Wed, 16 Feb 2011

Package vegan updated to version 1.17-7 with previous version 1.17-6 dated 2011-01-10

Title: Community Ecology Package
Description: Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Helene Wagner
Maintainer: Jari Oksanen

Diff between vegan versions 1.17-6 dated 2011-01-10 and 1.17-7 dated 2011-02-16

 DESCRIPTION                  |    8 +-
 R/anova.ccabyaxis.R          |   27 +++++++--
 R/anova.ccabyterm.R          |    9 ++-
 R/as.preston.R               |   34 ++++++++---
 R/capscale.R                 |   24 ++++++--
 R/cca.formula.R              |    1 
 R/eigenvals.R                |   36 ++++++++++++
 R/fitted.capscale.R          |   11 ++-
 R/kendall.post.R             |    2 
 R/nestednodf.R               |    3 -
 R/nestedtemp.R               |    8 +-
 R/ordiParseFormula.R         |    7 +-
 R/ordiplot3d.R               |    2 
 R/orditkplot.R               |    8 +-
 R/plot.cascadeKM.R           |    6 --
 R/plot.cca.R                 |    2 
 R/plot.specaccum.R           |   23 ++++---
 R/predict.rda.R              |   10 ++-
 R/prestondistr.R             |    8 +-
 R/prestonfit.R               |   11 ++-
 R/print.MOStest.R            |    2 
 R/rda.formula.R              |    1 
 R/rgl.renyiaccum.R           |    2 
 R/showvarparts.R             |    4 -
 R/simulate.rda.R             |   59 +++++++++++++++++++
 R/specaccum.R                |    2 
 data/BCI.rda                 |binary
 data/dune.env.rda            |binary
 data/dune.rda                |binary
 data/mite.env.rda            |binary
 data/mite.pcnm.rda           |binary
 data/pyrifos.rda             |binary
 data/varechem.rda            |binary
 data/varespec.rda            |binary
 inst/ChangeLog               |   31 ++++++++++
 inst/NEWS                    |   24 ++++++++
 inst/doc/FAQ-vegan.pdf       |binary
 inst/doc/decision-vegan.pdf  |binary
 inst/doc/decision-vegan.tex  |   18 +++---
 inst/doc/diversity-vegan.pdf |binary
 inst/doc/diversity-vegan.tex |   70 +++++++++++------------
 inst/doc/intro-vegan.pdf     |binary
 inst/doc/intro-vegan.tex     |   49 ++++++++--------
 man/anova.cca.Rd             |    4 +
 man/capscale.Rd              |    7 ++
 man/cca.object.Rd            |   27 +++++++--
 man/eigenvals.Rd             |    9 ++-
 man/fisherfit.Rd             |  128 +++++++++++++++++++++++--------------------
 man/simulate.rda.Rd          |   30 ++++++----
 man/specaccum.Rd             |   12 ++--
 50 files changed, 494 insertions(+), 225 deletions(-)

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Package readBrukerFlexData updated to version 1.0.1 with previous version 1.0 dated 2011-02-15

Title: Reads files generated by MALDI-TOF MS of Bruker Daltonics' *flex series
Description: readBrukerFlexData supports direct file import of acqu and fid files generated by MALDI-TOF mass spectrometer of Bruker Daltonics' *flex series; successfully tested for Bruker Daltonics' Autoflex MS
Author: Sebastian Gibb
Maintainer: Sebastian Gibb

Diff between readBrukerFlexData versions 1.0 dated 2011-02-15 and 1.0.1 dated 2011-02-16

 DESCRIPTION                       |   15 ++++++++-------
 NEWS                              |    4 ++++
 R/readBrukerFlexData.R            |   28 ++++++++++++++--------------
 man/double2singlePrecision.Rd     |    2 +-
 man/hpc.Rd                        |   12 +++++-------
 man/readBrukerFlexData.package.Rd |    8 ++++----
 man/readBrukerFlexDir.Rd          |   10 +++++-----
 man/readBrukerFlexFile.Rd         |   30 +++++++++++++++++-------------
 8 files changed, 58 insertions(+), 51 deletions(-)

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Package forecast updated to version 2.13 with previous version 2.12 dated 2011-01-19

Title: Forecasting functions for time series
Description: Methods and tools for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.
Author: Rob J Hyndman
Maintainer: Rob J Hyndman

Diff between forecast versions 2.12 dated 2011-01-19 and 2.13 dated 2011-02-16

 ChangeLog           |    9 ++++++++-
 DESCRIPTION         |    8 ++++----
 NAMESPACE           |   37 ++++++++++++++++++++-----------------
 R/errors.R          |   17 ++++++++++-------
 R/forecast.R        |    7 ++++++-
 R/forecast2.R       |   11 +++++++----
 R/season.R          |   35 +++++++++++++++++++++++++++++++++++
 R/simulate.R        |   14 ++++++++++++++
 man/forecast.stl.Rd |only
 9 files changed, 104 insertions(+), 34 deletions(-)

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New package ggcolpairs with initial version 0.2.3
Package: ggcolpairs
Type: Package
Title: Combination of GGplot2 plots into a matrix based on data columns.
Version: 0.2.3
Date: 2011-2-15
Author: Fernando Fuentes , George Ostrouchov
Maintainer: Fernando Fuentes
Description: The ggcolpairs package allows the creation of a plot matrix based on column parameters from a dataset.
Depends: ggplot2
License: GPL-2
LazyLoad: yes
Packaged: 2011-02-16 06:03:03 UTC; nan
Repository: CRAN
Date/Publication: 2011-02-16 11:36:51

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Package bgmm updated to version 1.2 with previous version 1.1 dated 2011-02-11

Title: Gaussian Mixture Modeling algorithms. Including the belief-based mixture modeling.
Description:
Author: Przemyslaw Biecek \& Ewa Szczurek
Maintainer: Przemyslaw Biecek

Diff between bgmm versions 1.1 dated 2011-02-11 and 1.2 dated 2011-02-16

 DESCRIPTION            |    6 +++---
 R/bgmm.r               |    2 +-
 R/get.simple.beliefs.r |   17 ++++++++++-------
 3 files changed, 14 insertions(+), 11 deletions(-)

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Package RcppArmadillo updated to version 0.2.12 with previous version 0.2.11 dated 2011-01-08

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 (currently version 1.1.20). 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 GNU LGPL version 3 or later, while RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is license under GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Romain Francois, Dirk Eddelbuettel and Doug Bates

Diff between RcppArmadillo versions 0.2.11 dated 2011-01-08 and 0.2.12 dated 2011-02-16

 RcppArmadillo-0.2.11/RcppArmadillo/inst/include/armadillo_bits/syslib_proto.hpp            |only
 RcppArmadillo-0.2.12/RcppArmadillo/ChangeLog                                               |    6 
 RcppArmadillo-0.2.12/RcppArmadillo/DESCRIPTION                                             |   17 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/NEWS                                               |   12 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/doc/RcppArmadillo-unitTests.pdf                    |binary
 RcppArmadillo-0.2.12/RcppArmadillo/inst/doc/unitTests-results/RcppArmadillo-unitTests.html |    6 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/doc/unitTests-results/RcppArmadillo-unitTests.txt  |   30 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/README                                     |    1 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo                                  |   13 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/Base.hpp                    |   15 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/Col_meat.hpp                |   14 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/Col_proto.hpp               |    8 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/Cube_meat.hpp               |    6 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/Mat_meat.hpp                |   20 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/Mat_proto.hpp               |   15 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/Row_meat.hpp                |   14 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/Row_proto.hpp               |    8 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/arma_config.hpp             |   10 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/arma_version.hpp            |    8 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/arrayops_meat.hpp           |only
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/arrayops_proto.hpp          |  448 +---------
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/auxlib_meat.hpp             |   63 -
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/auxlib_proto.hpp            |   10 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/compiler_setup.hpp          |    8 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/config.hpp                  |   20 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/debug.hpp                   |   27 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/fn_conv_to.hpp              |   60 -
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/fn_prod.hpp                 |   40 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/glue_solve_meat.hpp         |   10 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/glue_solve_proto.hpp        |    4 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/injector_meat.hpp           |    6 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/op_dot_meat.hpp             |    2 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/op_prod_meat.hpp            |   29 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/op_reshape_meat.hpp         |    8 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/op_trans_meat.hpp           |    2 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/op_trimat_meat.hpp          |    4 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/podarray_meat.hpp           |    4 
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/subview_cube_meat.hpp       |   50 -
 RcppArmadillo-0.2.12/RcppArmadillo/inst/include/armadillo_bits/subview_meat.hpp            |    8 
 39 files changed, 339 insertions(+), 667 deletions(-)

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