Title: An individual-based population genetic simulation environment
Diff between rmetasim versions 1.1.09 dated 2009-10-08 and 1.1.10 dated 2010-01-22
Description: An interface between R and the metasim simulation engine.
Facilitates the use of the metasim engine to build and run
individual based population genetics simulations. The
simulation environment is documented in: Allan Strand. Metasim
1.0: an individual-based environment for simulating population
genetics of complex population dynamics. Mol. Ecol. Notes,
2:373-376, 2002. (Please contact Allan Strand with comments,
bug reports, etc). This version represents a significant
alteration of function names that hopefully increases
consistency and reduces the chances of collisions with other
packages naming conventions. For a spatially-explicit, but
slower, package with a similar interface, see kernelPop
Author: Allan Strand
Maintainer: Allan Strand
CHANGELOG | 6 +++++
DESCRIPTION | 8 +++----
NAMESPACE | 1
R/landscape.mig.matrix.R |only
man/landscape.mig.matrix.Rd |only
src/FastAllele.cc | 7 ++++--
src/FastSeqAllele.cc | 7 +++---
src/Landscape.cc | 20 +++++++++++++------
src/RandLib.cc | 6 +++--
src/TransMat.cc | 14 +++++++------
src/metasim.h | 5 ++--
src/rmetasim.cc | 45 +++++++++++++++++++++++++++++++++++---------
src/rmetasim.h | 2 -
13 files changed, 86 insertions(+), 35 deletions(-)
Title: Model-Based Clustering / Normal Mixture Modeling
Diff between mclust versions 3.4 dated 2009-12-16 and 3.4.1 dated 2010-01-22
Description: Model-based clustering and normal mixture modeling
including Bayesian regularization
Author: Chris Fraley and Adrian Raftery
Maintainer: Chris Fraley
CHANGELOG | 2 ++
CITATION | 3 +--
DESCRIPTION | 8 ++++----
LICENSE | 3 +--
man/Defaults.Mclust.Rd | 3 ++-
man/mclustModel.Rd | 36 +++++++++++++++++++++++++++++++-----
6 files changed, 41 insertions(+), 14 deletions(-)
Title: Various programming utilities
Diff between R.utils versions 1.3.0 dated 2010-01-03 and 1.3.2 dated 2010-01-22
Description: This package provides utility classes and methods useful
when programming in R and developing R packages.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
DESCRIPTION | 8 ++--
R/999.NonDocumentedObjects.R | 6 +++
R/999.package.R | 6 ---
R/System.R | 70 ++++++++++++++++++++++++++++++++++++++++++
R/eps.R | 5 ++-
R/sourceDirectory.R | 4 +-
R/sourceTo.R | 9 ++++-
inst/NEWS | 16 +++++++++
man/Non-documented_objects.Rd | 6 +++
man/R.utils-package.Rd | 6 ---
man/System.Rd | 3 +
man/eps.Rd | 3 +
man/sourceDirectory.Rd | 2 -
13 files changed, 123 insertions(+), 21 deletions(-)
Title: R object-oriented programming with or without references
Diff between R.oo versions 1.6.6 dated 2010-01-03 and 1.6.7 dated 2010-01-22
Description: Methods and classes for object-oriented programming in R
with or without references. Large effort has been made on
making definition of methods as simple as possible with a
minimum of maintenance for package developers. The package has
been developed since 2001 and is now considered very stable.
This is a cross-platform package implemented in pure R that
defines standard S3 classes without any tricks.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
DESCRIPTION | 10 ++++------
R/999.package.R | 32 +++++++++++++++++++++++++-------
R/ASCII.R | 3 ++-
inst/NEWS | 4 ++++
man/R.oo-package.Rd | 28 +++++++++++++++++++++++-----
man/charToInt.Rd | 3 ++-
6 files changed, 60 insertions(+), 20 deletions(-)
Title: SegClust : a package for Segmentation and
Segmentation/Clustering.
Diff between segclust versions 0.74 dated 2008-12-01 and 0.75 dated 2010-01-22
Description: SegClust corresponds to the implementation of the
statistical model described in : Picard et al., A
segmentation/clustering model for the analysis of array CGH
data. Biometrics, 63(3) 2007. Segmentation functions are also
available (from Picard et al. A statistical approach for array
CGH data analysis. BMC Bioinformatics. 2005 Feb 11;6:27).
Author: Franck Picard
Maintainer: Mark Hoebeke
DESCRIPTION | 18 +++++++++++++-----
man/segmean.Rd | 2 +-
src/Segmentation_mean.cc | 3 +--
src/Segmentation_mixt.cc | 21 +++++++++++++--------
src/helperfuncs.h | 8 +++++++-
5 files changed, 35 insertions(+), 17 deletions(-)
Title: Reads, annotates, and normalizes reverse phase protein array
data
Diff between RPPanalyzer versions 1.0 dated 2010-01-18 and 1.0.2 dated 2010-01-22
Description: Reads in sampledescription and slidedescription files and
annotates the expression values taken from gpr files. After
Normalization data can be presented in boxplots, heatmaps or
dotplots.
Author: Heiko Mannsperger with contributions of Stephan Gade
Maintainer: Heiko Mannsperger
RPPanalyzer-1.0.2/RPPanalyzer/DESCRIPTION | 7 ++++---
RPPanalyzer-1.0/RPPanalyzer/data/S10.gpr |only
RPPanalyzer-1.0/RPPanalyzer/data/S10_2.gpr |only
RPPanalyzer-1.0/RPPanalyzer/data/S3.gpr |only
RPPanalyzer-1.0/RPPanalyzer/data/S5.gpr |only
RPPanalyzer-1.0/RPPanalyzer/data/S6.gpr |only
RPPanalyzer-1.0/RPPanalyzer/data/S7.gpr |only
RPPanalyzer-1.0/RPPanalyzer/data/S8.gpr |only
RPPanalyzer-1.0/RPPanalyzer/data/S8_2.gpr |only
RPPanalyzer-1.0/RPPanalyzer/data/S9.gpr |only
RPPanalyzer-1.0/RPPanalyzer/data/S9_2.gpr |only
RPPanalyzer-1.0/RPPanalyzer/man/subsetdataI.Rd |only
12 files changed, 4 insertions(+), 3 deletions(-)
Title: R/KEA interface
Diff between RKEA versions 0.0-2 dated 2009-06-25 and 0.0-3 dated 2010-01-22
Description: An R interface to KEA (Version 5.0). KEA (for Keyphrase
Extraction Algorithm) allows for extracting keyphrases from
text documents. It can be either used for free indexing or for
indexing with a controlled vocabulary. For more information see
http://www.nzdl.org/Kea/.
Author: Ingo Feinerer, Kurt Hornik
Maintainer: Kurt Hornik
DESCRIPTION | 9 ++++-----
inst/doc/kea.pdf |binary
inst/java/snowball.jar |only
inst/java/weka.jar |only
4 files changed, 4 insertions(+), 5 deletions(-)
Title: Kalman filter and smoothers for exponential family state space
models.
Diff between KFAS versions 0.5.1 dated 2010-01-12 and 0.5.2 dated 2010-01-22
Description: Package KFAS provides functions for Kalman filtering,
state, disturbance and simulation smoothing, forecasting and
simulation of state space models. All functions can use exact
diffuse initialisation when distributions of some or all
elements of initial state vector are unknown. Filtering, state
smoothing and simulation functions use sequential processing
algorithm, which is faster than standard approach, and it also
allows singularity of prediction error variance matrix. KFAS
also contains function for computing the likelihood of
exponential family state space models and function for state
smoothing of exponential family state space models.
Author: Jouni Helske
Maintainer: Jouni Helske
DESCRIPTION | 8 ++++----
R/KFAS.R | 11 ++++++-----
src/eflik.f90 | 2 +-
src/eflik0.f90 | 2 +-
src/kf.f90 | 44 +++++++++++++++++++++++---------------------
src/ks.f90 | 9 +++++----
src/simsmoother.f90 | 15 ++++++++-------
7 files changed, 48 insertions(+), 43 deletions(-)
Title: Tools for Scraping Data from HTML and XML Documents
Diff between scrapeR versions 0.1.3 dated 2010-01-17 and 0.1.4 dated 2010-01-22
Description: Tools for Scraping Data from Web-Based Documents
Author: Ryan M. Acton
Maintainer: Ryan M. Acton
DESCRIPTION | 6 +++---
R/functions.R | 15 ++++++++++-----
man/scrapeR-package.Rd | 2 +-
3 files changed, 14 insertions(+), 9 deletions(-)
Title: Relative survival regression
Diff between relsurv versions 1.5.2 dated 2009-10-26 and 1.5.3 dated 2010-01-22
Description: Various functions for regression in relative survival.
Author: Maja Pohar Perme
Maintainer: Maja Pohar Perme
DESCRIPTION | 6 +++---
R/Rcode.r | 34 ++++++++++++++++++++++++----------
2 files changed, 27 insertions(+), 13 deletions(-)
Title: A graphical user interface for data mining in R using GTK
Diff between rattle versions 2.5.15 dated 2010-01-15 and 2.5.17 dated 2010-01-22
Description: Rattle (the R Analytic Tool To Learn Easily) provides a
Gnome (RGtk2) based interface to R functionality for data
mining. The aim is to provide a simple and intuitive interface
that allows a user to quickly load data from a CSV file (or via
ODBC), transform and explore the data, build and evaluate
models, and export models as PMML (predictive modelling markup
language) or as scores. All of this with knowing little about
R. All R commands are logged and commented through the log tab
and so available to the user as a script file or as an aide to
the user to interact directly with R itself. Rattle also
exports a number of utility functions and the graphical user
interface, invoked as rattle(), does not need to be run to
deploy these.
Author: Graham Williams
Maintainer: Graham Williams
rattle-2.5.15/rattle/po/R-ja.po.091221 |only
rattle-2.5.15/rattle/po/R-ja.po.091222 |only
rattle-2.5.15/rattle/po/R-ja.po.091223 |only
rattle-2.5.15/rattle/po/R-ja.poi.091223072033 |only
rattle-2.5.15/rattle/po/R-ja.poi.091223072546 |only
rattle-2.5.15/rattle/po/R-ja.poi.091223072735 |only
rattle-2.5.15/rattle/po/R-ja.poi.091223101117 |only
rattle-2.5.15/rattle/po/R-ja.poi.091223H1328 |only
rattle-2.5.15/rattle/po/R-ja.poi.091223H1706 |only
rattle-2.5.15/rattle/po/R-ja.poi.091224095345 |only
rattle-2.5.15/rattle/po/R-ja.poi.100109093641 |only
rattle-2.5.15/rattle/po/R-ja.poi.100109151122 |only
rattle-2.5.15/rattle/po/R-ja.poi.100109151915 |only
rattle-2.5.15/rattle/po/R-ja.poi.100109152051 |only
rattle-2.5.15/rattle/po/R-ja.poi.100110123843 |only
rattle-2.5.15/rattle/po/R-ja.poi.100110142602 |only
rattle-2.5.15/rattle/po/R-ja.poi.100110150856 |only
rattle-2.5.15/rattle/po/R-ja.poi.100110152605 |only
rattle-2.5.15/rattle/po/R-ja.poi.100110153059 |only
rattle-2.5.15/rattle/po/R-ja.poi.100110160134 |only
rattle-2.5.15/rattle/po/R-ja.poi.100110160335 |only
rattle-2.5.15/rattle/po/R-ja.poi.100110160345 |only
rattle-2.5.15/rattle/po/R-ja.poi.100110160424 |only
rattle-2.5.15/rattle/po/R-ja.poi.100111205954 |only
rattle-2.5.15/rattle/po/messages.pot |only
rattle-2.5.17/rattle/DESCRIPTION | 20
rattle-2.5.17/rattle/R/associate.R | 6
rattle-2.5.17/rattle/R/biclust.R |only
rattle-2.5.17/rattle/R/clara.R |only
rattle-2.5.17/rattle/R/cluster.R | 7
rattle-2.5.17/rattle/R/data.R | 76
rattle-2.5.17/rattle/R/explore.R | 600 -
rattle-2.5.17/rattle/R/hclust.R | 13
rattle-2.5.17/rattle/R/help.R | 2
rattle-2.5.17/rattle/R/kmeans.R | 19
rattle-2.5.17/rattle/R/log.R | 8
rattle-2.5.17/rattle/R/model.R | 37
rattle-2.5.17/rattle/R/random_forest.R | 10
rattle-2.5.17/rattle/R/rattle.R | 193
rattle-2.5.17/rattle/R/rpart.R | 13
rattle-2.5.17/rattle/R/textview.R | 8
rattle-2.5.17/rattle/R/transform.R | 4
rattle-2.5.17/rattle/R/zzz.R | 2
rattle-2.5.17/rattle/inst/etc/rattle.glade | 113
rattle-2.5.17/rattle/inst/etc/textviews.xml | 62
rattle-2.5.17/rattle/inst/etc/tooltips.xml | 3
rattle-2.5.17/rattle/inst/po/ja/LC_MESSAGES/R-rattle.mo |binary
rattle-2.5.17/rattle/inst/po/no |only
rattle-2.5.17/rattle/man/centers.hclust.Rd | 6
rattle-2.5.17/rattle/man/internal.Rd | 2
rattle-2.5.17/rattle/man/rattle.print.rpart.Rd | 12
rattle-2.5.17/rattle/man/rattle.print.summary.multinom.Rd | 6
rattle-2.5.17/rattle/po/Makefile | 24
rattle-2.5.17/rattle/po/R-ja.po | 2887 +++++--
rattle-2.5.17/rattle/po/R-ja.poh | 2
rattle-2.5.17/rattle/po/R-ja.poi | 2869 +++++--
rattle-2.5.17/rattle/po/R-no.po |only
rattle-2.5.17/rattle/po/R-no.poi |only
rattle-2.5.17/rattle/po/R-rattle.header |only
rattle-2.5.17/rattle/po/R-rattle.pot | 5055 +++++++++++++-
rattle-2.5.17/rattle/po/new.poi | 2885 +++++--
61 files changed, 12028 insertions(+), 2916 deletions(-)
Title: Various plotting functions
Diff between plotrix versions 2.7-2 dated 2009-10-26 and 2.8 dated 2010-01-22
Description: Lots of plots, various labeling, axis and color scaling
functions.
Author: Jim Lemon, Ben Bolker, Sander Oom, Eduardo Klein, Barry
Rowlingson, Hadley Wickham, Anupam Tyagi, Olivier Eterradossi,
Gabor Grothendieck, Michael Toews, John Kane, Rolf Turner, Carl
Witthoft, Julian Stander, Thomas Petzoldt, Remko Duursma, Elisa
Biancotto, Ofir Levy
Maintainer: Jim Lemon
plotrix-2.7-2/plotrix/R/piper.diagram.R |only
plotrix-2.7-2/plotrix/man/convert.meq.Rd |only
plotrix-2.7-2/plotrix/man/p.ions.Rd |only
plotrix-2.7-2/plotrix/man/piper.coords.Rd |only
plotrix-2.7-2/plotrix/man/piper.diagram.Rd |only
plotrix-2.7-2/plotrix/man/piper.points.Rd |only
plotrix-2.7-2/plotrix/man/piper.set.Rd |only
plotrix-2.7-2/plotrix/man/piper.text.Rd |only
plotrix-2.8/plotrix/DESCRIPTION | 18 +++++++++---------
plotrix-2.8/plotrix/INDEX | 7 +------
plotrix-2.8/plotrix/NEWS | 9 +++++++++
plotrix-2.8/plotrix/R/barp.R | 13 +++++++------
plotrix-2.8/plotrix/R/brkdn.plot.R | 10 ++++------
plotrix-2.8/plotrix/R/dendrite.R | 2 ++
plotrix-2.8/plotrix/R/getMarginWidth.R | 2 ++
plotrix-2.8/plotrix/R/hierobarp.R | 12 ++++++------
plotrix-2.8/plotrix/R/legendg.R |only
plotrix-2.8/plotrix/R/stackpoly.R | 18 +++++++-----------
plotrix-2.8/plotrix/R/staircase.plot.R | 10 +++++-----
plotrix-2.8/plotrix/man/ablineclip.Rd | 2 +-
plotrix-2.8/plotrix/man/addtable2plot.Rd | 2 +-
plotrix-2.8/plotrix/man/arctext.Rd | 2 +-
plotrix-2.8/plotrix/man/axis.break.Rd | 2 +-
plotrix-2.8/plotrix/man/axis.mult.Rd | 2 +-
plotrix-2.8/plotrix/man/barp.Rd | 20 +++++++++++++-------
plotrix-2.8/plotrix/man/bin.wind.records.Rd | 2 +-
plotrix-2.8/plotrix/man/boxed.labels.Rd | 6 +++---
plotrix-2.8/plotrix/man/brkdn.plot.Rd | 4 ++--
plotrix-2.8/plotrix/man/bumpchart.Rd | 2 +-
plotrix-2.8/plotrix/man/centipede.plot.Rd | 4 ++--
plotrix-2.8/plotrix/man/clock24.plot.Rd | 2 +-
plotrix-2.8/plotrix/man/clplot.Rd | 2 +-
plotrix-2.8/plotrix/man/cluster.overplot.Rd | 4 ++--
plotrix-2.8/plotrix/man/color.gradient.Rd | 2 +-
plotrix-2.8/plotrix/man/color.id.Rd | 2 +-
plotrix-2.8/plotrix/man/color.legend.Rd | 6 +++---
plotrix-2.8/plotrix/man/color.scale.Rd | 7 ++++++-
plotrix-2.8/plotrix/man/color.scale.lines.Rd | 2 +-
plotrix-2.8/plotrix/man/color2D.matplot.Rd | 4 ++--
plotrix-2.8/plotrix/man/count.overplot.Rd | 2 +-
plotrix-2.8/plotrix/man/cylindrect.Rd | 2 +-
plotrix-2.8/plotrix/man/diamondplot.Rd | 2 +-
plotrix-2.8/plotrix/man/dispersion.Rd | 2 +-
plotrix-2.8/plotrix/man/draw.circle.Rd | 2 +-
plotrix-2.8/plotrix/man/draw.tilted.sector.Rd | 4 ++--
plotrix-2.8/plotrix/man/fan.plot.Rd | 2 +-
plotrix-2.8/plotrix/man/feather.plot.Rd | 2 +-
plotrix-2.8/plotrix/man/floating.pie.Rd | 3 +--
plotrix-2.8/plotrix/man/fullaxis.Rd | 2 +-
plotrix-2.8/plotrix/man/furc.Rd | 2 +-
plotrix-2.8/plotrix/man/gantt.chart.Rd | 8 ++++----
plotrix-2.8/plotrix/man/gap.barplot.Rd | 4 ++--
plotrix-2.8/plotrix/man/gap.boxplot.Rd | 10 +++++-----
plotrix-2.8/plotrix/man/gap.plot.Rd | 4 ++--
plotrix-2.8/plotrix/man/get.breaks.Rd | 2 +-
plotrix-2.8/plotrix/man/get.gantt.info.Rd | 4 ++--
plotrix-2.8/plotrix/man/get.segs.Rd | 2 +-
plotrix-2.8/plotrix/man/get.soil.texture.Rd | 2 +-
plotrix-2.8/plotrix/man/get.triprop.Rd | 2 +-
plotrix-2.8/plotrix/man/getIntersectList.Rd | 2 +-
plotrix-2.8/plotrix/man/getMarginWidth.Rd | 9 ++++++++-
plotrix-2.8/plotrix/man/hexagon.Rd | 2 +-
plotrix-2.8/plotrix/man/hierobarp.Rd | 12 +++++++-----
plotrix-2.8/plotrix/man/hierobarp.svymean.Rd | 2 +-
plotrix-2.8/plotrix/man/hierobarp.svyprop.Rd | 2 +-
plotrix-2.8/plotrix/man/hierobrk.Rd | 8 ++++----
plotrix-2.8/plotrix/man/intersectDiagram.Rd | 4 ++--
plotrix-2.8/plotrix/man/legendg.Rd |only
plotrix-2.8/plotrix/man/lengthKey.Rd | 2 +-
plotrix-2.8/plotrix/man/listDepth.Rd | 2 +-
plotrix-2.8/plotrix/man/makeDendrite.Rd | 2 +-
plotrix-2.8/plotrix/man/makeIntersectList.Rd | 2 +-
plotrix-2.8/plotrix/man/multhist.Rd | 8 ++++----
plotrix-2.8/plotrix/man/oz.windrose.Rd | 3 +--
plotrix-2.8/plotrix/man/oz.windrose.legend.Rd | 2 +-
plotrix-2.8/plotrix/man/pasteCols.Rd | 2 +-
plotrix-2.8/plotrix/man/pie.labels.Rd | 2 +-
plotrix-2.8/plotrix/man/pie3D.Rd | 2 +-
plotrix-2.8/plotrix/man/pie3D.labels.Rd | 4 ++--
plotrix-2.8/plotrix/man/plot.dendrite.Rd | 2 +-
plotrix-2.8/plotrix/man/plotCI.Rd | 17 ++++++++++-------
plotrix-2.8/plotrix/man/polar.plot.Rd | 2 +-
plotrix-2.8/plotrix/man/polygon.shadow.Rd | 2 +-
plotrix-2.8/plotrix/man/pyramid.plot.Rd | 2 +-
plotrix-2.8/plotrix/man/qt.plot.Rd | 2 +-
plotrix-2.8/plotrix/man/radial.plot.Rd | 2 +-
plotrix-2.8/plotrix/man/revaxis.Rd | 4 ++--
plotrix-2.8/plotrix/man/sizeplot.Rd | 2 +-
plotrix-2.8/plotrix/man/sizetree.Rd | 2 +-
plotrix-2.8/plotrix/man/smoothColors.Rd | 7 ++++++-
plotrix-2.8/plotrix/man/soil.texture.Rd | 6 +++---
plotrix-2.8/plotrix/man/soil.texture.uk.Rd | 6 +++---
plotrix-2.8/plotrix/man/stackpoly.Rd | 22 ++++++++++++++++++----
plotrix-2.8/plotrix/man/staircase.plot.Rd | 5 +++--
plotrix-2.8/plotrix/man/staxlab.Rd | 2 +-
plotrix-2.8/plotrix/man/std.error.Rd | 2 +-
plotrix-2.8/plotrix/man/sumDendrite.Rd | 2 +-
plotrix-2.8/plotrix/man/symbolbox.Rd | 2 +-
plotrix-2.8/plotrix/man/tab.title.Rd | 2 +-
plotrix-2.8/plotrix/man/thigmophobe.Rd | 2 +-
plotrix-2.8/plotrix/man/thigmophobe.labels.Rd | 4 ++--
plotrix-2.8/plotrix/man/triax.abline.Rd | 2 +-
plotrix-2.8/plotrix/man/triax.frame.Rd | 2 +-
plotrix-2.8/plotrix/man/triax.plot.Rd | 4 +---
plotrix-2.8/plotrix/man/triax.points.Rd | 2 +-
plotrix-2.8/plotrix/man/twoord.plot.Rd | 2 +-
plotrix-2.8/plotrix/man/vectorField.Rd | 2 +-
plotrix-2.8/plotrix/man/weighted.hist.Rd | 6 +++---
plotrix-2.8/plotrix/man/zoomInPlot.Rd | 2 +-
109 files changed, 239 insertions(+), 197 deletions(-)
Title: a tentative logging package
Diff between logging versions 0.2-9014 dated 2010-01-15 and 0.2-9100 dated 2010-01-22
Description: a logging package emulating the python logging package.
Author: Mario Frasca
Maintainer: Mario Frasca
DESCRIPTION | 6 +++---
R/logger.R | 4 ++--
R/version.R | 6 +++---
dist/logging.tar.gz |binary
4 files changed, 8 insertions(+), 8 deletions(-)
Title: Completing ranks
Diff between crank versions 1.0 dated 2008-05-21 and 1.0-1 dated 2010-01-22
Description: Functions for completing and recalculating rankings.
Author: Jim Lemon
Maintainer: Jim Lemon
DESCRIPTION | 10 ++++++----
NEWS |only
man/cats2ranks.Rd | 14 +++++++-------
man/fillArow.Rd | 15 +++++++--------
man/fillArows.Rd | 11 +++++------
man/getLWargs.Rd | 6 +++---
man/listBuilder.Rd | 20 ++++++++++----------
man/listCrawler.Rd | 21 ++++++++++++---------
man/lw.FriedmanTest.Rd | 6 +++---
man/lwscreen.Rd | 7 +++----
man/meanranks.Rd | 15 +++++++--------
man/muranks.Rd | 24 ++++++++++++------------
man/page.trend.test.Rd | 6 +++---
man/permute.Rd | 10 +++++-----
man/print.cats2ranks.Rd | 4 ++--
man/print.lwstat.Rd | 4 ++--
man/print.meanranks.Rd | 4 ++--
man/print.page.trend.test.Rd | 4 ++--
18 files changed, 91 insertions(+), 90 deletions(-)
Title: Clinical significance functions.
Diff between clinsig versions 1.0-1 dated 2009-03-16 and 1.0-2 dated 2010-01-22
Description: Functions for calculating clinical significance.
Author: Jim Lemon
Maintainer: Jim Lemon
DESCRIPTION | 10 +++----
NEWS |only
R/spreadout.R | 65 ++++++++++++++++++++++++++++++++++-----------------
man/clinsig.Rd | 2 -
man/hist.clinsig.Rd | 4 +--
man/plot.clinsig.Rd | 4 +--
man/print.clinsig.Rd | 4 +--
7 files changed, 56 insertions(+), 33 deletions(-)
Title: SNP-Haplotype Adaptive REgression (SHARE)
Diff between SHARE versions 1.0.2 dated 2009-07-22 and 1.0.4 dated 2010-01-22
Description: An adaptive algorithm to select the most informative set
of SNPs for genetic association
Author: James Y. Dai
Maintainer: Ting-Yuan Liu
DESCRIPTION | 8
R/cshare.R | 6
inst/doc/SHARE.pdf | 2062 ++++++++++++++++-----------------
inst/extdata/unphasedPermuPValue.RData |binary
4 files changed, 1036 insertions(+), 1040 deletions(-)
Title: Hidden Markov Models
Diff between HiddenMarkov versions 1.2-8 dated 2009-10-11 and 1.3-0 dated 2010-01-22
Description: Contains functions for the analysis of Discrete Time
Hidden Markov Models, Markov Modulated GLMs and the Markov
Modulated Poisson Process. It includes functions for
simulation, parameter estimation, and the Viterbi algorithm.
See the topic "HiddenMarkov" for an introduction to the
package, and "Changes" for a list of recent changes. The
algorithms are based of those of Walter Zucchini.
Author: David Harte
Maintainer: David Harte
HiddenMarkov-1.2-8/HiddenMarkov/R/Baum.Welch.R |only
HiddenMarkov-1.2-8/HiddenMarkov/R/Baum.Welch.mmpp.R |only
HiddenMarkov-1.2-8/HiddenMarkov/R/Baum.Welch0.mmpp.R |only
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HiddenMarkov-1.2-8/HiddenMarkov/R/Viterbi.mmglm.R |only
HiddenMarkov-1.2-8/HiddenMarkov/R/Viterbihmm.R |only
HiddenMarkov-1.2-8/HiddenMarkov/R/as.mmglm.R |only
HiddenMarkov-1.2-8/HiddenMarkov/R/backward0.mmpp.R |only
HiddenMarkov-1.2-8/HiddenMarkov/R/forward0.mmpp.R |only
HiddenMarkov-1.2-8/HiddenMarkov/R/logLik.mmglm.R |only
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HiddenMarkov-1.2-8/HiddenMarkov/R/residuals.mmglm.R |only
HiddenMarkov-1.2-8/HiddenMarkov/R/residualshmm.R |only
HiddenMarkov-1.2-8/HiddenMarkov/R/sim.hmm.R |only
HiddenMarkov-1.2-8/HiddenMarkov/R/sim.hmm1.R |only
HiddenMarkov-1.2-8/HiddenMarkov/R/sim.markov.R |only
HiddenMarkov-1.2-8/HiddenMarkov/R/sim.mmpp.R |only
HiddenMarkov-1.2-8/HiddenMarkov/R/simulate.mmglm.R |only
HiddenMarkov-1.2-8/HiddenMarkov/R/summary.mmglm.R |only
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HiddenMarkov-1.3-0/HiddenMarkov/R/BaumWelch.mmglmlong1.R |only
HiddenMarkov-1.3-0/HiddenMarkov/R/Estep.mmglm1.R |only
HiddenMarkov-1.3-0/HiddenMarkov/R/Mstep.mmglm1.R |only
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HiddenMarkov-1.3-0/HiddenMarkov/R/as.dthmm.R | 2
HiddenMarkov-1.3-0/HiddenMarkov/R/as.mmglm0.R |only
HiddenMarkov-1.3-0/HiddenMarkov/R/deprecated.R |only
HiddenMarkov-1.3-0/HiddenMarkov/R/dmmglm.R |only
HiddenMarkov-1.3-0/HiddenMarkov/R/forwardback.dthmm.R |only
HiddenMarkov-1.3-0/HiddenMarkov/R/logLik.mmglm0.R |only
HiddenMarkov-1.3-0/HiddenMarkov/R/mmglm.R | 12
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HiddenMarkov-1.3-0/HiddenMarkov/R/summary.mmglm0.R |only
HiddenMarkov-1.3-0/HiddenMarkov/R/summary.mmglm1.R |only
HiddenMarkov-1.3-0/HiddenMarkov/R/summary.mmglmlong1.R |only
HiddenMarkov-1.3-0/HiddenMarkov/inst/doc/index.html | 19
HiddenMarkov-1.3-0/HiddenMarkov/man/BaumWelch.Rd | 54 +
HiddenMarkov-1.3-0/HiddenMarkov/man/Changes.Rd | 14
HiddenMarkov-1.3-0/HiddenMarkov/man/Estep.Rd | 16
HiddenMarkov-1.3-0/HiddenMarkov/man/HiddenMarkov-dthmm-deprecated.Rd | 4
HiddenMarkov-1.3-0/HiddenMarkov/man/HiddenMarkov-internal.Rd | 13
HiddenMarkov-1.3-0/HiddenMarkov/man/HiddenMarkov.Rd | 13
HiddenMarkov-1.3-0/HiddenMarkov/man/Mstep.Rd | 10
HiddenMarkov-1.3-0/HiddenMarkov/man/Transform-Parameters.Rd |only
HiddenMarkov-1.3-0/HiddenMarkov/man/Viterbi.Rd | 20
HiddenMarkov-1.3-0/HiddenMarkov/man/bwcontrol.Rd | 2
HiddenMarkov-1.3-0/HiddenMarkov/man/compdelta.Rd | 12
HiddenMarkov-1.3-0/HiddenMarkov/man/dthmm.Rd | 40 -
HiddenMarkov-1.3-0/HiddenMarkov/man/forwardback.Rd | 21
HiddenMarkov-1.3-0/HiddenMarkov/man/logLik.Rd | 10
HiddenMarkov-1.3-0/HiddenMarkov/man/mchain.Rd | 2
HiddenMarkov-1.3-0/HiddenMarkov/man/mmglm-2nd-level-functions.Rd |only
HiddenMarkov-1.3-0/HiddenMarkov/man/mmglm.Rd | 275 ++++++++--
HiddenMarkov-1.3-0/HiddenMarkov/man/mmpp-2nd-level-functions.Rd | 2
HiddenMarkov-1.3-0/HiddenMarkov/man/neglogLik.Rd | 10
HiddenMarkov-1.3-0/HiddenMarkov/man/probhmm.Rd | 14
HiddenMarkov-1.3-0/HiddenMarkov/man/residuals.Rd | 12
HiddenMarkov-1.3-0/HiddenMarkov/man/simulate.Rd | 18
HiddenMarkov-1.3-0/HiddenMarkov/man/summary.Rd | 14
70 files changed, 447 insertions(+), 171 deletions(-)
Title: Computation of functional similarities between GO terms and gene
products; GO enrichement analysis
Diff between GOSim versions 1.2.1.0 dated 2010-01-14 and 1.2.1.1 dated 2010-01-22
Description: This package implements several functions useful for
computing similarities between GO terms and gene products based
on their GO annotation. Moreover it allows for computing a GO
enrichment analysis
Author: Holger Froehlich
Maintainer: Holger Froehlich
.project | 36 +-
DESCRIPTION | 11
R/termSimilarity.R | 3
inst/doc/GOSim.pdf | 872 ++++++++++++++++++++++++++---------------------------
4 files changed, 463 insertions(+), 459 deletions(-)
Title: An interface for creating GUIs modeled in part after traits UI
module for python.
Diff between traitr versions 0.1 dated 2010-01-15 and 0.3 dated 2010-01-22
Description: An inteface for creating GUIs modeled in part after the
traits UI module for pyton. The basic design takes advantage of
model-view-controller design pattern. The overall interface
makes basic dialogs quite easy to produce.
Author: John Verzani
Maintainer: John Verzani
ChangeLog |only
DESCRIPTION | 11 +-
NEWS | 23 +++++
R/base.R | 203 +++++++++++++++++++++++++++++++++----------------
R/container.R | 21 ++++-
R/controller.R | 31 +++++--
R/dialog.R | 31 ++++---
R/editor.R | 40 +++++++--
R/helpers.R | 15 +++
R/itemgroup.R | 61 +++++++++-----
R/items.R | 134 ++++++++++++++++++++------------
R/model.R | 37 +++++++-
R/traitR-package.R | 15 +++
R/view.R | 89 ++++++++++++++++-----
README | 8 -
TODO.txt | 15 +--
inst/doc/df-scroll.png |only
inst/doc/traitr.Rnw | 63 +++++++++++++++
inst/doc/traitr.pdf |binary
inst/doc/traitr.rel |only
man/dfEditItem.Rd | 6 -
testing/test-mvc.R | 2
22 files changed, 586 insertions(+), 219 deletions(-)
Title: R code for Stock Synthesis
Diff between r4ss versions 1.03 dated 2010-01-13 and 1.04 dated 2010-01-22
Description: Functions for reading output, plotting, exploring and
manipulating input files for Richard Methot's Stock Synthesis
fisheries stock assessment modeling platform.
Author: Ian Taylor, Ian Stewart, Tommy Garrison, Andre Punt, John
Wallace, and other contributors
Maintainer: Ian Taylor
DESCRIPTION | 8 ++++----
R/RebuildPlot.R |only
R/SSv3_output.R | 18 +++++++++---------
R/SSv3_plots.R | 43 ++++++++++++++++++++++++-------------------
inst/doc/r4ss_vignette.pdf |binary
man/RebuildPlot.Rd |only
man/SS_parlines.Rd | 2 +-
man/r4ss-package.Rd | 4 ++--
8 files changed, 40 insertions(+), 35 deletions(-)
Title: Utilities to fit paired comparison models for preferences
Diff between prefmod versions 0.8-16 dated 2009-06-14 and 0.8-18 dated 2010-01-22
Description: Generates design matrix for analysing real paired
comparisons and derived paired comparison data (Likert type
items / ratings or rankings) using a loglinear approach. Fits
loglinear Bradley-Terry model (LLBT) exploting an eliminate
feature. Computes pattern models for paired comparisons,
rankings, and ratings. Some treatment of missing values (MCAR
and MNAR). Fits latent class (mixture) models for paired
comparison, rating and ranking patterns.
Author: Reinhold Hatzinger
Maintainer: Reinhold Hatzinger
DESCRIPTION | 11 ++++-----
NAMESPACE | 3 ++
R/NIblcontrib.R | 6 ++++
R/NIgroupscontrib.R | 9 -------
R/alldistPC.R |only
R/covdesign.R | 6 +++-
R/llbtPC.fit.R | 18 +++++++++-----
R/normalize.R | 50 ++++++++++++++++++++++++-----------------
R/npml.parts.R |only
R/pattL.fit.R | 3 +-
R/pattLrep.fit.R | 3 +-
R/pattPC.fit.R | 7 ++++-
R/pattR.fit.R | 6 +++-
R/pattnpml.fit.R |only
R/plotworth.R | 5 +++-
R/splitCovs.R | 58 +++++++++++++++++++++++++++++++++---------------
data/euro55.2.des.rda |only
man/euro55.2.des.Rd |only
man/pattPC.fit.Rd | 2 -
man/pattnpml.fit.Rd |only
man/prefmod-package.Rd | 4 +--
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22 files changed, 120 insertions(+), 71 deletions(-)
Title: Simulate and test marker dosage for dominant markers in
autopolyploids
Diff between polySegratio versions 0.2-2 dated 2009-11-18 and 0.2-3 dated 2010-01-22
Description: Perform classic chi-squared tests and Ripol et al(1999)
binomial confidence interval approach for autopolyploid
dominant markers. Also, dominant markers may be generated for
families of offspring where either one or both of the parents
possess the marker. Missing values and misclassified markers
may be generated at random.
Author: Peter Baker
Maintainer: Peter Baker
polySegratio-0.2-2/polySegratio/TODO |only
polySegratio-0.2-2/polySegratio/inst/doc/polySegratio-commands.pdf |only
polySegratio-0.2-2/polySegratio/inst/doc/polySegratio-overview.pdf-old |only
polySegratio-0.2-3/polySegratio/DESCRIPTION | 12
polySegratio-0.2-3/polySegratio/inst/doc/polySegratio-overview.pdf |binary
polySegratio-0.2-3/polySegratio/inst/doc/tmp/tmp-007.eps | 180 -
polySegratio-0.2-3/polySegratio/inst/doc/tmp/tmp-007.pdf | 200 +-
polySegratio-0.2-3/polySegratio/inst/doc/tmp/tmp-009.eps | 492 ++---
polySegratio-0.2-3/polySegratio/inst/doc/tmp/tmp-009.pdf | 504 ++---
polySegratio-0.2-3/polySegratio/inst/doc/tmp/tmp-010.eps | 882 ++++-----
polySegratio-0.2-3/polySegratio/inst/doc/tmp/tmp-010.pdf | 934 ++++------
polySegratio-0.2-3/polySegratio/man/polySegratio-package.Rd | 2
12 files changed, 1583 insertions(+), 1623 deletions(-)
Title: Parallelised Estimation of Prediction Error
Diff between peperr versions 1.1-4 dated 2009-09-28 and 1.1-5 dated 2010-01-22
Description: Package peperr is designed for prediction error estimation
through resampling techniques, possibly accelerated by parallel
execution on a compute cluster. Newly developed model fitting
routines can be easily incorporated.
Author: Christine Porzelius, Harald Binder
Maintainer: Christine Porzelius
DESCRIPTION | 6 +++---
R/peperr.R | 9 ++++-----
R/pmpec.R | 2 +-
changeLog | 3 +++
4 files changed, 11 insertions(+), 9 deletions(-)
Title: Multi-state Path-Dependent Models in Discrete Time
Diff between mspath versions 0.9-6 dated 2010-01-21 and 0.9-7 dated 2010-01-22
Description: Functions for fitting path-dependent (non-Markov)
multi-state models to categorical processes observed at
arbitrary times, optionally with misclassified responses, and
covariates on transition or misclassification rates. Uses
discrete-time approximation. Based on the Jackson's msm
package v 0.3.1, with an interface as compatible as possible.
Author: Ross Boylan
Maintainer: Ross Boylan
ChangeLog | 4
DESCRIPTION | 8
inst/doc/mspath-program.pdf |binary
inst/doc/mspath-program.ps |28407 ++++++++++++++++++++++++++------------------
man/expit.Rd | 2
man/logit.Rd | 2
src/trueSrc/Coefficient.eps | 8660 ++++++-------
src/trueSrc/Coefficient.pdf |binary
8 files changed, 21640 insertions(+), 15443 deletions(-)
Title: procedures for automated interpolation
Diff between intamap versions 1.3-1 dated 2009-11-19 and 1.3-3 dated 2010-01-22
Description: A package that provides classes and methods for automated
spatial interpolation.
Author: Edzer Pebesma
Maintainer: Edzer J. Pebesma
DESCRIPTION | 8 -
R/estimateAnisotropy.R | 24 +++--
R/pointKriging.R | 41 +++++++-
R/spCopPred.R | 2
R/transGaussian.R | 50 ++++++++--
man/estimateAnisotropy.Rd | 15 ++-
man/intamap-package.Rd | 10 ++
man/interpolate.Rd | 7 +
man/rotateAnisotropicData.Rd | 15 +--
tests/idw.Rout.save | 52 +++-------
tests/interpolate.Rout.save | 204 +++++++++----------------------------------
11 files changed, 192 insertions(+), 236 deletions(-)
Title: Multivariate Statistical Analysis in Chemometrics
Diff between chemometrics versions 0.5 dated 2009-11-08 and 0.6 dated 2010-01-22
Description: This package is the R companion to the book "Introduction
to Multivariate Statistical Analysis in Chemometrics" written
by K. Varmuza and P. Filzmoser (2009)
Author: P. Filzmoser and K. Varmuza
Maintainer: P. Filzmoser
DESCRIPTION | 8 ++++----
R/RPvectors.R |only
man/RPvectors.Rd |only
3 files changed, 4 insertions(+), 4 deletions(-)
Title: Another Multidimensional Analysis Package
Diff between amap versions 0.8-4 dated 2009-10-23 and 0.8-5 dated 2010-01-22
Description: Tools for Clustering and Principal Component Analysis
(With robusts methods, and parallelized functions).
Author: Antoine Lucas
Maintainer: Antoine Lucas
DESCRIPTION | 8 ++++----
inst/doc/amap.pdf |binary
src/distance_T.cpp | 6 +++---
3 files changed, 7 insertions(+), 7 deletions(-)
Title: Rcpp R/C++ interface package
Diff between Rcpp versions 0.7.2 dated 2010-01-13 and 0.7.3 dated 2010-01-22
Description: R/C++ interface classes and examples The Rcpp library maps
data types betweeen R and C++, and includes support for R types
real, integer, character, vector, matrix, Date, datetime (i.e.
POSIXct) at microsecond resolution, data frame, and function.
Transfer to and from simple SEXP objects is particular easy.
Calling R functions from C++ is also supported.
C++ code can be 'inlined' by using the 'inline' package which will
create a C++ function and compile, link and load it given the
'inlined' character argument which makes C++ integration very
easy.
Several examples are included.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by
Simon Urbanek and David Reiss; based on code written during
2005 and 2006 by Dominick Samperi
Maintainer: Dirk Eddelbuettel
DESCRIPTION | 13 -
INDEX | 2
NAMESPACE | 3
R/Rcpp.package.skeleton.R |only
R/RcppLdpath.R | 43 ++++-
R/exceptions.R | 42 ++++-
R/zzz.R | 4
cleanup | 1
configure | 179 ++++++++++++++++++++---
configure.in | 80 ++++++++--
inst/ChangeLog | 149 +++++++++++++++++++
inst/discovery |only
inst/doc/Rcpp-unitTests.html | 10 -
inst/doc/Rcpp-unitTests.pdf |binary
inst/doc/Rcpp-unitTests.txt | 240 ++++++++++++++++----------------
inst/skeleton |only
inst/unitTests/runit.CharacterVector.R | 4
inst/unitTests/runit.ComplexVector.R | 4
inst/unitTests/runit.ExpressionVector.R | 43 +++++
inst/unitTests/runit.Function.R | 5
inst/unitTests/runit.GenericVector.R | 4
inst/unitTests/runit.IntegerVector.R | 4
inst/unitTests/runit.Language.R | 8 -
inst/unitTests/runit.NumericVector.R | 3
inst/unitTests/runit.Pairlist.R | 8 -
inst/unitTests/runit.RawVector.R | 3
inst/unitTests/runit.environments.R | 16 ++
inst/unitTests/runit.evaluator.R | 20 --
inst/unitTests/runit.wrap.R | 12 +
man/Rcpp.package.skeleton.Rd |only
src/CharacterVector.cpp | 45 ------
src/ComplexVector.cpp | 24 ---
src/Environment.cpp | 51 ++++--
src/Evaluator.cpp | 44 +++--
src/ExpressionVector.cpp | 56 ++++---
src/Function.cpp | 16 --
src/GenericVector.cpp | 39 +----
src/IntegerVector.cpp | 31 ----
src/Language.cpp | 2
src/LogicalVector.cpp | 36 ----
src/Makevars.in | 2
src/Makevars.win | 1
src/NumericVector.cpp | 30 ----
src/Pairlist.cpp | 12 -
src/Promise.cpp | 2
src/RObject.cpp | 3
src/RawVector.cpp | 32 ----
src/Rcpp/CharacterVector.h | 40 ++---
src/Rcpp/ComplexVector.h | 37 ++--
src/Rcpp/Environment.h | 47 ++++--
src/Rcpp/Evaluator.h | 26 +--
src/Rcpp/ExpressionVector.h | 46 ++++--
src/Rcpp/Function.h | 28 ---
src/Rcpp/GenericVector.h | 33 ++--
src/Rcpp/IntegerVector.h | 59 +++++--
src/Rcpp/Language.h | 8 -
src/Rcpp/LogicalVector.h | 66 +++++---
src/Rcpp/NumericVector.h | 58 +++++--
src/Rcpp/Pairlist.h | 11 -
src/Rcpp/Promise.h | 4
src/Rcpp/RObject.h | 20 +-
src/Rcpp/RawVector.h | 54 +++++--
src/Rcpp/VectorBase.h |only
src/RcppCommon.cpp | 40 -----
src/RcppCommon.h | 29 ++-
src/VectorBase.cpp |only
src/exceptions.cpp | 16 +-
67 files changed, 1166 insertions(+), 782 deletions(-)
Title: SQLite interface for R
Diff between RSQLite versions 0.8-1 dated 2010-01-07 and 0.8-2 dated 2010-01-22
Description: Database Interface R driver for SQLite. This package
embeds the SQLite database engine in R and provides an
interface compliant with the DBI package. The source for the
SQLite engine (version 3.6.21) is included.
Author: David A. James
Maintainer: Seth Falcon
DESCRIPTION | 6 +++---
inst/NEWS | 4 ++++
src/RS-DBI.h | 16 +++++++++-------
3 files changed, 16 insertions(+), 10 deletions(-)