Folks in the New Jersey area no longer need to trek over to New York City to meet other R users. Now there's NewJerseyR, a new R user group put together by Mango Solutions. The first meeting will in Iselin on September 16, with speakers from Mango, Pfizer, and Bristol Myers Squibb. Full details at the NewJerseyR website, linked below.
NewJerseyR: NewJerseyR home page
Title: Boruta -- a tool for finding significant attributes in
information systems
Description: Boruta is a feature selection algorithm based on a
randomForest predictor. It selects the full set of all
important attributes by comparing original attributes
importance with datum importance of their randomised copies.
Author: Algorithm by Witold R. Rudnicki , R
implementation by Miron B. Kursa .
Maintainer: Miron B. Kursa
Diff between Boruta versions 1.2 dated 2010-05-08 and 1.3 dated 2010-09-02
DESCRIPTION | 8 ++++---- R/Boruta.R | 16 ++++++++-------- inst/CITATION |only inst/NEWS | 6 +++++- man/Boruta.Rd | 6 +++++- 5 files changed, 22 insertions(+), 14 deletions(-)
Title: Supervised Clustering of Predictor Variables such as Genes
Description: Methodology for supervised grouping aka "clustering" of
potentially many predictor variables, such as genes etc.
Author: Marcel Dettling and Martin Maechler
Maintainer: Martin Maechler
Diff between supclust versions 1.0-5 dated 2005-05-18 and 1.0-6 dated 2010-09-02
DESCRIPTION | 25 +++-- R/pelora-utils.R | 15 +-- R/pelora.R | 159 +++++++++++++++--------------------- man/coef.pelora.Rd | 17 --- man/dlda.Rd | 17 ++- man/fitted.pelora.Rd | 18 +--- man/fitted.wilma.Rd | 15 --- man/margin.Rd | 2 man/pelora.Rd | 8 - man/plot.pelora.Rd | 16 --- man/plot.wilma.Rd | 25 +---- man/predict.pelora.Rd | 20 +--- man/predict.wilma.Rd | 24 ++--- man/print.pelora.Rd | 21 +--- man/print.wilma.Rd | 13 -- man/score.Rd | 2 man/sign.change.Rd | 2 man/signflip.Rd | 2 man/standardize.genes.Rd | 2 man/summary.pelora.Rd | 16 --- man/summary.wilma.Rd | 13 -- man/wilma.Rd | 4 src/pelora.c | 6 - src/wilma.c | 8 - tests/pelora-ex.Rout.save | 138 +++++++++++++++---------------- tests/wilma-ex.Rout.save | 202 +++++----------------------------------------- 26 files changed, 268 insertions(+), 522 deletions(-)
Title: Functions for soil texture plot, classification and
transformation
Description: "The Soil Texture Wizard" is a set of R functions designed
to produce texture triangles (also called texture plots,
texture diagrams, texture ternary plots), classify and
transform soil textures data. These functions virtually allows
to plot any soil texture triangle / classification into any
triangle geometry (isosceles, right-angled triangles, etc.).
This set of function is expected to be useful to people using
soil textures data from different soil texture classification
or different particle size systems. Several texture triangles
are predefined: USDA; FAO (which is also the triangle for the
soil map of Europe); Aisne (France); GEPPA (France); German
triangle (Bodenkundliche Kartieranleitung 1994); Soil Survey of
England and Wales (UK); Australian triangle; Belgian triangle;
Canadian triangle; ISSS triangle; Romanian traingle. The Soil
Texture Wizard is initially develloped from the functions
'soil.texture()' from the package 'plotrix' by Jim Lemon et al.
Author: Julien MOEYS , contributions
from Wei Shangguan.
Maintainer: Julien MOEYS
Diff between soiltexture versions 1.0 dated 2010-08-18 and 1.01 dated 2010-09-02
soiltexture-1.0/soiltexture/inst/doc2 |only soiltexture-1.01/soiltexture/DESCRIPTION | 13 - soiltexture-1.01/soiltexture/R/soiltexture.R | 129 +++++----- soiltexture-1.01/soiltexture/inst/doc/CC-By-SA-nonported-88x31.PNG |only soiltexture-1.01/soiltexture/inst/doc/Sweave.sty |only soiltexture-1.01/soiltexture/inst/doc/TT.env.Rd |only soiltexture-1.01/soiltexture/inst/doc/julienmoeysmailaddress-322-24.png |only soiltexture-1.01/soiltexture/inst/doc/julienmoeysmailaddress-382-25.png |only soiltexture-1.01/soiltexture/inst/doc/soiltexture_vignette.R |only soiltexture-1.01/soiltexture/inst/doc/soiltexture_vignette.Rnw |only soiltexture-1.01/soiltexture/inst/doc/soiltexture_vignette.bib |only soiltexture-1.01/soiltexture/inst/doc/soiltexture_vignette.pdf |binary soiltexture-1.01/soiltexture/inst/doc/transformations.R |only soiltexture-1.01/soiltexture/inst/doc/transformations.Rnw |only soiltexture-1.01/soiltexture/inst/doc/transformations.pdf |only soiltexture-1.01/soiltexture/inst/doc/version.txt |only soiltexture-1.01/soiltexture/man/TT.text.transf.Xm.Rd | 20 - soiltexture-1.01/soiltexture/man/soiltexture-package.Rd | 4 18 files changed, 89 insertions(+), 77 deletions(-)
Title: Statistical Catch-at-Age Plotting Environment
Description: Import and plot results from statistical catch-at-age
models, used in fisheries stock assessments.
Author: Arni Magnusson
Maintainer: Arni Magnusson
Diff between scape versions 1.1-2 dated 2010-09-01 and 1.1-4 dated 2010-09-02
DESCRIPTION | 8 ++++---- NEWS | 4 ++-- data/x.cod.R | 2 +- data/x.ling.R | 2 +- data/x.oreo.R | 2 +- data/x.sbw.R | 2 +- inst/doc/Rplots.pdf | 4 ++-- inst/doc/dsc-vignette.pdf |binary inst/doc/gallery.pdf |binary inst/doc/mymodel.pdf |binary man/plotB.Rd | 8 ++------ man/plotCA.Rd | 10 +++------- man/plotCL.Rd | 8 ++------ man/plotIndex.Rd | 8 ++------ man/plotLA.Rd | 8 ++------ man/plotN.Rd | 8 ++------ man/plotSel.Rd | 6 +----- 17 files changed, 26 insertions(+), 54 deletions(-)
Title: Interface between R and GGobi
Description: The rggobi package provides a command-line interface to
GGobi, an interactive and dynamic graphics package. Rggobi
complements GGobi's graphical user interface, providing a way
to fluidly transition between analysis and exploration, as well
as automating common tasks.
Author: Duncan Temple Lang , Debby
Swayne , Hadley Wickham
, Michael Lawrence
Maintainer: Hadley Wickham
Diff between rggobi versions 2.1.14 dated 2009-05-10 and 2.1.16 dated 2010-09-02
rggobi-2.1.14/rggobi/man/as-data-frame-GGobiData-10.rd |only rggobi-2.1.14/rggobi/man/check-versions-qe.rd |only rggobi-2.1.14/rggobi/man/close-GGobi-jj.rd |only rggobi-2.1.14/rggobi/man/close-GGobiDisplay-3v.rd |only rggobi-2.1.14/rggobi/man/connecting-edges-cn.rd |only rggobi-2.1.14/rggobi/man/dataset-GGobiDisplay-f1.rd |only rggobi-2.1.14/rggobi/man/dataset-numeric-h2.rd |only rggobi-2.1.14/rggobi/man/dataset-up.rd |only rggobi-2.1.14/rggobi/man/dim-GGobiData-9t.rd |only rggobi-2.1.14/rggobi/man/dimnames-GGobiData-ib.rd |only rggobi-2.1.14/rggobi/man/display-GGobiData-iu.rd |only rggobi-2.1.14/rggobi/man/displays-GGobi-4v.rd |only rggobi-2.1.14/rggobi/man/edges---GGobi-b7.rd |only rggobi-2.1.14/rggobi/man/edges---GGobiData-3u.rd |only rggobi-2.1.14/rggobi/man/excluded-54.rd |only rggobi-2.1.14/rggobi/man/excluded-GGobiData-5p.rd |only rggobi-2.1.14/rggobi/man/ggobi-GGobiDisplay-zb.rd |only rggobi-2.1.14/rggobi/man/ggobi-count-bo.rd |only rggobi-2.1.14/rggobi/man/ggobi-data-add-variable-o9.rd |only rggobi-2.1.14/rggobi/man/ggobi-data-remove-variable-36.rd |only rggobi-2.1.14/rggobi/man/ggobi-display-get-tour-projection-ih.rd |only rggobi-2.1.14/rggobi/man/ggobi-gtk-main-window-c4.rd |only rggobi-2.1.14/rggobi/man/ggobi-set-data-frame-k0.rd |only rggobi-2.1.14/rggobi/man/ggobi-symbol-34.rd |only rggobi-2.1.14/rggobi/man/glyph-colour-GGobiData-fz.rd |only rggobi-2.1.14/rggobi/man/glyph-size---GGobiData-c8.rd |only rggobi-2.1.14/rggobi/man/glyph-type---GGobiData-2r.rd |only rggobi-2.1.14/rggobi/man/glyph-type-GGobiData-2i.rd |only rggobi-2.1.14/rggobi/man/ids-GGobiData-2v.rd |only rggobi-2.1.14/rggobi/man/length-GGobiDisplay-a1.rd |only rggobi-2.1.14/rggobi/man/mapGlyphType-5p.rd |only rggobi-2.1.14/rggobi/man/names---GGobiData-ga.rd |only rggobi-2.1.14/rggobi/man/names-GGobi-ol.rd |only rggobi-2.1.14/rggobi/man/ncol-GGobiData-fi.rd |only rggobi-2.1.14/rggobi/man/pmode-la.rd |only rggobi-2.1.14/rggobi/man/print-GGobi-b6.rd |only rggobi-2.1.14/rggobi/man/print-GGobiData-7s.rd |only rggobi-2.1.14/rggobi/man/rownames---GGobiData-2d.rd |only rggobi-2.1.14/rggobi/man/rownames-GGobiData-n8.rd |only rggobi-2.1.14/rggobi/man/shadowed-GGobiData-8a.rd |only rggobi-2.1.14/rggobi/man/summary-GGobiData-wb.rd |only rggobi-2.1.14/rggobi/man/valid-ggobi-mk.rd |only rggobi-2.1.14/rggobi/man/variables--hh.rd |only rggobi-2.1.14/rggobi/man/variables-GGobiDisplay-zm.rd |only rggobi-2.1.14/rggobi/man/variables-cf.rd |only rggobi-2.1.16/rggobi/DESCRIPTION | 11 ++++------ rggobi-2.1.16/rggobi/R/data.r | 2 + rggobi-2.1.16/rggobi/R/datasets.r | 6 +++-- rggobi-2.1.16/rggobi/R/display-tour.r | 5 ++-- rggobi-2.1.16/rggobi/R/display-variables.r | 3 +- rggobi-2.1.16/rggobi/R/display.r | 1 rggobi-2.1.16/rggobi/R/edges.r | 2 + rggobi-2.1.16/rggobi/R/ggobi.r | 5 +++- rggobi-2.1.16/rggobi/aclocal.m4 | 4 +-- rggobi-2.1.16/rggobi/man/GGobiCall-n1.rd | 2 - rggobi-2.1.16/rggobi/man/as-RGtkObject-8g.rd | 4 +-- rggobi-2.1.16/rggobi/man/as-data-frame-GGobiData-i6.rd |only rggobi-2.1.16/rggobi/man/check-versions-xs.rd |only rggobi-2.1.16/rggobi/man/clean-ggobi-bw.rd | 2 - rggobi-2.1.16/rggobi/man/close-GGobi-kz.rd |only rggobi-2.1.16/rggobi/man/close-GGobiDisplay-ke.rd |only rggobi-2.1.16/rggobi/man/colorscheme-6n.rd | 2 - rggobi-2.1.16/rggobi/man/connecting-edges-vf.rd |only rggobi-2.1.16/rggobi/man/dataset-GGobiDisplay-gk.rd |only rggobi-2.1.16/rggobi/man/dataset-mn.rd |only rggobi-2.1.16/rggobi/man/dataset-numeric-gd.rd |only rggobi-2.1.16/rggobi/man/dim-GGobiData-ok.rd |only rggobi-2.1.16/rggobi/man/dimnames---GGobiData-ds.rd | 4 +-- rggobi-2.1.16/rggobi/man/dimnames-GGobiData-x0.rd |only rggobi-2.1.16/rggobi/man/display-GGobiData-vz.rd |only rggobi-2.1.16/rggobi/man/display-ce.rd | 4 +-- rggobi-2.1.16/rggobi/man/displays-GGobi-n2.rd |only rggobi-2.1.16/rggobi/man/displays-kj.rd | 4 +-- rggobi-2.1.16/rggobi/man/edges---GGobi-m7.rd |only rggobi-2.1.16/rggobi/man/edges---GGobiData-qe.rd |only rggobi-2.1.16/rggobi/man/edges---GGobiDisplay-1y.rd | 2 - rggobi-2.1.16/rggobi/man/edges--p8.rd | 4 +-- rggobi-2.1.16/rggobi/man/edges-lk.rd | 4 +-- rggobi-2.1.16/rggobi/man/excluded---GGobiData-3z.rd | 2 - rggobi-2.1.16/rggobi/man/excluded-GGobiData-ic.rd |only rggobi-2.1.16/rggobi/man/excluded-ec.rd |only rggobi-2.1.16/rggobi/man/get--GGobi-7p.rd | 4 +-- rggobi-2.1.16/rggobi/man/get--GGobiData-9v.rd | 8 +++---- rggobi-2.1.16/rggobi/man/ggobi-GGobiDisplay-zh.rd |only rggobi-2.1.16/rggobi/man/ggobi-check-structs-qq.rd | 4 --- rggobi-2.1.16/rggobi/man/ggobi-count-u4.rd |only rggobi-2.1.16/rggobi/man/ggobi-data-add-variable-xu.rd |only rggobi-2.1.16/rggobi/man/ggobi-data-remove-variable-bv.rd |only rggobi-2.1.16/rggobi/man/ggobi-data-set-variable-43.rd | 4 +-- rggobi-2.1.16/rggobi/man/ggobi-default-20.rd | 2 - rggobi-2.1.16/rggobi/man/ggobi-display-get-tour-projection-p0.rd |only rggobi-2.1.16/rggobi/man/ggobi-display-make-type-3r.rd | 4 +-- rggobi-2.1.16/rggobi/man/ggobi-display-set-tour-projection-2n.rd | 4 +-- rggobi-2.1.16/rggobi/man/ggobi-display-types-9g.rd | 4 +-- rggobi-2.1.16/rggobi/man/ggobi-find-file-fe.rd | 2 - rggobi-2.1.16/rggobi/man/ggobi-get-2m.rd | 2 - rggobi-2.1.16/rggobi/man/ggobi-gtk-main-window-l6.rd |only rggobi-2.1.16/rggobi/man/ggobi-gtk-menu-bar-j4.rd | 2 - rggobi-2.1.16/rggobi/man/ggobi-pcp-c7.rd | 2 - rggobi-2.1.16/rggobi/man/ggobi-set-data-file-be.rd | 4 +-- rggobi-2.1.16/rggobi/man/ggobi-set-data-frame-vy.rd |only rggobi-2.1.16/rggobi/man/ggobi-symbol-ec.rd |only rggobi-2.1.16/rggobi/man/ggobi-version-ao.rd | 2 - rggobi-2.1.16/rggobi/man/glyph-colour---GGobiData-u7.rd | 4 +-- rggobi-2.1.16/rggobi/man/glyph-colour-GGobiData-p2.rd |only rggobi-2.1.16/rggobi/man/glyph-size---GGobiData-9w.rd |only rggobi-2.1.16/rggobi/man/glyph-size-GGobiData-3t.rd | 2 - rggobi-2.1.16/rggobi/man/glyph-type---GGobiData-r1.rd |only rggobi-2.1.16/rggobi/man/glyph-type-GGobiData-og.rd |only rggobi-2.1.16/rggobi/man/ids---GGobiData-mw.rd | 4 +-- rggobi-2.1.16/rggobi/man/ids-GGobiData-yu.rd |only rggobi-2.1.16/rggobi/man/length-GGobiDisplay-gt.rd |only rggobi-2.1.16/rggobi/man/mapGlyphType-t9.rd |only rggobi-2.1.16/rggobi/man/names---GGobiData-p2.rd |only rggobi-2.1.16/rggobi/man/names-GGobi-pt.rd |only rggobi-2.1.16/rggobi/man/names-GGobiData-c0.rd | 4 +-- rggobi-2.1.16/rggobi/man/ncol-GGobiData-p3.rd |only rggobi-2.1.16/rggobi/man/nrow-GGobiData-om.rd | 4 +-- rggobi-2.1.16/rggobi/man/pmode-ix.rd |only rggobi-2.1.16/rggobi/man/pmodes-tc.rd | 2 - rggobi-2.1.16/rggobi/man/print-GGobi-yo.rd |only rggobi-2.1.16/rggobi/man/print-GGobiData-ja.rd |only rggobi-2.1.16/rggobi/man/print-GGobiDisplay-o0.rd | 4 +-- rggobi-2.1.16/rggobi/man/rownames---GGobiData-rg.rd |only rggobi-2.1.16/rggobi/man/rownames-GGobiData-pv.rd |only rggobi-2.1.16/rggobi/man/selected-GGobiData-xv.rd | 4 +-- rggobi-2.1.16/rggobi/man/shadowed---GGobiData-h7.rd | 2 - rggobi-2.1.16/rggobi/man/shadowed-GGobiData-8b.rd |only rggobi-2.1.16/rggobi/man/summary-GGobi-c4.rd | 4 +-- rggobi-2.1.16/rggobi/man/summary-GGobiData-mm.rd |only rggobi-2.1.16/rggobi/man/valid-ggobi-uv.rd |only rggobi-2.1.16/rggobi/man/variable-index-h9.rd | 4 +-- rggobi-2.1.16/rggobi/man/variables--1i.rd |only rggobi-2.1.16/rggobi/man/variables-2n.rd |only rggobi-2.1.16/rggobi/man/variables-GGobiDisplay-si.rd |only rggobi-2.1.16/rggobi/src/Makevars | 4 +-- rggobi-2.1.16/rggobi/src/RSGGobiEntryPoints.h | 4 +-- rggobi-2.1.16/rggobi/src/ggobi.c | 2 - 138 files changed, 88 insertions(+), 81 deletions(-)
Title: Low-level R to Java interface
Description: Low-level interface to Java VM very much like .C/.Call and
friends. Allows creation of objects, calling methods and
accessing fields.
Author: Simon Urbanek
Maintainer: Simon Urbanek
Diff between rJava versions 0.8-4 dated 2010-04-29 and 0.8-5 dated 2010-09-02
DESCRIPTION | 4 - NEWS | 13 +++ inst/java/boot/RJavaClassLoader$RJavaObjectInputStream.class |binary inst/java/boot/RJavaClassLoader.class |binary inst/java/boot/RJavaClassLoader.java | 10 ++- inst/javadoc/ArrayDimensionException.html | 4 - inst/javadoc/ArrayWrapper.html | 4 - inst/javadoc/ArrayWrapper_Test.html | 4 - inst/javadoc/DummyPoint.html | 4 - inst/javadoc/FlatException.html | 4 - inst/javadoc/NotAnArrayException.html | 4 - inst/javadoc/NotComparableException.html | 4 - inst/javadoc/ObjectArrayException.html | 4 - inst/javadoc/PrimitiveArrayException.html | 4 - inst/javadoc/RJavaArrayIterator.html | 4 - inst/javadoc/RJavaArrayTools.ArrayDimensionMismatchException.html | 4 - inst/javadoc/RJavaArrayTools.html | 4 - inst/javadoc/RJavaArrayTools_Test.html | 4 - inst/javadoc/RJavaClassLoader.html | 4 - inst/javadoc/RJavaComparator.html | 4 - inst/javadoc/RJavaImport.html | 4 - inst/javadoc/RJavaTools.html | 4 - inst/javadoc/RJavaTools_Test.DummyNonStaticClass.html | 4 - inst/javadoc/RJavaTools_Test.TestException.html | 4 - inst/javadoc/RJavaTools_Test.html | 4 - inst/javadoc/RectangularArrayBuilder.html | 4 - inst/javadoc/RectangularArrayBuilder_Test.html | 4 - inst/javadoc/RectangularArrayExamples.html | 4 - inst/javadoc/RectangularArraySummary.html | 4 - inst/javadoc/TestException.html | 4 - inst/javadoc/allclasses-frame.html | 4 - inst/javadoc/allclasses-noframe.html | 4 - inst/javadoc/constant-values.html | 4 - inst/javadoc/deprecated-list.html | 4 - inst/javadoc/help-doc.html | 4 - inst/javadoc/index-all.html | 4 - inst/javadoc/index.html | 2 inst/javadoc/overview-tree.html | 4 - inst/javadoc/package-frame.html | 4 - inst/javadoc/package-summary.html | 4 - inst/javadoc/package-tree.html | 4 - inst/javadoc/serialized-form.html | 4 - inst/jri/JRIEngine.jar |binary inst/jri/REngine.jar |binary jri/NEWS | 9 ++ jri/Rengine.java | 16 ++-- jri/src/Rengine.c | 33 ++++------ jri/src/jri.h | 8 +- src/java/RJavaClassLoader$RJavaObjectInputStream.class |binary src/java/RJavaClassLoader.class |binary src/java/RJavaClassLoader.java | 10 ++- src/rJava.h | 2 52 files changed, 144 insertions(+), 107 deletions(-)
Title: Toolkit implementation of the gWidgets API for use with web
pages
Description: Port of the gWidgets API to program dynamic websites. Can
be used with R's dynamic help web server to serve local files.
This provides a convenient means to make local GUIs for users
without concern for external GUI toolkits. Also, in combination
with RApache,
http://biostat.mc.vanderbilt.edu/rapache/index.html, this
framework can be used to make public websites powered by R. The
Ext JavaScript libararies (www.extjs.com) are used to create
and manipulate the widgets dynamically.
Author: John Verzani
Maintainer: John Verzani
Diff between gWidgetsWWW versions 0.0-19 dated 2010-06-19 and 0.0-21 dated 2010-09-02
gWidgetsWWW-0.0-19/gWidgetsWWW/R/gcodemirror.R |only gWidgetsWWW-0.0-19/gWidgetsWWW/inst/basehtml/codemirror |only gWidgetsWWW-0.0-21/gWidgetsWWW/ChangeLog | 9 gWidgetsWWW-0.0-21/gWidgetsWWW/DESCRIPTION | 23 - gWidgetsWWW-0.0-21/gWidgetsWWW/NAMESPACE | 2 gWidgetsWWW-0.0-21/gWidgetsWWW/NEWS | 12 gWidgetsWWW-0.0-21/gWidgetsWWW/R/LocalVersion.R | 156 +++++++--- gWidgetsWWW-0.0-21/gWidgetsWWW/R/aaa.R | 1 gWidgetsWWW-0.0-21/gWidgetsWWW/R/common.R | 18 + gWidgetsWWW-0.0-21/gWidgetsWWW/R/gcanvas.R | 4 gWidgetsWWW-0.0-21/gWidgetsWWW/R/gcommandline.R | 2 gWidgetsWWW-0.0-21/gWidgetsWWW/R/gdf.R | 8 gWidgetsWWW-0.0-21/gWidgetsWWW/R/ggooglemaps.R | 25 - gWidgetsWWW-0.0-21/gWidgetsWWW/R/ggroup.R | 12 gWidgetsWWW-0.0-21/gWidgetsWWW/R/gsvg.R | 4 gWidgetsWWW-0.0-21/gWidgetsWWW/R/gtext.R | 5 gWidgetsWWW-0.0-21/gWidgetsWWW/R/gwebvis.R |only gWidgetsWWW-0.0-21/gWidgetsWWW/R/gwindow.R | 57 ++- gWidgetsWWW-0.0-21/gWidgetsWWW/TODO.txt | 1 gWidgetsWWW-0.0-21/gWidgetsWWW/inst/Examples/ex-clt.R | 10 gWidgetsWWW-0.0-21/gWidgetsWWW/inst/Examples/ex-widgets.R | 7 gWidgetsWWW-0.0-21/gWidgetsWWW/inst/doc/gWidgetsWWW.pdf |binary gWidgetsWWW-0.0-21/gWidgetsWWW/man/gWidgetsWWW-undocumented.Rd | 1 gWidgetsWWW-0.0-21/gWidgetsWWW/man/gwebvis.Rd |only gWidgetsWWW-0.0-21/gWidgetsWWW/man/localServerStart.Rd | 5 25 files changed, 245 insertions(+), 117 deletions(-)
Title: Binary R server
Description: Rserve acts as a socket server (TCP/IP or local sockets)
which allows binary requests to be sent to R. Every connection
has a separate workspace and working directory. Client-side
implementations are available for popular languages such as
C/C++ and Java, allowing any application to use facilities of R
without the need of linking to R code. Rserve supports remote
connection, user authentication and file transfer. A simple R
client is included in this package as well.
Author: Simon Urbanek
Maintainer: Simon Urbanek
Diff between Rserve versions 0.6-1 dated 2010-05-25 and 0.6-2 dated 2010-09-02
DESCRIPTION | 4 NEWS | 31 + clients/cxx/Rconnection.cc | 62 +++ clients/cxx/Rconnection.h | 35 ++ clients/cxx/Rsrv.h | 6 clients/cxx/configure | 293 +++++++++--------- clients/java-new/Rserve/protocol/REXPFactory.java | 51 +-- clients/java-new/Rserve/test/test.java | 29 + configure | 299 +++++++++---------- src/Makefile.win | 15 src/Rserv.c | 81 +++-- src/Rsrv.h | 6 src/client/cxx/Rconnection.cc | 62 +++ src/client/cxx/Rconnection.h | 35 ++ src/client/cxx/Rsrv.h | 6 src/client/cxx/configure | 293 +++++++++--------- src/client/java-new/Rserve/protocol/REXPFactory.java | 51 +-- src/client/java-new/Rserve/test/test.java | 29 + src/winembed.c | 34 +- 19 files changed, 900 insertions(+), 522 deletions(-)
Title: SPArse Matrix
Description: Set of function for sparse matrix algebra. Differences
with SparseM/Matrix are: (1) we only support (essentially) one
sparse matrix format, (2) based on transparent and simple
structure(s), (3) tailored for MCMC calculations within GMRF.
(4) S3 and S4 like-"compatible" ... and it is fast.
Author: Reinhard Furrer
Maintainer: Reinhard Furrer
Diff between spam versions 0.22-0 dated 2010-06-09 and 0.23-0 dated 2010-09-02
DESCRIPTION | 8 ++++---- R/apply.R | 2 +- R/definitions.R | 2 +- R/dist.R | 2 +- R/foreign.R | 2 +- R/helper.R | 2 +- R/kronecker.R | 2 +- R/mle.R | 2 +- R/permutation.R | 2 +- R/plotting.R | 2 +- R/profile.R | 2 +- R/spam_solve.R | 2 +- R/xybind.R | 2 +- demo/article-jss-example1.R | 22 +++++++++++----------- demo/article-jss-example2.R | 24 ++++++++++++------------ demo/article-jss.R | 14 +++++++------- demo/cholesky.R | 2 +- demo/spam.R | 2 +- demo/timing.R | 2 +- inst/CITATION |only inst/NEWS | 9 +++++++++ man/Oral.Rd | 2 +- man/SPAM.Rd | 11 +++++++---- man/UScounties.Rd | 4 ++-- man/USprecip.Rd | 2 +- man/allequal.Rd | 2 +- man/apply.Rd | 2 +- man/bandwidth.Rd | 11 +++++------ man/bdiag.Rd | 2 +- man/chol.Rd | 2 +- man/complexity.Rd | 2 +- man/det.Rd | 2 +- man/diag.Rd | 2 +- man/dim.Rd | 2 +- man/display.Rd | 26 +++++++++++++------------- man/foreign.Rd | 2 +- man/germany.Rd | 4 ++-- man/history.spam.Rd | 5 +++-- man/image.Rd | 2 +- man/import.Rd | 5 ++--- man/isSymmetric.Rd | 2 +- man/kronecker.Rd | 10 +++++----- man/lu.tri.Rd | 2 +- man/math.Rd | 2 +- man/math2.Rd | 2 +- man/mle.Rd | 2 +- man/nearestdist.Rd | 2 +- man/operations.Rd | 2 +- man/options.Rd | 2 +- man/ordering.Rd | 2 +- man/permutation.Rd | 2 +- man/powerboost.Rd | 2 +- man/print.Rd | 2 +- man/rmvnorm.Rd | 2 +- man/solve.Rd | 2 +- man/spam-class.Rd | 2 +- man/spam.chol.NgPeyton-class.Rd | 2 +- man/spam.creation.Rd | 2 +- man/spam.internal.Rd | 2 +- man/summary.Rd | 2 +- man/todo.Rd | 2 +- man/triplet.Rd | 2 +- man/version.Rd | 2 +- man/xybind.Rd | 2 +- tests/demo_article-jss-example1.R | 2 +- tests/demo_article-jss-example1.Rout.save | 6 +++--- tests/demo_article-jss-example2.R | 2 +- tests/demo_article-jss-example2.Rout.save | 11 ++++++----- tests/demo_article-jss.R | 2 +- tests/demo_article-jss.Rout.save | 6 +++--- tests/demo_cholesky.R | 2 +- tests/demo_cholesky.Rout.save | 6 +++--- tests/demo_spam.R | 2 +- tests/demo_spam.Rout.save | 6 +++--- tests/demo_timing.R | 2 +- tests/demo_timing.Rout.save | 6 +++--- tests/displays.R | 2 +- tests/displays.Rout.save | 6 +++--- tests/dist.R | 2 +- tests/dist.Rout.save | 6 +++--- tests/foreign.R | 2 +- tests/foreign.Rout.save | 4 ++-- tests/helper.R | 2 +- tests/helper.Rout.save | 6 +++--- tests/kronecker.R | 2 +- tests/kronecker.Rout.save | 6 +++--- tests/mle.R | 2 +- tests/mle.Rout.save | 6 +++--- tests/overall.R | 2 +- tests/overall.Rout.save | 6 +++--- tests/permutation.R | 2 +- tests/permutation.Rout.save | 6 +++--- tests/solve.R | 2 +- tests/solve.Rout.save | 6 +++--- tests/xybind.R | 2 +- tests/xybind.Rout.save | 6 +++--- 96 files changed, 198 insertions(+), 186 deletions(-)
Title: Read data from files readable by gnumeric
Description: Read data files readable by gnumeric into R. Can read
whole sheet or a range, from several file formats, including
the native format of gnumeric. Reading is done by using
ssconvert (a file converter utility included in the gnumeric
distribution http://projects.gnome.org/gnumeric/) to convert
the requested part to CSV. From gnumeric files (but not other
formats) can list sheet names and sheet sizes or read all
sheets.
Author: Karoly Antal .
Maintainer: Karoly Antal
Diff between gnumeric versions 0.5-3 dated 2009-09-18 and 0.6-1 dated 2010-09-02
DESCRIPTION | 8 ++++---- R/read.gnumeric.R | 28 +++++++++++++++++++++++----- changelog | 13 ++++++++++++- man/read.gnumeric.sheet.Rd | 22 +++++++++++++--------- man/read.gnumeric.sheets.Rd | 13 ++++++++++--- 5 files changed, 62 insertions(+), 22 deletions(-)
Title: Multidimensional Numerical Integration
Description: R2Cuba implements four general-purpose multidimensional
integration algorithms: Vegas, Suave, Divonne and Cuhre
Author: The Cuba library has been written by Thomas Hahn
(http://wwwth.mppmu.mpg.de/members/hahn); Interface to R was
written by Annie Bouvier and Kięn Kięu
Maintainer: Annie Bouvier
Diff between R2Cuba versions 1.0-5 dated 2010-09-01 and 1.0-6 dated 2010-09-02
DESCRIPTION | 9 +++++---- man/R2Cuba-package.Rd | 7 ++++--- 2 files changed, 9 insertions(+), 7 deletions(-)
Title: FISH Based Normalization and Copy Number inference of SNP
microarray data
Description: Normalizes the data from a file containing the raw values
of the SNP probes of microarrray data by using the FISH probes
and their corresponding CNs.
Author: Adrian Andronache , Luca Agnelli
Maintainer: Adrian Andronache , Luca Agnelli
Diff between FBN versions 1.4 dated 2010-02-03 and 1.5 dated 2010-09-02
DESCRIPTION | 8 ++++---- R/FBNormalization.R | 38 ++++++++++++++++++++++++++++++-------- man/FBN-package.Rd | 4 ++-- man/FBNormalization.Rd | 6 ++++-- 4 files changed, 40 insertions(+), 16 deletions(-)
Title: Text Analysis Utilities
Description: Utilities for text analysis
Author: Christian Buchta, Kurt Hornik, Ingo Feinerer, David Meyer
Maintainer: Kurt Hornik
Diff between tau versions 0.0-9 dated 2010-08-10 and 0.0-10 dated 2010-09-02
DESCRIPTION | 9 +++++---- R/sysdata.rda |binary 2 files changed, 5 insertions(+), 4 deletions(-)
Title: Cluster ensembles
Description: CLUster Ensembles
Author: Kurt Hornik, with contributions from Walter Boehm
Maintainer: Kurt Hornik
Diff between clue versions 0.3-34 dated 2010-04-27 and 0.3-35 dated 2010-09-02
DESCRIPTION | 11 ++++++----- R/dissimilarity.R | 14 ++++++++++++++ R/membership.R | 15 +++++++++++++-- R/objects.R | 2 +- R/partition.R | 9 ++++++++- R/pclust.R | 14 +++++++++----- R/registration.R | 3 +++ inst/doc/clue.pdf |binary man/cl_dissimilarity.Rd | 8 ++++++++ man/pclust.Rd | 4 ++-- 10 files changed, 64 insertions(+), 16 deletions(-)
Title: Latent position and cluster models for statistical networks
Description: A package to fit and simulate latent position and cluster
models for statistical networks.
Author: Pavel N. Krivitsky , Mark S. Handcock
, based on original code from
"latentnetHRT", and code from other packages of `statnet'
project
Maintainer: Pavel N. Krivitsky
Diff between latentnet versions 2.3-0 dated 2010-04-07 and 2.4-0 dated 2010-09-02
ChangeLog | 17 ++++++ DESCRIPTION | 12 ++-- R/bayesmbc.R | 12 ++-- R/ergmm.MCMC.C.R | 36 ++++++------- R/ergmm.R | 9 +-- R/ergmm.get.model.R | 6 +- R/ergmm.initvals.R | 121 ++++++++++++++++++++++++++++++--------------- R/ergmm.par.R | 10 +-- R/ergmm.statseval.R | 14 ----- R/ergmm.tuner.R | 35 ++++++++----- R/gof.ergmm.R | 2 R/label.switching.R | 2 R/mcmc.diagnostics.ergmm.R | 6 +- R/plot.ergmm.R | 2 R/summary.ergmm.R | 8 +- R/utilities.R | 3 - man/as.mcmc.list.ergmm.Rd | 13 ++-- man/ergmm.object.Rd | 5 - man/latentnet-internal.Rd | 5 + man/summary.ergmm.Rd | 42 ++++++++++++++- 20 files changed, 231 insertions(+), 129 deletions(-)
Title: Smoothed minimax concave penalization (SMCP) method for
genome-wide association studies.
Description: A package containing functions for genome-wide association
studies.
Author: Jin (Gordon) Liu
Maintainer: Jin (Gordon) Liu
Diff between SMCP versions 1.1.2 dated 2010-08-30 and 1.1.3 dated 2010-09-02
DESCRIPTION | 12 ++++++------ R/SMCP.R | 2 +- man/SMCP.Rd | 15 +++++++-------- 3 files changed, 14 insertions(+), 15 deletions(-)
We've covered how to generate random numbers in R before, but what if you want to go beyond generating one random number at a time? What if you want to generate two, or three or more random numbers, and what's more, you want them to be correlated?
JD Long lays out the way in a couple of posts at his Cerebral Mastication blog. If you want to generate bivariate (or trivariate, or more) random multivariate Normal variates, it's pretty easy, as JD points out. Just use the mvrnorm function from the MASS package in R, specify the covariance matrix, and you're all set.
But what if the random variables need to follow some other marginal distribution than Normal? This is a common task for simulations, where you may know the distributions you want for each variable, but need a way to specify the covariance structure. This is where copulas come in handy, as explained in JD's second post, complete with R code implementing a simulation.
Cerebral Mastication: Even Simpler Multivariate Correlated Simulations
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification
and regression models
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer and Allan Engelhardt
Maintainer: Max Kuhn
Diff between caret versions 4.58 dated 2010-08-29 and 4.59 dated 2010-09-01
DESCRIPTION | 8 +- R/rfe.R | 90 ++++++++++++++++++------- R/selectByFilter.R | 156 +++++++++++++++++++++++++++++++++++--------- inst/NEWS | 12 +++ inst/doc/caretMisc.pdf |binary inst/doc/caretSelection.R | 83 ++++++++++++++++++----- inst/doc/caretSelection.Rnw | 79 ++++++++++++++++++++-- inst/doc/caretSelection.pdf |binary inst/doc/caretTrain.pdf |binary inst/doc/caretVarImp.pdf |binary man/nullModel.Rd | 8 +- man/trainControl.Rd | 2 12 files changed, 351 insertions(+), 87 deletions(-)
Title: Time wave analysis and graphical representation
Description: seewave provides functions for analysing, manipulating,
displaying, editing and synthesizing time waves (particularly
sound). This package processes time analysis (oscillograms and
envelopes), spectral content, resonance quality factor,
entropy, cross correlation and autocorrelation, zero-crossing,
dominant frequency, analytic signal, frequency coherence, 2D
and 3D spectrograms and many other analyses.
Author: Jerome Sueur , Thierry Aubin
, Caroline Simonis
Maintainer: Jerome Sueur
Diff between seewave versions 1.5.8 dated 2010-06-15 and 1.5.9 dated 2010-09-01
DESCRIPTION | 12 NAMESPACE | 2 NEWS | 15 - R/seewave.r | 602 +++++++++++++++++++++++++++--------------------- inst/doc/seewave_IO.pdf |binary man/autoc.Rd | 25 + man/corenv.Rd | 3 man/covspectro.Rd | 3 man/csh.Rd | 7 man/dfreq.Rd | 7 man/dynspec.Rd | 10 man/ffilter.Rd | 5 man/fund.Rd | 3 man/lfs.Rd | 12 man/meanspec.Rd | 17 - man/oscillo.Rd | 7 man/seewave.package.Rd | 4 man/spec.Rd | 7 man/spectro.Rd | 15 + man/spectro3D.Rd | 7 man/wf.Rd | 7 21 files changed, 455 insertions(+), 315 deletions(-)
Title: Statistical Catch-at-Age Plotting Environment
Description: Import and plot results from statistical catch-at-age
models, used in fisheries stock assessments.
Author: Arni Magnusson
Maintainer: Arni Magnusson
Diff between scape versions 1.1-0 dated 2010-08-31 and 1.1-2 dated 2010-09-01
DESCRIPTION | 8 NEWS | 6 R/importCol.R | 33 data/x.cod.R | 853 ++++---- data/x.ling.R | 3920 ++++++++++++++++++++--------------------- data/x.oreo.R | 4376 +++++++++++++++++++++++----------------------- data/x.sbw.R | 785 ++++---- inst/doc/Rplots.pdf | 2937 ++++++++++-------------------- inst/doc/dsc-vignette.pdf |binary inst/doc/gallery.pdf |binary inst/doc/mymodel.pdf |binary man/importCol.Rd | 7 man/x.cod.Rd | 4 man/x.ling.Rd | 4 man/x.oreo.Rd | 5 man/x.sbw.Rd | 4 16 files changed, 6122 insertions(+), 6820 deletions(-)
Title: P2BAT
Description: This package provides data analysis via the pbat program,
and an alternative internal implementation of the power
calculations via simulation only. For analysis, this package
provides a frontend to the PBAT software, automatically reading
in the output from the pbat program and displaying the
corresponding figure when appropriate (i.e. PBAT-logrank). It
includes support for multiple processes and clusters. For
analysis, users must download PBAT (developed by Christoph
Lange) and accept it's license, available on the PBAT webpage.
Both the data analysis and power calculations have command line
and graphical interfaces using tcltk.
Author: Thomas Hoffmann , with contributions from
Christoph Lange
Maintainer: Thomas Hoffmann
Diff between pbatR versions 2.2-0 dated 2009-11-23 and 2.2-2 dated 2010-09-01
DESCRIPTION | 8 +++---- R/createCommandfile.R | 55 ++++++++++++++++++++++++++++++++++++++++---------- R/pbat.m.R | 2 - R/pbatGUI.R | 5 ++-- man/pbat.Rd | 8 ++++--- src/kludge.cpp | 25 ++++++++++++---------- src/powerSim.cpp | 20 ++++++++++-------- src/thmalloc.h |only 8 files changed, 83 insertions(+), 40 deletions(-)
Title: Interface between GMT Map-Making Software and R
Description: Interface between the GMT map-making software and R,
enabling the user to manipulate geographic data within R and
call GMT commands to draw and annotate maps in postscript
format. The 'gmt' package is about interactive data analysis,
rapidly visualizing subsets and summaries of geographic data,
while performing statistical analysis in the R console.
Author: Arni Magnusson
Maintainer: Arni Magnusson
Diff between gmt versions 1.1-7 dated 2010-08-28 and 1.1-8 dated 2010-09-01
DESCRIPTION | 8 ++++---- NEWS | 4 ++-- man/gmt-package.Rd | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Efficient selection of undirected graphical models for
high-dimensional datasets
Description: gRapHD is designed for efficient selection of
high-dimensional undirected graphical models. The package
provides tools for selecting trees, forests and decomposable
models minimizing information criteria such as AIC or BIC, and
for displaying the independence graphs of the models. It has
also some useful tools for analysing graphical structures. It
supports the use of discrete, continuous, or both types of
variables.
Author: Gabriel Coelho Goncalves de Abreu ,
Rodrigo Labouriau , David Edwards
.
Maintainer: Gabriel Coelho Goncalves de Abreu
Diff between gRapHD versions 0.1.7 dated 2010-08-17 and 0.1.8 dated 2010-09-01
DESCRIPTION | 6 ++--- R/functions.r | 66 +++++++++++++++++++++++++++++++--------------------------- man/fit.rd | 7 ++++-- 3 files changed, 44 insertions(+), 35 deletions(-)
Title: Multidimensional Numerical Integration
Description: R2Cuba implements four general-purpose multidimensional
integration algorithms: Vegas, Suave, Divonne and Cuhre
Author: The Cuba library has been written by Thomas Hahn
(http://wwwth.mppmu.mpg.de/members/hahn); Interface to R was
written by Annie Bouvier and Kięn Kięu
Maintainer: Annie Bouvier
Diff between R2Cuba versions 1.0-4 dated 2010-02-08 and 1.0-5 dated 2010-09-01
DESCRIPTION | 8 ++++---- R/commoncuba.R | 7 +++++-- R/cuhre.R | 3 ++- R/divonne.R | 3 ++- R/suave.R | 3 ++- R/vegas.R | 3 ++- man/R2Cuba-package.Rd | 4 ++-- man/cuhre.Rd | 1 + src/cuhre_Cuhre.c | 1 - src/cuhre_common.c | 2 +- src/vegas_Vegas.c | 3 ++- tests/kk.Rout.save | 10 +++++++--- 12 files changed, 30 insertions(+), 18 deletions(-)
Title: A package for statistical analysis in epidemiology.
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data,
including interval censored data and representation of
multistate data. Also some useful functions for tabulation and
plotting. Contains some epidemiological datasets.
Author: Bendix Carstensen, Martyn Plummer, Esa Laara, Michael Hills et.
al.
Maintainer: Bendix Carstensen
Diff between Epi versions 1.1.15 dated 2010-06-19 and 1.1.17 dated 2010-09-01
Epi-1.1.15/Epi/inst/doc/Rplots.pdf |only Epi-1.1.15/Epi/man/mstate.Lexis.Rd |only Epi-1.1.17/Epi/CHANGES | 20 + Epi-1.1.17/Epi/DESCRIPTION | 10 Epi-1.1.17/Epi/NAMESPACE | 9 Epi-1.1.17/Epi/R/MS.boxes.R | 7 Epi-1.1.17/Epi/R/lexis.R | 9 Epi-1.1.17/Epi/R/stack.Lexis.R | 68 ++--- Epi-1.1.17/Epi/inst/doc/Follow-up.pdf | 424 ++++++++++++++++------------------ Epi-1.1.17/Epi/man/msdata.Lexis.Rd |only Epi-1.1.17/Epi/man/plot.Lexis.Rd | 9 Epi-1.1.17/Epi/man/transform.Lexis.Rd | 9 12 files changed, 291 insertions(+), 274 deletions(-)
Title: Wrapper package for design of experiments functionality
Description: This package creates various kinds of designs for
(industrial) experiments. It uses, and sometimes enhances,
design generation routines from other packages. Initially,
response surface designs from package rsm and latin hypercube
samples from package lhs have been implemented.
Author: Ulrike Groemping
Maintainer: Ulrike Groemping
Diff between DoE.wrapper versions 0.8 dated 2010-08-10 and 0.8-1 dated 2010-09-01
DESCRIPTION | 8 ++++---- inst/NEWS | 3 +++ man/Dopt.augment.Rd | 3 +-- man/Dopt.design.Rd | 3 +-- 4 files changed, 9 insertions(+), 8 deletions(-)
Title: A software package for annotation and identification of the KEGG
pathways.
Description: SubpathwayMiner is an R-based software for flexible
pathway identification. (1) SubpathwayMiner can provide users
with sub-pathway annotation and identification of metabolic
pathways based on enzyme commission (EC) numbers. (2)
SubpathwayMiner can provide users with sub-pathway annotation
and identification based on KEGG Orthology (KO) identifiers.
(3) SubpathwayMiner can provide annotation and identification
of entire pathways. (4) SubpathwayMiner can support most of
organisms in the KEGG GENE database. (5) Data can be
automatically updated on demand by the user. (6)
SubpathwayMiner can provide identification of disease related
sub-pathways.(new!) The version 3.1 use a new approach to store
organism-related data (e.g., gene-enzyme relation data), which
make the running time of the function updateOrgAndIdType reduce
significantly compared with the old version. Therefore, the
environment variables of organisms will be provided no longer
for reducing size of the software package. When using this
tool, please cite: Li, C., Li, X., Miao, Y., Wang, Q., Jiang,
W., Xu, C., Li, J., Han, J., Zhang, F., Gong, B. et al. (2009)
SubpathwayMiner: a software package for flexible identification
of pathways. Nucleic Acids Res, 37, e131. Full text:
http://nar.oxfordjournals.org/cgi/content/full/37/19/e131
Author: Chunquan Li
Maintainer: Chunquan Li
Diff between SubpathwayMiner versions 3.0 dated 2010-06-01 and 3.1 dated 2010-09-01
SubpathwayMiner-3.0/SubpathwayMiner/R/id.R |only SubpathwayMiner-3.0/SubpathwayMiner/data/ath_ncbi-geneid.rda |only SubpathwayMiner-3.0/SubpathwayMiner/data/cel_ncbi-geneid.rda |only SubpathwayMiner-3.0/SubpathwayMiner/data/dme_ncbi-geneid.rda |only SubpathwayMiner-3.0/SubpathwayMiner/data/eco_ncbi-geneid.rda |only SubpathwayMiner-3.0/SubpathwayMiner/data/hsa_ensembl-hsa.rda |only SubpathwayMiner-3.0/SubpathwayMiner/data/hsa_ncbi-gi.rda |only SubpathwayMiner-3.0/SubpathwayMiner/data/inData.rda |only SubpathwayMiner-3.0/SubpathwayMiner/data/mmu_ncbi-geneid.rda |only SubpathwayMiner-3.0/SubpathwayMiner/data/osa_ncbi-geneid.rda |only SubpathwayMiner-3.0/SubpathwayMiner/data/pathwayClass.rda |only SubpathwayMiner-3.0/SubpathwayMiner/data/sce_ncbi-geneid.rda |only SubpathwayMiner-3.0/SubpathwayMiner/data/sce_ncbi-gi.rda |only SubpathwayMiner-3.0/SubpathwayMiner/data/sce_sgd-sce.rda |only SubpathwayMiner-3.0/SubpathwayMiner/man/KO2gene.Rd |only SubpathwayMiner-3.0/SubpathwayMiner/man/KOuGraph.Rd |only SubpathwayMiner-3.0/SubpathwayMiner/man/background.Rd |only SubpathwayMiner-3.0/SubpathwayMiner/man/dGraph.Rd |only SubpathwayMiner-3.0/SubpathwayMiner/man/ec2gene.Rd |only SubpathwayMiner-3.0/SubpathwayMiner/man/gene2KO.Rd |only SubpathwayMiner-3.0/SubpathwayMiner/man/gene2ec.Rd |only SubpathwayMiner-3.0/SubpathwayMiner/man/gene2path.Rd |only SubpathwayMiner-3.0/SubpathwayMiner/man/getEnzymeFromGene.Rd |only SubpathwayMiner-3.0/SubpathwayMiner/man/getGeneFromEnzyme.Rd |only SubpathwayMiner-3.0/SubpathwayMiner/man/getGeneFromKO.Rd |only SubpathwayMiner-3.0/SubpathwayMiner/man/getGeneFromPathway.Rd |only SubpathwayMiner-3.0/SubpathwayMiner/man/getKOFromGene.Rd |only SubpathwayMiner-3.0/SubpathwayMiner/man/getPathwayFromGene.Rd |only SubpathwayMiner-3.0/SubpathwayMiner/man/getPathwayNameFromId.Rd |only SubpathwayMiner-3.0/SubpathwayMiner/man/keggpathid2name.Rd |only SubpathwayMiner-3.0/SubpathwayMiner/man/kpidList.Rd |only SubpathwayMiner-3.0/SubpathwayMiner/man/mpidList.Rd |only SubpathwayMiner-3.0/SubpathwayMiner/man/path2gene.Rd |only SubpathwayMiner-3.0/SubpathwayMiner/man/uGraph.Rd |only SubpathwayMiner-3.1/SubpathwayMiner/DESCRIPTION | 24 + SubpathwayMiner-3.1/SubpathwayMiner/R/D2P.R | 3 SubpathwayMiner-3.1/SubpathwayMiner/R/ann.R | 11 SubpathwayMiner-3.1/SubpathwayMiner/R/go2go.R | 156 ++++++---- SubpathwayMiner-3.1/SubpathwayMiner/R/graph.R | 2 SubpathwayMiner-3.1/SubpathwayMiner/R/initialize.R | 82 ++--- SubpathwayMiner-3.1/SubpathwayMiner/R/ko.R | 4 SubpathwayMiner-3.1/SubpathwayMiner/R/visualize.R | 10 SubpathwayMiner-3.1/SubpathwayMiner/data/hsa_ncbi-geneid.rda |binary SubpathwayMiner-3.1/SubpathwayMiner/inst/doc/Rplots.pdf | 85 +++-- SubpathwayMiner-3.1/SubpathwayMiner/inst/doc/SubpathwayMiner.Rnw | 38 +- SubpathwayMiner-3.1/SubpathwayMiner/inst/doc/SubpathwayMiner.pdf |binary SubpathwayMiner-3.1/SubpathwayMiner/inst/localdata |only SubpathwayMiner-3.1/SubpathwayMiner/man/Ke2gEnvironment.Rd | 24 - SubpathwayMiner-3.1/SubpathwayMiner/man/SubpathwayMiner-internal.Rd | 22 - SubpathwayMiner-3.1/SubpathwayMiner/man/cutoffAnn.Rd | 3 SubpathwayMiner-3.1/SubpathwayMiner/man/generateNetwork.Rd | 18 - SubpathwayMiner-3.1/SubpathwayMiner/man/getAnn.Rd | 8 SubpathwayMiner-3.1/SubpathwayMiner/man/getDefaultBackground.Rd | 4 SubpathwayMiner-3.1/SubpathwayMiner/man/getDefaultGraph.Rd | 8 SubpathwayMiner-3.1/SubpathwayMiner/man/getDefaultKOPathway.Rd | 2 SubpathwayMiner-3.1/SubpathwayMiner/man/getDefaultKOUndirectedGraph.Rd | 2 SubpathwayMiner-3.1/SubpathwayMiner/man/getDefaultMetabolicPathway.Rd | 2 SubpathwayMiner-3.1/SubpathwayMiner/man/getDefaultUndirectedGraph.Rd | 2 SubpathwayMiner-3.1/SubpathwayMiner/man/getKOAnn.Rd | 16 - SubpathwayMiner-3.1/SubpathwayMiner/man/getKcSubGraph.Rd | 19 - SubpathwayMiner-3.1/SubpathwayMiner/man/getKcsmpAnn.Rd | 9 SubpathwayMiner-3.1/SubpathwayMiner/man/getMpAnn.Rd | 9 SubpathwayMiner-3.1/SubpathwayMiner/man/go2go.Rd |only SubpathwayMiner-3.1/SubpathwayMiner/man/gotoKEGG.Rd | 24 - SubpathwayMiner-3.1/SubpathwayMiner/man/ke2g.Rd | 17 - SubpathwayMiner-3.1/SubpathwayMiner/man/plotAnn.Rd | 16 - SubpathwayMiner-3.1/SubpathwayMiner/man/plotKOAnn.Rd | 16 - SubpathwayMiner-3.1/SubpathwayMiner/man/printAnn.Rd | 4 SubpathwayMiner-3.1/SubpathwayMiner/man/updateGraphs.Rd | 9 SubpathwayMiner-3.1/SubpathwayMiner/man/updateKOGraphs.Rd | 5 SubpathwayMiner-3.1/SubpathwayMiner/man/updateOrgAndIdType.Rd | 22 - 71 files changed, 397 insertions(+), 279 deletions(-)
Title: Construct time delay gene regulatory network
Description: GeneReg is an R package for inferring time delay gene
regulatory network using time course gene expression profiles.
The main idea of time delay linear model is to fit a linear
regression model using a set of putative regulators to estimate
the transcription pattern of a specific target gene.
Author: Tao Huang
Maintainer: Tao Huang
Diff between GeneReg versions 1.1.1 dated 2009-12-14 and 1.1.2 dated 2010-09-01
DESCRIPTION | 10 +++++++--- R/plot.R | 3 ++- R/timedelay.lm.R | 3 ++- data/mut.expr.data.rda |binary data/tf.list.rda |binary data/wt.expr.data.rda |binary man/GeneReg-package.Rd | 8 ++++---- man/plot.GeneReg.Rd | 5 ++++- man/timedelay.lm.Rd | 5 ++++- man/timedelay.lm.batch.Rd | 5 ++++- man/timedelay.univariate.lm.Rd | 4 ++++ 11 files changed, 31 insertions(+), 12 deletions(-)
Vol. 36, Book Review 3, Sep 2010
Graphics for Statistics and Data Analysis with R
Kevin J. Keen
Chapman and Hall/CRC, 2010
ISBN: 9781584880875
by Hadley Wickham, Garrett Grolemund at September 01, 2010 07:00 AM
Maria Wolters, self-styled "Science-Mum of two" and speech and language technology researcher, has a great blog post about the one tool she couldn't live without: R. Maria says R is her "favourite tool for analysing experimental results and modelling the resulting patterns of behaviour and preferences", and explains why:
R is a programming language for everything statistical. It’s free, it’s open source, and it’s being maintained by statisticians for statisticians. Its origin means that it is a pain to learn. It takes a while until one has cleared a path through the data structures, including the various conventions for extracting information from objects that store the results of painstaking statistical analyses, and I am still often baffled myself.
But the payoff is magnificent. Clear (modulo coding ability), open, replicable analyses. R is the ultimate in replicable research. If you give people your data set and your source code, they can repeat every single step of your reasoning. There are no paywalls, no limits of affordability, no packages that are indispensable for the analysis, but that your department hasn’t paid for.
This issue of "replicable analysis" is an important one: the ability to know that you can re-run your analysis at any time in the future (assuming you still have access to the same hardware, or at least a virtual instance of it) and verify the results, without having to worry about the software no longer being available, is crucial. It also means that third parties can reproduce your results where necessary. The fact that it really is necessary to support good science is the topic that Fritz Leisch covered in this excellent keynote speech at this year's UseR! conference.
Speech and Science: The one tool I couldn’t live without
Title: Extensible Time Series
Description: Provide for uniform handling of R's different time-based
data classes by extending zoo, maximizing native format
information preservation and allowing for user level
customization and extension, while simplifying cross-class
interoperability.
Author: Jeffrey A. Ryan, Josh M. Ulrich
Maintainer: Jeffrey A. Ryan
Diff between xts versions 0.7-4 dated 2010-08-04 and 0.7-5 dated 2010-08-31
xts-0.7-4/xts/inst/unitTests/report.html |only xts-0.7-4/xts/inst/unitTests/report.txt |only xts-0.7-4/xts/inst/unitTests/reportSummary.txt |only xts-0.7-5/xts/DESCRIPTION | 10 - xts-0.7-5/xts/NEWS | 26 +++++ xts-0.7-5/xts/R/endpoints.R | 2 xts-0.7-5/xts/R/index.R | 1 xts-0.7-5/xts/R/indexTZ.R | 17 ++- xts-0.7-5/xts/R/origin.fix.R | 2 xts-0.7-5/xts/R/toperiod.R | 10 + xts-0.7-5/xts/R/xts.R | 15 ++ xts-0.7-5/xts/R/xts.methods.R | 6 - xts-0.7-5/xts/R/xtsible.R | 4 xts-0.7-5/xts/inst/doc/xts.pdf |binary xts-0.7-5/xts/man/xts-package.Rd | 6 - xts-0.7-5/xts/src/coredata.c | 3 xts-0.7-5/xts/src/subset.c | 129 ++++++++++++++++++++++++- 17 files changed, 203 insertions(+), 28 deletions(-)
Title: Chronological objects which can handle dates and times
Description: Chronological objects which can handle dates and times
Author: S original by David James , R port
by Kurt Hornik .
Maintainer: Kurt Hornik
Diff between chron versions 2.3-35 dated 2010-04-05 and 2.3-36 dated 2010-08-31
ChangeLog | 9 ++++++++- DESCRIPTION | 8 ++++---- R/chron.R | 6 +++--- 3 files changed, 15 insertions(+), 8 deletions(-)
Title: Bayesian Estimation of the GARCH(1,1) Model with Student-t
Innovations
Description: This package provides the bayesGARCH function which
performs the Bayesian estimation of the GARCH(1,1) model with
Student's t innovations.
Author: David Ardia
Maintainer: David Ardia
Diff between bayesGARCH versions 1-00.05 dated 2009-11-25 and 1-00.06 dated 2010-08-31
bayesGARCH-1-00.05/bayesGARCH/man/addPriorConditions.Rd |only bayesGARCH-1-00.06/bayesGARCH/COPYRIGHTS | 2 bayesGARCH-1-00.06/bayesGARCH/DESCRIPTION | 8 - bayesGARCH-1-00.06/bayesGARCH/NAMESPACE | 1 bayesGARCH-1-00.06/bayesGARCH/NEWS | 7 + bayesGARCH-1-00.06/bayesGARCH/R/functions.R | 11 -- bayesGARCH-1-00.06/bayesGARCH/R/onload.R | 2 bayesGARCH-1-00.06/bayesGARCH/R/sampler.R | 20 ++- bayesGARCH-1-00.06/bayesGARCH/THANKS | 3 bayesGARCH-1-00.06/bayesGARCH/demo/bayesGARCH.R | 14 -- bayesGARCH-1-00.06/bayesGARCH/inst/CITATION | 8 - bayesGARCH-1-00.06/bayesGARCH/man/bayesGARCH.Rd | 85 ++++++++++++---- 12 files changed, 103 insertions(+), 58 deletions(-)
Title: Normalised prediction distribution errors for nonlinear
mixed-effect models
Description: Routines to compute normalised prediction distribution
errors, a metric designed to evaluate non-linear mixed effect
models such as those used in pharmacokinetics and
pharmacodynamics
Author: Emmanuelle Comets, Karl Brendel and France Mentré
Maintainer: Emmanuelle Comets
Diff between npde versions 1.2 dated 2008-04-02 and 1.2.1 dated 2010-08-31
DESCRIPTION | 16 +++++++++++----- man/calcnpde.Rd | 4 ++-- man/computenpde.Rd | 4 ++-- man/computepd.Rd | 4 ++-- man/graphnpde.Rd | 4 ++-- man/plotnpde.Rd | 7 +++---- man/plotpd.Rd | 10 ++++------ man/readobs.Rd | 4 ++-- 8 files changed, 28 insertions(+), 25 deletions(-)
Title: Nearest Neighbor Autocovariates
Description: Computes nearest neighbor autocovariates
Author: A. I. McLeod and M. S. Islam
Maintainer:
Diff between nnc versions 1.13 dated 2010-08-30 and 1.14 dated 2010-08-31
DESCRIPTION | 8 +-- NEWS | 2 inst/doc/Rplots.pdf | 101 ++++++++++++++++++++++------------------------- inst/doc/nncVignette.pdf |binary man/nnc-package.Rd | 8 +-- man/nncTest.Rd | 7 +++ 6 files changed, 64 insertions(+), 62 deletions(-)
Title: Pharmacometric tools for data preparation, modeling, simulation,
and reporting
Description: Pharmacometric tools for common data preparation tasks,
stratified bootstrap resampling of data sets, NONMEM control
stream creation/editing, NONMEM model execution, creation of
standard and user-defined diagnostic plots, execution and
summary of bootstrap and predictive check results,
implementation of simulations from posterior parameter
distributions, reporting of output tables and creation of a
detailed analysis log.
Author: Metrum Institute (http://metruminstitute.org): Bill Knebel,
Leonid Gibianski, Tim Bergsma
Maintainer: Tim Bergsma
Diff between MIfuns versions 4.0.17 dated 2010-08-31 and 4.0.18 dated 2010-08-31
DESCRIPTION | 8 ++++---- R/PLOTR.R | 41 ++++++++++++++++++++++++++--------------- man/MIfuns-package.Rd | 4 ++-- man/dataFormat.Rd | 2 -- man/dataSynthesis.Rd | 3 --- 5 files changed, 32 insertions(+), 26 deletions(-)
Title: Statistical Catch-at-Age Plotting Environment
Description: Import and plot results from statistical catch-at-age
models, used in fisheries stock assessments.
Author: Arni Magnusson
Maintainer: Arni Magnusson
Diff between scape versions 1.0-9 dated 2009-04-21 and 1.1-0 dated 2010-08-31
scape-1.0-9/scape/INDEX |only scape-1.0-9/scape/inst/CHANGES |only scape-1.0-9/scape/inst/doc/mymodel.txt |only scape-1.1-0/scape/DESCRIPTION | 17 +++---- scape-1.1-0/scape/NEWS |only scape-1.1-0/scape/R/importCol.R | 37 +++++++++------ scape-1.1-0/scape/R/plotB.R | 31 ++++--------- scape-1.1-0/scape/R/plotCA.R | 48 +++++++++----------- scape-1.1-0/scape/R/plotCL.R | 48 +++++++++----------- scape-1.1-0/scape/R/plotIndex.R | 66 ++++++++++++++-------------- scape-1.1-0/scape/R/plotLA.R | 49 +++++++++----------- scape-1.1-0/scape/R/plotN.R | 44 ++++++++---------- scape-1.1-0/scape/R/plotSel.R | 38 +++++++--------- scape-1.1-0/scape/inst/doc/Rplots.pdf |only scape-1.1-0/scape/inst/doc/dsc-vignette.Rnw |only scape-1.1-0/scape/inst/doc/dsc-vignette.pdf |only scape-1.1-0/scape/inst/doc/dsc.pdf |binary scape-1.1-0/scape/inst/doc/gallery.Rnw |only scape-1.1-0/scape/inst/doc/gallery.pdf |only scape-1.1-0/scape/inst/doc/mymodel.Rnw |only scape-1.1-0/scape/inst/doc/mymodel.pdf |only scape-1.1-0/scape/man/importCol.Rd | 14 ++--- scape-1.1-0/scape/man/plotB.Rd | 25 ++++++---- scape-1.1-0/scape/man/plotCA.Rd | 31 +++++++------ scape-1.1-0/scape/man/plotCL.Rd | 33 ++++++++------ scape-1.1-0/scape/man/plotIndex.Rd | 39 +++++++++------- scape-1.1-0/scape/man/plotLA.Rd | 38 +++++++++------- scape-1.1-0/scape/man/plotN.Rd | 31 ++++++++----- scape-1.1-0/scape/man/plotSel.Rd | 33 ++++++++------ scape-1.1-0/scape/man/scape-package.Rd | 8 +-- scape-1.1-0/scape/man/x.cod.Rd | 10 ++-- scape-1.1-0/scape/man/x.ling.Rd | 8 ++- scape-1.1-0/scape/man/x.oreo.Rd | 9 ++- scape-1.1-0/scape/man/x.sbw.Rd | 8 ++- 34 files changed, 349 insertions(+), 316 deletions(-)
Title: For mapping global data : rworldmap
Description: Enables mapping of country level and gridded user
datasets.
Author: , with contributions from Joe
Scutt-Phillips, Barry Rowlingson, Roger Bivand & Pru Foster
Maintainer: Andy South
Diff between rworldmap versions 0.107 dated 2010-02-03 and 0.110 dated 2010-08-31
DESCRIPTION | 18 R/getMap.r | 16 R/joinData2Map.R |only R/mapBars.r |only R/mapBubbles.r | 6 R/mapCountryData.R | 50 R/mapGriddedData.r | 78 R/mapPies.r |only R/mapPolys.R |only R/rwmGetColours.R | 3 R/setMapExtents.R | 6 R/zzz.r | 2 inst/doc/Rplots.pdf |234591 --------------------------------------------- inst/doc/rworldmap.Rnw | 2 inst/doc/rworldmap.pdf |binary inst/doc/rworldmapFAQ.pdf |binary man/joinCountryData2Map.Rd | 10 man/joinData2Map.Rd |only man/mapBars.Rd |only man/mapCountryData.Rd | 28 man/mapPies.Rd |only man/mapPolys.Rd |only man/rworldmap-package.Rd | 23 man/wrld_coarse.Rd | 14 24 files changed, 619 insertions(+), 234228 deletions(-)
Title: Bayesian graphical models using MCMC
Description: Interface to the JAGS MCMC library
Author: Martyn Plummer
Maintainer: Martyn Plummer
Diff between rjags versions 2.1.0-6 dated 2010-07-29 and 2.1.0-7 dated 2010-08-31
DESCRIPTION | 8 ++++---- R/jags.R | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Statistical inference for partially observed Markov processes
Description: Inference methods for partially-observed Markov processes
Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner,
Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael
Lavine, Daniel C. Reuman
Maintainer: Aaron A. King
Diff between pomp versions 0.32-1 dated 2010-08-24 and 0.32-5 dated 2010-08-31
DESCRIPTION | 10 - R/euler.R | 6 R/plugins.R | 14 +- R/pomp-fun.R | 4 R/pomp.R | 8 - R/probe.R | 11 - R/trajectory-pomp.R | 31 ++-- data/dacca.rda |binary data/euler.sir.rda |binary data/gillespie.sir.rda |binary data/ou2.rda |binary data/ricker.rda |only inst/ChangeLog | 64 +++++++++ inst/data-R/euler.sir.R | 8 - inst/data-R/gillespie.sir.R | 2 inst/data-R/ou2.R | 8 - inst/data-R/ricker.R |only inst/doc/advanced_topics_in_pomp.Rnw | 18 +- inst/doc/advanced_topics_in_pomp.pdf |binary inst/doc/intro_to_pomp.Rnw | 11 - inst/doc/intro_to_pomp.pdf |binary inst/doc/pomp.bib | 21 ++- inst/examples/sir.R | 8 - inst/examples/sir.c | 226 ++++------------------------------- man/plugins.Rd | 4 man/ricker.Rd |only src/R_init_pomp.c |only src/cholmodel.c | 6 src/ou2.c | 36 ++--- src/ricker.c |only src/sir.c | 38 ++--- tests/ou2-probe-match.R | 11 + tests/ou2-probe-match.Rout.save | 30 ++++ tests/ricker.R |only tests/ricker.Rout.save |only 35 files changed, 261 insertions(+), 314 deletions(-)
Title: Visualization using Eulerian tours and Hamiltonian
decompositions
Description: Eulerian tours and Hamiltonian decompositions of complete
graphs are used to ameliorate order effects in statistical
graphics.
Author: C.B. Hurley and R.W. Oldford
Maintainer: Catherine Hurley
Diff between PairViz versions 1.0 dated 2008-10-28 and 1.1 dated 2010-08-31
PairViz-1.0/PairViz/man/pvpcp.Rd |only PairViz-1.1/PairViz/DESCRIPTION | 15 - PairViz-1.1/PairViz/NAMESPACE | 6 PairViz-1.1/PairViz/R/catpcp.R |only PairViz-1.1/PairViz/R/desaturate_color.R |only PairViz-1.1/PairViz/R/egraph.R | 89 +++++++- PairViz-1.1/PairViz/R/eulerian.R | 21 +- PairViz-1.1/PairViz/R/guidedpcp.R | 39 ++- PairViz-1.1/PairViz/R/hamorder.R | 11 - PairViz-1.1/PairViz/R/mcplot.R | 36 ++- PairViz-1.1/PairViz/R/pathweights.R | 52 +++-- PairViz-1.1/PairViz/R/specialg.R |only PairViz-1.1/PairViz/R/table_plot.R | 57 +++-- PairViz-1.1/PairViz/demo/00Index | 2 PairViz-1.1/PairViz/demo/cat_pcp.R | 104 ++-------- PairViz-1.1/PairViz/demo/demo_fns.R |only PairViz-1.1/PairViz/demo/euler.R | 102 +++++++-- PairViz-1.1/PairViz/demo/mcplots.R | 35 ++- PairViz-1.1/PairViz/demo/pcp.R | 280 ++++++++++++++++++--------- PairViz-1.1/PairViz/demo/rating.R |only PairViz-1.1/PairViz/demo/stars.R | 62 ++++- PairViz-1.1/PairViz/demo/stepwise.R | 163 +++++++++++---- PairViz-1.1/PairViz/man/desaturate_color.Rd |only PairViz-1.1/PairViz/man/etour.Rd | 11 - PairViz-1.1/PairViz/man/eulerian.Rd | 8 PairViz-1.1/PairViz/man/even_graph.Rd | 10 PairViz-1.1/PairViz/man/find_path.Rd | 9 PairViz-1.1/PairViz/man/guided_pcp.Rd | 18 + PairViz-1.1/PairViz/man/hpaths.Rd | 3 PairViz-1.1/PairViz/man/mc_plot.Rd | 6 PairViz-1.1/PairViz/man/mk_complete_graph.Rd | 2 PairViz-1.1/PairViz/man/mk_even_graph.Rd | 12 - PairViz-1.1/PairViz/man/order_best.Rd | 2 PairViz-1.1/PairViz/man/overlayci.Rd | 6 PairViz-1.1/PairViz/man/overview.Rd | 2 PairViz-1.1/PairViz/man/path_cor.Rd | 1 PairViz-1.1/PairViz/man/pathweights.Rd | 9 PairViz-1.1/PairViz/man/pcp.Rd |only PairViz-1.1/PairViz/man/specialg.Rd |only PairViz-1.1/PairViz/man/spreadout.Rd |only PairViz-1.1/PairViz/man/tableplot.Rd | 11 - 41 files changed, 766 insertions(+), 418 deletions(-)
Title: Multiscale Analysis for Density Functions
Description: Given independent and identically distributed observations
X(1), ..., X(n) from a density f, this package provides five
methods to perform a multiscale analysis about f as well as the
necessary critical values. The first method, introduced in
Duembgen and Walther (2008), provides simultaneous confidence
statements for the existence and location of local increases
(or decreases) of f, based on all intervals I(all) spanned by
any two observations X(j), X(k). The second method approximates
the latter approach by using only a subset of I(all) and is
therefore computationally much more efficient, but
asymptotically equivalent. Omitting the additive correction
term Gamma in either method offers another two approaches which
are more powerful on small scales and less powerful on large
scales, however, not asymptotically minimax optimal anymore.
Finally, the block procedure is a compromise between adding
Gamma or not, having intermediate power properties. The latter
is again asymptotically equivalent to the first and was
introduced in Rufibach and Walther (2010).
Author: Kaspar Rufibach and Guenther
Walther
Maintainer: Kaspar Rufibach
Diff between modehunt versions 1.0.4 dated 2009-03-04 and 1.0.5 dated 2010-08-31
modehunt-1.0.4/modehunt/CHANGES |only modehunt-1.0.4/modehunt/R/blocks.R |only modehunt-1.0.4/modehunt/R/criticalValuesAll.R |only modehunt-1.0.4/modehunt/R/criticalValuesApprox.R |only modehunt-1.0.4/modehunt/R/dlin.R |only modehunt-1.0.4/modehunt/R/minimalIntervals.R |only modehunt-1.0.4/modehunt/R/modeHunting.R |only modehunt-1.0.4/modehunt/R/modeHuntingApprox.R |only modehunt-1.0.4/modehunt/R/modeHuntingBlock.R |only modehunt-1.0.4/modehunt/R/myRound.R |only modehunt-1.0.4/modehunt/R/plin.R |only modehunt-1.0.4/modehunt/R/preProcessX.R |only modehunt-1.0.4/modehunt/R/qlin.R |only modehunt-1.0.4/modehunt/R/rlin.R |only modehunt-1.0.5/modehunt/DESCRIPTION | 52 ++++++++++++-------- modehunt-1.0.5/modehunt/NEWS |only modehunt-1.0.5/modehunt/R/blocks.r |only modehunt-1.0.5/modehunt/R/criticalValuesAll.r |only modehunt-1.0.5/modehunt/R/criticalValuesApprox.r |only modehunt-1.0.5/modehunt/R/dlin.r |only modehunt-1.0.5/modehunt/R/minimalIntervals.r |only modehunt-1.0.5/modehunt/R/modeHunting.r |only modehunt-1.0.5/modehunt/R/modeHuntingApprox.r |only modehunt-1.0.5/modehunt/R/modeHuntingBlock.r |only modehunt-1.0.5/modehunt/R/myRound.r |only modehunt-1.0.5/modehunt/R/plin.r |only modehunt-1.0.5/modehunt/R/preProcessX.r |only modehunt-1.0.5/modehunt/R/qlin.r |only modehunt-1.0.5/modehunt/R/rlin.r |only modehunt-1.0.5/modehunt/data/cvModeAll.rda |binary modehunt-1.0.5/modehunt/data/cvModeApprox.rda |binary modehunt-1.0.5/modehunt/data/cvModeBlock.rda |binary modehunt-1.0.5/modehunt/man/blocks.Rd | 10 +-- modehunt-1.0.5/modehunt/man/criticalValuesAll.Rd | 6 +- modehunt-1.0.5/modehunt/man/criticalValuesApprox.Rd | 8 +-- modehunt-1.0.5/modehunt/man/cvModeAll.Rd | 4 - modehunt-1.0.5/modehunt/man/cvModeApprox.Rd | 4 - modehunt-1.0.5/modehunt/man/cvModeBlock.Rd | 4 - modehunt-1.0.5/modehunt/man/lin.Rd | 8 +-- modehunt-1.0.5/modehunt/man/minimalIntervals.Rd | 6 +- modehunt-1.0.5/modehunt/man/modeHunting.Rd | 6 +- modehunt-1.0.5/modehunt/man/modeHuntingApprox.Rd | 6 +- modehunt-1.0.5/modehunt/man/modeHuntingBlock.Rd | 6 +- modehunt-1.0.5/modehunt/man/modehunt-package.Rd | 31 ++++++++--- modehunt-1.0.5/modehunt/man/myRound.Rd | 2 modehunt-1.0.5/modehunt/man/preProcessX.Rd | 2 46 files changed, 89 insertions(+), 66 deletions(-)
Title: Least squares, logistic, and Cox-regression with ordered
predictors
Description: In biomedical studies, researchers are often interested in
assessing the association between one or more ordinal
explanatory variables and an outcome variable, at the same time
adjusting for covariates of any type. The outcome variable may
be continuous, binary, or represent censored survival times. In
the absence of a precise knowledge of the response function,
using monotonicity constraints on the ordinal variables
improves efficiency in estimating parameters, especially when
sample sizes are small. This package implements an active set
algorithm that efficiently computes such estimators.
Author: Kaspar Rufibach
Maintainer: Kaspar Rufibach
Diff between OrdFacReg versions 1.0.1 dated 2009-09-28 and 1.0.2 dated 2010-08-31
OrdFacReg-1.0.1/OrdFacReg/CHANGES |only OrdFacReg-1.0.1/OrdFacReg/R/Abeta.R |only OrdFacReg-1.0.1/OrdFacReg/R/LSEsubspace.R |only OrdFacReg-1.0.1/OrdFacReg/R/constraintMats.R |only OrdFacReg-1.0.1/OrdFacReg/R/coxDeriv.R |only OrdFacReg-1.0.1/OrdFacReg/R/coxLoglik.R |only OrdFacReg-1.0.1/OrdFacReg/R/coxSubspace.R |only OrdFacReg-1.0.1/OrdFacReg/R/dummy.R |only OrdFacReg-1.0.1/OrdFacReg/R/expandBeta.R |only OrdFacReg-1.0.1/OrdFacReg/R/indexDummy.R |only OrdFacReg-1.0.1/OrdFacReg/R/lmLSE.R |only OrdFacReg-1.0.1/OrdFacReg/R/lmSS.R |only OrdFacReg-1.0.1/OrdFacReg/R/logRegDeriv.R |only OrdFacReg-1.0.1/OrdFacReg/R/logRegLoglik.R |only OrdFacReg-1.0.1/OrdFacReg/R/logRegSubspace.R |only OrdFacReg-1.0.1/OrdFacReg/R/maxStep.R |only OrdFacReg-1.0.1/OrdFacReg/R/ordFacReg.R |only OrdFacReg-1.0.1/OrdFacReg/R/ordFacRegCox.R |only OrdFacReg-1.0.1/OrdFacReg/R/phi_jl.R |only OrdFacReg-1.0.1/OrdFacReg/R/prepareData.R |only OrdFacReg-1.0.1/OrdFacReg/R/setminus.R |only OrdFacReg-1.0.1/OrdFacReg/R/shrinkBeta.R |only OrdFacReg-1.0.2/OrdFacReg/DESCRIPTION | 8 ++++---- OrdFacReg-1.0.2/OrdFacReg/NEWS |only OrdFacReg-1.0.2/OrdFacReg/R/Abeta.r |only OrdFacReg-1.0.2/OrdFacReg/R/LSEsubspace.r |only OrdFacReg-1.0.2/OrdFacReg/R/constraintMats.r |only OrdFacReg-1.0.2/OrdFacReg/R/coxDeriv.r |only OrdFacReg-1.0.2/OrdFacReg/R/coxLoglik.r |only OrdFacReg-1.0.2/OrdFacReg/R/coxSubspace.r |only OrdFacReg-1.0.2/OrdFacReg/R/dummy.r |only OrdFacReg-1.0.2/OrdFacReg/R/expandBeta.r |only OrdFacReg-1.0.2/OrdFacReg/R/indexDummy.r |only OrdFacReg-1.0.2/OrdFacReg/R/lmLSE.r |only OrdFacReg-1.0.2/OrdFacReg/R/lmSS.r |only OrdFacReg-1.0.2/OrdFacReg/R/logRegDeriv.r |only OrdFacReg-1.0.2/OrdFacReg/R/logRegLoglik.r |only OrdFacReg-1.0.2/OrdFacReg/R/logRegSubspace.r |only OrdFacReg-1.0.2/OrdFacReg/R/maxStep.r |only OrdFacReg-1.0.2/OrdFacReg/R/ordFacReg.r |only OrdFacReg-1.0.2/OrdFacReg/R/ordFacRegCox.r |only OrdFacReg-1.0.2/OrdFacReg/R/phi_jl.r |only OrdFacReg-1.0.2/OrdFacReg/R/prepareData.r |only OrdFacReg-1.0.2/OrdFacReg/R/setminus.r |only OrdFacReg-1.0.2/OrdFacReg/R/shrinkBeta.r |only OrdFacReg-1.0.2/OrdFacReg/man/internal.Rd | 10 +++++----- OrdFacReg-1.0.2/OrdFacReg/man/ordFacReg-package.Rd | 8 ++++---- OrdFacReg-1.0.2/OrdFacReg/man/ordFacReg.Rd | 10 +++++----- OrdFacReg-1.0.2/OrdFacReg/man/ordFacRegCox.Rd | 8 ++++---- OrdFacReg-1.0.2/OrdFacReg/man/prepareData.Rd | 6 +++--- 50 files changed, 25 insertions(+), 25 deletions(-)
Title: Pharmacometric tools for data preparation, modeling, simulation,
and reporting
Description: Pharmacometric tools for common data preparation tasks,
stratified bootstrap resampling of data sets, NONMEM control
stream creation/editing, NONMEM model execution, creation of
standard and user-defined diagnostic plots, execution and
summary of bootstrap and predictive check results,
implementation of simulations from posterior parameter
distributions, reporting of output tables and creation of a
detailed analysis log.
Author: Metrum Institute (http://metruminstitute.org): Bill Knebel,
Leonid Gibianski, Tim Bergsma
Maintainer: Tim Bergsma
Diff between MIfuns versions 4.0.16 dated 2010-08-28 and 4.0.17 dated 2010-08-31
DESCRIPTION | 12 NAMESPACE |only R/NONR.R | 2 R/PLOTR.R | 2 R/covariatePlots.R | 2 R/diagnosticPlots.R | 1 R/lookup.R | 1 R/params.R | 1 R/plot.nm.R | 10 R/read.cwres.data.R | 6 R/runCommand.R | 2 R/runNonmem.R | 2 R/runlog.R | 1 R/simpar.R | 1 R/xyplot.ext.R | 2 R/zzz.R | 28 inst/sample/nonmem/1005.boot/CombRunLog.csv | 1200 - inst/sample/nonmem/1005.boot/log.csv |17400 ++++++++++++++-------------- inst/sample/nonmem/1005/1005.ctl | 2 inst/sample/nonmem/1005/1005.lst | 67 inst/sample/nonmem/1005/diagnostics.pdf | 242 inst/sample/nonmem/1105/1105.ctl | 9 inst/sample/nonmem/1105/1105.lst | 31 inst/sample/nonmem/ctl/1005.ctl | 2 inst/sample/nonmem/ctl/1105.ctl | 19 inst/sample/script/assemble.pdf |binary inst/sample/script/assemble.tex | 3 inst/sample/script/model-bivariate.pdf | 4 inst/sample/script/model-covplot.pdf | 4 inst/sample/script/model-diamondBack.pdf | 4 inst/sample/script/model-stripplot.pdf | 4 inst/sample/script/model.R | 23 inst/sample/script/model.Rnw | 23 inst/sample/script/model.pdf |binary inst/sample/script/model.tex | 184 inst/test/nm6/out/1/1.lst | 10 inst/test/nm6/out/1/1.tab | 2 inst/test/nm6/out/1/TestPlots.pdf | 4 inst/test/nm6/out/1/cwtab1 | 2 inst/test/nm6/out/1/diagnostics.pdf | 164 inst/test/nm6/out/1001.boot/1001.lst | 8 inst/test/nm6/out/1001/1001.lst | 6 inst/test/nm6/out/1001/TestPlots.pdf | 4 inst/test/nm6/out/1001/diagnostics.pdf | 164 inst/test/nm6/out/1002.boot/1002.lst | 12 inst/test/nm6/out/1002/1002.lst | 12 inst/test/nm6/out/1002/TestPlots.pdf | 4 inst/test/nm6/out/1002/diagnostics.pdf | 164 inst/test/nm6/out/1003.boot/1003.lst | 6 inst/test/nm6/out/1003/1003.lst | 6 inst/test/nm6/out/1003/TestPlots.pdf | 4 inst/test/nm6/out/1003/diagnostics.pdf | 164 inst/test/nm6/out/2/2.lst | 4 inst/test/nm6/out/2/2.tab | 2 inst/test/nm6/out/2/TestPlots.pdf | 4 inst/test/nm6/out/2/cwtab1 | 2 inst/test/nm6/out/2/diagnostics.pdf | 254 inst/test/nm7/out/1/1.lst | 24 inst/test/nm7/out/1/diagnostics.pdf | 164 inst/test/nm7/out/1/nmprd4p.mod |binary inst/test/nm7/out/1001.boot/1001.lst | 22 inst/test/nm7/out/1001.boot/nmprd4p.mod |binary inst/test/nm7/out/1001/1001.lst | 22 inst/test/nm7/out/1001/diagnostics.pdf | 164 inst/test/nm7/out/1001/nmprd4p.mod |binary inst/test/nm7/out/1002.boot/1002.lst | 22 inst/test/nm7/out/1002.boot/nmprd4p.mod |binary inst/test/nm7/out/1002/1002.lst | 24 inst/test/nm7/out/1002/diagnostics.pdf | 164 inst/test/nm7/out/1002/nmprd4p.mod |binary inst/test/nm7/out/1003.boot/1003.lst | 20 inst/test/nm7/out/1003.boot/nmprd4p.mod |binary inst/test/nm7/out/1003/1003.lst | 24 inst/test/nm7/out/1003/diagnostics.pdf | 164 inst/test/nm7/out/1003/nmprd4p.mod |binary inst/test/nm7/out/1003/profile.pdf | 4 inst/test/nm7/out/2/2.lst | 20 inst/test/nm7/out/2/diagnostics.pdf | 256 inst/test/nm7/out/2/nmprd4p.mod |binary inst/test/nm7/out/bootlog.csv | 6 inst/test/nm7/out/runlog.csv | 6 man/MIfuns-package.Rd | 4 man/NONR.Rd | 6 man/PLOTR.Rd | 3 man/accept.Rd | 2 man/acceptance.Rd | 2 man/diagnosticPlots.Rd | 2 man/lookup.Rd | 2 man/panel.densitystrip.Rd | 5 man/panel.hist.Rd | 2 man/panel.stratify.Rd | 2 man/params.Rd | 2 man/partab.Rd | 2 man/plot.nm.Rd | 3 man/rlog.Rd | 3 man/snap.Rd | 1 96 files changed, 10457 insertions(+), 10986 deletions(-)
Title: genome-wide SNP association analysis
Description: a package for genome-wide association analysis between
quantitative or binary traits and single-nucleiotide
polymorphisms (SNPs).
Author: Yurii Aulchenko, Maksim Struchalin
Maintainer: Yurii Aulchenko
Diff between GenABEL versions 1.6-2 dated 2010-08-08 and 1.6-4 dated 2010-08-31
GenABEL-1.6-2/GenABEL/R/ss_slot_wrappers.R |only GenABEL-1.6-2/GenABEL/man/phdata.Rd |only GenABEL-1.6-4/GenABEL/CHANGES.LOG | 19 GenABEL-1.6-4/GenABEL/DESCRIPTION | 8 GenABEL-1.6-4/GenABEL/NAMESPACE | 38 GenABEL-1.6-4/GenABEL/R/GenABEL-package.R | 3 GenABEL-1.6-4/GenABEL/R/add.plot.R | 31 GenABEL-1.6-4/GenABEL/R/ccfast.R | 70 + GenABEL-1.6-4/GenABEL/R/check.marker.R | 47 + GenABEL-1.6-4/GenABEL/R/descriptives.scan.R | 46 - GenABEL-1.6-4/GenABEL/R/descriptives.trait.R | 8 GenABEL-1.6-4/GenABEL/R/egscore.R | 76 + GenABEL-1.6-4/GenABEL/R/emp.ccfast.R | 2 GenABEL-1.6-4/GenABEL/R/emp.grammar.R | 2 GenABEL-1.6-4/GenABEL/R/emp.mmscore.R | 2 GenABEL-1.6-4/GenABEL/R/emp.qtscore.R | 2 GenABEL-1.6-4/GenABEL/R/export.merlin.R | 40 - GenABEL-1.6-4/GenABEL/R/export.plink.R |only GenABEL-1.6-4/GenABEL/R/formetascore.R | 71 + GenABEL-1.6-4/GenABEL/R/grammar.R | 9 GenABEL-1.6-4/GenABEL/R/ibs.R | 4 GenABEL-1.6-4/GenABEL/R/mlreg.R | 60 + GenABEL-1.6-4/GenABEL/R/mmscore.R | 65 + GenABEL-1.6-4/GenABEL/R/plot.scan.gwaa.R | 44 - GenABEL-1.6-4/GenABEL/R/polygenic.R | 8 GenABEL-1.6-4/GenABEL/R/qtscore.R | 153 ++- GenABEL-1.6-4/GenABEL/R/scan.haplo.R | 22 GenABEL-1.6-4/GenABEL/R/snp.subset.R | 14 GenABEL-1.6-4/GenABEL/R/ss.R | 936 ++++++++++++++++++------ GenABEL-1.6-4/GenABEL/R/summary.gwaa.data.R | 11 GenABEL-1.6-4/GenABEL/R/summary.scan.gwaa.R |only GenABEL-1.6-4/GenABEL/R/summary.snp.data.R | 9 GenABEL-1.6-4/GenABEL/R/zzz.R | 2 GenABEL-1.6-4/GenABEL/TODO | 2 GenABEL-1.6-4/GenABEL/data/ge03d2.clean.RData |binary GenABEL-1.6-4/GenABEL/data/ge03d2ex.RData |binary GenABEL-1.6-4/GenABEL/data/ge03d2ex.clean.RData |binary GenABEL-1.6-4/GenABEL/demo/ge03d2.R | 2 GenABEL-1.6-4/GenABEL/demo/srdta.R | 2 GenABEL-1.6-4/GenABEL/demo/srdtawin.R | 2 GenABEL-1.6-4/GenABEL/man/GenABEL-package.Rd | 3 GenABEL-1.6-4/GenABEL/man/check.marker.Rd | 4 GenABEL-1.6-4/GenABEL/man/descriptives.scan.Rd | 3 GenABEL-1.6-4/GenABEL/man/egscore.old.Rd | 10 GenABEL-1.6-4/GenABEL/man/emp.ccfast.Rd | 8 GenABEL-1.6-4/GenABEL/man/emp.qtscore.Rd | 2 GenABEL-1.6-4/GenABEL/man/estlambda.Rd | 2 GenABEL-1.6-4/GenABEL/man/export.merlin.Rd | 9 GenABEL-1.6-4/GenABEL/man/export.plink.Rd |only GenABEL-1.6-4/GenABEL/man/gwaa.data-class.Rd | 14 GenABEL-1.6-4/GenABEL/man/ibs.Rd | 3 GenABEL-1.6-4/GenABEL/man/plot.scan.gwaa.Rd | 4 GenABEL-1.6-4/GenABEL/man/qtscore.Rd | 4 GenABEL-1.6-4/GenABEL/man/qvaluebh95.Rd | 4 GenABEL-1.6-4/GenABEL/man/scan.glm.Rd | 12 GenABEL-1.6-4/GenABEL/man/scan.gwaa-class.Rd | 50 + GenABEL-1.6-4/GenABEL/man/snp.data-class.Rd | 83 +- GenABEL-1.6-4/GenABEL/man/summary.scan.gwaa.Rd |only GenABEL-1.6-4/GenABEL/man/summary.snp.data.Rd | 8 59 files changed, 1472 insertions(+), 561 deletions(-)
Vol. 36, Issue 9, Aug 2010
Abstract:
Cluster ensembles have emerged as a powerful meta-learning paradigm that provides improved accuracy and robustness by aggregating several input data clusterings. In particular, link-based similarity methods have recently been introduced with superior performance to the conventional co-association approach. This paper presents a MATLAB package, LinkCluE, that implements the link-based cluster ensemble framework. A variety of functional methods for evaluating clustering results, based on both internal and external criteria, are also provided. Additionally, the underlying algorithms together with the sample uses of the package with interesting real and synthetic datasets are demonstrated herein.
by Natthakan Iam-on, Simon Garrett at August 31, 2010 07:00 AM
Vol. 36, Issue 8, Aug 2010
Abstract:
The 3-dimensional representation and inspection of complex data is a frequently used strategy in many data analysis domains. Existing data mining software often lacks functionality that would enable users to explore 3D data interactively, especially if one wishes to make dynamic graphical representations directly viewable on the web.
In this paper we present vrmlgen, a software package for the statistical programming language R to create 3D data visualizations in web formats like the Virtual Reality Markup Language (VRML) and LiveGraphics3D. vrmlgen can be used to generate 3D charts and bar plots, scatter plots with density estimation contour surfaces, and visualizations of height maps, 3D object models and parametric functions. For greater flexibility, the user can also access low-level plotting methods through a unified interface and freely group different function calls together to create new higher-level plotting methods. Additionally, we present a web tool allowing users to visualize 3D data online and test some of vrmlgen's features without the need to install any software on their computer.
by Enrico Glaab, Jonathan M. Garibaldi, Natalio Krasnogor at August 31, 2010 07:00 AM
Vol. 36, Code Snippet 1, Aug 2010
Title: TK Rplot
Description: simple mechanism for placing R graphics in a Tk widget
Author: Luke Tierney
Maintainer: Luke Tierney
Diff between tkrplot versions 0.0-18 dated 2008-04-01 and 0.0-19 dated 2010-08-31
DESCRIPTION | 6 ++++-- src/Makevars.win | 2 +- 2 files changed, 5 insertions(+), 3 deletions(-)
Title: Testthat code. Tools to make testing fun :)
Description: A testing package specifically tailored for R that's fun,
flexible and easy to set up.
Author: Hadley Wickham
Maintainer: Hadley Wickham
Diff between testthat versions 0.2 dated 2010-07-25 and 0.3 dated 2010-08-31
testthat-0.2/testthat/ideas.r |only testthat-0.2/testthat/load.r |only testthat-0.2/testthat/man/create_traceback.Rd |only testthat-0.2/testthat/man/try_capture_stack.Rd |only testthat-0.2/testthat/tests/test-basics.r |only testthat-0.2/testthat/tests/test-failure.r |only testthat-0.2/testthat/tests/test-reporter.r |only testthat-0.2/testthat/tests/test-throws-error.r |only testthat-0.2/testthat/tests/test-watcher.r |only testthat-0.3/testthat/DESCRIPTION | 13 - testthat-0.3/testthat/NAMESPACE | 25 +- testthat-0.3/testthat/NEWS | 31 +++ testthat-0.3/testthat/R/aaa-classes.r | 2 testthat-0.3/testthat/R/auto-test.r | 6 testthat-0.3/testthat/R/colour-text.r | 10 - testthat-0.3/testthat/R/expect-that.r | 16 + testthat-0.3/testthat/R/expectation.r | 2 testthat-0.3/testthat/R/expectations.r | 209 ++++++++++++++++++++---- testthat-0.3/testthat/R/library.r | 4 testthat-0.3/testthat/R/reporter-minimal.r | 1 testthat-0.3/testthat/R/reporter-stop.r | 34 +++ testthat-0.3/testthat/R/reporter-summary.r | 21 +- testthat-0.3/testthat/R/reporter-zzz.r | 8 testthat-0.3/testthat/R/reporter.r | 11 - testthat-0.3/testthat/R/test-files.r | 29 ++- testthat-0.3/testthat/R/test-package.r |only testthat-0.3/testthat/R/test-that.r | 61 +------ testthat-0.3/testthat/R/utils.r |only testthat-0.3/testthat/R/watcher.r | 2 testthat-0.3/testthat/README.md |only testthat-0.3/testthat/TODO | 5 testthat-0.3/testthat/inst |only testthat-0.3/testthat/man/equals.Rd | 10 - testthat-0.3/testthat/man/expect_that.Rd | 7 testthat-0.3/testthat/man/gives_warning.Rd |only testthat-0.3/testthat/man/is_a.Rd | 4 testthat-0.3/testthat/man/is_equivalent_to.Rd | 12 + testthat-0.3/testthat/man/is_false.Rd | 4 testthat-0.3/testthat/man/is_identical_to.Rd | 10 - testthat-0.3/testthat/man/is_true.Rd | 4 testthat-0.3/testthat/man/matches.Rd | 13 + testthat-0.3/testthat/man/prints_text.Rd | 6 testthat-0.3/testthat/man/shows_message.Rd |only testthat-0.3/testthat/man/source_dir.Rd | 3 testthat-0.3/testthat/man/test_dir.Rd | 3 testthat-0.3/testthat/man/test_package.Rd |only testthat-0.3/testthat/man/test_that.Rd | 4 testthat-0.3/testthat/man/throws_error.Rd | 7 testthat-0.3/testthat/tests/test-all.R |only 49 files changed, 409 insertions(+), 168 deletions(-)
Title: Smooth Estimation of GPD Shape Parameter
Description: Given independent and identically distributed observations
X(1), ..., X(n) from a Generalized Pareto distribution with
shape parameter gamma in [-1,0], this package offers several
estimates to compute estimates of gamma. The estimates are
based on the principle of replacing the order statistics by
quantiles of a distribution function based on a log--concave
density function. This procedure is justified by the fact that
the GPD density is log--concave for gamma in [-1,0].
Author: Kaspar Rufibach and Samuel
Mueller
Maintainer: Kaspar Rufibach
Diff between smoothtail versions 1.1.4 dated 2009-10-15 and 2.0.0 dated 2010-08-31
smoothtail-1.1.4/smoothtail/R/dgpd.R |only smoothtail-1.1.4/smoothtail/R/falk.R |only smoothtail-1.1.4/smoothtail/R/falkMVUE.R |only smoothtail-1.1.4/smoothtail/R/pgpd.R |only smoothtail-1.1.4/smoothtail/R/pickands.R |only smoothtail-1.1.4/smoothtail/R/qgpd.R |only smoothtail-1.1.4/smoothtail/R/rgpd.R |only smoothtail-2.0.0/smoothtail/CHANGES | 4 + smoothtail-2.0.0/smoothtail/DESCRIPTION | 10 +-- smoothtail-2.0.0/smoothtail/R/dgpd.r |only smoothtail-2.0.0/smoothtail/R/falk.r |only smoothtail-2.0.0/smoothtail/R/falkMVUE.r |only smoothtail-2.0.0/smoothtail/R/generalizedPick.r | 56 ++++++++++-------- smoothtail-2.0.0/smoothtail/R/lambdaGenPick.r | 22 +++---- smoothtail-2.0.0/smoothtail/R/pgpd.r |only smoothtail-2.0.0/smoothtail/R/pickands.r |only smoothtail-2.0.0/smoothtail/R/qgpd.r |only smoothtail-2.0.0/smoothtail/R/rgpd.r |only smoothtail-2.0.0/smoothtail/man/falk.Rd | 15 +++- smoothtail-2.0.0/smoothtail/man/falkMVUE.Rd | 15 +++- smoothtail-2.0.0/smoothtail/man/generalizedPick.Rd | 15 +++- smoothtail-2.0.0/smoothtail/man/pickands.Rd | 14 +++- smoothtail-2.0.0/smoothtail/man/smoothtail-package.Rd | 44 +++++++------- 23 files changed, 118 insertions(+), 77 deletions(-)
Title: Modeling evolution in paleontological time-series
Description: This package facilitates analysis of paleontological
sequences of trait values from an evolving lineage. Functions
are provided to fit, using maximum likelihood, evolutionary
models including unbiased random walks, directional evolution,
stasis, and Ornstein-Uhlenbeck models. Newly added since
version (0.3-1) are functions to analyze punctuations and
models in which evolutionary dynamics change over the course of
a time-series of trait values.
Author: Gene Hunt
Maintainer: Gene Hunt
Diff between paleoTS versions 0.3-2 dated 2010-05-08 and 0.3-3 dated 2010-08-31
DESCRIPTION | 10 +++++----- R/plot.paleoTS.R | 2 +- man/stickleback.Rd | 8 +++++--- 3 files changed, 11 insertions(+), 9 deletions(-)
Title: Robust Loss Development Using MCMC
Description: Loss Development for Insurance Triangles
Author: Christopher W. Laws, Frank A. Schmid
Maintainer: Christopher W. Laws
Diff between lossDev versions 0.9.3 dated 2010-07-06 and 0.9.4 dated 2010-08-31
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inst/doc/charts/lossDev-zeroPayments5050.pdf |18520 inst/doc/charts/lossDev-zeroPaymentsCurve.eps | 418 inst/doc/charts/lossDev-zeroPaymentsCurve.pdf | 469 inst/doc/charts/lossDev-zeroPaymentsScale.eps |18338 inst/doc/charts/lossDev-zeroPaymentsScale.pdf |18521 inst/doc/lossDev.Rnw | 2 inst/doc/lossDev.pdf |binary man/AnnualAggLossDevModelOutputWithZeros-class.Rd | 6 man/BreakAnnualAggLossDevModelInput-class.Rd | 4 man/BreakAnnualAggLossDevModelOutputWithZeros-class.Rd | 4 man/QQPlot,AnnualAggLossDevModelOutput-method.Rd | 4 man/QQPlot.Rd | 5 man/StandardAnnualAggLossDevModelInput-class.Rd | 4 man/StandardAnnualAggLossDevModelOutputWithZeros-class.Rd | 4 man/autoregressiveParameter,AnnualAggLossDevModelOutput-method.Rd | 8 man/autoregressiveParameter.Rd | 9 man/calendarYearEffect,AnnualAggLossDevModelOutput-method.Rd | 10 man/calendarYearEffect.Rd | 11 man/calendarYearEffectAutoregressiveParameter,AnnualAggLossDevModelOutput-method.Rd | 8 man/calendarYearEffectAutoregressiveParameter.Rd | 9 man/calendarYearEffectErrorTracePlot,AnnualAggLossDevModelOutput-method.Rd | 4 man/calendarYearEffectErrorTracePlot.Rd | 5 man/calendarYearEffectErrors,AnnualAggLossDevModelOutput-method.Rd | 10 man/calendarYearEffectErrors.Rd | 11 man/consumptionPath,BreakAnnualAggLossDevModelOutput-method.Rd | 4 man/consumptionPath,StandardAnnualAggLossDevModelOutput-method.Rd | 4 man/consumptionPath.Rd | 7 man/consumptionPathTracePlot,BreakAnnualAggLossDevModelOutput-method.Rd | 4 man/consumptionPathTracePlot,StandardAnnualAggLossDevModelOutput-method.Rd | 4 man/consumptionPathTracePlot.Rd | 5 man/degreesOfFreedom.Rd | 1 man/exposureGrowth,AnnualAggLossDevModelOutput-method.Rd | 4 man/exposureGrowth.Rd | 5 man/exposureGrowthAutoregressiveParameter.Rd | 1 man/exposureGrowthTracePlot,AnnualAggLossDevModelOutput-method.Rd | 4 man/exposureGrowthTracePlot.Rd | 5 man/finalCumulativeDiff,AnnualAggLossDevModelOutputWithZeros-method.Rd | 6 man/finalCumulativeDiff.Rd | 1 man/firstYearInNewRegime,BreakAnnualAggLossDevModelOutput-method.Rd | 4 man/firstYearInNewRegime.Rd | 5 man/firstYearInNewRegimeTracePlot,BreakAnnualAggLossDevModelOutput-method.Rd | 4 man/firstYearInNewRegimeTracePlot.Rd | 5 man/getJagsData.Rd | 1 man/getJagsInits.Rd | 1 man/getModelOutputNodes.Rd | 1 man/getTriDim.Rd | 1 man/gompertzParameters,AnnualAggLossDevModelOutputWithZeros-method.Rd | 1 man/gompertzParameters.Rd | 1 man/lossDevelopmentFactors,AnnualAggLossDevModelOutput-method.Rd | 4 man/lossDevelopmentFactors.Rd | 5 man/mcmcACF,BreakAnnualAggLossDevModelOutput-method.Rd | 4 man/mcmcACF,StandardAnnualAggLossDevModelOutput-method.Rd | 4 man/mcmcACF.Rd | 5 man/meanExposureGrowth.Rd | 1 man/numberOfKnots,BreakAnnualAggLossDevModelOutput-method.Rd | 6 man/numberOfKnots,StandardAnnualAggLossDevModelOutput-method.Rd | 6 man/numberOfKnots.Rd | 7 man/predictedPayments,AnnualAggLossDevModelOutputWithZeros-method.Rd | 4 man/predictedPayments.Rd | 1 man/probablityOfPayment.Rd | 1 man/rateOfDecay,BreakAnnualAggLossDevModelOutput-method.Rd | 6 man/rateOfDecay,StandardAnnualAggLossDevModelOutput-method.Rd | 6 man/rateOfDecay.Rd | 9 man/rateOfDecayTracePlot,BreakAnnualAggLossDevModelOutput-method.Rd | 4 man/rateOfDecayTracePlot,StandardAnnualAggLossDevModelOutput-method.Rd | 4 man/rateOfDecayTracePlot.Rd | 5 man/runLossDevModel.Rd | 1 man/scaleParameter.Rd | 1 man/skewnessParameter.Rd | 1 man/standardDeviationForScaleInnovation,AnnualAggLossDevModelOutput-method.Rd | 6 man/standardDeviationForScaleInnovation.Rd | 5 man/standardDeviationOfCalendarYearEffect,AnnualAggLossDevModelOutput-method.Rd | 8 man/standardDeviationOfCalendarYearEffect.Rd | 9 man/standardDeviationOfExposureGrowth,AnnualAggLossDevModelOutput-method.Rd | 6 man/standardDeviationOfExposureGrowth.Rd | 1 man/standardDeviationVsDevelopmentTime.Rd | 1 man/stochasticInflation,AnnualAggLossDevModelOutput-method.Rd | 6 man/stochasticInflation.Rd | 7 man/stochasticInflationRhoParameter,AnnualAggLossDevModelOutput-method.Rd | 6 man/stochasticInflationRhoParameter.Rd | 7 man/stochasticInflationStationaryMean,AnnualAggLossDevModelOutput-method.Rd | 6 man/stochasticInflationStationaryMean.Rd | 7 man/tailFactor,BreakAnnualAggLossDevModelOutput-method.Rd | 4 man/tailFactor,BreakAnnualAggLossDevModelOutputWithZeros-method.Rd | 10 man/tailFactor,StandardAnnualAggLossDevModelOutput-method.Rd | 4 man/tailFactor,StandardAnnualAggLossDevModelOutputWithZeros-method.Rd | 10 man/tailFactor.Rd | 5 man/triResi,AnnualAggLossDevModelOutput-method.Rd | 4 man/triResi.Rd | 5 src/Makevars.win | 98 src/distributions/DSpline.cpp | 684 src/distributions/DSpline.h | 446 src/samplers/ExpandableArray.cpp | 142 src/samplers/ExpandableArray.h | 94 src/samplers/Knots.cpp | 1280 src/samplers/Knots.h | 266 src/samplers/RJumpSpline.cpp | 1548 src/samplers/RJumpSpline.h | 378 src/samplers/RJumpSplineFactory.cpp | 272 src/samplers/RJumpSplineFactory.h | 130 src/samplers/lapack.h | 180 187 files changed, 589478 insertions(+), 589541 deletions(-)
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