Sun, 14 Oct 2012

Package spatstat updated to version 1.29-0 with previous version 1.28-2 dated 2012-08-23

Title: Spatial Point Pattern analysis, model-fitting, simulation, tests
Description: A package for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, and space-time point patterns in any number of dimensions. Contains over 1000 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 and tessellations. Exploratory methods include K-functions, 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 etc. Point process models can be fitted to point pattern data using functions ppm, kppm, slrm similar to glm. Models may include dependence on covariates, interpoint interaction, cluster formation and dependence on marks. Fitted models can be simulated automatically. Also provides facilities for formal inference (such as chi-squared tests) and model diagnostics (including simulation envelopes, residuals, residual plots and Q-Q plots).
Author: Adrian Baddeley and Rolf Turner with substantial contributions of code by Kasper Klitgaard Berthelsen; Abdollah Jalilian; Marie-Colette van Lieshout; Ege Rubak; Dominic Schuhmacher; and Rasmus Waagepetersen. Additional contributions by Q.W. Ang; S. Azaele; C. Beale; R. Bernhardt; T. Bendtsen; B. Biggerstaff; R. Bivand; F. Bonneu; J. Burgos; S. Byers; Y.M. Chang; J.B. Chen; I. Chernayavsky; Y.C. Chin; B. Christensen; J.-F. Coeurjolly; M. de la Cruz; P. Dalgaard; P.J. Diggle; I. Dryden; S. Eglen; N. Funwi-Gabga; A. Gault; M. Genton; P. Grabarnik; C. Graf; J. Franklin; U. Hahn; A. Hardegen; M. Hering; M.B. Hansen; M. Hazelton; J. Heikkinen; K. Hornik; R. Ihaka; A. Jammalamadaka; R. John-Chandran; D. Johnson; M. Kuhn; J. Laake; F. Lavancier; T. Lawrence; R.A. Lamb; J. Lee; G.P. Leser; H.T. Li; B. Madin; R. Mark; J. Mateu; P. McCullagh; U. Mehlig; S. Meyer; X.C. Mi; J. Moller; E. Mudrak; L.S. Nielsen; F. Nunes; J. Oehlschlaegel; T. Onkelinx; E. Parilov; J. Picka; S. Protsiv; A. Raftery; M. Reiter; T.O. Richardson; B.D. Ripley; B. Rowlingson; J. Rudge; F. Safavimanesh; A. Sarkka; K. Schladitz; B.T. Scott; G.C. Shen; V. Shcherbakov; I.-M. Sintorn; Y. Song; M. Spiess; M. Stevenson; K. Stucki; M. Sumner; P. Surovy; B. Taylor; B. Turlach; A. van Burgel; T. Verbeke; A. Villers; H. Wang; H. Wendrock; J. Wild; S. Wong and M.E. Zamboni.
Maintainer: Adrian Baddeley

Diff between spatstat versions 1.28-2 dated 2012-08-23 and 1.29-0 dated 2012-10-14

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Package bibtex updated to version 0.3-3 with previous version 0.3-2 dated 2012-09-13

Title: bibtex parser
Description: Utility to parse a bibtex file
Author: Romain Francois
Maintainer: Kurt Hornik

Diff between bibtex versions 0.3-2 dated 2012-09-13 and 0.3-3 dated 2012-10-14

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Package Rcpp updated to version 0.9.15 with previous version 0.9.14 dated 2012-10-01

Title: Seamless R and C++ Integration
Description: The Rcpp package provides R functions as well as a C++ library which facilitate the integration of R and C++. R data types (SEXP) are matched to C++ objects in a class hierarchy. All R types are supported (vectors, functions, environment, etc ...) and each type is mapped to a dedicated class. For example, numeric vectors are represented as instances of the Rcpp::NumericVector class, environments are represented as instances of Rcpp::Environment, functions are represented as Rcpp::Function, etc ... The "Rcpp-introduction" vignette provides a good entry point to Rcpp. Conversion from C++ to R and back is driven by the templates Rcpp::wrap and Rcpp::as which are highly flexible and extensible, as documented in the "Rcpp-extending" vignette. Rcpp also provides Rcpp modules, a framework that allows exposing C++ functions and classes to the R level. The "Rcpp-modules" vignette details the current set of features of Rcpp-modules. Rcpp includes a concept called Rcpp sugar that brings many R functions into C++. Sugar takes advantage of lazy evaluation and expression templates to achieve great performance while exposing a syntax that is much nicer to use than the equivalent low-level loop code. The "Rcpp-sugar" vignette gives an overview of the feature. Several examples are included, and over 800 unit tests in over 360 unit test functions provide additional usage examples. An earlier version of Rcpp, containing what we now call the 'classic Rcpp API' was written during 2005 and 2006 by Dominick Samperi. This code has been factored out of Rcpp into the package RcppClassic, and it is still available for code relying on the older interface. New development should always use this Rcpp package instead.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel

Diff between Rcpp versions 0.9.14 dated 2012-10-01 and 0.9.15 dated 2012-10-14

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New package rebird with initial version 0.1
Package: rebird
Version: 0.1
Date: 2012-1-28
Description: A programmatic interface to the eBird database
Title: Interface to eBird
License: BSD
Author: Rafael Maia, Scott Chamberlain
Maintainer: Rafael Maia
URL: https://github.com/ropensci/rebird
Depends: RJSONIO, RCurl, plyr
Collate: 'notable.R' 'ebirdgeo.R' 'ebirdhotspot.R' 'ebirdloc.R' 'ebirdregion.R' 'nearestobs.R' 'rebird-package.R'
Packaged: 2012-10-14 02:06:22 UTC; rmaia
Repository: CRAN
Date/Publication: 2012-10-14 06:49:30

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Package Rcmdr updated to version 1.9-2 with previous version 1.9-1 dated 2012-09-18

Title: R Commander
Description: A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre], Liviu Andronic [ctb], Michael Ash [ctb], Milan Bouchet-Valat [ctb], Theophilius Boye [ctb], Stefano Calza [ctb], Andy Chang [ctb], Philippe Grosjean [ctb], Richard Heiberger [ctb], Kosar Karimi Pour [ctb], G. Jay Kerns [ctb], Renaud Lancelot [ctb], Matthieu Lesnoff [ctb], Uwe Ligges [ctb], Samir Messad [ctb], Martin Maechler [ctb], Robert Muenchen [ctb], Duncan Murdoch [ctb], Erich Neuwirth [ctb], Dan Putler [ctb], Brian Ripley [ctb], Miroslav Ristic [ctb], Peter Wolf [ctb]
Maintainer: John Fox

Diff between Rcmdr versions 1.9-1 dated 2012-09-18 and 1.9-2 dated 2012-10-14

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Package numDeriv updated to version 2012.9-1 with previous version 2012.3-1 dated 2012-03-27

Title: Accurate Numerical Derivatives
Description: This package provide methods for calculating (usually) accurate numerical first and second order derivatives. Accurate calculations are done using Richardson's extrapolation or, when applicable, a complex step derivative is available. A simple difference method is also provided. Simple difference is (usually) less accurate but is much quicker than Richardson's extrapolation and provides a useful cross-check. Methods are provided for real scalar and vector valued functions.
Author: Paul Gilbert and Ravi Varadhan
Maintainer: Paul Gilbert

Diff between numDeriv versions 2012.3-1 dated 2012-03-27 and 2012.9-1 dated 2012-10-14

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New package lda with initial version 1.3.2
Package: lda
Type: Package
Title: Collapsed Gibbs sampling methods for topic models.
Version: 1.3.2
Date: 2012-05-22
Author: Jonathan Chang
Maintainer: Jonathan Chang
Description: This package implements latent Dirichlet allocation (LDA) and related models. This includes (but is not limited to) sLDA, corrLDA, and the mixed-membership stochastic blockmodel. Inference for all of these models is implemented via a fast collapsed Gibbs sampler writtten in C. Utility functions for reading/writing data typically used in topic models, as well as tools for examining posterior distributions are also included.
License: LGPL
LazyLoad: yes
Suggests: Matrix, reshape2, ggplot2 (>= 0.9.1), penalized
Packaged: 2012-10-14 02:29:36 UTC; jonchang
Depends: R (>= 2.10)
Repository: CRAN
Date/Publication: 2012-10-14 06:49:32

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Package gMCP updated to version 0.8-0 with previous version 0.7-12 dated 2012-08-02

Title: Graph Based Multiple Comparison Procedures
Description: This package provides functions and a graphical user interface for graphical described multiple test procedures.
Author: Kornelius Rohmeyer, Florian Klinglmueller (parametric tests, adaptive designs), Bjoern Bornkamp (power simulations)
Maintainer: Kornelius Rohmeyer

Diff between gMCP versions 0.7-12 dated 2012-08-02 and 0.8-0 dated 2012-10-14

 DESCRIPTION                                                                |    6 
 MD5                                                                        |  165 +-
 NAMESPACE                                                                  |    9 
 NEWS                                                                       |   40 
 R/analysis.R                                                               |    3 
 R/calcPower.R                                                              |    3 
 R/convertFromOldClassDefinition.R                                          |    3 
 R/doRUnitTests.R                                                           |   37 
 R/exampleGraphs.R                                                          |  133 +
 R/gMCP.R                                                                   |   36 
 R/graph2latex.R                                                            |   51 
 R/graphMCP.R                                                               |   57 
 R/graphTest.R                                                              |    8 
 R/helperGUI.R                                                              |   15 
 R/matrix2graph.R                                                           |   12 
 R/misc.R                                                                   |   10 
 R/onLoad.R                                                                 |   36 
 R/rqmvnorm.R                                                               |    9 
 R/subVariables.R                                                           |   27 
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 inst/java-src/org/af/gMCP/gui/ReproducableLog.java                         |    9 
 inst/java-src/org/af/gMCP/gui/datatable/CellEditorE.java                   |   10 
 inst/java-src/org/af/gMCP/gui/datatable/CloseTabPanel.java                 |only
 inst/java-src/org/af/gMCP/gui/datatable/DataFramePanel.java                |   89 +
 inst/java-src/org/af/gMCP/gui/datatable/DataTable.java                     |   12 
 inst/java-src/org/af/gMCP/gui/datatable/RDataFrameRef.java                 |    4 
 inst/java-src/org/af/gMCP/gui/datatable/SingleDataFramePanel.java          |only
 inst/java-src/org/af/gMCP/gui/dialogs/GraphSendToArchiveDialog.java        |    2 
 inst/java-src/org/af/gMCP/gui/dialogs/MatrixCreationDialog.java            |   18 
 inst/java-src/org/af/gMCP/gui/dialogs/ParameterDialog.java                 |   61 
 inst/java-src/org/af/gMCP/gui/dialogs/PowerDialogParameterUncertainty.java |  680 ++++++----
 inst/java-src/org/af/gMCP/gui/dialogs/PowersettingsToXML.java              |only
 inst/java-src/org/af/gMCP/gui/dialogs/TextFileViewer.java                  |    7 
 inst/java-src/org/af/gMCP/gui/graph/DView.java                             |    2 
 inst/java-src/org/af/gMCP/gui/graph/Edge.java                              |  120 -
 inst/java-src/org/af/gMCP/gui/graph/GraphMCP.java                          |  152 +-
 inst/java-src/org/af/gMCP/gui/graph/GraphPanel.java                        |only
 inst/java-src/org/af/gMCP/gui/graph/GraphView.java                         |   89 -
 inst/java-src/org/af/gMCP/gui/graph/LaTeXTool.java                         |only
 inst/java-src/org/af/gMCP/gui/graph/NetList.java                           |  341 +++--
 inst/java-src/org/af/gMCP/gui/graph/NetListPopUpMenu.java                  |    7 
 inst/java-src/org/af/gMCP/gui/graph/NetListSelectionPopUpMenu.java         |only
 inst/java-src/org/af/gMCP/gui/graph/Node.java                              |  261 ++-
 inst/java-src/org/af/gMCP/gui/graph/NodeListener.java                      |    6 
 inst/java-src/org/af/gMCP/gui/graph/PPanel.java                            |  186 +-
 inst/java-src/org/af/gMCP/gui/graph/PView.java                             |  557 ++++----
 inst/java-src/org/af/gMCP/gui/graph/Physics.java                           |only
 inst/java-src/org/af/gMCP/gui/graph/PrintableObject.java                   |    6 
 inst/java-src/org/af/gMCP/gui/graph/SubFamily.java                         |only
 inst/java-src/org/af/gMCP/gui/graph/UpdateEdge.java                        |    4 
 inst/java-src/org/af/gMCP/gui/graph/UpdateNode.java                        |   48 
 inst/java-src/org/af/gMCP/gui/graph/annotations                            |only
 inst/java-src/org/af/gMCP/gui/options/GeneralPanel.java                    |   56 
 inst/java-src/org/af/gMCP/gui/options/MiscPanel.java                       |   18 
 inst/java-src/org/af/gMCP/gui/options/NumericPanel.java                    |   31 
 inst/java-src/org/af/gMCP/gui/options/OptionsDialog.java                   |    5 
 inst/java-src/org/af/gMCP/gui/pdf                                          |only
 inst/java-src/tests/InteractionTest.java                                   |    7 
 inst/java-src/tests/LoadSaveTest.java                                      |   25 
 inst/java-src/tests/PPanelTest.java                                        |    4 
 inst/java-src/tests/TestSuite.java                                         |   11 
 inst/java/afcommons.jar                                                    |binary
 inst/java/gsrmtp.jar                                                       |binary
 inst/unitTests/runit.entangled.R                                           |only
 inst/unitTests/runit.power.R                                               |   16 
 man/calcPower.Rd                                                           |    2 
 man/entangled.Rd                                                           |only
 man/exampleGraphs.Rd                                                       |   21 
 man/graphGUI.Rd                                                            |   16 
 man/graphMCP.Rd                                                            |    3 
 man/graphTest.Rd                                                           |    6 
 man/placeNodes.Rd                                                          |    8 
 man/replaceVariables.Rd                                                    |    4 
 man/rqmvnorm.Rd                                                            |    3 
 man/substituteEps.Rd                                                       |    4 
 src/gMCP.c                                                                 |    4 
 src/mcp.c                                                                  |  254 +--
 86 files changed, 3005 insertions(+), 1600 deletions(-)

More information about gMCP at CRAN
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Package cluster updated to version 1.14.3 with previous version 1.14.2 dated 2012-02-08

Title: Cluster Analysis Extended Rousseeuw et al.
Description: Cluster Analysis, extended original from Peter Rousseeuw, Anja Struyf and Mia Hubert.
Author: Martin Maechler, based on S original by Peter Rousseeuw , Anja.Struyf@uia.ua.ac.be and Mia.Hubert@uia.ua.ac.be, and initial R port by Kurt.Hornik@R-project.org
Maintainer: Martin Maechler

Diff between cluster versions 1.14.2 dated 2012-02-08 and 1.14.3 dated 2012-10-14

 DESCRIPTION                              |   12 ++++---
 MD5                                      |   32 +++++++++---------
 R/0aaa.R                                 |    6 +++
 R/clara.q                                |    2 -
 R/clusGap.R                              |    6 ++-
 R/daisy.q                                |    6 ++-
 R/mona.q                                 |    2 -
 inst/po/de/LC_MESSAGES/R-cluster.mo      |binary
 inst/po/en@quot/LC_MESSAGES/R-cluster.mo |binary
 inst/po/pl                               |only
 man/clusGap.Rd                           |   41 ++++++++++++++---------
 po/R-cluster.pot                         |   35 ++++++--------------
 po/R-de.po                               |   53 +++++++++++++++++--------------
 po/R-en@quot.po                          |   43 ++++++++-----------------
 po/R-pl.po                               |only
 po/update-me.sh                          |    3 +
 tests/clara-NAs.Rout.save                |    9 +++--
 tests/mona.Rout.save                     |   24 ++++++++------
 18 files changed, 143 insertions(+), 131 deletions(-)

More information about cluster at CRAN
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New package enaR with initial version 1.01
Package: enaR
Type: Package
Title: Tools ecological network analysis (ena)
Version: 1.01
Date: 2012-10-10
Author: M.K. Lau, S.R. Borrett, D.E. Hines
Maintainer: Matthew K. Lau
Description: Functions for the analysis of ecological networks
Depends: statnet, MASS, stringr, xlsx
License: GPL-2
Packaged: 2012-10-12 23:38:42 UTC; Aeolus
Repository: CRAN
Date/Publication: 2012-10-14 06:15:54

More information about enaR at CRAN
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