Title: Significance analysis of sequencing data based on a Poisson log
linear model
Diff between PoissonSeq versions 1.1 dated 2011-09-08 and 1.1.1 dated 2012-10-09
Description: This package implements a method for normalization,
testing, and false discovery rate estimation for RNA-sequencing
data. The description of the method is in Li J, Witten DM,
Johnstone I, Tibshirani R (2012). Normalization, testing, and
false discovery rate estimation for RNA-sequencing data.
Biostatistics 13(3): 523-38. We estimate the sequencing depths
of experiments using a new method based on Poisson
goodness-of-fit statistic, calculate a score statistic on the
basis of a Poisson log-linear model, and then estimate the
false discovery rate using a modified version of permutation
plug-in method. A more detailed instruction as well as sample
data is available at
http://www.stanford.edu/~junli07/research.html. In Version
1.1.1, we changed the way of calculating log foldchange for
two-class data. The FDR estimation part remains unchanged.
Author: Jun Li
Maintainer: Jun Li
DESCRIPTION | 31 +++++++++++++++++--------------
MD5 | 8 ++++----
R/ps_main.R | 10 +++++-----
R/ps_other.R | 13 ++++++++++---
man/PS.Main.Rd | 4 ++--
5 files changed, 38 insertions(+), 28 deletions(-)
Title: Companion to Applied Regression
Diff between car versions 2.0-14 dated 2012-09-20 and 2.0-15 dated 2012-10-09
Description: This package accompanies J. Fox and S. Weisberg, An R
Companion to Applied Regression, Second Edition, Sage, 2011.
Author: John Fox [aut, cre], Sanford Weisberg [aut], Douglas Bates
[ctb], David Firth [ctb], Michael Friendly [ctb], Gregor
Gorjanc [ctb], Spencer Graves [ctb], Richard Heiberger [ctb],
Rafael Laboissiere [ctb], Georges Monette [ctb], Henric Nilsson
[ctb], Derek Ogle [ctb], Brian Ripley [ctb], Achim Zeileis
[ctb], R-Core [ctb]
Maintainer: John Fox
DESCRIPTION | 17 +--
MD5 | 34 +++---
NAMESPACE | 4
NEWS | 10 +
R/Boot.R | 77 +++++++++++--
R/compareCoefs.R | 2
R/marginalModelPlot.R | 248 ++++++++++++++++++++++++++++++--------------
R/recode.R | 4
R/residualPlots.R | 4
R/scatterplotSmoothers.R | 48 ++++++--
R/utility-functions.R | 66 +++++++++++
man/Anova.Rd | 4
man/Boot.Rd | 26 +++-
man/ScatterplotSmoothers.Rd | 10 +
man/car-package.Rd | 70 ++++++------
man/marginalModelPlot.Rd | 39 ++++--
man/recode.Rd | 10 +
man/residualPlots.Rd | 3
18 files changed, 478 insertions(+), 198 deletions(-)
Title: Toolkit for Weighting and Analysis of Nonequivalent Groups
Diff between twang versions 1.2-6 dated 2012-09-18 and 1.2-7 dated 2012-10-09
Description: This package offers functions for propensity score
estimating and weighting, nonresponse weighting, and diagnosis
of the weights. This package was originally developed by Drs.
Ridgeway, McCaffrey, and Morral. Burgette, Griffin and
McCaffrey updated the package in 2011.
Author: Greg Ridgeway
Maintainer: Lane Burgette
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
R/get.weights.R | 2 +-
data/egsingle.RData |binary
data/lalonde.RData |binary
data/lindner.RData |binary
data/raceprofiling.RData |binary
inst/doc/twang.pdf |binary
8 files changed, 12 insertions(+), 12 deletions(-)
Title: Computation of functional similarities between GO terms and gene
products; GO enrichment analysis
Diff between GOSim versions 1.2.7.2 dated 2012-08-02 and 1.2.7.7 dated 2012-10-09
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
GOSim-1.2.7.2/GOSim/.project |only
GOSim-1.2.7.2/GOSim/R/GOSim.R |only
GOSim-1.2.7.2/GOSim/inst/doc/GOSim.Rnw |only
GOSim-1.2.7.7/GOSim/DESCRIPTION | 12 +++----
GOSim-1.2.7.7/GOSim/MD5 | 34 ++++++++++------------
GOSim-1.2.7.7/GOSim/R/GOenrichment.R | 5 +--
GOSim-1.2.7.7/GOSim/R/geneSimilarity.R | 37 ++++++++++++------------
GOSim-1.2.7.7/GOSim/R/general.R | 12 +++----
GOSim-1.2.7.7/GOSim/R/manifold_embedding.R | 6 +--
GOSim-1.2.7.7/GOSim/R/termSimilarity.R | 18 +++++------
GOSim-1.2.7.7/GOSim/data/ICsBPhumanall.rda |binary
GOSim-1.2.7.7/GOSim/data/ICsCChumanall.rda |binary
GOSim-1.2.7.7/GOSim/data/ICsMFhumanall.rda |binary
GOSim-1.2.7.7/GOSim/inst/doc/GOSim.pdf |binary
GOSim-1.2.7.7/GOSim/man/filterGO.Rd | 5 +--
GOSim-1.2.7.7/GOSim/man/getGOInfo.Rd | 2 -
GOSim-1.2.7.7/GOSim/man/getGeneSim.Rd | 4 +-
GOSim-1.2.7.7/GOSim/man/getGeneSimPrototypes.Rd | 2 -
GOSim-1.2.7.7/GOSim/man/getTermSim.Rd | 2 -
GOSim-1.2.7.7/GOSim/man/setEvidenceLevel.Rd | 10 +++---
20 files changed, 75 insertions(+), 74 deletions(-)
Title: General network (HTTP/FTP/...) client interface for R
Diff between RCurl versions 1.95-0.1 dated 2012-10-02 and 1.95-1.1 dated 2012-10-09
Description: The package allows one to compose general HTTP requests
and provides convenient functions to fetch URIs, get & post
forms, etc. and process the results returned by the Web server.
This provides a great deal of control over the HTTP/FTP/...
connection and the form of the request while providing a
higher-level interface than is available just using R socket
connections. Additionally, the underlying implementation is
robust and extensive, supporting FTP/FTPS/TFTP (uploads and
downloads), SSL/HTTPS, telnet, dict, ldap, and also supports
cookies, redirects, authentication, etc.
Author: Duncan Temple Lang
Maintainer: Duncan Temple Lang
RCurl-1.95-0.1/RCurl/CRAN_changes |only
RCurl-1.95-0.1/RCurl/src/Makevars |only
RCurl-1.95-1.1/RCurl/DESCRIPTION | 6 +++---
RCurl-1.95-1.1/RCurl/MD5 | 12 +++++-------
RCurl-1.95-1.1/RCurl/R/curlAuthConstants.R | 4 ++--
RCurl-1.95-1.1/RCurl/R/form.S | 2 +-
RCurl-1.95-1.1/RCurl/README.windows | 5 +++++
RCurl-1.95-1.1/RCurl/src/json.c | 3 ++-
8 files changed, 18 insertions(+), 14 deletions(-)
Title: Classification and regression trees
Diff between tree versions 1.0-31 dated 2012-08-06 and 1.0-32 dated 2012-10-09
Description: Classification and Regression Trees.
Author: Brian Ripley
Maintainer: Brian Ripley
ChangeLog | 4 ++++
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/treemisc.R | 20 ++++++++++++++------
man/text.tree.Rd | 11 ++++++-----
src/init.c | 6 +++++-
6 files changed, 38 insertions(+), 21 deletions(-)
Title: R tools for integrating phylogenies and ecology
Diff between picante versions 1.5-1 dated 2012-10-02 and 1.5-2 dated 2012-10-09
Description: Phylocom integration, community analyses, null-models,
traits and evolution in R
Author: Steven W. Kembel
Maintainer: Steven W. Kembel
picante-1.5-1/picante/R/pic3.R |only
picante-1.5-1/picante/man/pic3.Rd |only
picante-1.5-2/picante/DESCRIPTION | 8 ++++----
picante-1.5-2/picante/MD5 | 12 +++++-------
picante-1.5-2/picante/R/traitgram.R | 18 ++++++++----------
picante-1.5-2/picante/inst/doc/picante-intro.pdf |binary
picante-1.5-2/picante/man/picante-package.Rd | 4 ++--
picante-1.5-2/picante/man/traitgram.Rd | 5 ++---
8 files changed, 21 insertions(+), 26 deletions(-)
Title: Functions to assess the strength and significance of
relationship of species site group associations
Diff between indicspecies versions 1.6.3 dated 2012-06-27 and 1.6.5 dated 2012-10-09
Description: This package provides a set of functions to assess the
strength of species site group associations. It is also
possible to check the statistical significance of such
associations.
Author: Miquel De Caceres, Florian Jansen
Maintainer: Miquel De Caceres
DESCRIPTION | 7 +++--
MD5 | 12 ++++-----
R/multipatt.r | 56 +++++++++++++++++++-------------------------
R/signassoc.r | 26 ++------------------
man/indicspecies-package.Rd | 3 +-
man/multipatt.Rd | 14 +++--------
man/signassoc.Rd | 21 +++++++---------
7 files changed, 55 insertions(+), 84 deletions(-)
Title: Toolkit implementation of gWidgets for tcltk package
Diff between gWidgetstcltk versions 0.0-52 dated 2012-06-20 and 0.0-53 dated 2012-10-09
Description: Port of the gWidgets API to the tcltk package. Requires TK
8.5 or greater for the tile (ttk)widgets
http://www.tcl.tk/software/tcltk/8.5.tml. This is the default
on Windows. Under linux, Tk must be installed. Under Mac OS X
(10.5) there are two options: native Tk or X11. For the native
one, Tk must be upgraded. See www.tcl.tk to download source.
Under the Mac it compiles and installs cleanly. For X11, tcltk
libraries can be downloaded to augment the R binary package.
See http://cran.r-project.org/bin/macosx/tools/. The gdf
function requires the add on Tk package TkTable
(http://tktable.sourceforge.net/).
Author: John Verzani
Maintainer: John Verzani
DESCRIPTION | 10
MD5 | 123 ++++
NEWS | 9
R/aaaGenerics.R | 9
R/aaaHandlers.R | 2
R/aaaR5classes.R | 2
R/dnd.R | 43 -
R/gaction.R | 21
R/gdf.R | 963 +++++++++++++++++++-------------------
R/gdialogs.R | 4
R/gfile.R | 7
R/glayout.R | 2
R/zzz.R | 37 +
inst/tklibs/autoscroll.tcl |only
inst/tklibs/tablelist5.6 |only
man/gWidgetstcltk-undocumented.Rd | 3
16 files changed, 718 insertions(+), 517 deletions(-)
Title: SNP-set (Sequence) Kernel Association Test
Diff between SKAT versions 0.78 dated 2012-09-06 and 0.79 dated 2012-10-09
Description: Kernel based SNP set test
Author: Seunggeun Lee, Larisa Miropolsky and Micheal Wu
Maintainer: Seunggeun (Shawn) Lee
DESCRIPTION | 6 +++---
MD5 | 16 ++++++++--------
R/Main.R | 7 +++++--
R/Power_Corr.R | 33 +++++++++++++++++++++++++++++++--
inst/doc/SKAT.Rnw | 34 +++++++++++++++++++++++++++++++---
inst/doc/SKAT.pdf |binary
man/Power_Continuous.rd | 15 +++++++++++----
man/Power_Logistic.rd | 15 +++++++++++----
man/SKAT.rd | 17 +++++++++++------
9 files changed, 111 insertions(+), 32 deletions(-)
Title: gWidgets API for building toolkit-independent, interactive GUIs
Diff between gWidgets versions 0.0-50 dated 2012-04-03 and 0.0-52 dated 2012-10-09
Description: gWidgets provides a toolkit-independent API for building
interactive GUIs. At least one of the 'gWidgetsXXX packages',
such as gWidgetstcltk, needs to be installed. Some icons are on
loan from the scigraphica project
http://scigraphica.sourceforge.net.
Author: John Verzani. Based on the iwidgets code of Simon Urbanek and
suggestions by Simon Urbanek, Philippe Grosjean and Michael
Lawrence
Maintainer: John Verzani
DESCRIPTION | 12 ++++----
MD5 | 64 ++++++++++++++++++++++----------------------
NEWS | 14 +++++++++
R/gcommandline.R | 26 ++++++++---------
R/ggenericwidget.R | 22 +++++++--------
R/ghelp.R | 56 +++++++++++++++++++-------------------
R/glabel.R | 6 ++--
R/guiWidget.R | 3 ++
inst/doc/addingToolkit.pdf |binary
inst/doc/gWidgets.Rnw | 13 ++++----
inst/doc/gWidgets.pdf |binary
inst/tests/test-gcalendar.R | 2 -
inst/tests/test-gimage.R | 1
man/gWidgets-dialogs.Rd | 2 -
man/gWidgets-dnd.Rd | 4 +-
man/gWidgets-handlers.Rd | 6 ++--
man/gbutton.Rd | 8 ++---
man/gcheckboxgroup.Rd | 6 ++--
man/gcombobox.Rd | 4 +-
man/gformlayout.Rd | 8 ++---
man/ggraphics.Rd | 10 +++---
man/ggroup.Rd | 6 ++--
man/ghelp.Rd | 10 +++---
man/gimage.Rd | 2 -
man/gmenu.Rd | 6 ++--
man/gnotebook.Rd | 4 +-
man/gpanedgroup.Rd | 6 ++--
man/gradio.Rd | 4 +-
man/gseparator.Rd | 6 ++--
man/gslider.Rd | 6 ++--
man/gstatusbar.Rd | 6 ++--
man/gtable.Rd | 16 +++++------
man/gwindow.Rd | 4 +-
33 files changed, 179 insertions(+), 164 deletions(-)
Title: Regularization paths for regression models with grouped
covariates
Diff between grpreg versions 2.1-0 dated 2012-07-28 and 2.2-0 dated 2012-10-09
Description: Efficient algorithms for fitting the regularization path
of linear or logistic regression models with grouped penalties,
such as group lasso, group MCP, and group SCAD. The algorithms
are based on the idea of either locally approximated coordinate
descent or group descent, depending on the penalty.
Author: Patrick Breheny
Maintainer: Patrick Breheny
DESCRIPTION | 8 +++---
MD5 | 34 +++++++++++++--------------
NEWS | 14 ++++++++++-
R/cv.grpreg.R | 55 ++++++++++++++------------------------------
R/grpreg.R | 6 +++-
R/logLik.R | 3 --
R/loss.R | 15 ++++++++----
R/orthogonalize.R | 5 ++--
R/plot.R | 26 +++++++++++++-------
R/plot.cv.R | 38 ++++++++++++++----------------
R/predict.R | 7 ++++-
R/select.R | 2 -
inst/tests/agreement.R | 2 -
inst/tests/extra-features.R | 8 +++++-
man/cv.grpreg.Rd | 34 +++++++--------------------
man/grpreg.Rd | 2 -
man/plot.grpreg.Rd | 7 ++++-
man/predict.Rd | 12 ++++++++-
18 files changed, 145 insertions(+), 133 deletions(-)