Mon, 22 Sep 2014

Package secr updated to version 2.9.0 with previous version 2.8.2 dated 2014-04-30

Title: Spatially explicit capture-recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford

Diff between secr versions 2.8.2 dated 2014-04-30 and 2.9.0 dated 2014-09-22

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 secr-2.9.0/secr/NAMESPACE                           |   29 +
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 secr-2.9.0/secr/R/DENSITY.R                         |   22 -
 secr-2.9.0/secr/R/Dsurface.R                        |   14 
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 117 files changed, 2871 insertions(+), 1528 deletions(-)

More information about secr at CRAN
Permanent link

Package testthat updated to version 0.9 with previous version 0.8.1 dated 2014-02-21

Title: Testthat code. Tools to make testing fun :)
Description: A testing package specifically tailored for R that's fun, flexible and easy to set up.
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham

Diff between testthat versions 0.8.1 dated 2014-02-21 and 0.9 dated 2014-09-22

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More information about testthat at CRAN
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New package pingr with initial version 1.0.0
Package: pingr
Title: Check If a Remote Computer is Up
Version: 1.0.0
Authors@R: "Gabor Csardi [aut,cre]"
Description: Check if a remote computer is up. It can either just call the system ping command, or check a specified TCP port.
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/gaborcsardi/pingr
BugReports: https://github.com/gaborcsardi/pingr/issues
Suggests: testthat
Packaged: 2014-09-22 18:46:33 UTC; gaborcsardi
Author: "Gabor Csardi" [aut, cre]
Maintainer: "Gabor Csardi"
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-09-22 21:26:59

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New package mpath with initial version 0.1-14
Package: mpath
Title: Regularized Linear Models
Version: 0.1-14
Author: Zhu Wang, with contributions from Achim Zeileis, Simon Jackman, Brian Ripley, Trevor Hastie, Rob Tibshirani, Balasubramanian Narasimhan, Gil Chu and Patrick Breheny
Maintainer: Zhu Wang
Description: Algorithms for fitting model-based penalized coefficient paths. Currently the models include penalized Poisson, negative binomial, zero-inflated Poisson and zero-inflated negative binomial regression models. The penalties include least absolute shrinkage and selection operator (LASSO), smoothly clipped absolute deviation (SCAD) and minimax concave penalty (MCP), and each possibly combining with L_2 penalty.
Imports: MASS,glmnet,pscl,numDeriv
Depends: methods
License: GPL-2
Packaged: 2014-09-22 17:32:25.925 UTC; zhu
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-09-22 21:27:03

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Package sglasso updated to version 1.1-0 with previous version 1.0-1 dated 2014-06-17

Title: Lasso method for RCON(V,E) models
Description: RCON(V, E) models (Højsgaard, et al.,2008) are a kind of restriction of the Gaussian Graphical Models defined by a set of equality constraints on the entries of the concentration matrix. sglasso package implements the structured graphical lasso (sglasso) estimator proposed in Abbruzzo et al. (2014) for the weighted l1-penalized RCON(V, E) model. Two cyclic coordinate algorithms are implemented to compute the sglasso estimator, i.e., a cyclic coordinate minimization (CCM) algorithm and a cyclic coordinate descent (CCD) algorithm.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro

Diff between sglasso versions 1.0-1 dated 2014-06-17 and 1.1-0 dated 2014-09-22

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New package GENLIB with initial version 1.0
Package: GENLIB
Type: Package
Title: Genealogical Data Analysis
Version: 1.0
Date: 2012-04-04
Authors@R: c( person("Louis", "Houde", role="aut"), person("Jean-Francois", "Lefebvre", role="aut", email="mroygagn@uottawa.ca"), person("Valery", "Roy-Lagace", role="aut"), person("Sebastien", "Lemieux", role="aut"), person("Michael J.", "Fromberger", role="ctb"), person("Marie-Helene", "Roy-Gagnon", role="cre", email="jf_lef@yahoo.ca"))
Description: Genealogical data analysis including descriptive statistics (e.g., kinship and inbreeding coefficients) and gene-dropping simulations.
License: GPL (>= 2)
LazyLoad: yes
Depends: R (>= 3.0), Rcpp (>= 0.9.10)
Imports: kinship2, methods, bootstrap, Matrix, lattice, quadprog, foreach, parallel, doParallel
LinkingTo: Rcpp
Packaged: 2014-09-22 14:22:08 UTC; sainte-justine\lefjea01
Author: Louis Houde [aut], Jean-Francois Lefebvre [aut], Valery Roy-Lagace [aut], Sebastien Lemieux [aut], Michael J. Fromberger [ctb], Marie-Helene Roy-Gagnon [cre]
Maintainer: Marie-Helene Roy-Gagnon
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-09-22 18:46:51

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New package documair with initial version 0.6-0
Package: documair
Version: 0.6-0
Date: 2014-09-06
Type: Package
Title: Automatic Documentation for R packages
Author: Jean-Baptiste Denis , Regis Pouillot , Kien Kieu
Maintainer: Jean-Baptiste Denis
Description: Production of R packages from tagged comments introduced within the code and a minimum of additional documentation files.
License: GPL (>= 2.15)
Packaged: 2014-09-17 09:35:38 UTC; rforge
Repository: CRAN
Repository/R-Forge/Project: riskassessment
Repository/R-Forge/Revision: 283
Repository/R-Forge/DateTimeStamp: 2014-09-17 09:16:39
Date/Publication: 2014-09-22 17:22:20
NeedsCompilation: yes

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Package proxy updated to version 0.4-13 with previous version 0.4-12 dated 2014-01-15

Title: Distance and Similarity Measures
Description: Provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.
Author: David Meyer [aut, cre], Christian Buchta [aut]
Maintainer: David Meyer

Diff between proxy versions 0.4-12 dated 2014-01-15 and 0.4-13 dated 2014-09-22

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Package predictmeans updated to version 0.99 with previous version 0.98 dated 2014-09-03

Title: Calculate Predicted Means for Linear Models
Description: This package provides functions to diagnose and make inferences from various linear models, such as those obtained from 'aov', 'lm', 'glm', 'gls', 'lme', and 'lmer'. Inferences include predicted means and standard errors, contrasts, multiple comparisons, permutation tests and graphs.
Author: Dongwen Luo, Siva Ganesh and John Koolaard
Maintainer: Dongwen Luo

Diff between predictmeans versions 0.98 dated 2014-09-03 and 0.99 dated 2014-09-22

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Package flexsurv updated to version 0.5 with previous version 0.3 dated 2014-01-20

Title: Flexible parametric survival and multi-state models
Description: Flexible parametric models for time-to-event data, including the Royston-Parmar spline model, generalized gamma and generalized F distributions. Any user-defined parametric distribution can be fitted, given at least an R function defining the probability density or hazard. There are also tools for fitting and predicting from fully parametric multi-state models.
Author: Christopher Jackson
Maintainer: Christopher Jackson

Diff between flexsurv versions 0.3 dated 2014-01-20 and 0.5 dated 2014-09-22

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New package fAssets with initial version 3011.82
Package: fAssets
Title: Rmetrics - Analysing and Modelling Financial Assets
Date: 2014-09-17
Version: 3011.82
Author: Rmetrics Core Team, Diethelm Wuertz [aut], Tobias Setz [cre] Yohan Chalabi [ctb]
Maintainer: Tobias Setz
Description: Environment for teaching "Financial Engineering and Computational Finance".
Depends: R (>= 2.15.1), timeDate, timeSeries, fBasics
Imports: fMultivar, robustbase, MASS, sn
Suggests: methods, mnormt, ecodist, mvnormtest, energy, RUnit
Note: SEVERAL PARTS ARE STILL PRELIMINARY AND MAY BE CHANGED IN THE FUTURE. THIS TYPICALLY INCLUDES FUNCTION AND ARGUMENT NAMES, AS WELL AS DEFAULTS FOR ARGUMENTS AND RETURN VALUES.
LazyData: yes
License: GPL (>= 2)
URL: https://www.rmetrics.org
Packaged: 2014-09-22 10:28:15 UTC; Tobi
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-22 14:10:47

More information about fAssets at CRAN
Permanent link

Package dendextend updated to version 0.17.5 with previous version 0.17.1 dated 2014-08-19

Title: Extending R's dendrogram functionality
Description: The dendextend package offers a set of functions for extending dendrogram objects in R, letting you visualize and compare trees of hierarchical clusterings. You can (1) Adjust a trees graphical parameters - the color, size, type, etc of its branches, nodes and labels. (2) Visually and statistically compare different dendrograms to one another.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com), Gavin Simpson [ctb], Gregory Jefferis [ctb] (imported code from his dendroextras package), Marco Gallotta [ctb] (a.k.a: marcog), Johan Renaudie [ctb] (https://github.com/plannapus), The R Core Team [ctb] (Thanks for the Infastructure, and code in the examples), Kurt Hornik [ctb], Uwe Ligges [ctb], Andrej-Nikolai Spiess [ctb], Steve Horvath [ctb], Peter Langfelder [ctb], skullkey [ctb], Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram), Yoav Benjamini [ths]
Maintainer: Tal Galili

Diff between dendextend versions 0.17.1 dated 2014-08-19 and 0.17.5 dated 2014-09-22

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Package rpf updated to version 0.39 with previous version 0.38 dated 2014-09-04

Title: Response Probability Functions
Description: The purpose of this package is to factor out logic and math common to Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as core support code suitable for more specialized IRT packages to build upon. Complete access to optimized C functions are made available with R_RegisterCCallable.
Author: Joshua Pritikin [cre, aut], Jonathan Weeks [ctb], Li Cai [ctb], Carrie Houts [ctb], Phil Chalmers [ctb]
Maintainer: Joshua Pritikin

Diff between rpf versions 0.38 dated 2014-09-04 and 0.39 dated 2014-09-22

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Package RcppArmadillo updated to version 0.4.450.1.0 with previous version 0.4.400.0 dated 2014-08-19

Title: Rcpp Integration for Armadillo Templated Linear Algebra Library
Description: R and Armadillo integration using Rcpp Armadillo is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. A delayed evaluation approach is employed (during compile time) to combine several operations into one, and to reduce (or eliminate) the need for temporaries. This is accomplished through recursive templates and template meta-programming. This library is useful if C++ has been decided as the language of choice (due to speed and/or integration capabilities), rather than another language. The RcppArmadillo package includes the header files from the templated Armadillo library. Thus users do not need to install Armadillo itself in order to use RcppArmadillo. This Armadillo integration provides a nice illustration of the capabilities of the Rcpp package for seamless R and C++ integration. Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel

Diff between RcppArmadillo versions 0.4.400.0 dated 2014-08-19 and 0.4.450.1.0 dated 2014-09-22

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Package RandomFields updated to version 3.0.42 with previous version 3.0.35 dated 2014-08-12

Title: Simulation and Analysis of Random Fields
Description: Simulation of Gaussian and extreme value random fields; conditional simulation; kriging; maximum likelihood estimation
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Peter Menck [aut], Sebastian Gross [aut], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather

Diff between RandomFields versions 3.0.35 dated 2014-08-12 and 3.0.42 dated 2014-09-22

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Package polysat updated to version 1.3-3 with previous version 1.3-2 dated 2013-09-06

Title: Tools for Polyploid Microsatellite Analysis
Description: polysat is a collection of tools to handle microsatellite data of any ploidy (and samples of mixed ploidy) where allele copy number is not known in partially heterozygous genotypes. It can import and export data in ABI GeneMapper, Structure, ATetra, Tetrasat/Tetra, GenoDive, SPAGeDi, POPDIST, STRand, and binary presence/absence formats. It can calculate pairwise distances between individuals using a stepwise mutation model or infinite alleles model, with or without taking ploidies and allele frequencies into account. These distances can be used for the calculation of clonal diversity statistics or used for further analysis in R. Allelic diversity statistics are also available. polysat can assist the user in estimating the ploidy of samples, and lastly it can estimate allele frequencies in populations, calculate pairwise Fst values based on those frequencies, and export allele frequencies to SPAGeDi and adegenet.
Author: Lindsay V. Clark
Maintainer: "Lindsay V. Clark"

Diff between polysat versions 1.3-2 dated 2013-09-06 and 1.3-3 dated 2014-09-22

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New package mpmi with initial version 0.41
Package: mpmi
Type: Package
Title: Mixed-pair mutual information estimators
Version: 0.41
Date: 2014-22-09
Author: Chris Pardy
Maintainer: Chris Pardy
Description: Uses a kernel smoothing approach to calculate Mutual Information for comparisons between all types of variables including continuous vs continuous, continuous vs discrete and discrete vs discrete. Uses a nonparametric bias correction giving Bias Corrected Mutual Information (BCMI). Implemented efficiently in Fortran 95 with OpenMP and suited to large genomic datasets.
License: GPL-3
URL: http://r-forge.r-project.org/projects/mpmi/
Depends: KernSmooth
Packaged: 2014-09-22 03:35:34 UTC; cp
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-09-22 07:59:19

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Package maps updated to version 2.3-9 with previous version 2.3-7 dated 2014-06-03

Title: Draw Geographical Maps
Description: Display of maps. Projection code and larger maps are in separate packages (mapproj and mapdata).
Author: Original S code by Richard A. Becker and Allan R. Wilks. R version by Ray Brownrigg . Enhancements by Thomas P Minka
Maintainer: Ray Brownrigg

Diff between maps versions 2.3-7 dated 2014-06-03 and 2.3-9 dated 2014-09-22

 DESCRIPTION           |    8 ++++----
 MD5                   |    6 +++---
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 4 files changed, 14 insertions(+), 14 deletions(-)

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Permanent link

New package IBrokers with initial version 0.9-12
Package: IBrokers
Type: Package
Title: R API to Interactive Brokers Trader Workstation
Version: 0.9-12
Date: 2014-09-22
Depends: xts, zoo
Author: Jeffrey A. Ryan
Maintainer: Joshua M. Ulrich
Description: Provides native R access to Interactive Brokers Trader Workstation API.
License: GPL-3
Packaged: 2014-09-22 02:44:36 UTC; josh
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-22 07:59:21

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Package DescTools updated to version 0.99.8.1 with previous version 0.99.8 dated 2014-09-20

Title: Tools for descriptive statistics
Description: DescTools contains a bunch of basic statistic functions and convenience wrappers for efficiently describing data, creating specific plots, doing reports using MS Word, Excel or PowerPoint. The package's intention is to offer a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell. Includes R source code and/or documentation previously published by (in alphabetical order): Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian Baddeley, Ben Bolker, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne Chhay, Michael Dewey, Harold C. Doran, Stephane Dray, Charles Dupont, Jeff Enos, Claus Ekstrom, Martin Elff, John Fox, Tal Galili, Matthias Gamer, Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E. Harrell Jr, Michael Hoehle, Christian W. Hoffmann, Markus Huerzeler, Wallace W. Hui, Rob J. Hyndman, Pablo J. Villacorta Iglesias, Matthias Kohl, Mikko Korpela, Detlew Labes, Friederich Leisch, Jim Lemon, Martin Maechler, Arni Magnusson, Daniel Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao, Yongyi Min, Markus Naepflin, Daniel Navarro, Klaus Nordhausen, Derek Ogle, Nick Parsons, Sandrine Pavoine, Roland Rapold, William Revelle, Tyler Rinker, Caroline Rodriguez, Venkatraman E. Seshan, Greg Snow, Michael Smithson, Werner A. Stahel, Yves Tille, Adrian Trapletti, Kevin Ushey, Jeremy VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Peter Wolf, Daniel Wollschlaeger, Achim Zeileis
Maintainer: Andri Signorell

Diff between DescTools versions 0.99.8 dated 2014-09-20 and 0.99.8.1 dated 2014-09-22

 DESCRIPTION                     |    9 -
 MD5                             |   12 -
 R/DescTools-internal.R          |  250 ++++++++++++++++++++--------------------
 inst/doc/DescTools.pdf          |binary
 inst/doc/DescToolsCompanion.pdf |binary
 man/DescTools-package.Rd        |   12 -
 src/pointinpolygon.c            |    2 
 7 files changed, 143 insertions(+), 142 deletions(-)

More information about DescTools at CRAN
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