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

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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

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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

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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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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>

Diff between prodlim versions 1.5.5 dated 2015-10-05 and 1.5.7 dated 2015-12-19

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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

 DESCRIPTION |    8 ++++----
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 3 files changed, 14 insertions(+), 8 deletions(-)

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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

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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>

Diff between gets versions 0.3 dated 2015-11-26 and 0.4 dated 2015-12-19

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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>

Diff between dynsim versions 1.2 dated 2015-07-24 and 1.2.1 dated 2015-12-19

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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>

Diff between seriation versions 1.1-2 dated 2015-08-23 and 1.1-3 dated 2015-12-19

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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>

Diff between R.rsp versions 0.20.0 dated 2015-02-19 and 0.21.0 dated 2015-12-19

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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>

Diff between raster versions 2.4-30 dated 2015-12-10 and 2.5-2 dated 2015-12-19

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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>

Diff between QCA versions 1.1-4 dated 2014-12-28 and 2.0 dated 2015-12-19

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 39 files changed, 30 insertions(+), 284 deletions(-)

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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

More information about plspm.formula at CRAN
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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>

Diff between FWDselect versions 2.0.1 dated 2015-10-11 and 2.1.0 dated 2015-12-19

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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>

Diff between cowplot versions 0.5.0 dated 2015-07-01 and 0.6.0 dated 2015-12-19

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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>

Diff between aqp versions 1.9.2 dated 2015-12-04 and 1.9.3 dated 2015-12-19

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More information about aqp at CRAN
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