Package: yest
Version: 0.3
Date: 2007-02-07
Title: Gaussian Independence Models
Author: Petr Simecek  
Maintainer: Petr Simecek 
Depends: R (>= 2.4.0), graphics, MASS
Description: Model selection and variance estimation in Gaussian independence models
License: GPL version 2 or newer
URL: http://5r.matfyz.cz/models
Packaged: Wed Jul  4 06:04:57 2007; psim8003

Package: scagnostics
Type: Package
Title: Compute scagnostics.
Version: 0.1.0
Date: 2006-09-29
Author: Heike Hofmann, , Lee Wilkinson ,  Hadley Wickham , Duncan Temple Lang, Anushka Anand
Maintainer: Hadley Wickham 
Description: Calculates Tukey's scagnostics.  Scagnostics describe various measures of interest for pairs of variables, based on their appearance on a scatterplot.  They are useful tool for weeding out interesting or unusual scatterplots from a scatterplot matrix, without having to look at ever individual plot.
Depends: R
Suggests: rggobi
LazyData: yes
License: GPL
Packaged: Fri Jun 29 17:34:17 2007; hadley

Package: penalized
Version: 0.9-0
Date: 2007-07-02
Title: Penalized estimation in Generalized Linear Models
Author: Jelle Goeman 
Maintainer: Jelle Goeman 
Depends: R, methods, survival
Imports: survival
Suggests: 
Description: L1 (lasso) and L2 (ridge) estimation in Generalized Linear Models and in the Cox Proportional Hazards model
License: GPL version 2 or newer
Collate: objects.R user.R core.R contrasts.R Brent.R plotpath.R cox.R logit.R linear.R
LazyLoad: yes
ZipData: yes
URL: http://www.msbi.nl/goeman
Packaged: Mon Jul  2 13:44:12 2007; jjgoeman

Package: ljr
Version: 1.0-0
Date: 2007-06-08
Title: Logistic Joinpoint Regression
Author: Michal Czajkowski, Ryan Gill, Greg Rempala
Maintainer: Ryan Gill 
Description: Fits and tests logistic joinpoint models.
License: GPL (version 2 or later)
Packaged: Wed Jun 13 04:26:11 2007; rsgill01

Package: grasp
Version: 2.5-4
Date: 2007-06-28
Title: Generalized Regression Analysis and Spatial Prediction for R
Author: Anthony Lehmann (anthony.lehmann@unige.ch), Fabien Fivaz (fabien.fivaz@unine.ch), John Leathwick and Jake Overton, with contributions from many specialists from around the world
Description: GRASP is a general method for making spatial predictions of response variables (RV) using point surveys of the RV and spatial coverages of Predictor variables (PV). Originally, GRASP was developed to analyse, model and predict vegetation distribution over New Zealand. It has been used in all sorts of applications since then. (A. Lehmann, J.R. Leathwick & J.McC. Overton, 2002. GRASP. Ecological Modelling, 157: 189-207)
Maintainer: Fabien Fivaz 
Depends: R (>= 2.0), gam (>= 0.93), mda (>= 0.3)
License: GPL version 2 or newer
URL: http://www.r-project.org, http://www.unige.ch/ia/climat/grasp
Packaged: Sat Jul  7 20:40:30 2007; hornik

Package: AcceptanceSampling
Type: Package
Title: Creation and evaluation of Acceptance Sampling Plans
Version: 0.1-1
Date: 2007-05-15
Author: Andreas Kiermeier 
Maintainer: Andreas Kiermeier 
Description: This package provides functionality for creating and
	evaluating acceptance sampling plans. Plans can be single,
	double or multiple sampling plans
Depends: methods, R(>= 2.4.0), stats
Imports: graphics
License: GPL version 2 or newer
LazyLoad: yes
Packaged: Fri Jun 29 13:41:17 2007; SFVLAXK

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 diveMove-0.8.0/diveMove/R/AllClass.R                  |    4 
 diveMove-0.8.0/diveMove/R/AllGenerics.R               |   10 +
 diveMove-0.8.0/diveMove/R/AllMethod.R                 |   17 ++-
 diveMove-0.8.0/diveMove/R/austFilter.R                |    4 
 diveMove-0.8.0/diveMove/R/bouts.R                     |only
 diveMove-0.8.0/diveMove/R/calibrate.R                 |    6 -
 diveMove-0.8.0/diveMove/R/detDive.R                   |    2 
 diveMove-0.8.0/diveMove/R/detPhase.R                  |    2 
 diveMove-0.8.0/diveMove/R/distSpeed.R                 |    2 
 diveMove-0.8.0/diveMove/R/diveStats.R                 |    2 
 diveMove-0.8.0/diveMove/R/oneDiveStats.R              |    2 
 diveMove-0.8.0/diveMove/R/plotTD.R                    |   97 +++++++++---------
 diveMove-0.8.0/diveMove/R/readLocs.R                  |    2 
 diveMove-0.8.0/diveMove/R/readTDR.R                   |    2 
 diveMove-0.8.0/diveMove/R/speedStats.R                |    2 
 diveMove-0.8.0/diveMove/R/stampDive.R                 |    2 
 diveMove-0.8.0/diveMove/R/zoc.R                       |    2 
 diveMove-0.8.0/diveMove/R/zzz.R                       |    3 
 diveMove-0.8.0/diveMove/README                        |    7 +
 diveMove-0.8.0/diveMove/inst/doc/diveMove.pdf         |binary
 diveMove-0.8.0/diveMove/man/TDR-accessors.Rd          |    2 
 diveMove-0.8.0/diveMove/man/TDR-class.Rd              |    2 
 diveMove-0.8.0/diveMove/man/TDRcalibrate-accessors.Rd |    2 
 diveMove-0.8.0/diveMove/man/TDRcalibrate-class.Rd     |    2 
 diveMove-0.8.0/diveMove/man/austFilter.Rd             |   18 +--
 diveMove-0.8.0/diveMove/man/bout-methods.Rd           |only
 diveMove-0.8.0/diveMove/man/bout-misc.Rd              |only
 diveMove-0.8.0/diveMove/man/bouts2MLE.Rd              |only
 diveMove-0.8.0/diveMove/man/bouts2NLS.Rd              |only
 diveMove-0.8.0/diveMove/man/calibrateDepth.Rd         |    6 -
 diveMove-0.8.0/diveMove/man/calibrateSpeed.Rd         |    2 
 diveMove-0.8.0/diveMove/man/detDive-internal.Rd       |    2 
 diveMove-0.8.0/diveMove/man/detPhase-internal.Rd      |    2 
 diveMove-0.8.0/diveMove/man/distSpeed.Rd              |    2 
 diveMove-0.8.0/diveMove/man/diveMove-internal.Rd      |    2 
 diveMove-0.8.0/diveMove/man/diveMove-package.Rd       |   21 +--
 diveMove-0.8.0/diveMove/man/diveStats.Rd              |    2 
 diveMove-0.8.0/diveMove/man/dives.Rd                  |    4 
 diveMove-0.8.0/diveMove/man/extractDive-methods.Rd    |    2 
 diveMove-0.8.0/diveMove/man/labDive-internal.Rd       |    2 
 diveMove-0.8.0/diveMove/man/plotTDR-methods.Rd        |    2 
 diveMove-0.8.0/diveMove/man/readLocs.Rd               |    2 
 diveMove-0.8.0/diveMove/man/readTDR.Rd                |    2 
 diveMove-0.8.0/diveMove/man/rqPlot.Rd                 |    2 
 diveMove-0.8.0/diveMove/man/timeBudget-methods.Rd     |    2 
 diveMove-0.8.0/diveMove/man/zoc.Rd                    |    2 
 50 files changed, 226 insertions(+), 125 deletions(-)

 DESCRIPTION    |    6 +++---
 R/genCluster.R |   31 ++++++++++++++++++++++++++-----
 tests/Makefile |   16 ++++++++--------
 3 files changed, 37 insertions(+), 16 deletions(-)

 DESCRIPTION    |    6 +++---
 R/simple.bp.R  |    2 +-
 man/lm.dibp.Rd |    3 ---
 3 files changed, 4 insertions(+), 7 deletions(-)

 backtest-0.1-2/backtest/inst/doc/Rplots.ps                 |only
 backtest-0.1-2/backtest/inst/doc/backtest-020.eps          |only
 backtest-0.1-2/backtest/inst/doc/backtest-020.pdf          |only
 backtest-0.1-2/backtest/inst/doc/backtest-021.eps          |only
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 backtest-0.1-2/backtest/inst/doc/backtest.tex              |only
 backtest-0.2-0/backtest/ChangeLog                          |   11 
 backtest-0.2-0/backtest/DESCRIPTION                        |    8 
 backtest-0.2-0/backtest/R/backtest.R                       |  104 +++-
 backtest-0.2-0/backtest/R/backtest.compute.R               |only
 backtest-0.2-0/backtest/R/backtest.function.R              |  274 +++++++------
 backtest-0.2-0/backtest/R/calc.turnover.R                  |   42 -
 backtest-0.2-0/backtest/R/categorize.R                     |    8 
 backtest-0.2-0/backtest/R/overlaps.compute.R               |only
 backtest-0.2-0/backtest/inst/doc/backtest.Rnw              |   13 
 backtest-0.2-0/backtest/inst/doc/backtest.pdf              |binary
 backtest-0.2-0/backtest/man/backtest-class.Rd              |    4 
 backtest-0.2-0/backtest/man/backtest.Rd                    |   50 +-
 backtest-0.2-0/backtest/tests/backtest.function.test.R     |   21 
 backtest-0.2-0/backtest/tests/backtest.function.test.RData |binary
 backtest-0.2-0/backtest/tests/backtest.summary.test.R      |   14 
 backtest-0.2-0/backtest/tests/bucketize.test2.R            |only
 backtest-0.2-0/backtest/tests/bucketize.test2.RData        |only
 backtest-0.2-0/backtest/tests/calc.true.weight.test.R      |only
 backtest-0.2-0/backtest/tests/calc.true.weight.test.RData  |only
 backtest-0.2-0/backtest/tests/calc.turnover.test.RData     |binary
 backtest-0.2-0/backtest/tests/overlaps.compute.test.R      |only
 backtest-0.2-0/backtest/tests/overlaps.compute.test.RData  |only
 35 files changed, 325 insertions(+), 224 deletions(-)

 DESCRIPTION   |    8 ++++----
 R/aws.r       |   29 +++++++++++------------------
 R/awstindex.r |    8 ++++----
 R/haws.r      |    1 +
 R/laws.r      |    4 ++--
 5 files changed, 22 insertions(+), 28 deletions(-)

 ape-1.10-1/ape/Changes                |only
 ape-1.10-2/ape/Changes.txt            |only
 ape-1.10-2/ape/DESCRIPTION            |    6 
 ape-1.10-2/ape/R/as.phylo.R           |    6 
 ape-1.10-2/ape/R/as.phylo.formula.R   |   16 -
 ape-1.10-2/ape/R/compar.ou.R          |    4 
 ape-1.10-2/ape/R/dist.topo.R          |  136 ++++++++++------
 ape-1.10-2/ape/R/mrca.R               |   13 -
 ape-1.10-2/ape/R/plot.phylo.R         |  280 ++++++++++++++++++++++------------
 ape-1.10-2/ape/R/read.GenBank.R       |    4 
 ape-1.10-2/ape/R/root.R               |    4 
 ape-1.10-2/ape/R/which.edge.R         |    7 
 ape-1.10-2/ape/man/all.equal.phylo.Rd |    3 
 ape-1.10-2/ape/man/ape-internal.Rd    |    1 
 ape-1.10-2/ape/man/as.phylo.Rd        |    3 
 ape-1.10-2/ape/man/boot.phylo.Rd      |   81 ++++++++-
 ape-1.10-2/ape/man/diversi.gof.Rd     |   12 -
 ape-1.10-2/ape/man/plot.phylo.Rd      |    9 -
 ape-1.10-2/ape/src/bipartition.c      |  165 ++++++++++++++++----
 19 files changed, 526 insertions(+), 224 deletions(-)

 analogue-0.3-3/analogue/R/Screeplot.R                  |only
 analogue-0.3-3/analogue/R/k.R                          |only
 analogue-0.3-3/analogue/man/Screeplot.Rd               |only
 analogue-0.3-3/analogue/man/k.Rd                       |only
 analogue-0.4-0/analogue/DESCRIPTION                    |    9 -
 analogue-0.4-0/analogue/R/RMSEP.R                      |   23 ++
 analogue-0.4-0/analogue/R/analog.R                     |    6 
 analogue-0.4-0/analogue/R/bayesF.R                     |    1 
 analogue-0.4-0/analogue/R/bootstrap.R                  |  105 ++++++------
 analogue-0.4-0/analogue/R/cma.R                        |   41 +----
 analogue-0.4-0/analogue/R/distance.R                   |   28 ++-
 analogue-0.4-0/analogue/R/fitted.mat.R                 |    4 
 analogue-0.4-0/analogue/R/getK.R                       |only
 analogue-0.4-0/analogue/R/internal.R                   |   72 +++++++-
 analogue-0.4-0/analogue/R/join.R                       |   35 ++--
 analogue-0.4-0/analogue/R/mat.R                        |   79 +++++++--
 analogue-0.4-0/analogue/R/mcarlo.R                     |   26 ++-
 analogue-0.4-0/analogue/R/plot.cma.R                   |    1 
 analogue-0.4-0/analogue/R/plot.mat.R                   |    4 
 analogue-0.4-0/analogue/R/predict.mat.R                |   36 ++--
 analogue-0.4-0/analogue/R/reconPlot.R                  |  139 ++++++++---------
 analogue-0.4-0/analogue/R/residuals.bootstrap.mat.R    |   31 +--
 analogue-0.4-0/analogue/R/roc.R                        |   49 +++++
 analogue-0.4-0/analogue/R/screeplot.R                  |only
 analogue-0.4-0/analogue/R/summary.analog.R             |    2 
 analogue-0.4-0/analogue/R/summary.bootstrap.mat.R      |   25 +--
 analogue-0.4-0/analogue/R/summary.cma.R                |   29 +++
 analogue-0.4-0/analogue/R/summary.mat.R                |    9 -
 analogue-0.4-0/analogue/R/summary.predict.mat.R        |   14 -
 analogue-0.4-0/analogue/R/zzz.R                        |    2 
 analogue-0.4-0/analogue/inst/COPYING                   |    2 
 analogue-0.4-0/analogue/inst/ChangeLog                 |   86 ++++++++++
 analogue-0.4-0/analogue/inst/TODO                      |    2 
 analogue-0.4-0/analogue/man/RMSEP.Rd                   |   38 +++-
 analogue-0.4-0/analogue/man/analogue-internal.Rd       |    2 
 analogue-0.4-0/analogue/man/analogue-package.Rd        |   12 -
 analogue-0.4-0/analogue/man/bootstrap.Rd               |   21 +-
 analogue-0.4-0/analogue/man/cma.Rd                     |   31 ---
 analogue-0.4-0/analogue/man/distance.Rd                |   13 +
 analogue-0.4-0/analogue/man/fitted.mat.Rd              |    2 
 analogue-0.4-0/analogue/man/getK.Rd                    |only
 analogue-0.4-0/analogue/man/join.Rd                    |   22 +-
 analogue-0.4-0/analogue/man/mat.Rd                     |   64 +++++--
 analogue-0.4-0/analogue/man/mcarlo.Rd                  |   30 ++-
 analogue-0.4-0/analogue/man/minDC.Rd                   |    8 
 analogue-0.4-0/analogue/man/plot.mat.Rd                |    4 
 analogue-0.4-0/analogue/man/plot.minDC.Rd              |    7 
 analogue-0.4-0/analogue/man/predict.mat.Rd             |   23 +-
 analogue-0.4-0/analogue/man/reconPlot.Rd               |   68 +++++---
 analogue-0.4-0/analogue/man/residuals.bootstrap.mat.Rd |   34 ++--
 analogue-0.4-0/analogue/man/residuals.mat.Rd           |    7 
 analogue-0.4-0/analogue/man/roc.Rd                     |   29 ++-
 analogue-0.4-0/analogue/man/screeplot.Rd               |only
 analogue-0.4-0/analogue/man/summary.bootstrap.mat.Rd   |  105 +++++++++---
 analogue-0.4-0/analogue/man/summary.cma.Rd             |   11 -
 analogue-0.4-0/analogue/man/summary.predict.mat.Rd     |   19 --
 56 files changed, 918 insertions(+), 492 deletions(-)