
 inst/include/boost/geometry/geometries/multi_point.hpp                                       |    6 
 inst/include/boost/geometry/geometries/multi_polygon.hpp                                     |   11 
 inst/include/boost/geometry/geometries/point.hpp                                             |   62 
 inst/include/boost/geometry/geometries/point_xy.hpp                                          |   10 
 inst/include/boost/geometry/geometries/pointing_segment.hpp                                  |   13 
 inst/include/boost/geometry/geometries/polygon.hpp                                           |   10 
 inst/include/boost/geometry/geometries/ring.hpp                                              |    5 
 inst/include/boost/geometry/geometries/segment.hpp                                           |   21 
 inst/include/boost/geometry/geometry.hpp                                                     |    7 
 inst/include/boost/geometry/index/detail/assert.hpp                                          |   10 
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 inst/include/boost/geometry/index/detail/rtree/node/node_elements.hpp                        |   17 
 inst/include/boost/geometry/index/detail/rtree/pack_create.hpp                               |   90 
 inst/include/boost/geometry/index/detail/rtree/quadratic/redistribute_elements.hpp           |    5 
 inst/include/boost/geometry/index/detail/rtree/query_iterators.hpp                           |   27 
 inst/include/boost/geometry/index/detail/rtree/rstar/insert.hpp                              |   20 
 inst/include/boost/geometry/index/detail/rtree/utilities/are_boxes_ok.hpp                    |   20 
 inst/include/boost/geometry/index/detail/rtree/visitors/children_box.hpp                     |    4 
 inst/include/boost/geometry/index/detail/rtree/visitors/distance_query.hpp                   |    8 
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 inst/include/boost/geometry/index/detail/rtree/visitors/remove.hpp                           |   15 
 inst/include/boost/geometry/index/detail/rtree/visitors/spatial_query.hpp                    |   10 
 inst/include/boost/geometry/index/indexable.hpp                                              |   27 
 inst/include/boost/geometry/index/rtree.hpp                                                  |  368 
 inst/include/boost/geometry/io/svg/svg_mapper.hpp                                            |   21 
 inst/include/boost/geometry/io/wkt/read.hpp                                                  |  146 
 inst/include/boost/geometry/io/wkt/write.hpp                                                 |   19 
 inst/include/boost/geometry/iterators/concatenate_iterator.hpp                               |    1 
 inst/include/boost/geometry/iterators/detail/segment_iterator/value_type.hpp                 |   38 
 inst/include/boost/geometry/iterators/flatten_iterator.hpp                                   |   19 
 inst/include/boost/geometry/iterators/point_iterator.hpp                                     |    1 
 inst/include/boost/geometry/multi/multi.hpp                                                  |   73 
 inst/include/boost/geometry/policies/is_valid/failing_reason_policy.hpp                      |   14 
 inst/include/boost/geometry/policies/relate/intersection_points.hpp                          |   32 
 inst/include/boost/geometry/policies/robustness/get_rescale_policy.hpp                       |   56 
 inst/include/boost/geometry/policies/robustness/rescale_policy.hpp                           |   17 
 inst/include/boost/geometry/policies/robustness/segment_ratio.hpp                            |   38 
 inst/include/boost/geometry/strategies/agnostic/hull_graham_andrew.hpp                       |    3 
 inst/include/boost/geometry/strategies/agnostic/relate.hpp                                   |   30 
 inst/include/boost/geometry/strategies/agnostic/simplify_douglas_peucker.hpp                 |    2 
 inst/include/boost/geometry/strategies/buffer.hpp                                            |   14 
 inst/include/boost/geometry/strategies/cartesian/box_in_box.hpp                              |   29 
 inst/include/boost/geometry/strategies/cartesian/buffer_end_round.hpp                        |   10 
 inst/include/boost/geometry/strategies/cartesian/buffer_join_miter.hpp                       |    4 
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 inst/include/boost/geometry/strategies/cartesian/buffer_join_round_by_divide.hpp             |    1 
 inst/include/boost/geometry/strategies/cartesian/buffer_point_circle.hpp                     |    3 
 inst/include/boost/geometry/strategies/cartesian/buffer_side_straight.hpp                    |   39 
 inst/include/boost/geometry/strategies/cartesian/cart_intersect.hpp                          |   27 
 inst/include/boost/geometry/strategies/cartesian/centroid_bashein_detmer.hpp                 |   24 
 inst/include/boost/geometry/strategies/cartesian/centroid_weighted_length.hpp                |   41 
 inst/include/boost/geometry/strategies/cartesian/point_in_box.hpp                            |   11 
 inst/include/boost/geometry/strategies/cartesian/side_of_intersection.hpp                    |  248 
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 inst/include/boost/geometry/strategies/spherical/distance_cross_track_point_box.hpp          |  293 
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 inst/include/boost/get_pointer.hpp                                                           |   28 
 inst/include/boost/heap/binomial_heap.hpp                                                    |    5 
 inst/include/boost/heap/detail/tree_iterator.hpp                                             |   18 
 inst/include/boost/heap/fibonacci_heap.hpp                                                   |   14 
 inst/include/boost/heap/pairing_heap.hpp                                                     |    2 
 inst/include/boost/interprocess/containers/pair.hpp                                          |    1 
 inst/include/boost/interprocess/detail/config_begin.hpp                                      |    5 
 inst/include/boost/interprocess/detail/config_end.hpp                                        |    3 
 inst/include/boost/interprocess/detail/os_thread_functions.hpp                               |   23 
 inst/include/boost/interprocess/detail/posix_time_types_wrk.hpp                              |    5 
 inst/include/boost/interprocess/detail/std_fwd.hpp                                           |   38 
 inst/include/boost/interprocess/detail/utilities.hpp                                         |   26 
 inst/include/boost/interprocess/detail/win32_api.hpp                                         |   45 
 inst/include/boost/interprocess/detail/workaround.hpp                                        |    3 
 inst/include/boost/interprocess/exceptions.hpp                                               |   53 
 inst/include/boost/interprocess/interprocess_fwd.hpp                                         |   13 
 inst/include/boost/interprocess/mapped_region.hpp                                            |    4 
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 inst/include/boost/interprocess/streams/vectorstream.hpp                                     |    4 
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 inst/include/boost/intrusive/avl_set.hpp                                                     |  398 
 inst/include/boost/intrusive/avltree.hpp                                                     |  232 
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 inst/include/boost/intrusive/bstree_algorithms.hpp                                           |    4 
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 inst/include/boost/intrusive/detail/has_member_function_callable_with.hpp                    |   13 
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 inst/include/boost/intrusive/detail/is_stateful_value_traits.hpp                             |    2 
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 inst/include/boost/intrusive/detail/key_nodeptr_comp.hpp                                     |   28 
 inst/include/boost/intrusive/detail/list_iterator.hpp                                        |    2 
 inst/include/boost/intrusive/detail/math.hpp                                                 |   30 
 inst/include/boost/intrusive/detail/mpl.hpp                                                  |  320 
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 inst/include/boost/intrusive/detail/parent_from_member.hpp                                   |    4 
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 inst/include/boost/intrusive/detail/slist_iterator.hpp                                       |    2 
 inst/include/boost/intrusive/detail/std_fwd.hpp                                              |   28 
 inst/include/boost/intrusive/detail/transform_iterator.hpp                                   |   13 
 inst/include/boost/intrusive/detail/tree_iterator.hpp                                        |   27 
 inst/include/boost/intrusive/detail/tree_value_compare.hpp                                   |only
 inst/include/boost/intrusive/hashtable.hpp                                                   | 2352 +++--
 inst/include/boost/intrusive/intrusive_fwd.hpp                                               |   32 
 inst/include/boost/intrusive/list.hpp                                                        |  167 
 inst/include/boost/intrusive/options.hpp                                                     |   11 
 inst/include/boost/intrusive/pointer_plus_bits.hpp                                           |   14 
 inst/include/boost/intrusive/pointer_traits.hpp                                              |   14 
 inst/include/boost/intrusive/rbtree.hpp                                                      |  236 
 inst/include/boost/intrusive/rbtree_algorithms.hpp                                           |    8 
 inst/include/boost/intrusive/set.hpp                                                         |  398 
 inst/include/boost/intrusive/sg_set.hpp                                                      |  398 
 inst/include/boost/intrusive/sgtree.hpp                                                      |  304 
 inst/include/boost/intrusive/slist.hpp                                                       |  206 
 inst/include/boost/intrusive/splay_set.hpp                                                   |  424 -
 inst/include/boost/intrusive/splaytree.hpp                                                   |  255 
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 inst/include/boost/intrusive/treap_set.hpp                                                   |  406 -
 inst/include/boost/intrusive/unordered_set.hpp                                               | 1933 ----
 inst/include/boost/iterator/is_lvalue_iterator.hpp                                           |   26 
 inst/include/boost/iterator/is_readable_iterator.hpp                                         |   16 
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 inst/include/boost/lambda/detail/operator_return_type_traits.hpp                             |   39 
 inst/include/boost/lambda/detail/operators.hpp                                               |   18 
 inst/include/boost/lambda/detail/return_type_traits.hpp                                      |   25 
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 inst/include/boost/lexical_cast/detail/converter_lexical_streams.hpp                         |    1 
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 inst/include/boost/lexical_cast/detail/is_character.hpp                                      |   19 
 inst/include/boost/lexical_cast/detail/lcast_unsigned_converters.hpp                         |    1 
 inst/include/boost/lexical_cast/try_lexical_convert.hpp                                      |   66 
 inst/include/boost/locale                                                                    |only
 inst/include/boost/log                                                                       |only
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 inst/include/boost/math/concepts/std_real_concept.hpp                                        |    2 
 inst/include/boost/math/constants/constants.hpp                                              |   14 
 inst/include/boost/math/cstdfloat/cstdfloat_iostream.hpp                                     |    5 
 inst/include/boost/math/cstdfloat/cstdfloat_limits.hpp                                       |    2 
 inst/include/boost/math/distributions/bernoulli.hpp                                          |    2 
 inst/include/boost/math/distributions/binomial.hpp                                           |    2 
 inst/include/boost/math/distributions/detail/hypergeometric_pdf.hpp                          |    2 
 inst/include/boost/math/distributions/detail/hypergeometric_quantile.hpp                     |   46 
 inst/include/boost/math/distributions/exponential.hpp                                        |    4 
 inst/include/boost/math/distributions/extreme_value.hpp                                      |    4 
 inst/include/boost/math/distributions/fisher_f.hpp                                           |    4 
 inst/include/boost/math/distributions/geometric.hpp                                          |    2 
 inst/include/boost/math/distributions/hypergeometric.hpp                                     |   44 
 inst/include/boost/math/distributions/inverse_gaussian.hpp                                   |   15 
 inst/include/boost/math/distributions/negative_binomial.hpp                                  |    2 
 inst/include/boost/math/distributions/non_central_beta.hpp                                   |    6 
 inst/include/boost/math/distributions/non_central_chi_squared.hpp                            |   58 
 inst/include/boost/math/distributions/non_central_t.hpp                                      |    4 
 inst/include/boost/math/distributions/rayleigh.hpp                                           |    2 
 inst/include/boost/math/distributions/skew_normal.hpp                                        |   18 
 inst/include/boost/math/distributions/triangular.hpp                                         |   12 
 inst/include/boost/math/distributions/uniform.hpp                                            |   21 
 inst/include/boost/math/policies/error_handling.hpp                                          |  124 
 inst/include/boost/math/policies/policy.hpp                                                  |  108 
 inst/include/boost/math/special_functions.hpp                                                |    2 
 inst/include/boost/math/special_functions/bernoulli.hpp                                      |    2 
 inst/include/boost/math/special_functions/bessel.hpp                                         |   34 
 inst/include/boost/math/special_functions/bessel_prime.hpp                                   |    8 
 inst/include/boost/math/special_functions/beta.hpp                                           |  183 
 inst/include/boost/math/special_functions/detail/bernoulli_details.hpp                       |   20 
 inst/include/boost/math/special_functions/detail/bessel_derivatives_linear.hpp               |   16 
 inst/include/boost/math/special_functions/detail/bessel_ik.hpp                               |    6 
 inst/include/boost/math/special_functions/detail/bessel_jn.hpp                               |    7 
 inst/include/boost/math/special_functions/detail/bessel_jy_asym.hpp                          |   18 
 inst/include/boost/math/special_functions/detail/bessel_jy_derivatives_series.hpp            |    5 
 inst/include/boost/math/special_functions/detail/bessel_yn.hpp                               |   34 
 inst/include/boost/math/special_functions/detail/lanczos_sse2.hpp                            |    2 
 inst/include/boost/math/special_functions/detail/polygamma.hpp                               |    8 
 inst/include/boost/math/special_functions/detail/t_distribution_inv.hpp                      |   40 
 inst/include/boost/math/special_functions/ellint_2.hpp                                       |   13 
 inst/include/boost/math/special_functions/ellint_d.hpp                                       |   10 
 inst/include/boost/math/special_functions/fpclassify.hpp                                     |   22 
 inst/include/boost/math/special_functions/gamma.hpp                                          |   20 
 inst/include/boost/math/special_functions/math_fwd.hpp                                       |   25 
 inst/include/boost/math/special_functions/nonfinite_num_facets.hpp                           |    5 
 inst/include/boost/math/special_functions/owens_t.hpp                                        |   84 
 inst/include/boost/math/special_functions/powm1.hpp                                          |   31 
 inst/include/boost/math/special_functions/relative_difference.hpp                            |only
 inst/include/boost/math/special_functions/trigamma.hpp                                       |   28 
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 inst/include/boost/math/special_functions/zeta.hpp                                           |  182 
 inst/include/boost/math/tools/big_constant.hpp                                               |    8 
 inst/include/boost/math/tools/config.hpp                                                     |   77 
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 inst/include/boost/math/tools/detail/polynomial_horner1_19.hpp                               |   40 
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 inst/include/boost/math/tools/detail/polynomial_horner3_3.hpp                                |   10 
 inst/include/boost/math/tools/detail/polynomial_horner3_4.hpp                                |   10 
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 inst/include/boost/math/tools/detail/rational_horner1_17.hpp                                 |   36 
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 inst/include/boost/math/tools/detail/rational_horner1_2.hpp                                  |    6 
 inst/include/boost/math/tools/detail/rational_horner1_20.hpp                                 |   42 
 inst/include/boost/math/tools/detail/rational_horner1_3.hpp                                  |    8 
 inst/include/boost/math/tools/detail/rational_horner1_4.hpp                                  |   10 
 inst/include/boost/math/tools/detail/rational_horner1_5.hpp                                  |   12 
 inst/include/boost/math/tools/detail/rational_horner1_6.hpp                                  |   14 
 inst/include/boost/math/tools/detail/rational_horner1_7.hpp                                  |   16 
 inst/include/boost/math/tools/detail/rational_horner1_8.hpp                                  |   18 
 inst/include/boost/math/tools/detail/rational_horner1_9.hpp                                  |   20 
 inst/include/boost/math/tools/detail/rational_horner2_10.hpp                                 |   22 
 inst/include/boost/math/tools/detail/rational_horner2_11.hpp                                 |   24 
 inst/include/boost/math/tools/detail/rational_horner2_12.hpp                                 |   26 
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 inst/include/boost/math/tools/detail/rational_horner2_14.hpp                                 |   30 
 inst/include/boost/math/tools/detail/rational_horner2_15.hpp                                 |   32 
 inst/include/boost/math/tools/detail/rational_horner2_16.hpp                                 |   34 
 inst/include/boost/math/tools/detail/rational_horner2_17.hpp                                 |   36 
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 inst/include/boost/math/tools/detail/rational_horner2_19.hpp                                 |   40 
 inst/include/boost/math/tools/detail/rational_horner2_2.hpp                                  |   10 
 inst/include/boost/math/tools/detail/rational_horner2_20.hpp                                 |   42 
 inst/include/boost/math/tools/detail/rational_horner2_3.hpp                                  |   10 
 inst/include/boost/math/tools/detail/rational_horner2_4.hpp                                  |   10 
 inst/include/boost/math/tools/detail/rational_horner2_5.hpp                                  |   12 
 inst/include/boost/math/tools/detail/rational_horner2_6.hpp                                  |   14 
 inst/include/boost/math/tools/detail/rational_horner2_7.hpp                                  |   16 
 inst/include/boost/math/tools/detail/rational_horner2_8.hpp                                  |   18 
 inst/include/boost/math/tools/detail/rational_horner2_9.hpp                                  |   20 
 inst/include/boost/math/tools/detail/rational_horner3_10.hpp                                 |   22 
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 inst/include/boost/math/tools/detail/rational_horner3_2.hpp                                  |   10 
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 inst/include/boost/math/tools/detail/rational_horner3_9.hpp                                  |   20 
 inst/include/boost/math/tools/fraction.hpp                                                   |   18 
 inst/include/boost/math/tools/minima.hpp                                                     |    2 
 inst/include/boost/math/tools/precision.hpp                                                  |  136 
 inst/include/boost/math/tools/promotion.hpp                                                  |   21 
 inst/include/boost/math/tools/rational.hpp                                                   |   32 
 inst/include/boost/math/tools/real_cast.hpp                                                  |    4 
 inst/include/boost/math/tools/roots.hpp                                                      |  451 -
 inst/include/boost/math/tools/series.hpp                                                     |   16 
 inst/include/boost/math/tools/toms748_solve.hpp                                              |    6 
 inst/include/boost/math/tools/traits.hpp                                                     |    7 
 inst/include/boost/math/tools/workaround.hpp                                                 |    4 
 inst/include/boost/math/tr1.hpp                                                              |    5 
 inst/include/boost/move/core.hpp                                                             |   65 
 inst/include/boost/move/default_delete.hpp                                                   |    6 
 inst/include/boost/move/detail/fwd_macros.hpp                                                |  266 
 inst/include/boost/move/detail/iterator_traits.hpp                                           |   18 
 inst/include/boost/move/detail/meta_utils.hpp                                                |  201 
 inst/include/boost/move/detail/meta_utils_core.hpp                                           |   26 
 inst/include/boost/move/detail/move_helpers.hpp                                              |  313 
 inst/include/boost/move/detail/std_ns_begin.hpp                                              |only
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 inst/include/boost/move/detail/workaround.hpp                                                |   10 
 inst/include/boost/move/unique_ptr.hpp                                                       |   26 
 inst/include/boost/move/utility_core.hpp                                                     |   78 
 inst/include/boost/mpi/collectives.hpp                                                       |  138 
 inst/include/boost/mpi/collectives/gatherv.hpp                                               |only
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 inst/include/boost/mpi/collectives/scatterv.hpp                                              |only
 inst/include/boost/mpi/communicator.hpp                                                      |   64 
 inst/include/boost/mpi/config.hpp                                                            |   25 
 inst/include/boost/mpi/datatype.hpp                                                          |   12 
 inst/include/boost/mpi/detail/forward_skeleton_iarchive.hpp                                  |   21 
 inst/include/boost/mpi/detail/forward_skeleton_oarchive.hpp                                  |   21 
 inst/include/boost/mpi/detail/ignore_skeleton_oarchive.hpp                                   |   22 
 inst/include/boost/mpi/detail/mpi_datatype_oarchive.hpp                                      |    9 
 inst/include/boost/mpi/nonblocking.hpp                                                       |   12 
 inst/include/boost/mpi/packed_iarchive.hpp                                                   |   22 
 inst/include/boost/mpi/packed_oarchive.hpp                                                   |   20 
 inst/include/boost/mpl/aux_/insert_range_impl.hpp                                            |   35 
 inst/include/boost/mpl/empty_base.hpp                                                        |   16 
 inst/include/boost/mpl/empty_sequence.hpp                                                    |    3 
 inst/include/boost/mpl/map/aux_/insert_range_impl.hpp                                        |only
 inst/include/boost/mpl/map/aux_/item.hpp                                                     |    3 
 inst/include/boost/mpl/map/map0.hpp                                                          |    1 
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 inst/include/boost/mpl/set/aux_/item.hpp                                                     |    2 
 inst/include/boost/mpl/set/set0.hpp                                                          |    1 
 inst/include/boost/mpl/string.hpp                                                            |    2 
 inst/include/boost/multi_index/detail/archive_constructed.hpp                                |    4 
 inst/include/boost/multi_index/detail/bucket_array.hpp                                       |    5 
 inst/include/boost/multi_index/detail/copy_map.hpp                                           |   15 
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 inst/include/boost/multi_index/detail/index_loader.hpp                                       |    5 
 inst/include/boost/multi_index/detail/index_matcher.hpp                                      |    5 
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 inst/include/boost/multi_index/detail/ord_index_impl.hpp                                     |only
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 inst/include/boost/multi_index/detail/seq_index_ops.hpp                                      |    6 
 inst/include/boost/multi_index/detail/value_compare.hpp                                      |    9 
 inst/include/boost/multi_index/hashed_index.hpp                                              |    2 
 inst/include/boost/multi_index/identity.hpp                                                  |   14 
 inst/include/boost/multi_index/member.hpp                                                    |    4 
 inst/include/boost/multi_index/ordered_index.hpp                                             | 1461 ---
 inst/include/boost/multi_index/ordered_index_fwd.hpp                                         |   93 
 inst/include/boost/multi_index/sequenced_index.hpp                                           |    8 
 inst/include/boost/multiprecision/cpp_bin_float.hpp                                          |   70 
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 inst/include/boost/multiprecision/cpp_dec_float.hpp                                          |  213 
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 inst/include/boost/multiprecision/detail/default_ops.hpp                                     |   48 
 inst/include/boost/multiprecision/detail/functions/pow.hpp                                   |   10 
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 inst/include/boost/multiprecision/mpfr.hpp                                                   |  121 
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 inst/include/boost/none.hpp                                                                  |   12 
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 inst/include/boost/numeric/odeint/integrate/detail/integrate_n_steps.hpp                     |   18 
 inst/include/boost/numeric/odeint/integrate/detail/integrate_times.hpp                       |   26 
 inst/include/boost/numeric/odeint/integrate/integrate_adaptive.hpp                           |    2 
 inst/include/boost/numeric/odeint/integrate/integrate_const.hpp                              |  203 
 inst/include/boost/numeric/odeint/integrate/integrate_n_steps.hpp                            |   82 
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 inst/include/boost/numeric/odeint/stepper/bulirsch_stoer.hpp                                 |   20 
 inst/include/boost/numeric/odeint/stepper/bulirsch_stoer_dense_out.hpp                       |   46 
 inst/include/boost/numeric/odeint/stepper/controlled_runge_kutta.hpp                         |  236 
 inst/include/boost/numeric/odeint/stepper/dense_output_runge_kutta.hpp                       |   20 
 inst/include/boost/numeric/odeint/stepper/generation/generation_controlled_runge_kutta.hpp   |   14 
 inst/include/boost/numeric/odeint/stepper/generation/generation_dense_output_runge_kutta.hpp |   13 
 inst/include/boost/numeric/odeint/stepper/generation/generation_rosenbrock4.hpp              |    7 
 inst/include/boost/numeric/odeint/stepper/generation/make_controlled.hpp                     |   22 
 inst/include/boost/numeric/odeint/stepper/generation/make_dense_output.hpp                   |   22 
 inst/include/boost/numeric/odeint/stepper/rosenbrock4_controller.hpp                         |   32 
 inst/include/boost/numeric/odeint/stepper/rosenbrock4_dense_output.hpp                       |   11 
 inst/include/boost/numeric/odeint/util/detail/less_with_sign.hpp                             |   10 
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 inst/include/boost/numeric/odeint/util/resize.hpp                                            |    2 
 inst/include/boost/numeric/odeint/util/resizer.hpp                                           |    2 
 inst/include/boost/numeric/odeint/util/same_size.hpp                                         |    2 
 inst/include/boost/numeric/odeint/util/unwrap_reference.hpp                                  |    2 
 inst/include/boost/numeric/ublas/storage.hpp                                                 |    6 
 inst/include/boost/operators.hpp                                                             |   14 
 inst/include/boost/optional/optional.hpp                                                     |   54 
 inst/include/boost/optional/optional_io.hpp                                                  |    4 
 inst/include/boost/parameter/aux_/arg_list.hpp                                               |   31 
 inst/include/boost/parameter/aux_/cast.hpp                                                   |    6 
 inst/include/boost/parameter/aux_/parenthesized_type.hpp                                     |   84 
 inst/include/boost/parameter/aux_/set.hpp                                                    |    3 
 inst/include/boost/parameter/aux_/tagged_argument.hpp                                        |    4 
 inst/include/boost/parameter/aux_/unwrap_cv_reference.hpp                                    |    6 
 inst/include/boost/parameter/binding.hpp                                                     |   30 
 inst/include/boost/parameter/keyword.hpp                                                     |   30 
 inst/include/boost/parameter/name.hpp                                                        |   20 
 inst/include/boost/parameter/preprocessor.hpp                                                |  113 
 inst/include/boost/parameter/value_type.hpp                                                  |   30 
 inst/include/boost/phoenix/config.hpp                                                        |   68 
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 inst/include/boost/phoenix/statement/detail/preprocessed/catch_push_back_10.hpp              |  324 
 inst/include/boost/phoenix/statement/detail/preprocessed/catch_push_back_20.hpp              |  692 +
 inst/include/boost/phoenix/statement/detail/preprocessed/catch_push_back_30.hpp              | 1052 ++
 inst/include/boost/phoenix/statement/detail/preprocessed/catch_push_back_40.hpp              | 1428 +++
 inst/include/boost/phoenix/statement/detail/preprocessed/catch_push_back_50.hpp              | 1886 ++++
 inst/include/boost/phoenix/statement/detail/preprocessed/try_catch_eval_10.hpp               |   38 
 inst/include/boost/phoenix/statement/detail/preprocessed/try_catch_eval_20.hpp               |   78 
 inst/include/boost/phoenix/statement/detail/preprocessed/try_catch_eval_30.hpp               |  118 
 inst/include/boost/phoenix/statement/detail/preprocessed/try_catch_eval_40.hpp               |  158 
 inst/include/boost/phoenix/statement/detail/preprocessed/try_catch_eval_50.hpp               |  198 
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 inst/include/boost/polygon/polygon_45_set_data.hpp                                           |    4 
 inst/include/boost/polygon/polygon_90_set_data.hpp                                           |    6 
 inst/include/boost/polygon/polygon_set_data.hpp                                              |    6 
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 inst/include/boost/preprocessor/seq/size.hpp                                                 |    1 
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 inst/include/boost/program_options/detail/config_file.hpp                                    |   16 
 inst/include/boost/program_options/detail/parsers.hpp                                        |    3 
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 inst/include/boost/progress.hpp                                                              |    7 
 inst/include/boost/property_tree/detail/rapidxml.hpp                                         |    2 
 inst/include/boost/ptr_container                                                             |only
 inst/include/boost/python.hpp                                                                |    3 
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 inst/include/boost/python/back_reference.hpp                                                 |   31 
 inst/include/boost/python/bases.hpp                                                          |   18 
 inst/include/boost/python/class.hpp                                                          |   45 
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 inst/include/boost/python/converter/object_manager.hpp                                       |   74 
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 inst/include/boost/python/copy_non_const_reference.hpp                                       |    2 
 inst/include/boost/python/data_members.hpp                                                   |    4 
 inst/include/boost/python/default_call_policies.hpp                                          |    2 
 inst/include/boost/python/detail/borrowed_ptr.hpp                                            |   30 
 inst/include/boost/python/detail/config.hpp                                                  |    3 
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 inst/include/boost/python/detail/cv_category.hpp                                             |    2 
 inst/include/boost/python/detail/destroy.hpp                                                 |   49 
 inst/include/boost/python/detail/force_instantiate.hpp                                       |   14 
 inst/include/boost/python/detail/msvc_typeinfo.hpp                                           |   19 
 inst/include/boost/python/detail/referent_storage.hpp                                        |   10 
 inst/include/boost/python/detail/string_literal.hpp                                          |   38 
 inst/include/boost/python/detail/type_list.hpp                                               |    4 
 inst/include/boost/python/detail/value_is_xxx.hpp                                            |   30 
 inst/include/boost/python/extract.hpp                                                        |    3 
 inst/include/boost/python/handle.hpp                                                         |   27 
 inst/include/boost/python/init.hpp                                                           |   22 
 inst/include/boost/python/make_constructor.hpp                                               |    9 
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 inst/include/boost/python/object/class_metadata.hpp                                          |    4 
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 inst/include/boost/python/object/pointer_holder.hpp                                          |    6 
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 inst/include/boost/python/object_items.hpp                                                   |    3 
 inst/include/boost/python/object_slices.hpp                                                  |    4 
 inst/include/boost/python/opaque_pointer_converter.hpp                                       |   13 
 inst/include/boost/python/other.hpp                                                          |   62 
 inst/include/boost/python/proxy.hpp                                                          |    4 
 inst/include/boost/python/ptr.hpp                                                            |   63 
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 inst/include/boost/python/register_ptr_to_python.hpp                                         |    2 
 inst/include/boost/python/return_arg.hpp                                                     |    2 
 inst/include/boost/python/return_internal_reference.hpp                                      |    2 
 inst/include/boost/python/suite/indexing/indexing_suite.hpp                                  |    4 
 inst/include/boost/python/to_python_converter.hpp                                            |    5 
 inst/include/boost/python/to_python_value.hpp                                                |    5 
 inst/include/boost/python/type_id.hpp                                                        |   28 
 inst/include/boost/python/with_custodian_and_ward.hpp                                        |    4 
 inst/include/boost/random.hpp                                                                |    5 
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 inst/include/boost/random/chi_squared_distribution.hpp                                       |    6 
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 inst/include/boost/random/seed_seq.hpp                                                       |   16 
 inst/include/boost/random/shuffle_order.hpp                                                  |    2 
 inst/include/boost/random/subtract_with_carry.hpp                                            |    4 
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 inst/include/boost/random/uniform_01.hpp                                                     |   32 
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 inst/include/boost/random/uniform_smallint.hpp                                               |   32 
 inst/include/boost/range/adaptor/filtered.hpp                                                |   43 
 inst/include/boost/range/adaptor/strided.hpp                                                 |    2 
 inst/include/boost/range/detail/common.hpp                                                   |    5 
 inst/include/boost/range/difference_type.hpp                                                 |   22 
 inst/include/boost/range/iterator.hpp                                                        |   32 
 inst/include/boost/range/iterator_range_core.hpp                                             |    4 
 inst/include/boost/range/size.hpp                                                            |    9 
 inst/include/boost/range/size_type.hpp                                                       |   33 
 inst/include/boost/range/sub_range.hpp                                                       |    4 
 inst/include/boost/rational.hpp                                                              |   54 
 inst/include/boost/regex/config.hpp                                                          |   58 
 inst/include/boost/regex/icu.hpp                                                             |  166 
 inst/include/boost/regex/pattern_except.hpp                                                  |    4 
 inst/include/boost/regex/v4/basic_regex.hpp                                                  |   31 
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 inst/include/boost/regex/v4/fileiter.hpp                                                     |   18 
 inst/include/boost/regex/v4/instances.hpp                                                    |   21 
 inst/include/boost/regex/v4/iterator_traits.hpp                                              |    4 
 inst/include/boost/regex/v4/match_results.hpp                                                |   34 
 inst/include/boost/regex/v4/mem_block_cache.hpp                                              |    2 
 inst/include/boost/regex/v4/perl_matcher.hpp                                                 |   55 
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 inst/include/boost/regex/v4/regex_grep.hpp                                                   |    2 
 inst/include/boost/regex/v4/regex_iterator.hpp                                               |    6 
 inst/include/boost/regex/v4/regex_match.hpp                                                  |    2 
 inst/include/boost/regex/v4/regex_raw_buffer.hpp                                             |    4 
 inst/include/boost/regex/v4/regex_replace.hpp                                                |    8 
 inst/include/boost/regex/v4/regex_search.hpp                                                 |    4 
 inst/include/boost/regex/v4/regex_split.hpp                                                  |    8 
 inst/include/boost/regex/v4/regex_token_iterator.hpp                                         |    6 
 inst/include/boost/regex/v4/regex_traits.hpp                                                 |   16 
 inst/include/boost/regex/v4/regex_traits_defaults.hpp                                        |   14 
 inst/include/boost/regex/v4/regex_workaround.hpp                                             |    7 
 inst/include/boost/regex/v4/states.hpp                                                       |   26 
 inst/include/boost/regex/v4/sub_match.hpp                                                    |  143 
 inst/include/boost/regex/v4/u32regex_iterator.hpp                                            |    4 
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 inst/include/boost/serialization/access.hpp                                                  |    8 
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 inst/include/boost/serialization/collections_load_imp.hpp                                    |  153 
 inst/include/boost/serialization/config.hpp                                                  |   17 
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 inst/include/boost/serialization/extended_type_info_no_rtti.hpp                              |   10 
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 inst/include/boost/serialization/factory.hpp                                                 |    1 
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 inst/include/boost/serialization/level.hpp                                                   |    8 
 inst/include/boost/serialization/list.hpp                                                    |   20 
 inst/include/boost/serialization/nvp.hpp                                                     |    5 
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 inst/include/boost/serialization/vector.hpp                                                  |   25 
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 inst/include/boost/smart_ptr/detail/yield_k.hpp                                              |    9 
 inst/include/boost/smart_ptr/scoped_ptr.hpp                                                  |   10 
 inst/include/boost/smart_ptr/shared_ptr.hpp                                                  |   49 
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 inst/include/boost/spirit/home/classic/utility/impl/chset.ipp                                |    6 
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 inst/include/boost/spirit/home/karma/detail/output_iterator.hpp                              |   12 
 inst/include/boost/spirit/home/karma/detail/string_generate.hpp                              |   34 
 inst/include/boost/spirit/home/karma/directive/duplicate.hpp                                 |    2 
 inst/include/boost/spirit/home/karma/directive/left_alignment.hpp                            |    4 
 inst/include/boost/spirit/home/karma/nonterminal/rule.hpp                                    |   11 
 inst/include/boost/spirit/home/karma/numeric/detail/real_utils.hpp                           |    2 
 inst/include/boost/spirit/home/karma/string/lit.hpp                                          |    3 
 inst/include/boost/spirit/home/lex/argument.hpp                                              |   10 
 inst/include/boost/spirit/home/lex/lexer/lexertl/functor_data.hpp                            |    2 
 inst/include/boost/spirit/home/lex/lexer/string_token_def.hpp                                |    1 
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 inst/include/boost/spirit/home/qi/detail/attributes.hpp                                      |    2 
 inst/include/boost/spirit/home/qi/nonterminal/rule.hpp                                       |   10 
 inst/include/boost/spirit/home/qi/numeric/detail/numeric_utils.hpp                           |   64 
 inst/include/boost/spirit/home/qi/numeric/detail/real_impl.hpp                               |  125 
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 inst/include/boost/spirit/home/support/char_class.hpp                                        |    1 
 inst/include/boost/spirit/home/support/char_encoding/ascii.hpp                               |   29 
 inst/include/boost/spirit/home/support/detail/endian/endian.hpp                              |   21 
 inst/include/boost/spirit/home/support/detail/lexer/parser/parser.hpp                        |    2 
 inst/include/boost/spirit/home/support/detail/lexer/state_machine.hpp                        |    2 
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 inst/include/boost/spirit/home/x3/char/negated_char_parser.hpp                               |    6 
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 inst/include/boost/spirit/home/x3/nonterminal.hpp                                            |    4 
 inst/include/boost/spirit/home/x3/nonterminal/debug_handler_state.hpp                        |    4 
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 inst/include/boost/spirit/home/x3/numeric/int.hpp                                            |    4 
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 inst/include/boost/spirit/home/x3/operator.hpp                                               |    4 
 inst/include/boost/spirit/home/x3/operator/alternative.hpp                                   |   15 
 inst/include/boost/spirit/home/x3/operator/and_predicate.hpp                                 |    6 
 inst/include/boost/spirit/home/x3/operator/detail/alternative.hpp                            |   35 
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 inst/include/boost/spirit/home/x3/operator/difference.hpp                                    |    8 
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 inst/include/boost/spirit/home/x3/operator/list.hpp                                          |    6 
 inst/include/boost/spirit/home/x3/operator/not_predicate.hpp                                 |    6 
 inst/include/boost/spirit/home/x3/operator/optional.hpp                                      |    6 
 inst/include/boost/spirit/home/x3/operator/plus.hpp                                          |    6 
 inst/include/boost/spirit/home/x3/operator/sequence.hpp                                      |   15 
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 inst/include/boost/spirit/home/x3/support/numeric_utils/pow10.hpp                            |    4 
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 inst/include/boost/spirit/home/x3/support/traits/attribute_category.hpp                      |    4 
 inst/include/boost/spirit/home/x3/support/traits/attribute_of.hpp                            |    4 
 inst/include/boost/spirit/home/x3/support/traits/attribute_type.hpp                          |    4 
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 inst/include/boost/spirit/home/x3/support/traits/handles_container.hpp                       |    4 
 inst/include/boost/spirit/home/x3/support/traits/has_attribute.hpp                           |    4 
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 inst/include/boost/spirit/home/x3/support/traits/is_substitute.hpp                           |    4 
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 inst/include/boost/spirit/home/x3/support/traits/move_to.hpp                                 |    8 
 inst/include/boost/spirit/home/x3/support/traits/numeric_traits.hpp                          |    4 
 inst/include/boost/spirit/home/x3/support/traits/optional_traits.hpp                         |    4 
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 inst/include/boost/spirit/home/x3/support/traits/print_token.hpp                             |    4 
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 inst/include/boost/spirit/home/x3/support/traits/value_traits.hpp                            |    4 
 inst/include/boost/spirit/home/x3/support/traits/variant_find_substitute.hpp                 |    4 
 inst/include/boost/spirit/home/x3/support/traits/variant_has_substitute.hpp                  |    4 
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 inst/include/boost/spirit/repository/home/karma/nonterminal/subrule.hpp                      |    4 
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 inst/include/boost/spirit/repository/home/qi/nonterminal/subrule.hpp                         |    4 
 inst/include/boost/spirit/repository/home/qi/operator/keywords.hpp                           |    4 
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 inst/include/boost/test/auto_unit_test.hpp                                                   |   12 
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 inst/include/boost/test/detail/enable_warnings.hpp                                           |   24 
 inst/include/boost/test/detail/fwd_decl.hpp                                                  |   11 
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 inst/include/boost/test/execution_monitor.hpp                                                |  521 -
 inst/include/boost/test/floating_point_comparison.hpp                                        |  284 
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 inst/include/boost/test/impl/unit_test_parameters.ipp                                        | 1000 +-
 inst/include/boost/test/impl/xml_log_formatter.ipp                                           |  109 
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 inst/include/boost/test/included/prg_exec_monitor.hpp                                        |    4 
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 inst/include/boost/test/output/compiler_log_formatter.hpp                                    |   24 
 inst/include/boost/test/output/plain_report_formatter.hpp                                    |   13 
 inst/include/boost/test/output/xml_log_formatter.hpp                                         |   22 
 inst/include/boost/test/output/xml_report_formatter.hpp                                      |   12 
 inst/include/boost/test/prg_exec_monitor.hpp                                                 |   35 
 inst/include/boost/test/progress_monitor.hpp                                                 |   48 
 inst/include/boost/test/results_collector.hpp                                                |   82 
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 inst/include/boost/test/unit_test_log.hpp                                                    |   49 
 inst/include/boost/test/unit_test_log_formatter.hpp                                          |  213 
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 inst/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp                              |   18 
 inst/include/boost/test/utils/basic_cstring/compare.hpp                                      |   50 
 inst/include/boost/test/utils/basic_cstring/io.hpp                                           |    8 
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 inst/include/boost/thread/futures/launch.hpp                                                 |    1 
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 inst/include/boost/thread/pthread/condition_variable_fwd.hpp                                 |  170 
 inst/include/boost/thread/pthread/once_atomic.hpp                                            |    4 
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 inst/include/boost/thread/win32/thread_primitives.hpp                                        |   62 
 inst/include/boost/timer/timer.hpp                                                           |    2 
 inst/include/boost/type_index/detail/compile_time_type_info.hpp                              |   12 
 inst/include/boost/type_index/stl_type_index.hpp                                             |    1 
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 inst/include/boost/type_traits/add_rvalue_reference.hpp                                      |   10 
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 inst/include/boost/type_traits/detail/has_prefix_operator.hpp                                |   25 
 inst/include/boost/type_traits/detail/ice_and.hpp                                            |    7 
 inst/include/boost/type_traits/detail/ice_eq.hpp                                             |    7 
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 inst/include/boost/type_traits/has_bit_and.hpp                                               |   38 
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 inst/include/boost/type_traits/has_divides_assign.hpp                                        |   36 
 inst/include/boost/type_traits/has_equal_to.hpp                                              |   40 
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 inst/include/boost/type_traits/has_greater_equal.hpp                                         |   40 
 inst/include/boost/type_traits/has_left_shift.hpp                                            |   38 
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 inst/include/boost/type_traits/has_less_equal.hpp                                            |   40 
 inst/include/boost/type_traits/has_logical_and.hpp                                           |   32 
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 inst/include/boost/type_traits/has_post_decrement.hpp                                        |   22 
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 inst/include/boost/utility/string_ref.hpp                                                    |    6 
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Package abn updated to version 0.86 with previous version 0.85 dated 2014-12-09

Title: Modelling Multivariate Data with Additive Bayesian Networks
Description: Bayesian network analysis is a form of probabilistic graphical models which derives from empirical data a directed acyclic graph, DAG, describing the dependency structure between random variables. An additive Bayesian network model consists of a form of a DAG where each node comprises a generalized linear model, GLM. Additive Bayesian network models are equivalent to Bayesian multivariate regression using graphical modelling, they generalises the usual multivariable regression, GLM, to multiple dependent variables. 'abn' provides routines to help determine optimal Bayesian network models for a given data set, where these models are used to identify statistical dependencies in messy, complex data. The additive formulation of these models is equivalent to multivariate generalised linear modelling (including mixed models with iid random effects). The usual term to describe this model selection process is structure discovery. The core functionality is concerned with model selection - determining the most robust empirical model of data from interdependent variables. Laplace approximations are used to estimate goodness of fit metrics and model parameters, and wrappers are also included to the INLA package which can be obtained from http://www.r-inla.org. It is recommended the testing version, which can be downloaded by running: source("http://www.math.ntnu.no/inla/givemeINLA-testing.R"). A comprehensive set of documented case studies, numerical accuracy/quality assurance exercises, and additional documentation are available from the abn website.
Author: Fraser Ian Lewis [aut], Marta Pittavino [cre, ctb], Reinhard Furrer [ctb]
Maintainer: Marta Pittavino <marta.pittavino@math.uzh.ch>

Diff between abn versions 0.85 dated 2014-12-09 and 0.86 dated 2015-12-28

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Package uniah updated to version 0.3 with previous version 0.2 dated 2015-12-16

Title: Unimodal Additive Hazards Model
Description: Nonparametric estimation of a unimodal or U-shape covariate effect under additive hazards model.
Author: Yunro Chung [cre], Anastasia Ivanova, Michael G. Hudgens and Jason P. Fine
Maintainer: Yunro Chung <yunro@live.unc.edu>

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Package Rsolnp updated to version 1.16 with previous version 1.15 dated 2014-11-24

Title: General Non-Linear Optimization
Description: General Non-linear Optimization Using Augmented Lagrange Multiplier Method.
Author: Alexios Ghalanos and Stefan Theussl
Maintainer: Alexios Ghalanos <alexios@4dscape.com>

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Package rmgarch updated to version 1.3-0 with previous version 1.2-9 dated 2015-07-02

Title: Multivariate GARCH Models
Description: Feasible multivariate GARCH models including DCC, GO-GARCH and Copula-GARCH.
Author: Alexios Ghalanos <alexios@4dscape.com>
Maintainer: Alexios Ghalanos <alexios@4dscape.com>

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Package lamW updated to version 1.0.0 with previous version 0.1-2 dated 2015-10-08

Title: Lambert-W Function
Description: Implements both real-valued branches of the Lambert-W function, also known as the product logarithm, without the need for installing the entire GSL.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>

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Package BiasedUrn updated to version 1.07 with previous version 1.06.1 dated 2013-12-29

Title: Biased Urn Model Distributions
Description: Statistical models of biased sampling in the form of univariate and multivariate noncentral hypergeometric distributions, including Wallenius' noncentral hypergeometric distribution and Fisher's noncentral hypergeometric distribution (also called extended hypergeometric distribution). See vignette("UrnTheory") for explanation of these distributions.
Author: Agner Fog
Maintainer: Agner Fog <agner@agner.org>

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Package BEST updated to version 0.4.0 with previous version 0.3.0 dated 2015-07-01

Title: Bayesian Estimation Supersedes the t-Test
Description: An alternative to t-tests, producing posterior estimates for group means and standard deviations and their differences and effect sizes.
Author: John K. Kruschke and Mike Meredith
Maintainer: Mike Meredith <mmeredith@wcs.org>

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Sun, 27 Dec 2015

Package selectiveInference updated to version 1.1.2 with previous version 1.1.1 dated 2015-09-30

Title: Tools for Post-Selection Inference
Description: New tools for post-selection inference, for use with forward stepwise regression, least angle regression, the lasso, and the many means problem.
Author: Ryan Tibshirani, Rob Tibshirani, Jonathan Taylor, Joshua Loftus, Stephen Reid
Maintainer: Rob Tibshirani <tibs@stanford.edu>

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Package SACCR updated to version 1.1 with previous version 1.0 dated 2015-10-11

Title: SA Counterparty Credit Risk under Basel III
Description: Computes the Exposure-At-Default based on standardized approach of the Basel III Regulatory framework (SA-CCR). It also includes an object-oriented solution for the generation of the trades.
Author: Tasos Grivas
Maintainer: Tasos Grivas <info@openriskcalculator.com>

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Package qiimer updated to version 0.9.4 with previous version 0.9.2 dated 2014-01-02

Title: Work with QIIME Output Files in R
Description: Open QIIME output files in R, compute statistics, and create plots from the data.
Author: Kyle Bittinger <kylebittinger@gmail.com>
Maintainer: Kyle Bittinger <kylebittinger@gmail.com>

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New package phonics with initial version 0.5.4
Package: phonics
Type: Package
Title: Phonetic Spelling Algorithms
Version: 0.5.4
Date: 2015-12-27
Author: "James P. Howard, II" <jh@jameshoward.us>
Maintainer: "James P. Howard, II" <jh@jameshoward.us>
Description: Provides a collection of phonetic algorithms including Soundex, Metaphone, NYSIIS, Caverphone, and others.
License: BSD_2_clause + file LICENSE
LazyData: TRUE
Imports: Rcpp (>= 0.12.1)
Suggests: testthat
LinkingTo: Rcpp, BH
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2015-12-27 15:20:11 UTC; howardjp
Repository: CRAN
Date/Publication: 2015-12-27 23:51:08

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Package listenv updated to version 0.6.0 with previous version 0.5.0 dated 2015-10-30

Title: Environments Behaving (Almost) as Lists
Description: List environments are environments that have list-like properties. For instance, the elements of a list environment are ordered and can be accessed and iterated over using index subsetting, e.g. 'x <- listenv(a=1, b=2); for (i in seq_along(x)) x[[i]] <- x[[i]]^2; y <- as.list(x)'.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

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Package lessR updated to version 3.4 with previous version 3.3.6 dated 2015-11-05

Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function, variable labels, color themes, and a built-in help system. A confirmatory factor analysis of multiple indicator measurement models is also available as are pedagogical routines for data simulation such as for the Central Limit Theorem. Compatible with 'RStudio' and 'knitr' including generation of 'knitr' instructions for interpretative output.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>

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Package DTRlearn updated to version 1.2 with previous version 1.1 dated 2015-10-28

Title: Learning Algorithms for Dynamic Treatment Regimes
Description: Dynamic treatment regimens (DTRs) are sequential decision rules tailored at each stage by time-varying subject-specific features and intermediate outcomes observed in previous stages. This package implements three methods: O-learning (Zhao et. al. 2012,2014), Q-learning (Murphy et. al. 2007; Zhao et.al. 2009) and P-learning (Liu et. al. 2014, 2015) to estimate the optimal DTRs.
Author: Ying Liu, Yuanjia Wang, Donglin Zeng
Maintainer: Ying Liu <yl2802@cumc.columbia.edu>

Diff between DTRlearn versions 1.1 dated 2015-10-28 and 1.2 dated 2015-12-27

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Package Blaunet updated to version 2.0.1 with previous version 1.0.1 dated 2014-04-14

Title: Calculate and Analyze Blau Status for Measuring Social Distance
Description: An integrated set of tools to calculate and analyze Blau statuses quantifying social distance between individuals belonging to organizations. Relational (network) data may be incorporated for additional analyses.
Author: Cheng Wang*, Michael Genkin*, George Berry, Liyuan Chen, Matthew Brashears *Both authors contributed equally to this work and their names are randomly ordered
Maintainer: Cheng Wang <cwang3@nd.edu>

Diff between Blaunet versions 1.0.1 dated 2014-04-14 and 2.0.1 dated 2015-12-27

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Permanent link

Package MissingDataGUI updated to version 0.2-4 with previous version 0.2-2 dated 2014-09-14

Title: A GUI for Missing Data Exploration
Description: Provides numeric and graphical summaries for the missing values from both categorical and quantitative variables. A variety of imputation methods are applied, including the univariate imputations like fixed or random values, multivariate imputations like the nearest neighbors and multiple imputations, and imputations conditioned on a categorical variable.
Author: Xiaoyue Cheng, Dianne Cook, Heike Hofmann
Maintainer: Xiaoyue Cheng <xycheng@unomaha.edu>

Diff between MissingDataGUI versions 0.2-2 dated 2014-09-14 and 0.2-4 dated 2015-12-27

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Package RGA updated to version 0.3.2 with previous version 0.3.1 dated 2015-12-01

Title: A Google Analytics API Client
Description: Provides functions for accessing and retrieving data from the Google Analytics APIs (https://developers.google.com/analytics/). Supports OAuth 2.0 authorization. Package provides access to the Management, Core Reporting, Multi-Channel Funnels Reporting, Real Time Reporting and Metadata APIs. Access to all the Google Analytics accounts which the user has access to. Auto-pagination to return more than 10,000 rows of the results by combining multiple data requests. Also package provides shiny app to explore the core reporting API dimensions and metrics.
Author: Artem Klevtsov [aut, cre], Philipp Upravitelev [ctb], Olga Shramko [ctb]
Maintainer: Artem Klevtsov <a.a.klevtsov@gmail.com>

Diff between RGA versions 0.3.1 dated 2015-12-01 and 0.3.2 dated 2015-12-27

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New package MultAlloc with initial version 1.2
Package: MultAlloc
Type: Package
Title: Optimal Allocation in Stratified Sampling
Version: 1.2
Date: 2015-12-26
Author: Jose Brito, Pedro Silva, Nelson Maculan and Gustavo Semaan
Maintainer: Jose Brito <jambrito@gmail.com>
Description: Integer Programming Formulations Applied to Univariate and Multivariate Allocation Problems.
Imports: Rglpk
License: GPL-2
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-26 22:11:58 UTC; andre
Repository: CRAN
Date/Publication: 2015-12-27 10:25:54

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Package meteoForecast updated to version 0.49 with previous version 0.48 dated 2015-10-22

Title: Numerical Weather Predictions
Description: Access to several Numerical Weather Prediction services both in raster format and as a time series for a location. Currently it works with GFS, MeteoGalicia, NAM, and RAP.
Author: Oscar Perpinan Lamigueiro [cre, aut], Marcelo Pinho Almeida [ctb]
Maintainer: Oscar Perpinan Lamigueiro <oscar.perpinan@gmail.com>

Diff between meteoForecast versions 0.48 dated 2015-10-22 and 0.49 dated 2015-12-27

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New package identifyr with initial version 0.1
Package: identifyr
Type: Package
Title: Clean Unique Identifiers
Version: 0.1
Date: 2015-12-21
Author: George Miranda [aut, cre]
Maintainer: George Miranda <georgemirandajr@gmail.com>
Description: A fast way to clean unique identifiers used by the Los Angeles County Probation Department.
License: GPL
LazyData: TRUE
Imports: stringr (>= 1.0.0), magrittr (>= 1.5)
RoxygenNote: 5.0.1
Suggests: testthat
URL: https://github.com/georgemirandajr/identifyr
BugReports: https://github.com/georgemirandajr/identifyr/issues
NeedsCompilation: no
Packaged: 2015-12-26 22:49:41 UTC; e525902
Repository: CRAN
Date/Publication: 2015-12-27 10:26:03

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New package cdfquantreg with initial version 1.0.0
Package: cdfquantreg
Type: Package
Title: Quantile Regression for Random Variables on the Unit Interval
Version: 1.0.0
Date: 2015-12-25
Authors@R: c(person(given = "Yiyun", family = "Shou", email = "yiyun.shou@anu.edu.au", role = c("aut", "cre")), person(given = "Michael", family = "Smithson", email = "Michael.Smithson@anu.edu.au", role = "aut"))
Description: Employs a two-parameter family of distributions for modelling random variables on the (0, 1) interval by applying the cumulative distribution function (cdf) of one parent distribution to the quantile function of another.
Depends: R (>= 3.1.0)
License: GPL-3
Imports: pracma (>= 1.8), Formula (>= 1.2), stats, MASS
Suggests: knitr, R2OpenBUGS
VignetteBuilder: knitr
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-26 09:09:37 UTC; samsung
Author: Yiyun Shou [aut, cre], Michael Smithson [aut]
Maintainer: Yiyun Shou <yiyun.shou@anu.edu.au>
Repository: CRAN
Date/Publication: 2015-12-27 10:26:01

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Sat, 26 Dec 2015

New package oasis with initial version 0.99.5
Package: oasis
Type: Package
Title: Multiple Sclerosis Lesion Segmentation using Magnetic Resonance Imaging (MRI)
Version: 0.99.5
Date: 2015-12-26
Authors@R: c(person(given = "Elizabeth M.", "Sweeney", email = "emsweene@jhsph.edu", role = c("aut", "cre")), person(given = "John", family = "Muschelli", email = "muschellij2@gmail.com", role = c("aut")), person( given = "R. Taki", family = "Shinohara", email = "rshi@mail.med.upenn.edu", role = c("aut")))
Maintainer: Elizabeth M. Sweeney <emsweene@jhsph.edu>
Description: Trains and makes predictions from the OASIS method, described in detail in the paper "OASIS is Automated Statistical Inference for Segmentation, with applications to multiple sclerosis lesion segmentation in MRI" <doi:10.1016/j.nicl.2013.03.002>. OASIS is a method for multiple sclerosis (MS) lesion segmentation on structural magnetic resonance image (MRI) studies. OASIS creates probability maps of lesion presence using the FLAIR, T2, T1, and PD structural MRI volumes. This packages allows for training of the OASIS model and prediction of OASIS probability maps from a trained model with user supplied studies that have a gold standard lesion segmentation masks. The package will also create OASIS probability maps for MRI studies using the OASIS model from the OASIS paper if no gold standard lesion segmentation masks are available.
Depends: fslr (>= 1.5.0)
Imports: stats, parallel, oro.nifti
Suggests: downloader
License: GPL-2
LazyLoad: yes
LazyData: yes
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-26 18:11:17 UTC; johnmuschelli
Author: Elizabeth M. Sweeney [aut, cre], John Muschelli [aut], R. Taki Shinohara [aut]
Repository: CRAN
Date/Publication: 2015-12-26 21:18:11

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Package lcmm updated to version 1.7.4 with previous version 1.7.3.0 dated 2015-10-23

Title: Extended Mixed Models Using Latent Classes and Latent Processes
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method.
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima <cecile.proust-lima@inserm.fr>

Diff between lcmm versions 1.7.3.0 dated 2015-10-23 and 1.7.4 dated 2015-12-26

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New package validateRS with initial version 1.0.0
Package: validateRS
Type: Package
Title: One-Sided Multivariate Testing Procedures for Rating Systems
Version: 1.0.0
Date: 2015-12-24
Author: Coppens F., Mayer M., Millischer L., Resch F., Sauer S., Schulze K.
Maintainer: Coppens F. <francois.coppens@nbb.be>
Description: An implementation of statistical tests for the validation of rating systems as described in the ECB Working paper ''Advances in multivariate back-testing for credit risk underestimation'', by F. Coppens, M. Mayer, L. Millischer, F. Resch, S. Sauer, K. Schulze (ECB WP series, forthcoming).
Depends: truncnorm, triangle, reshape2, data.table
License: EUPL
Packaged: 2015-12-26 08:57:42 UTC; Karine
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-12-26 10:04:35

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New package TransferEntropy with initial version 1.0
Package: TransferEntropy
Type: Package
Title: The Transfer Entropy Package
Version: 1.0
Date: 2015-12-26
Authors@R: c( person("Ghazaleh", "Haratinezhad Torbati", email = "ghazale.hnt@gmail.com", role = c("aut","cre")), person("Glenn", "Lawyer", email = "lawyer@mpi-inf.mpg.de", role = c("aut")) )
Maintainer: Ghazaleh Haratinezhad Torbati <ghazale.hnt@gmail.com>
Description: Estimates the transfer entropy from one time series to another, where each time series consists of continuous random variables. The transfer entropy is an extension of mutual information which takes into account the direction of information flow, under the assumption that the underlying processes can be described by a Markov model. Two estimation methods are provided. The first calculates transfer entropy as the difference of mutual information. Mutual information is estimated using the Kraskov method, which builds on a nearest-neighbor framework (see package references). The second estimation method estimate transfer entropy via the a generalized correlation sum.
License: GPL (>= 2) | file LICENSE
Depends: R (>= 3.0.0)
Imports: Rcpp (>= 0.11.6)
LinkingTo: Rcpp
URL: https://github.com/Healthcast/TransEnt
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-12-26 09:45:09
Packaged: 2015-12-26 00:45:12 UTC; ghazale
Author: Ghazaleh Haratinezhad Torbati [aut, cre], Glenn Lawyer [aut]

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Package spacetime updated to version 1.1-5 with previous version 1.1-4 dated 2015-04-24

Title: Classes and Methods for Spatio-Temporal Data
Description: Classes and methods for spatio-temporal data, including space-time regular lattices, sparse lattices, irregular data, and trajectories; utility functions for plotting data as map sequences (lattice or animation) or multiple time series; methods for spatial and temporal selection and subsetting, as well as for spatial/temporal/spatio-temporal matching or aggregation, retrieving coordinates, print, summary, etc.
Author: Edzer Pebesma [cre, aut], Benedikt Graeler [ctb], Tom Gottfried [ctb], Robert J. Hijmans [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

Diff between spacetime versions 1.1-4 dated 2015-04-24 and 1.1-5 dated 2015-12-26

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New package NNLM with initial version 0.4.0
Package: NNLM
Type: Package
Title: Fast and Versatile Non-Negative Matrix Factorization
Description: This is a package for Non-Negative Linear Models (NNLM). It implements fast sequential coordinate descent algorithms for non-negative linear regression and non-negative matrix factorization. It supports mean square error and Kullback-Leibler divergence loss. Many other features are also implemented, including missing value imputation, domain knowledge integration, designable W and H matrices and multiple forms of regularizations.
Version: 0.4.0
Date: 2015-12-15
Authors@R: c(person("Xihui", "Lin", email = "xihuil.silence@gmail.com", role = c("aut", "cre")), person("Paul C Boutros", role = "aut", email = "Paul.Boutros@oicr.on.ca"))
Depends: R (>= 3.0.1)
Imports: Rcpp (>= 0.11.0), stats, utils
LinkingTo: Rcpp, RcppArmadillo, RcppProgress
LazyData: yes
LazyLoad: yes
NeedsCompilation: yes
Suggests: testthat, knitr, rmarkdown, mice, missForest, ISOpureR
VignetteBuilder: knitr
RoxygenNote: 5.0.0
License: BSD_2_clause + file LICENSE
BugReports: https://github.com/linxihui/NNLM/issues
URL: https://github.com/linxihui/NNLM
Packaged: 2015-12-26 04:37:25 UTC; xlin
Author: Xihui Lin [aut, cre], Paul C Boutros [aut]
Maintainer: Xihui Lin <xihuil.silence@gmail.com>
Repository: CRAN
Date/Publication: 2015-12-26 09:45:05

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Fri, 25 Dec 2015

Package ShapeSelectForest updated to version 1.2 with previous version 1.1 dated 2015-09-06

Title: Shape Selection for Landsat Time Series of Forest Dynamics
Description: Landsat satellites collect important data about global forest conditions. Documentation about Landsat's role in forest disturbance estimation is available at the site <http://landsat.gsfc.nasa.gov/?p=9513>. By constrained quadratic B-splines, this package delivers an optimal shape-restricted trajectory to a time series of Landsat imagery for the purpose of modeling annual forest disturbance dynamics to behave in an ecologically sensible manner assuming one of seven possible "shapes", namely, flat, decreasing, one-jump (decreasing, jump up, decreasing), inverted vee (increasing then decreasing), vee (decreasing then increasing), linear increasing, and double-jump (decreasing, jump up, decreasing, jump up, decreasing). The main routine selects the best shape according to the minimum Bayes information criterion (BIC) or the cone information criterion (CIC), which is defined as the log of the estimated predictive squared error. The package also provides parameters summarizing the temporal pattern including year(s) of inflection, magnitude of change, pre- and post-inflection rates of growth or recovery. In addition, it contains routines for converting a flat map of disturbance agents to time-series disturbance maps and a graphical routine displaying the fitted trajectory of Landsat imagery.
Author: Mary C. Meyer, Xiyue Liao, Elizabeth Freeman, Gretchen G. Moisen
Maintainer: Xiyue Liao <xiyue@rams.colostate.edu>

Diff between ShapeSelectForest versions 1.1 dated 2015-09-06 and 1.2 dated 2015-12-25

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Package OutbreakTools updated to version 0.1-14 with previous version 0.1-13 dated 2015-03-23

Title: Basic Tools for the Analysis of Disease Outbreaks
Description: Implements basic tools for storing, handling and visualizing disease outbreak data, as well as simple analysis tools. OutbreakTools defines the new formal class obkData which can be used to store any case-base outbreak data, and provides summaries for these objects, alongside a range of functions for subsetting and data manipulation. It implements a range of graphics for visualising timelines, maps, contact networks and genetic analyses. It also includes a simple case-base outbreak simulation tool.
Author: The Hackout team (In alphabetic order: David Aanensen, Marc Baguelin, Paul Birrell, Simon Cauchemez, Anton Camacho, Caroline Colijn, Anne Cori, Xavier Didelot, Ken Eames, Christophe Fraser, Simon Frost, Niel Hens, Joseph Hugues, Thibaut Jombart, Lulla Opatowski, Oliver Ratmann, Samuel Soubeyrand, Marc Suchard, Jacco Wallinga, Rolf Ypma)
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>

Diff between OutbreakTools versions 0.1-13 dated 2015-03-23 and 0.1-14 dated 2015-12-25

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New package TideHarmonics with initial version 0.1-0
Package: TideHarmonics
Version: 0.1-0
Date: 2016-01-04
Title: Harmonic Analysis of Tides
Author: Alec Stephenson.
Maintainer: Alec Stephenson <alec_stephenson@hotmail.com>
Depends: R (>= 2.10)
Description: Implements harmonic analysis of tidal and sea-level data. Over 400 harmonic tidal constituents can be estimated, all with daily nodal corrections. Time-varying mean sea-levels can also be used.
LazyData: yes
License: BSD_3_clause + file LICENSE
NeedsCompilation: no
Packaged: 2015-12-25 03:12:40 UTC; ste6an
Repository: CRAN
Date/Publication: 2015-12-25 14:27:19

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Package Matching updated to version 4.9-2 with previous version 4.8-3.4 dated 2013-10-29

Title: Multivariate and Propensity Score Matching with Balance Optimization
Description: Provides functions for multivariate and propensity score matching and for finding optimal balance based on a genetic search algorithm. A variety of univariate and multivariate metrics to determine if balance has been obtained are also provided.
Author: Jasjeet Singh Sekhon <sekhon@berkeley.edu>
Maintainer: Jasjeet Singh Sekhon <sekhon@berkeley.edu>

Diff between Matching versions 4.8-3.4 dated 2013-10-29 and 4.9-2 dated 2015-12-25

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Package evd updated to version 2.3-2 with previous version 2.3-0 dated 2012-08-30

Title: Functions for Extreme Value Distributions
Description: Extends simulation, distribution, quantile and density functions to univariate and multivariate parametric extreme value distributions, and provides fitting functions which calculate maximum likelihood estimates for univariate and bivariate maxima models, and for univariate and bivariate threshold models.
Author: Alec Stephenson. Function fbvpot by Chris Ferro.
Maintainer: Alec Stephenson <alec_stephenson@hotmail.com>

Diff between evd versions 2.3-0 dated 2012-08-30 and 2.3-2 dated 2015-12-25

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Thu, 24 Dec 2015

New package telegram with initial version 0.1
Package: telegram
Title: R Wrapper Around the Telegram Bot API
Version: 0.1
Authors@R: person("Luca", "Braglia", email = "lbraglia@gmail.com", role = c("aut", "cre"))
Description: R wrapper around the Telegram Bot API (http://core.telegram.org/bots/api) to access Telegram's messaging facilities with ease (eg you send messages, images, files from R to your smartphone).
URL: http://github.com/lbraglia/telegram
BugReports: http://github.com/lbraglia/telegram/issues
Imports: R6, httr
Depends: R (>= 3.2.3)
License: GPL-3
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-24 13:15:41 UTC; l
Author: Luca Braglia [aut, cre]
Maintainer: Luca Braglia <lbraglia@gmail.com>
Repository: CRAN
Date/Publication: 2015-12-24 14:45:31

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New package shock with initial version 1.0
Package: shock
Type: Package
Title: Slope Heuristic for Block-Diagonal Covariance Selection in High Dimensional Gaussian Graphical Models
Version: 1.0
Date: 2015-12-24
Author: Emilie Devijver, Melina Gallopin
Maintainer: Melina Gallopin <melina.gallopin@gmail.com>
Description: Block-diagonal covariance selection for high dimensional Gaussian graphical models. The selection procedure is based on the slope heuristics.
License: GPL (>= 3)
Imports: glasso, mvtnorm, capushe, GGMselect, igraph, stats
Packaged: 2015-12-24 12:24:32 UTC; gallopin
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-12-24 14:45:29

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Package randomForestSRC updated to version 2.0.5 with previous version 2.0.0 dated 2015-12-07

Title: Random Forests for Survival, Regression and Classification (RF-SRC)
Description: A unified treatment of Breiman's random forests for survival, regression and classification problems based on Ishwaran and Kogalur's random survival forests (RSF) package. The package runs in both serial and parallel (OpenMP) modes. Now extended to include multivariate and unsupervised forests.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur <ubk@kogalur.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>

Diff between randomForestSRC versions 2.0.0 dated 2015-12-07 and 2.0.5 dated 2015-12-24

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New package r.jive with initial version 1.2
Package: r.jive
Type: Package
Title: Perform JIVE Decompositions for Multi-Source Data
Version: 1.2
Date: 2015-12-15
Author: Michael J. O'Connell and Eric F. Lock
Maintainer: Michael J. O'Connell <oconn725@umn.edu>
Description: Performs the JIVE decompositions on a list of data sets when the data share a dimension, returning low-rank matrices that capture the joint and individual structure of the data. It provides two methods of rank selection when the rank is unknown, a permutation test and a BIC selection algorithm. Also included in the package are three plotting functions for visualizing the variance attributed to each data source: a bar plot that shows the percentages of the variability attributable to joint and individual structure, a heatmap that shows the structure of the variability, and principal component plots.
License: GPL-3
Imports: SpatioTemporal, gplots, graphics, stats
Suggests: knitr, rmarkdown
Depends: R(>= 2.10.0)
VignetteBuilder: knitr
Packaged: 2015-12-24 05:47:56 UTC; Eric
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-12-24 13:46:48

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Package plotKML updated to version 0.5-4 with previous version 0.5-3 dated 2015-07-09

Title: Visualization of Spatial and Spatio-Temporal Objects in Google Earth
Description: Writes sp-class, spacetime-class, raster-class and similar spatial and spatio-temporal objects to KML following some basic cartographic rules.
Author: Tomislav Hengl [cre, aut], Pierre Roudier [ctb], Dylan Beaudette [ctb], Edzer Pebesma [ctb], Michael Blaschek [ctb]
Maintainer: Tomislav Hengl <tom.hengl@isric.org>

Diff between plotKML versions 0.5-3 dated 2015-07-09 and 0.5-4 dated 2015-12-24

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New package multifwf with initial version 0.2.2
Package: multifwf
Type: Package
Title: Read Fixed Width Format Files Containing Lines of Different Type
Version: 0.2.2
Date: 2015-12-23
Author: Panos Rontogiannis
Maintainer: Panos Rontogiannis <p.g.ronto@gmail.com>
Description: Read a table of fixed width formatted data of different types into a data.frame for each type.
Depends: R (>= 3.1.1)
License: GPL (>= 2)
URL: https://github.com/prontog/multifwf
BugReports: https://github.com/prontog/multifwf/issues
RoxygenNote: 5.0.1
Imports: utils
Suggests: testthat
NeedsCompilation: no
Packaged: 2015-12-24 11:55:11 UTC; p.rontogiannis
Repository: CRAN
Date/Publication: 2015-12-24 13:46:32

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New package MediaK with initial version 1.0
Package: MediaK
Type: Package
Date: 2015-12-23
Title: Calculate MeDiA_K Distance
Version: 1.0
Author: Zizhuo Ren, Hesen Peng, Tianwei Yu
Maintainer: Zizhuo Ren<zizhuoren@gmail.com>
Description: Calculates MeDiA_K (means Mean Distance Association by K-nearest neighbor) in order to detect nonlinear associations.
License: GPL
LazyData: TRUE
Imports: Rcpp (>= 0.11.3)
LinkingTo: Rcpp, RcppEigen
Packaged: 2015-12-24 09:33:04 UTC; renzizhuo
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-12-24 13:46:16

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Package dynRB updated to version 0.5 with previous version 0.4 dated 2015-08-11

Title: Dynamic Range Boxes
Description: Improves the concept of multivariate range boxes, which is highly susceptible for outliers and does not consider the distribution of the data. The package uses dynamic range boxes to overcome these problems.
Author: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>, Wolfgang Trutschnig <Wolfgang.Trutschnig@sbg.ac.at>, Robert R. Junker <Robert.Junker@sbg.ac.at>, Jonas Kuppler <Jonas.Kuppler@uni-duesseldorf.de>, Arne Bathke <Arne.Bathke@sbg.ac.at>
Maintainer: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>

Diff between dynRB versions 0.4 dated 2015-08-11 and 0.5 dated 2015-12-24

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Package DataCombine updated to version 0.2.18 with previous version 0.2.9 dated 2015-02-11

Title: Tools for Easily Combining and Cleaning Data Sets
Description: Tools for combining and cleaning data sets, particularly with grouped and time series data.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>

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Package apcluster updated to version 1.4.2 with previous version 1.4.1 dated 2014-12-09

Title: Affinity Propagation Clustering
Description: The 'apcluster' package implements Frey's and Dueck's Affinity Propagation clustering in R. The algorithms are largely analogous to the 'Matlab' code published by Frey and Dueck. The package further provides leveraged affinity propagation and an algorithm for exemplar-based agglomerative clustering that can also be used to join clusters obtained from affinity propagation. Various plotting functions are available for analyzing clustering results.
Author: Ulrich Bodenhofer, Johannes Palme, Chrats Melkonian, Andreas Kothmeier
Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>

Diff between apcluster versions 1.4.1 dated 2014-12-09 and 1.4.2 dated 2015-12-24

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Package XNomial updated to version 1.0.4 with previous version 1.0.1 dated 2014-02-08

Title: Exact Goodness-of-Fit Test for Multinomial Data with Fixed Probabilities
Description: Tests whether a set of counts fit a given expected ratio. For example, a genetic cross might be expected to produce four types in the relative frequencies of 9:3:3:1. To see whether a set of observed counts fits this expectation, one can examine all possible outcomes with xmulti() or a random sample of them with xmonte() and find the probability of an observation deviating from the expectation by at least as much as the observed. As a measure of deviation from the expected, one can use the log-likelihood ratio, the multinomial probability, or the classic chi-square statistic. A histogram of the test statistic can also be plotted and compared with the asymptotic curve.
Author: Bill Engels <wrengels@wisc.edu>
Maintainer: Bill Engels <wrengels@wisc.edu>

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Package ss3sim updated to version 0.9.0 with previous version 0.8.2 dated 2014-03-09

Title: Fisheries Stock Assessment Simulation Testing with Stock Synthesis
Description: The ss3sim package develops a framework for fisheries stock assessment simulation testing with Stock Synthesis 3 (SS3).
Author: Sean Anderson [aut, cre], Cole Monnahan [aut], Kelli Johnson [aut], Kotaro Ono [aut], Juan Valero [aut], Curry Cunningham [aut], Allan Hicks [aut], Felipe Hurtado-Ferro [aut], Peter Kuriyama [aut], Roberto Licandeo [aut], Carey McGilliard [aut], Melissa Muradian [ctb], Merrill Rudd [aut], Christine Stawitz [aut], Cody Szuwalski [aut], Ian Taylor [aut], Katyana Vert-pre [aut], Athol Whitten [aut]
Maintainer: Sean Anderson <sean@seananderson.ca>

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Package SchemaOnRead updated to version 1.0.2 with previous version 1.0.1 dated 2015-11-03

Title: Automated Schema on Read
Description: Provides schema-on-read tools including a single function call (e.g., schemaOnRead('filename')) that reads text ('TXT'), comma separated value ('CSV'), raster image ('BMP', 'PNG', 'GIF', 'TIFF', and 'JPG'), R data ('RDS'), HDF5 ('H5'), NetCDF ('CS'), spreadsheet ('XLS', 'XLSX', 'ODS', and 'DIF'), Weka Attribute-Relation File Format ('ARFF'), Epi Info ('REC'), SPSS ('SAV'), Systat ('SYS'), and Stata ('DTA') files. It also recursively reads folders (e.g., schemaOnRead('folder')), returning a nested list of the contained elements.
Author: Michael North [aut, cre]
Maintainer: Michael North <north@anl.gov>

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New package cffdrs with initial version 1.7
Package: cffdrs
Type: Package
Title: Canadian Forest Fire Danger Rating System
Version: 1.7
Date: 2015-12-22
Author: Xianli Wang, Alan Cantin, Marc-Andre Parisien, Mike Wotton, Kerry Anderson, Brett Moore, and Mike Flannigan
Maintainer: Alan Cantin <Alan.Cantin@Canada.ca>
Depends: R(>= 3.2.2), rgdal, raster, foreach, data.table, spatial.tools
Imports: doParallel
Description: This project provides a group of new functions to calculate the outputs of the two main components of the Canadian Forest Fire Danger Rating System (CFFDRS) at various time scales: the Fire Weather Index (FWI) System and the Fire Behaviour Prediction (FBP) System. Some functions have two versions, table and raster based.
License: GPL-2
URL: https://r-forge.r-project.org/projects/cffdrs/
BugReports: https://r-forge.r-project.org/tracker/?func=browse&group_id=1970&atid=5372
Repository: CRAN
Repository/R-Forge/Project: cffdrs
Repository/R-Forge/Revision: 54
Repository/R-Forge/DateTimeStamp: 2015-12-23 18:11:16
Date/Publication: 2015-12-24 08:19:07
NeedsCompilation: no
Packaged: 2015-12-23 18:25:36 UTC; rforge

More information about cffdrs at CRAN
Permanent link

Package brainGraph updated to version 0.55.0 with previous version 0.48.0 dated 2015-12-09

Title: Graph Theory Analysis of Brain MRI Data
Description: A set of tools for performing graph theory analysis of brain MRI data. It is best suited to data from a Freesurfer analysis (cortical thickness, volumes, local gyrification index, surface area), but also works with e.g., tractography data from FSL. It contains a graphical user interface for graph visualization and data exploration.
Author: Christopher G. Watson <cgwatson@bu.edu>
Maintainer: Christopher G. Watson <cgwatson@bu.edu>

Diff between brainGraph versions 0.48.0 dated 2015-12-09 and 0.55.0 dated 2015-12-24

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 R/check_resid.R                    |    2 
 R/choose_edges.R                   |    8 -
 R/corr_matrix.R                    |   12 +-
 R/count_homologous.R               |    7 +
 R/count_interlobar.R               |   19 ++--
 R/dti_create_mats.R                |    9 +-
 R/edge_asymmetry.R                 |   39 +++++---
 R/get_resid.R                      |   88 ++++++++++++++------
 R/graph_contract_brain.R           |    5 -
 R/graph_efficiency.R               |   39 ++++++--
 R/individ_contrib.R                |only
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 R/permute_group.R                  |   21 ++--
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 R/sim_rand_graph_par.R             |    6 -
 R/small_world.R                    |    9 --
 R/spatial_dist.R                   |    8 +
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 man/choose.edges.Rd                |    2 
 man/color.edges.Rd                 |    2 
 man/color.vertices.Rd              |    2 
 man/corr.matrix.Rd                 |    2 
 man/count_homologous.Rd            |    2 
 man/count_interlobar.Rd            |    9 --
 man/dti_create_mats.Rd             |    9 +-
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 man/graph.contract.brain.Rd        |    2 
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 man/robustness.Rd                  |    2 
 man/rotation.Rd                    |    2 
 man/set.brainGraph.attributes.Rd   |    2 
 man/sim.rand.graph.clust.Rd        |    2 
 man/sim.rand.graph.par.Rd          |    2 
 man/small.world.Rd                 |    2 
 man/spatial.dist.Rd                |    2 
 man/update_brainGraph_gui.Rd       |    2 
 man/vec.transform.Rd               |    2 
 man/vertex_attr_dt.Rd              |    2 
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 man/within_module_deg_z_score.Rd   |    2 
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More information about brainGraph at CRAN
Permanent link

Wed, 23 Dec 2015

Package r4ss updated to version 1.24.0 with previous version 1.22.1 dated 2014-07-12

Title: R Code for Stock Synthesis
Description: A collection of R functions for use with Stock Synthesis, a fisheries stock assessment modeling platform written in ADMB by Dr. Richard D. Methot at the NOAA Northwest Fisheries Science Center. The functions include tools for summarizing and plotting results, manipulating files, visualizing model parameterizations, and various other common stock assessment tasks.
Author: Ian G. Taylor, Ian J. Stewart, Allan C. Hicks, Tommy M. Garrison, Andre E. Punt, John R. Wallace, Chantel R. Wetzel, James T. Thorson, Yukio Takeuchi, Kotaro Ono, Cole C. Monnahan, Christine C. Stawitz, Z. Teresa A'mar, Athol R. Whitten, Kelli F. Johnson, Robbie L. Emmet, Sean C. Anderson, and other contributors.
Maintainer: Ian Taylor <Ian.Taylor@noaa.gov>

Diff between r4ss versions 1.22.1 dated 2014-07-12 and 1.24.0 dated 2015-12-23

 DESCRIPTION                  |   26 
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 NAMESPACE                    |  225 +++---
 NEWS.md                      |only
 R/IOTCmove.R                 |    1 
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 R/PinerPlot.R                |  116 ++-
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 R/SS_html.R                  |   28 
 R/SS_makedatlist.R           |   15 
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 R/SS_parlines.R              |   16 
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 R/SS_readdat.R               |   16 
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 R/SS_writestarter.R          |   29 
 R/SSgetoutput.R              |    5 
 R/SSplotBiology.R            |  903 ++++++++++++++++++++----
 R/SSplotCatch.R              |   27 
 R/SSplotCohorts.R            |    8 
 R/SSplotComparisons.R        |  956 +++++++++++++++++---------
 R/SSplotComps.R              | 1577 ++++++++++++++++++++++++-------------------
 R/SSplotData.R               |   23 
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 R/SSplotMnwt.R               |    8 
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 R/SSplotNumbers.R            |  206 ++++-
 R/SSplotPars.R               |   95 +-
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 R/SSplotRecdevs.R            |   17 
 R/SSplotRecdist.R            |    8 
 R/SSplotRetroRecruits.R      |   33 
 R/SSplotSPR.R                |   39 -
 R/SSplotSelex.R              |   20 
 R/SSplotSpawnrecruit.R       |  118 ++-
 R/SSplotSummaryF.R           |    8 
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 R/SSplotTimeseries.R         |   57 +
 R/SSplotYield.R              |   12 
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 R/SStableComparisons.R       |   30 
 R/bubble3.R                  |   61 +
 R/getADMBHessian.R           |    2 
 R/make_multifig.R            |  521 ++++++++++----
 R/mcmc.nuisance.R            |   12 
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 README.md                    |   56 +
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 man/SSplotMCMC_ExtraSelex.Rd |   73 +
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 man/SSplotMovementMap.Rd     |  131 +--
 man/SSplotMovementRates.Rd   |  143 +--
 man/SSplotNumbers.Rd         |  168 ++--
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 144 files changed, 11088 insertions(+), 8476 deletions(-)

More information about r4ss at CRAN
Permanent link

New package multisom with initial version 1.0
Package: multisom
Type: Package
Title: Clustering a Dataset using Multi-SOM Algorithm
Version: 1.0
Date: 2015-12-22
Author: Sarra Chair and Malika Charrad
Maintainer: Sarra Chair<sarra.chair@gmail.com>
Description: Implements two version of Multi-SOM algorithm namely stochastic Multi-SOM and batch Multi-SOM. The package determines also the best number of clusters and offers to the user the best clustering scheme from different results.
License: GPL-2
Depends: R (>= 3.1.3),class, kohonen
URL: https://sites.google.com/site/malikacharrad/research/multisom-package
NeedsCompilation: no
Repository: CRAN
Packaged: 2015-12-23 20:07:40 UTC; chaira
Date/Publication: 2015-12-23 23:47:40

More information about multisom at CRAN
Permanent link

Package MRIaggr updated to version 1.1.5 with previous version 1.1.4 dated 2015-11-08

Title: Management, Display, and Processing of Medical Imaging Data
Description: Provide a compact storage for medical imaging data with access and display possibilities. Basic tools for processing brain imaging data are proposed like extraction of brain voxels, morphological image segmentation, and filtering / normalization of contrast parameters. Specific tools are also provided for blood perfusion imaging to calculate hypoperfusion and reperfusion volumes.
Author: Brice Ozenne
Maintainer: Brice Ozenne <brice.ozenne@orange.fr>

Diff between MRIaggr versions 1.1.4 dated 2015-11-08 and 1.1.5 dated 2015-12-23

 DESCRIPTION                         |    8 
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 R/Functions_Potts.R                 |   15 
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 17 files changed, 770 insertions(+), 670 deletions(-)

More information about MRIaggr at CRAN
Permanent link

Package dotwhisker updated to version 0.2.0.2 with previous version 0.2.0.1 dated 2015-10-06

Title: Dot-and-Whisker Plots of Regression Results
Description: Quick and easy dot-and-whisker plots of regression results.
Author: Frederick Solt <frederick-solt@uiowa.edu>, Yue Hu <yue-hu-1@uiowa.edu>
Maintainer: Yue Hu <yue-hu-1@uiowa.edu>

Diff between dotwhisker versions 0.2.0.1 dated 2015-10-06 and 0.2.0.2 dated 2015-12-23

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 vignettes/dotwhisker-vignette.Rmd |   13 ++++++++++++-
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 16 files changed, 83 insertions(+), 39 deletions(-)

More information about dotwhisker at CRAN
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Package BlandAltmanLeh updated to version 0.3.1 with previous version 0.2.1 dated 2015-12-15

Title: Plots (Slightly Extended) Bland-Altman Plots
Description: Bland-Altman Plots using either base graphics or ggplot2, augmented with confidence intervals, with detailed return values and a sunflowerplot option for data with ties.
Author: Bernhard Lehnert
Maintainer: Bernhard Lehnert <bernhard.lehnert@uni-greifswald.de>

Diff between BlandAltmanLeh versions 0.2.1 dated 2015-12-15 and 0.3.1 dated 2015-12-23

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 9 files changed, 313 insertions(+), 210 deletions(-)

More information about BlandAltmanLeh at CRAN
Permanent link

Package vcdExtra updated to version 0.6-12 with previous version 0.6-11 dated 2015-09-17

Title: 'vcd' Extensions and Additions
Description: Provides additional data sets, methods and documentation to complement the 'vcd' package for Visualizing Categorical Data and the 'gnm' package for Generalized Nonlinear Models. In particular, 'vcdExtra' extends mosaic, assoc and sieve plots from 'vcd' to handle 'glm()' and 'gnm()' models and adds a 3D version in 'mosaic3d'. Additionally, methods are provided for comparing and visualizing lists of 'glm' and 'loglm' objects. This package is now a support package for the book, "Discrete Data Analysis with R" by Michael Friendly and David Meyer.
Author: Michael Friendly [aut, cre], Heather Turner [ctb], Achim Zeileis [ctb], Duncan Murdoch [ctb], David Firth [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>

Diff between vcdExtra versions 0.6-11 dated 2015-09-17 and 0.6-12 dated 2015-12-23

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More information about vcdExtra at CRAN
Permanent link

Package sweidnumbr updated to version 1.0.0 with previous version 0.8.2 dated 2015-12-05

Title: Handling of Swedish Identity Numbers
Description: Structural handling of identity numbers used in the Swedish administration such as personal identity numbers ('personnummer') and organizational identity numbers ('organisationsnummer').
Author: Mans Magnusson and Erik Bulow
Maintainer: Mans Magnusson <mons.magnusson@gmail.com>

Diff between sweidnumbr versions 0.8.2 dated 2015-12-05 and 1.0.0 dated 2015-12-23

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More information about sweidnumbr at CRAN
Permanent link

Package interplot updated to version 0.1.1.0 with previous version 0.1.0.2 dated 2015-07-23

Title: Plot the Effects of Variables in Interaction Terms
Description: Plots the conditional coefficients ("marginal effects") of variables included in multiplicative interaction terms.
Author: Frederick Solt <frederick-solt@uiowa.edu>, Yue Hu <yue-hu-1@uiowa.edu>
Maintainer: Yue Hu <yue-hu-1@uiowa.edu>

Diff between interplot versions 0.1.0.2 dated 2015-07-23 and 0.1.1.0 dated 2015-12-23

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 NAMESPACE                        |   11 -
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 README.md                        |    5 
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 17 files changed, 1119 insertions(+), 300 deletions(-)

More information about interplot at CRAN
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New package gSEM with initial version 0.4.3.3
Package: gSEM
Type: Package
Title: Semi-Supervised Generalized Structural Equation Modelling
Description: Conducts a semi-gSEM statistical analysis (semi-supervised generalized structural equation modeling) on a data frame of coincident observations of multiple continuous variables, via two functions sgSEMp1() and sgSEMp2(), representing fittings based on two statistical principles. Principle 1 determines the univariate relationships in the spirit of the Markovian process. The relationship between each pair of system elements, including predictors and the system level response, is determined with the Markovian property that assumes the value of the current predictor is sufficient in relating to the next level variable, i.e., the relationship is independent of the specific value of the preceding-level variable to the current predictor, given the current value. Principle 2 resembles the multiple regression principle in the way multiple predictors are considered simultaneously. Specifically, the first-level predictors to the system level variable, such as, Time and unit level variables, acted on the system level variable collectively by an additive model. This collective additive model can be found with a generalized stepwise variable selection (using the step() function in R, which performs variable selection on the basis of AIC) and this proceeds iteratively.
Version: 0.4.3.3
Author: Junheng Ma <jxm216@case.edu>, Nicholas Wheeler <nrw16@case.edu>, Yifan Xu <ethan.yifanxu@case.edu>, Wenyu Du <wxd97@case.edu>, Abdulkerim Gok <axg515@case.edu>, Jiayang Sun <jiayang.sun@case.edu>
Maintainer: Junheng Ma <jxm216@case.edu>
Depends: R (>= 2.14.0)
Imports: knitr, MASS, htmlwidgets, DiagrammeR
License: GPL (>= 2)
LazyData: true
NeedsCompilation: no
Packaged: 2015-12-23 14:30:51 UTC; Junheng Ma
RoxygenNote: 5.0.1
Repository: CRAN
Date/Publication: 2015-12-23 16:13:42

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New package ecd with initial version 0.6.4
Package: ecd
Type: Package
Title: Elliptic Distribution Based on Elliptic Curves
Version: 0.6.4
Date: 2015-12-23
Authors@R: person(given = "Stephen", family = "Lihn", middle = "H-T.", email = "stevelihn@gmail.com", role = c("aut", "cre"))
Author: Stephen H-T. Lihn [aut, cre]
Maintainer: Stephen H-T. Lihn <stevelihn@gmail.com>
Description: An implementation of the univariate elliptic distribution and elliptic option pricing model. It provides detailed functionality and data sets for the distribution and modelling. Especially, it contains functions for the computation of density, probability, quantile, fitting procedures, option prices, volatility smile. It also comes with sample financial data, and plotting routines.
Depends: R (>= 3.1.2)
Imports: stats, Rmpfr, polynom, xts, zoo, optimx, moments, parallel, graphics, methods, yaml, RSQLite
Suggests: knitr, testthat, roxygen2, ghyp, fOptions
License: Artistic-2.0
Encoding: latin1
LazyData: true
Collate: 'ecd-adj-gamma-method.R' 'ecd-asymp-stats-method.R' 'ecd-ccdf-method.R' 'ecd-cdf-method.R' 'ecd-numericMpfr-class.R' 'ecdq-class.R' 'ecd-package.R' 'ecd-class.R' 'ecd-constructor.R' 'ecd-cubic-method.R' 'ecd-cusp-a2r-method.R' 'ecd-cusp-constructor.R' 'ecd-cusp-std-moment-method.R' 'ecd-data-config-internal.R' 'ecd-data-method.R' 'ecd-data-stats-method.R' 'ecd-df2ts-method.R' 'ecd-discr-generic.R' 'ecd-distribution-method.R' 'ecld-class.R' 'ecd-ecldOrEcd-class.R' 'ecd-ellipticity-generic.R' 'ecd-estimate-const-method.R' 'ecd-fit-data-method.R' 'ecd-fit-ts-conf-method.R' 'ecd-has-quantile-method.R' 'ecd-imgf-method.R' 'ecd-integrate-method.R' 'ecd-integrate-pdf-generic.R' 'ecd-is-numericMpfr-internal.R' 'ecd-jinv-generic.R' 'ecd-lag-method.R' 'ecd-manage-hist-tails-method.R' 'ecd-max-kurtosis-method.R' 'ecd-model-internal.R' 'ecd-moment-generic.R' 'ecd-mp2f-method.R' 'ecd-mpfr-method.R' 'ecd-mpfr-qagi-method.R' 'ecd-mpnum-method.R' 'ecd-ogf-method.R' 'ecd-pdf-method.R' 'ecd-plot-2x2-generic.R' 'ecd-polar-constructor.R' 'ecd-quantilize-generic.R' 'ecd-rational-method.R' 'ecd-read-csv-by-symbol-method.R' 'ecd-read-symbol-conf-method.R' 'ecd-sd-method.R' 'ecd-setup-const-method.R' 'ecd-solve-cusp-asym-method.R' 'ecd-solve-generic.R' 'ecd-solve-sym-generic.R' 'ecd-solve-trig-generic.R' 'ecd-standardfit-method.R' 'ecd-stats-method.R' 'ecd-toString-method.R' 'ecd-ts-lag-stats-method.R' 'ecd-uniroot-method.R' 'ecd-y-slope-generic.R' 'ecd-y0-isomorphic-method.R' 'ecdattr-class.R' 'ecdattr-constructor.R' 'ecdattr-enrich-method.R' 'ecdattr-pairs-method.R' 'ecdattr-pairs-polar-method.R' 'ecdb-class.R' 'ecdb-bootstrap-generic.R' 'ecdb-constructor.R' 'ecdb-dbSendQuery-method.R' 'ecdb-ecdattr-generic.R' 'ecdb-helpers-internal.R' 'ecdb-history-generic.R' 'ecdb-protectiveCommit-method.R' 'ecdb-read-generic.R' 'ecdb-summary-generic.R' 'ecdb-write-generic.R' 'ecdq-constructor.R' 'ecld-cdf-method.R' 'ecld-const-method.R' 'ecld-constructor.R' 'ecld-gamma-method.R' 'ecld-imgf-method.R' 'ecld-imnt-method.R' 'ecld-ivol-ogf-star-method.R' 'ecld-mgf-term-method.R' 'ecld-moment-method.R' 'ecld-mpnum-method.R' 'ecld-mu-D-method.R' 'ecld-ogf-method.R' 'ecld-ogf-star-method.R' 'ecld-op-V-method.R' 'ecld-pdf-method.R' 'ecld-sd-method.R' 'ecld-sged-method.R' 'ecld-solve-method.R' 'ecld-y-slope-method.R' 'ecop-bs-implied-volatility-method.R' 'ecop-bs-option-price-method.R' 'ecop-opt-class.R' 'ecop-class.R' 'ecop-constructor.R' 'ecop-plot-option-method.R' 'ecop-polyfit-option-method.R' 'ecop-read-csv-by-symbol.R'
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-23 12:47:36 UTC; slihn
Repository: CRAN
Date/Publication: 2015-12-23 16:17:00

More information about ecd at CRAN
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New package cofeatureR with initial version 1.0.0
Package: cofeatureR
Title: Generate Cofeature Matrices
Version: 1.0.0
Authors@R: person("Fong Chun", "Chan", , email = "fongchunchan@gmail.com", role = c("aut", "cre"))
Description: Generate cofeature (feature by sample) matrices. The package utilizies ggplot2::geom_tile to generate the matrix allowing for easy additions from the base matrix.
Depends: R (>= 3.1.0)
Imports: ggplot2 (>= 1.0.0), dplyr (>= 0.4.3), lazyeval (>= 0.1.10)
URL: https://github.com/tinyheero/cofeatureR
BugReports: https://github.com/tinyheero/cofeatureR/issues
License: MIT + file LICENSE
LazyData: true
NeedsCompilation: no
Packaged: 2015-12-23 12:02:57 UTC; fongchun
Author: Fong Chun Chan [aut, cre]
Maintainer: Fong Chun Chan <fongchunchan@gmail.com>
Repository: CRAN
Date/Publication: 2015-12-23 15:48:12

More information about cofeatureR at CRAN
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Package sprm updated to version 1.2.1 with previous version 1.2 dated 2015-10-15

Title: Sparse and Non-Sparse Partial Robust M Regression and Classification
Description: Robust dimension reduction methods for regression and discriminant analysis are implemented that yield estimates with a partial least squares alike interpretability. Partial robust M regression (PRM) is robust to both vertical outliers and leverage points. Sparse partial robust M regression (SPRM) is a related robust method with sparse coefficient estimate, and therefore with intrinsic variable selection. For bianry classification related discriminant methods are PRM-DA and SPRM-DA.
Author: Sven Serneels, BASF Corp and Irene Hoffmann
Maintainer: Irene Hoffmann <irene.hoffmann@tuwien.ac.at>

Diff between sprm versions 1.2 dated 2015-10-15 and 1.2.1 dated 2015-12-23

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 sprm-1.2.1/sprm/MD5                 |   44 ++++++++++++++----------------------
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 sprm-1.2.1/sprm/R/daprpr.R          |    5 ++++
 sprm-1.2.1/sprm/R/prmda.R           |    2 -
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Package Rknots updated to version 1.3.1 with previous version 1.3.0 dated 2015-12-22

Title: Topological Analysis of Knotted Proteins, Biopolymers and 3D Structures
Description: Contains functions for the topological analysis of polymers, with a focus on protein structures.
Author: Federico Comoglio and Maurizio Rinaldi
Maintainer: Federico Comoglio <federico.comoglio@gmail.com>

Diff between Rknots versions 1.3.0 dated 2015-12-22 and 1.3.1 dated 2015-12-23

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 MD5                           |   14 +++++++-------
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 vignettes/Rknots_vignette.Rmd |    2 +-
 8 files changed, 20 insertions(+), 22 deletions(-)

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Package vardpoor updated to version 0.4.8 with previous version 0.4.6 dated 2015-10-08

Title: Variance Estimation for Sample Surveys by the Ultimate Cluster Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>

Diff between vardpoor versions 0.4.6 dated 2015-10-08 and 0.4.8 dated 2015-12-23

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Package surveyplanning updated to version 1.0 with previous version 0.8 dated 2015-11-30

Title: Survey Planning Tools
Description: Tools for sample survey planning, including sample size calculation, estimation of expected precision for the estimates of totals, and calculation of optimal sample size allocation.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Janis Jukams [aut]
Maintainer: Juris Breidaks <rcsb@csb.gov.lv>

Diff between surveyplanning versions 0.8 dated 2015-11-30 and 1.0 dated 2015-12-23

 DESCRIPTION                   |    8 +++---
 MD5                           |   18 +++++++-------
 R/dom_optimal_allocation.R    |   53 ++++++++++++++++++++++++++++--------------
 R/expvar.R                    |   14 -----------
 R/optsize.R                   |   47 ++++++++++++++++++++++---------------
 man/dom_optimal_allocation.Rd |   18 ++++++++------
 man/expsize.Rd                |    5 ++-
 man/expvar.Rd                 |   10 +++----
 man/optsize.Rd                |   10 +++++--
 man/surveyplanning-package.Rd |    4 +--
 10 files changed, 107 insertions(+), 80 deletions(-)

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Package seqHMM updated to version 1.0.3 with previous version 1.0.2-1 dated 2015-12-19

Title: Hidden Markov Models for Life Sequences and Other Multivariate, Multichannel Categorical Time Series
Description: Designed for fitting hidden (latent) Markov models and mixture hidden Markov models for social sequence data and other categorical time series. Also some more restricted versions of these type of models are available: Markov models, mixture Markov models, and latent class models. The package supports models for one or multiple subjects with one or multiple parallel sequences (channels). External covariates can be added to explain cluster membership in mixture models. The package provides functions for evaluating and comparing models, as well as functions for easy plotting of multichannel sequence data and hidden Markov models. Models are estimated using maximum likelihood via the EM algorithm and/or direct numerical maximization with analytical gradients. All main algorithms are written in C++ with support for parallel computation.
Author: Jouni Helske, Satu Helske
Maintainer: Jouni Helske <jouni.helske@jyu.fi>

Diff between seqHMM versions 1.0.2-1 dated 2015-12-19 and 1.0.3 dated 2015-12-23

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 src/objective.cpp            |   60 -
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 68 files changed, 6555 insertions(+), 6533 deletions(-)

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New package LexisPlotR with initial version 0.2
Package: LexisPlotR
Type: Package
Title: Plot Lexis Diagrams for Demographic Purposes
Version: 0.2
Date: 2015-12-22
Authors@R: c(person("Philipp", "Ottolinger", , "philipp@ottolinger.de", role=c("aut","cre")), person("Marieke", "Smilde-Becker", role="ctb"))
Author: Philipp Ottolinger [aut, cre], Marieke Smilde-Becker [ctb]
Maintainer: Philipp Ottolinger <philipp@ottolinger.de>
Description: Functions to plot Lexis Diagrams for Demographic purposes.
Depends: R (>= 3.0.0), ggplot2 (>= 1.0.1)
License: GPL-2
URL: https://github.com/ottlngr/LexisPlotR
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-23 09:11:52 UTC; philipp
Repository: CRAN
Date/Publication: 2015-12-23 10:21:12

More information about LexisPlotR at CRAN
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Package kergp updated to version 0.2.0 with previous version 0.1.0 dated 2015-06-22

Title: Gaussian Process Laboratory
Description: Gaussian Process models with customised covariance kernels.
Author: Yves Deville, David Ginsbourger, Olivier Roustant. Contributors: Nicolas Durrande.
Maintainer: Yves Deville <deville.yves@alpestat.com>

Diff between kergp versions 0.1.0 dated 2015-06-22 and 0.2.0 dated 2015-12-23

 kergp-0.1.0/kergp/inst                 |only
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New package heemod with initial version 0.1.0
Package: heemod
Title: Models for Health Economic Evaluation
Version: 0.1.0
Author: Kevin Zarca [aut], Antoine Filipovic-Pierucci [aut,cre]
Maintainer: Antoine Filipovic-Pierucci <pierucci@gmail.com>
Description: Health Economic Evaluation MODelling (HEEMOD). Markov models (homogenous and non-homogenous) for health economic evaluation. Model comparison, sensitivity and probabilistic analysis.
Depends: R (>= 3.2.2)
Imports: lazyeval, dplyr, purrr
License: GPL (>= 3)
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 5.0.1
Suggests: testthat, knitr
NeedsCompilation: no
Packaged: 2015-12-23 09:41:33 UTC; antoine
Repository: CRAN
Date/Publication: 2015-12-23 10:53:09

More information about heemod at CRAN
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Package toaster updated to version 0.4.1 with previous version 0.3.1 dated 2015-11-03

Title: Big Data in-Database Analytics with Teradata Aster
Description: A consistent set of tools to perform in-database analytics on Teradata Aster Big Data Discovery Platform. toaster (a.k.a 'to Aster') embraces simple 2-step approach: compute in Aster - visualize and analyze in R. Its `compute` functions use combination of SQL and SQL/MR functions running in Aster database - highly scalable parallel and distributed analytical platform. Then `create` functions visualize results with boxplots, scatterplots, histograms, heatmaps, word clouds, maps, or slope graphs. Advanced options such as faceting, coloring, labeling, and others are supported with most functions.
Author: Gregory Kanevsky [aut, cre], Nick Switanek [aut]
Maintainer: Gregory Kanevsky <gregory.kanevsky@teradata.com>

Diff between toaster versions 0.3.1 dated 2015-11-03 and 0.4.1 dated 2015-12-23

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 tests/testthat/test-computeTfIdf.R        |   17 ++++
 tests/testthat/test-createBoxplot.R       |    2 
 tests/testthat/test-createClusterPlots.R  |only
 tests/testthat/test-misc.R                |only
 tests/testthat/test-utils.R               |   44 +++++++++++
 52 files changed, 582 insertions(+), 124 deletions(-)

More information about toaster at CRAN
Permanent link

Package spatstat updated to version 1.44-0 with previous version 1.43-0 dated 2015-10-08

Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing spatial data, mainly Spatial Point Patterns, including multi-type/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, and point patterns on a linear network. Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference. Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks. Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported. Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods. A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above. Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>, Rolf Turner <r.turner@auckland.ac.nz> and Ege Rubak <rubak@math.aau.dk>, with substantial contributions of code by Kasper Klitgaard Berthelsen; Ute Hahn; Abdollah Jalilian; Marie-Colette van Lieshout; Tuomas Rajala; Dominic Schuhmacher; and Rasmus Waagepetersen. Additional contributions by Q.W. Ang; S. Azaele; M. Baddeley; C. Beale; M. Bell; R. Bernhardt; T. Bendtsen; A. Bevan; B. Biggerstaff; A. Bilgrau; L. Bischof; C. Biscio; R. Bivand; J.M. Blanco Moreno; F. Bonneu; J. Burgos; S. Byers; Y.M. Chang; J.B. Chen; I. Chernayavsky; Y.C. Chin; B. Christensen; J.-F. Coeurjolly; R. Corria Ainslie; M. de la Cruz; P. Dalgaard; S. Das; P.J. Diggle; P. Donnelly; I. Dryden; S. Eglen; A. El-Gabbas; B. Fandohan; O. Flores; E.D. Ford; P. Forbes; S. Frank; J. Franklin; N. Funwi-Gabga; O. Garcia; A. Gault; J. Geldmann; M. Genton; S. Ghalandarayeshi; J. Gilbey; J. Goldstick; P. Grabarnik; C. Graf; U. Hahn; A. Hardegen; M.B. Hansen; M. Hazelton; J. Heikkinen; M. Hering; M. Herrmann; K. Hingee; K. Hornik; P. Hunziker; J. Hywood; R. Ihaka; A. Jammalamadaka; R. John-Chandran; D. Johnson; M. Khanmohammadi; R. Klaver; P. Kovesi; M. Kuhn; J. Laake; F. Lavancier; T. Lawrence; R.A. Lamb; J. Lee; G.P. Leser; H.T. Li; G. Limitsios; A. Lister; B. Madin; M. Maechler; J. Marcus; K. Marchikanti; R. Mark; J. Mateu; P. McCullagh; U. Mehlig; S. Meyer; X.C. Mi; L. De Middeleer; R.K. Milne; E. Miranda; J. Moller; E. Mudrak; G.M. Nair; N. Nava; L.S. Nielsen; F. Nunes; J.R. Nyengaard; J. Oehlschlaegel; T. Onkelinx; S. O'Riordan; E. Parilov; J. Picka; N. Picard; M. Porter; S. Protsiv; A. Raftery; S. Rakshit; B. Ramage; P. Ramon; X. Raynaud, M. Reiter; I. Renner; T.O. Richardson; B.D. Ripley; E. Rosenbaum; B. Rowlingson; J. Rudokas; J. Rudge; C. Ryan; F. Safavimanesh; A. Sarkka; C. Schank; K. Schladitz; S. Schutte; B.T. Scott; O. Semboli; F. Semecurbe; V. Shcherbakov; G.C. Shen; P. Shi; H.-J. Ship; I.-M. Sintorn; Y. Song; M. Spiess; M. Stevenson; K. Stucki; M. Sumner; P. Surovy; B. Taylor; T. Thorarinsdottir; B. Turlach; T. Tvedebrink; K. Ummer; M. Uppala; A. van Burgel; T. Verbeke; M. Vihtakari; A. Villers; F. Vinatier; S. Voss; H. Wang; H. Wendrock; J. Wild; C. Witthoft; S. Wong; M. Woringer; M.E. Zamboni and A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

Diff between spatstat versions 1.43-0 dated 2015-10-08 and 1.44-0 dated 2015-12-23

 DESCRIPTION                      |   25 
 MD5                              | 2291 ++++++++++++-----------
 NAMESPACE                        |   59 
 NEWS                             |  197 ++
 R/Gest.R                         |    2 
 R/Gmulti.R                       |    2 
 R/Hest.R                         |   42 
 R/Iest.R                         |  129 -
 R/Kcom.R                         |    2 
 R/Kmeasure.R                     |   18 
 R/Kmulti.R                       |    2 
 R/Tstat.R                        |    8 
 R/addvar.R                       |    2 
 R/allstats.R                     |    2 
 R/alltypes.R                     |    2 
 R/anova.mppm.R                   |   11 
 R/badgey.R                       |    2 
 R/beginner.R                     |    2 
 R/boundingbox.R                  |    9 
 R/bw.optim.R                     |    2 
 R/bw.ppl.R                       |    2 
 R/by.ppp.R                       |    2 
 R/clarkevans.R                   |    4 
 R/clickpoly.R                    |    2 
 R/clickppp.R                     |    2 
 R/close3Dpairs.R                 |  255 +-
 R/closepairs.R                   |    2 
 R/clusterinfo.R                  |   35 
 R/colourtables.R                 |    2 
 R/compareFit.R                   |    2 
 R/convexify.R                    |only
 R/covariates.R                   |    2 
 R/daogenton.R                    |  105 -
 R/dclftest.R                     |  138 +
 R/defaultwin.R                   |    2 
 R/deldir.R                       |   37 
 R/density.ppp.R                  |    7 
 R/detpointprocfamilyfun.R        |    7 
 R/dg.R                           |    2 
 R/dgs.R                          |    2 
 R/diagnoseppm.R                  |    6 
 R/diagram.R                      |    2 
 R/distances.psp.R                |    4 
 R/distcdf.R                      |   40 
 R/distfunlpp.R                   |   16 
 R/dppm.R                         |    2 
 R/dummy.R                        |   12 
 R/effectfun.R                    |   15 
 R/envelope.R                     |  103 -
 R/envelope3.R                    |   12 
 R/envelopelpp.R                  |   21 
 R/eval.fasp.R                    |  117 -
 R/eval.fv.R                      |  127 -
 R/eval.im.R                      |   86 
 R/evalcovar.R                    |  706 +++----
 R/fardist.R                      |    2 
 R/fasp.R                         |  148 -
 R/fiksel.R                       |    2 
 R/formulae.R                     |    6 
 R/funxy.R                        |    2 
 R/fv.R                           |  363 ++-
 R/hardcore.R                     |    2 
 R/hybrid.R                       |    4 
 R/hybrid.family.R                |    4 
 R/hyperframe.R                   |   16 
 R/hypersub.R                     |   26 
 R/idw.R                          |    2 
 R/infline.R                      |    6 
 R/intensity.R                    |    2 
 R/interact.R                     |    8 
 R/interactions.R                 |  127 -
 R/iplot.R                        |    2 
 R/iplotlayered.R                 |    4 
 R/ippm.R                         |   17 
 R/istat.R                        |    2 
 R/kppm.R                         |  119 -
 R/layered.R                      |    4 
 R/linearK.R                      |    2 
 R/lineardisc.R                   |    2 
 R/linearmrkcon.R                 |   42 
 R/linearpcf.R                    |    2 
 R/linequad.R                     |  211 +-
 R/linfun.R                       |    2 
 R/linim.R                        |   74 
 R/linnet.R                       |    6 
 R/lixellate.R                    |only
 R/logistic.R                     |    9 
 R/lpp.R                          |   10 
 R/lppm.R                         |   69 
 R/lurking.R                      |  577 +++--
 R/markcorr.R                     |    2 
 R/marks.R                        |    2 
 R/measures.R                     |   29 
 R/mpl.R                          |   16 
 R/mppm.R                         |  916 ++++-----
 R/multihard.R                    |    2 
 R/nnclean.R                      |    2 
 R/nncorr.R                       |   22 
 R/nndistlpp.R                    |  351 ++-
 R/nnmark.R                       |   72 
 R/objsurf.R                      |    2 
 R/options.R                      |   22 
 R/ord.R                          |    2 
 R/ord.family.R                   |    2 
 R/ordthresh.R                    |    2 
 R/pairpiece.R                    |    2 
 R/pairs.im.R                     |    2 
 R/pairwise.R                     |    2 
 R/plot.anylist.R                 |   16 
 R/plot.fv.R                      |   17 
 R/plot.owin.R                    |    7 
 R/plot.ppp.R                     |    4 
 R/plot3d.R                       |    2 
 R/poisson.R                      |    2 
 R/pp3.R                          |    2 
 R/ppmclass.R                     |   45 
 R/ppqq.R                         |   93 
 R/ppx.R                          |  101 -
 R/predictmppm.R                  |  676 +++----
 R/profilepl.R                    |    6 
 R/progress.R                     |  226 +-
 R/psp.R                          |    5 
 R/pspcross.R                     |    2 
 R/psstG.R                        |    2 
 R/quadratcount.R                 |   24 
 R/quadratresample.R              |    5 
 R/quadrattest.R                  |   14 
 R/quadscheme.R                   |    2 
 R/rPerfect.R                     |   87 
 R/random.R                       |  102 -
 R/randomNS.R                     |    2 
 R/randommk.R                     |   10 
 R/randomtess.R                   |    2 
 R/reduceformula.R                |   60 
 R/relrisk.ppm.R                  |   24 
 R/residppm.R                     |    2 
 R/resolve.defaults.R             |    2 
 R/rhohat.R                       |    2 
 R/rmh.default.R                  |   16 
 R/rmhcontrol.R                   |    2 
 R/rmhmodel.R                     |   55 
 R/rmhmodel.ppm.R                 |   10 
 R/rmhtemper.R                    |    2 
 R/satpiece.R                     |    2 
 R/saturated.R                    |    2 
 R/sigtrace.R                     |   30 
 R/slrm.R                         |   27 
 R/smooth.ppp.R                   |    8 
 R/softcore.R                     |    2 
 R/split.ppx.R                    |    2 
 R/stienen.R                      |    2 
 R/strauss.R                      |    2 
 R/strausshard.R                  |    2 
 R/studpermutest.R                |    7 
 R/summary.quad.R                 |   92 
 R/superimpose.R                  |    5 
 R/symbolmap.R                    |    6 
 R/terse.R                        |   14 
 R/tess.R                         |   34 
 R/texture.R                      |    2 
 R/treebranches.R                 |    2 
 R/triangulate.R                  |   26 
 R/triplets.R                     |    2 
 R/unique.ppp.R                   |    6 
 R/update.ppm.R                   |    2 
 R/util.R                         |   92 
 R/varblock.R                     |   14 
 R/varcount.R                     |only
 R/window.R                       |   35 
 R/wingeom.R                      |    7 
 R/xysegment.R                    |    2 
 R/zclustermodel.R                |only
 build/vignette.rds               |binary
 data/Kovesi.rda                  |binary
 data/amacrine.rda                |binary
 data/anemones.rda                |binary
 data/ants.rda                    |binary
 data/austates.rda                |binary
 data/bdspots.rda                 |binary
 data/bei.rda                     |binary
 data/betacells.rda               |binary
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 data/bronzefilter.rda            |binary
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 data/flu.rda                     |binary
 data/ganglia.rda                 |binary
 data/gordon.rda                  |binary
 data/gorillas.rda                |binary
 data/hamster.rda                 |binary
 data/heather.rda                 |binary
 data/humberside.rda              |binary
 data/hyytiala.rda                |binary
 data/japanesepines.rda           |binary
 data/lansing.rda                 |binary
 data/letterR.rda                 |binary
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 data/mucosa.rda                  |binary
 data/murchison.rda               |binary
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 data/osteo.rda                   |binary
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 data/ponderosa.rda               |binary
 data/pyramidal.rda               |binary
 data/redwood.rda                 |binary
 data/redwoodfull.rda             |binary
 data/residualspaper.rda          |binary
 data/shapley.rda                 |binary
 data/simba.rda                   |binary
 data/simdat.rda                  |binary
 data/simplenet.rda               |binary
 data/spiders.rda                 |binary
 data/sporophores.rda             |binary
 data/spruces.rda                 |binary
 data/swedishpines.rda            |binary
 data/urkiola.rda                 |binary
 data/vesicles.rda                |binary
 data/waka.rda                    |binary
 data/waterstriders.rda           |binary
 demo/spatstat.R                  |    5 
 demo/sumfun.R                    |    2 
 inst/doc/datasets.pdf            |binary
 inst/doc/getstart.pdf            |binary
 inst/doc/replicated.pdf          |binary
 inst/doc/shapefiles.pdf          |binary
 inst/doc/updates.R               |   22 
 inst/doc/updates.Rnw             | 3752 ++++-----------------------------------
 inst/doc/updates.pdf             |binary
 man/AreaInter.Rd                 |    9 
 man/BadGey.Rd                    |    9 
 man/CDF.Rd                       |   10 
 man/Concom.Rd                    |    9 
 man/DiggleGatesStibbard.Rd       |   15 
 man/DiggleGratton.Rd             |    9 
 man/Emark.Rd                     |   11 
 man/Extract.anylist.Rd           |    9 
 man/Extract.fasp.Rd              |   10 
 man/Extract.fv.Rd                |    9 
 man/Extract.hyperframe.Rd        |    9 
 man/Extract.im.Rd                |    9 
 man/Extract.influence.ppm.Rd     |    9 
 man/Extract.layered.Rd           |    9 
 man/Extract.leverage.ppm.Rd      |    9 
 man/Extract.linnet.Rd            |    9 
 man/Extract.listof.Rd            |    9 
 man/Extract.lpp.Rd               |    9 
 man/Extract.msr.Rd               |    9 
 man/Extract.owin.Rd              |    9 
 man/Extract.ppp.Rd               |    9 
 man/Extract.ppx.Rd               |   40 
 man/Extract.psp.Rd               |    9 
 man/Extract.quad.Rd              |   10 
 man/Extract.solist.Rd            |   11 
 man/Extract.splitppp.Rd          |    9 
 man/Extract.tess.Rd              |   10 
 man/F3est.Rd                     |    6 
 man/Fest.Rd                      |   10 
 man/Fiksel.Rd                    |    9 
 man/Finhom.Rd                    |    8 
 man/Frame.Rd                     |   14 
 man/G3est.Rd                     |    6 
 man/Gcom.Rd                      |    8 
 man/Gcross.Rd                    |   10 
 man/Gdot.Rd                      |   10 
 man/Gest.Rd                      |   10 
 man/Geyer.Rd                     |   10 
 man/Gfox.Rd                      |    6 
 man/Ginhom.Rd                    |    8 
 man/Gmulti.Rd                    |   10 
 man/Gres.Rd                      |    8 
 man/Hardcore.Rd                  |   10 
 man/Hest.Rd                      |   41 
 man/HierHard.Rd                  |   12 
 man/HierStrauss.Rd               |   12 
 man/HierStraussHard.Rd           |   12 
 man/Hybrid.Rd                    |   10 
 man/Iest.Rd                      |   10 
 man/Jcross.Rd                    |   10 
 man/Jdot.Rd                      |   10 
 man/Jest.Rd                      |   10 
 man/Jinhom.Rd                    |    8 
 man/Jmulti.Rd                    |   10 
 man/K3est.Rd                     |    6 
 man/Kcom.Rd                      |    8 
 man/Kcross.Rd                    |   10 
 man/Kcross.inhom.Rd              |   10 
 man/Kdot.Rd                      |   10 
 man/Kdot.inhom.Rd                |   10 
 man/Kest.Rd                      |    7 
 man/Kest.fft.Rd                  |   23 
 man/Kinhom.Rd                    |   10 
 man/Kmark.Rd                     |   10 
 man/Kmeasure.Rd                  |   10 
 man/Kmodel.Rd                    |   10 
 man/Kmodel.dppm.Rd               |   14 
 man/Kmodel.kppm.Rd               |   10 
 man/Kmodel.ppm.Rd                |    6 
 man/Kmulti.Rd                    |   10 
 man/Kmulti.inhom.Rd              |   10 
 man/Kres.Rd                      |    8 
 man/Kscaled.Rd                   |   10 
 man/Ksector.Rd                   |   14 
 man/LambertW.Rd                  |   10 
 man/Lcross.Rd                    |   10 
 man/Lcross.inhom.Rd              |   10 
 man/Ldot.Rd                      |   10 
 man/Ldot.inhom.Rd                |   10 
 man/LennardJones.Rd              |   10 
 man/Lest.Rd                      |   10 
 man/Linhom.Rd                    |   10 
 man/Math.im.Rd                   |   14 
 man/Math.linim.Rd                |   14 
 man/MultiHard.Rd                 |   12 
 man/MultiStrauss.Rd              |   12 
 man/MultiStraussHard.Rd          |   12 
 man/Ord.Rd                       |   10 
 man/OrdThresh.Rd                 |   10 
 man/PPversion.Rd                 |   11 
 man/PairPiece.Rd                 |   10 
 man/Pairwise.Rd                  |   10 
 man/Penttinen.Rd                 |   10 
 man/Poisson.Rd                   |   10 
 man/Replace.im.Rd                |   10 
 man/SatPiece.Rd                  |   10 
 man/Saturated.Rd                 |   10 
 man/Smooth.Rd                    |   10 
 man/Smooth.fv.Rd                 |   10 
 man/Smooth.msr.Rd                |    6 
 man/Smooth.ppp.Rd                |    7 
 man/Smoothfun.ppp.Rd             |   12 
 man/Softcore.Rd                  |   10 
 man/Strauss.Rd                   |   12 
 man/StraussHard.Rd               |   12 
 man/Triplets.Rd                  |   10 
 man/Tstat.Rd                     |    6 
 man/Window.Rd                    |   14 
 man/WindowOnly.Rd                |   12 
 man/adaptive.density.Rd          |   17 
 man/add.texture.Rd               |    9 
 man/addvar.Rd                    |    7 
 man/affine.Rd                    |   10 
 man/affine.im.Rd                 |   10 
 man/affine.linnet.Rd             |   10 
 man/affine.lpp.Rd                |   10 
 man/affine.owin.Rd               |   10 
 man/affine.ppp.Rd                |   10 
 man/affine.psp.Rd                |   10 
 man/affine.tess.Rd               |   10 
 man/allstats.Rd                  |   10 
 man/alltypes.Rd                  |   10 
 man/angles.psp.Rd                |   10 
 man/anova.lppm.Rd                |    6 
 man/anova.mppm.Rd                |   16 
 man/anova.ppm.Rd                 |   10 
 man/anova.slrm.Rd                |    8 
 man/ants.Rd                      |    2 
 man/anylist.Rd                   |   14 
 man/append.psp.Rd                |   10 
 man/applynbd.Rd                  |   10 
 man/area.owin.Rd                 |   10 
 man/areaGain.Rd                  |   10 
 man/areaLoss.Rd                  |   10 
 man/as.box3.Rd                   |   10 
 man/as.boxx.Rd                   |   14 
 man/as.data.frame.hyperframe.Rd  |   10 
 man/as.data.frame.im.Rd          |   10 
 man/as.data.frame.owin.Rd        |   14 
 man/as.data.frame.ppp.Rd         |   10 
 man/as.data.frame.psp.Rd         |   10 
 man/as.function.fv.Rd            |   10 
 man/as.function.im.Rd            |   14 
 man/as.fv.Rd                     |   13 
 man/as.hyperframe.Rd             |   10 
 man/as.hyperframe.ppx.Rd         |   10 
 man/as.im.Rd                     |   10 
 man/as.interact.Rd               |   10 
 man/as.layered.Rd                |   14 
 man/as.linim.Rd                  |    9 
 man/as.linnet.linim.Rd           |   14 
 man/as.linnet.psp.Rd             |   14 
 man/as.lpp.Rd                    |   10 
 man/as.mask.Rd                   |   10 
 man/as.mask.psp.Rd               |   10 
 man/as.matrix.im.Rd              |   10 
 man/as.matrix.owin.Rd            |   10 
 man/as.owin.Rd                   |   14 
 man/as.polygonal.Rd              |   24 
 man/as.ppm.Rd                    |   14 
 man/as.ppp.Rd                    |   10 
 man/as.psp.Rd                    |   10 
 man/as.rectangle.Rd              |   10 
 man/as.solist.Rd                 |   14 
 man/as.tess.Rd                   |   10 
 man/auc.Rd                       |   14 
 man/bdist.pixels.Rd              |   10 
 man/bdist.points.Rd              |   10 
 man/bdist.tiles.Rd               |   10 
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 man/berman.test.Rd               |   12 
 man/bind.fv.Rd                   |   10 
 man/blur.Rd                      |   10 
 man/border.Rd                    |   10 
 man/bounding.box.xy.Rd           |   10 
 man/boundingbox.Rd               |   10 
 man/box3.Rd                      |   10 
 man/boxx.Rd                      |   10 
 man/branchlabelfun.Rd            |   14 
 man/bw.diggle.Rd                 |   10 
 man/bw.frac.Rd                   |   10 
 man/bw.ppl.Rd                    |   10 
 man/bw.relrisk.Rd                |   10 
 man/bw.scott.Rd                  |   10 
 man/bw.smoothppp.Rd              |   10 
 man/bw.stoyan.Rd                 |   10 
 man/by.im.Rd                     |   10 
 man/by.ppp.Rd                    |   10 
 man/cauchy.estK.Rd               |    6 
 man/cauchy.estpcf.Rd             |    6 
 man/cbind.hyperframe.Rd          |   10 
 man/cdf.test.Rd                  |   10 
 man/cdf.test.mppm.Rd             |   16 
 man/centroid.owin.Rd             |   12 
 man/chicago.Rd                   |    2 
 man/chop.tess.Rd                 |   10 
 man/chorley.Rd                   |    2 
 man/circdensity.Rd               |   14 
 man/circumradius.Rd              |    4 
 man/clarkevans.Rd                |    6 
 man/clarkevans.test.Rd           |    6 
 man/clickbox.Rd                  |   10 
 man/clickdist.Rd                 |   14 
 man/clickjoin.Rd                 |    4 
 man/clickpoly.Rd                 |   10 
 man/clickppp.Rd                  |   10 
 man/clip.infline.Rd              |   10 
 man/closepairs.Rd                |   10 
 man/closepairs.pp3.Rd            |   12 
 man/closing.Rd                   |   10 
 man/clusterfield.Rd              |   14 
 man/clusterfit.Rd                |   14 
 man/clusterkernel.Rd             |   14 
 man/clusterradius.Rd             |   14 
 man/clusterset.Rd                |   10 
 man/coef.mppm.Rd                 |   16 
 man/coef.ppm.Rd                  |   10 
 man/coef.slrm.Rd                 |    8 
 man/collapse.fv.Rd               |   10 
 man/colourmap.Rd                 |   10 
 man/colourtools.Rd               |   10 
 man/commonGrid.Rd                |   10 
 man/compareFit.Rd                |    8 
 man/compatible.Rd                |   10 
 man/compatible.fasp.Rd           |   10 
 man/compatible.fv.Rd             |   10 
 man/compatible.im.Rd             |   10 
 man/complement.owin.Rd           |   10 
 man/concatxy.Rd                  |   10 
 man/connected.Rd                 |   10 
 man/connected.ppp.Rd             |   10 
 man/contour.im.Rd                |   14 
 man/contour.imlist.Rd            |   14 
 man/convexhull.Rd                |   10 
 man/convexhull.xy.Rd             |   10 
 man/convexify.Rd                 |only
 man/convolve.im.Rd               |   10 
 man/coords.Rd                    |   10 
 man/copyExampleFiles.Rd          |   14 
 man/corners.Rd                   |   10 
 man/crossdist.Rd                 |    6 
 man/crossdist.default.Rd         |    6 
 man/crossdist.lpp.Rd             |    6 
 man/crossdist.pp3.Rd             |    6 
 man/crossdist.ppp.Rd             |    6 
 man/crossdist.ppx.Rd             |    6 
 man/crossdist.psp.Rd             |   10 
 man/crossing.psp.Rd              |   10 
 man/cut.im.Rd                    |   10 
 man/cut.ppp.Rd                   |   10 
 man/data.ppm.Rd                  |   10 
 man/dclf.progress.Rd             |   21 
 man/dclf.sigtrace.Rd             |   38 
 man/dclf.test.Rd                 |   46 
 man/default.dummy.Rd             |   10 
 man/default.expand.Rd            |   10 
 man/default.rmhcontrol.Rd        |   10 
 man/delaunay.Rd                  |   14 
 man/delaunayDistance.Rd          |   14 
 man/delaunayNetwork.Rd           |   14 
 man/deletebranch.Rd              |   14 
 man/deltametric.Rd               |   10 
 man/demohyper.Rd                 |    2 
 man/demopat.Rd                   |    2 
 man/density.lpp.Rd               |    2 
 man/density.ppp.Rd               |   22 
 man/density.psp.Rd               |   10 
 man/density.splitppp.Rd          |   10 
 man/deriv.fv.Rd                  |   10 
 man/detpointprocfamilyfun.Rd     |   14 
 man/dfbetas.ppm.Rd               |    6 
 man/dg.envelope.Rd               |   24 
 man/dg.progress.Rd               |   46 
 man/dg.sigtrace.Rd               |   45 
 man/dg.test.Rd                   |   47 
 man/diagnose.ppm.Rd              |   10 
 man/diameter.Rd                  |   10 
 man/diameter.box3.Rd             |   10 
 man/diameter.boxx.Rd             |   10 
 man/diameter.linnet.Rd           |    4 
 man/diameter.owin.Rd             |   10 
 man/dilated.areas.Rd             |   10 
 man/dilation.Rd                  |   10 
 man/dim.detpointprocfamily.Rd    |   14 
 man/dirichlet.Rd                 |   10 
 man/dirichletAreas.Rd            |   14 
 man/dirichletVertices.Rd         |   14 
 man/dirichletWeights.Rd          |   10 
 man/disc.Rd                      |   10 
 man/discpartarea.Rd              |   10 
 man/discretise.Rd                |   10 
 man/discs.Rd                     |   14 
 man/distcdf.Rd                   |   13 
 man/distfun.Rd                   |   10 
 man/distfun.lpp.Rd               |   16 
 man/distmap.Rd                   |   10 
 man/distmap.owin.Rd              |   10 
 man/distmap.ppp.Rd               |   10 
 man/distmap.psp.Rd               |   10 
 man/dkernel.Rd                   |    4 
 man/dmixpois.Rd                  |   12 
 man/domain.Rd                    |   14 
 man/dppBessel.Rd                 |   10 
 man/dppCauchy.Rd                 |   14 
 man/dppGauss.Rd                  |   14 
 man/dppMatern.Rd                 |   14 
 man/dppPowerExp.Rd               |   14 
 man/dppapproxkernel.Rd           |   14 
 man/dppapproxpcf.Rd              |   14 
 man/dppeigen.Rd                  |   14 
 man/dppkernel.Rd                 |   14 
 man/dppm.Rd                      |   16 
 man/dppparbounds.Rd              |   14 
 man/dppspecden.Rd                |   14 
 man/dppspecdenrange.Rd           |   14 
 man/dummify.Rd                   |    4 
 man/dummy.ppm.Rd                 |   10 
 man/duplicated.ppp.Rd            |   10 
 man/edge.Ripley.Rd               |   10 
 man/edge.Trans.Rd                |   10 
 man/edges.Rd                     |   12 
 man/edges2triangles.Rd           |   10 
 man/edges2vees.Rd                |   10 
 man/edit.hyperframe.Rd           |   14 
 man/edit.ppp.Rd                  |   14 
 man/eem.Rd                       |   10 
 man/effectfun.Rd                 |   10 
 man/ellipse.Rd                   |   10 
 man/emend.Rd                     |   14 
 man/emend.ppm.Rd                 |   10 
 man/endpoints.psp.Rd             |   10 
 man/envelope.Rd                  |   58 
 man/envelope.envelope.Rd         |   10 
 man/envelope.lpp.Rd              |   29 
 man/envelope.pp3.Rd              |   28 
 man/eroded.areas.Rd              |   10 
 man/erosion.Rd                   |   10 
 man/eval.fasp.Rd                 |   10 
 man/eval.fv.Rd                   |   10 
 man/eval.im.Rd                   |   10 
 man/eval.linim.Rd                |   10 
 man/ewcdf.Rd                     |   10 
 man/exactMPLEstrauss.Rd          |   10 
 man/expand.owin.Rd               |   10 
 man/fardist.Rd                   |   14 
 man/fasp.object.Rd               |   10 
 man/fitin.Rd                     |   10 
 man/fitted.lppm.Rd               |   14 
 man/fitted.mppm.Rd               |   16 
 man/fitted.ppm.Rd                |   10 
 man/fitted.slrm.Rd               |    8 
 man/fixef.mppm.Rd                |   16 
 man/flipxy.Rd                    |   10 
 man/foo.Rd                       |   14 
 man/formula.fv.Rd                |   10 
 man/formula.ppm.Rd               |    6 
 man/fourierbasis.Rd              |   14 
 man/fryplot.Rd                   |   10 
 man/funxy.Rd                     |   10 
 man/fv.Rd                        |   10 
 man/fv.object.Rd                 |   10 
 man/fvnames.Rd                   |   10 
 man/gauss.hermite.Rd             |   12 
 man/gridcentres.Rd               |   10 
 man/gridweights.Rd               |   10 
 man/grow.boxx.Rd                 |only
 man/grow.rectangle.Rd            |   12 
 man/harmonic.Rd                  |   10 
 man/harmonise.Rd                 |   12 
 man/harmonise.fv.Rd              |   12 
 man/harmonise.im.Rd              |   10 
 man/harmonise.owin.Rd            |   10 
 man/heather.Rd                   |    4 
 man/hextess.Rd                   |   10 
 man/hierpair.family.Rd           |   12 
 man/hist.im.Rd                   |   10 
 man/hopskel.Rd                   |   14 
 man/humberside.Rd                |    2 
 man/hybrid.family.Rd             |   10 
 man/hyperframe.Rd                |   10 
 man/identify.ppp.Rd              |   10 
 man/identify.psp.Rd              |   10 
 man/idw.Rd                       |   10 
 man/im.Rd                        |   10 
 man/im.apply.Rd                  |   10 
 man/im.object.Rd                 |   10 
 man/imcov.Rd                     |   10 
 man/improve.kppm.Rd              |   10 
 man/incircle.Rd                  |   10 
 man/increment.fv.Rd              |   14 
 man/infline.Rd                   |   10 
 man/influence.ppm.Rd             |    6 
 man/inforder.family.Rd           |   10 
 man/inside.boxx.Rd               |only
 man/inside.owin.Rd               |   10 
 man/integral.im.Rd               |   14 
 man/integral.linim.Rd            |   14 
 man/integral.msr.Rd              |   14 
 man/intensity.Rd                 |   10 
 man/intensity.dppm.Rd            |   14 
 man/intensity.lpp.Rd             |   10 
 man/intensity.ppm.Rd             |    6 
 man/intensity.ppp.Rd             |   10 
 man/intensity.ppx.Rd             |   14 
 man/intensity.quadratcount.Rd    |   10 
 man/interp.colourmap.Rd          |   10 
 man/interp.im.Rd                 |   10 
 man/intersect.owin.Rd            |   14 
 man/intersect.tess.Rd            |   10 
 man/invoke.symbolmap.Rd          |   12 
 man/iplot.Rd                     |   10 
 man/ippm.Rd                      |   10 
 man/is.convex.Rd                 |   10 
 man/is.dppm.Rd                   |    6 
 man/is.empty.Rd                  |   10 
 man/is.hybrid.Rd                 |   10 
 man/is.im.Rd                     |   10 
 man/is.lpp.Rd                    |   10 
 man/is.marked.Rd                 |   10 
 man/is.marked.ppm.Rd             |   10 
 man/is.marked.ppp.Rd             |   10 
 man/is.multitype.Rd              |   10 
 man/is.multitype.ppm.Rd          |   10 
 man/is.multitype.ppp.Rd          |   10 
 man/is.owin.Rd                   |   10 
 man/is.ppm.Rd                    |   10 
 man/is.ppp.Rd                    |   10 
 man/is.rectangle.Rd              |   10 
 man/is.stationary.Rd             |   14 
 man/is.subset.owin.Rd            |   10 
 man/istat.Rd                     |   10 
 man/kaplan.meier.Rd              |   10 
 man/kernel.factor.Rd             |    4 
 man/km.rs.Rd                     |   10 
 man/kppm.Rd                      |   15 
 man/latest.news.Rd               |   10 
 man/layered.Rd                   |   10 
 man/layerplotargs.Rd             |   10 
 man/layout.boxes.Rd              |   10 
 man/lengths.psp.Rd               |   10 
 man/letterR.Rd                   |    2 
 man/levelset.Rd                  |   10 
 man/leverage.ppm.Rd              |    6 
 man/lgcp.estK.Rd                 |    8 
 man/lgcp.estpcf.Rd               |    8 
 man/linearK.Rd                   |    6 
 man/linearKcross.Rd              |    6 
 man/linearKcross.inhom.Rd        |    6 
 man/linearKdot.Rd                |    6 
 man/linearKdot.inhom.Rd          |    6 
 man/linearKinhom.Rd              |    6 
 man/lineardisc.Rd                |    6 
 man/linearmarkconnect.Rd         |    6 
 man/linearmarkequal.Rd           |    6 
 man/linearpcf.Rd                 |    6 
 man/linearpcfcross.Rd            |    6 
 man/linearpcfcross.inhom.Rd      |    6 
 man/linearpcfdot.Rd              |    6 
 man/linearpcfdot.inhom.Rd        |    6 
 man/linearpcfinhom.Rd            |    6 
 man/linfun.Rd                    |   10 
 man/linim.Rd                     |    6 
 man/linnet.Rd                    |    4 
 man/lixellate.Rd                 |only
 man/localK.Rd                    |   10 
 man/localKinhom.Rd               |   10 
 man/localpcf.Rd                  |   10 
 man/logLik.dppm.Rd               |   14 
 man/logLik.kppm.Rd               |   14 
 man/logLik.mppm.Rd               |   16 
 man/logLik.ppm.Rd                |   38 
 man/logLik.slrm.Rd               |    8 
 man/lohboot.Rd                   |   10 
 man/lpp.Rd                       |    4 
 man/lppm.Rd                      |    6 
 man/lurking.Rd                   |   10 
 man/lut.Rd                       |   10 
 man/markconnect.Rd               |   10 
 man/markcorr.Rd                  |   10 
 man/markcrosscorr.Rd             |   14 
 man/marks.Rd                     |   10 
 man/marks.psp.Rd                 |   10 
 man/marks.tess.Rd                |   14 
 man/markstat.Rd                  |   10 
 man/marktable.Rd                 |   10 
 man/markvario.Rd                 |   10 
 man/matclust.estK.Rd             |    6 
 man/matclust.estpcf.Rd           |    6 
 man/maxnndist.Rd                 |    8 
 man/mean.im.Rd                   |   10 
 man/mergeLevels.Rd               |   14 
 man/methods.box3.Rd              |   10 
 man/methods.boxx.Rd              |   10 
 man/methods.dppm.Rd              |    6 
 man/methods.fii.Rd               |    6 
 man/methods.funxy.Rd             |   10 
 man/methods.kppm.Rd              |    6 
 man/methods.layered.Rd           |   10 
 man/methods.linfun.Rd            |   21 
 man/methods.linim.Rd             |   23 
 man/methods.linnet.Rd            |   15 
 man/methods.lpp.Rd               |   16 
 man/methods.lppm.Rd              |   39 
 man/methods.objsurf.Rd           |    8 
 man/methods.pp3.Rd               |   10 
 man/methods.ppx.Rd               |   10 
 man/methods.rho2hat.Rd           |    6 
 man/methods.rhohat.Rd            |    6 
 man/methods.slrm.Rd              |    6 
 man/methods.units.Rd             |   10 
 man/methods.zclustermodel.Rd     |only
 man/midpoints.psp.Rd             |   10 
 man/mincontrast.Rd               |    6 
 man/miplot.Rd                    |   10 
 man/model.depends.Rd             |   10 
 man/model.frame.ppm.Rd           |   14 
 man/model.images.Rd              |   14 
 man/model.matrix.ppm.Rd          |   14 
 man/model.matrix.slrm.Rd         |   10 
 man/moribund.Rd                  |   12 
 man/mppm.Rd                      |   14 
 man/msr.Rd                       |    6 
 man/multiplicity.ppp.Rd          |   10 
 man/nearest.raster.point.Rd      |   10 
 man/nearestsegment.Rd            |   10 
 man/nestsplit.Rd                 |   14 
 man/nnclean.Rd                   |    2 
 man/nncorr.Rd                    |   10 
 man/nncross.Rd                   |   10 
 man/nncross.lpp.Rd               |   30 
 man/nncross.pp3.Rd               |   10 
 man/nndensity.Rd                 |   10 
 man/nndist.Rd                    |    6 
 man/nndist.lpp.Rd                |   15 
 man/nndist.pp3.Rd                |    6 
 man/nndist.ppx.Rd                |    6 
 man/nndist.psp.Rd                |   10 
 man/nnfun.Rd                     |   10 
 man/nnfun.lpp.Rd                 |   10 
 man/nnmap.Rd                     |   10 
 man/nnmark.Rd                    |   14 
 man/nnorient.Rd                  |   12 
 man/nnwhich.Rd                   |    6 
 man/nnwhich.lpp.Rd               |   14 
 man/nnwhich.pp3.Rd               |    6 
 man/nnwhich.ppx.Rd               |    6 
 man/npfun.Rd                     |    8 
 man/npoints.Rd                   |   10 
 man/nsegments.Rd                 |   26 
 man/objsurf.Rd                   |    2 
 man/opening.Rd                   |   10 
 man/ord.family.Rd                |   10 
 man/osteo.Rd                     |    2 
 man/overlap.owin.Rd              |   10 
 man/owin.Rd                      |   10 
 man/owin.object.Rd               |   10 
 man/padimage.Rd                  |   14 
 man/pairdist.Rd                  |    6 
 man/pairdist.default.Rd          |    6 
 man/pairdist.lpp.Rd              |    6 
 man/pairdist.pp3.Rd              |    6 
 man/pairdist.ppp.Rd              |    6 
 man/pairdist.ppx.Rd              |    6 
 man/pairdist.psp.Rd              |   10 
 man/pairorient.Rd                |   12 
 man/pairs.im.Rd                  |   10 
 man/pairsat.family.Rd            |   10 
 man/pairwise.family.Rd           |   10 
 man/panel.contour.Rd             |   14 
 man/parameters.Rd                |   14 
 man/parres.Rd                    |   10 
 man/pcf.Rd                       |   10 
 man/pcf.fasp.Rd                  |   10 
 man/pcf.fv.Rd                    |   10 
 man/pcf.ppp.Rd                   |   10 
 man/pcf3est.Rd                   |    6 
 man/pcfcross.Rd                  |   10 
 man/pcfcross.inhom.Rd            |   10 
 man/pcfdot.Rd                    |   10 
 man/pcfdot.inhom.Rd              |   10 
 man/pcfinhom.Rd                  |   10 
 man/pcfmulti.Rd                  |   10 
 man/perimeter.Rd                 |   10 
 man/periodify.Rd                 |   10 
 man/persp.im.Rd                  |   14 
 man/perspPoints.Rd               |   14 
 man/pixelcentres.Rd              |   12 
 man/pixellate.Rd                 |   10 
 man/pixellate.owin.Rd            |   10 
 man/pixellate.ppp.Rd             |   10 
 man/pixellate.psp.Rd             |   14 
 man/pixelquad.Rd                 |   10 
 man/plot.anylist.Rd              |   14 
 man/plot.bermantest.Rd           |   12 
 man/plot.cdftest.Rd              |   10 
 man/plot.colourmap.Rd            |   10 
 man/plot.dppm.Rd                 |   10 
 man/plot.envelope.Rd             |   10 
 man/plot.fasp.Rd                 |   10 
 man/plot.fv.Rd                   |   10 
 man/plot.hyperframe.Rd           |   10 
 man/plot.im.Rd                   |   10 
 man/plot.imlist.Rd               |   14 
 man/plot.influence.ppm.Rd        |    6 
 man/plot.kppm.Rd                 |   28 
 man/plot.layered.Rd              |   10 
 man/plot.leverage.ppm.Rd         |    6 
 man/plot.linim.Rd                |    6 
 man/plot.linnet.Rd               |    4 
 man/plot.listof.Rd               |   10 
 man/plot.lpp.Rd                  |   10 
 man/plot.lppm.Rd                 |    6 
 man/plot.mppm.Rd                 |   16 
 man/plot.msr.Rd                  |   10 
 man/plot.onearrow.Rd             |   14 
 man/plot.owin.Rd                 |   10 
 man/plot.plotppm.Rd              |   10 
 man/plot.pp3.Rd                  |   14 
 man/plot.ppm.Rd                  |   10 
 man/plot.ppp.Rd                  |   10 
 man/plot.psp.Rd                  |   10 
 man/plot.quad.Rd                 |   10 
 man/plot.quadratcount.Rd         |   10 
 man/plot.quadrattest.Rd          |   10 
 man/plot.scan.test.Rd            |   10 
 man/plot.slrm.Rd                 |    8 
 man/plot.solist.Rd               |   14 
 man/plot.splitppp.Rd             |   10 
 man/plot.symbolmap.Rd            |   12 
 man/plot.tess.Rd                 |   10 
 man/plot.textstring.Rd           |   14 
 man/plot.texturemap.Rd           |   12 
 man/plot.yardstick.Rd            |   14 
 man/pointsOnLines.Rd             |   10 
 man/pool.Rd                      |   10 
 man/pool.anylist.Rd              |   14 
 man/pool.envelope.Rd             |   10 
 man/pool.fasp.Rd                 |   10 
 man/pool.fv.Rd                   |   14 
 man/pool.quadrattest.Rd          |   10 
 man/pool.rat.Rd                  |   10 
 man/pp3.Rd                       |   10 
 man/ppm.Rd                       |  113 -
 man/ppm.object.Rd                |   10 
 man/ppm.ppp.Rd                   |   94 
 man/ppp.Rd                       |   10 
 man/ppp.object.Rd                |   10 
 man/ppx.Rd                       |   10 
 man/predict.dppm.Rd              |   14 
 man/predict.kppm.Rd              |   10 
 man/predict.lppm.Rd              |    4 
 man/predict.mppm.Rd              |   16 
 man/predict.ppm.Rd               |    8 
 man/predict.slrm.Rd              |    8 
 man/print.im.Rd                  |   10 
 man/print.owin.Rd                |   10 
 man/print.ppm.Rd                 |   10 
 man/print.ppp.Rd                 |   10 
 man/print.psp.Rd                 |   10 
 man/print.quad.Rd                |   10 
 man/profilepl.Rd                 |   10 
 man/progressreport.Rd            |   14 
 man/project2segment.Rd           |   10 
 man/project2set.Rd               |   14 
 man/pseudoR2.Rd                  |only
 man/psp.Rd                       |   10 
 man/psp.object.Rd                |   10 
 man/psst.Rd                      |    8 
 man/psstA.Rd                     |    8 
 man/psstG.Rd                     |    8 
 man/qqplot.ppm.Rd                |   10 
 man/quad.object.Rd               |   10 
 man/quad.ppm.Rd                  |   10 
 man/quadrat.test.Rd              |   10 
 man/quadrat.test.mppm.Rd         |   16 
 man/quadrat.test.splitppp.Rd     |   10 
 man/quadratcount.Rd              |   10 
 man/quadratresample.Rd           |   10 
 man/quadrats.Rd                  |   10 
 man/quadscheme.Rd                |   10 
 man/quadscheme.logi.Rd           |   12 
 man/quantess.Rd                  |   14 
 man/quantile.density.Rd          |   14 
 man/quantile.ewcdf.Rd            |   10 
 man/quantile.im.Rd               |   10 
 man/quasirandom.Rd               |   12 
 man/rCauchy.Rd                   |    6 
 man/rDGS.Rd                      |   18 
 man/rDiggleGratton.Rd            |   22 
 man/rGaussPoisson.Rd             |   10 
 man/rHardcore.Rd                 |   16 
 man/rLGCP.Rd                     |   10 
 man/rMatClust.Rd                 |   10 
 man/rMaternI.Rd                  |   19 
 man/rMaternII.Rd                 |   21 
 man/rMosaicField.Rd              |   10 
 man/rMosaicSet.Rd                |   10 
 man/rNeymanScott.Rd              |   10 
 man/rPenttinen.Rd                |only
 man/rPoissonCluster.Rd           |   10 
 man/rQuasi.Rd                    |   12 
 man/rSSI.Rd                      |   14 
 man/rStrauss.Rd                  |   16 
 man/rStraussHard.Rd              |   21 
 man/rThomas.Rd                   |   10 
 man/rVarGamma.Rd                 |    6 
 man/ranef.mppm.Rd                |   16 
 man/range.fv.Rd                  |    8 
 man/raster.x.Rd                  |   12 
 man/rat.Rd                       |   10 
 man/rcell.Rd                     |   10 
 man/rcellnumber.Rd               |   10 
 man/rdpp.Rd                      |   14 
 man/reach.Rd                     |   10 
 man/reach.dppm.Rd                |   14 
 man/reduced.sample.Rd            |   10 
 man/redwood.Rd                   |    2 
 man/redwoodfull.Rd               |    2 
 man/reflect.Rd                   |   10 
 man/relevel.im.Rd                |   14 
 man/reload.or.compute.Rd         |   10 
 man/relrisk.Rd                   |   14 
 man/relrisk.ppm.Rd               |   14 
 man/relrisk.ppp.Rd               |   10 
 man/rescale.Rd                   |   10 
 man/rescale.im.Rd                |   10 
 man/rescale.owin.Rd              |   10 
 man/rescale.ppp.Rd               |   10 
 man/rescale.psp.Rd               |   10 
 man/rescue.rectangle.Rd          |   10 
 man/residuals.dppm.Rd            |   14 
 man/residuals.kppm.Rd            |   14 
 man/residuals.mppm.Rd            |   16 
 man/residuals.ppm.Rd             |   10 
 man/residualspaper.Rd            |    4 
 man/rgbim.Rd                     |   10 
 man/rho2hat.Rd                   |    2 
 man/rhohat.Rd                    |   26 
 man/ripras.Rd                    |   10 
 man/rjitter.Rd                   |   10 
 man/rknn.Rd                      |   10 
 man/rlabel.Rd                    |   10 
 man/rlinegrid.Rd                 |   10 
 man/rmh.Rd                       |   10 
 man/rmh.default.Rd               |   10 
 man/rmh.ppm.Rd                   |   10 
 man/rmhcontrol.Rd                |   10 
 man/rmhexpand.Rd                 |   10 
 man/rmhmodel.Rd                  |   10 
 man/rmhmodel.default.Rd          |   45 
 man/rmhmodel.list.Rd             |   10 
 man/rmhmodel.ppm.Rd              |   42 
 man/rmhstart.Rd                  |   10 
 man/rmpoint.Rd                   |   10 
 man/rmpoispp.Rd                  |   10 
 man/rnoise.Rd                    |   14 
 man/roc.Rd                       |   14 
 man/rose.Rd                      |   14 
 man/rotate.Rd                    |   10 
 man/rotate.im.Rd                 |   10 
 man/rotate.owin.Rd               |   10 
 man/rotate.ppp.Rd                |   10 
 man/rotate.psp.Rd                |   10 
 man/rotmean.Rd                   |   14 
 man/round.ppp.Rd                 |   10 
 man/rounding.Rd                  |   10 
 man/rpoint.Rd                    |   10 
 man/rpoisline.Rd                 |   10 
 man/rpoislinetess.Rd             |   10 
 man/rpoislpp.Rd                  |    4 
 man/rpoispp.Rd                   |   21 
 man/rpoispp3.Rd                  |   10 
 man/rpoisppOnLines.Rd            |   24 
 man/rpoisppx.Rd                  |   10 
 man/rshift.Rd                    |   10 
 man/rshift.ppp.Rd                |   10 
 man/rshift.psp.Rd                |   10 
 man/rshift.splitppp.Rd           |   10 
 man/rstrat.Rd                    |   10 
 man/rsyst.Rd                     |   10 
 man/rtemper.Rd                   |   14 
 man/rthin.Rd                     |   10 
 man/run.simplepanel.Rd           |   10 
 man/runifdisc.Rd                 |   10 
 man/runiflpp.Rd                  |    4 
 man/runifpoint.Rd                |   10 
 man/runifpoint3.Rd               |   10 
 man/runifpointOnLines.Rd         |   10 
 man/runifpointx.Rd               |   10 
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More information about spatstat at CRAN
Permanent link

Package SpatialTools updated to version 1.0.2 with previous version 1.0.1 dated 2015-11-30

Title: Tools for Spatial Data Analysis
Description: Tools for spatial data analysis. Emphasis on kriging. Provides functions for prediction and simulation. Intended to be relatively straightforward, fast, and flexible.
Author: Joshua French <joshua.french@ucdenver.edu>
Maintainer: Joshua French <joshua.french@ucdenver.edu>

Diff between SpatialTools versions 1.0.1 dated 2015-11-30 and 1.0.2 dated 2015-12-23

 DESCRIPTION |    8 ++++----
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More information about SpatialTools at CRAN
Permanent link

Package rdryad updated to version 0.2.0 with previous version 0.1.1 dated 2013-01-30

Title: Access for Dryad Web Services
Description: Interface to the Dryad Solr API, their OAI-PMH service, and fetch datasets.
Author: Scott Chamberlain [aut, cre], Carl Boettiger [aut], Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between rdryad versions 0.1.1 dated 2013-01-30 and 0.2.0 dated 2015-12-23

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Permanent link

New package population with initial version 0.1
Package: population
Type: Package
Title: Models for Simulating Populations
Version: 0.1
Date: 2015-12-23
Author: Guillaume Chapron
Maintainer: Guillaume Chapron <gchapron@carnivoreconservation.org>
Description: Run population simulations using an Individual-Based Model (IBM) compiled in C.
License: GPL-3
Depends: parallel, abind
NeedsCompilation: yes
Packaged: 2015-12-22 23:43:42 UTC; Guillaume
Repository: CRAN
Date/Publication: 2015-12-23 06:53:09

More information about population at CRAN
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New package PAactivPAL with initial version 1.0
Package: PAactivPAL
Type: Package
Title: Summarize Daily Physical Activity from 'activPAL' Accelerometer Data
Version: 1.0
Date: 2015-12-18
Author: Yukun Zhang [aut,cre], Haocheng Li [aut], Sarah Keadle [ctb], Charles Matthews [ctb], Raymond Carroll [ctb]
Maintainer: Yukun Zhang <yukzhang@ucalgary.ca>
Description: Summarize physical activity (Mets, Proportion, Total, etc.) in the given time period from accelerometer data. This package has been tested by data exported from 'activPAL'. 'activPAL' is a wearable device for medical and healthcare research application developed by PAL Technologies, Glasgow, Scotland. A simulated accelerometer sample dataset is provided in this package. See https://github.com/YukunZhang/PAactivPAL1.0 for more information.
License: GPL-2
Imports: stats
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-23 05:49:24 UTC; Yukun Zhang
Repository: CRAN
Date/Publication: 2015-12-23 06:58:06

More information about PAactivPAL at CRAN
Permanent link

Package gistr updated to version 0.3.6 with previous version 0.3.4 dated 2015-10-09

Title: Work with 'GitHub' 'Gists'
Description: Work with 'GitHub' 'gists' from 'R' (e.g., http://en.wikipedia.org/ wiki/GitHub#Gist, https://help.github.com/articles/about-gists/). A 'gist' is simply one or more files with code/text/images/etc. This package allows the user to create new 'gists', update 'gists' with new files, rename files, delete files, get and delete 'gists', star and 'un-star' 'gists', fork 'gists', open a 'gist' in your default browser, get embed code for a 'gist', list 'gist' 'commits', and get rate limit information when 'authenticated'. Some requests require authentication and some do not. 'Gists' website: https:// gist.github.com/.
Author: Ramnath Vaidyanathan [aut], Karthik Ram [aut], Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between gistr versions 0.3.4 dated 2015-10-09 and 0.3.6 dated 2015-12-23

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Package ftsa updated to version 4.6 with previous version 4.5 dated 2015-11-12

Title: Functional Time Series Analysis
Description: Functions for visualizing, modeling, forecasting and hypothesis testing of functional time series.
Author: Rob J Hyndman and Han Lin Shang
Maintainer: Han Lin Shang <hanlin.shang@anu.edu.au>

Diff between ftsa versions 4.5 dated 2015-11-12 and 4.6 dated 2015-12-23

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Package batteryreduction updated to version 0.1.1 with previous version 0.1.0 dated 2015-10-12

Title: An R Package for Data Reduction by Battery Reduction
Description: Battery reduction is a method used in data reduction. It uses Gram-Schmidt orthogonal rotations to find out a subset of variables best representing the original set of variables.
Author: Chunqiao Luo [aut, cre], Ralph D'Agostino [aut] (This package is derived from Battery Reduction Macro at http://www.lexjansen.com/nesug/nesug92/NESUG92090.pdf)
Maintainer: Chunqiao Luo <chunqiaoluo@gmail.com>

Diff between batteryreduction versions 0.1.0 dated 2015-10-12 and 0.1.1 dated 2015-12-23

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More information about batteryreduction at CRAN
Permanent link

Tue, 22 Dec 2015

New package weathermetrics with initial version 1.2.0
Package: weathermetrics
Type: Package
Title: Functions to Convert Between Weather Metrics
Version: 1.2.0
Date: 2015-12-18
Authors@R: c(person("Brooke", "Anderson", email = "brooke.anderson@colostate.edu", role = c("aut", "cre")), person("Roger", "Peng", email = "rdpeng@gmail.com", role = c("aut")))
Description: Functions to convert between Celsius and Fahrenheit, to convert between dew point temperature and relative humidity, and to calculate heat index.
URL: https://github.com/geanders/weathermetrics/
BugReports: https://github.com/geanders/weathermetrics/issues
License: MIT + file LICENSE
LazyData: true
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-12-22 19:36:32 UTC; brookeanderson
Author: Brooke Anderson [aut, cre], Roger Peng [aut]
Maintainer: Brooke Anderson <brooke.anderson@colostate.edu>
Repository: CRAN
Date/Publication: 2015-12-22 23:04:33

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New package Rknots with initial version 1.3.0
Package: Rknots
Type: Package
Title: Topological Analysis of Knotted Proteins, Biopolymers and 3D Structures
Version: 1.3.0
Date: 2015-12-15
Depends: R (>= 2.14.0), methods, rgl, rSymPy, bio3d
Suggests: knitr
VignetteBuilder: knitr
Author: Federico Comoglio and Maurizio Rinaldi
Maintainer: Federico Comoglio <federico.comoglio@gmail.com>
Description: The Rknots package contains functions for the topological analysis of polymers, with a focus on protein structures.
License: GPL-2
LazyData: yes
Packaged: 2015-12-22 21:37:32 UTC; federico
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-12-22 23:07:17

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New package gear with initial version 0.1.1
Package: gear
Type: Package
Title: Geostatistical Analysis in R
Version: 0.1.1
Date: 2015-12-22
Author: Joshua French
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Description: Implements common geostatistical methods in a clean, straightforward, efficient manner. A quasi reboot of the SpatialTools R package.
License: GPL (>= 2)
Imports: sp, parallel, lattice, stats, optimx
Suggests: testthat, gstat, geoR, spam, Matrix
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-22 19:38:13 UTC; jfrench
Repository: CRAN
Date/Publication: 2015-12-22 23:10:27

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Package colourlovers updated to version 0.2.0 with previous version 0.1.4 dated 2014-12-20

Title: R Client for the COLOURlovers API
Description: Provides access to the COLOURlovers <http://www.colourlovers.com/> API, which offers color inspiration and color palettes.
Author: Thomas J. Leeper
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>

Diff between colourlovers versions 0.1.4 dated 2014-12-20 and 0.2.0 dated 2015-12-22

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Package plotROC updated to version 2.0.0 with previous version 1.3.3 dated 2015-03-16

Title: Generate Useful ROC Curve Charts for Print and Interactive Use
Description: Most ROC curve plots obscure the cutoff values and inhibit interpretation and comparison of multiple curves. This attempts to address those shortcomings by providing plotting and interactive tools. Functions are provided to generate an interactive ROC curve plot for web use, and print versions. A Shiny application implementing the functions is also included.
Author: Michael C Sachs
Maintainer: Michael C Sachs <sachsmc@gmail.com>

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Package Lock5withR updated to version 1.2.2 with previous version 1.2.0 dated 2015-12-18

Title: Datasets for 'Statistics: Unlocking the Power of Data'
Description: Data sets and other utilities for 'Statistics: Unlocking the Power of Data' by Lock, Lock, Lock, Lock and Lock (ISBN : 978-0-470-60187-7, http://lock5stat.com/).
Author: Randall Pruim
Maintainer: Randall Pruim <rpruim@calvin.edu>

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New package IMP with initial version 0.1
Package: IMP
Type: Package
Title: Interactive Model Performance Evaluation
Version: 0.1
Date: 2015-12-18
Authors@R: person("Anup", "Nair", email = "nairanup50695@gmail.com", role = c("aut","cre"))
Description: Contains functions for evaluating & comparing the performance of Binary classification models. Functions can be called either statically or interactively (as Shiny Apps).
License: GPL
LazyData: TRUE
Imports: dplyr, ggplot2, stats, tidyr, shiny
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-22 18:31:42 UTC; anup.a.nair
Author: Anup Nair [aut, cre]
Maintainer: Anup Nair <nairanup50695@gmail.com>
Repository: CRAN
Date/Publication: 2015-12-22 20:50:44

More information about IMP at CRAN
Permanent link

Package crmPack updated to version 0.1.6 with previous version 0.1.5 dated 2015-11-12

Title: Object-Oriented Implementation of CRM Designs
Description: Implements a wide range of model-based dose escalation designs, ranging from classical and modern continual reassessment methods (CRMs) based on dose-limiting toxicity endpoints to dual-endpoint designs taking into account a biomarker/efficacy outcome. The focus is on Bayesian inference, making it very easy to setup a new design with its own JAGS code. However, it is also possible to implement 3+3 designs for comparison or models with non-Bayesian estimation. The whole package is written in a modular form in the S4 class system, making it very flexible for adaptation to new models, escalation or stopping rules.
Author: Daniel Sabanes Bove <sabanesd@roche.com>, Wai Yin Yeung <w.yeung1@lancaster.ac.uk>, Giuseppe Palermo <giuseppe.palermo@roche.com>, Thomas Jaki <jaki.thomas@gmail.com>
Maintainer: Daniel Sabanes Bove <sabanesd@roche.com>

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Package TcGSA updated to version 0.10.1 with previous version 0.9.8 dated 2014-04-28

Title: Time-Course Gene Set Analysis
Description: Implementation of TcGSA, a method for analyzing longitudinal gene-expression data at the gene set level.
Author: Boris P. Hejblum [aut, cre], Damien Chimits [aut]
Maintainer: Boris P. Hejblum <bhejblum@hsph.harvard.edu>

Diff between TcGSA versions 0.9.8 dated 2014-04-28 and 0.10.1 dated 2015-12-22

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Package simsalapar updated to version 1.0-7 with previous version 1.0-6 dated 2015-12-14

Title: Tools for Simulation Studies in Parallel
Description: Tools for setting up ("design"), conducting, and evaluating large-scale simulation studies with graphics and tables, including parallel computations.
Author: Marius Hofert and Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>

Diff between simsalapar versions 1.0-6 dated 2015-12-14 and 1.0-7 dated 2015-12-22

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Package betalink updated to version 2.2.0 with previous version 2.1.0 dated 2015-08-15

Title: Beta-Diversity of Species Interactions
Description: Measures of beta-diversity in networks, and easy visualization of why two networks are different.
Author: Timothee Poisot <tim@poisotlab.io>
Maintainer: Timothee Poisot <tim@poisotlab.io>

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Package archiDART updated to version 1.2 with previous version 1.1 dated 2015-06-08

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 (2015) 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>

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Package recalls (with last version 0.1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-05-09 0.1.0

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Package tcR updated to version 2.2.1.7 with previous version 2.2.1 dated 2015-11-07

Title: Advanced Data Analysis of Immune Receptor Repertoires
Description: Platform for the advanced analysis of T cell receptor and Immunoglobulin repertoires data and visualisation of the analysis results.
Author: Vadim Nazarov
Maintainer: Vadim Nazarov <vdm.nazarov@gmail.com>

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Package spdep updated to version 0.5-92 with previous version 0.5-88 dated 2015-03-17

Title: Spatial Dependence: Weighting Schemes, Statistics and Models
Description: A collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree; a collection of tests for spatial autocorrelation, including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross product statistic, Empirical Bayes estimates and Assunção/Reis Index, Getis/Ord G and multicoloured join count statistics, local Moran's I and Getis/Ord G, saddlepoint approximations and exact tests for global and local Moran's I; and functions for estimating spatial simultaneous autoregressive (SAR) lag and error models, impact measures for lag models, weighted and unweighted SAR and CAR spatial regression models, semi-parametric and Moran eigenvector spatial filtering, GM SAR error models, and generalized spatial two stage least squares models.
Author: Roger Bivand [cre, aut], Micah Altman [ctb], Luc Anselin [ctb], Renato Assunção [ctb], Olaf Berke [ctb], Andrew Bernat [ctb], Guillaume Blanchet [ctb], Eric Blankmeyer [ctb], Marilia Carvalho [ctb], Bjarke Christensen [ctb], Yongwan Chun [ctb], Carsten Dormann [ctb], Stéphane Dray [ctb], Virgilio Gómez-Rubio [ctb], Martin Gubri [ctb], Rein Halbersma [ctb], Elias Krainski [ctb], Pierre Legendre [ctb], Nicholas Lewin-Koh [ctb], Hongfei Li [ctb], Jielai Ma [ctb], Giovanni Millo [ctb], Werner Mueller [ctb], Hisaji Ono [ctb], Pedro Peres-Neto [ctb], Gianfranco Piras [ctb], Markus Reder [ctb], Michael Tiefelsdorf [ctb], Danlin Yu [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

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Package spcosa updated to version 0.3-6 with previous version 0.3-5 dated 2013-05-02

Title: Spatial Coverage Sampling and Random Sampling from Compact Geographical Strata
Description: Spatial coverage sampling and random sampling from compact geographical strata created by k-means.
Author: Dennis Walvoort [aut, cre, cph], Dick Brus [aut, cph], Jaap de Gruijter [aut, cph]
Maintainer: Dennis Walvoort <dennis.Walvoort@wur.nl>

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Package Rvcg updated to version 0.13.1 with previous version 0.13.0 dated 2015-12-15

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; the authors of VCGLIB for the included version of the code
Maintainer: Stefan Schlager <zarquon42@gmail.com>

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Package RPublica updated to version 0.1.3 with previous version 0.1.2 dated 2014-12-20

Title: ProPublica API Client
Description: Client for accessing data journalism APIs from ProPublica <http://www.propublica.org/>.
Author: Thomas J. Leeper [aut, cre], Jeroen Ooms [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>

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Package RcmdrPlugin.KMggplot2 updated to version 0.2-2 with previous version 0.2-1 dated 2015-12-14

Title: An Rcmdr Plug-in for Kaplan-Meier Plots and Other Plots by Using the ggplot2 Package
Description: A GUI front-end for ggplot2 allows Kaplan-Meier plot, histogram, Q-Q plot, box plot, errorbar plot, scatter plot, line chart, pie chart, bar chart, contour plot, and distribution plot.
Author: Triad sou. and Kengo NAGASHIMA
Maintainer: Triad sou. <triadsou@gmail.com>

Diff between RcmdrPlugin.KMggplot2 versions 0.2-1 dated 2015-12-14 and 0.2-2 dated 2015-12-22

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Package kequate updated to version 1.5.0 with previous version 1.4.0 dated 2014-06-04

Title: The Kernel Method of Test Equating
Description: Implements the kernel method of test equating using the CB, EG, SG, NEAT CE/PSE and NEC designs, supporting gaussian, logistic and uniform kernels and unsmoothed and pre-smoothed input data.
Author: Bjorn Andersson, Kenny Branberg and Marie Wiberg
Maintainer: Bjorn Andersson <bjoern.h.andersson@gmail.com>

Diff between kequate versions 1.4.0 dated 2014-06-04 and 1.5.0 dated 2015-12-22

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New package lumendb with initial version 0.2.0
Package: lumendb
Type: Package
Title: Lumen Database API Client
Version: 0.2.0
Date: 2015-12-22
Authors@R: c(person("Thomas J.", "Leeper", role = c("aut", "cre"), email = "thosjleeper@gmail.com"))
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Description: A simple client for the Lumen Database <https://lumendatabase.org/> (formerly Chilling Effects) API.
License: GPL (>= 2)
URL: https://github.com/leeper/lumendb
BugReports: https://github.com/leeper/lumendb/issues
Imports: httr
Suggests: testthat
NeedsCompilation: no
Packaged: 2015-12-22 07:52:49 UTC; Thomas
Author: Thomas J. Leeper [aut, cre]
Repository: CRAN
Date/Publication: 2015-12-22 14:37:03

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New package HSAR with initial version 0.3.6
Package: HSAR
Type: Package
Title: Hierarchical Spatial Autoregressive Model (HSAR)
Version: 0.3.6
Date: 2015-12-21
Author: Guanpeng Dong, Richard Harris, Angelos Mimis
Maintainer: Angelos Mimis <mimis@panteion.gr>
Description: A library of the Hierarchical Spatial Autoregressive Model (HSAR), based on a Bayesian Markov Chain Monte Carlo (MCMC) algorithm.
License: GPL (>= 2)
Depends: R (>= 2.7.0)
Imports: spdep, Rcpp
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Repository: CRAN
Packaged: 2015-12-22 08:25:37 UTC; Angelos
Date/Publication: 2015-12-22 14:36:40

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Package federalregister updated to version 0.2.0 with previous version 0.1.2 dated 2014-08-06

Title: Client Package for the U.S. Federal Register API
Description: Access data from the Federal Register API <https://www.federalregister.gov/developers/api/v1>.
Author: Thomas J. Leeper
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>

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Package circlize updated to version 0.3.4 with previous version 0.3.3 dated 2015-11-26

Title: Circular Visualization
Description: Circular layout is an efficient way for the visualization of huge amounts of information. Here the circlize package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of this package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, circlize gives users more convenience and freedom to design figures for better understanding complex patterns behind multi-dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>

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Package sValues updated to version 0.1.4 with previous version 0.1.2 dated 2015-10-25

Title: Measures of the Sturdiness of Regression Coefficients
Description: The sValues package implements the s-values proposed by Ed. Leamer. It provides a context-minimal approach for sensitivity analysis using extreme bounds to assess the sturdiness of regression coefficients.
Author: Carlos Cinelli
Maintainer: Carlos Cinelli <carloscinelli@hotmail.com>

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Package SimDesign updated to version 0.5 with previous version 0.4.1 dated 2015-11-20

Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to help organize Monte Carlo simulations in R. The package controls the structure and back-end of Monte Carlo simulations by utilizing a general generate-analyse-summarise strategy. The functions provided control common simulation issues such as re-simulating non-convergent results, support parallel back-end and MPI distributed computations, save and restore temporary files, aggregate results across independent nodes, and provide native support for debugging.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>

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Package rmarkdown updated to version 0.9 with previous version 0.8.1 dated 2015-10-09

Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre], Joe Cheng [aut], Yihui Xie [aut], Jonathan McPherson [aut], Winston Chang [aut], Jeff Allen [aut], Hadley Wickham [aut], Aron Atkins [aut], Rob Hyndman [aut], RStudio, Inc. [cph], jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/rmd/h/jquery-AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. [ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library)
Maintainer: JJ Allaire <jj@rstudio.com>

Diff between rmarkdown versions 0.8.1 dated 2015-10-09 and 0.9 dated 2015-12-22

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Package aSPU updated to version 1.39 with previous version 1.38 dated 2015-10-26

Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based and some pathway based association tests (Pathway based Sum of Powered Score tests ('SPUpath'), adaptive 'SPUpath' ('aSPUpath') test, 'GEEaSPU' test for multiple traits - single 'SNP' (single-nucleotide-polymorphism) association in generalized estimation equations, 'MTaSPUs' test for multiple traits - single 'SNP' association with Genome Wide Association Studies ('GWAS') summary statistics, Gene-based Association Test that uses an extended Simes procedure ('GATES'), Hybrid Set-based Test ('HYST') and extended version of 'GATES' test for pathway-based association testing ('GATES-Simes'). ). The tests can be used with genetic and other data sets with covariates. The response variable is binary or quantitative. Summary; (1) Single trait-'SNP' set association with individual-level data ('aSPU', 'aSPUw'), (2) Single trait-'SNP' set association with summary statistics ('aSPUs'), (3) Single trait-pathway association with individual-level data ('aSPUpath'), (4) Single trait-pathway association with summary statistics ('aSPUsPath'), (5) Multiple traits-single 'SNP' association with individual-level data ('GEEaSPU'), (6) Multiple traits-single SNP association with summary statistics ('MTaSPUs').
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak@umn.edu>

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Mon, 21 Dec 2015

Package wq updated to version 0.4.5 with previous version 0.4.4 dated 2015-07-30

Title: Exploring Water Quality Monitoring Data
Description: Functions to assist in the processing and exploration of data from environmental monitoring programs. The package name stands for "water quality" and reflects the original focus on time series data for physical and chemical properties of water, as well as the plankton. Intended for programs that sample approximately monthly at discrete stations, a feature of many legacy data sets. Most of the functions should be useful for analysis of similar-frequency time series regardless of the subject matter.
Author: Alan D. Jassby and James E. Cloern
Maintainer: Alan Jassby <wq@fastmail.net>

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Package visNetwork updated to version 0.2.0 with previous version 0.1.2 dated 2015-10-30

Title: Network Visualization using 'vis.js' Library
Description: Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.
Author: Almende B.V. [aut, cph] (vis.js library in htmlwidgets/lib, http://visjs.org, http://www.almende.com/home), Benoit Thieurmel [aut, cre] (R interface)
Maintainer: Benoit Thieurmel <bt@datak.fr>

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Package systemicrisk updated to version 0.3 with previous version 0.2 dated 2015-03-19

Title: A Toolbox for Systemic Risk
Description: A toolbox for systemic risk based on liabilities matrices. Contains a Gibbs sampler for liabilities matrices where only row and column sums of the liabilities matrix as well as some other fixed entries are observed. Includes models for power law distribution on the degree distribution.
Author: Axel Gandy and Luitgard A.M. Veraart
Maintainer: Axel Gandy <a.gandy@imperial.ac.uk>

Diff between systemicrisk versions 0.2 dated 2015-03-19 and 0.3 dated 2015-12-21

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More information about systemicrisk at CRAN
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Package rms updated to version 4.4-1 with previous version 4.4-0 dated 2015-09-28

Title: Regression Modeling Strategies
Description: Regression modeling, testing, estimation, validation, graphics, prediction, and typesetting by storing enhanced model design attributes in the fit. 'rms' is a collection of functions that assist with and streamline modeling. It also contains functions for binary and ordinal logistic regression models, ordinal models for continuous Y with a variety of distribution families, and the Buckley-James multiple regression model for right-censored responses, and implements penalized maximum likelihood estimation for logistic and ordinary linear models. 'rms' works with almost any regression model, but it was especially written to work with binary or ordinal regression models, Cox regression, accelerated failure time models, ordinary linear models, the Buckley-James model, generalized least squares for serially or spatially correlated observations, generalized linear models, and quantile regression.
Author: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
Maintainer: Frank E Harrell Jr <f.harrell@vanderbilt.edu>

Diff between rms versions 4.4-0 dated 2015-09-28 and 4.4-1 dated 2015-12-21

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Package precrec updated to version 0.2.0 with previous version 0.1.1 dated 2015-12-04

Title: Calculate Accurate Precision-Recall and ROC Curves
Description: Accurate calculations and visualization of Precision-Recall and ROC curves.
Author: Takaya Saito [aut, cre], Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>

Diff between precrec versions 0.1.1 dated 2015-12-04 and 0.2.0 dated 2015-12-21

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New package nnetpredint with initial version 1.2
Package: nnetpredint
Type: Package
Title: Prediction Intervals of Multi-Layer Neural Networks
Version: 1.2
Date: 2015-12-21
Suggests: MASS, nnet, neuralnet
Imports: stats, RSNNS
Author: Xichen Ding <rockingdingo@gmail.com>
Maintainer: Xichen Ding <rockingdingo@gmail.com>
Description: Computing prediction intervals of neural network models (e.g.backpropagation) at certain confidence level. It can take the output from models trained by other packages like 'nnet', 'neuralnet', 'RSNNS', etc.
License: GPL (>= 2)
Repository: CRAN
Repository/R-Forge/Project: nnetpredint
Repository/R-Forge/Revision: 7
Repository/R-Forge/DateTimeStamp: 2015-12-21 12:31:51
Date/Publication: 2015-12-21 21:35:34
NeedsCompilation: no
Packaged: 2015-12-21 13:05:10 UTC; rforge

More information about nnetpredint at CRAN
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Package CFC updated to version 1.0.1 with previous version 1.0.0 dated 2015-12-18

Title: Cause-Specific Framework for Competing-Risk Analysis
Description: Numerical integration of cause-specific survival curves to arrive at cause-specific cumulative incidence functions, with three usage modes: 1) Convenient API for parametric survival regression followed by competing-risk analysis, 2) API for CFC, accepting user-specified survival functions in R, and 3) Same as 2, but accepting survival functions in C++.
Author: Mansour T.A. Sharabiani, Alireza S. Mahani
Maintainer: Alireza S. Mahani <alireza.s.mahani@gmail.com>

Diff between CFC versions 1.0.0 dated 2015-12-18 and 1.0.1 dated 2015-12-21

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More information about CFC at CRAN
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New package aws.signature with initial version 0.2.0
Package: aws.signature
Type: Package
Title: Amazon Web Services Request Signatures
Version: 0.2.0
Date: 2015-12-21
Author: Thomas J. Leeper
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Description: Generates request signatures for Amazon Web Services (AWS) APIs.
License: GPL (>= 2)
Imports: digest
Suggests: testthat
URL: https://github.com/cloudyr/aws.signature
BugReports: https://github.com/cloudyr/aws.signature/issues
NeedsCompilation: no
Packaged: 2015-12-21 19:05:41 UTC; Thomas
Repository: CRAN
Date/Publication: 2015-12-21 22:00:53

More information about aws.signature at CRAN
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New package auRoc with initial version 0.1-0
Package: auRoc
Title: Various Methods to Estimate the AUC
Version: 0.1-0
Author: Dai Feng
Description: Estimate the AUC using a variety of methods as follows: (1) frequentist nonparametric methods based on the Mann-Whitney statistic or kernel methods. (2) frequentist parametric methods using the likelihood ratio test based on higher-order asymptotic results, the signed log-likelihood ratio test, the Wald test, or the approximate ''t'' solution to the Behrens-Fisher problem. (3) Bayesian parametric MCMC methods.
Maintainer: Dai Feng <dai_feng@merck.com>
Depends: R (>= 3.0.2), rjags (>= 3-11), ProbYX(>= 1.1)
Imports: coda(>= 0.16-1), MBESS(>= 3.3.3)
License: GPL
NeedsCompilation: no
Packaged: 2015-12-21 20:29:11 UTC; fengd
Repository: CRAN
Date/Publication: 2015-12-21 21:57:32

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Package paleofire updated to version 1.1.8 with previous version 1.1.7 dated 2015-11-12

Title: Analysis of Charcoal Records from the Global Charcoal Database
Description: Tools to extract and analyse charcoal sedimentary data stored in the Global Charcoal Database. Main functionalities includes data extraction and sites selection, transformation and interpolation of the charcoal records as well as compositing.
Author: Global Paleofire Working Group <paleofire@univ-fcomte.fr>
Maintainer: Olivier Blarquez <blarquez@gmail.com>

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Package FSA updated to version 0.8.4 with previous version 0.8.3 dated 2015-10-22

Title: Functions for Simple Fisheries Stock Assessment Methods
Description: Functions to perform a variety of simple fish stock assessment methods. Detailed vignettes are available on the fishR website listed below.
Author: Derek Ogle [aut, cre]
Maintainer: Derek Ogle <derek@derekogle.com>

Diff between FSA versions 0.8.3 dated 2015-10-22 and 0.8.4 dated 2015-12-21

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Package statebins updated to version 1.2.2 with previous version 1.0 dated 2014-08-27

Title: U.S. State Cartogram Heatmaps in R; an Alternative to Choropleth Maps for USA States
Description: Cartogram heatmaps are an alternative to choropleth maps for USA States and are based on work by the Washington Post graphics department in their report on "The states most threatened by trade". "State bins" preserve as much of the geographic placement of the states as possible but has the look and feel of a traditional heatmap. Functions are provided that allow for use of a binned, discrete scale, a continuous scale or manually specified colors depending on what is needed for the underlying data.
Author: Bob Rudis (@hrbrmstr)
Maintainer: Bob Rudis <bob@rudis.net>

Diff between statebins versions 1.0 dated 2014-08-27 and 1.2.2 dated 2015-12-21

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Package scmamp updated to version 0.2.5 with previous version 0.2.4 dated 2015-12-01

Title: Statistical Comparison of Multiple Algorithms in Multiple Problems
Description: Given a matrix with results of different algorithms for different problems, the package uses statistical tests and corrections to assess the differences between algorithms.
Author: Borja Calvo [aut, cre], Guzman Santafe [aut]
Maintainer: Borja Calvo <borja.calvo@ehu.eus>

Diff between scmamp versions 0.2.4 dated 2015-12-01 and 0.2.5 dated 2015-12-21

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Package rgdal updated to version 1.1-3 with previous version 1.1-1 dated 2015-11-02

Title: Bindings for the Geospatial Data Abstraction Library
Description: Provides bindings to Frank Warmerdam's Geospatial Data Abstraction Library (GDAL) (>= 1.6.3) and access to projection/transformation operations from the PROJ.4 library. The GDAL and PROJ.4 libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both GDAL raster and OGR vector map data can be imported into R, and GDAL raster data and OGR vector data exported. Use is made of classes defined in the sp package. Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and Expat) are provided on CRAN.
Author: Roger Bivand [cre, aut], Tim Keitt [aut], Barry Rowlingson [aut], Edzer Pebesma [ctb], Michael Sumner [ctb], Robert Hijmans [ctb], Even Rouault [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

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Package NlcOptim updated to version 0.3 with previous version 0.2 dated 2015-10-26

Title: Solve Nonlinear Optimization with Nonlinear Constraints
Description: Optimization for nonlinear objective and constraint functions. Linear or nonlinear equality and inequality constraints are allowed. It accepts the input parameters as a constrained matrix.
Author: Xianyan Chen <xychen@uga.edu>, Xiangrong Yin <yinxiangrong@uky.edu>
Maintainer: Xianyan Chen <xychen@uga.edu>

Diff between NlcOptim versions 0.2 dated 2015-10-26 and 0.3 dated 2015-12-21

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Package morse updated to version 2.1.1 with previous version 2.1.0 dated 2015-12-14

Title: MOdelling Tools for Reproduction and Survival Data in Ecotoxicology
Description: Tools for ecotoxicologists and regulators dedicated to the mathematical and statistical modelling of bioassay data. They use advanced and innovative methods for a valuable quantitative environmental risk assessment.
Author: Marie Laure Delignette-Muller [aut], Philippe Ruiz [aut], Sandrine Charles [aut], Wandrille Duchemin [ctb], Christelle Lopes [ctb], Guillaume Kon- Kam-king [ctb], Philippe Veber [aut]
Maintainer: Philippe Ruiz <philippe.ruiz@univ-lyon1.fr>

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Package metricsgraphics updated to version 0.9.0 with previous version 0.8.5 dated 2015-06-14

Title: Create Interactive Charts with the JavaScript 'MetricsGraphics' Library
Description: Provides an 'htmlwidgets' interface to the 'MetricsGraphics.js' ('D3'-based) charting library which is geared towards displaying time-series data. Chart types include line charts, scatterplots, histograms and rudimentary bar charts. Support for laying out multiple charts into a grid layout is also provided. All charts are interactive and many have an option for line, label and region annotations.
Author: Bob Rudis [aut, cre], Ali Almossawi [ctb, cph] (MetricsGraphics library), Hamilton Ulmer [ctb, cph] (MetricsGraphics library), Mozilla [cph] (MetricsGraphics library), jQuery Foundation and contributors [ctb, cph] (jQuery library)
Maintainer: Bob Rudis <bob@rudis.net>

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 metricsgraphics-0.9.0/metricsgraphics/man/mjs_histogram.Rd                                                     |    8 
 metricsgraphics-0.9.0/metricsgraphics/man/mjs_labs.Rd                                                          |    5 
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More information about metricsgraphics at CRAN
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Package dygraphs updated to version 0.6 with previous version 0.5 dated 2015-10-20

Title: Interface to Dygraphs Interactive Time Series Charting Library
Description: An R interface to the 'dygraphs' JavaScript charting library (a copy of which is included in the package). Provides rich facilities for charting time-series data in R, including highly configurable series- and axis-display and interactive features like zoom/pan and series/point highlighting.
Author: Dan Vanderkam [aut, cph] (dygraphs library in htmlwidgets/lib, http://dygraphs.com/), JJ Allaire [aut, cre] (R interface), RStudio [cph], jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/htmlwidgets/lib/jquery/AUTHORS.txt)
Maintainer: JJ Allaire <jj@rstudio.com>

Diff between dygraphs versions 0.5 dated 2015-10-20 and 0.6 dated 2015-12-21

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Package diversitree updated to version 0.9-8 with previous version 0.9-7 dated 2014-02-20

Title: Comparative Phylogenetic Analyses of Diversification
Description: Contains a number of comparative phylogenetic methods, mostly focusing on analysing diversification and character evolution. Contains implementations of 'BiSSE' (Binary State Speciation and Extinction) and its unresolved tree extensions, 'MuSSE' (Multiple State Speciation and Extinction), 'QuaSSE', 'GeoSSE', and 'BiSSE-ness' Other included methods include Markov models of discrete and continuous trait evolution and constant rate speciation and extinction.
Author: Richard G. FitzJohn <fitzjohn@zoology.ubc.ca>, with 'GeoSSE' and 'ClaSSE' by Emma E. Goldberg <eeg@uic.edu>, and 'BiSSE-ness' by Karen Magnuson-Ford.
Maintainer: Richard G. FitzJohn <rich.fitzjohn@gmail.com>

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Package BDgraph updated to version 2.26 with previous version 2.25 dated 2015-11-19

Title: Bayesian Graph Selection Based on Birth-Death MCMC Approach
Description: Provides statistical tools for Bayesian structure learning in undirected graphical models with either continuous or discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi <a.mohammadi@rug.nl>

Diff between BDgraph versions 2.25 dated 2015-11-19 and 2.26 dated 2015-12-21

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New package surveyoutliers with initial version 0.0
Package: surveyoutliers
Type: Package
Title: Helps Manage Outliers in Sample Surveys
Version: 0.0
Date: 2015-12-14
Author: Robert Clark
Maintainer: "Robert Clark" <rclark@uow.edu.au>
Imports: stats
Description: At present, the only functionality is the calculation of optimal one-sided winsorizing cutoffs. The main function is optimal.onesided.cutoff.bygroup. It calculates the optimal tuning parameter for one-sided winsorisation, and so calculates winsorised values for a variable of interest. See the help file for this function for more details and an example.
License: GPL-2 | GPL-3
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-21 09:11:38 UTC; rclark
Repository: CRAN
Date/Publication: 2015-12-21 11:33:36

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New package ProbYX with initial version 1.1-0
Package: ProbYX
Type: Package
Title: Inference for the Stress-Strength Model R = P(Y<X)
Version: 1.1-0
Date: 2015-12-17
Author: Giuliana Cortese
Maintainer: Giuliana Cortese <gcortese@stat.unipd.it>
Depends: R (>= 3.0-0), rootSolve
Description: Confidence intervals and point estimation for R under various parametric model assumptions; likelihood inference based on classical first-order approximations and higher-order asymptotic procedures.
License: GPL-2
LazyLoad: yes
Imports: stats, graphics
Packaged: 2015-12-21 08:36:35 UTC; Giuliana
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-12-21 11:33:28

More information about ProbYX at CRAN
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Package openair updated to version 1.6.7 with previous version 1.6.5 dated 2015-11-03

Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air pollution data. Data are typically hourly time series and both monitoring data and dispersion model output can be analysed. Many functions can also be applied to other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre], Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>

Diff between openair versions 1.6.5 dated 2015-11-03 and 1.6.7 dated 2015-12-21

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Package coala updated to version 0.3.0 with previous version 0.2.1 dated 2015-11-17

Title: A Framework for Coalescent Simulation
Description: Coalescent simulators can rapidly simulate biological sequences evolving according to a given model of evolution. You can use this package to specify such models, to conduct the simulations and to calculate additional statistics from the results. It relies on existing simulators for doing the simulation, and currently supports the programs 'ms', 'msms' and 'scrm'. It also supports finite-sites mutation models by combining the simulators with the program 'seq-gen'.
Author: Paul Staab [aut, cre], Dirk Metzler [aut, ths]
Maintainer: Paul Staab <develop@paulstaab.de>

Diff between coala versions 0.2.1 dated 2015-11-17 and 0.3.0 dated 2015-12-21

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New package VARsignR with initial version 0.1.3
Package: VARsignR
Version: 0.1.3
Date: 2015-12-19
Title: Sign Restrictions, Bayesian, Vector Autoregression Models
Authors@R: c(person("Christian", "Danne", email = "dannec@tcd.ie", role = c("aut", "cre")))
Author: Christian Danne [aut, cre]
Maintainer: Christian Danne <dannec@tcd.ie>
Depends: R (>= 3.2)
Imports: HI, minqa, mvnfast, utils, stats, methods, grDevices, graphics
Description: Provides routines for identifying structural shocks in vector autoregressions (VARs) using sign restrictions.
License: GPL (>= 3)
License_is_FOSS: yes
License_restricts_use: no
SystemRequirements: gcc (>= 4.0)
NeedsCompilation: no
Packaged: 2015-12-21 00:17:42 UTC; christian
Repository: CRAN
Date/Publication: 2015-12-21 08:54:51
Suggests: knitr
VignetteBuilder: knitr

More information about VARsignR at CRAN
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New package VarfromPDB with initial version 1.1.0
Package: VarfromPDB
Type: Package
Title: Capture the Genes and Variants Related to a Genetic Disease from Public Databases
Version: 1.1.0
Depends: R (>= 3.0.0), stringr, XML, XML2R, RCurl
biocViews: Software
Date: 2015-12-21
Author: Zongfu Cao
Maintainer: Zongfu Cao <caozongfu@gmail.com>
Description: Captures and compiles the genes and variants related to a disease, a phenotype or a clinical feature based on the public databases including HPO (Human Phenotype Ontology, http://human-phenotype-ontology.github.io/about.html), Orphanet (http://www.orpha.net/consor/cgi-bin/index.php), OMIM (Online Mendelian Inheritance in Man, http://www.omim.org), ClinVar (http://www.ncbi.nlm.nih.gov/clinvar), and Uniprot (Universal Protein Resource, http://www.uniprot.org). HPO provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. HPO currently contains approximately 11,000 terms and over 115,000 annotations to hereditary diseases. Orphanet is the reference portal for information on rare diseases and orphan drugs, whose aim is to help improve the diagnosis, care and treatment of patients with rare diseases. OMIM is a continuously updated catalog of human genes and genetic disorders and traits, with particular focus on the molecular relationship between genetic variation and phenotypic expression. ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. Uniprot focuses on amino acid altering variants imported from Ensembl Variation databases. For Homo sapiens, the variants including human polymorphisms and disease mutations in the Uniprot are manually curated from UniProtKB/Swiss-Prot.
License: GPL-2
NeedsCompilation: no
Packaged: 2015-12-21 03:03:13 UTC; Administrator
Repository: CRAN
Date/Publication: 2015-12-21 08:54:53

More information about VarfromPDB at CRAN
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Package PhySortR updated to version 1.0.3 with previous version 1.0.2 dated 2015-12-16

Title: A Fast, Flexible Tool for Sorting Phylogenetic Trees
Description: Screens and sorts phylogenetic trees in both traditional and extended Newick format. Allows for the fast and flexible screening (within a tree) of Exclusive clades that comprise only the target taxa and/or Non-Exclusive clades that includes a defined portion of non-target taxa.
Author: Timothy Stephens [aut, cre, trl] (R port), Debashish Bhattacharya [aut], Mark Ragan [aut], Cheong Xin Chan [aut, cph] (Original Perl implementation)
Maintainer: Timothy Stephens <timothy.stephens1@uqconnect.edu.au>

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Package ltsa updated to version 1.4.6 with previous version 1.4.5 dated 2015-08-22

Title: Linear Time Series Analysis
Description: Methods of developing linear time series modelling. Methods are given for loglikelihood computation, forecasting and simulation.
Author: A.I. McLeod, Hao Yu, Zinovi Krougly
Maintainer: A.I. McLeod <aimcleod@uwo.ca>

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Package gridGraphics updated to version 0.1-5 with previous version 0.1-3 dated 2015-02-09

Title: Redraw Base Graphics Using 'grid' Graphics
Description: Functions to convert a page of plots drawn with the graphics package into identical output drawn with the grid package. The result looks like the original graphics-based plot, but consists of grid grobs and viewports that can then be manipulated with grid functions (e.g., edit grobs and revisit viewports).
Author: Paul Murrell [cre, aut]
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>

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Package ggswissmaps updated to version 0.0.6 with previous version 0.0.2 dated 2014-11-07

Title: Offers Various Swiss Maps as ggplot2 Objects
Description: Offers various swiss maps as ggplot2 objects and gives the possibility to add layers of data on the maps. Data are publicly available from the swiss federal statistical office.
Author: Sandro Petrillo Burri [aut, cre], Eric Stephani [aut], Lisa Bottinelli [ctb]
Maintainer: Sandro Petrillo Burri <gibo.gaf@gmail.com>

Diff between ggswissmaps versions 0.0.2 dated 2014-11-07 and 0.0.6 dated 2015-12-21

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Package clusrank updated to version 0.1-1 with previous version 0.1-0 dated 2015-12-14

Title: Wilcoxon Rank Sum Test for Clustered Data
Description: Non-parametric tests (Wilcoxon rank sum test and Wilcoxon signed rank test) for clustered data.
Author: Yujing Jiang [aut, cre], Jun Yan [ctb]
Maintainer: Yujing Jiang <yujing.jiang@uconn.edu>

Diff between clusrank versions 0.1-0 dated 2015-12-14 and 0.1-1 dated 2015-12-21

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Package clogitboost updated to version 1.1 with previous version 1.0 dated 2015-11-26

Title: Boosting Conditional Logit Model
Description: A set of functions to fit a boosting conditional logit model.
Author: Haolun Shi and Guosheng Yin
Maintainer: Haolun Shi <shl2003@connect.hku.hk>

Diff between clogitboost versions 1.0 dated 2015-11-26 and 1.1 dated 2015-12-21

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Package choroplethr updated to version 3.3.1 with previous version 3.3.0 dated 2015-09-28

Title: Simplify the Creation of Choropleth Maps in R
Description: Choropleths are thematic maps where geographic regions, such as states, are colored according to some metric, such as the number of people who live in that state. This package simplifies this process by 1. Providing ready-made functions for creating choropleths of common maps. 2. Providing data and API connections to interesting data sources for making choropleths. 3. Providing a framework for creating choropleths from arbitrary shapefiles. 4. Overlaying those maps over reference maps from Google Maps. Please see the vignettes for more details.
Author: Ari Lamstein <arilamstein@gmail.com>[cre, aut], Brian P Johnson <brian@pjohnson.info> [ctb, frontend animation code]
Maintainer: Ari Lamstein <arilamstein@gmail.com>

Diff between choroplethr versions 3.3.0 dated 2015-09-28 and 3.3.1 dated 2015-12-21

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Sun, 20 Dec 2015

Package W3CMarkupValidator updated to version 0.1-5 with previous version 0.1-4 dated 2015-06-24

Title: R Interface to W3C Markup Validation Services
Description: R interface to a W3C Markup Validation service. See <http://validator.w3.org/> for more information.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

Diff between W3CMarkupValidator versions 0.1-4 dated 2015-06-24 and 0.1-5 dated 2015-12-20

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Package marketeR (with last version 0.1.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2015-10-21 0.1.1
2015-09-10 0.1.0

Permanent link
Package stylo updated to version 0.6.3 with previous version 0.6.2-1 dated 2015-11-19

Title: Functions for a Variety of Stylometric Analyses
Description: A number of functions, supplemented by GUI, to perform various analyses in the field of computational stylistics, authorship attribution, etc.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont
Maintainer: Maciej Eder <maciejeder@gmail.com>

Diff between stylo versions 0.6.2-1 dated 2015-11-19 and 0.6.3 dated 2015-12-20

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Package plotrix updated to version 3.6-1 with previous version 3.6 dated 2015-10-20

Title: Various Plotting Functions
Description: Lots of plots, various labeling, axis and color scaling functions.
Author: Jim Lemon, Ben Bolker, Sander Oom, Eduardo Klein, Barry Rowlingson, Hadley Wickham, Anupam Tyagi, Olivier Eterradossi, Gabor Grothendieck, Michael Toews, John Kane, Rolf Turner, Carl Witthoft, Julian Stander, Thomas Petzoldt, Remko Duursma, Elisa Biancotto, Ofir Levy, Christophe Dutang, Peter Solymos, Robby Engelmann, Michael Hecker, Felix Steinbeck, Hans Borchers, Henrik Singmann, Ted Toal, Derek Ogle
Maintainer: Jim Lemon <drjimlemon@gmail.com>

Diff between plotrix versions 3.6 dated 2015-10-20 and 3.6-1 dated 2015-12-20

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Package OAIHarvester updated to version 0.2-0 with previous version 0.1-7 dated 2014-04-02

Title: Harvest Metadata Using OAI-PMH v2.0
Description: Harvest metadata using the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH) version 2.0.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

Diff between OAIHarvester versions 0.1-7 dated 2014-04-02 and 0.2-0 dated 2015-12-20

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New package depth.plot with initial version 0.1
Package: depth.plot
Type: Package
Title: Multivariate Analogy of Quantiles
Version: 0.1
Date: 2015-12-19
Authors@R: c(person("Omker","Mahalanobish",email="omker.scorpio@gmail.com",role="aut"),person("Somedip","Karmakar",email="somedip@yahoo.co.in",role=c("cre","aut")))
Maintainer: Somedip Karmakar <somedip@yahoo.co.in>
Description: Could be used to obtain spatial depths, spatial ranks and outliers of multivariate random variables. Could also be used to visualize DD-plots (a multivariate generalization of QQ-plots).
Imports: mvtnorm , stats , graphics
License: GPL-2
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-20 11:01:29 UTC; omahala
Author: Omker Mahalanobish [aut], Somedip Karmakar [cre, aut]
Repository: CRAN
Date/Publication: 2015-12-20 15:33:19

More information about depth.plot at CRAN
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New package ContaminatedMixt with initial version 1.0
Package: ContaminatedMixt
Type: Package
Title: Model-Based Clustering and Classification with the Multivariate Contaminated Normal Distribution
Version: 1.0
Date: 2015-11-29
Author: Antonio Punzo, Angelo Mazza, Paul D. McNicholas
Maintainer: Angelo Mazza <a.mazza@unict.it>
Description: Fits mixtures of multivariate contaminated normal distributions (with eigen-decomposed scale matrices) via the expectation conditional- maximization algorithm under a clustering or classification paradigm.
License: GPL-2
LazyLoad: yes
Depends: R (>= 2.15.0)
Imports: mixture, mnormt, mclust
NeedsCompilation: no
Packaged: 2015-12-20 11:03:47 UTC; Angelo
Repository: CRAN
Date/Publication: 2015-12-20 15:34:15

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Package qicharts updated to version 0.4.3 with previous version 0.4.2 dated 2015-10-24

Title: Quality Improvement Charts
Description: Functions for making run charts and basic Shewhart control charts for measure and count data. The main function, qic(), creates run and control charts and has a simple interface with a rich set of options to control data analysis and plotting, including options for automatic data aggregation by subgroups, easy analysis of before-and-after data, exclusion of one or more data points from analysis, and splitting charts into sequential time periods. Missing values and empty subgroups are handled gracefully.
Author: Jacob Anhoej [aut, cre], Timo Roeder [ctb]
Maintainer: Jacob Anhoej <jacob@anhoej.net>

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Package plotly updated to version 2.0.16 with previous version 2.0.3 dated 2015-11-25

Title: Create Interactive Web Graphics via Plotly's JavaScript Graphing Library
Description: Easily translate ggplot2 graphs to an interactive web-based version and/or create custom web-based visualizations directly from R. Once uploaded to a plotly account, plotly graphs (and the data behind them) can be viewed and modified in a web browser.
Author: Carson Sievert [aut, cre], Chris Parmer [aut, cph], Toby Hocking [aut], Scott Chamberlain [aut], Karthik Ram [aut], Marianne Corvellec [aut], Pedro Despouy [aut]
Maintainer: Carson Sievert <cpsievert1@gmail.com>

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Package lctools updated to version 0.2-4 with previous version 0.2-3 dated 2015-07-05

Title: Local Correlation, Spatial Inequalities, Geographically Weighted Regression and Other Tools
Description: The main purpose of lctools is to provide researchers and educators with easy-to-learn user friendly tools for calculating key spatial statistics and to apply simple as well as advanced methods of spatial analysis in real data. These include: Local Pearson and Geographically Weighted Pearson Correlation Coefficients, Spatial Inequality Measures (Gini, Spatial Gini, LQ, Focal LQ), Spatial Autocorrelation (Global and Local Moran's I), several Geographically Weighted Regression techniques and other Spatial Analysis tools (other geographically weighted statistics). This package also contains functions for measuring the significance of each statistic calculated, mainly based on Monte Carlo simulations.
Author: Stamatis Kalogirou [aut, cre]
Maintainer: Stamatis Kalogirou <skalo@hua.gr>

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Package ggthemes updated to version 3.0.0 with previous version 2.2.1 dated 2015-07-01

Title: Extra Themes, Scales and Geoms for `ggplot2`
Description: Some extra themes, geoms, and scales for `ggplot2`. Provides `ggplot2` themes and scales that replicate the look of plots by Edward Tufte, Stephen Few, `Fivethirtyeight`, `The Economist`, `Stata`, `Excel`, and `The Wall Street Journal`, among others. Provides `geoms` for Tufte's box plot and range frame.
Author: Jeffrey B. Arnold [aut, cre], Gergely Daroczi [ctb], Bo Werth [ctb], Brian Weitzner [ctb], Joshua Kunst [ctb], Baptise Auguie [ctb], Bob Rudis [ctb], Hadley Wickham [ctb, cph] (Code from the ggplot2 package.), Justin Talbot [ctb] (Code from the labeling package)
Maintainer: Jeffrey B. Arnold <jeffrey.arnold@gmail.com>

Diff between ggthemes versions 2.2.1 dated 2015-07-01 and 3.0.0 dated 2015-12-20

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 ggthemes-3.0.0/ggthemes/NAMESPACE                             |   26 
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 ggthemes-3.0.0/ggthemes/R/excel.R                             |   19 
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 ggthemes-3.0.0/ggthemes/R/fivethirtyeight.R                   |   15 
 ggthemes-3.0.0/ggthemes/R/gdocs.R                             |   50 
 ggthemes-3.0.0/ggthemes/R/geom-rangeframe.R                   |  139 +-
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More information about ggthemes at CRAN
Permanent link

Package GERGM updated to version 0.6.2 with previous version 0.5.1 dated 2015-12-04

Title: Estimation and Fit Diagnostics for Generalized Exponential Random Graph Models
Description: Estimation and diagnosis of the convergence of Generalized Exponential Random Graph Models (GERGM) via Gibbs sampling or Metropolis Hastings with exponential down weighting.
Author: Matthew J. Denny <mdenny@psu.edu>, James D. Wilson <jdwilson1212@gmail.com>, Skyler Cranmer <cranmer.12@osu.edu >, Bruce A. Desmarais <bdesmarais@psu.edu>, Shankar Bhamidi <bhamidi@email.unc.edu>
Maintainer: Matthew J. Denny <mdenny@psu.edu>

Diff between GERGM versions 0.5.1 dated 2015-12-04 and 0.6.2 dated 2015-12-20

 GERGM-0.5.1/GERGM/man/GERGM.Rd                                     |only
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 GERGM-0.6.2/GERGM/NAMESPACE                                        |    1 
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 GERGM-0.6.2/GERGM/R/Helper_Functions.R                             |    8 
 GERGM-0.6.2/GERGM/R/Log_Likelihood_and_MPLE_Objective.R            |   62 ++
 GERGM-0.6.2/GERGM/R/MCMCMLE.R                                      |  133 +++--
 GERGM-0.6.2/GERGM/R/Network_Statistic_Calculation_Functions.R      |   12 
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 GERGM-0.6.2/GERGM/R/Parse_Formula_Object.R                         |    3 
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 31 files changed, 790 insertions(+), 362 deletions(-)

More information about GERGM at CRAN
Permanent link

Sat, 19 Dec 2015

New package TITAN2 with initial version 2.1
Package: TITAN2
Type: Package
Title: Threshold Indicator Taxa Analysis
Version: 2.1
Authors@R: c(person("Matthew E.", "Baker", email = "mbaker@umbc.edu", role = c("aut", "cph")), person("Ryan S.", "King",email = "Ryan_S_King@baylor.edu", role = c("aut", "cph")), person("David", "Kahle", email = "david.kahle@gmail.com", role = c("aut", "cph", "cre")))
Maintainer: David Kahle <david.kahle@gmail.com>
Description: Uses indicator species scores across binary partitions of a sample set to detect congruence in taxon-specific changes of abundance and occurrence frequency along an environmental gradient as evidence of an ecological community threshold. Relevant references include: Baker, ME and RS King. 2010. A new method for detecting and interpreting biodiversity and ecological community thresholds. Methods in Ecology and Evolution 1(1): 25:37. King, RS and ME Baker. 2010. Considerations for identifying and interpreting ecological community thresholds. Journal of the North American Benthological Association 29(3):998-1008. Baker ME and RS King. 2013. Of TITAN and straw men: an appeal for greater understanding of community data. Freshwater Science 32(2):489-506.
VignetteBuilder: knitr
Depends: R (>= 2.15.0)
Imports: parallel
Suggests: knitr, rmarkdown
License: GPL-2
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-19 16:00:55 UTC; david_kahle
Author: Matthew E. Baker [aut, cph], Ryan S. King [aut, cph], David Kahle [aut, cph, cre]
Repository: CRAN
Date/Publication: 2015-12-19 18:49:09

More information about TITAN2 at CRAN
Permanent link

New package modules with initial version 0.1.0
Package: modules
Title: Self Contained Units of Source Code
Version: 0.1.0
Date: 2015-12-18
Authors@R: person("Sebastian", "Warnholz", email = "wahani@gmail.com", role = c("aut", "cre"))
Description: Provides modules as an organizational unit for source code. Modules enforce to be more rigorous when defining dependencies and have a local search path. They can be used as a sub unit within packages or in scripts.
BugReports: https://github.com/wahani/modules/issues
Depends: R (>= 3.2.2), aoos, methods
License: GPL-3 | file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: disposables, testthat, devtools, knitr, parallel
RoxygenNote: 5.0.1
Collate: 'NAMESPACE.R' 'module.R' 'module-class.R' 'module-coercion.R' 'module-helper.R'
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-12-19 17:18:36 UTC; sebastian
Author: Sebastian Warnholz [aut, cre]
Maintainer: Sebastian Warnholz <wahani@gmail.com>
Repository: CRAN
Date/Publication: 2015-12-19 19:07:23

More information about modules at CRAN
Permanent link

Package ggmap updated to version 2.6 with previous version 2.5.2 dated 2015-08-21

Title: Spatial Visualization with ggplot2
Description: A collection of functions to visualize spatial data and models on top of static maps from various online sources (e.g Google Maps and Stamen Maps). It includes tools common to those tasks, including functions for geolocation and routing.
Author: David Kahle [aut, cre], Hadley Wickham [aut]
Maintainer: David Kahle <david.kahle@gmail.com>

Diff between ggmap versions 2.5.2 dated 2015-08-21 and 2.6 dated 2015-12-19

 DESCRIPTION              |   20 +--
 MD5                      |  119 +++++++++---------
 NAMESPACE                |   11 +
 NEWS                     |  300 ++++++++++++++++++++++++++++-------------------
 R/XY2LonLat.R            |   29 ++--
 R/bb2bbox.R              |   19 ++
 R/file_drawer.R          |    6 
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 R/get_map.R              |    4 
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 R/ggmap.R                |   57 +++++---
 R/ggplot2.R              |   10 -
 R/help.R                 |    7 -
 R/inset.R                |   71 ++++++-----
 R/inset_raster.R         |  108 ++++++++++++----
 R/mapdist.R              |   40 ++++--
 R/qmap.R                 |   14 +-
 R/qmplot.R               |   62 +++++----
 R/route.R                |  170 +++++++++++++++-----------
 R/theme_nothing.R        |   30 ++--
 README.md                |   25 ++-
 man/LonLat2XY.Rd         |    7 -
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 man/XY2LonLat.Rd         |   17 ++
 man/bb2bbox.Rd           |   23 ++-
 man/calc_zoom.Rd         |    2 
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 man/distQueryCheck.Rd    |    2 
 man/file_drawer.Rd       |    8 +
 man/geocode.Rd           |   34 +++--
 man/geom_leg.Rd          |  190 +++++++++++++++++++++++++----
 man/get_cloudmademap.Rd  |    2 
 man/get_googlemap.Rd     |   12 +
 man/get_map.Rd           |    2 
 man/get_navermap.Rd      |    3 
 man/get_openstreetmap.Rd |    3 
 man/get_stamenmap.Rd     |    8 -
 man/ggimage.Rd           |    3 
 man/gglocator.Rd         |    5 
 man/ggmap.Rd             |   54 +++++---
 man/ggmapplot.Rd         |    2 
 man/hadley.Rd            |    2 
 man/inset.Rd             |    6 
 man/inset_raster.Rd      |   34 +++--
 man/legs2route.Rd        |    4 
 man/make_bbox.Rd         |    3 
 man/mapdist.Rd           |   39 ++++--
 man/mutate_geocode.Rd    |    5 
 man/print.ggmap.Rd       |    5 
 man/qmap.Rd              |    4 
 man/qmplot.Rd            |   11 -
 man/revgeocode.Rd        |    4 
 man/route.Rd             |   41 ++----
 man/routeQueryCheck.Rd   |    2 
 man/theme_inset.Rd       |   23 +--
 man/theme_nothing.Rd     |    8 -
 man/wind.Rd              |    2 
 man/zips.Rd              |    2 
 61 files changed, 1122 insertions(+), 637 deletions(-)

More information about ggmap at CRAN
Permanent link

New package seqHMM with initial version 1.0.2-1
Package: seqHMM
Title: Hidden Markov Models for Life Sequences and Other Multivariate, Multichannel Categorical Time Series
Version: 1.0.2-1
Date: 2015-12-18
Author: Jouni Helske, Satu Helske
Maintainer: Jouni Helske <jouni.helske@jyu.fi>
Description: Designed for fitting hidden (latent) Markov models and mixture hidden Markov models for social sequence data and other categorical time series. Also some more restricted versions of these type of models are available: Markov models, mixture Markov models, and latent class models. The package supports models for one or multiple subjects with one or multiple parallel sequences (channels). External covariates can be added to explain cluster membership in mixture models. The package provides functions for evaluating and comparing models, as well as functions for easy plotting of multichannel sequence data and hidden Markov models. Models are estimated using maximum likelihood via the EM algorithm and/or direct numerical maximization with analytical gradients. All main algorithms are written in C++ with support for parallel computation.
LazyData: true
LinkingTo: Rcpp, RcppArmadillo
Depends: R (>= 3.0.0)
Imports: gridBase, igraph, Matrix, nloptr, numDeriv, Rcpp (>= 0.11.3), TraMineR (>= 1.8-8), graphics, grDevices, grid, methods, stats, utils
Suggests: MASS, nnet, knitr
License: GPL (>= 2)
Encoding: UTF-8
BugReports: https://github.com/helske/seqHMM/issues
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2015-12-18 13:14:56 UTC; jovetale
Repository: CRAN
Date/Publication: 2015-12-19 16:15:27

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Permanent link

Package RcppTOML updated to version 0.0.5 with previous version 0.0.4 dated 2015-07-16

Title: 'Rcpp' Bindings to Parser for Tom's Obvious Markup Language
Description: The configuration format defined by 'TOML' (which expands to "Tom's Obvious Markup Language") specifies an excellent format (described at <https://github.com/toml-lang/toml>) suitable for both human editing as well as the common uses of a machine-readable format. This package uses 'Rcpp' to connect the 'cpptoml' parser written by Chase Geigle (in modern C++11) to R.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppTOML versions 0.0.4 dated 2015-07-16 and 0.0.5 dated 2015-12-19

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Package prodlim updated to version 1.5.7 with previous version 1.5.5 dated 2015-10-05

Title: Product-Limit Estimation for Censored Event History Analysis
Description: Fast and user friendly implementation of nonparametric estimators for censored event history (survival) analysis. Kaplan-Meier and Aalen-Johansen method.
Author: Thomas A. Gerds
Maintainer: Thomas A. Gerds <tag@biostat.ku.dk>

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Package pnea updated to version 1.2.3 with previous version 1.2.2 dated 2015-12-11

Title: Parametric Network Enrichment Analysis
Description: Includes functions and examples to compute Parametric Network Enrichment Analysis.
Author: Mirko Signorelli, Veronica Vinciotti and Ernst C. Wit
Maintainer: Mirko Signorelli <m.signorelli@rug.nl>

Diff between pnea versions 1.2.2 dated 2015-12-11 and 1.2.3 dated 2015-12-19

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New package MTurkRGUI with initial version 0.1.5
Package: MTurkRGUI
Version: 0.1.5
Date: 2015-12-18
Title: A Graphical User Interface for MTurkR
Authors@R: c(person("Thomas J.", "Leeper", role = c("aut", "cre"), email = "thosjleeper@gmail.com"))
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Imports: MTurkR, tcltk, grDevices, utils, XML, curl
Description: A graphical user interface (GUI) for the MTurkR package.
License: GPL-2
URL: https://github.com/leeper/MTurkRGUI
BugReports: https://github.com/leeper/MTurkRGUI/issues
NeedsCompilation: no
Packaged: 2015-12-19 10:07:35 UTC; Thomas
Author: Thomas J. Leeper [aut, cre]
Repository: CRAN
Date/Publication: 2015-12-19 16:15:14

More information about MTurkRGUI at CRAN
Permanent link

Package gets updated to version 0.4 with previous version 0.3 dated 2015-11-26

Title: General-to-Specific (GETS) Modelling and Indicator Saturation Methods
Description: Automated multi-path General-to-Specific (GETS) modelling of the mean and variance of a regression, and indicator saturation methods for detecting and testing for structural breaks in the mean.
Author: Genaro Sucarrat [aut, cre], Felix Pretis [aut], James Reade [aut]
Maintainer: Genaro Sucarrat <genaro.sucarrat@bi.no>

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Package dynsim updated to version 1.2.1 with previous version 1.2 dated 2015-07-24

Title: Dynamic Simulations of Autoregressive Relationships
Description: Dynamic simulations and graphical depictions of autoregressive relationships.
Author: Christopher Gandrud [aut, cre], Laron K. Williams [aut], Guy D. Whitten [aut]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>

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Package bujar updated to version 0.2-1 with previous version 0.1-5 dated 2015-10-27

Title: Buckley-James Regression for Survival Data with High-Dimensional Covariates
Description: Buckley-James regression for right-censoring survival data with high-dimensional covariates. Implementations for survival data include boosting with componentwise linear least squares, componentwise smoothing splines, regression trees and MARS. Other high-dimensional tools include penalized regression for survival data.
Author: Zhu Wang and others (see COPYRIGHTS)
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>

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Package seriation updated to version 1.1-3 with previous version 1.1-2 dated 2015-08-23

Title: Infrastructure for Ordering Objects Using Seriation
Description: Infrastructure for seriation with an implementation of several seriation/sequencing techniques to reorder matrices, dissimilarity matrices, and dendrograms. Also provides (optimally) reordered heatmaps, color images and clustering visualizations like dissimilarity plots, and visual assessment of cluster tendency plots (VAT and iVAT).
Author: Michael Hahsler [aut, cre, cph], Christian Buchta [aut, cph], Kurt Hornik [aut, cph], Fionn Murtagh [ctb, cph], Michael Brusco [ctb, cph], Stephanie Stahl [ctb, cph], Hans-Friedrich Koehn [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

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Package R.rsp updated to version 0.21.0 with previous version 0.20.0 dated 2015-02-19

Title: Dynamic Generation of Scientific Reports
Description: The RSP markup language makes any text-based document come alive. RSP provides a powerful markup for controlling the content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr documents (and more), e.g. 'Today's date is <%=Sys.Date()%>'. Contrary to many other literate programming languages, with RSP it is straightforward to loop over mixtures of code and text sections, e.g. in month-by-month summaries. RSP has also several preprocessing directives for incorporating static and dynamic contents of external files (local or online) among other things. Functions rstring() and rcat() make it easy to process RSP strings, rsource() sources an RSP file as it was an R script, while rfile() compiles it (even online) into its final output format, e.g. rfile('report.tex.rsp') generates 'report.pdf' and rfile('report.md.rsp') generates 'report.html'. RSP is ideal for self-contained scientific reports and R package vignettes. It's easy to use - if you know how to write an R script, you'll be up and running within minutes.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

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Package raster updated to version 2.5-2 with previous version 2.4-30 dated 2015-12-10

Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
Author: Robert J. Hijmans [cre, aut], Jacob van Etten [ctb], Joe Cheng [ctb], Matteo Mattiuzzi [ctb], Michael Sumner [ctb], Jonathan A. Greenberg [ctb], Oscar Perpinan Lamigueiro [ctb], Andrew Bevan [ctb], Etienne B. Racine [ctb], Ashton Shortridge [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>

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Package QCA updated to version 2.0 with previous version 1.1-4 dated 2014-12-28

Title: Qualitative Comparative Analysis
Description: Starting with version 2.0, the package QCA acts as an aggregator for the various packages dealing with Qualitative Comparative Analysis. For the moment, it is a gateway to the QCAGUI package, but more related packages are expected to be loaded at runtime.
Author: Adrian Dusa [aut, cre, cph], Alrik Thiem [aut] (from version 1.0-0, up to version 1.1-3)
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>

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New package plspm.formula with initial version 1.0
Package: plspm.formula
Type: Package
Title: Formula Based PLS Path Modeling Utilities
Version: 1.0
Date: 2015-12-17
Authors@R: c(person("ACHIEPO", "Odilon Yapo M.", role=c("aut", "cre"), email = "kingodilon@gmail.com"))
Author: ACHIEPO Odilon Yapo M. [aut, cre]
Maintainer: ACHIEPO Odilon Yapo M. <kingodilon@gmail.com>
Description: The main objective is to make easy the PLS Path Modeling with R using the package 'plspm'. It compute automatically the inner matrix and the outer list the 'plspm' function need simply by specify the model using formulas.
Depends: R (>= 2.15.0)
Imports: plspm
Repository: CRAN
License: GPL (>= 2.0)
LazyLoad: yes
LazyData: yes
NeedsCompilation: no
Packaged: 2015-12-19 01:31:32 UTC; kodilon
Date/Publication: 2015-12-19 09:53:54

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Package FWDselect updated to version 2.1.0 with previous version 2.0.1 dated 2015-10-11

Title: Selecting Variables in Regression Models
Description: A simple method to select the best model or best subset of variables using different types of data (binary, Gaussian or Poisson) and applying it in different contexts (parametric or non-parametric).
Author: Marta Sestelo [aut, cre], Nora M. Villanueva [aut], Javier Roca-Pardinas [aut]
Maintainer: Marta Sestelo <sestelo@uvigo.es>

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Package cowplot updated to version 0.6.0 with previous version 0.5.0 dated 2015-07-01

Title: Streamlined Plot Theme and Plot Annotations for 'ggplot2'
Description: Some helpful extensions and modifications to the 'ggplot2' library. In particular, this package makes it easy to combine multiple 'ggplot2' plots into one and label them with letters, e.g. A, B, C, etc., as is often required for scientific publications. The package also provides a streamlined and clean theme that is used in the Wilke lab, hence the package name, which stands for Claus O. Wilke's plot library.
Author: Claus O. Wilke [aut, cre], Hadley Wickham [cph]
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>

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Package bst updated to version 0.3-11 with previous version 0.3-4 dated 2014-06-23

Title: Gradient Boosting
Description: Functional gradient descent algorithm for a variety of convex and nonconvex loss functions, for both classical and robust regression and classification problems. HingeBoost is implemented for binary and multi-class classification, with unequal misclassification costs for binary case. The algorithm can fit linear and nonlinear classifiers.
Author: Zhu Wang [aut, cre], Torsten Hothorn [ctb]
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>

Diff between bst versions 0.3-4 dated 2014-06-23 and 0.3-11 dated 2015-12-19

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Package aqp updated to version 1.9.3 with previous version 1.9.2 dated 2015-12-04

Title: Algorithms for Quantitative Pedology
Description: A collection of algorithms related to modeling of soil resources, soil classification, soil profile aggregation, and visualization.
Author: Dylan Beaudette <debeaudette@ucdavis.edu>, Pierre Roudier <roudierp@landcareresearch.co.nz>
Maintainer: Dylan Beaudette <debeaudette@ucdavis.edu>

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Fri, 18 Dec 2015

Package VBLPCM updated to version 2.4.4 with previous version 2.4.3 dated 2014-03-07

Title: Variational Bayes Latent Position Cluster Model for Networks
Description: Fit and simulate latent position and cluster models for network data, using a fast Variational Bayes approximation.
Author: Michael Salter-Townshend
Maintainer: Michael Salter-Townshend <mike.saltertownshend@gmail.com>

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Package UpSetR updated to version 1.0.2 with previous version 1.0.1 dated 2015-12-17

Title: A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets
Description: Creates visualizations of intersecting sets using a novel matrix design, along with visualizations of several common set, element and attribute related tasks.
Author: Jake Conway [cre], Nils Gehlenborg [aut]
Maintainer: Jake Conway <jake_conway@student.uml.edu>

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Package SpatialVx updated to version 0.3 with previous version 0.2-4 dated 2015-06-01

Title: Spatial Forecast Verification
Description: Spatial forecast verification arose from verifying high-resolution forecasts, where coarser-resolution models generally are favored even when a human forecaster finds the higher-resolution model to be considerably better. Most newly proposed methods, which largely come from image analysis, computer vision, and similar, are available, with more on the way.
Author: Eric Gilleland <EricG@ucar.edu>
Maintainer: Eric Gilleland <EricG@ucar.edu>

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Package geosphere updated to version 1.5-1 with previous version 1.4-3 dated 2015-07-01

Title: Spherical Trigonometry
Description: Spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations.
Author: Robert J. Hijmans [cre, aut], Ed Williams [ctb], Chris Vennes [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>

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Package directlabels updated to version 2015.12.16 with previous version 2013.6.15 dated 2013-07-22

Title: Direct Labels for Multicolor Plots
Description: An extensible framework for automatically placing direct labels onto multicolor lattice or ggplot2 plots. Label positions are described using Positioning Methods which can be re-used across several different plots. There are heuristics for examining "trellis" and "ggplot" objects and inferring an appropriate Positioning Method.
Author: Toby Dylan Hocking
Maintainer: Toby Dylan Hocking <tdhock5@gmail.com>

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New package binaryLogic with initial version 0.2.6
Package: binaryLogic
Title: Binary Logic
Description: Convert to binary numbers (Base2). Shift, rotate, summary. Based on logical vector.
Version: 0.2.6
Author: Daniel Dörrhöfer <ddo@openmailbox.org>
Maintainer: Daniel Dörrhöfer <ddo@openmailbox.org>
URL: https://github.com/d4ndo/binaryLogic
BugReports: https://github.com/d4ndo/binaryLogic/issues
Depends: R (>= 3.0.2)
Suggests: testthat
License: GPL-3 + file LICENSE
LazyData: true
Encoding: UTF-8
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-18 14:42:38 UTC; daniel
Repository: CRAN
Date/Publication: 2015-12-18 23:23:52

More information about binaryLogic at CRAN
Permanent link

Package astrochron updated to version 0.5 with previous version 0.4.3 dated 2015-07-01

Title: A Computational Tool for Astrochronology
Description: Routines for astrochronologic testing, astronomical time scale construction, and time series analysis. Also included are a range of statistical analysis and modeling routines that are relevant to time scale development and paleoclimate analysis.
Author: Stephen Meyers
Maintainer: Stephen Meyers <smeyers@geology.wisc.edu>

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Package picasso updated to version 0.5.0 with previous version 0.4.7 dated 2015-09-15

Title: Pathwise Calibrated Sparse Shooting Algorithm
Description: Implements the pathwise calibrated sparse shooting algorithm (PICASSO) for high dimensional regularized sparse linear regression, sparse logistic regression, and sparse undirected graphical model estimation. As a pathwise coordinate optimization algorithm, PICASSO exploits warm start initialization, active set updating, and strong rule for coordinate preselection to boost computation, and attains a linear convergence to a unique sparse local optimum with optimal statistical properties. Moreover, users can choose different regularizers, including L1, MCP, and SCAD regularizers. The computation is memory-optimized using the sparse matrix output.
Author: Xingguo Li, Tuo Zhao, Tong Zhang and Han Liu
Maintainer: Xingguo Li <xingguo.leo@gmail.com>

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Package pcadapt updated to version 2.1 with previous version 2.0.1 dated 2015-11-09

Title: Principal Component Analysis for Outlier Detection
Description: Methods to detect genetic markers involved in biological adaptation. 'pcadapt' provides statistical tools for outlier detection based on Principal Component Analysis.
Author: Keurcien Luu, Michael G.B. Blum
Maintainer: Keurcien Luu <keurcien.luu@imag.fr>

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Package likeLTD updated to version 6.0.1 with previous version 6.0.0 dated 2015-12-16

Title: Tools to Evaluate DNA Profile Evidence
Description: Tools to determine DNA profile Weight of Evidence. For further information see the likeLTD guide provided, or the paper under citation.
Author: David Balding, Adrian Timpson, Christopher Steele, Mayeul d'Avezac, James Hetherington.
Maintainer: Christopher Steele <c.steele.11@ucl.ac.uk>

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New package bodenmiller with initial version 0.1
Package: bodenmiller
Type: Package
Title: Profilling of Peripheral Blood Mononuclear Cells using CyTOF
Version: 0.1
Depends: R (>= 3.1.0)
Suggests: ggplot2, dplyr, reshape2, RColorBrewer, knitr, rmarkdown
Authors@R: c(person('Yann','Abraham',email='yann.abraham@gmail.com',role=c('aut','cre')), person('Bernd','Bodenmiller',email='bernd.bodenmiller@imls.uzh.ch',role='aut'))
Description: This data package contains a subset of the Bodenmiller et al, Nat Biotech 2012 dataset for testing single cell, high dimensional analysis and visualization methods.
License: CC0
LazyData: TRUE
URL: https://github.com/yannabraham/bodenmiller
BugReports: https://github.com/yannabraham/bodenmiller/issues
VignetteBuilder: knitr
Packaged: 2015-12-18 14:34:35 UTC; ABRAHYA1
Author: Yann Abraham [aut, cre], Bernd Bodenmiller [aut]
Maintainer: Yann Abraham <yann.abraham@gmail.com>
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-12-18 22:45:47

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Package phenex updated to version 1.1-9 with previous version 1.0-7 dated 2014-02-11

Title: Auxiliary Functions for Phenological Data Analysis
Description: Provides some easy-to-use functions for spatial analyses of (plant-) phenological data sets and satellite observations of vegetation.
Author: Lange, Maximilian and Doktor, Daniel
Maintainer: Daniel Doktor <daniel.doktor@ufz.de>

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Package equateIRT updated to version 1.2-2 with previous version 1.2-1 dated 2015-11-26

Title: Direct, Chain and Average Equating Coefficients with Standard Errors Using IRT Methods
Description: Computation of direct, chain and average (bisector) equating coefficients with standard errors using Item Response Theory (IRT) methods for dichotomous items.
Author: Michela Battauz
Maintainer: Michela Battauz <michela.battauz@uniud.it>

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Package confreq updated to version 1.4 with previous version 1.3-1 dated 2015-05-01

Title: Configural Frequencies Analysis Using Log-Linear Modeling
Description: Offers several functions for Configural Frequencies Analysis (CFA), which is a useful statistical tool for the analysis of multiway contingency tables. CFA was introduced by G. A. Lienert as 'Konfigurations Frequenz Analyse - KFA'.
Author: Joerg-Henrik Heine, R.W. Alexandrowicz (function stirling_cfa() ) and intensive package testing by Mark Stemmler
Maintainer: Joerg-Henrik Heine <jhheine@googlemail.com>

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Package needs updated to version 0.0.2 with previous version 0.0.1 dated 2015-12-15

Title: Attaches and Installs Packages
Description: A simple function for easier package loading and auto-installation.
Author: Josh Katz [aut, cre]
Maintainer: Josh Katz <josh.katz@nytimes.com>

Diff between needs versions 0.0.1 dated 2015-12-15 and 0.0.2 dated 2015-12-18

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New package mangoTraining with initial version 1.0-6
Package: mangoTraining
Type: Package
Title: Mango Solutions Training Datasets
Version: 1.0-6
Date: 2015-07-07
Author: Mango Solutions <rin24hours@mango-solutions.com>
Maintainer: Aimee Gott <agott@mango-solutions.com>
Contact: Mango Solutions <rin24hours@mango-solutions.com>
Description: Datasets designed to be used in conjunction with Mango Solutions training materials and the book SAMS Teach Yourself R in 24 Hours (ISBN: 978-0-672-33848-9).
URL: http://www.mango-solutions.com
Depends: R (>= 2.10.0)
License: GPL-2
LazyLoad: yes
LazyData: yes
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-18 09:45:27 UTC; agott
Repository: CRAN
Date/Publication: 2015-12-18 11:08:07

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Package Hmisc updated to version 3.17-1 with previous version 3.17-0 dated 2015-09-21

Title: Harrell Miscellaneous
Description: Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX code, and recoding variables.
Author: Frank E Harrell Jr <f.harrell@vanderbilt.edu>, with contributions from Charles Dupont and many others.
Maintainer: Frank E Harrell Jr <f.harrell@vanderbilt.edu>

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Package gimms updated to version 0.4.0 with previous version 0.3.0 dated 2015-11-13

Title: Download and Process GIMMS NDVI3g Data
Description: We provide a set of functions to retrieve information about GIMMS NDVI3g files currently available online; download and re-arrange the bi-monthly datasets according to creation time; import downloaded files from native binary (ENVI) format directly into R based on the widely applied 'raster' package; calculate monthly value composites (e.g. maximum value composites, MVC) from the bi-monthly input data; and derive long-term monotonous trends from the Mann-Kendall trend test, optionally featuring pre-whitening to account for lag-1 autocorrelation.
Author: Florian Detsch [cre, aut]
Maintainer: Florian Detsch <admin@environmentalinformatics-marburg.de>

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Package ggplot2 updated to version 2.0.0 with previous version 1.0.1 dated 2015-03-17

Title: An Implementation of the Grammar of Graphics
Description: An implementation of the grammar of graphics in R. It combines the advantages of both base and lattice graphics: conditioning and shared axes are handled automatically, and you can still build up a plot step by step from multiple data sources. It also implements a sophisticated multidimensional conditioning system and a consistent interface to map data to aesthetic attributes. See http://ggplot2.org for more information, documentation and examples.
Author: Hadley Wickham [aut, cre], Winston Chang [aut], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package CFC updated to version 1.0.0 with previous version 0.7.0 dated 2015-03-12

Title: Cause-Specific Framework for Competing-Risk Analysis
Description: Numerical integration of cause-specific survival curves to arrive at cause-specific cumulative incidence functions, with three usage modes: 1) Convenient API for parametric survival regression followed by competing-risk analysis, 2) API for CFC, accepting user-specified survival functions in R, and 3) Same as 2, but accepting survival functions in C++.
Author: Mansour T.A. Sharabiani, Alireza S. Mahani
Maintainer: Alireza S. Mahani <alireza.s.mahani@gmail.com>

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New package Ultimixt with initial version 2.0
Package: Ultimixt
Type: Package
Title: Bayesian Analysis of a Non-Informative Parametrization for Gaussian Mixture Distributions
Version: 2.0
Date: 2015-12-10
Author: Kaniav Kamary, Kate Lee
Maintainer: Kaniav Kamary <kamary@ceremade.dauphine.fr>
Depends: coda, gtools, graphics, grDevices, stats
Description: A generic reference Bayesian analysis of unidimensional mixtures of Gaussian distributions obtained by a location-scale parameterisation of the model is implemented. Included functions can be applied to produce a Bayesian analysis of Gaussian mixtures with an arbitrary number of components, with no need to define the prior distribution.
License: GPL (>= 2.0)
NeedsCompilation: no
Packaged: 2015-12-17 16:49:57 UTC; kamary
Repository: CRAN
Date/Publication: 2015-12-18 06:43:04

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New package TextoMineR with initial version 1.1
Package: TextoMineR
Type: Package
Title: Textual Statistics
Version: 1.1
Date: 2015-12-17
Author: Monica Becue-Bertaut, Daria M. Hernandez, Belchin Kostov, Josep A. Sanchez
Maintainer: Monica Becue-Bertaut <monica.becue@upc.edu>
Description: Multidimensional statistical methods for textual analysis.
License: GPL (>= 2.0)
Depends: FactoMineR, stringr, tm, gdata, MASS
Packaged: 2015-12-17 21:15:31 UTC; Usuario
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-12-18 06:43:01

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Package SEMID updated to version 0.2 with previous version 0.1 dated 2013-08-16

Title: Identifiability of Linear Structural Equation Models
Description: Provides routines to check identifiability or non-identifiability of linear structural equation models as described in Drton, Foygel & Sullivant (Ann. Statist., 2011) and Foygel, Draisma & Drton (Ann. Statist., 2012). The routines are based on the graphical representation of structural equation models by a path diagram/mixed graph.
Author: Rina Foygel Barber <rina@uchicago.edu>, Mathias Drton <md5@uw.edu>, Luca Weihs <lucaw@uw.edu>.
Maintainer: Mathias Drton <md5@uw.edu>

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New package sankey with initial version 1.0.0
Package: sankey
Title: Sankey Diagrams
Version: 1.0.0
Author: Gabor Csardi, January Weiner
Maintainer: Gabor Csardi <gcsardi@mango-solutions.com>
Description: Sankey plots illustrate the flow of information or material.
License: GPL (>= 2)
LazyData: true
URL: https://github.com/mangothecat/sankey
BugReports: https://github.com/mangothecat/sankey/issues
Suggests: testthat
Imports: simplegraph, utils, graphics, grDevices
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-17 20:57:12 UTC; gaborcsardi
Repository: CRAN
Date/Publication: 2015-12-18 06:43:38

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Package recommenderlab updated to version 0.1-8 with previous version 0.1-7 dated 2015-07-24

Title: Lab for Developing and Testing Recommender Algorithms
Description: Provides a research infrastructure to test and develop recommender algorithms.
Author: Michael Hahsler [aut, cre, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>

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Package PortfolioEffectHFT updated to version 1.4 with previous version 1.3 dated 2015-11-10

Title: High Frequency Portfolio Analytics by PortfolioEffect
Description: R interface to PortfolioEffect cloud service for backtesting high frequency trading (HFT) strategies, intraday portfolio analysis and optimization. Includes auto-calibrating model pipeline for market microstructure noise, risk factors, price jumps/outliers, tail risk (high-order moments) and price fractality (long memory). Constructed portfolios could use client-side market data or access HF intraday price history for all major US Equities. See https://www.portfolioeffect.com/ for more information on the PortfolioEffect high frequency portfolio analytics platform.
Author: Aleksey Zemnitskiy [aut, cre], Andrey Kostin [aut], Oleg Nechaev [aut], Craig Otis and others [ctb, cph] (OpenFAST library), Daniel Lemire, Muraoka Taro and others [ctb, cph] (JavaFastPFOR library), Joe Walnes, Jorg Schaible and others [ctb, cph] (XStream library), Dain Sundstrom [ctb, cph] (Snappy library), Extreme! Lab, Indiana University [ctb, cph] (XPP3 library), The Apache Software Foundation [ctb, cph] (Apache Log4j and Commons Lang libraries), Google, Inc. [ctb, cph] (GSON library), Free Software Foundation [ctb, cph] (GNU Trove and GNU Crypto libraries)
Maintainer: Aleksey Zemnitskiy <aleksey.zemnitskiy@portfolioeffect.com>

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Package pbdMPI updated to version 0.3-0 with previous version 0.2-5 dated 2014-10-05

Title: Programming with Big Data -- Interface to MPI
Description: An efficient interface to MPI by utilizing S4 classes and methods with a focus on Single Program/Multiple Data ('SPMD') parallel programming style, which is intended for batch parallel execution.
Author: Wei-Chen Chen [aut, cre], George Ostrouchov [aut], Drew Schmidt [aut], Pragneshkumar Patel [aut], Hao Yu [aut], Christian Heckendorf [ctb] (FreeBSD), Brian Ripley [ctb] (Windows HPC Pack 2012), R Core team [ctb] (some functions are modified from the base packages)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>

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 pbdMPI-0.3-0/pbdMPI/R/spmd_reduce_obj.r                                  |    8 
 pbdMPI-0.3-0/pbdMPI/R/spmd_scatterv.r                                    |   21 
 pbdMPI-0.3-0/pbdMPI/R/spmd_scatterv_obj.r                                |    6 
 pbdMPI-0.3-0/pbdMPI/R/spmd_send.r                                        |   12 
 pbdMPI-0.3-0/pbdMPI/R/spmd_sendrecv.r                                    |   52 -
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 pbdMPI-0.3-0/pbdMPI/R/spmd_tool.r                                        |   25 
 pbdMPI-0.3-0/pbdMPI/R/spmd_utility.r                                     |   16 
 pbdMPI-0.3-0/pbdMPI/R/spmd_wait.r                                        |    7 
 pbdMPI-0.3-0/pbdMPI/R/windows/zzz.r                                      |    9 
 pbdMPI-0.3-0/pbdMPI/R/zzz.r.in                                           |   16 
 pbdMPI-0.3-0/pbdMPI/README.md                                            |only
 pbdMPI-0.3-0/pbdMPI/demo/00Index                                         |    2 
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 pbdMPI-0.3-0/pbdMPI/demo/pbdLapply.r                                     |    7 
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 pbdMPI-0.3-0/pbdMPI/inst/CITATION                                        |    8 
 pbdMPI-0.3-0/pbdMPI/inst/doc/pbdMPI-guide.Rnw                            |   27 
 pbdMPI-0.3-0/pbdMPI/inst/doc/pbdMPI-guide.pdf                            |binary
 pbdMPI-0.3-0/pbdMPI/inst/examples/test_cs/named.client.r                 |    4 
 pbdMPI-0.3-0/pbdMPI/inst/examples/test_cs/named.server.r                 |    4 
 pbdMPI-0.3-0/pbdMPI/inst/examples/test_cs/simple.client.r                |    4 
 pbdMPI-0.3-0/pbdMPI/inst/examples/test_cs/simple.server.r                |    4 
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 pbdMPI-0.3-0/pbdMPI/inst/examples/test_long_vector/send_recv.r           |    2 
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 pbdMPI-0.3-0/pbdMPI/inst/examples/test_rmpi/allgather_spmd.r             |    2 
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 pbdMPI-0.3-0/pbdMPI/inst/examples/test_rmpi/g