Wed, 03 Jun 2009

Package primer updated to version 0.2 with previous version 0.1 dated 2009-03-27

Author: M Henry H Stevens
Title: Functions and data for the forthcoming, A Primer of Ecology with R
Description: Functions are primarily functions for systems of ordinary differential equations, difference equations, and eigenanalysis and projection of demographic matrices; data are for examples.

Diff between primer versions 0.1 dated 2009-03-27 and 0.2 dated 2009-06-03

 primer-0.1/primer/R/myQ.R               |only
 primer-0.1/primer/man/myQ.Rd            |only
 primer-0.2/primer/DESCRIPTION           |    8 ++++----
 primer-0.2/primer/R/chesson.R           |only
 primer-0.2/primer/man/BSsucc.Rd         |   11 ++++++-----
 primer-0.2/primer/man/CandG.Rd          |    8 +++++---
 primer-0.2/primer/man/ClostExp.Rd       |    8 +++++---
 primer-0.2/primer/man/DemoBoot.Rd       |   13 +++++++------
 primer-0.2/primer/man/DemoInfo.Rd       |    8 ++++----
 primer-0.2/primer/man/MetaSim.Rd        |   18 ++++++++++++------
 primer-0.2/primer/man/PopSim.Rd         |    2 +-
 primer-0.2/primer/man/ProjMat.Rd        |    8 ++++----
 primer-0.2/primer/man/SIR.Rd            |   10 ++++++----
 primer-0.2/primer/man/SIRbd.Rd          |   15 ++++++++++-----
 primer-0.2/primer/man/SIRf.Rd           |   11 +++++++----
 primer-0.2/primer/man/chesson.Rd        |only
 primer-0.2/primer/man/clogistic.Rd      |   22 +++++++++++++++++-----
 primer-0.2/primer/man/compcol.Rd        |   12 +++++++-----
 primer-0.2/primer/man/compcolM.Rd       |   11 +++++++----
 primer-0.2/primer/man/dlogistic.Rd      |    4 ++--
 primer-0.2/primer/man/dlvcomp2.Rd       |   11 +++++++----
 primer-0.2/primer/man/fruitdat.Rd       |    8 +++++---
 primer-0.2/primer/man/gotelli.Rd        |   16 ++++++++--------
 primer-0.2/primer/man/hanski.Rd         |    9 +++++----
 primer-0.2/primer/man/igp.Rd            |   10 ++++++----
 primer-0.2/primer/man/lande.Rd          |   10 +++++-----
 primer-0.2/primer/man/levins.Rd         |   12 ++++--------
 primer-0.2/primer/man/lvcomp2.Rd        |    7 +++----
 primer-0.2/primer/man/lvcomp3.Rd        |    6 +++---
 primer-0.2/primer/man/lvcompg.Rd        |   10 +++++-----
 primer-0.2/primer/man/pimmlawton.Rd     |   31 +++++++++++++++++++------------
 primer-0.2/primer/man/predpreyLV.Rd     |    6 +++---
 primer-0.2/primer/man/predpreyRM.Rd     |   12 ++++++++----
 primer-0.2/primer/man/primer-package.Rd |    7 ++++---
 primer-0.2/primer/man/ross.Rd           |    6 ++++--
 primer-0.2/primer/man/scheffer.Rd       |   13 +++++++++----
 primer-0.2/primer/man/seeddat.Rd        |    9 ++++++---
 primer-0.2/primer/man/sparrows.Rd       |    6 +++---
 primer-0.2/primer/man/stagedat.Rd       |    4 ++--
 primer-0.2/primer/man/succniche.Rd      |   13 ++++++++-----
 primer-0.2/primer/man/thetalogistic.Rd  |    6 ++++--
 primer-0.2/primer/man/weeds.Rd          |   17 ++++++++++-------
 42 files changed, 235 insertions(+), 163 deletions(-)

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Package BCE updated to version 1.3 with previous version 1.1 dated 2008-05-08

Author: Karel Van den Meersche , Karline Soetaert
Title: Bayesian composition estimator: estimating sample (taxonomic) composition from biomarker data
Description: Function to estimates taxonomic compositions from biomarker data, using a Bayesian approach.

Diff between BCE versions 1.1 dated 2008-05-08 and 1.3 dated 2009-06-03

 DESCRIPTION       |   27 +++++++++++++++++----------
 NAMESPACE         |    2 +-
 R/BCE.r           |   19 +++++++++++--------
 R/tlsce.r         |only
 man/BCE.Rd        |   29 +++++++++++++++++------------
 man/export.bce.Rd |    2 +-
 man/pairs.bce.Rd  |    6 +++---
 man/tlsce.Rd      |only
 8 files changed, 50 insertions(+), 35 deletions(-)

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New package tnet with initial version 0.0.6
Type: Package
Package: tnet
Version: 0.0.6
Date: 2009-06-01
Title: Analysis of weighted and longitudinal networks
Author: Tore Opsahl
Maintainer: Tore Opsahl
Depends: R (>= 2.7.0), graph, RBGL
Suggests: network, sna
Description: R package to analyse weighted and longitudinal networks.
License: file LICENSE
Packaged: 2009-06-02 23:02:47 UTC; Tore Opsahl
Repository: CRAN
Date/Publication: 2009-06-03 17:31:37

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New package oblique.tree with initial version 1.0
Package: oblique.tree
Type: Package
Title: Oblique Trees for Classification Data
Version: 1.0
Date: 2009-03-17
Author: Alfred Truong
Maintainer: Alfred Truong
Description: Grows Oblique Trees to Classification Data.
License: GPL-3
Depends: tree
Imports: nnet, glmnet
Packaged: Wed Jun 3 01:00:53 2009; Alfred
Repository: CRAN
Date/Publication: 2009-06-03 17:31:33

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New package cmm with initial version 0.1
Package: cmm
Type: Package
Title: Categorical Marginal Models
Version: 0.1
Date: 2009-05-26
Author: Wicher Bergsma and Andries van der Ark
Maintainer: Wicher Bergsma
Description: Quite extensive package for the estimation of marginal models for categorical data.
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2009-06-03 08:23:19 UTC; a
Repository: CRAN
Date/Publication: 2009-06-03 17:31:22

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New package countrycode with initial version 0.1
Package: countrycode
Type: Package
Title: Converts country names and coding schemes
Version: 0.1
Date: 2009-05-31
Author: Vincent Arel-Bundock
Maintainer: Vincent Arel-Bundock
Description: Standardizes country names, converts them into one of seven coding schemes, and assigns region descriptors
License: GPL-3
LazyLoad: yes
LazyData: yes
Packaged: 2009-06-03 05:10:26 UTC; vincent
Repository: CRAN
Date/Publication: 2009-06-03 17:31:28

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New package freqMAP with initial version 0.1
Package: freqMAP
Type: Package
Title: Frequency Moving Average Plots (MAP) of Multinomial Data by a Continuous Covariate
Version: 0.1
Date: 2009-05-29
Author: Colin McCulloch
Maintainer: Colin McCulloch
Description: A frequency moving average plot (MAP) is estimated from a multinomial data and a continuous covariate. The frequency MAP is a moving average estimate of category frequencies, where frequency means and posterior bounds are estimated. Comparisons of two frequency MAPs as well as odds ratios can be plotted.
License: GPL (>= 2)
LazyLoad: yes
Packaged: Tue Jun 2 20:39:21 2009; colin
Repository: CRAN
Date/Publication: 2009-06-03 17:31:30

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Package clim.pact updated to version 2.2-36 with previous version 2.2-35 dated 2009-05-27

Author: Rasmus E. Benestad
Title: Climate analysis and empirical-statistical downscaling (ESD) package for monthly and daily data.
Description: The package contains R functions for retrieving data, making climate analysis and downscaling of monthly mean and daily mean global climate scenarios. (Windows-users may need to obtain the 'ncdf' package from URL 'http://www.stats.ox.ac.uk/pub/RWin/' to get clim.pact to work). The package is also described in the book 'Empirical-Statistical Downscaling (http://www.worldscibooks.com/environsci/6908.html)

Diff between clim.pact versions 2.2-35 dated 2009-05-27 and 2.2-36 dated 2009-06-03

 DESCRIPTION    |    8 ++---
 R/ds.R         |    1 
 R/eof.R        |   26 +++++++++++++++---
 R/map.R        |    5 +++
 R/objDS.R      |   40 +++++++++++++++-------------
 R/plotDS.R     |    8 ++++-
 R/plotEOF.R    |   79 +++++++++++++++++++++++++++++++--------------------------
 man/objDS.Rd   |    3 +-
 man/plotEOF.Rd |    3 +-
 9 files changed, 106 insertions(+), 67 deletions(-)

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Package bipartite updated to version 0.92 with previous version 0.91 dated 2009-05-06

Author: Carsten F. Dormann and Bernd Gruber, with additional code from Mariano Devoto, Jochen Fruend, Jose Iriondo and Diego Vazquez, also based on C-code developed by Nils Bluethgen and by Miguel Rodriguez-Girones.
Title: Visualising bipartite networks and calculating some ecological indices.
Description: Bipartite provides functions to viualise webs and calculate a series of indices commonly used to describe pattern in ecological webs. It focusses on webs consisting of only two trophic levels, e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the webs topology.

Diff between bipartite versions 0.91 dated 2009-05-06 and 0.92 dated 2009-06-03

 bipartite-0.91/bipartite/Jochentest.txt           |only
 bipartite-0.91/bipartite/vazquez_et_al_ms.pdf     |only
 bipartite-0.92/bipartite/DESCRIPTION              |   16 -
 bipartite-0.92/bipartite/R/empty.R                |   13 
 bipartite-0.92/bipartite/R/functspec.r            |    3 
 bipartite-0.92/bipartite/R/networklevel.R         |    3 
 bipartite-0.92/bipartite/R/nodespec.r             |    4 
 bipartite-0.92/bipartite/R/visweb.R               |  296 ++++++++++------------
 bipartite-0.92/bipartite/R/wine.r                 |   39 ++
 bipartite-0.92/bipartite/R/zzz.R                  |    4 
 bipartite-0.92/bipartite/man/C.score.Rd           |    2 
 bipartite-0.92/bipartite/man/bipartite-package.Rd |   14 -
 bipartite-0.92/bipartite/man/networklevel.Rd      |    2 
 bipartite-0.92/bipartite/man/swap.web.Rd          |    2 
 bipartite-0.92/bipartite/man/vazquez.example.rd   |   18 -
 bipartite-0.92/bipartite/man/visweb.Rd            |    8 
 bipartite-0.92/bipartite/man/wine.rd              |   14 -
 17 files changed, 227 insertions(+), 211 deletions(-)

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Package bigmemory updated to version 3.7 with previous version 3.6 dated 2009-05-04

Author: Michael J. Kane and John W. Emerson
Title: Manage massive matrices in R using C++, with support for shared memory and memory-mapped files.
Description: Use C++ to create, store, access, and manipulate massive matrices. Matrices may optionally be allocated to shared memory and/or may use memory-mapped files.

Diff between bigmemory versions 3.6 dated 2009-05-04 and 3.7 dated 2009-06-03

 bigmemory-3.6/bigmemory/R/is.filebacked.R         |only
 bigmemory-3.6/bigmemory/README                    |only
 bigmemory-3.6/bigmemory/SHM                       |only
 bigmemory-3.6/bigmemory/src/writedescr.txt        |only
 bigmemory-3.7/bigmemory/DESCRIPTION               |    8 
 bigmemory-3.7/bigmemory/NAMESPACE                 |    4 
 bigmemory-3.7/bigmemory/R/bigmatrix.R             |  414 +++++++++-------------
 bigmemory-3.7/bigmemory/R/bigmatrixLib.R          |    6 
 bigmemory-3.7/bigmemory/R/bigmatrixShm.R          |  122 ++++--
 bigmemory-3.7/bigmemory/configure.Rout            |    2 
 bigmemory-3.7/bigmemory/man/big.matrix-class.Rd   |    5 
 bigmemory-3.7/bigmemory/man/big.matrix.Rd         |   18 
 bigmemory-3.7/bigmemory/man/big.sub.matrix.Rd     |only
 bigmemory-3.7/bigmemory/man/bigmemory-package.Rd  |    4 
 bigmemory-3.7/bigmemory/man/colmean.Rd            |    4 
 bigmemory-3.7/bigmemory/man/write.big.matrix.Rd   |   12 
 bigmemory-3.7/bigmemory/src/BigMatrix.cpp         |  291 +++++++++------
 bigmemory-3.7/bigmemory/src/BigMatrix.h           |   96 ++++-
 bigmemory-3.7/bigmemory/src/BigMatrixAccessor.hpp |   11 
 bigmemory-3.7/bigmemory/src/CbigmemoRy.cpp        |  181 +++++++--
 bigmemory-3.7/bigmemory/src/CbigmemoRyLib.cpp     |   42 +-
 bigmemory-3.7/bigmemory/src/TODO.txt              |only
 22 files changed, 712 insertions(+), 508 deletions(-)

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Package ctv updated to version 0.5-2 with previous version 0.5-1 dated 2009-02-11

Author: Achim Zeileis, Kurt Hornik
Title: CRAN Task Views
Description: Server-side and client-side tools for task views to CRAN-style repositories

Diff between ctv versions 0.5-1 dated 2009-02-11 and 0.5-2 dated 2009-06-03

 COPYRIGHTS                            |    2 
 DESCRIPTION                           |   12 
 NEWS                                  |    5 
 R/ctv-server.R                        |   14 
 inst/ctv/Bayesian.ctv                 |  599 +++++++++++--------------
 inst/ctv/ChemPhys.ctv                 |    4 
 inst/ctv/Cluster.ctv                  |  142 ++++-
 inst/ctv/Distributions.ctv            |   32 -
 inst/ctv/Distributions.html           |only
 inst/ctv/Econometrics.ctv             |   17 
 inst/ctv/Environmetrics.ctv           |    4 
 inst/ctv/ExperimentalDesign.ctv       |   33 -
 inst/ctv/Finance.ctv                  |  157 ++++--
 inst/ctv/HighPerformanceComputing.ctv |   90 ++-
 inst/ctv/MedicalImaging.ctv           |only
 inst/ctv/Multivariate.ctv             |   17 
 inst/ctv/Optimization.ctv             |   40 +
 inst/ctv/Psychometrics.ctv            |   28 +
 inst/ctv/SocialSciences.ctv           |    3 
 inst/ctv/Spatial.ctv                  |   98 ++--
 inst/ctv/Survival.ctv                 |  814 +++++++++++++++++++++-------------
 inst/ctv/TimeSeries.ctv               |   27 -
 inst/ctv/gR.ctv                       |  222 +++++----
 inst/doc/ctv-howto.pdf                |binary
 man/ctv-server.Rd                     |    2 
 25 files changed, 1439 insertions(+), 923 deletions(-)

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