Title: Selected ISO codes
Diff between ISOcodes versions 2011.01.08 dated 2011-01-08 and 2011.07.31 dated 2011-07-31
Description: ISO language, territory, currency, script and character
codes. Provides ISO 639 language codes, ISO 3166 territory
codes, ISO 4217 currency codes, ISO 15924 script codes, and the
ISO 8859 character codes as well as the UN M.49 area codes.
Author: Christian Buchta and Kurt Hornik
Maintainer: Kurt Hornik
DESCRIPTION | 8 ++++----
data/ISO_15924.rda |binary
data/ISO_3166_1.rda |binary
data/ISO_3166_2.rda |binary
data/ISO_3166_3.rda |binary
data/ISO_4217.rda |binary
data/ISO_4217_Historic.rda |binary
data/ISO_639_2.rda |binary
data/ISO_639_3.rda |binary
data/ISO_639_3_Retirements.rda |binary
data/ISO_639_5.rda |binary
data/ISO_8859.rda |binary
data/UN_M.49_Countries.rda |binary
data/UN_M.49_Regions.rda |binary
14 files changed, 4 insertions(+), 4 deletions(-)
Title: Interface between R and the Google Visualisation API
Diff between googleVis versions 0.2.7 dated 2011-07-23 and 0.2.8 dated 2011-07-31
Description: googleVis provides an interface between R and the Google
Visualisation API to create interactive charts for web pages.
The functions of the package allow the user to visualise data
stored in R data frames with the Google Visualisation API
without uploading the data to Google. The output of a googleVis
function is html code that contains the data and references to
JavaScript functions hosted by Google. googleVis makes use of
the internal R HTTP server to display the output locally. A
browser with Flash and Internet connection is required. Please
visit the project web site for more information and examples.
Author: Markus Gesmann, Diego de Castillo
Maintainer: Markus Gesmann
DESCRIPTION | 20 ++++++++---------
LICENSE | 53 -----------------------------------------------
NEWS | 14 ++++++++++++
R/gvis.R | 16 ++++++++++----
R/gvisCoreCharts.R | 6 ++++-
R/gvisMethods.R | 4 +--
R/zzz.R | 24 +++++++++++++--------
THANKS | 2 -
inst/doc/googleVis.Rnw | 25 ++++++++++++++++------
inst/doc/googleVis.bib | 6 ++---
inst/doc/googleVis.pdf |binary
inst/rsp/index.rsp | 2 -
man/googleVis-package.Rd | 28 ++++++++++++++++--------
man/gvisBarChart.Rd | 25 +++++++++++++++++++++-
man/gvisGeoMap.Rd | 5 ++--
man/gvisPieChart.Rd | 15 +++++++++++++
16 files changed, 143 insertions(+), 102 deletions(-)
Title: Analysis of Spatially Distributed Data
Diff between RSurvey versions 0.6-2 dated 2011-05-30 and 0.6-3 dated 2011-07-31
Description: This package is a processing program for spatially
distributed data. It features graphing tools, query building,
and polygon clipping. A graphical user interface is provided.
Author: Jason C. Fisher
Maintainer: Jason C. Fisher
RSurvey-0.6-2/RSurvey/COPYING |only
RSurvey-0.6-3/RSurvey/DESCRIPTION | 8 -
RSurvey-0.6-3/RSurvey/NAMESPACE |only
RSurvey-0.6-3/RSurvey/R/AutocropPolygon.R | 42 ++-----
RSurvey-0.6-3/RSurvey/R/Data.R | 22 +--
RSurvey-0.6-3/RSurvey/R/ImportData.R | 34 ++++-
RSurvey-0.6-3/RSurvey/R/OpenRSurvey.R | 128 ++++++++++++++++-----
RSurvey-0.6-3/RSurvey/R/Plot2d.R | 54 ++++++---
RSurvey-0.6-3/RSurvey/R/ProcessData.R | 153 +++++++++-----------------
RSurvey-0.6-3/RSurvey/R/SetConfiguration.R | 15 --
RSurvey-0.6-3/RSurvey/R/SetPreferences.R | 54 ++++-----
RSurvey-0.6-3/RSurvey/R/ViewData.R | 4
RSurvey-0.6-3/RSurvey/R/WriteFile.R | 3
RSurvey-0.6-3/RSurvey/README.md | 15 +-
RSurvey-0.6-3/RSurvey/data/project.rda |binary
RSurvey-0.6-3/RSurvey/man/AddAxis.Rd | 2
RSurvey-0.6-3/RSurvey/man/Autocrop.Rd | 2
RSurvey-0.6-3/RSurvey/man/AutocropPolygon.Rd | 24 +---
RSurvey-0.6-3/RSurvey/man/CheckEntry.Rd | 5
RSurvey-0.6-3/RSurvey/man/CutoutPolygon.Rd | 7 -
RSurvey-0.6-3/RSurvey/man/Data.Rd | 26 ++--
RSurvey-0.6-3/RSurvey/man/EditDateFormat.Rd | 4
RSurvey-0.6-3/RSurvey/man/EditFunction.Rd | 12 +-
RSurvey-0.6-3/RSurvey/man/EditLimits.Rd | 4
RSurvey-0.6-3/RSurvey/man/EvalFunction.Rd | 4
RSurvey-0.6-3/RSurvey/man/GetFile.Rd | 12 +-
RSurvey-0.6-3/RSurvey/man/ImportData.Rd | 15 +-
RSurvey-0.6-3/RSurvey/man/ManageData.Rd | 29 ++--
RSurvey-0.6-3/RSurvey/man/ManagePolygons.Rd | 12 +-
RSurvey-0.6-3/RSurvey/man/OpenRSurvey.Rd | 6 -
RSurvey-0.6-3/RSurvey/man/Plot2d.Rd | 41 +++---
RSurvey-0.6-3/RSurvey/man/Plot3d.Rd | 8 -
RSurvey-0.6-3/RSurvey/man/PlotTimeSeries.Rd | 4
RSurvey-0.6-3/RSurvey/man/ProcessData.Rd | 86 +++++++++-----
RSurvey-0.6-3/RSurvey/man/RSurvey-package.Rd | 4
RSurvey-0.6-3/RSurvey/man/ReadData.Rd | 12 +-
RSurvey-0.6-3/RSurvey/man/Rename.Rd | 6 -
RSurvey-0.6-3/RSurvey/man/SetConfiguration.Rd | 14 +-
RSurvey-0.6-3/RSurvey/man/SetPolygonLimits.Rd | 16 +-
RSurvey-0.6-3/RSurvey/man/SetPreferences.Rd | 18 +--
RSurvey-0.6-3/RSurvey/man/SummarizeData.Rd | 6 -
RSurvey-0.6-3/RSurvey/man/ViewData.Rd | 8 -
RSurvey-0.6-3/RSurvey/man/WriteFile.Rd | 13 +-
RSurvey-0.6-3/RSurvey/man/project.Rd |only
44 files changed, 497 insertions(+), 435 deletions(-)
Title: Data Structures and Algorithms for Relations
Diff between relations versions 0.5-10 dated 2011-04-26 and 0.5-11 dated 2011-07-31
Description: Data structures and algorithms for k-ary relations with
arbitrary domains, featuring relational algebra, predicate
functions, and fitters for consensus relations.
Author: Kurt Hornik and David Meyer
Maintainer: Kurt Hornik
DESCRIPTION | 10 +++++-----
R/operators.R | 8 +++++++-
data/Cetacea.rda |binary
data/Felines.rda |binary
data/SVM_Benchmarking_Classification.rda |binary
data/SVM_Benchmarking_Classification_Consensus.rda |binary
data/SVM_Benchmarking_Regression.rda |binary
data/SVM_Benchmarking_Regression_Consensus.rda |binary
inst/NEWS.Rd |only
inst/doc/relations.pdf |binary
10 files changed, 12 insertions(+), 6 deletions(-)
Title: Lattice Graphics
Diff between lattice versions 0.19-30 dated 2011-06-30 and 0.19-31 dated 2011-07-31
Description: Lattice is a powerful and elegant high-level data
visualization system, with an emphasis on multivariate data,
that is sufficient for typical graphics needs, and is also
flexible enough to handle most nonstandard requirements. See
?Lattice for an introduction.
Author: Deepayan Sarkar
Maintainer: Deepayan Sarkar
lattice-0.19-30/lattice/COPYING |only
lattice-0.19-31/lattice/DESCRIPTION | 8 ++++----
lattice-0.19-31/lattice/GPL-2 |only
lattice-0.19-31/lattice/GPL-3 |only
lattice-0.19-31/lattice/LICENSE |only
5 files changed, 4 insertions(+), 4 deletions(-)
Title: General Smoothing Splines
Diff between gss versions 2.0-0 dated 2011-07-24 and 2.0-1 dated 2011-07-31
Description: A comprehensive package for structural multivariate
function estimation using smoothing splines.
Author: Chong Gu
Maintainer: Chong Gu
ChangeLog | 42 ++++++++++++++++++++++++------------------
DESCRIPTION | 8 ++++----
R/family.cv.R | 2 +-
R/gssanova1.R | 2 +-
R/project.sscox.R | 2 +-
R/project.ssden.R | 2 +-
man/buffalo.Rd | 2 +-
src/drkl.f | 2 +-
src/ratfor/drkl.r | 2 +-
9 files changed, 35 insertions(+), 29 deletions(-)
Title: A framework for comparing the performance of MCMC samplers
Diff between SamplerCompare versions 1.1 dated 2011-03-21 and 1.2 dated 2011-07-31
More information about SamplerCompare at CRAN
Description: This package consists of two components: a framework for
running sets of MCMC samplers on sets of distributions with a
variety of tuning parameters and plotting functions to
visualize the results of those simulations. See sc-intro.pdf
for an introduction. Version 1.2 adds a mechanism for loading
external simulations.
Author: Madeleine Thompson
Maintainer: Madeleine Thompson
SamplerCompare-1.1/SamplerCompare/inst/doc/sc-intro.bib |only
SamplerCompare-1.2/SamplerCompare/DESCRIPTION | 16
SamplerCompare-1.2/SamplerCompare/NAMESPACE | 4
SamplerCompare-1.2/SamplerCompare/R/00dist-util.R | 14
SamplerCompare-1.2/SamplerCompare/R/compare-samplers.R | 129 ++--
SamplerCompare-1.2/SamplerCompare/R/comparison-plot.R | 5
SamplerCompare-1.2/SamplerCompare/R/distributions.R | 8
SamplerCompare-1.2/SamplerCompare/R/univar-eigen.R | 19
SamplerCompare-1.2/SamplerCompare/inst/doc/ex-compare-results.Rfrag |only
SamplerCompare-1.2/SamplerCompare/inst/doc/ex-compare-samplers.Rfrag | 11
SamplerCompare-1.2/SamplerCompare/inst/doc/ex-final-compare.Rfrag | 12
SamplerCompare-1.2/SamplerCompare/inst/doc/glue.pdf |binary
SamplerCompare-1.2/SamplerCompare/inst/doc/jss668.bib |only
SamplerCompare-1.2/SamplerCompare/inst/doc/sc-intro.Rnw | 303 ++++++----
SamplerCompare-1.2/SamplerCompare/inst/doc/sc-intro.pdf |binary
SamplerCompare-1.2/SamplerCompare/man/SamplerCompare-package.Rd | 11
SamplerCompare-1.2/SamplerCompare/man/compare.samplers.Rd | 13
SamplerCompare-1.2/SamplerCompare/man/comparison.plot.Rd | 5
SamplerCompare-1.2/SamplerCompare/man/make.dist.Rd | 10
SamplerCompare-1.2/SamplerCompare/man/simulation.result.Rd |only
SamplerCompare-1.2/SamplerCompare/tests/test-samplers.R | 21
21 files changed, 366 insertions(+), 215 deletions(-)
Permanent link
Title: DBI/RJDBC interface to h2 Database
Diff between RH2 versions 0.1-2.5 dated 2011-07-23 and 0.1-2.6 dated 2011-07-31
Description: DBI/RJDBC interface to h2 database. h2 version 1.3.158 is
included.
Author: G. Grothendieck. Author of h2 is Thomas Mueller.
Maintainer: G. Grothendieck
DESCRIPTION | 10 +++++-----
NEWS | 4 ++++
2 files changed, 9 insertions(+), 5 deletions(-)
Title: Multivariate Autoregressive State-Space Modeling
Diff between MARSS versions 1.1 dated 2010-10-19 and 2.3 dated 2011-07-31
Description: The MARSS package fits constrained and unconstrained
linear multivariate autoregressive state-space (MARSS) models
to multivariate time series data via priamarily an
Expectation-Maximization (EM) algorithm, although fitting via
the BFGS algorithm (using the optim function) is also provided.
Functions are provided for parametric and innovations
bootstrapping, Kalman filter and smoothing, bootstrap model
selection criteria (AICb), confidences intervals via the
hessian approximation and via bootstrapping and calculation of
auxilliary residuals for detecting outliers and shocks. The
user guide shows examples of using MARSS for parameter
estimation for a variety of applications, model selection,
dynamic factor analysis, outlier and shock detection, and
addition of covariates. Type RShowDoc("UserGuide",
package="MARSS") at the R command line to open the MARSS user
guide.
Author: Eli Holmes, Eric Ward, and Kellie Wills, NOAA, Seattle, USA
Maintainer: eli.holmes@noaa.gov
MARSS-1.1/MARSS/R/find.degenerate.R |only
MARSS-1.1/MARSS/R/show.doc.R |only
MARSS-1.1/MARSS/inst/doc/Case_Study_1.xRnw |only
MARSS-1.1/MARSS/inst/doc/Case_Study_2.xRnw |only
MARSS-1.1/MARSS/inst/doc/Case_Study_3.xRnw |only
MARSS-1.1/MARSS/inst/doc/Case_Study_5.xRnw |only
MARSS-1.1/MARSS/inst/doc/Manual.pdf |only
MARSS-1.1/MARSS/inst/doc/Manual.xRnw |only
MARSS-1.1/MARSS/inst/doc/Quick_Examples.xRnw |only
MARSS-1.1/MARSS/inst/doc/builduserguide.Rnw |only
MARSS-1.1/MARSS/inst/doc/builduserguide.pdf |only
MARSS-1.1/MARSS/inst/doc/cbe.bst |only
MARSS-1.1/MARSS/inst/doc/figures |only
MARSS-1.1/MARSS/inst/doc/footmisc.sty |only
MARSS-1.1/MARSS/inst/doc/hanging.sty |only
MARSS-1.1/MARSS/inst/doc/svmono.cls |only
MARSS-1.1/MARSS/inst/doc/tex |only
MARSS-1.1/MARSS/inst/doc/xxMakefile |only
MARSS-1.1/MARSS/inst/doc/xxMakefile.win |only
MARSS-1.1/MARSS/man/find.degenerate.Rd |only
MARSS-1.1/MARSS/man/show.doc.Rd |only
MARSS-2.3/MARSS/DESCRIPTION | 27
MARSS-2.3/MARSS/NAMESPACE | 9
MARSS-2.3/MARSS/R/CSEGriskfigure.R | 11
MARSS-2.3/MARSS/R/CSEGtmufigure.R | 7
MARSS-2.3/MARSS/R/MARSS.R | 22
MARSS-2.3/MARSS/R/MARSSLLprofile.R | 2
MARSS-2.3/MARSS/R/MARSSaic.R | 2
MARSS-2.3/MARSS/R/MARSSboot.R | 2
MARSS-2.3/MARSS/R/MARSScheckdims.R | 10
MARSS-2.3/MARSS/R/MARSScheckpar.R | 4
MARSS-2.3/MARSS/R/MARSShatyt.r |only
MARSS-2.3/MARSS/R/MARSSinits.R | 6
MARSS-2.3/MARSS/R/MARSSkem.r | 986 ++++++++++++++++-----------
MARSS-2.3/MARSS/R/MARSSkemcheck.r | 69 -
MARSS-2.3/MARSS/R/MARSSkf.R | 363 ++++++---
MARSS-2.3/MARSS/R/MARSSkfas.r |only
MARSS-2.3/MARSS/R/MARSSoptim.r | 92 +-
MARSS-2.3/MARSS/R/MARSSparamCIs.R | 4
MARSS-2.3/MARSS/R/MARSSresids.R |only
MARSS-2.3/MARSS/R/MARSSsettings.R | 92 +-
MARSS-2.3/MARSS/R/MARSSsimulate.R | 44 +
MARSS-2.3/MARSS/R/as_marssm.R | 78 +-
MARSS-2.3/MARSS/R/checkPopWrap.R | 92 +-
MARSS-2.3/MARSS/R/describe_marssm.R | 2
MARSS-2.3/MARSS/R/diaghelpers.r | 27
MARSS-2.3/MARSS/R/is_marssMLE.r | 27
MARSS-2.3/MARSS/R/is_marssm.R | 32
MARSS-2.3/MARSS/R/marssm.R | 2
MARSS-2.3/MARSS/R/popWrap.R | 44 -
MARSS-2.3/MARSS/R/print_marssMLE.r | 6
MARSS-2.3/MARSS/R/print_marssm.R | 4
MARSS-2.3/MARSS/data/graywhales.rda |binary
MARSS-2.3/MARSS/data/grouse.rda |binary
MARSS-2.3/MARSS/data/harborSeal.rda |binary
MARSS-2.3/MARSS/data/harborSealWA.rda |binary
MARSS-2.3/MARSS/data/ivesDataByWeek.rda |only
MARSS-2.3/MARSS/data/ivesDataLP.rda |binary
MARSS-2.3/MARSS/data/kestrel.rda |only
MARSS-2.3/MARSS/data/okanaganRedds.rda |only
MARSS-2.3/MARSS/data/prairiechicken.rda |binary
MARSS-2.3/MARSS/data/rockfish.rda |only
MARSS-2.3/MARSS/data/wilddogs.rda |binary
MARSS-2.3/MARSS/inst/doc/Case_study_1.R | 46 -
MARSS-2.3/MARSS/inst/doc/Case_study_2.R | 84 +-
MARSS-2.3/MARSS/inst/doc/Case_study_3.R | 16
MARSS-2.3/MARSS/inst/doc/Case_study_4.R |only
MARSS-2.3/MARSS/inst/doc/Case_study_5.R | 18
MARSS-2.3/MARSS/inst/doc/Case_study_6.R |only
MARSS-2.3/MARSS/inst/doc/Case_study_7.R |only
MARSS-2.3/MARSS/inst/doc/Case_study_8.R |only
MARSS-2.3/MARSS/inst/doc/Makefile |only
MARSS-2.3/MARSS/inst/doc/UserGuide.Rnw | 2
MARSS-2.3/MARSS/inst/doc/UserGuide.pdf |binary
MARSS-2.3/MARSS/inst/doc/UserGuide.tex |only
MARSS-2.3/MARSS/inst/doc/changes.Rnw | 45 +
MARSS-2.3/MARSS/inst/doc/changes.pdf |binary
MARSS-2.3/MARSS/inst/doc/changes.tex |only
MARSS-2.3/MARSS/inst/doc/index.html | 8
MARSS-2.3/MARSS/man/CSEGriskfigure.Rd | 5
MARSS-2.3/MARSS/man/CSEGtmufigure.Rd | 78 +-
MARSS-2.3/MARSS/man/MARSS-package.Rd | 122 +--
MARSS-2.3/MARSS/man/MARSS.Rd | 101 +-
MARSS-2.3/MARSS/man/MARSSLLprofile.Rd | 4
MARSS-2.3/MARSS/man/MARSSaic.Rd | 4
MARSS-2.3/MARSS/man/MARSSboot.Rd | 8
MARSS-2.3/MARSS/man/MARSScheckdims.Rd | 56 -
MARSS-2.3/MARSS/man/MARSShatyt.Rd |only
MARSS-2.3/MARSS/man/MARSShessian.Rd | 70 -
MARSS-2.3/MARSS/man/MARSSinits.Rd | 88 +-
MARSS-2.3/MARSS/man/MARSSinnovationsboot.Rd | 2
MARSS-2.3/MARSS/man/MARSSkem.Rd | 58 -
MARSS-2.3/MARSS/man/MARSSkemcheck.Rd | 46 -
MARSS-2.3/MARSS/man/MARSSkf.Rd | 56 -
MARSS-2.3/MARSS/man/MARSSmcinit.Rd | 116 +--
MARSS-2.3/MARSS/man/MARSSoptim.Rd | 18
MARSS-2.3/MARSS/man/MARSSoptions.Rd | 78 +-
MARSS-2.3/MARSS/man/MARSSparamCIs.Rd | 4
MARSS-2.3/MARSS/man/MARSSresids.Rd |only
MARSS-2.3/MARSS/man/allowed.rd | 38 -
MARSS-2.3/MARSS/man/checkPopWrap.Rd | 4
MARSS-2.3/MARSS/man/graywhales.Rd | 14
MARSS-2.3/MARSS/man/harborSeal.Rd | 62 -
MARSS-2.3/MARSS/man/is.blockdiag.Rd | 3
MARSS-2.3/MARSS/man/is.marssMLE.Rd | 14
MARSS-2.3/MARSS/man/marssm.Rd | 12
MARSS-2.3/MARSS/man/plankton.Rd | 55 -
MARSS-2.3/MARSS/man/popWrap.Rd | 16
MARSS-2.3/MARSS/man/stdInnov.Rd | 72 -
109 files changed, 2000 insertions(+), 1489 deletions(-)
Title: Categorical Regression Splines
Diff between crs versions 0.15-0 dated 2011-06-24 and 0.15-2 dated 2011-07-30
Description: This package provides for estimating regression splines
that handle a mix of continuous and categorical (discrete) data
often encountered in applied settings. I would like to
gratefully acknowledge support from the Natural Sciences and
Engineering Research Council of Canada (NSERC:www.nserc.ca),
the Social Sciences and Humanities Research Council of Canada
(SSHRC:www.sshrc.ca), and the Shared Hierarchical Academic
Research Computing Network (SHARCNET:www.sharcnet.ca).
Author: Jeffrey S. Racine
Maintainer: Jeffrey S. Racine
crs-0.15-0/crs/COPYING |only
crs-0.15-0/crs/R/is.snomadr.R |only
crs-0.15-2/crs/CHANGELOG | 56
crs-0.15-2/crs/COPYRIGHTS |only
crs-0.15-2/crs/DESCRIPTION | 10
crs-0.15-2/crs/NAMESPACE | 13
crs-0.15-2/crs/R/crs.R | 958 +++++++++++-----
crs-0.15-2/crs/R/crscv.R | 2
crs-0.15-2/crs/R/crsiv.R | 9
crs-0.15-2/crs/R/frscv.R | 64 -
crs-0.15-2/crs/R/frscvNOMAD.R | 80 -
crs-0.15-2/crs/R/glp.model.matrix.R |only
crs-0.15-2/crs/R/kernel.R | 22
crs-0.15-2/crs/R/krscv.R | 150 +-
crs-0.15-2/crs/R/krscvNOMAD.R | 102 +
crs-0.15-2/crs/R/np.regression.glp.R |only
crs-0.15-2/crs/R/snomadr.R | 278 ++--
crs-0.15-2/crs/R/spline.R | 227 ++-
crs-0.15-2/crs/R/util.R | 79 +
crs-0.15-2/crs/R/zzz.R | 2
crs-0.15-2/crs/README | 4
crs-0.15-2/crs/crsver | 2
crs-0.15-2/crs/demo/00Index | 20
crs-0.15-2/crs/demo/crsiv_exog_persp.R | 12
crs-0.15-2/crs/demo/radial_constrained_first_partial.R |only
crs-0.15-2/crs/demo/radial_constrained_mean.R |only
crs-0.15-2/crs/demo/radial_constrained_second_partial.R |only
crs-0.15-2/crs/demo/radial_constrained_test.R |only
crs-0.15-2/crs/demo/radial_persp.R | 6
crs-0.15-2/crs/demo/radial_rgl.R | 7
crs-0.15-2/crs/demo/sine_rgl.R |only
crs-0.15-2/crs/demo/spline.R |only
crs-0.15-2/crs/inst/doc/crs.Rnw | 97 +
crs-0.15-2/crs/inst/doc/crs.bib | 45
crs-0.15-2/crs/inst/doc/crs.pdf |binary
crs-0.15-2/crs/inst/doc/crs_faq.pdf |binary
crs-0.15-2/crs/inst/doc/spline_primer.Rnw | 2
crs-0.15-2/crs/inst/doc/spline_primer.pdf |binary
crs-0.15-2/crs/man/crs-package.Rd | 10
crs-0.15-2/crs/man/crs.Rd | 66 -
crs-0.15-2/crs/man/crsiv.Rd | 11
crs-0.15-2/crs/man/data-cps71.Rd | 11
crs-0.15-2/crs/man/data-wage1.Rd | 18
crs-0.15-2/crs/man/frscv.Rd | 33
crs-0.15-2/crs/man/frscvNOMAD.Rd | 50
crs-0.15-2/crs/man/glp.model.matrix.Rd |only
crs-0.15-2/crs/man/krscv.Rd | 39
crs-0.15-2/crs/man/krscvNOMAD.Rd | 56
crs-0.15-2/crs/man/npglpreg.Rd |only
crs-0.15-2/crs/mkcrspkg.sh | 2
crs-0.15-2/crs/src/snomadr.cpp | 51
51 files changed, 1654 insertions(+), 940 deletions(-)
Title: An R package for changepoint analysis
Diff between changepoint versions 0.4.1 dated 2011-06-05 and 0.5 dated 2011-07-30
Description: Implements various mainstream and specialised changepoint
methods for finding single and multiple changepoints within
data. Many popular non-parametric and frequentist methods are
included. The cpt.mean, cpt.var, cpt.meanvar functions should
be your first point of call.
Author: Rebecca Killick
Maintainer: Rebecca Killick
DESCRIPTION | 11 +--
NAMESPACE |only
NEWS | 8 ++
R/cpt.R | 2
R/cpt.class.R | 151 +++++++++++++++++++++------------------------
R/zzz.R | 20 +----
man/changepoint-package.Rd | 4 -
man/cpt.var.Rd | 4 -
8 files changed, 97 insertions(+), 103 deletions(-)
Title: Serialize R objects to JSON, JavaScript Object Notation
Diff between RJSONIO versions 0.7-3 dated 2011-06-06 and 0.8-1 dated 2011-07-30
Description: This is a package that allows conversion to and from data
in Javascript object notation (JSON) format. This allows R
objects to be inserted into Javascript/ECMAScript/ActionScript
code and allows R programmers to read and convert JSON content
to R objects. This is an alternative to rjson package. That
version is too slow for converting large R objects to JSON and
is not extensible, but a very useful prototype. It is fast for
parsing. This package uses methods, vectorized operations and C
code and callbacks to R functions for deserializing JSON
objects to R. Verison 0.4 of this package uses a new native
parser, implements the transformation code in C and allocates
memory efficiently (rather than concatenating because of event
driven parsing). The result is a significantly faster parsing
of large JSON documents.
Author: Duncan Temple Lang
Maintainer: Duncan Temple Lang
Changes | 21 +++++++++++++++++
Changes.html | 44 +++++++++++++++++++++++++++++++++---
Changes.xml | 28 ++++++++++++++++++++++
DESCRIPTION | 6 ++--
R/json.R | 39 ++++++++++++++++---------------
R/readJSON.R | 35 ++++++++++++++--------------
Web/index.html | 2 -
inst/doc/biblio.xml |only
inst/doc/overview.Rdb |only
inst/doc/overview.aux |only
inst/doc/overview.bbl |only
inst/doc/overview.bib |only
inst/doc/overview.blg |only
inst/doc/overview.html |only
inst/doc/overview.log |only
inst/doc/overview.out |only
inst/doc/overview.pdf |only
inst/doc/overview.tex |only
man/fromJSON.Rd | 12 +++++++++
man/toJSON.Rd | 13 +++++++++-
src/libjson/Source/JSONChildren.h | 2 +
src/libjson/Source/NumberToString.h | 7 +++++
src/libjson/bdr |only
src/rlibjson.c | 24 +++++++++----------
24 files changed, 176 insertions(+), 57 deletions(-)
Title: Tableplot, a visualization of large statistical datasets
Diff between tabplot versions 0.10 dated 2011-07-29 and 0.10-1 dated 2011-07-30
Description: A tableplot is a visualisation of a (large) statistical
dataset with a dozen of variables, both both numeric and
categorical. Each column represents a variable and each row bin
is an aggregate of a certain number of records. Numeric
variables are visualized as bar charts, and categorical
variables as stacked bar charts. Missing values are taken into
account. A GUI has been implemented which is used to easily
customize the tableplot. Also supports large ffdf datasets from
the ff package.
Author: Martijn Tennekes and Edwin de Jonge
Maintainer: Martijn Tennekes
DESCRIPTION | 23 +++++++++++++++++++----
R/pkg.R | 4 ++--
R/preprocess.data.table.R | 2 +-
R/preprocess.ffdf.R | 2 +-
Tableplot.jpg |only
inst/doc/enumitem.sty |only
inst/doc/tabplot-vignette.pdf |binary
man/tabplot-package.Rd | 4 ++--
8 files changed, 25 insertions(+), 10 deletions(-)
Title: Geographic analysis and modeling with raster data
Diff between raster versions 1.9-1 dated 2011-07-23 and 1.9-5 dated 2011-07-30
Description: Reading, writing, manipulating, analyzing and modeling of
gridded spatial data. The package implements basic and
high-level functions, as well as map algebra. Processing of
very large files is supported.
Author: Robert J. Hijmans & Jacob van Etten
Maintainer: Robert J. Hijmans
raster-1.9-1/raster/R/median.R |only
raster-1.9-5/raster/ChangeLog | 8 ++++
raster-1.9-5/raster/DESCRIPTION | 10 ++---
raster-1.9-5/raster/NAMESPACE | 2 -
raster-1.9-5/raster/R/as.data.frame.R |only
raster-1.9-5/raster/R/calc.R | 34 +++++++++++------
raster-1.9-5/raster/R/coerce.R | 8 +---
raster-1.9-5/raster/R/getValues.R | 15 +++++--
raster-1.9-5/raster/R/gridDistance.R | 2 -
raster-1.9-5/raster/R/imageplot2.R | 21 ++++++----
raster-1.9-5/raster/R/index.R | 21 ++++++++--
raster-1.9-5/raster/R/indexReplace.R | 23 +++++++----
raster-1.9-5/raster/R/indexReplaceBrick.R | 41 +++++----------------
raster-1.9-5/raster/R/plot.R | 13 ++++--
raster-1.9-5/raster/R/plotRGB.R | 54 ----------------------------
raster-1.9-5/raster/R/predict.R | 24 +++++++++++-
raster-1.9-5/raster/R/rasterToPoints.R | 9 ++--
raster-1.9-5/raster/R/read.R | 3 +
raster-1.9-5/raster/R/writeRaster.R | 11 +++--
raster-1.9-5/raster/inst/doc/Raster.pdf |binary
raster-1.9-5/raster/inst/doc/functions.pdf |binary
raster-1.9-5/raster/inst/doc/rasterfile.pdf |binary
raster-1.9-5/raster/man/Summary-methods.Rd | 30 +++++++--------
raster-1.9-5/raster/man/as.data.frame.Rd |only
raster-1.9-5/raster/man/extractIndex.Rd | 1
raster-1.9-5/raster/man/gridDistance.Rd | 8 ++--
raster-1.9-5/raster/man/plot.Rd | 24 +++++++-----
raster-1.9-5/raster/man/raster-package.Rd | 3 -
raster-1.9-5/raster/man/replacement.Rd | 1
29 files changed, 186 insertions(+), 180 deletions(-)
Title: Parallel nonparametric kernel smoothing methods for mixed data
types
Diff between npRmpi versions 0.40-7 dated 2011-06-09 and 0.40-9 dated 2011-07-30
Description: This package provides a variety of nonparametric (and
semiparametric) kernel methods that seamlessly handle a mix of
continuous, unordered, and ordered factor data types. This
package is a parallel implementation of the np package based on
the MPI specification that incorporates the Rmpi package (Hao
Yu
Author: Tristen Hayfield
Maintainer: Jeffrey S. Racine
npRmpi-0.40-7/npRmpi/COPYING |only
npRmpi-0.40-7/npRmpi/demo/n_2/.R.Rout |only
npRmpi-0.40-7/npRmpi/demo/n_2/npplreg_npRmpi.Rout |only
npRmpi-0.40-7/npRmpi/demo/n_2/tmp |only
npRmpi-0.40-7/npRmpi/demo/n_3 |only
npRmpi-0.40-7/npRmpi/demo/n_4 |only
npRmpi-0.40-7/npRmpi/demo/serial/.R.Rout |only
npRmpi-0.40-7/npRmpi/demo/serial/npplreg_serial.Rout |only
npRmpi-0.40-7/npRmpi/inst/doc/npRmpi.Rnw |only
npRmpi-0.40-7/npRmpi/inst/doc/npRmpi.pdf |only
npRmpi-0.40-7/npRmpi/inst/merge_np_Rmpi.tex |only
npRmpi-0.40-9/npRmpi/CHANGELOG | 24 ++
npRmpi-0.40-9/npRmpi/COPYRIGHTS |only
npRmpi-0.40-9/npRmpi/DESCRIPTION | 10 -
npRmpi-0.40-9/npRmpi/R/Rparutilities.R | 85 ++++----
npRmpi-0.40-9/npRmpi/R/np.plot.R | 6
npRmpi-0.40-9/npRmpi/R/np.plregression.R | 41 +++-
npRmpi-0.40-9/npRmpi/R/np.plregression.bw.R | 29 ++
npRmpi-0.40-9/npRmpi/R/np.singleindex.R | 144 ++++----------
npRmpi-0.40-9/npRmpi/R/np.singleindex.bw.R | 133 +++----------
npRmpi-0.40-9/npRmpi/R/sibandwidth.R | 9
npRmpi-0.40-9/npRmpi/R/util.R | 20 +-
npRmpi-0.40-9/npRmpi/R/zzz.R | 2
npRmpi-0.40-9/npRmpi/README | 159 ----------------
npRmpi-0.40-9/npRmpi/configure.ac | 19 +
npRmpi-0.40-9/npRmpi/data/cps71.rda |binary
npRmpi-0.40-9/npRmpi/inst/Rslaves.bat | 33 +--
npRmpi-0.40-9/npRmpi/inst/Rslaves32.bat |only
npRmpi-0.40-9/npRmpi/inst/Rslaves64.bat |only
npRmpi-0.40-9/npRmpi/inst/compile_npRmpi_MS_Windows.txt | 47 ++--
npRmpi-0.40-9/npRmpi/inst/doc/np_faq.pdf |binary
npRmpi-0.40-9/npRmpi/inst/install_npRmpi_MS_Windows.txt | 16 -
npRmpi-0.40-9/npRmpi/inst/install_npRmpi_SHARCNET.txt | 8
npRmpi-0.40-9/npRmpi/man/b.star.Rd | 4
npRmpi-0.40-9/npRmpi/man/data-oecd.Rd | 2
npRmpi-0.40-9/npRmpi/man/data-wage1.Rd | 2
npRmpi-0.40-9/npRmpi/man/gradients.Rd | 2
npRmpi-0.40-9/npRmpi/man/hosts.Rd | 8
npRmpi-0.40-9/npRmpi/man/mpi.spawn.Rslaves.Rd | 2
npRmpi-0.40-9/npRmpi/man/np-package.Rd | 2
npRmpi-0.40-9/npRmpi/man/np.cmstest.Rd | 2
npRmpi-0.40-9/npRmpi/man/np.condensity.Rd | 4
npRmpi-0.40-9/npRmpi/man/np.condensity.bw.Rd | 5
npRmpi-0.40-9/npRmpi/man/np.conmode.Rd | 2
npRmpi-0.40-9/npRmpi/man/np.deneqtest.Rd | 2
npRmpi-0.40-9/npRmpi/man/np.density.Rd | 2
npRmpi-0.40-9/npRmpi/man/np.density.bw.Rd | 2
npRmpi-0.40-9/npRmpi/man/np.deptest.Rd | 2
npRmpi-0.40-9/npRmpi/man/np.kernelsum.Rd | 2
npRmpi-0.40-9/npRmpi/man/np.plot.Rd | 2
npRmpi-0.40-9/npRmpi/man/np.plregression.Rd | 10 -
npRmpi-0.40-9/npRmpi/man/np.plregression.bw.Rd | 10 -
npRmpi-0.40-9/npRmpi/man/np.qcmstest.Rd | 2
npRmpi-0.40-9/npRmpi/man/np.qregression.Rd | 2
npRmpi-0.40-9/npRmpi/man/np.regression.Rd | 2
npRmpi-0.40-9/npRmpi/man/np.regression.bw.Rd | 2
npRmpi-0.40-9/npRmpi/man/np.sdeptest.Rd | 2
npRmpi-0.40-9/npRmpi/man/np.sigtest.Rd | 2
npRmpi-0.40-9/npRmpi/man/np.singleindex.Rd | 21 --
npRmpi-0.40-9/npRmpi/man/np.singleindex.bw.Rd | 19 -
npRmpi-0.40-9/npRmpi/man/np.smoothcoef.Rd | 2
npRmpi-0.40-9/npRmpi/man/np.smoothcoef.bw.Rd | 2
npRmpi-0.40-9/npRmpi/man/np.symtest.Rd | 2
npRmpi-0.40-9/npRmpi/man/np.unitest.Rd | 2
npRmpi-0.40-9/npRmpi/man/npseed.Rd | 2
npRmpi-0.40-9/npRmpi/man/se.Rd | 2
npRmpi-0.40-9/npRmpi/man/uocquantile.Rd | 2
npRmpi-0.40-9/npRmpi/npver | 2
npRmpi-0.40-9/npRmpi/src/Makevars.win | 7
npRmpi-0.40-9/npRmpi/src/Rmpi.c | 6
npRmpi-0.40-9/npRmpi/src/Rmpi.h | 1
npRmpi-0.40-9/npRmpi/src/jksum.c | 2
npRmpi-0.40-9/npRmpi/src/kernel.c | 2
npRmpi-0.40-9/npRmpi/src/kernele.c | 8
74 files changed, 372 insertions(+), 574 deletions(-)
Title: Nonparametric kernel smoothing methods for mixed data types
Diff between np versions 0.40-7 dated 2011-06-09 and 0.40-9 dated 2011-07-30
Description: This package provides a variety of nonparametric (and
semiparametric) kernel methods that seamlessly handle a mix of
continuous, unordered, and ordered factor data types. We would
like to gratefully acknowledge support from the Natural
Sciences and Engineering Research Council of Canada
(NSERC:www.nserc.ca), the Social Sciences and Humanities
Research Council of Canada (SSHRC:www.sshrc.ca), and the Shared
Hierarchical Academic Research Computing Network
(SHARCNET:www.sharcnet.ca).
Author: Tristen Hayfield
Maintainer: Jeffrey S. Racine
np-0.40-7/np/.tmp.sh |only
np-0.40-7/np/COPYING |only
np-0.40-7/np/nptest |only
np-0.40-9/np/CHANGELOG | 25 +++++
np-0.40-9/np/COPYRIGHTS |only
np-0.40-9/np/DESCRIPTION | 10 +-
np-0.40-9/np/R/np.plot.R | 65 +++++++++-----
np-0.40-9/np/R/np.plregression.R | 41 ++++++++-
np-0.40-9/np/R/np.plregression.bw.R | 29 +++++-
np-0.40-9/np/R/np.singleindex.R | 144 +++++++++------------------------
np-0.40-9/np/R/np.singleindex.bw.R | 133 +++++++-----------------------
np-0.40-9/np/R/sibandwidth.R | 12 ++
np-0.40-9/np/R/util.R | 20 +++-
np-0.40-9/np/R/zzz.R | 2
np-0.40-9/np/README |only
np-0.40-9/np/data/cps71.rda |binary
np-0.40-9/np/inst/doc/entropy_np.pdf |binary
np-0.40-9/np/inst/doc/np.pdf |binary
np-0.40-9/np/inst/doc/np_faq.pdf |binary
np-0.40-9/np/man/b.star.Rd | 2
np-0.40-9/np/man/data-oecd.Rd | 2
np-0.40-9/np/man/data-wage1.Rd | 2
np-0.40-9/np/man/gradients.Rd | 2
np-0.40-9/np/man/np-package.Rd | 17 ++-
np-0.40-9/np/man/np.cmstest.Rd | 10 --
np-0.40-9/np/man/np.condensity.Rd | 54 +++++-------
np-0.40-9/np/man/np.condensity.bw.Rd | 18 +---
np-0.40-9/np/man/np.conmode.Rd | 13 +-
np-0.40-9/np/man/np.deneqtest.Rd | 2
np-0.40-9/np/man/np.density.Rd | 30 ++----
np-0.40-9/np/man/np.density.bw.Rd | 31 ++-----
np-0.40-9/np/man/np.deptest.Rd | 2
np-0.40-9/np/man/np.kernelsum.Rd | 2
np-0.40-9/np/man/np.plot.Rd | 69 +++++++--------
np-0.40-9/np/man/np.plregression.Rd | 58 ++++++-------
np-0.40-9/np/man/np.plregression.bw.Rd | 36 ++++----
np-0.40-9/np/man/np.qcmstest.Rd | 2
np-0.40-9/np/man/np.qregression.Rd | 20 ++--
np-0.40-9/np/man/np.regression.Rd | 57 ++++---------
np-0.40-9/np/man/np.regression.bw.Rd | 6 -
np-0.40-9/np/man/np.sdeptest.Rd | 2
np-0.40-9/np/man/np.sigtest.Rd | 2
np-0.40-9/np/man/np.singleindex.Rd | 27 ------
np-0.40-9/np/man/np.singleindex.bw.Rd | 19 ----
np-0.40-9/np/man/np.smoothcoef.Rd | 2
np-0.40-9/np/man/np.smoothcoef.bw.Rd | 2
np-0.40-9/np/man/np.symtest.Rd | 2
np-0.40-9/np/man/np.unitest.Rd | 2
np-0.40-9/np/man/npseed.Rd | 2
np-0.40-9/np/man/se.Rd | 2
np-0.40-9/np/man/uocquantile.Rd | 2
np-0.40-9/np/npver | 2
np-0.40-9/np/src/jksum.c | 4
np-0.40-9/np/src/kernel.c | 2
np-0.40-9/np/src/kernele.c | 8 -
55 files changed, 447 insertions(+), 549 deletions(-)
Title: Text Classification Using Low-memory Multinomial Logistic
Regression
Diff between maxent versions 1.1 dated 2011-07-30 and 1.2 dated 2011-07-30
Description: maxent is an R package with tools for text classification
using multinomial logistic regression, also known as maximum
entropy. The focus of this maximum entropy classifier is to
minimize memory consumption on very large datasets,
particularly sparse document-term matrices represented by the
tm package.
Author: Timothy P. Jurka
Maintainer: Timothy P. Jurka
maxent-1.1/maxent/R/dtm_to_sparsem.R |only
maxent-1.1/maxent/R/print_weights.R |only
maxent-1.1/maxent/man/dtm_to_sparsem.Rd |only
maxent-1.1/maxent/man/print_weights.Rd |only
maxent-1.2/maxent/DESCRIPTION | 15 ++++++++-------
maxent-1.2/maxent/NAMESPACE | 6 +++++-
maxent-1.2/maxent/R/as.compressed.matrix.R |only
maxent-1.2/maxent/R/load.model.R |only
maxent-1.2/maxent/R/maxent.R | 22 +++++++++++-----------
maxent-1.2/maxent/R/predict.maxent.R | 20 ++++++++++----------
maxent-1.2/maxent/R/save.model.R |only
maxent-1.2/maxent/R/zzz.R | 6 +++---
maxent-1.2/maxent/man/as.compressed.matrix.Rd |only
maxent-1.2/maxent/man/load.model.Rd |only
maxent-1.2/maxent/man/maxent-class.Rd | 7 +++----
maxent-1.2/maxent/man/maxent-package.Rd | 17 ++++++-----------
maxent-1.2/maxent/man/maxent.Rd | 9 ++++-----
maxent-1.2/maxent/man/predict.maxent.Rd | 9 ++++-----
maxent-1.2/maxent/man/save.model.Rd |only
19 files changed, 54 insertions(+), 57 deletions(-)
Title: Multilayer optics
Diff between planar versions 1.0 dated 2011-07-27 and 1.1 dated 2011-07-30
Description: Solves the electromagnetic problem of reflection and
transmission at a multilayer planar interface. Also computes
the decay rates for a dipolar emitter near a multilayer
structure.
Author: baptiste Auguie
Maintainer: baptiste Auguie
DESCRIPTION | 13 ++++----
NAMESPACE | 21 +++++++-------
R/field-profile.r |only
R/planar-package.r | 4 +-
R/recursive.fresnel.r | 2 -
demo/field_enhancement.r | 63 +++++--------------------------------------
inst/doc/planar-vignette.pdf |binary
man/field.outside.Rd |only
man/planar-package.Rd | 4 +-
src/multilayer.cpp | 1
10 files changed, 30 insertions(+), 78 deletions(-)
Title: Fractional Factorial designs with 2-level factors
Diff between FrF2 versions 1.2-4 dated 2011-07-23 and 1.2-5 dated 2011-07-30
Description: This package creates regular and non-regular Fractional
Factorial designs. Furthermore, analysis tools for Fractional
Factorial designs with 2-level factors are offered (main
effects and interaction plots for all factors simultaneously,
cube plot for looking at the simultaneous effects of three
factors, full or half normal plot, alias structure in a more
readable format than with the built-in function alias). The
package is currently subject to intensive development. While
much of the intended functionality is already available, some
changes and improvements are still to be expected. Suggestions
are welcome.
Author: Ulrike Groemping
Maintainer: Ulrike Groemping
DESCRIPTION | 8 ++++----
R/FrF2.R | 40 +++++++++++++++++++++++++++++++++-------
inst/NEWS | 6 ++++++
man/FrF2.Rd | 13 ++++++++-----
4 files changed, 51 insertions(+), 16 deletions(-)
Title: Spatial and Phylogenetic Analysis of Community Diversity
Diff between spacodiR versions 0.11.04012011 dated 2011-04-05 and 0.11.07292011 dated 2011-07-30
Description: SPACoDi is primarily designed to characterise the
structure and phylogenetic diversity of communities using
abundance or presence-absence data of species among community
plots.
Author: Jonathan Eastman, Timothy Paine, and Olivier Hardy
Maintainer: Jonathan Eastman
ChangeLog | 3 +++
DESCRIPTION | 8 ++++----
R/dataManipulation.R | 2 +-
R/dataResampling.R | 2 +-
4 files changed, 9 insertions(+), 6 deletions(-)
Title: Derivative-free Optimization
Diff between dfoptim versions 2011.7-1 dated 2011-07-25 and 2011.7-2 dated 2011-07-30
Description: Derivative-Free optimization algorithms. These algorithms
do not require gradient information. More importantly, they can
be used to solve non-smooth optimization problems.
Author: Ravi Varadhan, Johns Hopkins University, and Hans W. Borchers
(ABB Corporate Research)
Maintainer: Ravi Varadhan
DESCRIPTION | 8 +++---
NAMESPACE | 1
NEWS | 4 +++
R/nmkb.R |only
demo/dfoptim.R | 69 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
man/nmkb.Rd |only
6 files changed, 77 insertions(+), 5 deletions(-)
Title: General Non-linear Optimization
Diff between Rsolnp versions 1.0-9 dated 2011-05-25 and 1.11 dated 2011-07-30
Description: General Non-linear Optimization Using Augmented Lagrange
Multiplier Method
Author: Alexios Ghalanos and Stefan Theussl
Maintainer: Alexios Ghalanos
ChangeLog | 11
DESCRIPTION | 10
NAMESPACE | 1
R/gosolnp.R | 208 +++++++++++++++++-
R/helpers.R | 5
R/solnp.R | 12 -
R/subnp.R | 562 --------------------------------------------------
data/dji30ret.rda |binary
man/Rsolnp-package.Rd | 4
man/gosolnp.Rd | 18 -
man/startpars.Rd |only
11 files changed, 240 insertions(+), 591 deletions(-)
Title: R Commander Plugin for (industrial) Design of Experiments
Diff between RcmdrPlugin.DoE versions 0.10-4 dated 2011-07-23 and 0.10-5 dated 2011-07-30
More information about RcmdrPlugin.DoE at CRAN
Description: WARNING: This package is currently in beta status! The
package provides a platform-independent GUI for design of
experiments. It is implemented as a plugin to the R-Commander,
which is a more general graphical user interface for statistics
in R based on tcl/tk. DoE functionality can be accessed through
the menu Design that is added to the R-Commander menus.
Author: Ulrike Groemping
Maintainer: Ulrike Groemping
DESCRIPTION | 8 ++++----
R/Menu.FrF2level.R | 2 +-
R/Menu.ccd.r | 17 +++++++++++++++++
inst/NEWS | 5 +++++
4 files changed, 27 insertions(+), 5 deletions(-)
Permanent link
Title: Regression Trees with Random Effects for Longitudinal (Panel)
Data
Diff between REEMtree versions 0.90.1 dated 2011-06-22 and 0.90.2 dated 2011-07-30
Description: This package estimates regression trees with random
effects as a way to use data mining techniques to describe
longitudinal or panel data.
Author: Rebecca Sela and Jeffrey Simonoff
Maintainer: Rebecca Sela
DESCRIPTION | 8 ++++----
R/EMtree-functions.r | 2 +-
man/AutoCorrelationLRtest.Rd | 2 +-
man/REEMtree-package.Rd | 3 +--
man/REEMtree.Rd | 5 ++---
man/REEMtree.object.Rd | 2 +-
man/fitted.REEMtree.Rd | 2 +-
man/is.Rd | 2 +-
man/logLik.Rd | 2 +-
man/plot.Rd | 2 +-
man/predict.Rd | 2 +-
man/print.Rd | 2 +-
man/ranef.REEMtree.Rd | 2 +-
man/residuals.REEMtree.Rd | 2 +-
man/simpleREEMdata.Rd | 2 +-
man/tree.Rd | 2 +-
16 files changed, 20 insertions(+), 22 deletions(-)
Title: Tableplot, a visualization of large statistical datasets
Diff between tabplot versions 0.9-1 dated 2011-01-25 and 0.10 dated 2011-07-29
Description: A tableplot is a visualisation of a (large) statistical
dataset with a dozen of variables, both both numeric and
categorical. Each column represents a variable and each row bin
is an aggregate of a certain number of records. Numeric
variables are visualized as bar charts, and categorical
variables as stacked bar charts. Missing values are taken into
account. A GUI has been implemented which is used to easily
customize the tableplot. Also supports large ffdf datasets from
the ff package.
Author: Martijn Tennekes and Edwin de Jonge
Maintainer: Martijn Tennekes
tabplot-0.10/tabplot/DESCRIPTION | 20
tabplot-0.10/tabplot/NAMESPACE | 17
tabplot-0.10/tabplot/R/brokenX.R | 2
tabplot-0.10/tabplot/R/cellplot.R |only
tabplot-0.10/tabplot/R/changeTabplot.R |only
tabplot-0.10/tabplot/R/columnsPlot.R |only
tabplot-0.10/tabplot/R/datetime2fac.R |only
tabplot-0.10/tabplot/R/generalFunctions.R |only
tabplot-0.10/tabplot/R/getFreqTable_DT.R |only
tabplot-0.10/tabplot/R/isTabplotUsable.R |only
tabplot-0.10/tabplot/R/num2fac.R | 22
tabplot-0.10/tabplot/R/onLoad.R |only
tabplot-0.10/tabplot/R/pkg.R |only
tabplot-0.10/tabplot/R/plotCatCol.R |only
tabplot-0.10/tabplot/R/plotColumns.R |only
tabplot-0.10/tabplot/R/plotNumCol.R |only
tabplot-0.10/tabplot/R/plot_tabplot.r |only
tabplot-0.10/tabplot/R/preprocess.data.table.R |only
tabplot-0.10/tabplot/R/preprocess.ffdf.R | 149 +--
tabplot-0.10/tabplot/R/summary_tabplot.R |only
tabplot-0.10/tabplot/R/tableGUI.R | 931 ++-------------------
tabplot-0.10/tabplot/R/tableGUI_functions.R |only
tabplot-0.10/tabplot/R/tableGUI_main_handlers.R |only
tabplot-0.10/tabplot/R/tableGUI_main_layout.R |only
tabplot-0.10/tabplot/R/tableGUI_n2f_handlers.r |only
tabplot-0.10/tabplot/R/tableGUI_n2f_layout.R |only
tabplot-0.10/tabplot/R/tableGUI_pal_functions.R |only
tabplot-0.10/tabplot/R/tableGUI_pal_handlers.R |only
tabplot-0.10/tabplot/R/tableGUI_pal_layout.r |only
tabplot-0.10/tabplot/R/tableplot.R | 129 +-
tabplot-0.10/tabplot/R/tableplot_checkBins.R |only
tabplot-0.10/tabplot/R/tableplot_checkDecreasing.R |only
tabplot-0.10/tabplot/R/tableplot_checkFromTo.R |only
tabplot-0.10/tabplot/R/tableplot_checkPals.R |only
tabplot-0.10/tabplot/R/tableplot_checkScales.R |only
tabplot-0.10/tabplot/R/tableplot_checktCols.R |only
tabplot-0.10/tabplot/R/tableplot_showPalettes.R |only
tabplot-0.10/tabplot/R/tabplotPalettes.R |only
tabplot-0.10/tabplot/R/tabplot_object.R |only
tabplot-0.10/tabplot/data |only
tabplot-0.10/tabplot/demo/ffdf.R | 2
tabplot-0.10/tabplot/demo/tableGUI.R | 3
tabplot-0.10/tabplot/demo/tableplot.R | 27
tabplot-0.10/tabplot/inst |only
tabplot-0.10/tabplot/man/changeTabplot.Rd |only
tabplot-0.10/tabplot/man/datetime2fac.Rd |only
tabplot-0.10/tabplot/man/num2fac.Rd | 63 -
tabplot-0.10/tabplot/man/plot.tabplot.Rd |only
tabplot-0.10/tabplot/man/summary.tabplot.Rd |only
tabplot-0.10/tabplot/man/tableGUI.Rd | 30
tabplot-0.10/tabplot/man/tableplot.Rd | 100 --
tabplot-0.10/tabplot/man/tableplot_showPalettes.Rd |only
tabplot-0.10/tabplot/man/tabplot-object.Rd |only
tabplot-0.10/tabplot/man/tabplot-package.Rd | 53 -
tabplot-0.10/tabplot/man/tabplotPalettes.Rd |only
tabplot-0.9-1/tabplot/R/plotTable.R |only
tabplot-0.9-1/tabplot/R/preprocess.data.frame.R |only
57 files changed, 440 insertions(+), 1108 deletions(-)
Title: Tools for splitting, applying and combining data
Diff between plyr versions 1.5.2 dated 2011-04-24 and 1.6 dated 2011-07-29
Description: plyr is a set of tools that solves a common set of
problems: you need to break a big problem down into manageable
pieces, operate on each pieces and then put all the pieces back
together. For example, you might want to fit a model to each
spatial location or time point in your study, summarise data by
panels or collapse high-dimensional arrays to simpler summary
statistics. The development of plyr has been generously
supported by BD (Becton Dickinson).
Author: Hadley Wickham
Maintainer: Hadley Wickham
plyr-1.5.2/plyr/inst/doc |only
plyr-1.5.2/plyr/man/data-baseball.rd |only
plyr-1.5.2/plyr/man/data-ozone.rd |only
plyr-1.6/plyr/DESCRIPTION | 8 -
plyr-1.6/plyr/NAMESPACE | 133 +++++++++++++++-------------
plyr-1.6/plyr/NEWS | 19 ++++
plyr-1.6/plyr/R/data.r |only
plyr-1.6/plyr/R/dimensions.r | 4
plyr-1.6/plyr/R/helper-arrange.r | 6 +
plyr-1.6/plyr/R/helper-col-wise.r | 2
plyr-1.6/plyr/R/helper-defaults.r | 1
plyr-1.6/plyr/R/helper-each.r | 9 -
plyr-1.6/plyr/R/helper-try.r | 1
plyr-1.6/plyr/R/immutable.r | 4
plyr-1.6/plyr/R/indexed-array.r | 4
plyr-1.6/plyr/R/indexed-data-frame.r | 4
plyr-1.6/plyr/R/indexed.r | 5 +
plyr-1.6/plyr/R/join.r | 4
plyr-1.6/plyr/R/loop-apply.r | 1
plyr-1.6/plyr/R/ply-array.r | 114 ++++++++----------------
plyr-1.6/plyr/R/ply-data-frame.r | 103 ++++-----------------
plyr-1.6/plyr/R/ply-list.r | 99 +++++---------------
plyr-1.6/plyr/R/ply-mapply.r | 3
plyr-1.6/plyr/R/ply-null.r | 3
plyr-1.6/plyr/R/ply-replicate.r | 6 +
plyr-1.6/plyr/R/progress.r | 17 ++-
plyr-1.6/plyr/R/quote.r | 42 +++++---
plyr-1.6/plyr/R/rbind-matrix.r | 1
plyr-1.6/plyr/R/rbind.r | 13 +-
plyr-1.6/plyr/R/simplify-array.r | 2
plyr-1.6/plyr/R/simplify-data-frame.r | 3
plyr-1.6/plyr/R/simplify-vector.r | 2
plyr-1.6/plyr/R/split-array.r | 2
plyr-1.6/plyr/R/split-data-frame.r | 3
plyr-1.6/plyr/R/split-indices.r | 1
plyr-1.6/plyr/R/split.r | 9 +
plyr-1.6/plyr/R/utils.r | 5 +
plyr-1.6/plyr/inst/tests/test-empty.r | 2
plyr-1.6/plyr/inst/tests/test-rbind.r | 30 +++++-
plyr-1.6/plyr/inst/tests/test-replicate.r |only
plyr-1.6/plyr/man-roxygen |only
plyr-1.6/plyr/man/a_ply.Rd | 52 ++++++----
plyr-1.6/plyr/man/aaply.Rd | 112 ++++++++++++++---------
plyr-1.6/plyr/man/adply.Rd | 89 ++++++++++++------
plyr-1.6/plyr/man/alply.Rd | 94 ++++++++++++-------
plyr-1.6/plyr/man/amv_dim.Rd | 13 +-
plyr-1.6/plyr/man/amv_dimnames.Rd | 16 +--
plyr-1.6/plyr/man/arrange.Rd | 27 ++---
plyr-1.6/plyr/man/as.data.frame.function.Rd | 30 +++---
plyr-1.6/plyr/man/as.list.split.Rd | 15 +--
plyr-1.6/plyr/man/as.quoted.Rd | 44 ++++-----
plyr-1.6/plyr/man/baseball.Rd |only
plyr-1.6/plyr/man/colwise.Rd | 40 ++++----
plyr-1.6/plyr/man/compact.Rd | 14 +-
plyr-1.6/plyr/man/count.Rd | 39 ++++----
plyr-1.6/plyr/man/create_progress_bar.Rd | 33 ++++--
plyr-1.6/plyr/man/d_ply.Rd | 40 +++++---
plyr-1.6/plyr/man/daply.Rd | 92 ++++++++++++-------
plyr-1.6/plyr/man/ddply.Rd | 93 ++++++++++++-------
plyr-1.6/plyr/man/defaults.Rd | 15 +--
plyr-1.6/plyr/man/desc.Rd | 24 ++---
plyr-1.6/plyr/man/dims.Rd | 13 +-
plyr-1.6/plyr/man/dlply.Rd | 84 +++++++++++------
plyr-1.6/plyr/man/each.Rd | 29 ++----
plyr-1.6/plyr/man/empty.Rd | 13 +-
plyr-1.6/plyr/man/eval.quoted.Rd | 22 ++--
plyr-1.6/plyr/man/failwith.Rd | 34 ++++---
plyr-1.6/plyr/man/get-split.Rd | 18 +--
plyr-1.6/plyr/man/id.Rd | 32 +++---
plyr-1.6/plyr/man/id_var.Rd | 6 -
plyr-1.6/plyr/man/idata.frame.Rd | 29 +++---
plyr-1.6/plyr/man/indexed_array.Rd | 23 ++--
plyr-1.6/plyr/man/indexed_df.Rd | 27 ++---
plyr-1.6/plyr/man/is.discrete.Rd | 19 ++--
plyr-1.6/plyr/man/is.formula.Rd | 9 +
plyr-1.6/plyr/man/isplit2.Rd | 6 -
plyr-1.6/plyr/man/join.Rd | 45 +++++----
plyr-1.6/plyr/man/join.keys.Rd | 19 ++--
plyr-1.6/plyr/man/l_ply.Rd | 38 +++++---
plyr-1.6/plyr/man/laply.Rd | 87 +++++++++++-------
plyr-1.6/plyr/man/ldply.Rd | 69 +++++++++-----
plyr-1.6/plyr/man/liply.Rd | 28 +++--
plyr-1.6/plyr/man/list_to_array.Rd | 26 +++--
plyr-1.6/plyr/man/list_to_dataframe.Rd | 25 +++--
plyr-1.6/plyr/man/list_to_vector.Rd | 18 ++-
plyr-1.6/plyr/man/llply.Rd | 85 ++++++++++-------
plyr-1.6/plyr/man/loop_apply.Rd | 20 ++--
plyr-1.6/plyr/man/m_ply.Rd | 43 +++++----
plyr-1.6/plyr/man/maply.Rd | 64 ++++++++-----
plyr-1.6/plyr/man/match_df.Rd | 35 ++++---
plyr-1.6/plyr/man/mdply.Rd | 62 +++++++------
plyr-1.6/plyr/man/mlply.Rd | 62 ++++++++-----
plyr-1.6/plyr/man/mutate.Rd | 39 ++++----
plyr-1.6/plyr/man/names.quoted.Rd | 15 +--
plyr-1.6/plyr/man/nunique.Rd | 14 +-
plyr-1.6/plyr/man/ozone.Rd |only
plyr-1.6/plyr/man/print.quoted.Rd | 9 +
plyr-1.6/plyr/man/print.split.Rd | 14 +-
plyr-1.6/plyr/man/progress_none.Rd | 15 ++-
plyr-1.6/plyr/man/progress_text.Rd | 26 +++--
plyr-1.6/plyr/man/progress_tk.Rd | 36 +++++--
plyr-1.6/plyr/man/progress_win.Rd | 32 ++++--
plyr-1.6/plyr/man/quickdf.Rd | 16 +--
plyr-1.6/plyr/man/quoted.Rd | 53 ++++++-----
plyr-1.6/plyr/man/r_ply.Rd | 41 +++++---
plyr-1.6/plyr/man/raply.Rd | 46 ++++++---
plyr-1.6/plyr/man/rbind.fill.Rd | 31 ++++--
plyr-1.6/plyr/man/rbind.fill.matrix.Rd | 43 +++++----
plyr-1.6/plyr/man/rdply.Rd | 39 +++++---
plyr-1.6/plyr/man/reduce_dim.Rd | 12 +-
plyr-1.6/plyr/man/rename.Rd | 21 ++--
plyr-1.6/plyr/man/rlply.Rd | 37 ++++---
plyr-1.6/plyr/man/round_any.Rd | 24 +++--
plyr-1.6/plyr/man/splat.Rd | 29 +++---
plyr-1.6/plyr/man/split_indices.Rd | 20 ++--
plyr-1.6/plyr/man/split_labels.Rd | 19 ++--
plyr-1.6/plyr/man/splitter_a.Rd | 46 ++++++---
plyr-1.6/plyr/man/splitter_d.Rd | 41 +++++---
plyr-1.6/plyr/man/strip_splits.Rd | 20 ++--
plyr-1.6/plyr/man/summarise.Rd | 35 +++----
plyr-1.6/plyr/man/true.Rd | 20 ++--
plyr-1.6/plyr/man/try_default.Rd | 31 +++---
plyr-1.6/plyr/man/tryapply.Rd | 9 +
plyr-1.6/plyr/man/unrowname.Rd | 12 +-
plyr-1.6/plyr/man/vaggregate.Rd | 43 +++++----
125 files changed, 2045 insertions(+), 1480 deletions(-)
Title: A replacement and extension of the optim() function
Diff between optimx versions 2011-2.27 dated 2011-03-01 and 2011-2.29 dated 2011-07-29
Description: Provides a replacement and extension of the optim()
function to unify and streamline optimization capabilities in R
for smooth, possibly box constrained functions of several or
many parameters
Author: John C Nash
Maintainer: John C Nash
DESCRIPTION | 8 ++++----
R/optimx.R | 3 ++-
2 files changed, 6 insertions(+), 5 deletions(-)
Title: R Interface to C API of COIN-OR Clp
Diff between clpAPI versions 1.1.5 dated 2011-07-28 and 1.1.6 dated 2011-07-29
Description: R Interface to C API of COIN-OR Clp, depends on COIN-OR
Clp Version >= 1.12.0
Author: Gabriel Gelius-Dietrich
Maintainer: Gabriel Gelius-Dietrich
DESCRIPTION | 8 ++++----
NEWS | 10 +++++++++-
configure | 22 +++++++++++-----------
configure.ac | 6 +++---
man/clpAPI-package.Rd | 4 ++--
src/Makevars.win | 2 +-
6 files changed, 30 insertions(+), 22 deletions(-)
More information about SpatioTemporal at CRAN
Permanent link
Title: Estimation, simulation and visualization of Hierarchical
Archimedean Copulae (HAC)
Diff between HAC versions 0.1-0 dated 2011-07-23 and 0.1-1 dated 2011-07-29
Description: Package provides the estimation of the structure and the
parameters, simulation methods and structural plots of
high-dimensional Hierarchical Archimedean Copulae (HAC).
Author: Ostap Okhrin
Maintainer: Ostap Okhrin
HAC-0.1-0/HAC/COPYING |only
HAC-0.1-1/HAC/DESCRIPTION | 23 ++++++++---------------
HAC-0.1-1/HAC/R/copula_plot.r | 6 +++---
3 files changed, 11 insertions(+), 18 deletions(-)
Title: Distance and Similarity Measures
Diff between proxy versions 0.4-6 dated 2010-02-06 and 0.4-7 dated 2011-07-29
Description: Provides an extensible framework for the effcient
calculation of auto- and cross-proximities, along with
implementations of the most popular ones.
Author: David Meyer and Christian Buchta
Maintainer: David Meyer
DESCRIPTION | 8 ++++----
NEWS | 5 +++++
R/database.R | 4 +++-
R/dist.R | 5 ++++-
inst/NEWS | 5 +++++
inst/doc/overview.pdf |binary
man/dist.Rd | 2 +-
7 files changed, 22 insertions(+), 7 deletions(-)
Title: Misc Functions of the Department of Statistics (e1071), TU Wien
Diff between e1071 versions 1.5-26 dated 2011-05-22 and 1.5-27 dated 2011-07-29
Description: Functions for latent class analysis, short time Fourier
transform, fuzzy clustering, support vector machines, shortest
path computation, bagged clustering, naive Bayes classifier,
...
Author: Evgenia Dimitriadou, Kurt Hornik, Friedrich Leisch, David
Meyer, and Andreas Weingessel
Maintainer: Friedrich Leisch
e1071-1.5-26/e1071/COPYING |only
e1071-1.5-27/e1071/DESCRIPTION | 8 ++++----
e1071-1.5-27/e1071/NEWS | 4 ++++
e1071-1.5-27/e1071/R/svm.R | 2 ++
e1071-1.5-27/e1071/README | 5 +++--
e1071-1.5-27/e1071/inst/doc/svmdoc.pdf |binary
e1071-1.5-27/e1071/man/svm.Rd | 4 +++-
e1071-1.5-27/e1071/src/Rsvm.c | 4 ++++
8 files changed, 20 insertions(+), 7 deletions(-)
Title: A Laboratory for Recursive Partytioning
Diff between party versions 0.9-99992 dated 2011-05-02 and 0.9-99993 dated 2011-07-29
Description: A computational toolbox for recursive partitioning. The
core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems,
including nominal, ordinal, numeric, censored as well as
multivariate response variables and arbitrary measurement
scales of the covariates. Based on conditional inference trees,
cforest() provides an implementation of Breiman's random
forests. The function mob() implements an algorithm for
recursive partitioning based on parametric models (e.g. linear
models, GLMs or survival regression) employing parameter
instability tests for split selection. Extensible functionality
for visualizing tree-structured regression models is available.
Author: Torsten Hothorn, Kurt Hornik, Carolin Strobl and Achim Zeileis
Maintainer: Torsten Hothorn
DESCRIPTION | 8
NEWS | 4
R/Plot.R | 2
R/Utils.R | 4
data/mammoexp.rda |binary
inst/doc/.build.timestamp |only
inst/doc/MOB.pdf |binary
inst/doc/MOB.tex |only
inst/doc/party.pdf |binary
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inst/documentation/html/Convenience_8c.html | 10
inst/documentation/html/Convenience_8c_af39bdd14f23726fdd6bf74888ffbf920_cgraph.map | 6
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inst/documentation/html/Distributions_8h_source.html | 2
inst/documentation/html/IndependenceTest_8c.html | 18
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inst/documentation/html/IndependenceTest_8h.html | 8
inst/documentation/html/IndependenceTest_8h_a84abb46c73e74364113fb61590f8faa0_cgraph.map | 2
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inst/documentation/html/LinearStatistic_8c.html | 32
inst/documentation/html/LinearStatistic_8c_source.html | 630 +++---
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inst/documentation/html/TestStatistic_8c.html | 8
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inst/documentation/html/TestStatistic_8h.html | 6
inst/documentation/html/TestStatistic_8h_source.html | 2
inst/documentation/html/TreeGrow_8c.html | 8
inst/documentation/html/TreeGrow_8c_a67d352c38f59d30c7b9954bf5d3a57ad_cgraph.map | 98 -
inst/documentation/html/TreeGrow_8c_a67d352c38f59d30c7b9954bf5d3a57ad_cgraph.md5 | 2
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inst/documentation/html/TreeGrow_8c_af9fe6e74563480c8eb5e4332fe9bca22_cgraph.md5 | 2
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inst/documentation/html/TreeGrow_8c_source.html | 2
inst/documentation/html/TreeGrow_8h.html | 4
inst/documentation/html/TreeGrow_8h_a67d352c38f59d30c7b9954bf5d3a57ad_cgraph.map | 98 -
inst/documentation/html/TreeGrow_8h_a67d352c38f59d30c7b9954bf5d3a57ad_cgraph.md5 | 2
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inst/documentation/html/TreeGrow_8h_source.html | 2
inst/documentation/html/Utils_8c.html | 265 +-
inst/documentation/html/Utils_8c_a46c7a1ff234b36c5417eea8a0a93464c_cgraph.map |only
inst/documentation/html/Utils_8c_a46c7a1ff234b36c5417eea8a0a93464c_cgraph.md5 |only
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inst/documentation/html/Utils_8c_a7d7d78de793f6a7b6fd0e2a4f8435908_cgraph.map |only
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inst/documentation/html/Utils_8c_a9aa84c21406d338bd7116cbe9444ea3c_cgraph.map | 6
inst/documentation/html/Utils_8c_a9aa84c21406d338bd7116cbe9444ea3c_cgraph.md5 | 2
inst/documentation/html/Utils_8c_a9aa84c21406d338bd7116cbe9444ea3c_cgraph.png |binary
inst/documentation/html/Utils_8c_ac0d5c2fe971923d7a1b1869dffabddb1_cgraph.map | 6
inst/documentation/html/Utils_8c_ac0d5c2fe971923d7a1b1869dffabddb1_cgraph.md5 | 2
inst/documentation/html/Utils_8c_ac0d5c2fe971923d7a1b1869dffabddb1_cgraph.png |binary
inst/documentation/html/Utils_8c_source.html | 912 +++++-----
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inst/documentation/html/Utils_8h_ac0d5c2fe971923d7a1b1869dffabddb1_cgraph.map | 6
inst/documentation/html/Utils_8h_ac0d5c2fe971923d7a1b1869dffabddb1_cgraph.md5 | 2
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inst/documentation/html/dir_91a45675702750ac58701b43283f1e46.html | 2
inst/documentation/html/dirs.html | 2
inst/documentation/html/files.html | 2
inst/documentation/html/globals.html | 3
inst/documentation/html/globals_0x62.html | 3
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inst/documentation/html/globals_defs.html | 2
inst/documentation/html/globals_func.html | 17
inst/documentation/html/globals_func_0x67.html | 3
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inst/documentation/html/globals_func_0x70.html | 3
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inst/documentation/html/globals_func_0x73.html | 3
inst/documentation/html/globals_func_0x75.html | 3
inst/documentation/html/globals_vars.html | 2
inst/documentation/html/graph_legend.html | 2
inst/documentation/html/main.html | 2
inst/documentation/html/mvt_8f.html | 2
inst/documentation/html/mvt_8f_source.html | 2
inst/documentation/html/mvt_8h.html | 2
inst/documentation/html/mvt_8h_source.html | 2
inst/documentation/html/pages.html | 2
inst/documentation/html/party_8h.html | 10
inst/documentation/html/party_8h_source.html | 2
inst/documentation/html/todo.html | 2
src/IndependenceTest.c | 9
src/LinearStatistic.c | 8
src/Node.c | 4
src/Predict.c | 14
src/Splits.c | 6
src/SurrogateSplits.c | 5
src/Utils.c | 26
src/Utils.h | 4
tests/Splits-regtest.R | 3
tests/Splits-regtest.Rout.save | 3
187 files changed, 2102 insertions(+), 2129 deletions(-)
Title: R interface to NLopt
Diff between nloptr versions 0.8.2 dated 2011-06-22 and 0.8.3 dated 2011-07-29
Description: nloptr is an R interface to NLopt. NLopt is a
free/open-source library for nonlinear optimization, providing
a common interface for a number of different free optimization
routines available online as well as original implementations
of various other algorithms. See
http://ab-initio.mit.edu/wiki/index.php/NLopt_Introduction for
more information on the available algorithms.
Author: Jelmer Ypma
Maintainer: Jelmer Ypma
nloptr-0.8.2/nloptr/COPYING |only
nloptr-0.8.2/nloptr/COPYING.LESSER |only
nloptr-0.8.3/nloptr/DESCRIPTION | 10 +--
nloptr-0.8.3/nloptr/INSTALL.windows |only
nloptr-0.8.3/nloptr/LICENSE |only
nloptr-0.8.3/nloptr/NAMESPACE | 2
nloptr-0.8.3/nloptr/R/check.derivatives.R |only
nloptr-0.8.3/nloptr/R/finite.diff.R |only
nloptr-0.8.3/nloptr/R/nloptr.R | 77 ++++++++++++++++++++++++-
nloptr-0.8.3/nloptr/inst/doc/nloptr.Rnw | 8 +-
nloptr-0.8.3/nloptr/inst/doc/nloptr.pdf |binary
nloptr-0.8.3/nloptr/man/check.derivatives.Rd |only
nloptr-0.8.3/nloptr/man/nloptr.Rd | 8 +-
nloptr-0.8.3/nloptr/src/Makevars | 30 +++++----
nloptr-0.8.3/nloptr/src/nloptr.c | 54 +++++++++++++----
nloptr-0.8.3/nloptr/tests/derivative_checker.R |only
nloptr-0.8.3/nloptr/tests/example.R | 4 -
17 files changed, 153 insertions(+), 40 deletions(-)
Title: Multivariate Dependence Modeling with Vines
Diff between vines versions 1.0.1 dated 2011-05-24 and 1.0.3 dated 2011-07-29
Description: Vines are graphical models for pair-copula constructions
that allow building high-dimensional distributions using
bivariate copulas and marginal density functions. This package
contains S4 classes for vines (C-vines and D-vines) and methods
for inference, goodness-of-fit tests, density evaluation,
distribution function evaluation, and simulation.
Author: Yasser González-Fernández
Maintainer: Yasser González-Fernández
vines-1.0.1/vines/COPYING |only
vines-1.0.3/vines/DESCRIPTION | 18 +++++++++---------
vines-1.0.3/vines/NEWS | 8 ++++++++
vines-1.0.3/vines/R/Vine.R | 4 ++--
vines-1.0.3/vines/R/dimnames.R | 4 ++--
vines-1.0.3/vines/R/dvine.R | 7 +++----
vines-1.0.3/vines/R/h.R | 4 ++--
vines-1.0.3/vines/R/hinverse.R | 6 +++---
vines-1.0.3/vines/R/pvine.R | 4 ++--
vines-1.0.3/vines/R/rvine.R | 8 ++++----
vines-1.0.3/vines/R/show.R | 4 ++--
vines-1.0.3/vines/R/vineFit.R | 4 ++--
vines-1.0.3/vines/R/vineFitML.R | 6 +++---
vines-1.0.3/vines/R/vineGoF.R | 4 ++--
vines-1.0.3/vines/R/vineIter.R | 10 +++++-----
vines-1.0.3/vines/R/vineOrder.R | 6 +++---
vines-1.0.3/vines/R/vinePIT.R | 4 ++--
vines-1.0.3/vines/R/vineParameters.R | 4 ++--
vines-1.0.3/vines/inst/CITATION | 4 ++--
vines-1.0.3/vines/man/CVine-class.Rd | 2 +-
vines-1.0.3/vines/man/DVine-class.Rd | 2 +-
vines-1.0.3/vines/man/RVine-class.Rd | 2 +-
vines-1.0.3/vines/man/Vine-class.Rd | 2 +-
vines-1.0.3/vines/man/h-methods.Rd | 22 +++++++++++-----------
vines-1.0.3/vines/man/hinverse-methods.Rd | 8 ++++----
vines-1.0.3/vines/man/vineFit.Rd | 4 ++--
vines-1.0.3/vines/man/vineOrder.Rd | 4 ++--
vines-1.0.3/vines/src/h.c | 4 ++--
vines-1.0.3/vines/src/h.h | 4 ++--
vines-1.0.3/vines/src/hinverse.c | 4 ++--
vines-1.0.3/vines/src/hinverse.h | 4 ++--
vines-1.0.3/vines/src/register.c | 4 ++--
vines-1.0.3/vines/tests/hfunctions.R | 13 +++++--------
33 files changed, 96 insertions(+), 92 deletions(-)
Title: classes and methods for spatio-temporal data
Diff between spacetime versions 0.5-1 dated 2011-07-23 and 0.5-2 dated 2011-07-29
Description: A package with classes and methods for spatio-temporal
data. In particular, space-time regular lattices, sparse
lattices, and irregular data are supported, with limited
support for trajectories, but not for topologies with S/T
interactions such as space-time prisms. Utility functions are
provided for plotting data as map sequences (lattice or
animation) or multiple time series; for spatial and temporal
selection, as well as methods for retrieving coordinates, for
subsetting, print, summary, etc.
Author: Edzer Pebesma, with contributions by Benedict Graeler and Tom
Gottfried
Maintainer: Edzer Pebesma
DESCRIPTION | 21 +++++++++++----------
R/STSDF-methods.R | 2 +-
R/coerce.R | 5 +++++
R/stplot.R | 8 ++++----
data/air.rda |binary
demo/CressieWikle.R | 17 +++++++----------
inst/doc/spacetime.Rnw | 4 +++-
inst/doc/spacetime.pdf |binary
inst/doc/sto.pdf |binary
inst/doc/stpg.pdf |binary
man/over.Rd | 6 ++++--
man/unstack.Rd | 14 +++++++-------
12 files changed, 42 insertions(+), 35 deletions(-)
Title: In-source documentation for R
Diff between roxygen2 versions 2.0 dated 2011-07-23 and 2.1 dated 2011-07-29
Description: A Doxygen-like in-source documentation system for Rd,
collation, and NAMESPACE.
Author: Hadley Wickham
Maintainer: Hadley Wickham
DESCRIPTION | 6 +++---
NAMESPACE | 1 +
NEWS | 30 ++++++++++++++++++++++++++++++
R/parse-srcref.R | 2 +-
R/rd-file-api.R | 4 ++--
R/rd-tag-api.R | 4 +++-
R/roclet-collate.R | 16 ++++++++--------
R/roclet-namespace.R | 2 +-
R/roclet-rd.R | 5 +++--
R/roxygenize.R | 14 +++++++++++---
README.md | 16 ++++++++--------
inst/tests/Rd-example-3.R |only
inst/tests/test-had.R | 32 +++++++++++++++++++++++++++++++-
man/roxygenize.Rd | 2 +-
14 files changed, 103 insertions(+), 31 deletions(-)
Title: Profile Output Processing Tools for R
Diff between proftools versions 0.0-3 dated 2010-07-30 and 0.0-4 dated 2011-07-29
Description: Tools for examining Rprof profile output.
Author: Luke Tierney
Maintainer: Luke Tierney
DESCRIPTION | 6 +++---
R/proftools.R | 8 ++++----
2 files changed, 7 insertions(+), 7 deletions(-)
Title: Robust PCA by Projection Pursuit
Diff between pcaPP versions 1.9-3 dated 2011-06-20 and 1.9-41 dated 2011-07-29
Description: Robust PCA by Projection Pursuit
Author: Peter Filzmoser, Heinrich Fritz, Klaudius Kalcher
Maintainer: Heinrich Fritz
pcaPP-1.9-3/pcaPP/src/L1Median.HoCr.cpp |only
pcaPP-1.9-3/pcaPP/src/L1Median.VardiZhang.cpp |only
pcaPP-1.9-3/pcaPP/src/R.meal.cpp |only
pcaPP-1.9-3/pcaPP/src/R.meal.h |only
pcaPP-1.9-3/pcaPP/src/package.cpp |only
pcaPP-1.9-3/pcaPP/src/package.h |only
pcaPP-1.9-41/pcaPP/DESCRIPTION | 6
pcaPP-1.9-41/pcaPP/src/L1Median.h | 7 -
pcaPP-1.9-41/pcaPP/src/L1Median_HoCr.cpp |only
pcaPP-1.9-41/pcaPP/src/L1Median_VardiZhang.cpp |only
pcaPP-1.9-41/pcaPP/src/ML_package.cpp |only
pcaPP-1.9-41/pcaPP/src/ML_package.h |only
pcaPP-1.9-41/pcaPP/src/Makevars | 4
pcaPP-1.9-41/pcaPP/src/PCAproj.cpp | 96 ++++++++++----
pcaPP-1.9-41/pcaPP/src/R_meal.cpp |only
pcaPP-1.9-41/pcaPP/src/R_meal.h |only
pcaPP-1.9-41/pcaPP/src/R_meal_BLAS.cpp |only
pcaPP-1.9-41/pcaPP/src/R_package.cpp |only
pcaPP-1.9-41/pcaPP/src/R_package.h |only
pcaPP-1.9-41/pcaPP/src/hess.cpp | 2
pcaPP-1.9-41/pcaPP/src/l1median.cpp | 13 +-
pcaPP-1.9-41/pcaPP/src/pcaPP.h | 3
pcaPP-1.9-41/pcaPP/src/smat.base.h | 100 +++++++++++++++
pcaPP-1.9-41/pcaPP/src/smat.cpp | 35 ++++-
pcaPP-1.9-41/pcaPP/src/smat.def.h | 2
pcaPP-1.9-41/pcaPP/src/smat.elop.h | 162 ++++++++++++++++++++++++-
pcaPP-1.9-41/pcaPP/src/smat.h | 1
pcaPP-1.9-41/pcaPP/src/smat.matop.h | 4
pcaPP-1.9-41/pcaPP/src/smat.meal.h | 50 ++++++-
pcaPP-1.9-41/pcaPP/src/smat_meal_passrng.h |only
pcaPP-1.9-41/pcaPP/src/smat_meal_passrng_hpp.h |only
31 files changed, 425 insertions(+), 60 deletions(-)
Title: GLM model selection and multimodel inference made easy
Diff between glmulti versions 1.0.1 dated 2011-04-15 and 1.0.2 dated 2011-07-29
Description: Automated model selection and model-averaging. Provides a
wrapper for glm and similar functions, automatically generating
all possible models (under constraints set by the user) with
the specified response and explanatory variables, and finding
the best models in terms of some Information Criterion (AIC,
AICc or BIC). Can handle very large numbers of candidate
models. Features a Genetic Algorithm to find the best models
when an exhaustive screening of the candidates is not feasible.
Author: Vincent Calcagno
Maintainer: Vincent Calcagno
ChangeLog | 5 +
DESCRIPTION | 10 +--
R/glmulti.r | 126 ++++++++++++++++++++++++++++++++++++++++++++-----
man/getfit-methods.Rd | 6 ++
man/glmulti-methods.Rd | 5 +
man/glmulti.Rd | 1
6 files changed, 136 insertions(+), 17 deletions(-)
Title: Estimation of Distribution Algorithms Based on Copula Theory
Diff between copulaedas versions 1.0.1 dated 2011-05-24 and 1.0.3 dated 2011-07-29
Description: This package contains implementations of various classes
of Estimation of Distribution Algorithms (EDAs) based on copula
theory: Copula EDAs and Vine EDAs. In this package, EDAs are
implemented using S4 classes with generic functions for its
main parts: seeding, selection, learning, sampling,
replacement, local optimization, termination, and reporting.
The package also includes the implementation of a group of
well-known optimization test problems and utility functions to
study the behavior of EDAs.
Author: Yasser González-Fernández
Maintainer: Yasser González-Fernández
copulaedas-1.0.1/copulaedas/COPYING |only
copulaedas-1.0.3/copulaedas/DESCRIPTION | 16 +++----
copulaedas-1.0.3/copulaedas/NEWS | 8 +++
copulaedas-1.0.3/copulaedas/R/CEDA.R | 8 +--
copulaedas-1.0.3/copulaedas/R/EDA.R | 4 -
copulaedas-1.0.3/copulaedas/R/VEDA.R | 4 -
copulaedas-1.0.3/copulaedas/R/criticalPopSize.R | 4 -
copulaedas-1.0.3/copulaedas/R/functions.R | 4 -
copulaedas-1.0.3/copulaedas/R/indepRuns.R | 4 -
copulaedas-1.0.3/copulaedas/R/margins.R | 4 -
copulaedas-1.0.3/copulaedas/R/misc.R | 4 -
copulaedas-1.0.3/copulaedas/R/optimize.R | 4 -
copulaedas-1.0.3/copulaedas/R/replace.R | 4 -
copulaedas-1.0.3/copulaedas/R/report.R | 4 -
copulaedas-1.0.3/copulaedas/R/run.R | 4 -
copulaedas-1.0.3/copulaedas/R/seed.R | 4 -
copulaedas-1.0.3/copulaedas/R/select.R | 4 -
copulaedas-1.0.3/copulaedas/R/terminate.R | 4 -
copulaedas-1.0.3/copulaedas/inst/CITATION | 4 -
copulaedas-1.0.3/copulaedas/man/CEDA-class.Rd | 28 ++++++------
copulaedas-1.0.3/copulaedas/man/EDA-class.Rd | 2
copulaedas-1.0.3/copulaedas/man/VEDA-class.Rd | 41 ++++++++++--------
copulaedas-1.0.3/copulaedas/man/edaCriticalPopSize.Rd | 3 -
23 files changed, 88 insertions(+), 78 deletions(-)
Title: Convert Rd to roxygen documentation and utilities to improve
documentation
Diff between Rd2roxygen versions 0.1-8 dated 2011-02-17 and 1.0-0 dated 2011-07-29
Description: Functions to convert Rd to roxygen documentation. It can
parse an Rd file to a list, create the roxygen documentation
and update the original R script (e.g. the one containing the
definition of the function) accordingly. This package also
provides utilities which can help developers build packages
using roxygen more easily. The formatR package can be used to
reformat the R code in the examples sections so that the code
will be more readable.
Author: Hadley Wickham and Yihui Xie
Maintainer: Yihui Xie
Rd2roxygen-0.1-8/Rd2roxygen/man/rm_undocumented.Rd |only
Rd2roxygen-1.0-0/Rd2roxygen/.gitignore |only
Rd2roxygen-1.0-0/Rd2roxygen/DESCRIPTION | 20 -
Rd2roxygen-1.0-0/Rd2roxygen/NAMESPACE | 8
Rd2roxygen-1.0-0/Rd2roxygen/NEWS |only
Rd2roxygen-1.0-0/Rd2roxygen/R/Rd2roxygen-package.R | 6
Rd2roxygen-1.0-0/Rd2roxygen/R/rd2roxygen.R | 12
Rd2roxygen-1.0-0/Rd2roxygen/R/utils.R | 315 ++++++------------
Rd2roxygen-1.0-0/Rd2roxygen/README | 6
Rd2roxygen-1.0-0/Rd2roxygen/inst/doc/Rd2roxygen.Rnw | 296 ++++++++--------
Rd2roxygen-1.0-0/Rd2roxygen/inst/doc/Rd2roxygen.bib | 22 -
Rd2roxygen-1.0-0/Rd2roxygen/inst/doc/Rd2roxygen.lyx | 295 ++++++++--------
Rd2roxygen-1.0-0/Rd2roxygen/inst/doc/Rd2roxygen.pdf |binary
Rd2roxygen-1.0-0/Rd2roxygen/inst/doc/clean-up.R | 2
Rd2roxygen-1.0-0/Rd2roxygen/man/Rd2roxygen-package.Rd | 32 +
Rd2roxygen-1.0-0/Rd2roxygen/man/Rd2roxygen.Rd | 50 +-
Rd2roxygen-1.0-0/Rd2roxygen/man/create_roxygen.Rd | 39 +-
Rd2roxygen-1.0-0/Rd2roxygen/man/parse_and_save.Rd | 32 +
Rd2roxygen-1.0-0/Rd2roxygen/man/parse_file.Rd | 34 +
Rd2roxygen-1.0-0/Rd2roxygen/man/reformat_code.Rd | 82 ++--
Rd2roxygen-1.0-0/Rd2roxygen/man/roxygen_and_build.Rd | 87 ++--
21 files changed, 669 insertions(+), 669 deletions(-)
Title: General-purpose optimisation with the Self-Organising Migrating
Algorithm
Diff between soma versions 1.0.0 dated 2010-12-13 and 1.1.0 dated 2011-07-28
Description: This package provides an R implementation of the
Self-Organising Migrating Algorithm, a general-purpose,
stochastic optimisation algorithm. The approach is similar to
that of genetic algorithms, although it is based on the idea of
a series of ``migrations'' by a fixed set of individuals,
rather than the development of successive generations. It can
be applied to any cost-minimisation problem with a bounded
parameter space, and is robust to local minima.
Author: Jon Clayden; based on the work of Ivan Zelinka
Maintainer: Jon Clayden
DESCRIPTION | 11 ++++++-----
NAMESPACE |only
NEWS |only
R/soma.R | 9 +++++++--
man/soma.Rd | 11 ++++++++++-
5 files changed, 23 insertions(+), 8 deletions(-)
Title: Robust Time Series Filters
Diff between robfilter versions 2.6.1 dated 2010-04-22 and 3.0 dated 2011-07-28
Description: A set of functions to filter time series based on concepts
from robust statistics.
Author: Roland Fried
Maintainer: Matthias Borowski
robfilter-2.6.1/robfilter/orig_man |only
robfilter-2.6.1/robfilter/privdata/readme |only
robfilter-3.0/robfilter/DESCRIPTION | 15 +--
robfilter-3.0/robfilter/NAMESPACE | 3
robfilter-3.0/robfilter/R/scarm.filter.R |only
robfilter-3.0/robfilter/data/const.Q.rda |only
robfilter-3.0/robfilter/data/const.rda |binary
robfilter-3.0/robfilter/data/critvals.rda |binary
robfilter-3.0/robfilter/data/dfs.rda |only
robfilter-3.0/robfilter/data/multi.ts.rda |binary
robfilter-3.0/robfilter/data/sysdata.rda |only
robfilter-3.0/robfilter/data/var.n.rda |only
robfilter-3.0/robfilter/inst/doc/getting_started.aux | 5 -
robfilter-3.0/robfilter/inst/doc/getting_started.dvi |only
robfilter-3.0/robfilter/inst/doc/getting_started.log | 93 ++++++++++---------
robfilter-3.0/robfilter/inst/doc/getting_started.pdf |binary
robfilter-3.0/robfilter/inst/doc/getting_started.tex | 69 ++++++++------
robfilter-3.0/robfilter/man/const.Q.Rd |only
robfilter-3.0/robfilter/man/dfs.Rd |only
robfilter-3.0/robfilter/man/dr.filter.Rd |only
robfilter-3.0/robfilter/man/lms.filter.Rd |only
robfilter-3.0/robfilter/man/lqd.filter.Rd |only
robfilter-3.0/robfilter/man/lts.filter.Rd |only
robfilter-3.0/robfilter/man/med.filter.Rd |only
robfilter-3.0/robfilter/man/rm.filter.Rd |only
robfilter-3.0/robfilter/man/robfilter-package.Rd |only
robfilter-3.0/robfilter/man/robreg.filter.Rd | 27 +----
robfilter-3.0/robfilter/man/scarm.filter.Rd |only
robfilter-3.0/robfilter/man/sizecor.Rd |only
robfilter-3.0/robfilter/man/timecor.Rd |only
robfilter-3.0/robfilter/man/var.n.Rd |only
31 files changed, 112 insertions(+), 100 deletions(-)
Title: Solve systems of non linear equations
Diff between nleqslv versions 1.8.5 dated 2011-05-15 and 1.8.6 dated 2011-07-28
Description: Solve a system of non linear equations using a Broyden or
a Newton method with a choice of global strategies such as
linesearch and trust region. There are options for using a
numerical or an analytical jacobian and fixed or automatic
scaling of parameters.
Author: Berend Hasselman
Maintainer: Berend Hasselman
DESCRIPTION | 8 ++--
NAMESPACE |only
NEWS | 7 +++
R/nleqslv.R | 6 +--
man/nleqslv.Rd | 4 +-
man/zznleqslv-iterationreport.Rd | 77 +++++++++++++++++++++------------------
src/nwddlg.f | 15 +++----
src/nwout.c | 20 +++++-----
src/nwpdlg.f | 8 ++--
9 files changed, 79 insertions(+), 66 deletions(-)
Title: Generalized Method of Moments and Generalized Empirical
Likelihood
Diff between gmm versions 1.3-6 dated 2011-04-07 and 1.3-8 dated 2011-07-28
Description: It is a complete suite to estimate models based on moment
conditions. It includes the two step Generalized method of
moments (GMM) of Hansen(1982), the iterated GMM and continuous
updated estimator (CUE) of Hansen-Eaton-Yaron(1996) and several
methods that belong to the Generalized Empirical Likelihood
(GEL) family of estimators, as presented by Smith(1997),
Kitamura(1997), Newey-Smith(2004) and Anatolyev(2005).
Author: Pierre Chausse
Maintainer: Pierre Chausse
DESCRIPTION | 12 +-
NEWS | 16 +++
R/FinRes.R | 52 +++++++++--
R/Methods.gmm.R | 20 +++-
R/gmm.R | 41 +++++++-
R/momentEstim.R | 221 +++++++++++++++++++++++++++++++++++++++++++-----
R/specTest.R | 14 ++-
data/Finance.rda |binary
inst/doc/gmm_with_R.pdf |binary
inst/doc/gmm_with_R.rnw | 4
man/gmm.Rd | 86 +++++++++---------
11 files changed, 372 insertions(+), 94 deletions(-)
Title: Neural Networks in R using the Stuttgart Neural Network
Simulator (SNNS)
Diff between RSNNS versions 0.4-0 dated 2011-06-21 and 0.4-1 dated 2011-07-28
Description: The Stuttgart Neural Network Simulator (SNNS) is a library
containing many standard implementations of neural networks.
This package wraps the SNNS functionality to make it available
from within R. Using the RSNNS low-level interface, all of the
algorithmic functionality and flexibility of SNNS can be
accessed. Furthermore, the package contains a convenient
high-level interface, so that the most common neural network
topologies and learning algorithms integrate seamlessly into R.
Author: Christoph Bergmeir
Maintainer: Christoph Bergmeir
RSNNS-0.4-0/RSNNS/COPYING.LIB |only
RSNNS-0.4-0/RSNNS/inst/doc/ChangeLog |only
RSNNS-0.4-1/RSNNS/ChangeLog |only
RSNNS-0.4-1/RSNNS/DESCRIPTION | 9 +++---
RSNNS-0.4-1/RSNNS/LICENSE |only
RSNNS-0.4-1/RSNNS/R/parser.R | 2 -
RSNNS-0.4-1/RSNNS/src/cc_glob.cpp | 12 ++++----
RSNNS-0.4-1/RSNNS/src/cc_learn.cpp | 9 +++---
RSNNS-0.4-1/RSNNS/src/init_f.cpp | 4 +-
RSNNS-0.4-1/RSNNS/src/kernel.cpp | 5 ++-
RSNNS-0.4-1/RSNNS/src/kr_art1.cpp | 4 +-
RSNNS-0.4-1/RSNNS/src/kr_io.cpp | 46 ++++++++++++++++++--------------
RSNNS-0.4-1/RSNNS/src/kr_mac.h | 6 ++--
RSNNS-0.4-1/RSNNS/src/kr_newpattern.cpp | 4 +-
RSNNS-0.4-1/RSNNS/src/kr_pat_scan.cpp | 3 +-
RSNNS-0.4-1/RSNNS/src/kr_td.cpp | 18 ++++++------
RSNNS-0.4-1/RSNNS/src/learn_f.cpp | 29 +++++++++-----------
RSNNS-0.4-1/RSNNS/src/prun_f.cpp | 6 ++--
RSNNS-0.4-1/RSNNS/src/tacoma_learn.cpp | 10 ++++--
RSNNS-0.4-1/RSNNS/src/update_f.cpp | 44 ++++++++++++++++++------------
20 files changed, 117 insertions(+), 94 deletions(-)
Title: Oracle database interface for R
Diff between ROracle versions 0.5-9 dated 2007-10-15 and 0.5-11 dated 2011-07-28
Description: Oracle database interface (DBI) driver for R. This is a
DBI-compliant Oracle driver based on the ProC/C++ embedded SQL.
It implements the DBI version 0.1-8 plus one extension.
Author: David A. James and Jake Luciani
Maintainer: David A. James
ROracle-0.5-11/ROracle/DESCRIPTION | 16 +++++++------
ROracle-0.5-11/ROracle/NAMESPACE |only
ROracle-0.5-11/ROracle/R/OraSupport.R | 8 +++++-
ROracle-0.5-11/ROracle/R/Oracle.R | 4 +--
ROracle-0.5-11/ROracle/R/S4R.R | 2 -
ROracle-0.5-11/ROracle/R/dbObjectId.R | 2 -
ROracle-0.5-11/ROracle/R/zzz.R | 6 ++---
ROracle-0.5-11/ROracle/configure | 3 --
ROracle-0.5-11/ROracle/configure.in | 2 -
ROracle-0.5-11/ROracle/inst/NEWS | 14 +++++++++++
ROracle-0.5-11/ROracle/inst/doc/DBI.pdf |binary
ROracle-0.5-11/ROracle/man/DBIPreparedStatement-class.Rd | 2 -
ROracle-0.5-11/ROracle/man/OraConnection-class.Rd | 2 -
ROracle-0.5-11/ROracle/man/OraDriver-class.Rd | 2 -
ROracle-0.5-11/ROracle/man/OraObject-class.Rd | 2 -
ROracle-0.5-11/ROracle/man/OraPreparedStatement-class.Rd | 2 -
ROracle-0.5-11/ROracle/man/OraResult-class.Rd | 2 -
ROracle-0.5-11/ROracle/man/Oracle.Rd | 4 +--
ROracle-0.5-11/ROracle/man/S4R.Rd | 2 -
ROracle-0.5-11/ROracle/man/dbCallProc-methods.Rd | 2 -
ROracle-0.5-11/ROracle/man/dbCommit-methods.Rd | 2 -
ROracle-0.5-11/ROracle/man/dbConnect-methods.Rd | 2 -
ROracle-0.5-11/ROracle/man/dbDataType-methods.Rd | 2 -
ROracle-0.5-11/ROracle/man/dbDriver-methods.Rd | 2 -
ROracle-0.5-11/ROracle/man/dbGetInfo-methods.Rd | 2 -
ROracle-0.5-11/ROracle/man/dbListTables-methods.Rd | 2 -
ROracle-0.5-11/ROracle/man/dbObjectId-class.Rd | 2 -
ROracle-0.5-11/ROracle/man/dbPrepareStatement-methods.Rd | 2 -
ROracle-0.5-11/ROracle/man/dbReadTable-methods.Rd | 2 -
ROracle-0.5-11/ROracle/man/dbSendQuery-methods.Rd | 2 -
ROracle-0.5-11/ROracle/man/dbSetDataMappings-methods.Rd | 2 -
ROracle-0.5-11/ROracle/man/fetch-methods.Rd | 2 -
ROracle-0.5-11/ROracle/man/isIdCurrent.Rd | 2 -
ROracle-0.5-11/ROracle/man/make.db.names-methods.Rd | 2 -
ROracle-0.5-11/ROracle/man/oraParseConParams.Rd | 2 -
ROracle-0.5-11/ROracle/man/oraSupport.Rd | 2 -
ROracle-0.5-11/ROracle/man/safe.write.Rd | 6 ++---
ROracle-0.5-11/ROracle/man/summary-methods.Rd | 2 -
ROracle-0.5-11/ROracle/src/Makefile.win | 2 -
ROracle-0.5-11/ROracle/src/RS-DBI.c | 6 ++---
ROracle-0.5-11/ROracle/src/RS-DBI.h | 2 -
ROracle-0.5-11/ROracle/src/RS-Oracle.h | 6 ++---
ROracle-0.5-11/ROracle/src/RS-Oracle.pc | 18 +++++++++------
ROracle-0.5-9/ROracle/sqlnet.log |only
ROracle-0.5-9/ROracle/src/ROracle.def |only
45 files changed, 87 insertions(+), 64 deletions(-)
Title: Medical image registration using the NiftyReg library
Diff between RNiftyReg versions 0.3.1 dated 2011-01-04 and 0.4.1 dated 2011-07-28
Description: This package provides an R interface to the NiftyReg image
registration tools
Author: Jon Clayden; based on original code by Marc Modat and Pankaj
Daga
Maintainer: Jon Clayden
.gitignore |only
DESCRIPTION | 9 +++++----
NAMESPACE |only
NEWS | 16 ++++++++++++++++
R/affine.R | 16 ++++++++--------
R/niftyreg.R | 43 ++++++++++++++++++++++++++++++-------------
R/xform.R | 4 ++--
R/zzz.R | 4 +---
man/niftyreg.Rd | 19 +++++++++++++------
9 files changed, 75 insertions(+), 36 deletions(-)
Title: Exploratory Chemometrics for Spectroscopy
Diff between ChemoSpec versions 1.46-4 dated 2011-03-27 and 1.47-1 dated 2011-07-28
Description: A collection of functions for plotting spectra (NMR, IR
etc) and carrying out various forms of top-down exploratory
data analysis, such as HCA, PCA and model-based clustering.
The design allows comparison of data from samples which fall
into groups such as treatment vs. control. Robust methods
appropriate for this type of high-dimensional data are
available. ChemoSpec is designed to be very user friendly and
suitable for people with limited background in R.
Author: Bryan A. Hanson DePauw University, Greencastle Indiana USA
Maintainer: Bryan A. Hanson
ChemoSpec-1.46-4/ChemoSpec/data/gasNIR.RData |only
ChemoSpec-1.46-4/ChemoSpec/inst/doc/graphics |only
ChemoSpec-1.46-4/ChemoSpec/man/gasNIR.Rd |only
ChemoSpec-1.47-1/ChemoSpec/DESCRIPTION | 11 -
ChemoSpec-1.47-1/ChemoSpec/NEWS | 19 +-
ChemoSpec-1.47-1/ChemoSpec/R/aovPCA.R |only
ChemoSpec-1.47-1/ChemoSpec/R/aovPCAloadings.R |only
ChemoSpec-1.47-1/ChemoSpec/R/aovPCAscores.R |only
ChemoSpec-1.47-1/ChemoSpec/R/avgFacLvls.R |only
ChemoSpec-1.47-1/ChemoSpec/R/classPCA.R | 8
ChemoSpec-1.47-1/ChemoSpec/R/hmapSpectra.R | 2
ChemoSpec-1.47-1/ChemoSpec/R/plotScores.R | 8
ChemoSpec-1.47-1/ChemoSpec/R/sPlotSpectra.R |only
ChemoSpec-1.47-1/ChemoSpec/R/splitSpectraGroups.R | 36 +++
ChemoSpec-1.47-1/ChemoSpec/data/datalist |only
ChemoSpec-1.47-1/ChemoSpec/inst/doc/.Rhistory |only
ChemoSpec-1.47-1/ChemoSpec/inst/doc/ChemoSpec.Rnw | 179 ++++++++++++-------
ChemoSpec-1.47-1/ChemoSpec/inst/doc/ChemoSpec.pdf |binary
ChemoSpec-1.47-1/ChemoSpec/inst/doc/aovPCA1.pdf |only
ChemoSpec-1.47-1/ChemoSpec/inst/doc/aovPCA2.pdf |only
ChemoSpec-1.47-1/ChemoSpec/inst/doc/chemometrics.bib | 50 +++++
ChemoSpec-1.47-1/ChemoSpec/man/ChemoSpec-package.Rd | 4
ChemoSpec-1.47-1/ChemoSpec/man/aovPCA.Rd |only
ChemoSpec-1.47-1/ChemoSpec/man/aovPCAloadings.Rd |only
ChemoSpec-1.47-1/ChemoSpec/man/aovPCAscores.Rd |only
ChemoSpec-1.47-1/ChemoSpec/man/avgFacLvls.Rd |only
ChemoSpec-1.47-1/ChemoSpec/man/classPCA.Rd | 6
ChemoSpec-1.47-1/ChemoSpec/man/colorSymbol.Rd | 2
ChemoSpec-1.47-1/ChemoSpec/man/sPlotSpectra.Rd |only
ChemoSpec-1.47-1/ChemoSpec/man/seXy.Rd | 2
ChemoSpec-1.47-1/ChemoSpec/man/splitSpectraGroups.Rd | 18 +
31 files changed, 252 insertions(+), 93 deletions(-)
Title: A general message and error reporting system
Diff between reportr versions 0.1.0 dated 2010-10-27 and 0.2.0 dated 2011-07-28
Description: The reportr package provides a system for reporting
messages, which provides certain useful features over the
standard R system, such as the incorporation of output
consolidation, message filtering, automatic generation of stack
traces for debugging, and conditional reporting based on the
current "output level".
Author: Jon Clayden
Maintainer: Jon Clayden
reportr-0.1.0/reportr/R/zzz.R |only
reportr-0.2.0/reportr/DESCRIPTION | 15 +-
reportr-0.2.0/reportr/NAMESPACE |only
reportr-0.2.0/reportr/NEWS |only
reportr-0.2.0/reportr/R/00_constants.R |only
reportr-0.2.0/reportr/R/infix.R | 9 +
reportr-0.2.0/reportr/R/reportr.R | 188 +++++++++++++++++++++++----------
reportr-0.2.0/reportr/man/infix.Rd | 13 +-
reportr-0.2.0/reportr/man/reportr.Rd | 46 +++++---
9 files changed, 187 insertions(+), 84 deletions(-)
Title: R to LaTeX and HTML
Diff between r2lh versions 0.6.1 dated 2010-07-01 and 0.7 dated 2011-07-28
Description: generate univariate and bivariate analyses in LaTeX or
HTML formats
Author: Christophe Genolini, Bernard Desgraupes, Lionel Riou Franca
Maintainer: Christophe Genolini
r2lh-0.6.1/r2lh/data/AIDSknowledge.rda |only
r2lh-0.7/r2lh/DESCRIPTION | 8 ++++----
r2lh-0.7/r2lh/man/r2lh-package.Rd | 4 ++--
r2lh-0.7/r2lh/r2lh-Ex.R |only
4 files changed, 6 insertions(+), 6 deletions(-)
Title: K-Means for Longitudinal Data (KmL)
Diff between kml versions 1.1.2 dated 2010-05-04 and 1.1.3 dated 2011-07-28
Description: KmL is an implementation of k-means specificaly design to
deal with longitudinal data. It provide facilities to deal with
missing value and propose a graphical interphace for chosing
the correct number of clusters.
Author: Christophe Genolini
Maintainer: Christophe Genolini
DESCRIPTION | 8 ++++----
kml-Ex.R |only
man/choice.Rd | 6 ------
man/kml-package.Rd | 4 ++--
4 files changed, 6 insertions(+), 12 deletions(-)
Title: Utilities from Seminar fuer Statistik ETH Zurich
Diff between sfsmisc versions 1.0-15 dated 2011-05-28 and 1.0-16 dated 2011-07-28
Description: Useful utilities ['goodies'] from Seminar fuer Statistik
ETH Zurich, quite a few related to graphics; many ported from
S-plus times.
Author: Martin Maechler and many others.
Maintainer: Martin Maechler
sfsmisc-1.0-15/sfsmisc/DESCRIPTION+ |only
sfsmisc-1.0-15/sfsmisc/man/boxplot.matrix.Rd |only
sfsmisc-1.0-16/sfsmisc/ChangeLog | 12 ++++++++++
sfsmisc-1.0-16/sfsmisc/DESCRIPTION | 10 ++++----
sfsmisc-1.0-16/sfsmisc/NAMESPACE | 1
sfsmisc-1.0-16/sfsmisc/R/misc-goodies.R | 32 ---------------------------
sfsmisc-1.0-16/sfsmisc/R/pd-matrix.R | 3 --
sfsmisc-1.0-16/sfsmisc/data/potatoes.rda |binary
sfsmisc-1.0-16/sfsmisc/inst/ChangeLog | 12 ++++++++++
sfsmisc-1.0-16/sfsmisc/man/posdefify.Rd | 5 ++--
10 files changed, 34 insertions(+), 41 deletions(-)
Title: Functions useful in the design and ANOVA of experiments
Diff between dae versions 2.1-2 dated 2011-01-26 and 2.1-7 dated 2011-07-28
Description: This package includes a number of functions that aid in
generating experimental designs and in examining their
canonical efficiency factors. It also includes functions that
facilitate diagnostic checking after an aov, especially when
the Error function has been used in the call to aov.
Author: Chris Brien
Maintainer: Chris Brien
DESCRIPTION | 8 ++++----
R/fac.functions.r | 3 ++-
R/proj.r | 47 +++++++++++++++++++++++++++++------------------
R/qqyeffects.r | 18 ++++++------------
R/rmvnorm.r | 18 +++++++++++-------
man/elements.Rd | 6 +++---
man/rmvnorm.Rd | 6 ++++--
7 files changed, 59 insertions(+), 47 deletions(-)
Title: Estimation, Diagnostic and Forecasting Functions for ARFIMA
models
Diff between afmtools versions 0.1.2 dated 2011-05-03 and 0.1.4 dated 2011-07-28
Description: A collection of estimation, forecasting and diagnostic
tools for autoregressive fractionally integrated moving-average
process (ARFIMA).
Author: Javier Contreras-Reyes, Georg M. Goerg, Wilfredo Palma
Maintainer: Javier Contreras-Reyes
DESCRIPTION | 6 ++---
R/pred.arfima.R | 2 -
data/TreeRing.rda |only
man/MammothCreek.Rd | 4 +--
man/TreeRing.Rd |only
man/afmtools-package.Rd | 6 +++--
man/check.parameters.arfima.Rd | 2 -
man/gw.test.Rd | 39 +++++++++++++----------------------
man/per.arfima.Rd | 18 +++++++---------
man/pi.j.Rd | 2 -
man/pred.arfima.Rd | 45 +++++++----------------------------------
man/rho.arma.Rd | 6 +----
man/rho.sowell.Rd | 36 +++-----------------------------
man/spectrum.arfima.Rd | 2 -
14 files changed, 48 insertions(+), 120 deletions(-)
Title: R/Weka interface jars
Diff between RWekajars versions 3.7.3-1 dated 2010-12-14 and 3.7.4-1 dated 2011-07-28
Description: External jars required for package RWeka.
Author: Kurt Hornik
Maintainer: Kurt Hornik
DESCRIPTION | 8 ++++----
inst/java/weka.jar |binary
2 files changed, 4 insertions(+), 4 deletions(-)
Title: R/Weka interface
Diff between RWeka versions 0.4-7 dated 2011-04-09 and 0.4-8 dated 2011-07-28
Description: An R interface to Weka (Version 3.7.4). Weka is a
collection of machine learning algorithms for data mining tasks
written in Java, containing tools for data pre-processing,
classification, regression, clustering, association rules, and
visualization. Package RWeka contains the interface code, the
Weka jar is in a separate package RWekajars. For more
information on Weka see http://www.cs.waikato.ac.nz/~ml/weka/.
Author: Kurt Hornik, with contributions from Christian Buchta, Torsten
Hothorn, Alexandros Karatzoglou, David Meyer, and Achim Zeileis
Maintainer: Kurt Hornik
CHANGELOG | 7
DESCRIPTION | 10 -
inst/arff/cpu.arff | 404 +++++++++++++++++++++++-----------------------
inst/arff/diabetes.arff |only
inst/arff/glass.arff |only
inst/arff/ionosphere.arff |only
inst/arff/vote.arff |only
inst/doc/RWeka.pdf |binary
inst/java/RWeka.jar |binary
9 files changed, 214 insertions(+), 207 deletions(-)
Title: Selecting variable subsets
Diff between subselect versions 0.10-1 dated 2009-12-13 and 0.11-1 dated 2011-07-27
Description: A collection of functions which (i) assess the quality of
variable subsets as surrogates for a full data set, in either
an exploratory data analysis or in the context of a
multivariate linear model, and (ii) search for subsets which
are optimal under various criteria.
Author: Jorge Orestes Cerdeira
Maintainer: Jorge Cadima
subselect-0.10-1/subselect/man/leaps.Rd |only
subselect-0.11-1/subselect/DESCRIPTION | 9
subselect-0.11-1/subselect/NAMESPACE | 4
subselect-0.11-1/subselect/R/anneal.R | 13
subselect-0.11-1/subselect/R/createHmat.R | 162 ++++++----
subselect-0.11-1/subselect/R/eleaps.R |only
subselect-0.11-1/subselect/R/genetic.R | 13
subselect-0.11-1/subselect/R/improve.R | 13
subselect-0.11-1/subselect/R/initialization.R |only
subselect-0.11-1/subselect/R/leaps.R | 184 -----------
subselect-0.11-1/subselect/R/validation.R | 29 +
subselect-0.11-1/subselect/R/validmat.R | 25 +
subselect-0.11-1/subselect/R/validnovcrit.R | 3
subselect-0.11-1/subselect/data |only
subselect-0.11-1/subselect/inst/CHANGELOG | 29 +
subselect-0.11-1/subselect/inst/doc |only
subselect-0.11-1/subselect/man/anneal.Rd | 45 +-
subselect-0.11-1/subselect/man/ccr12.Rd | 12
subselect-0.11-1/subselect/man/eleaps.Rd |only
subselect-0.11-1/subselect/man/farm.Rd |only
subselect-0.11-1/subselect/man/genetic.Rd | 28 +
subselect-0.11-1/subselect/man/glhHmat.Rd | 179 ++---------
subselect-0.11-1/subselect/man/glmHmat.Rd | 32 +
subselect-0.11-1/subselect/man/improve.Rd | 38 +-
subselect-0.11-1/subselect/man/ldaHmat.Rd | 9
subselect-0.11-1/subselect/man/lmHmat.Rd | 16
subselect-0.11-1/subselect/man/rm.Rd | 2
subselect-0.11-1/subselect/man/rv.Rd | 2
subselect-0.11-1/subselect/man/subselect-internal.Rd | 13
subselect-0.11-1/subselect/man/tau2.Rd | 13
subselect-0.11-1/subselect/man/trimmatrix.Rd | 2
subselect-0.11-1/subselect/man/wald.Rd | 16
subselect-0.11-1/subselect/man/xi2.Rd | 12
subselect-0.11-1/subselect/man/zeta2.Rd | 13
subselect-0.11-1/subselect/src/CCRcrt.cpp | 59 ++-
subselect-0.11-1/subselect/src/CCRcrt.h | 22 -
subselect-0.11-1/subselect/src/ErrMReals.h |only
subselect-0.11-1/subselect/src/GCDcrt.cpp | 24 -
subselect-0.11-1/subselect/src/GCDcrt.h | 16
subselect-0.11-1/subselect/src/MStcrt.cpp | 68 +++-
subselect-0.11-1/subselect/src/MStcrt.h | 35 +-
subselect-0.11-1/subselect/src/Qforms.cpp | 86 +++--
subselect-0.11-1/subselect/src/Qforms.h | 30 +
subselect-0.11-1/subselect/src/RMcrt.cpp | 107 ++++--
subselect-0.11-1/subselect/src/RMcrt.h | 26 +
subselect-0.11-1/subselect/src/RVcrt.cpp | 226 ++++++++------
subselect-0.11-1/subselect/src/RVcrt.h | 30 +
subselect-0.11-1/subselect/src/Rnk3CCRcrt.cpp | 69 ++--
subselect-0.11-1/subselect/src/Rnk3CCRcrt.h | 10
subselect-0.11-1/subselect/src/SRI_sscma.cpp | 80 +++-
subselect-0.11-1/subselect/src/SRI_sscma.h | 22 -
subselect-0.11-1/subselect/src/SR_datatrnsf.cpp | 182 ++++++-----
subselect-0.11-1/subselect/src/SR_intf.cpp | 13
subselect-0.11-1/subselect/src/SpecialArrays.cpp | 4
subselect-0.11-1/subselect/src/SpecialArrays.h | 167 ++++++++--
subselect-0.11-1/subselect/src/Sscma.cpp | 125 +++++--
subselect-0.11-1/subselect/src/Sscma.h | 24 +
subselect-0.11-1/subselect/src/Subsets.h | 6
subselect-0.11-1/subselect/src/VSQforms.cpp | 67 ++--
subselect-0.11-1/subselect/src/VSQforms.h | 14
subselect-0.11-1/subselect/src/Varsmbo.cpp | 306 +++++++++++--------
subselect-0.11-1/subselect/src/Vsmabo.h | 222 ++++++-------
subselect-0.11-1/subselect/src/Wrkf1.cpp | 266 ++++++++++++----
63 files changed, 1864 insertions(+), 1358 deletions(-)
Title: A Package for Running jags from R
Diff between R2jags versions 0.02-16 dated 2011-07-23 and 0.02-17 dated 2011-07-27
Description: Using this package to call jags from R.
Author: Yu-Sung Su
Maintainer: Yu-Sung Su
CHANGELOG | 4 ++++
DESCRIPTION | 12 ++++++------
R/jags.R | 27 +++++++++------------------
R/recompile.R | 2 +-
4 files changed, 20 insertions(+), 25 deletions(-)
Title: Ornstein-Uhlenbeck models for phylogenetic comparative
hypotheses
Diff between ouch versions 2.7-1 dated 2010-07-26 and 2.7-2 dated 2011-07-27
Description: Fit and compare Ornstein-Uhlenbeck models for evolution
along a phylogenetic tree.
Author: Aaron A. King
Maintainer: Aaron A. King
ouch-2.7-1/ouch/data/anolis.ssd.csv |only
ouch-2.7-1/ouch/data/bimac.csv |only
ouch-2.7-2/ouch/DESCRIPTION | 10 ++---
ouch-2.7-2/ouch/data/anolis.ssd.csv.gz |only
ouch-2.7-2/ouch/data/bimac.csv.gz |only
ouch-2.7-2/ouch/inst/ChangeLog | 18 ++++++++++
ouch-2.7-2/ouch/inst/NEWS | 56 ++++++++++++++++-----------------
ouch-2.7-2/ouch/man/hansen.Rd | 6 +--
8 files changed, 54 insertions(+), 36 deletions(-)
Title: Time Series Database Interface extension to connect to zip files
Diff between TSzip versions 2011.3-1 dated 2011-03-23 and 2011.6-1 dated 2011-07-27
Description: Provides TSdbi package methods to retrieve time series
data from zipped, as if the files form a database.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 12 ++++++------
LICENSE | 1 +
inst/doc/Guide.pdf |binary
3 files changed, 7 insertions(+), 6 deletions(-)
Title: Time Series Database Interface extension to connect to
spreadsheets
Diff between TSxls versions 2011.3-1 dated 2011-03-23 and 2011.6-1 dated 2011-07-27
Description: Provides TSdbi package methods to retrieve time series
data from spreadsheets, pretending the spreadsheet is a
database.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 12 ++++++------
LICENSE | 1 +
inst/doc/Guide.pdf |binary
3 files changed, 7 insertions(+), 6 deletions(-)
Title: Time Series Database Interface extensions for PADI Time Series
Server
Diff between TSpadi versions 2011.3-1 dated 2011-03-23 and 2011.6-1 dated 2011-07-27
Description: Provides methods for generics in the TSdbi package to
connect through a protocol for application database interface
(PADI) to a time series database (e.g. Fame).
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 14 +++++++-------
LICENSE | 1 +
inst/doc/Guide.pdf |binary
3 files changed, 8 insertions(+), 7 deletions(-)
Title: Time Series Database Interface extensions for get.hist.quote
Diff between TShistQuote versions 2011.3-1 dated 2011-03-23 and 2011.6-1 dated 2011-07-27
Description: Provides methods for generics in the TSdbi package to
retrieve data from historical quote URLs.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 14 +++++++-------
LICENSE | 1 +
inst/doc/Guide.pdf |binary
3 files changed, 8 insertions(+), 7 deletions(-)
Title: Time Series Database Interface extension to connect with
getSymbols
Diff between TSgetSymbol versions 2011.3-1 dated 2011-03-23 and 2011.6-1 dated 2011-07-27
Description: Provides methods for generics in the TSdbi package to
retrieve data with getSymbols, in particular from the Federal
Reserve FRED database.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 14 +++++++-------
LICENSE | 1 +
inst/doc/Guide.pdf |binary
3 files changed, 8 insertions(+), 7 deletions(-)
Title: Seamless R and C++ Integration
Diff between Rcpp versions 0.9.5 dated 2011-07-06 and 0.9.6 dated 2011-07-27
Description: The Rcpp package provides a C++ library which facilitates
the integration of R and C++.
R data types (SEXP) are matched to C++ objects in a class hierarchy.
All R types are supported (vectors, functions, environment, etc
...) and each type is mapped to a dedicated class. For
example, numeric vectors are represented as instances of the
Rcpp::NumericVector class, environments are represented as
instances of Rcpp::Environment, functions are represented as
Rcpp::Function, etc ... The "Rcpp-introduction" vignette
provides a good entry point to Rcpp.
Conversion from C++ to R and back is driven by the templates Rcpp::wrap
and Rcpp::as which are highly flexible and extensible, as
documented in the "Rcpp-extending" vignette.
Rcpp also provides Rcpp modules, a framework that allows exposing C++
functions and classes to the R level. The "Rcpp-modules"
vignette details the current set of features of Rcpp-modules.
Rcpp includes a concept called Rcpp sugar that brings many R functions
into C++. Sugar takes advantage of lazy evaluation and
expression templates to achieve great performance while
exposing a syntax that is much nicer to use than the equivalent
low-level loop code. The "Rcpp-sugar" vignette gives an
overview of the feature.
Several examples are included, and 753 unit tests in 338 unit test
functions provide additional usage examples.
An earlier version of Rcpp, containing what we now call the 'classic
Rcpp API' was written during 2005 and 2006 by Dominick Samperi.
This code has been factored out of Rcpp into the package
RcppClassic and it is still available for code relying on this
interface. New development should use this package instead.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by
Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel and Romain Francois
Rcpp-0.9.5/Rcpp/COPYING |only
Rcpp-0.9.6/Rcpp/ChangeLog | 42 ++++++-
Rcpp-0.9.6/Rcpp/DESCRIPTION | 8 -
Rcpp-0.9.6/Rcpp/inst/NEWS | 21 +++
Rcpp-0.9.6/Rcpp/inst/doc/Rcpp-FAQ.pdf |binary
Rcpp-0.9.6/Rcpp/inst/doc/Rcpp-extending.pdf |binary
Rcpp-0.9.6/Rcpp/inst/doc/Rcpp-introduction.pdf |binary
Rcpp-0.9.6/Rcpp/inst/doc/Rcpp-modules.pdf |binary
Rcpp-0.9.6/Rcpp/inst/doc/Rcpp-package.pdf |binary
Rcpp-0.9.6/Rcpp/inst/doc/Rcpp-quickref.pdf |binary
Rcpp-0.9.6/Rcpp/inst/doc/Rcpp-sugar.pdf |binary
Rcpp-0.9.6/Rcpp/inst/doc/Rcpp-unitTests.pdf |binary
Rcpp-0.9.6/Rcpp/inst/doc/unitTests-results/Rcpp-unitTests.html | 16 +-
Rcpp-0.9.6/Rcpp/inst/doc/unitTests-results/Rcpp-unitTests.txt | 44 +++----
Rcpp-0.9.6/Rcpp/inst/examples/Fibonacci |only
Rcpp-0.9.6/Rcpp/inst/examples/RcppGibbs |only
Rcpp-0.9.6/Rcpp/inst/include/Rcpp/XPtr.h | 58 +++++-----
Rcpp-0.9.6/Rcpp/inst/include/Rcpp/config.h | 2
Rcpp-0.9.6/Rcpp/inst/include/Rcpp/internal/wrap.h | 23 +++
Rcpp-0.9.6/Rcpp/inst/include/Rcpp/traits/is_eigen_base.h |only
Rcpp-0.9.6/Rcpp/inst/include/RcppCommon.h | 1
21 files changed, 145 insertions(+), 70 deletions(-)
Title: Package for analysis and visualization of metagenes
Diff between oposSOM versions 0.1-1 dated 2011-06-17 and 0.1-3 dated 2011-07-27
Description: This package translates microarray expression data into
metagenes and provides various visualizations and second level
analyses.
Author: Henry Wirth
Maintainer: Henry Wirth
DESCRIPTION | 8 ++++----
R/pipeline.r | 2 +-
data |only
man/oposSOM-package.Rd | 26 ++++++++++++++++++++++----
man/run.pipeline.Rd | 38 +++++++++++++++++++++++++++++++-------
man/tissues.Rd |only
6 files changed, 58 insertions(+), 16 deletions(-)
Title: opencpu object encoder/decoder
Diff between opencpu.encode versions 0.1 dated 2011-07-24 and 0.11 dated 2011-07-27
More information about opencpu.encode at CRAN
Description: Encodes R objects to a standardized JSON format
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
DESCRIPTION | 8 ++++----
R/depackageObject.R | 2 +-
R/packageObject.R | 2 +-
R/toJSON.integer.R | 8 ++------
R/toJSON.logical.R | 8 ++------
README.md |only
6 files changed, 10 insertions(+), 18 deletions(-)
Permanent link
Title: Server Side Scripting with R
Diff between SSSR versions 1.0.3 dated 2010-11-26 and 1.0.5 dated 2011-07-27
Description: A package for writing server side R scripts with session,
application and cookie support
Author: Mehmet Hakan Satman
Maintainer: Mehmet Hakan Satman
DESCRIPTION | 17 +++++------
NAMESPACE |only
R/SSSR.r | 78 +++++++++++++++++++++++++++++-----------------------
man/SSSR-package.Rd | 9 ++----
4 files changed, 56 insertions(+), 48 deletions(-)
More information about RcmdrPlugin.KMggplot2 at CRAN
Permanent link
Title: Practical Numerical Math Functions
Diff between pracma versions 0.7-3 dated 2011-07-23 and 0.7.5 dated 2011-07-27
Description: This package provides R implementations of functions in
numerical analysis, with a special view on on optimization and
time series routines. Uses Matlab/Octave function names where
appropriate to simplify porting.
Author: Hans W Borchers
Maintainer: HwB
pracma-0.7-3/pracma/doc/NEWS.Rd |only
pracma-0.7-3/pracma/inst/NEWS.pdf |only
pracma-0.7.5/pracma/DESCRIPTION | 10 +++++-----
pracma-0.7.5/pracma/NEWS | 15 ++++++++++++++-
pracma-0.7.5/pracma/R/rortho.R |only
pracma-0.7.5/pracma/data |only
pracma-0.7.5/pracma/doc/NEWS.pdf |only
pracma-0.7.5/pracma/inst/NEWS.Rd |only
pracma-0.7.5/pracma/man/rortho.Rd |only
pracma-0.7.5/pracma/man/titanium.Rd |only
10 files changed, 19 insertions(+), 6 deletions(-)
Title: Forward search for Mokken scale analysis
Diff between fwdmsa versions 0.1 dated 2010-07-08 and 0.2 dated 2011-07-27
Description: fwdmsa performs the Forward Search for Mokken scale
analysis. It detects outliers, it produces several types of
diagnostic plots.
Author: Wobbe P. Zijlstra
Maintainer: Wobbe P. Zijlstra
fwdmsa-0.1/fwdmsa/R/X.residual.R |only
fwdmsa-0.1/fwdmsa/R/coefH.R |only
fwdmsa-0.1/fwdmsa/R/coefZ.R |only
fwdmsa-0.1/fwdmsa/R/fs.MSA.R |only
fwdmsa-0.1/fwdmsa/R/fs.MSA.n1.R |only
fwdmsa-0.1/fwdmsa/R/memberR.R |only
fwdmsa-0.1/fwdmsa/R/memberX.R |only
fwdmsa-0.1/fwdmsa/R/plot.fs.class.n1.R |only
fwdmsa-0.1/fwdmsa/R/zzz.r |only
fwdmsa-0.1/fwdmsa/man/fs.MSA.Rd |only
fwdmsa-0.1/fwdmsa/man/fs.MSA.n1.Rd |only
fwdmsa-0.2/fwdmsa/DESCRIPTION | 10 +++++-----
fwdmsa-0.2/fwdmsa/R/coefh.R |only
fwdmsa-0.2/fwdmsa/R/coefz.R |only
fwdmsa-0.2/fwdmsa/R/count.R | 4 ++--
fwdmsa-0.2/fwdmsa/R/fs.msa.R |only
fwdmsa-0.2/fwdmsa/R/fs.msa.n1.R |only
fwdmsa-0.2/fwdmsa/R/memberr.R |only
fwdmsa-0.2/fwdmsa/R/memberx.R |only
fwdmsa-0.2/fwdmsa/R/observation.obj.func.R | 4 ++--
fwdmsa-0.2/fwdmsa/R/plot.fs.class.R | 4 ++--
fwdmsa-0.2/fwdmsa/R/plot.fs.n1.class.R |only
fwdmsa-0.2/fwdmsa/R/x.residual.R |only
fwdmsa-0.2/fwdmsa/man/fs.msa.Rd |only
fwdmsa-0.2/fwdmsa/man/fs.msa.n1.Rd |only
fwdmsa-0.2/fwdmsa/man/fwdmsa-package.Rd | 14 +++++++-------
fwdmsa-0.2/fwdmsa/man/plot.fs.class.Rd | 6 +++---
fwdmsa-0.2/fwdmsa/man/plot.fs.n1.class.Rd | 15 +++++++++------
28 files changed, 30 insertions(+), 27 deletions(-)
Title: CRAN Task Views
Diff between ctv versions 0.7-2 dated 2011-04-17 and 0.7-3 dated 2011-07-27
Description: Server-side and client-side tools for task views to
CRAN-style repositories
Author: Achim Zeileis, Kurt Hornik
Maintainer: Achim Zeileis
ctv-0.7-2/ctv/COPYING |only
ctv-0.7-2/ctv/COPYRIGHTS |only
ctv-0.7-3/ctv/DESCRIPTION | 8
ctv-0.7-3/ctv/NEWS | 6
ctv-0.7-3/ctv/R/ctv-server.R | 3
ctv-0.7-3/ctv/inst/ctv/Bayesian.ctv | 314 +++++++++++++-------
ctv-0.7-3/ctv/inst/ctv/ChemPhys.ctv | 12
ctv-0.7-3/ctv/inst/ctv/Cluster.ctv | 26 -
ctv-0.7-3/ctv/inst/ctv/Distributions.ctv | 203 ++++++++++--
ctv-0.7-3/ctv/inst/ctv/Econometrics.ctv | 24 +
ctv-0.7-3/ctv/inst/ctv/ExperimentalDesign.ctv | 23 +
ctv-0.7-3/ctv/inst/ctv/Finance.ctv | 21 -
ctv-0.7-3/ctv/inst/ctv/Genetics.ctv | 9
ctv-0.7-3/ctv/inst/ctv/HighPerformanceComputing.ctv | 14
ctv-0.7-3/ctv/inst/ctv/MachineLearning.ctv | 22 +
ctv-0.7-3/ctv/inst/ctv/Phylogenetics.ctv | 5
ctv-0.7-3/ctv/inst/ctv/Psychometrics.ctv | 6
ctv-0.7-3/ctv/inst/ctv/Spatial.ctv | 9
ctv-0.7-3/ctv/inst/ctv/Survival.ctv | 182 +++++++----
ctv-0.7-3/ctv/inst/ctv/TimeSeries.ctv | 23 +
ctv-0.7-3/ctv/inst/ctv/gR.ctv | 21 -
ctv-0.7-3/ctv/inst/doc/ctv-howto.pdf |binary
22 files changed, 661 insertions(+), 270 deletions(-)
Title: Graphical user interface for data mining in R
Diff between rattle versions 2.6.7 dated 2011-07-23 and 2.6.8 dated 2011-07-26
Description: Rattle (the R Analytic Tool To Learn Easily) provides a
Gnome (RGtk2) based interface to R functionality for data
mining. The aim is to provide a simple and intuitive interface
that allows a user to quickly load data from a CSV file (or via
ODBC), transform and explore the data, build and evaluate
models, and export models as PMML (predictive modelling markup
language) or as scores. All of this with knowing little about
R. All R commands are logged and commented through the log tab.
Thus they are available to the user as a script file or as an
aide for the user to learn R or to copy-and-paste directly into
R itself. Rattle also exports a number of utility functions and
the graphical user interface, invoked as rattle(), does not
need to be run to deploy these.
Author: Graham Williams
Maintainer: Graham Williams
DESCRIPTION | 8 ++++----
R/evaluate.R | 15 +++++++++++----
R/random_forest.R | 7 ++++++-
R/rattle.R | 4 ++--
data/weatherAUS.RData |binary
inst/.Rhistory |only
inst/ChangeLog | 8 ++++++++
inst/doc/rattle.pdf |binary
inst/po/de/LC_MESSAGES/R-rattle.mo |binary
inst/po/es/LC_MESSAGES/R-rattle.mo |binary
inst/po/fr/LC_MESSAGES/R-rattle.mo |binary
inst/po/ja/LC_MESSAGES/R-rattle.mo |binary
12 files changed, 31 insertions(+), 11 deletions(-)
Title: Tools for the analysis of air pollution data
Diff between openair versions 0.4-17 dated 2011-04-24 and 0.4-23 dated 2011-07-26
Description: Tools to analyse, interpret and understand air pollution
data. Data are typically hourly time series and both monitoring
data and dispersion model output can be analysed. Many
functions can also be applied to other data, including
meteorological and traffic data.
Author: David Carslaw and Karl Ropkins
Maintainer: David Carslaw
DESCRIPTION | 14
NAMESPACE | 11
NEWS | 79 ++++
R/GoogleMapsPlot.R |only
R/MannKendall.R | 137 +++----
R/TaylorDiagram.R |only
R/aqStats.R | 95 +++--
R/calcPercentile.R | 8
R/calendarPlot.R | 23 -
R/checkPrep.R | 16
R/conditionalQuantile.R | 55 +-
R/drawOpenKey.R | 12
R/import.2.R | 156 +++++++-
R/import.R | 30 +
R/importAURNCsv.R | 6
R/importSAQN.R |only
R/linearRelation.R | 8
R/modStats.R | 16
R/openair.generics.R | 6
R/percentileRose.R | 91 ++--
R/polarAnnulus.R | 338 +++++++++---------
R/polarFreq.R | 146 ++++---
R/polarPlot.R | 95 +++--
R/scatterPlot.R | 310 ++++++++++------
R/selectRunning.R | 12
R/smoothTrend.R | 84 ++--
R/timeAverage.R | 127 +++++-
R/timePlot.R | 160 ++++----
R/timeVariation.R | 98 ++---
R/trendLevel.R | 134 +++----
R/utilities.R | 97 ++++-
R/windRose.R | 231 +++++++-----
R/zzz.R | 16
chm |only
man/GoogleMapsPlot.Rd |only
man/TaylorDiagram.Rd |only
man/calcPercentile.Rd | 8
man/calendarPlot.Rd | 2
man/importAURN.Rd | 11
man/importKCL.Rd | 893 +++++++++++++++++++++++-------------------------
man/importSAQN.Rd |only
man/openair-package.Rd | 2
man/percentileRose.Rd | 13
man/polarAnnulus.Rd | 79 +---
man/polarFreq.Rd | 18
man/polarPlot.Rd | 24 -
man/scatterPlot.Rd | 77 ++--
man/smoothTrend.Rd | 26 -
man/timeAverage.Rd | 36 +
man/timePlot.Rd | 30 -
man/trendLevel.Rd | 2
man/windRose.Rd | 166 +++++---
52 files changed, 2325 insertions(+), 1673 deletions(-)
Title: Analysis of Oceanographic data
Diff between oce versions 0.4-1 dated 2011-07-23 and 0.5-1 dated 2011-07-26
Description: Supports the analysis of Oceanographic data, including ADP
measurements, CTD measurements, sectional data, sea-level time
series, coastline files, etc. Provides functions for
calculating seawater properties such as potential temperature
and density, as well as derived properties such as buoyancy
frequency and dynamic height.
Author: Dan Kelley
Maintainer: Dan Kelley
oce-0.4-1/oce/man/heading.Rd |only
oce-0.4-1/oce/man/pressure.Rd |only
oce-0.4-1/oce/man/velocity.Rd |only
oce-0.5-1/oce/.gitignore | 1
oce-0.5-1/oce/DESCRIPTION | 10 +-
oce-0.5-1/oce/NAMESPACE | 11 ++-
oce-0.5-1/oce/NEWS | 6 +
oce-0.5-1/oce/R/accessors.R | 117 +++++++++++++++++++++++++++++++++--
oce-0.5-1/oce/R/ctd.R | 60 ++++++++++++-----
oce-0.5-1/oce/R/drifter.R |only
oce-0.5-1/oce/R/misc.R | 16 +++-
oce-0.5-1/oce/R/oce.R | 4 -
oce-0.5-1/oce/R/pt.R | 9 ++
oce-0.5-1/oce/R/spectral.R | 15 +++-
oce-0.5-1/oce/data/argo.rda |only
oce-0.5-1/oce/data/datalist | 1
oce-0.5-1/oce/inst/doc/.Rhistory |only
oce-0.5-1/oce/inst/doc/oce.pdf |binary
oce-0.5-1/oce/man/accessors.Rd |only
oce-0.5-1/oce/man/addColumn.Rd | 11 +--
oce-0.5-1/oce/man/argo.Rd |only
oce-0.5-1/oce/man/ctdDecimate.Rd | 2
oce-0.5-1/oce/man/interpBarnes.Rd | 6 -
oce-0.5-1/oce/man/makeSection.Rd | 10 +-
oce-0.5-1/oce/man/plot.adp.Rd | 2
oce-0.5-1/oce/man/plot.ctd.scan.Rd | 2
oce-0.5-1/oce/man/plot.drifter.Rd |only
oce-0.5-1/oce/man/pwelch.Rd | 44 +++++++++----
oce-0.5-1/oce/man/read.coastline.Rd | 13 ++-
oce-0.5-1/oce/man/read.drifter.Rd |only
oce-0.5-1/oce/man/summary.drifter.Rd |only
31 files changed, 269 insertions(+), 71 deletions(-)
Title: Maximum Entropy Bootstrap for Time Series
Diff between meboot versions 1.1-1 dated 2009-12-06 and 1.1-2 dated 2011-07-26
Description: This package performs maximum entropy density based
dependent data bootstrap. An algorithm is provided to create a
population of time series (ensemble) without assuming
stationarity. The reference paper (Vinod, H.D., 2004) explains
how the algorithm satisfies the ergodic theorem and the central
limit theorem.
Author: Hrishikesh D. Vinod
Maintainer: Javier López-de-Lacalle
DESCRIPTION | 8 ++++----
inst/doc/meboot.pdf |binary
man/USconsum.Rd | 1 -
man/USfygt.Rd | 1 -
man/ullwan.Rd | 1 -
meboot-Ex.R |only
6 files changed, 4 insertions(+), 7 deletions(-)
Title: An R wrapper for the infochimps.com API services
Diff between infochimps versions 0.3 dated 2011-03-22 and 0.3.1 dated 2011-07-26
Description: This package provides functions to access all of the APIs
currently available infochimps.com. For more information see
http://api.infochimps.com/.
Author: Drew Conway
Maintainer: Drew Conway
DESCRIPTION | 8 ++++----
man/tw.PeopleSearch.Rd | 6 +++---
man/ufo.Rd | 6 +++---
man/wikipedia.abstracts.Rd | 6 +++---
4 files changed, 13 insertions(+), 13 deletions(-)
Title: Extensible Markov Model (EMM) for Data Stream Clustering in R
Diff between rEMM versions 1.0-0 dated 2010-07-13 and 1.0-2 dated 2011-07-26
Description: This package implements TRACDS (Temporal Relationships
between Clusters for Data Streams) which is a generalization of
Extensible Markov Model (EMM). TRACDS adds a temporal or order
model to data stream clustering by superimposing a dynamically
adapting Markov Chain. This package implements EMM (TRACDS on
top of tNN data stream clustering). Development of this package
was supported in part by NSF IIS-0948893.
Author: Michael Hahsler and Margaret H. Dunham
Maintainer: Michael Hahsler
rEMM-1.0-0/rEMM/inst/doc/rEMM.R |only
rEMM-1.0-0/rEMM/inst/doc/rEMM.Rnw_old |only
rEMM-1.0-2/rEMM/DESCRIPTION | 30 +++---
rEMM-1.0-2/rEMM/NAMESPACE | 18 ++-
rEMM-1.0-2/rEMM/R/AAA.R | 18 +++
rEMM-1.0-2/rEMM/R/AllClasses.R | 123 ++++++++++++++++++++++----
rEMM-1.0-2/rEMM/R/AllGenerics.R | 23 ++++
rEMM-1.0-2/rEMM/R/EMM.R | 50 +++++++++-
rEMM-1.0-2/rEMM/R/SimpleMC.R | 30 +++++-
rEMM-1.0-2/rEMM/R/TRACDS.R | 52 +++++++++--
rEMM-1.0-2/rEMM/R/build.R | 141 +++++------------------------
rEMM-1.0-2/rEMM/R/cluster.R | 123 ++++++++++++--------------
rEMM-1.0-2/rEMM/R/conversion.R |only
rEMM-1.0-2/rEMM/R/fade.R | 28 ++++-
rEMM-1.0-2/rEMM/R/map.R |only
rEMM-1.0-2/rEMM/R/merge.R | 58 +++++++-----
rEMM-1.0-2/rEMM/R/onload.R |only
rEMM-1.0-2/rEMM/R/plot.R | 160 +++++++++++++++++++++++++++-------
rEMM-1.0-2/rEMM/R/predict.R | 26 ++++-
rEMM-1.0-2/rEMM/R/prune.R | 19 ++++
rEMM-1.0-2/rEMM/R/recluster.R | 33 +++++--
rEMM-1.0-2/rEMM/R/remove.R | 37 +++++--
rEMM-1.0-2/rEMM/R/reset.R | 20 ++++
rEMM-1.0-2/rEMM/R/score.R | 19 ++++
rEMM-1.0-2/rEMM/R/synthetic_stream.R | 18 +++
rEMM-1.0-2/rEMM/R/tNN.R | 88 +++++++++++++++---
rEMM-1.0-2/rEMM/R/transition.R | 22 ++++
rEMM-1.0-2/rEMM/R/update.R |only
rEMM-1.0-2/rEMM/data/16S.rda |binary
rEMM-1.0-2/rEMM/data/Derwent.rda |binary
rEMM-1.0-2/rEMM/data/EMMTraffic.rda |binary
rEMM-1.0-2/rEMM/data/EMMsim.rda |binary
rEMM-1.0-2/rEMM/inst/doc/rEMM.Rnw | 94 ++++++++++++++-----
rEMM-1.0-2/rEMM/inst/doc/rEMM.pdf |binary
rEMM-1.0-2/rEMM/man/EMM-class.Rd | 21 +++-
rEMM-1.0-2/rEMM/man/EMM.Rd |only
rEMM-1.0-2/rEMM/man/TRACDS-class.Rd | 37 +++++--
rEMM-1.0-2/rEMM/man/build.Rd | 48 +++-------
rEMM-1.0-2/rEMM/man/cluster.Rd |only
rEMM-1.0-2/rEMM/man/conversion.Rd |only
rEMM-1.0-2/rEMM/man/merge.Rd | 4
rEMM-1.0-2/rEMM/man/plot.EMM.Rd | 13 +-
rEMM-1.0-2/rEMM/man/prune.Rd | 2
rEMM-1.0-2/rEMM/man/recluster.Rd | 2
rEMM-1.0-2/rEMM/man/remove.Rd | 4
rEMM-1.0-2/rEMM/man/tNN-class.Rd | 39 +++++---
rEMM-1.0-2/rEMM/man/update.Rd |only
47 files changed, 977 insertions(+), 423 deletions(-)
Title: Manage massive matrices with shared memory and memory-mapped
files
Diff between bigmemory versions 4.2.3 dated 2010-05-09 and 4.2.11 dated 2011-07-26
Description: Create, store, access, and manipulate massive matrices.
Matrices are allocated to shared memory and may use
memory-mapped files. Packages biganalytics, bigtabulate,
synchronicity, and bigalgebra provide advanced functionality.
Author: Michael J. Kane
Maintainer: Jay and Mike
bigmemory-4.2.11/bigmemory/DESCRIPTION | 10 -
bigmemory-4.2.11/bigmemory/NEWS | 21 ++
bigmemory-4.2.11/bigmemory/R/bigmemory.R | 72 ++++++++--
bigmemory-4.2.11/bigmemory/configure | 11 -
bigmemory-4.2.11/bigmemory/configure.win | 1
bigmemory-4.2.11/bigmemory/inst/doc/Overview.pdf |binary
bigmemory-4.2.11/bigmemory/inst/include/bigmemory/isna.hpp | 6
bigmemory-4.2.11/bigmemory/inst/include/boost/interprocess/detail/transform_iterator.hpp | 22 +--
bigmemory-4.2.11/bigmemory/man/bigmemory-package.Rd | 6
bigmemory-4.2.11/bigmemory/man/deepcopy.Rd | 8 -
bigmemory-4.2.11/bigmemory/src/BigMatrix.cpp | 4
bigmemory-4.2.11/bigmemory/src/bigmemory.cpp | 39 +++--
bigmemory-4.2.11/bigmemory/src/deepcopy.cpp |only
bigmemory-4.2.3/bigmemory/COPYING |only
bigmemory-4.2.3/bigmemory/inst/doc/Overview.tex |only
15 files changed, 141 insertions(+), 59 deletions(-)
Title: Gaussian Processes Tool-Kit
Diff between gptk versions 1.02 dated 2011-06-17 and 1.03 dated 2011-07-26
Description: The gptk package implements a general-purpose toolkit for
Gaussian process regression with an RBF covariance function.
Based on a MATLAB implementation by Neil D. Lawrence. See
inst/doc/index.html for more details.
Author: Alfredo A. Kalaitzis
Maintainer: Alfredo A. Kalaitzis
DESCRIPTION | 10 +++++-----
R/cmpndKernExpandParam.R | 2 +-
R/gpExpandParam.R | 1 -
R/gpPlot.R | 8 ++++----
R/kernExpandParam.R | 5 ++++-
inst/doc/index.html | 3 +++
6 files changed, 17 insertions(+), 12 deletions(-)
Title: spatial and spatio-temporal geostatistical modelling, prediction
and simulation
Diff between gstat versions 1.0-0 dated 2011-07-23 and 1.0-1 dated 2011-07-26
Description: variogram modelling; simple, ordinary and universal point
or block (co)kriging, sequential Gaussian or indicator
(co)simulation; variogram and variogram map plotting utility
functions.
Author: Edzer Pebesma
Maintainer: Edzer Pebesma
DESCRIPTION | 13 ++++++-------
R/variogram.default.R | 2 +-
inst/doc/gstat.pdf |binary
inst/doc/st.pdf |binary
man/predict.gstat.Rd | 2 +-
man/variogram.Rd | 5 +++--
6 files changed, 11 insertions(+), 11 deletions(-)
Title: Functions to operate on binary fingerprint data
Diff between fingerprint versions 3.4.4 dated 2011-06-04 and 3.4.5 dated 2011-07-26
Description: This package contains functions to manipulate binary
fingerprints of arbitrary length. A fingerprint is represented
by an object of S4 class 'fingerprint' which is internally
represented a vector of integers, such that each element
represents the position in the fingerprint that is set to 1.
The bitwise logical functions in R are overridden so that they
can be used directly with 'fingerprint' objects. A number of
distance metrics are also available (many contributed by
Michael Fadock). Fingerprints can be converted to Euclidean
vectors (i.e., points on the unit hypersphere) and can also be
folded using OR. Arbitrary fingerprint formats can be handled
via line handlers. Currently handlers are provided for CDK, MOE
and BCI fingerprint data.
Author: Rajarshi Guha
Maintainer: Rajarshi Guha
ChangeLog | 9 +++++++++
DESCRIPTION | 8 ++++----
R/matrix.R | 34 +++++++++++++---------------------
man/sim.Rd | 10 ++++++++--
4 files changed, 34 insertions(+), 27 deletions(-)
Title: Scientific Graphing Functions for Factorial Designs
Diff between sciplot versions 1.0-8 dated 2011-07-25 and 1.0-9 dated 2011-07-26
Description: A collection of functions that creates graphs with error
bars for data collected from one-way or higher factorial
designs.
Author: Manuel Morales
Maintainer: Manuel Morales
CHANGELOG | 4 +++-
DESCRIPTION | 6 +++---
R/bargraphCI.R | 4 ++--
R/lineplot.CI.R | 4 ++--
4 files changed, 10 insertions(+), 8 deletions(-)
Title: ODBC Database Access
Diff between RODBC versions 1.3-2 dated 2010-07-26 and 1.3-3 dated 2011-07-26
Description: An ODBC database interface
Author: Brian Ripley, and from 1999 to Oct 2002 Michael Lapsley
Maintainer: Brian Ripley
RODBC-1.3-2/RODBC/COPYING |only
RODBC-1.3-3/RODBC/ChangeLog | 8 ++
RODBC-1.3-3/RODBC/DESCRIPTION | 10 ++-
RODBC-1.3-3/RODBC/GPL-2 |only
RODBC-1.3-3/RODBC/inst/LICENCE | 2
RODBC-1.3-3/RODBC/inst/doc/RODBC.Rnw | 38 ++++++-------
RODBC-1.3-3/RODBC/inst/doc/RODBC.pdf |binary
RODBC-1.3-3/RODBC/inst/po/da |only
RODBC-1.3-3/RODBC/inst/po/de/LC_MESSAGES/R-RODBC.mo |binary
RODBC-1.3-3/RODBC/inst/po/de/LC_MESSAGES/RODBC.mo |binary
RODBC-1.3-3/RODBC/inst/po/en@quot/LC_MESSAGES/R-RODBC.mo |binary
RODBC-1.3-3/RODBC/inst/po/en@quot/LC_MESSAGES/RODBC.mo |binary
RODBC-1.3-3/RODBC/po/R-RODBC.pot | 13 +++-
RODBC-1.3-3/RODBC/po/R-da.po |only
RODBC-1.3-3/RODBC/po/R-de.po | 12 +++-
RODBC-1.3-3/RODBC/po/R-en@quot.po | 16 ++++-
RODBC-1.3-3/RODBC/po/RODBC.pot | 35 +++++++-----
RODBC-1.3-3/RODBC/po/da.po |only
RODBC-1.3-3/RODBC/po/de.po | 35 +++++++-----
RODBC-1.3-3/RODBC/po/en@quot.po | 43 +++++++++------
RODBC-1.3-3/RODBC/tests/DB2.Rout.save | 29 +++++-----
RODBC-1.3-3/RODBC/tests/Master.R | 2
RODBC-1.3-3/RODBC/tests/Notes | 2
RODBC-1.3-3/RODBC/tests/postgresql.Rout.save | 17 +++--
24 files changed, 166 insertions(+), 96 deletions(-)
Title: Software for Bayesian Inference
Diff between LaplacesDemon versions 11.07.15 dated 2011-07-23 and 11.07.27 dated 2011-07-26
Description: Laplace's Demon is software for Bayesian inference.
Author: Byron Hall
Maintainer: Byron Hall
CHANGELOG | 7 +
DESCRIPTION | 8 -
R/LaplacesDemon.R | 24 ++---
inst/CITATION | 2
inst/doc/BayesianInference.pdf |binary
inst/doc/Examples.Stex | 194 +++++++++++++++++++++++++++++++++++++++--
inst/doc/Examples.pdf |binary
inst/doc/LaplacesDemon.pdf |binary
inst/doc/References.bib | 2
man/LaplacesDemon.Rd | 23 ++--
10 files changed, 228 insertions(+), 32 deletions(-)
Title: Evolutionary Multiobjective Optimization Algorithms
Diff between emoa versions 0.4-5 dated 2011-06-30 and 0.4-7 dated 2011-07-26
Description: Collection of building blocks for the design and analysis
of evolutionary multiobjective optimization algorithms.
Author: Olaf Mersmann
Maintainer: Olaf Mersmann
ChangeLog | 46 +++++++++++++++
DESCRIPTION | 12 ++--
NAMESPACE | 13 ++++
R/crowding_distance.r | 2
R/dominance.r | 4 -
R/emoa.r | 13 +++-
R/front_edge.R |only
R/hypervolume.r | 4 -
R/indicators.r | 17 +++--
R/poly_mutation.r | 2
R/sb_crossover.r | 2
R/sympart.r | 2
R/utilities.r | 3 +
inst/unittests/runit-front_edge.R |only
inst/unittests/runit-id.r | 8 ++
man/which_points_on_edge.Rd |only
src/dominance.c | 4 -
src/front_edge.c |only
src/precomputed_weight_vectors.h |only
src/r_ind.c | 111 ++++++++++++++++++++++++++++++++------
src/weight_vectors.h |only
21 files changed, 199 insertions(+), 44 deletions(-)
Title: SciViews GUI API - Main package
Diff between SciViews versions 0.9-2 dated 2010-09-27 and 0.9-4 dated 2011-07-26
Description: Functions to install SciViews additions to R, and more
(various) tools
Author: Philippe Grosjean
Maintainer: Philippe Grosjean
DESCRIPTION | 8 ++++----
NEWS | 12 ++++++++++++
R/colors.R | 23 +++++++++++------------
R/pcomp.R | 4 ++--
build |only
man/colors.Rd | 8 +++-----
6 files changed, 32 insertions(+), 23 deletions(-)
Title: Overlays on Google map tiles in R
Diff between RgoogleMaps versions 1.1.9.11 dated 2011-07-23 and 1.1.9.13 dated 2011-07-26
Description: This package serves two purposes: (i) Provide a
comfortable R interface to query the Google server for static
maps, and (ii) Use the map as a background image to overlay
plots within R. This requires proper coordinate scaling. NOTE:
To do anything but downloading static map tiles, RgoogleMaps
needs EITHER png OR ReadImages OR rimage installed ! png
(default) is your package if you prefer png file format and
ReadImages or rimage if you prefer jpg format. In the latter
cases, you will also need the libjpeg library installed.
Author: Markus Loecher, Sense Networks
Maintainer: "Markus Loecher, Sense Networks"
DESCRIPTION | 11 ++++++-----
R/PlotOnStaticMap.R | 11 +++++++++--
R/ReadMapTile.R | 27 +++++++++++++++------------
R/myplot.imagematrix.R | 7 +++++++
inst/doc/RgoogleMaps-intro.Rnw | 2 +-
man/RgoogleMaps-package.Rd | 4 ++--
6 files changed, 40 insertions(+), 22 deletions(-)
Title: Get XKCD comic from R
Diff between RXKCD versions 1.0 dated 2011-07-23 and 1.2 dated 2011-07-26
Description: This package allows the visualization of your favorite
XKCD comic strip directly from R. XKCD web comic content is
provided under the Creative Commons Attribution-NonCommercial
2.5 License.
Author: Paolo Sonego
Maintainer: Paolo Sonego
RXKCD-1.0/RXKCD/COPYING |only
RXKCD-1.0/RXKCD/COPYRIGHTS |only
RXKCD-1.2/RXKCD/DESCRIPTION | 16 +++++++++-------
RXKCD-1.2/RXKCD/R/getXKCD.R | 8 ++++++--
RXKCD-1.2/RXKCD/inst/xkcd/xkcd.csv | 2 +-
5 files changed, 16 insertions(+), 10 deletions(-)
Title: Classification and Regression Training
Diff between caret versions 4.92 dated 2011-07-06 and 4.98 dated 2011-07-26
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
caret-4.92/caret/R/applyProcessing.R |only
caret-4.92/caret/R/processData.R |only
caret-4.92/caret/man/applyProcessing.Rd |only
caret-4.98/caret/DESCRIPTION | 8 +--
caret-4.98/caret/NAMESPACE | 15 ++++-
caret-4.98/caret/R/avNNet.R |only
caret-4.98/caret/R/bag.R | 8 +--
caret-4.98/caret/R/confusionMatrix.R | 58 +++++++++++++++++++++
caret-4.98/caret/R/createFolds.R | 21 +++++--
caret-4.98/caret/R/createGrid.R | 4 +
caret-4.98/caret/R/createModel.R | 29 +++++++++-
caret-4.98/caret/R/misc.R | 24 +++++++--
caret-4.98/caret/R/modelLookup.R | 28 ++++++++--
caret-4.98/caret/R/preProcess.R | 21 ++++++-
caret-4.98/caret/R/predictionFunction.R | 2
caret-4.98/caret/R/predictors.R | 5 +
caret-4.98/caret/R/probFunction.R | 2
caret-4.98/caret/R/sampling.R |only
caret-4.98/caret/R/selection.R | 2
caret-4.98/caret/R/train.default.R | 53 ++++++++++---------
caret-4.98/caret/R/trainControl.R | 11 +---
caret-4.98/caret/data/datalist |only
caret-4.98/caret/data/segmentationData.RData |binary
caret-4.98/caret/inst/NEWS | 69 ++++++++++++++++++++++++++
caret-4.98/caret/inst/doc/allPred.pdf |binary
caret-4.98/caret/inst/doc/caretMisc.Rnw | 31 ++++++++++-
caret-4.98/caret/inst/doc/caretMisc.pdf |binary
caret-4.98/caret/inst/doc/caretSelection.pdf |binary
caret-4.98/caret/inst/doc/caretTrain.Rnw | 50 +++++++++++++-----
caret-4.98/caret/inst/doc/caretTrain.pdf |binary
caret-4.98/caret/inst/doc/caretVarImp.Rnw | 4 -
caret-4.98/caret/inst/doc/caretVarImp.pdf |binary
caret-4.98/caret/inst/doc/compact.Rout |only
caret-4.98/caret/inst/doc/filteredPred.pdf |binary
caret-4.98/caret/man/avNNet.Rd |only
caret-4.98/caret/man/bag.Rd | 2
caret-4.98/caret/man/confusionMatrix.train.Rd |only
caret-4.98/caret/man/createDataPartition.Rd | 18 ++++--
caret-4.98/caret/man/pcaNNet.Rd | 6 +-
caret-4.98/caret/man/preProcess.Rd | 2
caret-4.98/caret/man/segmentationData.Rd | 6 +-
caret-4.98/caret/man/train.Rd | 3 -
caret-4.98/caret/man/trainControl.Rd | 8 ---
43 files changed, 384 insertions(+), 106 deletions(-)
Title: Robust Small Area Estimation
Diff between rsae versions 0.1-2 dated 2011-07-23 and 0.1-3 dated 2011-07-25
Description: Robust Small Area Estimation. Robust Basic Unit- and
Area-Level Models
Author: Tobias Schoch
Maintainer: Tobias Schoch
rsae-0.1-2/rsae/inst/doc/rsae-007.pdf |only
rsae-0.1-2/rsae/inst/doc/rsae-015.pdf |only
rsae-0.1-2/rsae/inst/doc/rsae-027.pdf |only
rsae-0.1-2/rsae/inst/doc/rsae-028.pdf |only
rsae-0.1-2/rsae/inst/doc/rsae-029.pdf |only
rsae-0.1-3/rsae/DESCRIPTION | 6 -
rsae-0.1-3/rsae/R/convergence.R |only
rsae-0.1-3/rsae/R/makedata.R | 10 +-
rsae-0.1-3/rsae/R/plot.meanssaemodel.R | 65 +++++++++++++------
rsae-0.1-3/rsae/R/print.fitsaemodel.R | 12 ++-
rsae-0.1-3/rsae/R/print.meanssaemodel.R | 15 +++-
rsae-0.1-3/rsae/R/print.saemodel.R | 6 +
rsae-0.1-3/rsae/R/robpredict.R | 45 +++++++------
rsae-0.1-3/rsae/R/rsae-internal.R | 44 ++++++++++++-
rsae-0.1-3/rsae/R/saemodel.R | 9 +-
rsae-0.1-3/rsae/R/summary.fitsaemodel.R | 107 ++++++++++++--------------------
rsae-0.1-3/rsae/inst/doc/rsae.Rnw | 93 ++++++++++++++++++++-------
rsae-0.1-3/rsae/inst/doc/rsae.pdf |binary
rsae-0.1-3/rsae/man/fitsaemodel.Rd | 9 +-
rsae-0.1-3/rsae/man/robpredict.Rd | 19 +++--
rsae-0.1-3/rsae/man/rsae-package.Rd | 2
rsae-0.1-3/rsae/src/rsae.f90 | 66 ++++++++++++++++++-
22 files changed, 344 insertions(+), 164 deletions(-)
Title: Easy handling of and access to files organized in structured
directories
Diff between R.filesets versions 1.0.2 dated 2011-06-25 and 1.1.0 dated 2011-07-25
Description: A file set refers to a set of files located in one or more
directories on the file system. This package provides classes
and methods to locate, setup, subset, navigate and iterate
suchs sets. The API is designed such that these classes can be
subsetted to provide a richer API for special file formats.
Moreover, a specific name format is defined such that filenames
and directories can be considered to have fullnames which
consists of a name followed by comma-separated tags. This adds
additional flexibility to identify file sets and individual
files. NOTE: This package's API should be considered to be in
an beta stage. Its main purpose is currently to support the
aroma.* packages, where it is one of the main core components;
if you decide to build on top of this package, please contact
the author first.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
DESCRIPTION | 12 +--
NAMESPACE |only
R/FullNameInterface.R | 19 +++++
R/TabularTextFile.R | 116 ++++++++++++++++++++++++++++++++++-
R/zzz.R | 10 ++-
inst/NEWS | 19 +++++
man/getTags.FullNameInterface.Rd | 7 +-
man/readDataFrame.TabularTextFile.Rd | 14 +++-
8 files changed, 184 insertions(+), 13 deletions(-)
Title: Testing, Monitoring and Dating Structural Changes
Diff between strucchange versions 1.4-4 dated 2011-05-13 and 1.4-5 dated 2011-07-25
Description: Testing, monitoring and dating structural changes in
(linear) regression models. strucchange features tests/methods
from the generalized fluctuation test framework as well as from
the F test (Chow test) framework. This includes methods to fit,
plot and test fluctuation processes (e.g., CUSUM, MOSUM,
recursive/moving estimates) and F statistics, respectively. It
is possible to monitor incoming data online using fluctuation
processes. Finally, the breakpoints in regression models with
structural changes can be estimated together with confidence
intervals. Emphasis is always given to methods for visualizing
the data.
Author: Achim Zeileis, Friedrich Leisch, Bruce Hansen, Kurt Hornik,
Christian Kleiber
Maintainer: Achim Zeileis
strucchange-1.4-4/strucchange/COPYING |only
strucchange-1.4-4/strucchange/COPYRIGHTS |only
strucchange-1.4-5/strucchange/DESCRIPTION | 10 ++---
strucchange-1.4-5/strucchange/NEWS | 11 ++++++
strucchange-1.4-5/strucchange/R/breakpoints.R | 1
strucchange-1.4-5/strucchange/R/recresid.R | 18 +++++++---
strucchange-1.4-5/strucchange/data/BostonHomicide.rda |binary
strucchange-1.4-5/strucchange/data/DJIA.rda |binary
strucchange-1.4-5/strucchange/data/GermanM1.rda |binary
strucchange-1.4-5/strucchange/data/Grossarl.rda |binary
strucchange-1.4-5/strucchange/data/PhillipsCurve.rda |binary
strucchange-1.4-5/strucchange/data/RealInt.rda |binary
strucchange-1.4-5/strucchange/data/SP2001.rda |binary
strucchange-1.4-5/strucchange/data/USIncExp.rda |binary
strucchange-1.4-5/strucchange/data/durab.rda |binary
strucchange-1.4-5/strucchange/data/scPublications.rda |binary
strucchange-1.4-5/strucchange/inst/doc/strucchange-intro.pdf |binary
strucchange-1.4-5/strucchange/man/recresid.Rd | 7 ++-
strucchange-1.4-5/strucchange/tests/strucchange-tests.Rout.save | 12 +++++-
19 files changed, 45 insertions(+), 14 deletions(-)
Title: An R client for the OGC Sensor Observation Service
Diff between sos4R versions 0.2-3 dated 2011-05-02 and 0.2-5 dated 2011-07-25
Description: sos4R is a client for Sensor Observation Services (SOS) as
specified by the Open Geospatial Consortium (OGC). It allows
users to retrieve metadata from SOS web services and to
interactively create requests for near real-time observation
data based on the available sensors, phenomena, observations et
cetera using thematic, temporal and spatial filtering.
Author: Daniel Nuest
Maintainer: Daniel Nuest
sos4R-0.2-3/sos4R/inst/doc/sensor.1.1.xml |only
sos4R-0.2-5/sos4R/DESCRIPTION | 8 +-
sos4R-0.2-5/sos4R/R/Defaults.R | 8 +-
sos4R-0.2-5/sos4R/R/SML-methods-coercion.R | 6 +
sos4R-0.2-5/sos4R/R/SML-methods.R | 14 ++--
sos4R-0.2-5/sos4R/R/SWE-methods-parsing.R | 6 -
sos4R-0.2-5/sos4R/demo/weathersos.R | 1
sos4R-0.2-5/sos4R/inst/CHANGES | 9 ++
sos4R-0.2-5/sos4R/inst/CITATION | 10 +-
sos4R-0.2-5/sos4R/inst/doc/err.response.RData |binary
sos4R-0.2-5/sos4R/inst/doc/exceptionResponse.RData |binary
sos4R-0.2-5/sos4R/inst/doc/mbari.RData |binary
sos4R-0.2-5/sos4R/inst/doc/mbari2.RData |binary
sos4R-0.2-5/sos4R/inst/doc/mySOS.RData |binary
sos4R-0.2-5/sos4R/inst/doc/mySOS2.RData |binary
sos4R-0.2-5/sos4R/inst/doc/mySOS2.disabled.RData |binary
sos4R-0.2-5/sos4R/inst/doc/mySensor.xml |only
sos4R-0.2-5/sos4R/inst/doc/obs.sept09.bbox.xml | 2
sos4R-0.2-5/sos4R/inst/doc/procs.descr.RData |binary
sos4R-0.2-5/sos4R/inst/doc/sos4R.Rnw | 55 ++++++++++-----
sos4R-0.2-5/sos4R/inst/doc/sos4R.pdf |binary
sos4R-0.2-5/sos4R/man/Defaults.Rd | 1
sos4R-0.2-5/sos4R/man/sos4R-package.Rd | 4 -
sos4R-0.2-5/sos4R/sandbox/mailinglist-support.R | 18 ++++-
sos4R-0.2-5/sos4R/sandbox/packaging.R | 73 +++++++++++----------
sos4R-0.2-5/sos4R/sandbox/testing.R | 13 +++
sos4R-0.2-5/sos4R/sos4R-Ex.R | 3
27 files changed, 155 insertions(+), 76 deletions(-)
Title: Simulation framework
Diff between simFrame versions 0.4.2 dated 2011-07-23 and 0.4.3 dated 2011-07-25
Description: A general framework for statistical simulation.
Author: Andreas Alfons
Maintainer: Andreas Alfons
simFrame-0.4.2/simFrame/.project |only
simFrame-0.4.2/simFrame/inst/doc/figure-UML.eps |only
simFrame-0.4.2/simFrame/inst/doc/figure-UML.pdf |only
simFrame-0.4.3/simFrame/DESCRIPTION | 10 +++++-----
simFrame-0.4.3/simFrame/NEWS | 8 ++++++++
simFrame-0.4.3/simFrame/R/aaaGenerics.R | 2 +-
simFrame-0.4.3/simFrame/R/cluster.R | 2 +-
simFrame-0.4.3/simFrame/data/eusilcP.RData |binary
simFrame-0.4.3/simFrame/inst/doc/UML.eps |only
simFrame-0.4.3/simFrame/inst/doc/UML.pdf |only
simFrame-0.4.3/simFrame/inst/doc/simFrame-eusilc.Rnw | 14 +++++++-------
simFrame-0.4.3/simFrame/inst/doc/simFrame-eusilc.pdf |binary
simFrame-0.4.3/simFrame/inst/doc/simFrame-intro.Rnw | 16 ++++++++--------
simFrame-0.4.3/simFrame/inst/doc/simFrame-intro.pdf |binary
simFrame-0.4.3/simFrame/inst/doc/simFrame.bib | 2 +-
simFrame-0.4.3/simFrame/man/accessors.Rd | 2 +-
simFrame-0.4.3/simFrame/man/simFrame-package.Rd | 6 +++---
17 files changed, 35 insertions(+), 27 deletions(-)
Title: IRT Separate Calibration Linking Methods
Diff between plink versions 1.3-0 dated 2011-02-12 and 1.3-1 dated 2011-07-25
Description: This package uses item response theory methods to compute
linking constants and conduct chain linking of unidimensional
or multidimensional tests for multiple groups under a common
item design. The unidimensional methods include the Mean/Mean,
Mean/Sigma, Haebara, and Stocking-Lord methods for dichotomous
(1PL, 2PL and 3PL) and/or polytomous (graded response, partial
credit/generalized partial credit, nominal, and multiple-choice
model) items. The multidimensional methods include the least
squares method and extensions of the Haebara and Stocking-Lord
method using single or multiple dilation parameters for
multidimensional extensions of all the unidimensional
dichotomous and polytomous item response models. The package
also includes functions for importing item and/or ability
parameters from common IRT software, conducting IRT true score
and observed score equating, and plotting item response
curves/surfaces, vector plots, and comparison plots for
examining parameter drift.
Author: Jonathan P. Weeks
Maintainer: Jonathan P. Weeks
plink-1.3-0/plink/inst/doc/Rplots.pdf |only
plink-1.3-1/plink/DESCRIPTION | 13 ++++++-------
plink-1.3-1/plink/R/mixed.R | 16 ++++++++++------
plink-1.3-1/plink/R/plink.R | 11 ++++++-----
plink-1.3-1/plink/inst/NEWS | 9 +++++++++
plink-1.3-1/plink/inst/doc/plink-UD.pdf |binary
6 files changed, 31 insertions(+), 18 deletions(-)
Title: Scientific Graphing Functions for Factorial Designs
Diff between sciplot versions 1.0-7 dated 2010-03-22 and 1.0-8 dated 2011-07-25
Description: A collection of functions that creates graphs with error
bars for data collected from one-way or higher factorial
designs.
Author: Manuel Morales
Maintainer: Manuel Morales
CHANGELOG | 1 +
DESCRIPTION | 6 +++---
R/bargraphCI.R | 2 +-
R/lineplot.CI.R | 4 ++--
4 files changed, 7 insertions(+), 6 deletions(-)
Title: Estimation of indicators on social exclusion and poverty
Diff between laeken versions 0.3 dated 2011-06-06 and 0.3.1 dated 2011-07-25
Description: Estimation of indicators on social exclusion and poverty,
as well as Pareto tail modeling for empirical income
distributions (including graphical tools).
Author: Andreas Alfons, Josef Holzer and Matthias Templ
Maintainer: Andreas Alfons
laeken-0.3.1/laeken/DESCRIPTION | 8 ++++----
laeken-0.3.1/laeken/NEWS | 8 ++++++++
laeken-0.3.1/laeken/R/paretoScale.R | 17 +++++++++++++----
laeken-0.3.1/laeken/inst/doc/laeken-pareto.Rnw | 3 +--
laeken-0.3.1/laeken/inst/doc/laeken-pareto.pdf |binary
laeken-0.3.1/laeken/inst/doc/laeken-standard.Rnw | 3 +--
laeken-0.3.1/laeken/inst/doc/laeken-standard.pdf |binary
laeken-0.3.1/laeken/inst/doc/laeken-variance.Rnw | 3 +--
laeken-0.3.1/laeken/inst/doc/laeken-variance.pdf |binary
laeken-0.3.1/laeken/inst/doc/laeken.bib | 2 +-
laeken-0.3.1/laeken/man/laeken-package.Rd | 4 ++--
laeken-0.3.1/laeken/man/paretoScale.Rd | 23 +++++++++++++++++++++--
laeken-0.3/laeken/inst/doc/laeken-pareto-007.eps |only
laeken-0.3/laeken/inst/doc/laeken-pareto-011.eps |only
laeken-0.3/laeken/inst/doc/laeken-pareto-012.eps |only
15 files changed, 52 insertions(+), 19 deletions(-)
Title: Collection of functions for statistical election audits
Diff between elec versions 0.1 dated 2009-05-04 and 0.1.2 dated 2011-07-25
Description: This is a bizzare collection of functions written to do
various sorts of statistical election audits. There are also
functions to generate simulated voting data, and simulated
"truth" so as to do simulations to check charactaristics of
these methods.
Author: Luke Miratrix
Maintainer: Luke Mirarix
elec-0.1.2/elec/DESCRIPTION | 8 +--
elec-0.1.2/elec/R/CAST.R |only
elec-0.1.2/elec/R/KM_package.R |only
elec-0.1.2/elec/R/elec_functions.R |only
elec-0.1.2/elec/R/trinomial.R |only
elec-0.1.2/elec/data/marin.rda |only
elec-0.1.2/elec/man/CAST.Rd | 10 +++-
elec-0.1.2/elec/man/KM.audit.Rd |only
elec-0.1.2/elec/man/KM.calc.sample.Rd |only
elec-0.1.2/elec/man/compute.stark.t.Rd | 2
elec-0.1.2/elec/man/elec-package.Rd | 51 +++++++++++++++--------
elec-0.1.2/elec/man/elec.data.Rd | 4 +
elec-0.1.2/elec/man/make.audit.Rd |only
elec-0.1.2/elec/man/make.opt.packed.bad.Rd |only
elec-0.1.2/elec/man/make.random.truth.Rd |only
elec-0.1.2/elec/man/make.sample.Rd | 9 +++-
elec-0.1.2/elec/man/marin.Rd |only
elec-0.1.2/elec/man/opt.sample.size.Rd |only
elec-0.1.2/elec/man/simulateIt.Rd |only
elec-0.1.2/elec/man/stark.test.Rd | 9 ++--
elec-0.1.2/elec/man/truth.looker.Rd |only
elec-0.1/elec/R/CAST.audit.R |only
elec-0.1/elec/R/CAST.calc.opt.cut.R |only
elec-0.1/elec/R/CAST.calc.sample.R |only
elec-0.1/elec/R/CAST.sample.R |only
elec-0.1/elec/R/TOT-internal.R |only
elec-0.1/elec/R/TTT-internal.R |only
elec-0.1/elec/R/audit.totals.to.OS.R |only
elec-0.1/elec/R/calc.overstatement.e_p.R |only
elec-0.1/elec/R/calc.pairwise.e_p.R |only
elec-0.1/elec/R/compute.audit.errors.R |only
elec-0.1/elec/R/compute.stark.t.R |only
elec-0.1/elec/R/countVotes.R |only
elec-0.1/elec/R/do.audit.R |only
elec-0.1/elec/R/elec.data.R |only
elec-0.1/elec/R/find.q.R |only
elec-0.1/elec/R/find.stark.SRS.p.R |only
elec-0.1/elec/R/find.stratification.R |only
elec-0.1/elec/R/foo-internal.R |only
elec-0.1/elec/R/fractionOfVotesBound.R |only
elec-0.1/elec/R/is.audit.plan.R |only
elec-0.1/elec/R/is.audit.plan.tri.R |only
elec-0.1/elec/R/make.Z.R |only
elec-0.1/elec/R/make.cartoon.R |only
elec-0.1/elec/R/make.ok.truth.R |only
elec-0.1/elec/R/make.sample.R |only
elec-0.1/elec/R/make.sample.from.totals.R |only
elec-0.1/elec/R/make.sample.from.totals.margin.R |only
elec-0.1/elec/R/make.truth.ex.bad.R |only
elec-0.1/elec/R/make.truth.opt.bad.R |only
elec-0.1/elec/R/make.truth.opt.bad.strat.R |only
elec-0.1/elec/R/maximumMarginBound.R |only
elec-0.1/elec/R/print.audit.plan.R |only
elec-0.1/elec/R/print.audit.plan.tri.R |only
elec-0.1/elec/R/print.elec.data.R |only
elec-0.1/elec/R/sim.race.R |only
elec-0.1/elec/R/stageElec-internal.R |only
elec-0.1/elec/R/stark.pairwise.test.R |only
elec-0.1/elec/R/stark.test.R |only
elec-0.1/elec/R/stark.test.Z.R |only
elec-0.1/elec/R/test.CAST.R |only
elec-0.1/elec/R/tri.audit.sim.R |only
elec-0.1/elec/R/tri.calc.sample.R |only
elec-0.1/elec/R/tri.sample.R |only
elec-0.1/elec/R/tri.sample.stats.R |only
elec-0.1/elec/R/trinomial.audit.R |only
elec-0.1/elec/R/trinomial.bound.R |only
elec-0.1/elec/R/weight.function.R |only
68 files changed, 62 insertions(+), 31 deletions(-)
Title: Species distribution modeling
Diff between dismo versions 0.7-1 dated 2011-07-04 and 0.7-2 dated 2011-07-25
Description: Functions for species distribution modeling, that is,
predicting entire geographic distributions form occurences at
specific sites.
Author: Robert J. Hijmans, Steven Phillips, John Leathwick and Jane
Elith
Maintainer:
DESCRIPTION | 10 +++++-----
R/domain.predict.R | 2 +-
inst/doc/brt.pdf |binary
inst/doc/sdm.pdf |binary
4 files changed, 6 insertions(+), 6 deletions(-)
Title: Derivative-free Optimization
Diff between dfoptim versions 2011.5-1 dated 2011-05-03 and 2011.7-1 dated 2011-07-25
Description: Derivative-Free optimization algorithms. These algorithms
do not require gradient information. More importantly, they can
be used to solve non-smooth optimization problems.
Author: Ravi Varadhan, Johns Hopkins University, and Hans W. Borchers
(ABB Corporate Research)
Maintainer: Ravi Varadhan
DESCRIPTION | 11 ++++++-----
NAMESPACE |only
NEWS | 16 ++++++++++++++--
R/hjk.R |only
demo/dfoptim.R | 5 +++++
man/dfoptim-package.Rd | 3 ++-
man/hookejeeves.Rd |only
7 files changed, 27 insertions(+), 8 deletions(-)
Title: Time Series Database Interface extensions for ODBC
Diff between TSodbc versions 2011.3-1 dated 2011-03-23 and 2011.6-1 dated 2011-07-25
Description: TSodbc provides an ODBC interface for TSdbi.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 14 +++++++-------
LICENSE | 1 +
inst/doc/Guide.pdf |binary
3 files changed, 8 insertions(+), 7 deletions(-)
Title: Time Series Database Interface extensions for fame
Diff between TSfame versions 2011.3-1 dated 2011-03-23 and 2011.7-1 dated 2011-07-25
Description: TSfame provides a fame interface for TSdbi.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 14 +++----
LICENSE | 1
NEWS | 9 ++++
R/TSdbiMethods.R | 92 +++++++++++++++++++++++++++++++++++++++----------
R/TSdbiMethodsFS.R | 97 +++++++++++++++++++++++++++++++++++++++-------------
inst/doc/Guide.Stex | 38 +++++++++++++++++++-
inst/doc/Guide.pdf |binary
man/TSdbiMethods.Rd | 41 ++++++++++++++++-----
tests/vintage.R |only
9 files changed, 232 insertions(+), 60 deletions(-)
Title: Time Series Database Interface
Diff between TSdbi versions 2011.3-1 dated 2011-03-23 and 2011.7-1 dated 2011-07-25
Description: TSdbi provides a common interface to time series
databases. The objective is to define a standard interface so
users can retrieve time series data from various sources with a
simple, common, set of commands, and so programs can be written
to be portable with respect to the data source. The SQL
implementations also provide a database table design, so users
needing to set up a time series database have a reasonably
complete way to do this easily. The interface provides for a
variety of options with respect to the representation of time
series in R. There is also a (not yet well tested) mechanism to
handle multilingual data documentation.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 10 +-
LICENSE | 1
NEWS | 14 +++
R/TSdbi.R | 179 ++++++++++++++++++++++++++++----------------
inst/TSsql/TSdbi.TSsql | 8 +
inst/TSsql/dbGetQuery.TSsql | 13 +--
inst/doc/Guide.pdf |binary
man/internal.Rd | 6 -
8 files changed, 152 insertions(+), 79 deletions(-)
Title: Time Series Database Interface extentions for SQLite
Diff between TSSQLite versions 2011.3-1 dated 2011-03-23 and 2011.7-1 dated 2011-07-25
Description: TSSQLite provides a SQLite interface for TSdbi.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 14 +++++++-------
LICENSE | 1 +
NEWS | 6 ++++++
R/TSdbiMethods.R | 14 +++++++-------
inst/doc/Guide.pdf |binary
man/TSdbiMethods.Rd | 28 ++++++++++++++--------------
6 files changed, 35 insertions(+), 28 deletions(-)
Title: Time Series Database Interface extensions for PostgreSQL
Diff between TSPostgreSQL versions 2011.3-1 dated 2011-03-23 and 2011.7-1 dated 2011-07-25
Description: TSPostgreSQL provides a PostgreSQL interface for TSdbi.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 14 +++++++-------
LICENSE | 1 +
NEWS | 5 +++++
R/TSdbiMethods.R | 14 +++++++-------
inst/doc/Guide.pdf |binary
man/TSdbiMethods.Rd | 28 ++++++++++++++--------------
6 files changed, 34 insertions(+), 28 deletions(-)
Title: Time Series Database Interface extensions for MySQL
Diff between TSMySQL versions 2011.3-1 dated 2011-03-23 and 2011.7-1 dated 2011-07-25
Description: TSMySQL provides a MySQL interface for TSdbi.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 14 +++++++-------
LICENSE | 1 +
NEWS | 5 +++++
R/TSdbiMethods.R | 14 +++++++-------
inst/doc/Guide.pdf |binary
man/TSdbiMethods.Rd | 28 ++++++++++++++--------------
6 files changed, 34 insertions(+), 28 deletions(-)
Title: Automating Mplus Model Estimation and Interpretation
Diff between MplusAutomation versions 0.4-2 dated 2011-03-19 and 0.4-3 dated 2011-07-25
More information about MplusAutomation at CRAN
Description: The MplusAutomation package leverages the flexibility of
the R language to automate latent variable model estimation and
interpretation using Mplus, a powerful latent variable modeling
program developed by Muthen and Muthen (www.statmodel.com).
Specifically, MplusAutomation provides routines for creating
related groups of models, running batches of models, and
extracting and tabulating model parameters and fit statistics.
Author: Michael Hallquist
Maintainer: Michael Hallquist
DESCRIPTION | 8 -
NAMESPACE | 5 -
NEWS | 13 ++-
R/createModels.R | 10 --
R/extractModIndices.R | 4
R/extractParameters.R | 53 +++++++-----
R/extractSaveData.R |only
R/parseOutput.R | 153 +++---------------------------------
R/utilityFunctions.R | 144 ++++++++++++++++++++++++++++++---
inst/doc/Vignette.pdf |binary
man/MplusAutomation-package.Rd | 4
man/extractModelParameters.Rd | 25 +++++
man/getSavedata_Bparams.Rd |only
man/testBParamCompoundConstraint.Rd |only
man/testBParamConstraint.Rd |only
15 files changed, 225 insertions(+), 194 deletions(-)
Permanent link
Title: Various programming utilities
Diff between R.utils versions 1.7.7 dated 2011-07-24 and 1.7.8 dated 2011-07-25
Description: This package provides utility classes and methods useful
when programming in R and developing R packages.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
DESCRIPTION | 8 ++++----
NAMESPACE | 2 +-
2 files changed, 5 insertions(+), 5 deletions(-)
Title: Dynamic generation of scientific reports
Diff between R.rsp versions 0.6.0 dated 2011-07-24 and 0.6.1 dated 2011-07-25
Description: An RSP document is a text-based document containing an
R-embedded template of the final document. An RSP document is
preprocessed, parsed and translated into an R script, which
when sourced generates the final document. This way it is
possible to dynamically generate reports in plain text, HTML,
TeX etc. It can also be used to enhance other literate
programming languanges such as Sweave. In addition to RSP,
this package also provides an internal cross-platform web
server and built-in dynamic RSP-embedded HTML help pages, which
can be launched by browseRsp(). If other packages provide RSP
help pages, these are automatically linked to as well.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
DESCRIPTION | 10 +++++-----
NAMESPACE | 4 ++--
inst/NEWS | 5 +++++
inst/doc/report.pdf |binary
4 files changed, 12 insertions(+), 7 deletions(-)
Title: A package for statistical analysis in epidemiology.
Diff between Epi versions 1.1.20 dated 2011-03-01 and 1.1.24 dated 2011-07-25
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
Epi-1.1.20/Epi/R/tabplot.R |only
Epi-1.1.20/Epi/data/DMconv.R |only
Epi-1.1.20/Epi/data/DMlate.R |only
Epi-1.1.20/Epi/data/DMrand.R |only
Epi-1.1.20/Epi/data/S.typh.R |only
Epi-1.1.20/Epi/data/bdendo.R |only
Epi-1.1.20/Epi/data/bdendo11.R |only
Epi-1.1.20/Epi/data/births.R |only
Epi-1.1.20/Epi/data/blcaIT.R |only
Epi-1.1.20/Epi/data/brv.R |only
Epi-1.1.20/Epi/data/diet.R |only
Epi-1.1.20/Epi/data/ewrates.R |only
Epi-1.1.20/Epi/data/gmortDK.R |only
Epi-1.1.20/Epi/data/hivDK.r |only
Epi-1.1.20/Epi/data/lep.R |only
Epi-1.1.20/Epi/data/lungDK.R |only
Epi-1.1.20/Epi/data/mortDK.R |only
Epi-1.1.20/Epi/data/nickel.R |only
Epi-1.1.20/Epi/data/occup.R |only
Epi-1.1.20/Epi/data/thoro.R |only
Epi-1.1.20/Epi/inst/doc/Rplots.pdf |only
Epi-1.1.20/Epi/man/tabplot.Rd |only
Epi-1.1.24/Epi/CHANGES | 50 +++++++++++++++++++++++++++++++---
Epi-1.1.24/Epi/DESCRIPTION | 14 ++++-----
Epi-1.1.24/Epi/NAMESPACE | 6 ++--
Epi-1.1.24/Epi/R/MS.boxes.R | 10 ++++--
Epi-1.1.24/Epi/R/Wald.R |only
Epi-1.1.24/Epi/R/apc.fit.R | 16 ++++------
Epi-1.1.24/Epi/R/ci.cum.R | 13 +++++++-
Epi-1.1.24/Epi/R/ci.lin.R | 13 +++++++-
Epi-1.1.24/Epi/R/cutLexis.R | 44 ++++++++++++++++-------------
Epi-1.1.24/Epi/R/pctab.R | 2 -
Epi-1.1.24/Epi/R/stack.Lexis.R | 16 ++++++----
Epi-1.1.24/Epi/data/DMconv.rda |only
Epi-1.1.24/Epi/data/DMlate.rda |only
Epi-1.1.24/Epi/data/DMrand.rda |only
Epi-1.1.24/Epi/data/S.typh.rda |only
Epi-1.1.24/Epi/data/bdendo.rda |only
Epi-1.1.24/Epi/data/bdendo11.rda |only
Epi-1.1.24/Epi/data/births.rda |only
Epi-1.1.24/Epi/data/blcaIT.rda |only
Epi-1.1.24/Epi/data/brv.rda |only
Epi-1.1.24/Epi/data/datalist |only
Epi-1.1.24/Epi/data/diet.rda |only
Epi-1.1.24/Epi/data/ewrates.rda |only
Epi-1.1.24/Epi/data/gmortDK.rda |only
Epi-1.1.24/Epi/data/hivDK.rda |only
Epi-1.1.24/Epi/data/lep.rda |only
Epi-1.1.24/Epi/data/lungDK.rda |only
Epi-1.1.24/Epi/data/mortDK.rda |only
Epi-1.1.24/Epi/data/nickel.rda |only
Epi-1.1.24/Epi/data/occup.rda |only
Epi-1.1.24/Epi/data/thoro.rda |only
Epi-1.1.24/Epi/inst/CITATION |only
Epi-1.1.24/Epi/inst/doc/Follow-up.pdf |binary
Epi-1.1.24/Epi/man/MS.boxes.Rd | 12 ++++----
Epi-1.1.24/Epi/man/cal.yr.Rd | 6 ++--
Epi-1.1.24/Epi/man/ci.cum.Rd | 26 ++++++++++-------
Epi-1.1.24/Epi/man/ci.lin.Rd | 37 +++++++++++++++++++++----
Epi-1.1.24/Epi/man/cutLexis.Rd | 37 ++++++++++++-------------
Epi-1.1.24/Epi/man/float.Rd | 6 ++--
Epi-1.1.24/Epi/man/ftrend.Rd | 6 ++--
Epi-1.1.24/Epi/man/pctab.Rd | 3 +-
63 files changed, 211 insertions(+), 106 deletions(-)
Title: Basic statistical functions for package ff
Diff between ffbase versions 0.2 dated 2011-04-07 and 0.2-1 dated 2011-07-25
Description: Implementation for min,max, mean, tabulate, table, with,
within. for package ff
Author: Edwin de Jonge
Maintainer: Edwin de Jonge
DESCRIPTION | 20 +++++++--------
NAMESPACE | 1
NEWS |only
R/Summary_ff.R | 2 -
R/chunkify.R | 1
R/compact.R |only
R/diff_ff.R | 1
inst/tests/testSummary.R | 1
inst/tests/testchunkify.R | 4 +--
inst/tests/testcut_ff.R | 2 -
inst/tests/testmin.ff.R | 2 -
inst/tests/testrisplit.R | 60 +++++++++++++++++++++++-----------------------
inst/tests/testsum_ff.R | 6 ++++
man/chunkify.Rd | 1
man/compact.Rd |only
tests/test_all.R | 2 -
16 files changed, 55 insertions(+), 48 deletions(-)
Title: Exact Calculation of WMTR
Diff between WMTregions versions 2.5.4 dated 2010-11-30 and 3.1.0.1 dated 2011-07-25
Description: R realization of an exact algorithm for calculating the
weighted-mean trimmed regions
Author: Pavel Bazovkin
Maintainer: Pavel Bazovkin
DESCRIPTION | 14
R/WMTR.R | 4
R/generTRsample.R | 4
R/loadWMTR.R | 4
R/visualWMTR.R | 44 ++
man/WMTR.Rd | 58 ++-
man/WMTregions-package.Rd | 33 +
man/generTRsample.Rd | 37 --
man/loadWMTR.Rd | 20 -
man/pointinTR.Rd | 13
man/showWMTR.Rd | 11
man/visualWMTR.Rd | 12
src/Agents.cpp | 804 ++++++++++++++++++++++++++++------------------
src/Makevars.win | 2
src/Objects.cpp | 357 +++++++++++++-------
15 files changed, 880 insertions(+), 537 deletions(-)
More information about RcmdrPlugin.mosaic at CRAN
Permanent link
Title: MCMC Generalised Linear Mixed Models
Diff between MCMCglmm versions 2.12 dated 2011-02-07 and 2.13 dated 2011-07-25
Description: MCMC Generalised Linear Mixed Models
Author: Jarrod Hadfield
Maintainer: Jarrod Hadfield
MCMCglmm-2.12/MCMCglmm/data/BTdata.tab |only
MCMCglmm-2.12/MCMCglmm/data/BTped.tab |only
MCMCglmm-2.12/MCMCglmm/data/PlodiaPO.tab |only
MCMCglmm-2.12/MCMCglmm/data/PlodiaR.tab |only
MCMCglmm-2.12/MCMCglmm/data/PlodiaRB.tab |only
MCMCglmm-2.12/MCMCglmm/data/SShorns.tab |only
MCMCglmm-2.12/MCMCglmm/inst/doc/CourseNotes.bbl |only
MCMCglmm-2.12/MCMCglmm/inst/doc/CourseNotes.blg |only
MCMCglmm-2.12/MCMCglmm/inst/doc/CourseNotes.idx |only
MCMCglmm-2.13/MCMCglmm/DESCRIPTION | 8
MCMCglmm-2.13/MCMCglmm/R/MCMCglmm.R | 127 ++++++-------
MCMCglmm-2.13/MCMCglmm/R/buildZ.R | 13 -
MCMCglmm-2.13/MCMCglmm/R/find.components.R | 4
MCMCglmm-2.13/MCMCglmm/R/inverseA.R | 5
MCMCglmm-2.13/MCMCglmm/R/sm2asreml.R | 10 -
MCMCglmm-2.13/MCMCglmm/data/BTdata.tab.gz |only
MCMCglmm-2.13/MCMCglmm/data/BTped.tab.gz |only
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MCMCglmm-2.13/MCMCglmm/data/SShorns.tab.gz |only
MCMCglmm-2.13/MCMCglmm/inst/doc/CourseNotes.pdf |binary
MCMCglmm-2.13/MCMCglmm/inst/doc/Lecture1-015.pdf |binary
MCMCglmm-2.13/MCMCglmm/inst/doc/Lecture1-027.pdf |binary
MCMCglmm-2.13/MCMCglmm/inst/doc/Lecture1-034.pdf |binary
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MCMCglmm-2.13/MCMCglmm/inst/doc/Lecture2-029.pdf |binary
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MCMCglmm-2.13/MCMCglmm/inst/doc/Lecture3-025.pdf |binary
MCMCglmm-2.13/MCMCglmm/inst/doc/Lecture4-005.pdf |binary
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MCMCglmm-2.13/MCMCglmm/inst/doc/Lecture6-006.pdf |binary
MCMCglmm-2.13/MCMCglmm/inst/doc/Lecture8-005.pdf |binary
MCMCglmm-2.13/MCMCglmm/inst/doc/Lecture8-021.pdf |binary
MCMCglmm-2.13/MCMCglmm/inst/doc/Lecture8-023.pdf |binary
MCMCglmm-2.13/MCMCglmm/inst/doc/Overview-Sol.pdf |binary
MCMCglmm-2.13/MCMCglmm/inst/doc/Overview-VCV.pdf |binary
MCMCglmm-2.13/MCMCglmm/inst/doc/Overview.pdf |binary
MCMCglmm-2.13/MCMCglmm/inst/doc/rgl1.pdf |binary
MCMCglmm-2.13/MCMCglmm/inst/doc/rgl2.pdf |binary
MCMCglmm-2.13/MCMCglmm/man/MCMCglmm.Rd | 35 ++-
MCMCglmm-2.13/MCMCglmm/man/MCMCglmmPackage.Rd | 3
MCMCglmm-2.13/MCMCglmm/man/predict.MCMCglmm.Rd | 28 +-
MCMCglmm-2.13/MCMCglmm/man/rtnorm.Rd | 2
MCMCglmm-2.13/MCMCglmm/man/sm2asreml.Rd | 2
MCMCglmm-2.13/MCMCglmm/src/MCMCglmm.cc | 209 ++++++++--------------
80 files changed, 207 insertions(+), 239 deletions(-)
Title: Neuwirth miscellaenous
Diff between ENmisc versions 1.0 dated 2011-01-03 and 1.2-0 dated 2011-07-25
Description: The ENmisc library contains utility function for different
purposes: mtapply and mlapply (multivariate version of tapply
and lapply), wtd.boxplot (a boxplot with weights), and a visual
interface to restructuring mosaic plots.
Author: Erich Neuwirth
Maintainer: Erich Neuwirth
CHANGES.txt |only
DESCRIPTION | 22 +++++++++++++---------
NAMESPACE | 4 +++-
R/mlapply.R |only
R/mosaicupanddown.R |only
R/wtd.boxplot.default.R | 4 ++--
R/zzz.R |only
man/ENmisc-package.Rd | 21 ++++++++++++++++-----
man/mlapply.Rd |only
man/mosaicPermDialog.Rd |only
man/mtapply.Rd | 8 ++++----
11 files changed, 38 insertions(+), 21 deletions(-)
Title: Classification and regression trees
Diff between tree versions 1.0-28 dated 2010-06-10 and 1.0-29 dated 2011-07-25
Description: Classification and Regression Trees.
Author: Brian Ripley
Maintainer: Brian Ripley
tree-1.0-28/tree/COPYING |only
tree-1.0-28/tree/INDEX |only
tree-1.0-28/tree/R/grow.q |only
tree-1.0-28/tree/R/plot.tree.sequence.q |only
tree-1.0-29/tree/DESCRIPTION | 8 ++++----
tree-1.0-29/tree/GPL-2 |only
tree-1.0-29/tree/R/plot.tree.sequence.R |only
tree-1.0-29/tree/R/tree.R |only
tree-1.0-29/tree/inst/LICENCE | 2 +-
9 files changed, 5 insertions(+), 5 deletions(-)
Title: Generalized Estimation Equation solver
Diff between gee versions 4.13-16 dated 2010-11-26 and 4.13-17 dated 2011-07-25
Description: Generalized Estimation Equation solver
Author: Vincent J Carey. Ported to R by Thomas Lumley (versions 3.13
and 4.4) and Brian Ripley
Maintainer: Brian Ripley
gee-4.13-16/gee/COPYING |only
gee-4.13-17/gee/ChangeLog | 4 ++++
gee-4.13-17/gee/DESCRIPTION | 11 ++++++-----
gee-4.13-17/gee/GPL-2 |only
gee-4.13-17/gee/R/ugee.R | 2 +-
5 files changed, 11 insertions(+), 6 deletions(-)
Title: memory-efficient storage of large data on disk and fast access
functions
Diff between ff versions 2.2-2 dated 2011-04-24 and 2.2-3 dated 2011-07-25
Description: The ff package provides data structures that are stored on
disk but behave (almost) as if they were in RAM by
transparently mapping only a section (pagesize) in main memory
- the effective virtual memory consumption per ff object. ff
supports R's standard atomic data types 'double', 'logical',
'raw' and 'integer' and non-standard atomic types boolean (1
bit), quad (2 bit unsigned), nibble (4 bit unsigned), byte (1
byte signed with NAs), ubyte (1 byte unsigned), short (2 byte
signed with NAs), ushort (2 byte unsigned), single (4 byte
float with NAs). For example 'quad' allows efficient storage of
genomic data as an 'A','T','G','C' factor. The unsigned types
support 'circular' arithmetic. There is also support for
close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date'
and custom close-to-atomic types. ff not only has native
C-support for vectors, matrices and arrays with flexible
dimorder (major column-order, major row-order and
generalizations for arrays). There is also a ffdf class not
unlike data.frames and import/export filters for csv files. ff
objects store raw data in binary flat files in native encoding,
and complement this with metadata stored in R as physical and
virtual attributes. ff objects have well-defined hybrid copying
semantics, which gives rise to certain performance improvements
through virtualization. ff objects can be stored and reopened
across R sessions. ff files can be shared by multiple ff R
objects (using different data en/de-coding schemes) in the same
process or from multiple R processes to exploit parallelism. A
wide choice of finalizer options allows to work with
'permanent' files as well as creating/removing 'temporary' ff
files completely transparent to the user. On certain
OS/Filesystem combinations, creating the ff files works without
notable delay thanks to using sparse file allocation. Several
access optimization techniques such as Hybrid Index
Preprocessing and Virtualization are implemented to achieve
good performance even with large datasets, for example virtual
matrix transpose without touching a single byte on disk.
Further, to reduce disk I/O, 'logicals' and non-standard data
types get stored native and compact on binary flat files i.e.
logicals take up exactly 2 bits to represent TRUE, FALSE and
NA. Beyond basic access functions, the ff package also provides
compatibility functions that facilitate writing code for ff and
ram objects and support for batch processing on ff objects
(e.g. as.ram, as.ff, ffapply). ff interfaces closely with
functionality from package 'bit': chunked looping, fast bit
operations and coercions between different objects that can
store subscript information ('bit', 'bitwhich', ff 'boolean',
ri range index, hi hybrid index). This allows to work
interactively with selections of large datasets and quickly
modify selection criteria. Further high-performance
enhancements can be made available upon request.
Author: Daniel Adler
Maintainer: Jens Oehlschl\xE4gel
DESCRIPTION | 8 ++--
NEWS | 15 +++++++++
R/ffsave.R | 82 +++++++++++++++++++++++++-------------------------
R/hi.R | 2 -
src/FSInfo_statfs.cpp | 2 -
5 files changed, 62 insertions(+), 47 deletions(-)
Title: Epidemiological calculator
Diff between epicalc versions 2.13.1.0 dated 2011-07-23 and 2.13.1.3 dated 2011-07-25
Description: Functions making R easy for epidemiological calculation.
Author: Virasakdi Chongsuvivatwong
Maintainer: Virasakdi Chongsuvivatwong
DESCRIPTION | 8 +++----
R/epicalc.R | 57 +++++++++++++++++++++++++++++++----------------------
man/setTitle.rd | 6 ++---
man/titleString.rd | 12 +++++------
4 files changed, 47 insertions(+), 36 deletions(-)
Title: Bayesian graphical models using MCMC
Diff between rjags versions 3-2 dated 2011-07-24 and 3-3 dated 2011-07-25
Description: Interface to the JAGS MCMC library
Author: Martyn Plummer
Maintainer: Martyn Plummer
DESCRIPTION | 8 ++++----
R/jags.R | 2 +-
R/jags.object.R | 9 +++++++--
configure | 2 +-
configure.ac | 2 +-
configure.ac.orig |only
foo |only
man/adapt.Rd | 47 ++++++++++++++++++++++++++++++-----------------
8 files changed, 44 insertions(+), 26 deletions(-)
Title: High-Dimensional Regression and CAR Score Variable Selection
Diff between care versions 1.1.0 dated 2011-07-23 and 1.1.1 dated 2011-07-25
Description: The "care" package implements the regression approach of
Zuber and Strimmer (2011) "High-dimensional regression and
variable selection using CAR scores" SAGMB 10: 34. CAR scores
measure the correlation between the response and the
Mahalanobis-decorrelated predictors. The squared CAR score is
a natural measure of variable importance and provides a
canonical ordering of variables. This package provides
functions for estimating CAR scores, for variable selection
using CAR scores, and for estimating corresponding regression
coefficients. Both shrinkage as well as empirical estimators
are available.
Author: Verena Zuber and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
care-1.1.0/care/R/car.models.R |only
care-1.1.0/care/man/car.models.Rd |only
care-1.1.1/care/DESCRIPTION | 25 +++++++++---------
care-1.1.1/care/NEWS | 9 ++++++
care-1.1.1/care/R/carscore.R | 25 ++++++++----------
care-1.1.1/care/R/slm.R | 28 ++++++++++----------
care-1.1.1/care/R/slm.models.R |only
care-1.1.1/care/man/care.package.Rd | 6 ++--
care-1.1.1/care/man/carscore.Rd | 31 ++++++++++++----------
care-1.1.1/care/man/lu2004.Rd | 4 +-
care-1.1.1/care/man/slm.Rd | 49 +++++++++++++++++++++++++++---------
care-1.1.1/care/man/slm.models.Rd |only
12 files changed, 108 insertions(+), 69 deletions(-)
Title: Quantile Regression
Diff between quantreg versions 4.69 dated 2011-06-22 and 4.71 dated 2011-07-24
Description: Quantile regression and related methods.
Author: Roger Koenker
Maintainer: Roger Koenker
DESCRIPTION | 6 +--
NAMESPACE |only
R/boot.R | 11 +++++
R/quantreg.R | 96 +++++++++++++++++++++++++++++++++----------------
inst/Changelog | 23 +++++++++++
inst/doc/engelcoef.pdf |binary
inst/doc/rq.pdf |binary
man/boot.rq.Rd | 8 +++-
man/rqs.fit.Rd |only
src/crq.f | 2 -
src/ratfor/rqs.r |only
src/rqs.f |only
12 files changed, 109 insertions(+), 37 deletions(-)
Title: Chronological objects which can handle dates and times
Diff between chron versions 2.3-39 dated 2010-12-07 and 2.3-40 dated 2011-07-24
Description: Chronological objects which can handle dates and times
Author: S original by David James
Maintainer: Kurt Hornik
chron-2.3-39/chron/COPYING |only
chron-2.3-40/chron/ChangeLog | 8 ++++++++
chron-2.3-40/chron/DESCRIPTION | 8 ++++----
chron-2.3-40/chron/README | 7 ++-----
4 files changed, 14 insertions(+), 9 deletions(-)
More information about opencpu.encode at CRAN
Permanent link
Title: General Smoothing Splines
Diff between gss versions 1.1-7 dated 2011-01-13 and 2.0-0 dated 2011-07-24
Description: A comprehensive package for structural multivariate
function estimation using smoothing splines.
Author: Chong Gu
Maintainer: Chong Gu
gss-1.1-7/gss/R/drkpk.R |only
gss-1.1-7/gss/R/grkpk.R |only
gss-1.1-7/gss/R/grkpk0.R |only
gss-1.1-7/gss/R/rkpk.R |only
gss-1.1-7/gss/R/rkpk0.R |only
gss-2.0-0/gss/ChangeLog | 18 +
gss-2.0-0/gss/DESCRIPTION | 8
gss-2.0-0/gss/INDEX | 41 ++
gss-2.0-0/gss/R/cdsscden.R |only
gss-2.0-0/gss/R/cdssden.R | 8
gss-2.0-0/gss/R/dsscden.R |only
gss-2.0-0/gss/R/family.R | 13
gss-2.0-0/gss/R/family.cv.R | 56 +--
gss-2.0-0/gss/R/family.proj.R | 77 +++--
gss-2.0-0/gss/R/family.surv.R | 4
gss-2.0-0/gss/R/gssanova.R | 450 ++++++++++++++++++++++++++++++--
gss-2.0-0/gss/R/gssanova0.R | 238 ++++++++++++++++
gss-2.0-0/gss/R/gssanova1.R |only
gss-2.0-0/gss/R/hzdrate.sshzd.R | 45 ++-
gss-2.0-0/gss/R/mkfun.poly.R | 51 +++
gss-2.0-0/gss/R/mkfun.tp.R | 14
gss-2.0-0/gss/R/mkterm.R | 38 ++
gss-2.0-0/gss/R/predict.ssanova.R | 36 +-
gss-2.0-0/gss/R/predict.ssanova0.R | 36 ++
gss-2.0-0/gss/R/predict.sscox.R |only
gss-2.0-0/gss/R/predict.ssllrm.R | 31 --
gss-2.0-0/gss/R/print.R | 46 ++-
gss-2.0-0/gss/R/project.gssanova.R | 28 +
gss-2.0-0/gss/R/project.ssanova.R | 16 -
gss-2.0-0/gss/R/project.ssanova9.R |only
gss-2.0-0/gss/R/project.sscden.R |only
gss-2.0-0/gss/R/project.sscden1.R |only
gss-2.0-0/gss/R/project.sscox.R |only
gss-2.0-0/gss/R/project.ssden.R | 50 ++-
gss-2.0-0/gss/R/project.sshzd.R | 16 -
gss-2.0-0/gss/R/project.sshzd1.R | 14
gss-2.0-0/gss/R/project.ssllrm.R | 32 --
gss-2.0-0/gss/R/ssanova.R | 439 ++++++++++++++++++++++++++++++-
gss-2.0-0/gss/R/ssanova0.R | 206 +++++++++++++-
gss-2.0-0/gss/R/ssanova9.R |only
gss-2.0-0/gss/R/sscden.R |only
gss-2.0-0/gss/R/sscden1.R |only
gss-2.0-0/gss/R/sscox.R |only
gss-2.0-0/gss/R/ssden.R | 218 +++++++++++++++
gss-2.0-0/gss/R/sshzd.R | 75 +++--
gss-2.0-0/gss/R/sshzd1.R | 62 +++-
gss-2.0-0/gss/R/ssllrm.R | 68 +---
gss-2.0-0/gss/R/summary.gssanova.R | 1
gss-2.0-0/gss/R/summary.ssanova.R | 15 -
gss-2.0-0/gss/R/summary.ssanova0.R | 7
gss-2.0-0/gss/R/summary.ssanova9.R |only
gss-2.0-0/gss/data/ColoCan.R |only
gss-2.0-0/gss/data/LakeAcidity.R | 35 +-
gss-2.0-0/gss/data/clim.R |only
gss-2.0-0/gss/data/penny.R |only
gss-2.0-0/gss/man/ColoCan.Rd |only
gss-2.0-0/gss/man/LakeAcid.Rd | 22 -
gss-2.0-0/gss/man/cdsscden.Rd |only
gss-2.0-0/gss/man/cdssden.Rd | 9
gss-2.0-0/gss/man/clim.Rd |only
gss-2.0-0/gss/man/drkpk.Rd | 18 +
gss-2.0-0/gss/man/dsscden.Rd |only
gss-2.0-0/gss/man/family.Rd | 11
gss-2.0-0/gss/man/gssanova.Rd | 11
gss-2.0-0/gss/man/gssanova0.Rd | 73 +++--
gss-2.0-0/gss/man/hzdrate.sshzd.Rd | 4
gss-2.0-0/gss/man/mkcov.Rd |only
gss-2.0-0/gss/man/mkfun.poly.Rd | 4
gss-2.0-0/gss/man/penny.Rd |only
gss-2.0-0/gss/man/predict.ssanova.Rd | 19 -
gss-2.0-0/gss/man/predict.sscox.Rd |only
gss-2.0-0/gss/man/predict.ssllrm.Rd | 6
gss-2.0-0/gss/man/print.Rd | 4
gss-2.0-0/gss/man/project.Rd | 15 -
gss-2.0-0/gss/man/rkpk.Rd | 11
gss-2.0-0/gss/man/ssanova.Rd | 4
gss-2.0-0/gss/man/ssanova0.Rd | 4
gss-2.0-0/gss/man/ssanova9.Rd |only
gss-2.0-0/gss/man/sscden.Rd |only
gss-2.0-0/gss/man/sscox.Rd |only
gss-2.0-0/gss/man/ssden.Rd | 33 ++
gss-2.0-0/gss/man/sshzd.Rd | 13
gss-2.0-0/gss/man/ssllrm.Rd | 12
gss-2.0-0/gss/man/summary.ssanova.Rd | 2
gss-2.0-0/gss/src/cdennewton.f |only
gss-2.0-0/gss/src/cdennewton10.f |only
gss-2.0-0/gss/src/dnewton.f | 366 +++++++++++++++-----------
gss-2.0-0/gss/src/drkl.f | 329 +++++++++++++++--------
gss-2.0-0/gss/src/hzdaux.f | 84 +++++
gss-2.0-0/gss/src/hzdnewton.f | 17 -
gss-2.0-0/gss/src/hzdnewton10.f | 14
gss-2.0-0/gss/src/llrmnewton.f | 16 -
gss-2.0-0/gss/src/ratfor/cdennewton.r |only
gss-2.0-0/gss/src/ratfor/cdennewton10.r |only
gss-2.0-0/gss/src/ratfor/dnewton.r | 147 ++++++----
gss-2.0-0/gss/src/ratfor/drkl.r | 185 ++++++++-----
gss-2.0-0/gss/src/ratfor/hzdaux.r | 55 +++
gss-2.0-0/gss/src/ratfor/hzdnewton.r | 11
gss-2.0-0/gss/src/ratfor/hzdnewton10.r | 11
gss-2.0-0/gss/src/ratfor/llrmnewton.r | 11
100 files changed, 3126 insertions(+), 887 deletions(-)
Title: Spatial Point Pattern analysis, model-fitting, simulation, tests
Diff between spatstat versions 1.22-3 dated 2011-06-17 and 1.23-0 dated 2011-07-24
Description: A package for analysing spatial data, mainly Spatial Point
Patterns, including multitype/marked points and spatial
covariates, in any two-dimensional spatial region. Also
supports three-dimensional point patterns, and space-time point
patterns in any number of dimensions. Contains over 1000
functions for plotting spatial data, exploratory data analysis,
model-fitting, simulation, spatial sampling, model diagnostics,
and formal inference. Data types include point patterns, line
segment patterns, spatial windows, pixel images and
tessellations. Exploratory methods include K-functions, nearest
neighbour distance and empty space statistics, Fry plots, pair
correlation function, kernel smoothed intensity, relative risk
estimation with cross-validated bandwidth selection, mark
correlation functions, segregation indices, mark dependence
diagnostics etc. Point process models can be fitted to point
pattern data using functions ppm, kppm, slrm similar to glm.
Models may include dependence on covariates, interpoint
interaction, cluster formation and dependence on marks. Fitted
models can be simulated automatically. Also provides facilities
for formal inference (such as chi-squared tests) and model
diagnostics (including simulation envelopes, residuals,
residual plots and Q-Q plots).
Author: Adrian Baddeley
Maintainer: Adrian Baddeley
spatstat-1.22-3/spatstat/man/internal.Rd |only
spatstat-1.23-0/spatstat/DESCRIPTION | 32 ++--
spatstat-1.23-0/spatstat/NAMESPACE |only
spatstat-1.23-0/spatstat/NEWS | 158 ++++++++++++++++++++++
spatstat-1.23-0/spatstat/R/First.R | 28 ++-
spatstat-1.23-0/spatstat/R/Gcom.R |only
spatstat-1.23-0/spatstat/R/Gmulti.R | 17 +-
spatstat-1.23-0/spatstat/R/Gres.R |only
spatstat-1.23-0/spatstat/R/Jmulti.R | 17 +-
spatstat-1.23-0/spatstat/R/Kcom.R |only
spatstat-1.23-0/spatstat/R/Kinhom.R | 27 +++
spatstat-1.23-0/spatstat/R/Kmulti.R | 32 ++--
spatstat-1.23-0/spatstat/R/Kmulti.inhom.R | 28 ++-
spatstat-1.23-0/spatstat/R/Kres.R |only
spatstat-1.23-0/spatstat/R/alltypes.R | 10 -
spatstat-1.23-0/spatstat/R/compareFit.R |only
spatstat-1.23-0/spatstat/R/density.ppp.R | 6
spatstat-1.23-0/spatstat/R/envelopelpp.R |only
spatstat-1.23-0/spatstat/R/fii.R | 5
spatstat-1.23-0/spatstat/R/fv.R | 133 +++++++++++++-----
spatstat-1.23-0/spatstat/R/interact.R | 11 +
spatstat-1.23-0/spatstat/R/linearK.R | 127 +++++++++++++++--
spatstat-1.23-0/spatstat/R/lineardisc.R |only
spatstat-1.23-0/spatstat/R/linearpcf.R |only
spatstat-1.23-0/spatstat/R/linequad.R |only
spatstat-1.23-0/spatstat/R/linim.R |only
spatstat-1.23-0/spatstat/R/lppm.R |only
spatstat-1.23-0/spatstat/R/mincontrast.R | 6
spatstat-1.23-0/spatstat/R/mpl.R | 11 -
spatstat-1.23-0/spatstat/R/options.R | 79 +++++++----
spatstat-1.23-0/spatstat/R/pcfcross.R | 28 ++-
spatstat-1.23-0/spatstat/R/pcfinhom.R | 40 ++++-
spatstat-1.23-0/spatstat/R/pcfmulti.inhom.R | 15 +-
spatstat-1.23-0/spatstat/R/plot.fv.R | 114 ++++++++++-----
spatstat-1.23-0/spatstat/R/ppmclass.R | 9 +
spatstat-1.23-0/spatstat/R/psst.R |only
spatstat-1.23-0/spatstat/R/psstA.R |only
spatstat-1.23-0/spatstat/R/psstG.R |only
spatstat-1.23-0/spatstat/R/rLGCP.R | 5
spatstat-1.23-0/spatstat/R/relrisk.R | 7
spatstat-1.23-0/spatstat/R/residppm.R | 48 +++++-
spatstat-1.23-0/spatstat/R/rhohat.R | 14 -
spatstat-1.23-0/spatstat/R/util.R | 34 ++++
spatstat-1.23-0/spatstat/data/amacrine.rda |binary
spatstat-1.23-0/spatstat/data/anemones.rda |binary
spatstat-1.23-0/spatstat/data/ants.rda |binary
spatstat-1.23-0/spatstat/data/bei.rda |binary
spatstat-1.23-0/spatstat/data/betacells.rda |binary
spatstat-1.23-0/spatstat/data/bramblecanes.rda |binary
spatstat-1.23-0/spatstat/data/bronzefilter.rda |binary
spatstat-1.23-0/spatstat/data/cells.rda |binary
spatstat-1.23-0/spatstat/data/chicago.rda |only
spatstat-1.23-0/spatstat/data/chorley.rda |binary
spatstat-1.23-0/spatstat/data/copper.rda |binary
spatstat-1.23-0/spatstat/data/datalist | 2
spatstat-1.23-0/spatstat/data/demopat.rda |binary
spatstat-1.23-0/spatstat/data/finpines.rda |binary
spatstat-1.23-0/spatstat/data/flu.rda |only
spatstat-1.23-0/spatstat/data/ganglia.rda |binary
spatstat-1.23-0/spatstat/data/hamster.rda |binary
spatstat-1.23-0/spatstat/data/heather.rda |binary
spatstat-1.23-0/spatstat/data/humberside.rda |binary
spatstat-1.23-0/spatstat/data/japanesepines.rda |binary
spatstat-1.23-0/spatstat/data/lansing.rda |binary
spatstat-1.23-0/spatstat/data/letterR.rda |binary
spatstat-1.23-0/spatstat/data/longleaf.rda |binary
spatstat-1.23-0/spatstat/data/murchison.rda |binary
spatstat-1.23-0/spatstat/data/nbfires.rda |binary
spatstat-1.23-0/spatstat/data/nztrees.rda |binary
spatstat-1.23-0/spatstat/data/osteo.rda |binary
spatstat-1.23-0/spatstat/data/ponderosa.rda |binary
spatstat-1.23-0/spatstat/data/redwood.rda |binary
spatstat-1.23-0/spatstat/data/redwoodfull.rda |binary
spatstat-1.23-0/spatstat/data/residualspaper.rda |binary
spatstat-1.23-0/spatstat/data/shapley.rda |binary
spatstat-1.23-0/spatstat/data/simdat.rda |binary
spatstat-1.23-0/spatstat/data/simplenet.rda |binary
spatstat-1.23-0/spatstat/data/spruces.rda |binary
spatstat-1.23-0/spatstat/data/swedishpines.rda |binary
spatstat-1.23-0/spatstat/data/urkiola.rda |binary
spatstat-1.23-0/spatstat/demo/data.R | 12 +
spatstat-1.23-0/spatstat/demo/diagnose.R | 23 +++
spatstat-1.23-0/spatstat/demo/spatstat.R | 28 ++-
spatstat-1.23-0/spatstat/inst/doc/shapefiles.pdf |binary
spatstat-1.23-0/spatstat/man/Gcom.Rd |only
spatstat-1.23-0/spatstat/man/Gres.Rd |only
spatstat-1.23-0/spatstat/man/Kcom.Rd |only
spatstat-1.23-0/spatstat/man/Kinhom.Rd | 36 ++++-
spatstat-1.23-0/spatstat/man/Kres.Rd |only
spatstat-1.23-0/spatstat/man/anova.lppm.Rd |only
spatstat-1.23-0/spatstat/man/as.interact.Rd |only
spatstat-1.23-0/spatstat/man/bei.Rd | 10 -
spatstat-1.23-0/spatstat/man/chicago.Rd |only
spatstat-1.23-0/spatstat/man/compareFit.Rd |only
spatstat-1.23-0/spatstat/man/density.ppp.Rd | 5
spatstat-1.23-0/spatstat/man/envelope.lpp.Rd |only
spatstat-1.23-0/spatstat/man/fitin.Rd | 1
spatstat-1.23-0/spatstat/man/flu.Rd |only
spatstat-1.23-0/spatstat/man/lgcp.estK.Rd | 4
spatstat-1.23-0/spatstat/man/lgcp.estpcf.Rd | 4
spatstat-1.23-0/spatstat/man/linearK.Rd | 30 +++-
spatstat-1.23-0/spatstat/man/linearKinhom.Rd |only
spatstat-1.23-0/spatstat/man/lineardisc.Rd |only
spatstat-1.23-0/spatstat/man/linearpcf.Rd |only
spatstat-1.23-0/spatstat/man/linearpcfinhom.Rd |only
spatstat-1.23-0/spatstat/man/linim.Rd |only
spatstat-1.23-0/spatstat/man/lppm.Rd |only
spatstat-1.23-0/spatstat/man/methods.lppm.Rd |only
spatstat-1.23-0/spatstat/man/npfun.Rd |only
spatstat-1.23-0/spatstat/man/pcfinhom.Rd | 48 ++++++
spatstat-1.23-0/spatstat/man/plot.fv.Rd | 32 +++-
spatstat-1.23-0/spatstat/man/plot.linim.Rd |only
spatstat-1.23-0/spatstat/man/predict.lppm.Rd |only
spatstat-1.23-0/spatstat/man/psst.Rd |only
spatstat-1.23-0/spatstat/man/psstA.Rd |only
spatstat-1.23-0/spatstat/man/psstG.Rd |only
spatstat-1.23-0/spatstat/man/rLGCP.Rd | 22 +--
spatstat-1.23-0/spatstat/man/relrisk.Rd | 17 +-
spatstat-1.23-0/spatstat/man/residuals.ppm.Rd | 56 +++++++
spatstat-1.23-0/spatstat/man/spatstat-internal.Rd |only
spatstat-1.23-0/spatstat/man/spatstat-package.Rd | 105 ++++++++++++--
spatstat-1.23-0/spatstat/man/spatstat.options.Rd | 53 +++++++
spatstat-1.23-0/spatstat/src/lineardisc.c |only
spatstat-1.23-0/spatstat/tests/fvproblems.R | 34 ++++
124 files changed, 1240 insertions(+), 323 deletions(-)
Title: Bayesian graphical models using MCMC
Diff between rjags versions 2.2.0-4 dated 2011-03-22 and 3-2 dated 2011-07-24
Description: Interface to the JAGS MCMC library
Author: Martyn Plummer
Maintainer: Martyn Plummer
.hgtags |only
DESCRIPTION | 10
NAMESPACE | 4
R/jags.R | 69 +++--
R/jags.object.R | 101 +++-----
R/read.data.R | 1
R/unix/zzz.R.in | 2
R/windows/zzz.R | 89 ++++---
configure | 578 +++++++++++++++++++++++++++---------------------
configure.ac | 16 +
man/control.Rd | 2
man/jags.model.Rd | 16 -
man/mcarray.object.Rd | 1
man/read.data.Rd | 41 +--
man/rjags-deprecated.Rd |only
src/Makevars.in | 4
src/Makevars.win | 2
src/jags.cc | 53 ++--
18 files changed, 567 insertions(+), 422 deletions(-)
Title: Locally stationary two-dimensional wavelet process estimation
scheme
Diff between LS2W versions 1.2 dated 2011-04-23 and 1.3 dated 2011-07-24
Description: Estimates two-dimensional local wavelet spectra
Author: Idris Eckley
Maintainer: Idris Eckley
DESCRIPTION | 10 -
R/summary.cddews.R | 4
data/textures.rda |binary
inst |only
man/A.Rd | 4
man/A2name.Rd | 103 +++++++++---------
man/D1Amat.Rd | 86 ++++++++-------
man/D2ACW.Rd | 147 +++++++++++++-------------
man/D2ACWmat.Rd | 281 +++++++++++++++++++++++++-------------------------
man/D2Amat.Rd | 132 +++++++++++------------
man/D2autoplot.Rd | 100 +++++++++--------
man/Haar2MA.diag.Rd | 92 ++++++++--------
man/Haar2MA.horiz.Rd | 94 ++++++++--------
man/Haar2MA.vert.Rd | 93 ++++++++--------
man/HaarMontage.Rd | 83 +++++++-------
man/LS2W-package.Rd | 180 ++++++++++++++++----------------
man/Phi1Dname.Rd | 102 +++++++++---------
man/PhiJ.Rd | 151 +++++++++++++-------------
man/Psi1Dname.Rd | 97 +++++++++--------
man/Psi2Dname.Rd | 84 ++++++++------
man/PsiJ.Rd | 254 ++++++++++++++++++++++-----------------------
man/cddews.Rd | 176 +++++++++++++++----------------
man/example.ls2w.Rd | 78 +++++++------
man/getdata.Rd | 69 ++++++------
man/imwd.Rd | 135 ++++++++++++------------
man/print.cddews.Rd | 86 +++++++--------
man/sample.stats.Rd | 70 ++++++------
man/specplot.Rd | 106 +++++++++---------
man/summary.cddews.Rd | 49 ++++----
man/threshold.imwd.Rd | 150 +++++++++++++-------------
30 files changed, 1544 insertions(+), 1472 deletions(-)
Title: Functions, data and code for count data.
Diff between COUNT versions 1.1.2 dated 2011-03-22 and 1.2.0 dated 2011-07-24
Description: Functions, data and code for Hilbe, J.M. 2009. Negative
Binomial Regression, 2nd Edition (Cambridge University Press)
Author: Joseph M Hilbe
Maintainer: Joseph M Hilbe
COUNT-1.1.2/COUNT/R/nb1syn.r |only
COUNT-1.1.2/COUNT/R/nbcsyn.r |only
COUNT-1.1.2/COUNT/man/nb1syn.Rd |only
COUNT-1.1.2/COUNT/man/nbcsyn.Rd |only
COUNT-1.2.0/COUNT/DESCRIPTION | 14 +++++++-------
COUNT-1.2.0/COUNT/R/ml.nb1.r | 6 +++---
COUNT-1.2.0/COUNT/R/ml.nb2.r | 6 +++---
COUNT-1.2.0/COUNT/R/ml.nbc.r | 2 +-
COUNT-1.2.0/COUNT/R/ml.pois.r |only
COUNT-1.2.0/COUNT/R/nb1_syn.r |only
COUNT-1.2.0/COUNT/R/nbc_syn.r |only
COUNT-1.2.0/COUNT/data/affairs.rda |binary
COUNT-1.2.0/COUNT/data/azdrg112.rda |binary
COUNT-1.2.0/COUNT/data/azpro.rda |binary
COUNT-1.2.0/COUNT/data/badhealth.rda |binary
COUNT-1.2.0/COUNT/data/fasttrakg.rda |binary
COUNT-1.2.0/COUNT/data/lbw.rda |binary
COUNT-1.2.0/COUNT/data/lbwgrp.rda |binary
COUNT-1.2.0/COUNT/data/loomis.rda |binary
COUNT-1.2.0/COUNT/data/mdvis.rda |binary
COUNT-1.2.0/COUNT/data/medpar.rda |binary
COUNT-1.2.0/COUNT/data/rwm.rda |binary
COUNT-1.2.0/COUNT/data/rwm5yr.rda |binary
COUNT-1.2.0/COUNT/data/ships.rda |binary
COUNT-1.2.0/COUNT/data/titanic.rda |binary
COUNT-1.2.0/COUNT/data/titgrp.rda |binary
COUNT-1.2.0/COUNT/man/logit_syn.Rd | 6 +++---
COUNT-1.2.0/COUNT/man/ml.nb1.Rd | 7 ++++++-
COUNT-1.2.0/COUNT/man/ml.nb2.Rd | 7 ++++++-
COUNT-1.2.0/COUNT/man/ml.pois.Rd |only
COUNT-1.2.0/COUNT/man/nb1_syn.Rd |only
COUNT-1.2.0/COUNT/man/nb2_syn.Rd | 2 +-
COUNT-1.2.0/COUNT/man/nbc_syn.Rd |only
33 files changed, 30 insertions(+), 20 deletions(-)
Title: Shenzhen Institutes of Advanced Technology Clustering Suite
Diff between siatclust versions 1.0.0 dated 2011-06-15 and 1.0.2 dated 2011-07-24
Description: A collection of cluster analysis tools and algorithms for
data mining developed at the Shenzhen Institutes of Advanced
Technology (SIAT) under the Senior International Scientist
program of the Chinese Academy of Sciences. Development of this
package is also supported by the Shenzhen High Technology
Development Fund within the Shenzhen Key Laboratory for High
Performance Data Mining.
Author: Graham J Williams, Joshua Z Huang, Xiaojun Chen, Qiang Wang
Maintainer: Graham Williams
DESCRIPTION | 8 ++--
R/ewkm.R | 19 +++++++++--
inst |only
man/ewkm.Rd | 27 +++++++++++++++-
src/ewkm.c | 98 ++++++++++++++++++++++++++++++++++++++++++++++--------------
tests |only
6 files changed, 121 insertions(+), 31 deletions(-)
Title: Statistical inference for partially observed Markov processes
Diff between pomp versions 0.38-3 dated 2011-06-09 and 0.38-5 dated 2011-07-24
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
DESCRIPTION | 10 +---
R/aaa.R | 7 +-
R/pfilter.R | 4 -
R/spect.R | 3 -
data/LondonYorke.rda |binary
data/blowflies.rda |binary
data/dacca.rda |binary
data/euler.sir.rda |binary
data/gillespie.sir.rda |binary
data/gompertz.rda |binary
data/ou2.rda |binary
data/ricker.rda |binary
data/rw2.rda |binary
data/verhulst.rda |binary
inst/ChangeLog | 87 +++++++++++++++++++++++++++++++++++
inst/NEWS | 9 +++
inst/doc/advanced_topics_in_pomp.Rnw | 2
inst/doc/advanced_topics_in_pomp.pdf |binary
inst/doc/intro_to_pomp.Rnw | 50 +++++++++++++++++---
inst/doc/intro_to_pomp.pdf |binary
man/eulermultinom.Rd | 6 --
src/SSA.f | 12 ++++
tests/fhn.Rout.save | 8 +--
tests/filtfail.Rout.save | 4 -
tests/gillespie.Rout.save | 8 ++-
tests/logistic.Rout.save | 2
tests/ou2-bsmc.Rout.save | 10 ++--
tests/ou2-forecast.Rout.save | 2
tests/ou2-kalman.Rout.save | 10 ++--
tests/ou2-mif.Rout.save | 2
tests/ou2-nlf.Rout.save | 4 -
tests/ou2-pmcmc.Rout.save | 8 ++-
tests/ou2-probe.Rout.save | 4 -
tests/ou2-procmeas.Rout.save | 2
tests/ou2-simulate.Rout.save | 4 -
tests/ou2-trajmatch.Rout.save | 44 ++++++++---------
tests/pfilter.Rout.save | 2
tests/pomppomp.Rout.save | 2
tests/ricker-probe.Rout.save | 8 +--
tests/ricker-spect.Rout.save | 8 ++-
tests/ricker.Rout.save | 18 +++----
tests/rw2.Rout.save | 8 +--
tests/sir-icfit.Rout.save | 52 ++++++++++----------
tests/sir.Rout.save | 30 ++++++------
tests/skeleton.Rout.save | 20 ++++----
tests/synlik.Rout.save | 2
46 files changed, 304 insertions(+), 148 deletions(-)
Title: A probe-level data file format used by aroma.affymetrix
[DEPRECATED]
Diff between aroma.apd versions 0.1.8 dated 2011-02-01 and 0.2.0 dated 2011-07-24
Description: THIS PACKAGE HAS BEEN DEPRECATED. (The (in-house) APD file
format was initially developed to store Affymetrix probe-level
data, e.g. normalized CEL intensites. Chip types can be added
to APD file and similar to methods in the affxparser package,
this package provides methods to read APDs organized by units
(probesets). In addition, the probe elements can be arranged
optimally such that the elements are guaranteed to be read in
order when, for instance, data is read unit by unit. This
speed up the read substantially. This package is supporting
the aroma.affymetrix package and not intended to be used
elsewhere.)
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
aroma.apd-0.1.8/aroma.apd/R/hide |only
aroma.apd-0.1.8/aroma.apd/inst/data-ex |only
aroma.apd-0.2.0/aroma.apd/DESCRIPTION | 15 +++++++--------
aroma.apd-0.2.0/aroma.apd/R/zzz.R | 27 +++++++++++++++++++++++++++
aroma.apd-0.2.0/aroma.apd/inst/NEWS | 10 ++++++++++
5 files changed, 44 insertions(+), 8 deletions(-)
Title: An R Package for the Calculation and Visualization of Student
Growth Percentiles.
Diff between SGP versions 0.1-0.0 dated 2011-06-18 and 0.3-5.0 dated 2011-07-24
Description: Functions to calculate student growth percentiles and
percentile growth projections/trajectories for students using
large scale, longitudinal assessment data. Functions use
quantile regression to estimate the conditional density
associated with each student's achievement history. Percentile
growth projections/trajectories are calculated using the
coefficient matrices derived from the quantile regression
analyses and specify what percentile growth is required for
students to reach future achievement targets.
Author: Damian W. Betebenner
Maintainer: Damian W. Betebenner
DESCRIPTION | 26 +
R/SGP-class.R | 4
R/abcSGP.R | 63 +++-
R/analyzeSGP.R | 112 +++++---
R/bubblePlot.R | 71 +++--
R/bubblePlot_Styles.R |only
R/combineSGP.R | 53 +++
R/growthAchievementPlot.R |only
R/prepareSGP.R | 9
R/studentGrowthPercentiles.R | 22 +
R/studentGrowthPlot.R | 3
R/studentGrowthProjections.R | 44 ++-
R/summarizeSGP.R | 20 +
R/visualizeSGP.R | 551 ++++++++++++++++++++++------------------
data/sgpData.rda |binary
data/sgpData_LONG.rda |binary
data/stateData.rda |binary
inst/CITATION | 4
inst/NEWS | 37 ++
man/SGP-package.Rd | 13
man/abcSGP.Rd | 16 +
man/analyzeSGP.Rd | 37 +-
man/bubblePlot.Rd | 22 +
man/bubblePlot_Styles.Rd |only
man/combineSGP.Rd | 14 -
man/growthAchievementPlot.Rd |only
man/studentGrowthPercentiles.Rd | 62 ++++
man/studentGrowthProjections.Rd | 5
man/summarizeSGP.Rd | 54 ++-
man/visualizeSGP.Rd | 219 ++++++++++-----
30 files changed, 972 insertions(+), 489 deletions(-)
Title: Various programming utilities
Diff between R.utils versions 1.7.5 dated 2011-04-27 and 1.7.7 dated 2011-07-24
Description: This package provides utility classes and methods useful
when programming in R and developing R packages.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
DESCRIPTION | 10 +++++-----
NAMESPACE | 9 ++++++++-
R/capitalize.R | 8 +-------
R/isReplicated.R |only
R/isSingle.R |only
incl/capitalize.Rex |only
incl/isReplicated.Rex |only
inst/NEWS | 11 +++++++++++
man/isReplicated.Rd |only
man/isSingle.Rd |only
10 files changed, 25 insertions(+), 13 deletions(-)
Title: Dynamic generation of scientific reports
Diff between R.rsp versions 0.5.4 dated 2011-06-25 and 0.6.0 dated 2011-07-24
Description: An RSP document is a text-based document containing an
R-embedded template of the final document. An RSP document is
preprocessed, parsed and translated into an R script, which
when sourced generates the final document. This way it is
possible to dynamically generate reports in plain text, HTML,
TeX etc. It can also be used to enhance other literate
programming languanges such as Sweave. In addition to RSP,
this package also provides an internal cross-platform web
server and built-in dynamic RSP-embedded HTML help pages, which
can be launched by browseRsp(). If other packages provide RSP
help pages, these are automatically linked to as well.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
DESCRIPTION | 10 +++----
NAMESPACE |only
R/zzz.R | 10 +++++++
inst/NEWS | 5 +++
inst/doc/index.html | 66 ++++++++++++++++++++++++++--------------------------
inst/doc/report.pdf |binary
6 files changed, 51 insertions(+), 40 deletions(-)
Title: Methods for accessing huge amounts of data [DEPRECATED]
Diff between R.huge versions 0.2.2 dated 2011-02-03 and 0.3.0 dated 2011-07-24
Description: THIS PACKAGE HAS BEEN DEPRECATED. Do not start building
new projects based on it. Cross-platform alternatives are the
following packages: bigmemory (CRAN), ff (CRAN), BufferedMatrix
(BioConductor). The main usage of it was inside the
aroma.affymetrix package. (The package currently provides a
class representing a matrix where the actual data is stored in
a binary format on the local file system. This way the size
limit of the data is set by the file system and not the
memory.)
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
DESCRIPTION | 12 +++++-------
NAMESPACE |only
R/zzz.R | 9 ++++++++-
inst/NEWS | 8 ++++++++
4 files changed, 21 insertions(+), 8 deletions(-)
Title: Analysis of Parent-Specific DNA Copy Numbers
Diff between PSCBS versions 0.11.7 dated 2011-07-23 and 0.12.0 dated 2011-07-24
Description: Segments allele-specific DNA copy number data to detect
regions with abnormal copy number within each parental
chromosome
Author: A.B. Olshen, H. Bengtsson, P. Neuvial, P.T. Spellman, R.A.
Olshen, V.E. Seshan
Maintainer: Henrik Bengtsson
DESCRIPTION | 8 ++++----
NAMESPACE |only
R/zzz.R | 11 +++++++++--
inst/NEWS | 8 ++++++++
4 files changed, 21 insertions(+), 6 deletions(-)
Title: Constrained L1-minimization for Inverse (covariance) Matrix
Estimation
Diff between clime versions 0.2 dated 2011-02-03 and 0.3 dated 2011-07-23
Description: A robust constrained L1 minimization method for estimating
a large sparse inverse covariance matrix (aka precision
matrix), and recovering its support for building graphical
models. The computation uses linear programming.
Author: T. Tony Cai, Weidong Liu and Xi (Rossi) Luo
Maintainer: Xi (Rossi) Luo
ChangeLog |only
DESCRIPTION | 8 ++++----
R/clime.R | 2 +-
R/likelihood.R | 4 +++-
4 files changed, 8 insertions(+), 6 deletions(-)
Title: A Collection of General Purpose Functions for R
Diff between caroline versions 0.5.1 dated 2011-06-07 and 0.5.4 dated 2011-07-23
Description: Great utilities that you won't be able to live without.
Author: David M. Schruth
Maintainer: David M. Schruth
DESCRIPTION | 8 ++++----
R/RAy.R | 22 +++++++++++++++-------
R/convert.R | 12 ++++++++----
R/plots.R | 11 ++++++++---
man/pies.Rd | 37 ++++++++++++++++++++++++-------------
man/raPlot.Rd | 20 +++++++++++++++++---
6 files changed, 76 insertions(+), 34 deletions(-)
Title: Overlays on Google map tiles in R
Diff between RgoogleMaps versions 1.1.9.8 dated 2011-06-29 and 1.1.9.11 dated 2011-07-23
Description: This package serves two purposes: (i) Provide a
comfortable R interface to query the Google server for static
maps, and (ii) Use the map as a background image to overlay
plots within R. This requires proper coordinate scaling. NOTE:
To do anything but downloading static map tiles, RgoogleMaps
needs EITHER png OR ReadImages OR rimage installed ! png
(default) is your package if you prefer png file format and
ReadImages or rimage if you prefer jpg format. In the latter
cases, you will also need the libjpeg library installed.
Author: Markus Loecher, Sense Networks
Maintainer: "Markus Loecher, Sense Networks"
DESCRIPTION | 22 ++++++++++------------
R/PlotOnStaticMap.R | 1 -
R/PlotPolysOnStaticMap.R | 40 ++++++++++++++++++++++++++++++++--------
R/ReadMapTile.R | 8 +++++---
man/GetMap.Rd | 2 +-
man/GetMap.bbox.Rd | 2 +-
man/PlotOnStaticMap.Rd | 2 +-
man/PlotPolysOnStaticMap.Rd | 3 ++-
man/RgoogleMaps-package.Rd | 6 +++---
9 files changed, 55 insertions(+), 31 deletions(-)
Title: Simulation of high-dimensional data and parallelized repeated
penalized regression
Diff between pensim versions 1.0.3 dated 2011-06-30 and 1.1.3 dated 2011-07-23
Description: Simulation of continuous, correlated high-dimensional data
with time to event or binary response, and parallelized
functions for Lasso, Ridge, and Elastic Net penalized
regression with repeated starts and two-dimensional tuning of
the Elastic Net.
Author: L. Waldron, M. Pintilie, M.-S. Tsao, F. A. Shepherd, C.
Huttenhower*, I. Jurisica* (*equal contribution)
Maintainer: Levi Waldron
Changelog | 8 ++++++++
DESCRIPTION | 11 ++++++-----
R/create.data.R | 10 ++++++++++
R/opt.nested.crossval.R |only
R/opt.splitval.R |only
man/create.data.Rd | 24 +++++++++++++++++++++---
man/opt.nested.crossval.Rd |only
man/opt.splitval.Rd |only
man/opt1D.Rd | 28 +++++++++++++++-------------
man/opt2D.Rd | 33 +++++++++++++++++----------------
man/pensim-package.Rd | 18 +++++++++---------
man/scan.l1l2.Rd | 16 ++++++++--------
12 files changed, 94 insertions(+), 54 deletions(-)
Title: rcdklib - CDK libraries packaged for R
Diff between rcdklibs versions 1.3.11 dated 2011-06-19 and 1.4.1 dated 2011-07-23
Description: This package provides the CDK libraries for use in the R
environment. Given the size of the library itself, this package
is not expected to change very frequently. To make use of the
CDK within R, it is suggested that you use the rcdk package.
Note that it is possible to directly interact with the CDK
using rJava. However rcdk exposes functionality in a more
idiomatic way
Author: Rajarshi Guha
Maintainer: Rajarshi Guha
DESCRIPTION | 8 ++++----
NEWS | 1 +
inst/cont/cdk.jar |binary
3 files changed, 5 insertions(+), 4 deletions(-)
Title: rcdk - Interface to the CDK Libraries
Diff between rcdk versions 3.1.1 dated 2011-06-19 and 3.1.2 dated 2011-07-23
Description: This package allows the user to access functionality in
the CDK, a Java framework for cheminformatics. This allows the
user to load molecules, evaluate fingerprints, calculate
molecular descriptors and so on. In addition the CDK API allows
the user to view structures in 2D.
Author: Rajarshi Guha
Maintainer: Rajarshi Guha
CHANGELOG | 4 ++++
DESCRIPTION | 8 ++++----
inst/cont/rcdk.jar |binary
inst/doc/rcdk.pdf |binary
4 files changed, 8 insertions(+), 4 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Diff between nlme versions 3.1-101 dated 2011-05-06 and 3.1-102 dated 2011-07-23
Description: Fit and compare Gaussian linear and nonlinear
mixed-effects models.
Author: Jose Pinheiro (S version), Douglas Bates (up to 2007), Saikat
DebRoy (up to 2002), Deepayan Sarkar (up to 2005), the R Core
team.
Maintainer: R-core
nlme-3.1-101/nlme/COPYING |only
nlme-3.1-102/nlme/ChangeLog | 20 +++++++++++++++++++-
nlme-3.1-102/nlme/DESCRIPTION | 8 ++++----
nlme-3.1-102/nlme/GPL-2 |only
nlme-3.1-102/nlme/LICENCE | 2 +-
nlme-3.1-102/nlme/R/newFunc.R | 2 +-
nlme-3.1-102/nlme/R/newMethods.R | 7 +++++--
nlme-3.1-102/nlme/inst/LICENCE | 2 +-
nlme-3.1-102/nlme/man/getData.lme.Rd | 6 +++++-
nlme-3.1-102/nlme/man/simulate.lme.Rd | 5 ++---
nlme-3.1-102/nlme/tests/lme.R | 19 ++++++++++++++++++-
nlme-3.1-102/nlme/tests/lme.Rout.save | 22 ++++++++++++++++++++--
nlme-3.1-102/nlme/tests/ss2.rda |only
13 files changed, 76 insertions(+), 17 deletions(-)
Title: Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase,
...
Diff between foreign versions 0.8-44 dated 2011-04-13 and 0.8-45 dated 2011-07-23
Description: Functions for reading and writing data stored by
statistical packages such as Minitab, S, SAS, SPSS, Stata,
Systat, ..., and for reading and writing dBase files.
Author: R-core members, Saikat DebRoy
Maintainer: R-core
foreign-0.8-44/foreign/COPYING |only
foreign-0.8-45/foreign/COPYRIGHTS | 12 ++++++------
foreign-0.8-45/foreign/ChangeLog | 11 +++++++++++
foreign-0.8-45/foreign/DESCRIPTION | 8 ++++----
foreign-0.8-45/foreign/GPL-2 |only
foreign-0.8-45/foreign/LICENCE | 4 ++--
foreign-0.8-45/foreign/src/file-handle.c | 1 +
7 files changed, 24 insertions(+), 12 deletions(-)
Title: Global Historical Climate Network Version 3
Diff between RghcnV3 versions 1.1 dated 2011-06-28 and 1.5 dated 2011-07-23
Description: The Rghcn package provides the core functions required to
download and format the GHCN V3 data and process it into
temperature series and temperature anomaly series. The data is
reformated so that integration with objects in the system is
straightforward. In addition, there are core functions required
to download and create land masks and functions to download and
import Sea Surface Temperature (SST) data.
Author: Steven Mosher
Maintainer: Steven Mosher
RghcnV3-1.1/RghcnV3/R/DataFunctions.R |only
RghcnV3-1.1/RghcnV3/R/Spatial.R |only
RghcnV3-1.1/RghcnV3/demo/DownloadAllV3.R |only
RghcnV3-1.1/RghcnV3/demo/MaskTest.R |only
RghcnV3-1.1/RghcnV3/man/createTemperature.Rd |only
RghcnV3-1.1/RghcnV3/man/intersectInvAnomalies.Rd |only
RghcnV3-1.1/RghcnV3/man/rasterizeAnomaly.Rd |only
RghcnV3-1.1/RghcnV3/man/whichStationsCAM.Rd |only
RghcnV3-1.5/RghcnV3/DESCRIPTION | 25 +-
RghcnV3-1.5/RghcnV3/R/Download.R | 66 ++++---
RghcnV3-1.5/RghcnV3/R/ReadFiles.R | 99 ++++++++---
RghcnV3-1.5/RghcnV3/R/Url.R | 9 -
RghcnV3-1.5/RghcnV3/R/annualize.R |only
RghcnV3-1.5/RghcnV3/R/anomalize.R |only
RghcnV3-1.5/RghcnV3/R/checkCriteria.R |only
RghcnV3-1.5/RghcnV3/R/createAnomaly.R |only
RghcnV3-1.5/RghcnV3/R/cropInv.R |only
RghcnV3-1.5/RghcnV3/R/getDemoFiles.R |only
RghcnV3-1.5/RghcnV3/R/getLonLat.R |only
RghcnV3-1.5/RghcnV3/R/getStations.R |only
RghcnV3-1.5/RghcnV3/R/intersectInvMts.R |only
RghcnV3-1.5/RghcnV3/R/intersectInvV3.R |only
RghcnV3-1.5/RghcnV3/R/intersectInvZoo.R |only
RghcnV3-1.5/RghcnV3/R/isInventory.R |only
RghcnV3-1.5/RghcnV3/R/isMts.R |only
RghcnV3-1.5/RghcnV3/R/isV3.R |only
RghcnV3-1.5/RghcnV3/R/keepIf.R |only
RghcnV3-1.5/RghcnV3/R/passesCamV3.R |only
RghcnV3-1.5/RghcnV3/R/passesCamZoo.R |only
RghcnV3-1.5/RghcnV3/R/rasterizeZoo.R |only
RghcnV3-1.5/RghcnV3/R/regionalAverage.R |only
RghcnV3-1.5/RghcnV3/R/removeNaStations.R |only
RghcnV3-1.5/RghcnV3/R/v3ToMts.R |only
RghcnV3-1.5/RghcnV3/R/v3ToZoo.R |only
RghcnV3-1.5/RghcnV3/R/windowV3.R |only
RghcnV3-1.5/RghcnV3/demo/00Index | 12 +
RghcnV3-1.5/RghcnV3/demo/Airports.R |only
RghcnV3-1.5/RghcnV3/demo/DemoSetup.R |only
RghcnV3-1.5/RghcnV3/demo/Global.R |only
RghcnV3-1.5/RghcnV3/demo/Gridding.R | 76 ++++++---
RghcnV3-1.5/RghcnV3/demo/Land.R |only
RghcnV3-1.5/RghcnV3/demo/LongRecords.R | 54 ++++--
RghcnV3-1.5/RghcnV3/demo/MaskCreate.R |only
RghcnV3-1.5/RghcnV3/demo/SST.R |only
RghcnV3-1.5/RghcnV3/demo/SSTmaps.R |only
RghcnV3-1.5/RghcnV3/demo/StationCount.R | 76 +++++++--
RghcnV3-1.5/RghcnV3/demo/Texas.R |only
RghcnV3-1.5/RghcnV3/inst |only
RghcnV3-1.5/RghcnV3/man/CRUTEMP3.MAPS.URL.Rd |only
RghcnV3-1.5/RghcnV3/man/CRUTEMP3.RESULTS.URL.Rd |only
RghcnV3-1.5/RghcnV3/man/FILE.PARAMETERS.Rd | 4
RghcnV3-1.5/RghcnV3/man/GHCN.V3.DATA.Rd | 4
RghcnV3-1.5/RghcnV3/man/GLOBE5.Rd | 84 +++++-----
RghcnV3-1.5/RghcnV3/man/HADCRUT3.MAPS.URL.Rd |only
RghcnV3-1.5/RghcnV3/man/HADCRUT3.RESULTS.URL.Rd |only
RghcnV3-1.5/RghcnV3/man/HADSST2.RESULTS.URL.Rd |only
RghcnV3-1.5/RghcnV3/man/OCEAN.MASK.URL.Rd | 4
RghcnV3-1.5/RghcnV3/man/RghcnV3-package.Rd | 192 ++++++++++++++---------
RghcnV3-1.5/RghcnV3/man/annualize.Rd |only
RghcnV3-1.5/RghcnV3/man/anomalize.Rd | 36 ++--
RghcnV3-1.5/RghcnV3/man/checkCriteria.Rd |only
RghcnV3-1.5/RghcnV3/man/createAnomaly.Rd | 27 +--
RghcnV3-1.5/RghcnV3/man/cropInv.Rd |only
RghcnV3-1.5/RghcnV3/man/downloadHadMaps.Rd |only
RghcnV3-1.5/RghcnV3/man/downloadMask.Rd | 22 +-
RghcnV3-1.5/RghcnV3/man/downloadSST.Rd | 18 +-
RghcnV3-1.5/RghcnV3/man/downloadV3.Rd | 23 +-
RghcnV3-1.5/RghcnV3/man/getDemoFiles.Rd |only
RghcnV3-1.5/RghcnV3/man/getLonLat.Rd | 8
RghcnV3-1.5/RghcnV3/man/getStations.Rd | 24 +-
RghcnV3-1.5/RghcnV3/man/intersectInvMts.Rd |only
RghcnV3-1.5/RghcnV3/man/intersectInvV3.Rd |only
RghcnV3-1.5/RghcnV3/man/intersectInvZoo.Rd |only
RghcnV3-1.5/RghcnV3/man/isInventory.Rd |only
RghcnV3-1.5/RghcnV3/man/isMts.Rd |only
RghcnV3-1.5/RghcnV3/man/isV3.Rd |only
RghcnV3-1.5/RghcnV3/man/keepIf.Rd |only
RghcnV3-1.5/RghcnV3/man/passesCamV3.Rd |only
RghcnV3-1.5/RghcnV3/man/passesCamZoo.Rd |only
RghcnV3-1.5/RghcnV3/man/rasterizeZoo.Rd |only
RghcnV3-1.5/RghcnV3/man/readHadMaps.Rd |only
RghcnV3-1.5/RghcnV3/man/readHadResults.Rd |only
RghcnV3-1.5/RghcnV3/man/readMask.Rd | 10 -
RghcnV3-1.5/RghcnV3/man/readMaskDeg1.Rd |only
RghcnV3-1.5/RghcnV3/man/regionalAverage.Rd |only
RghcnV3-1.5/RghcnV3/man/removeNaStations.Rd |only
RghcnV3-1.5/RghcnV3/man/v3ToMts.Rd |only
RghcnV3-1.5/RghcnV3/man/v3ToZoo.Rd |only
88 files changed, 547 insertions(+), 326 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Diff between MASS versions 7.3-13 dated 2011-04-13 and 7.3-14 dated 2011-07-23
Description: Functions and datasets to support Venables and Ripley,
'Modern Applied Statistics with S' (4th edition, 2002).
Author: S original by Venables & Ripley. R port by Brian Ripley,
following partial ports by Kurt Hornik and Albrecht Gebhardt
around 1998.
Maintainer: Brian Ripley
DESCRIPTION | 11 +++++------
R/boxcox.R | 1 +
R/corresp.R | 1 +
R/eqscplot.R | 2 --
R/lda.R | 3 ++-
R/logtrans.R | 1 +
R/mca.R | 1 +
R/profiles.R | 22 +++++++++-------------
R/truehist.R | 1 +
R/zzz.R | 5 +++++
inst/NEWS | 2 ++
src/MASS.c | 4 ++--
tests/Examples/MASS-Ex.Rout.save | 2 +-
tests/profile.R |only
14 files changed, 31 insertions(+), 25 deletions(-)
Title: WNOMINATE Roll Call Analysis Software.
Diff between wnominate versions 0.95 dated 2011-05-26 and 0.96 dated 2011-07-23
Description: Estimates Poole and Rosenthal W-NOMINATE scores from roll
call votes supplied though a 'rollcall' object from package
'pscl'.
Author: Keith Poole
Maintainer: Jeffrey Lewis
wnominate-0.95/wnominate/man/plot.skree.Rd |only
wnominate-0.96/wnominate/DESCRIPTION | 8 ++++----
wnominate-0.96/wnominate/HISTORY | 12 +++++++++---
wnominate-0.96/wnominate/NAMESPACE | 2 +-
wnominate-0.96/wnominate/R/methods.R | 6 +++---
wnominate-0.96/wnominate/R/wnominate.R | 17 ++++++++++++-----
wnominate-0.96/wnominate/inst/doc/wnominate.pdf |binary
wnominate-0.96/wnominate/inst/notused.Rnw |only
wnominate-0.96/wnominate/man/plot.angles.Rd | 2 +-
wnominate-0.96/wnominate/man/plot.coords.Rd | 2 +-
wnominate-0.96/wnominate/man/plot.cutlines.Rd | 2 +-
wnominate-0.96/wnominate/man/plot.nomObject.Rd | 2 +-
wnominate-0.96/wnominate/man/plot.scree.Rd |only
wnominate-0.96/wnominate/man/summary.nomObject.Rd | 2 +-
wnominate-0.96/wnominate/man/wnominate.Rd | 2 +-
15 files changed, 35 insertions(+), 22 deletions(-)
Title: Package contains a few functions to visualize statistical
circumstances.
Diff between visualizationTools versions 0.2.01 dated 2011-05-23 and 0.2.02 dated 2011-07-23
More information about visualizationTools at CRAN
Description: Package contains function to visualize a t-test, the power
of a t-test, control charts and the influence of regulating
them, Oc-curves, the Law of large Numbers and confidence
intervals.
Author: Thomas Roth Etienne Stockhausen
Maintainer: T. Roth
DESCRIPTION | 8 ++++----
R/plot.power.htest.R | 4 ++--
build/visualizationTools.pdf |binary
man/plot.power.htest.Rd | 16 +++++++++-------
man/visualizationTools-package.Rd | 5 +++--
5 files changed, 18 insertions(+), 15 deletions(-)
Permanent link
Title: Perform SQL Selects on R Data Frames
Diff between sqldf versions 0.4-1 dated 2011-06-29 and 0.4-1.2 dated 2011-07-23
Description: Manipulate R data frames using SQL.
Author: G. Grothendieck
Maintainer: G. Grothendieck
DESCRIPTION | 8 ++++----
R/sqldf.R | 11 +++++++----
inst/NEWS | 8 ++++++++
man/sqldf.Rd | 3 +++
4 files changed, 22 insertions(+), 8 deletions(-)
Title: A Set of Tools for Administering SHared Repositories
Diff between stashR versions 0.3-3 dated 2009-03-27 and 0.3-4 dated 2011-07-23
Description: A Set of Tools for Administering SHared Repositories
Author: Sandy Eckel, Roger D. Peng
Maintainer: Roger D. Peng
DESCRIPTION | 10 +++++-----
tests/tests.Rout.save | 11 ++++++-----
2 files changed, 11 insertions(+), 10 deletions(-)
Title: Sparklines and graphical tables for tex and html
Diff between sparkTable versions 0.1.3 dated 2010-09-13 and 0.9.1 dated 2011-07-23
Description: Create Sparklines and graphical tables for documents and
websites
Author: Alexander Kowarik, Bernhard Meindl, Stefan Zechner
Maintainer: Alexander Kowarik
sparkTable-0.1.3/sparkTable/R/basicFunctions.R |only
sparkTable-0.1.3/sparkTable/R/print.sparkTable.R |only
sparkTable-0.1.3/sparkTable/R/setPara.R |only
sparkTable-0.1.3/sparkTable/R/spark.R |only
sparkTable-0.1.3/sparkTable/R/sparkEPS.R |only
sparkTable-0.1.3/sparkTable/R/sparkHTML.R |only
sparkTable-0.1.3/sparkTable/R/sparkTable_Config.R |only
sparkTable-0.1.3/sparkTable/R/spark_init.R |only
sparkTable-0.1.3/sparkTable/R/zzz.r |only
sparkTable-0.1.3/sparkTable/inst |only
sparkTable-0.1.3/sparkTable/man/print.sparkTable.Rd |only
sparkTable-0.1.3/sparkTable/man/setPara.Rd |only
sparkTable-0.1.3/sparkTable/man/spark.Rd |only
sparkTable-0.1.3/sparkTable/man/sparkEPS.Rd |only
sparkTable-0.1.3/sparkTable/man/sparkHTML.Rd |only
sparkTable-0.1.3/sparkTable/man/sparkTable_config.Rd |only
sparkTable-0.1.3/sparkTable/man/spark_init.Rd |only
sparkTable-0.9.1/sparkTable/.project | 22 +++++++++----------
sparkTable-0.9.1/sparkTable/DESCRIPTION | 11 +++++----
sparkTable-0.9.1/sparkTable/NAMESPACE | 14 +++++-------
sparkTable-0.9.1/sparkTable/R/auxFunctions.r |only
sparkTable-0.9.1/sparkTable/R/classes.r |only
sparkTable-0.9.1/sparkTable/R/exports.r |only
sparkTable-0.9.1/sparkTable/R/methods.r |only
sparkTable-0.9.1/sparkTable/data/coordsEU.RData |only
sparkTable-0.9.1/sparkTable/data/debtEU.RData |only
sparkTable-0.9.1/sparkTable/data/popEU.RData |only
sparkTable-0.9.1/sparkTable/man/brp.Rd | 10 ++++++++
sparkTable-0.9.1/sparkTable/man/geoTable-class.Rd |only
sparkTable-0.9.1/sparkTable/man/getParameter.Rd |only
sparkTable-0.9.1/sparkTable/man/newGeoTable.Rd |only
sparkTable-0.9.1/sparkTable/man/newSparkBar.Rd |only
sparkTable-0.9.1/sparkTable/man/newSparkTable.Rd |only
sparkTable-0.9.1/sparkTable/man/plotGeoTable.Rd |only
sparkTable-0.9.1/sparkTable/man/plotSparkTable.Rd |only
sparkTable-0.9.1/sparkTable/man/plotSparks.Rd |only
sparkTable-0.9.1/sparkTable/man/reshapeExt.Rd |only
sparkTable-0.9.1/sparkTable/man/setParameter.Rd |only
sparkTable-0.9.1/sparkTable/man/sparkTable-class.Rd |only
sparkTable-0.9.1/sparkTable/man/sparkbar-class.Rd |only
sparkTable-0.9.1/sparkTable/man/sparkbox-class.Rd |only
sparkTable-0.9.1/sparkTable/man/sparkline-class.Rd |only
42 files changed, 33 insertions(+), 24 deletions(-)
Title: classes and methods for spatio-temporal data
Diff between spacetime versions 0.5-0 dated 2011-07-02 and 0.5-1 dated 2011-07-23
Description: A package with classes and methods for spatio-temporal
data. In particular, space-time regular lattices, sparse
lattices, and irregular data are supported, but no topologies
with S/T interactions sucha s space-time prisms. Utility
functions are provided, e.g. for plotting data as map sequences
or multiple time series; for spatial and temporal selection, as
well as methods for retrieving coordinates, for subsetting,
print, summary, etc.
Author: Edzer Pebesma, with contributions by Benedict Graeler and Tom
Gottfried
Maintainer: Edzer Pebesma
ChangeLog | 149 +++++++++++++++++++++++++++++++++++++++++++++++++
DESCRIPTION | 23 +++++--
R/STIDF-methods.R | 4 -
R/STSDF-methods.R | 2
data/air.rda |binary
demo/CressieWikle.R | 8 +-
inst/doc/spacetime.Rnw | 36 +++++++----
inst/doc/spacetime.pdf |binary
inst/doc/sto.Rnw | 2
inst/doc/sto.pdf |binary
inst/doc/stpg.Rnw |only
inst/doc/stpg.pdf |only
man/ST-class.Rd | 29 ++++++---
man/air.Rd | 6 -
man/stconstruct.Rd | 5 -
svn2cl.xsl |only
16 files changed, 223 insertions(+), 41 deletions(-)
Title: classes and methods for spatial data
Diff between sp versions 0.9-83 dated 2011-06-15 and 0.9-84 dated 2011-07-23
Description: A package that provides classes and methods for spatial
data. The classes document where the spatial location
information resides, for 2D or 3D data. Utility functions are
provided, e.g. for plotting data as maps, spatial selection, as
well as methods for retrieving coordinates, for subsetting,
print, summary, etc.
Author: Edzer Pebesma
Maintainer: Edzer Pebesma
ChangeLog | 4636 +++++++++++++++++++++++++++++++++++++++--------
DESCRIPTION | 10
NAMESPACE | 6
R/AAA.R | 23
R/GridTopology-methods.R | 7
R/Spatial-methods.R | 6
R/SpatialGrid-methods.R | 30
R/flipSGDF.R | 38
R/gridlines.R | 10
R/over.R | 2
R/projected.R | 39
R/spplot.R | 8
data/Rlogo.rda |binary
data/meuse.grid.rda |binary
data/meuse.rda |binary
data/meuse.riv.rda |binary
email |only
inst/ChangeLog | 4636 +++++++++++++++++++++++++++++++++++++++--------
inst/doc/over.pdf |binary
inst/doc/sp.pdf |binary
man/gridlines.Rd | 26
man/meuse.Rd | 128 -
man/meuse.grid.Rd | 84
man/over.Rd | 68
man/overlay.Rd | 5
tests/over.R |only
tests/spplot.Rout.save | 5
27 files changed, 8149 insertions(+), 1618 deletions(-)
Title: The skew-normal and skew-t distributions
Diff between sn versions 0.4-16 dated 2010-08-30 and 0.4-17 dated 2011-07-23
Description: Functions for manipulating skew-normal and skew-t
probability distributions, and for fitting them to data, in the
scalar and in the multivariate case.
Author: Adelchi Azzalini
Maintainer: Adelchi Azzalini
sn-0.4-16/sn/data/ais.R |only
sn-0.4-16/sn/data/frontier.R |only
sn-0.4-17/sn/DESCRIPTION | 7 +-
sn-0.4-17/sn/R/sn.R | 99 +++++++++++++++++++---------------------
sn-0.4-17/sn/data/ais.rda |only
sn-0.4-17/sn/data/frontier.rda |only
sn-0.4-17/sn/history.txt | 2
sn-0.4-17/sn/man/dmsn.Rd | 11 +++-
sn-0.4-17/sn/man/dmst.Rd | 11 +++-
sn-0.4-17/sn/man/sn-internal.Rd | 2
sn-0.4-17/sn/man/sn.mmle.Rd | 19 ++++++-
sn-0.4-17/sn/sn-Ex.R |only
12 files changed, 87 insertions(+), 64 deletions(-)
Title: (Standardised) Major Axis Estimation and Testing Routines
Diff between smatr versions 3.2.0 dated 2011-04-27 and 3.2.2 dated 2011-07-23
Description: This package provides methods of fitting bivariate lines
in allometry using the major axis (MA) or standardised major
axis (SMA), and for making inferences about such lines. The
available methods of inference include confidence intervals and
one-sample tests for slope and elevation, testing for a common
slope or elevation amongst several allometric lines,
constructing a confidence interval for a common slope or
elevation, and testing for no shift along a common axis,
amongst several samples.
Author: David Warton
Maintainer: David Warton
DESCRIPTION | 8 -
R/line.cis.R | 2
R/multcompmatrix.R |only
R/plot.sma.R | 6 -
R/print.sma.R | 29 ++++++
R/sma.R | 222 ++++++++++++++++++++++++++++++++------------------
data/leaflife.RData |binary
data/leafmeas.RData |binary
man/line.cis.Rd | 3
man/multcompmatrix.Rd |only
man/sma.Rd | 10 ++
11 files changed, 193 insertions(+), 87 deletions(-)
Title: Simulation framework
Diff between simFrame versions 0.4.1 dated 2011-03-21 and 0.4.2 dated 2011-07-23
Description: A general framework for statistical simulation.
Author: Andreas Alfons
Maintainer: Andreas Alfons
simFrame-0.4.1/simFrame/inst/doc/figures-eusilc |only
simFrame-0.4.1/simFrame/inst/doc/figures-intro |only
simFrame-0.4.2/simFrame/.project |only
simFrame-0.4.2/simFrame/DESCRIPTION | 8 ++++----
simFrame-0.4.2/simFrame/NEWS | 6 ++++++
simFrame-0.4.2/simFrame/R/sampling.R | 9 ++++++---
simFrame-0.4.2/simFrame/data/datalist |only
simFrame-0.4.2/simFrame/inst/doc/figure-UML.eps |only
simFrame-0.4.2/simFrame/inst/doc/figure-UML.pdf |only
simFrame-0.4.2/simFrame/inst/doc/simFrame-eusilc.Rnw | 2 +-
simFrame-0.4.2/simFrame/inst/doc/simFrame-eusilc.pdf |binary
simFrame-0.4.2/simFrame/inst/doc/simFrame-intro.Rnw | 4 ++--
simFrame-0.4.2/simFrame/inst/doc/simFrame-intro.pdf |binary
simFrame-0.4.2/simFrame/inst/doc/simFrame.bib | 2 +-
simFrame-0.4.2/simFrame/man/simFrame-package.Rd | 4 ++--
15 files changed, 22 insertions(+), 13 deletions(-)
Title: Stable Isotope Analysis in R
Diff between siar versions 4.1 dated 2011-03-31 and 4.1.1 dated 2011-07-23
Description: This package takes data on organism isotopes and fits a
Bayesian model to their dietary habits based upon a Gaussian
likelihood with a mixture dirichlet-distributed prior on the
mean. See siardemo() for an example. The latest version
includes SiBER metrics. Version 4.1.1 contains a bug fix to the
function standard.ellipse
Author: Andrew Parnell and Andrew Jackson
Maintainer: Andrew Parnell
DESCRIPTION | 11 ++++++-----
R/standard.ellipse.r | 4 +++-
2 files changed, 9 insertions(+), 6 deletions(-)
Title: Regression with Functional Data
Diff between refund versions 0.1-3 dated 2011-05-15 and 0.1-4 dated 2011-07-23
Description: Functions for regression with functional data. The
principal methods currently implemented are (I) regression of
scalar responses on functional predictors, by (longitudinal)
penalized functional regression and functional principal
component regression; and (II) regression of functional
responses on scalar predictors, by penalized OLS or GLS.
Author: Coordinating authors: Ciprian Crainiceanu
Maintainer: Lei Huang
DESCRIPTION | 14 ++--
R/lpfr.R | 146 ++++++++++++++++++++++++++++++++------------------
R/pfr.R | 139 +++++++++++++++++++++++++++++++----------------
data/DTI.rda |only
man/DTI.Rd |only
man/fpcr.Rd | 2
man/lpfr.Rd | 119 +++++++++++++++++++---------------------
man/pfr.Rd | 119 +++++++++++++++++++++++++++++++++++-----
man/refund-package.Rd | 5 +
9 files changed, 361 insertions(+), 183 deletions(-)
Title: Improved Foreign Function Interface (FFI) and Dynamic Bindings
to C Libraries (e.g. OpenGL)
Diff between rdyncall versions 0.7.2 dated 2011-04-27 and 0.7.3 dated 2011-07-23
Description: The package provides a cross-platform framework for
dynamic binding of C libraries using a flexible Foreign
Function Interface (FFI). The FFI supports almost all
fundamental C types, multiple calling conventions, symbolic
access to foreign C struct/union data types and wrapping of R
functions as C callback function pointers. Dynamic bindings to
shared C libraries are data-driven by cross-platform binding
specification using a compact plain text format ; an initial
repository of bindings to a couple of common C libraries
(OpenGL, SDL, Expat, glew, CUDA, OpenCL, ODE, R) comes with the
package. The package includes a variety of technology demos and
OS-specific notes for installation of shared libraries.
Author: Daniel Adler
Maintainer: Daniel Adler
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rdyncall-0.7.3/rdyncall/src/dyncall/test/syscall/syscall.c | 4
rdyncall-0.7.3/rdyncall/src/dyncall/test/thunk/Makefile.embedded |only
rdyncall-0.7.3/rdyncall/src/dyncall/test/thunk/Makefile.generic | 19
rdyncall-0.7.3/rdyncall/src/dyncall/test/thunk/test_thunk.c | 6
221 files changed, 1643 insertions(+), 1224 deletions(-)
Title: Graphical user interface for data mining in R
Diff between rattle versions 2.6.6 dated 2011-04-10 and 2.6.7 dated 2011-07-23
Description: Rattle (the R Analytic Tool To Learn Easily) provides a
Gnome (RGtk2) based interface to R functionality for data
mining. The aim is to provide a simple and intuitive interface
that allows a user to quickly load data from a CSV file (or via
ODBC), transform and explore the data, build and evaluate
models, and export models as PMML (predictive modelling markup
language) or as scores. All of this with knowing little about
R. All R commands are logged and commented through the log tab.
Thus they are available to the user as a script file or as an
aide for the user to learn R or to copy-and-paste directly into
R itself. Rattle also exports a number of utility functions and
the graphical user interface, invoked as rattle(), does not
need to be run to deploy these.
Author: Graham Williams
Maintainer: Graham Williams
DESCRIPTION | 25
R/associate.R | 79 +-
R/clara.R | 4
R/cluster.R | 7
R/ewkm.R |only
R/explore.R | 323 ++++----
R/rattle.R | 146 +++
R/transform.R | 380 ++++++----
data/locationsAUS.RData |binary
data/weather.RData |binary
data/weatherAUS.RData |binary
inst/CITATION | 2
inst/ChangeLog | 28
inst/doc/rattle.pdf |binary
inst/etc/rattle.ui | 1351 ++++++++++++++++++++-----------------
inst/etc/tooltips.xml | 11
inst/po/de/LC_MESSAGES/R-rattle.mo |binary
inst/po/es/LC_MESSAGES/R-rattle.mo |binary
inst/po/fr/LC_MESSAGES/R-rattle.mo |binary
inst/po/ja/LC_MESSAGES/R-rattle.mo |binary
man/grouper.Rd |only
man/internal.Rd | 3
man/rattle.Rd | 5
man/rattleInfo.Rd | 10
24 files changed, 1411 insertions(+), 963 deletions(-)
Title: Visualization methods for the raster package
Diff between rasterVis versions 0.10-2 dated 2011-07-06 and 0.10-3 dated 2011-07-23
Description: The raster package defines classes and methods for spatial
raster data access and manipulation. The rasterVis package
complements raster providing a set of methods for enhanced
visualization and interaction.
Author: Oscar Perpiñán Lamigueiro and Robert Hijmans
Maintainer: Oscar Perpiñán Lamigueiro
DESCRIPTION | 16 ++++++++--------
NAMESPACE | 6 ++++--
R/bwplot.R | 8 +++++---
R/density.R | 8 ++++----
R/histogram.R | 6 +++---
R/interactRaster.R | 11 ++++++++---
R/latticeRaster.R | 36 ++++++++++++++++++++++--------------
R/splom.R | 6 +++++-
man/bwplot-methods.Rd | 11 ++++++++---
man/chooseRegion.Rd | 23 ++++++++++++++++++++++-
man/densityplot-methods.Rd | 13 ++++++++++---
man/hexbinplot.Rd | 2 +-
man/histogram-methods.Rd | 12 +++++++++---
man/horizonplot-methods.Rd | 2 +-
man/hovmoller-methods.Rd | 2 +-
man/levelplot-methods.Rd | 10 +++++++++-
man/splom-methods.Rd | 2 +-
man/xyplot-methods.Rd | 2 +-
18 files changed, 122 insertions(+), 54 deletions(-)
Title: Geographic analysis and modeling with raster data
Diff between raster versions 1.8-39 dated 2011-07-05 and 1.9-1 dated 2011-07-23
Description: Reading, writing, manipulating, analyzing and modeling of
gridded spatial data. The package implements basic and
high-level functions, as well as map algebra. Processing of
very large files is supported.
Author: Robert J. Hijmans & Jacob van Etten
Maintainer: Robert J. Hijmans
raster-1.8-39/raster/R/gplot.R |only
raster-1.8-39/raster/R/plot3d.R |only
raster-1.8-39/raster/man/plot3d.Rd |only
raster-1.9-1/raster/ChangeLog | 14 +++
raster-1.9-1/raster/DESCRIPTION | 12 +-
raster-1.9-1/raster/NAMESPACE | 3
raster-1.9-1/raster/R/artith.R | 90 ++++++++++++++++++++-
raster-1.9-1/raster/R/as.raster.R |only
raster-1.9-1/raster/R/atan2.R | 2
raster-1.9-1/raster/R/blockSize.R | 3
raster-1.9-1/raster/R/cellStats.R | 2
raster-1.9-1/raster/R/crop.R | 7 +
raster-1.9-1/raster/R/dropLayer.R | 24 ++++-
raster-1.9-1/raster/R/extent.R | 10 ++
raster-1.9-1/raster/R/extentUnion.R | 2
raster-1.9-1/raster/R/flip.R | 37 +++-----
raster-1.9-1/raster/R/freq.R | 2
raster-1.9-1/raster/R/getData.R | 12 +-
raster-1.9-1/raster/R/image.R | 18 +++-
raster-1.9-1/raster/R/imageplot.R | 119 +++++++++-------------------
raster-1.9-1/raster/R/imageplot2.R |only
raster-1.9-1/raster/R/indexReplace.R | 73 +----------------
raster-1.9-1/raster/R/indexReplaceBrick.R |only
raster-1.9-1/raster/R/interpolate.R | 15 +--
raster-1.9-1/raster/R/is.na.R | 6 -
raster-1.9-1/raster/R/kml.R | 6 +
raster-1.9-1/raster/R/math.R | 6 -
raster-1.9-1/raster/R/multiCore.R | 3
raster-1.9-1/raster/R/overlayList.R | 6 -
raster-1.9-1/raster/R/plot.R | 21 +++-
raster-1.9-1/raster/R/plotRGB.R | 28 +++++-
raster-1.9-1/raster/R/plotRaster.R | 16 +--
raster-1.9-1/raster/R/plotRaster2.R |only
raster-1.9-1/raster/R/polygonToRaster.R | 4
raster-1.9-1/raster/R/predict.R | 2
raster-1.9-1/raster/R/resolution.R | 1
raster-1.9-1/raster/R/sampleRegular.R | 88 ++++++++++----------
raster-1.9-1/raster/R/scalebar.R | 83 ++++++++++++++++++-
raster-1.9-1/raster/R/setValues.R | 13 +--
raster-1.9-1/raster/R/spplot.R | 10 ++
raster-1.9-1/raster/R/stretch.R |only
raster-1.9-1/raster/R/subs.R | 11 ++
raster-1.9-1/raster/R/subset.R | 13 ++-
raster-1.9-1/raster/R/summary-methods.R | 8 -
raster-1.9-1/raster/R/unique.R | 23 +----
raster-1.9-1/raster/R/writeRaster.R | 2
raster-1.9-1/raster/R/zoom.R | 2
raster-1.9-1/raster/inst/doc/Raster.pdf |binary
raster-1.9-1/raster/inst/doc/functions.pdf |binary
raster-1.9-1/raster/inst/doc/rasterfile.pdf |binary
raster-1.9-1/raster/man/as.matrix.Rd | 4
raster-1.9-1/raster/man/as.raster.Rd |only
raster-1.9-1/raster/man/contour.Rd | 6 +
raster-1.9-1/raster/man/extent.Rd | 7 +
raster-1.9-1/raster/man/extractIndex.Rd |only
raster-1.9-1/raster/man/plot.Rd | 8 +
raster-1.9-1/raster/man/plotRGB.Rd | 6 -
raster-1.9-1/raster/man/raster-package.Rd | 5 -
raster-1.9-1/raster/man/replacement.Rd | 76 +++--------------
raster-1.9-1/raster/man/scalebar.Rd |only
raster-1.9-1/raster/man/spplot.Rd | 32 +------
raster-1.9-1/raster/man/writeValues.Rd | 6 -
62 files changed, 525 insertions(+), 422 deletions(-)
Title: spatial and spatio-temporal geostatistical modelling, prediction
and simulation
Diff between gstat versions 0.9-82 dated 2011-06-27 and 1.0-0 dated 2011-07-23
Description: variogram modelling; simple, ordinary and universal point
or block (co)kriging, sequential Gaussian or indicator
(co)simulation; variogram and variogram map plotting utility
functions.
Author: Edzer Pebesma
Maintainer: Edzer Pebesma
gstat-0.9-82/gstat/inst/doc/gstat.rnw |only
gstat-1.0-0/gstat/DESCRIPTION | 16 ++--
gstat-1.0-0/gstat/NAMESPACE | 2
gstat-1.0-0/gstat/R/gstat.formula.R | 4 +
gstat-1.0-0/gstat/R/plot.gstatVariogram.R | 3
gstat-1.0-0/gstat/R/variogram.ST.R |only
gstat-1.0-0/gstat/R/variogram.default.R | 48 +++++++++++--
gstat-1.0-0/gstat/R/variogram.formula.R | 8 +-
gstat-1.0-0/gstat/R/variogramST.R |only
gstat-1.0-0/gstat/data/coalash.rda |binary
gstat-1.0-0/gstat/data/fulmar.rda |binary
gstat-1.0-0/gstat/data/jura.rda |binary
gstat-1.0-0/gstat/data/meuse.all.rda |binary
gstat-1.0-0/gstat/data/meuse.alt.rda |binary
gstat-1.0-0/gstat/data/ncp.grid.rda |binary
gstat-1.0-0/gstat/data/oxford.rda |binary
gstat-1.0-0/gstat/data/pcb.rda |binary
gstat-1.0-0/gstat/data/sic2004.rda |binary
gstat-1.0-0/gstat/data/sic97.rda |binary
gstat-1.0-0/gstat/data/tull.rda |binary
gstat-1.0-0/gstat/data/vv.rda |only
gstat-1.0-0/gstat/data/walker.rda |binary
gstat-1.0-0/gstat/data/wind.rda |binary
gstat-1.0-0/gstat/inst/doc/gstat.Rnw |only
gstat-1.0-0/gstat/inst/doc/gstat.pdf |binary
gstat-1.0-0/gstat/inst/doc/ifgi-logo_int.pdf |only
gstat-1.0-0/gstat/inst/doc/st.Rnw |only
gstat-1.0-0/gstat/inst/doc/st.pdf |only
gstat-1.0-0/gstat/man/krige.Rd | 3
gstat-1.0-0/gstat/man/plot.gstatVariogram.Rd | 28 +++++--
gstat-1.0-0/gstat/man/variogram.Rd | 35 +++++++--
gstat-1.0-0/gstat/man/vv.Rd |only
gstat-1.0-0/gstat/src/data.c | 4 -
gstat-1.0-0/gstat/src/s.c | 34 +++++++--
gstat-1.0-0/gstat/src/sem.c | 96 +++++++++++++--------------
35 files changed, 190 insertions(+), 91 deletions(-)
Title: Tools to make developing R code easier
Diff between devtools versions 0.3 dated 2011-06-30 and 0.4 dated 2011-07-23
Description: Collection of package development tools
Author: Hadley Wickham
Maintainer: Hadley Wickham
DESCRIPTION | 11 ++---
NAMESPACE | 18 +++++---
NEWS | 48 ++++++++++++++++++++++
R/build.r | 54 +++++++++++++++++++++++-
R/check.r | 4 -
R/devel-mode.r | 15 +++++-
R/document.r | 58 ++++++++++++++------------
R/has-devel.r | 2
R/install.r | 11 ++---
R/load.r | 8 +++
R/os.r |only
R/package.r | 41 +++++++++++-------
R/release.r | 23 ++++++----
R/reload.r | 11 +++--
R/test.r | 1
R/vignettes.r | 1
R/wd.r |only
R/zzz.r |only
README.md | 91 +++++++++++++++++++++++++++---------------
inst/tests/test-description.r | 2
man/as.package.Rd | 18 +++-----
man/bash.Rd | 14 +++---
man/build.Rd | 28 +++++++++---
man/build_vignettes.Rd | 17 ++++---
man/build_win.Rd |only
man/changed_files.Rd | 8 ++-
man/check.Rd | 22 ++++------
man/check_doc.Rd |only
man/clear_cache.Rd | 2
man/clear_pkg_env.Rd | 8 ++-
man/dev_mode.Rd | 36 +++++++++-------
man/document.Rd | 20 ++++++---
man/env_name.Rd | 8 ++-
man/find_code.Rd | 6 +-
man/has_devel.Rd | 16 +++----
man/install.Rd | 24 +++++------
man/install_github.Rd | 21 ++++++---
man/is.package.Rd | 6 +-
man/load_all.Rd | 17 ++++---
man/load_c.Rd | 14 +++---
man/load_code.Rd | 24 +++++------
man/load_data.Rd | 24 +++++------
man/load_deps.Rd | 18 +++-----
man/load_pkg_description.Rd | 6 +-
man/md5.Rd | 6 +-
man/parse_collate.Rd | 6 +-
man/parse_deps.Rd | 10 +++-
man/pkg_env.Rd | 18 +++-----
man/release.Rd | 21 ++++++---
man/reload.Rd | 17 ++++---
man/run_examples.Rd | 26 ++++++------
man/show_news.Rd | 22 ++++++----
man/test.Rd | 16 ++++---
man/wd.Rd |only
man/with_locale.Rd | 6 +-
55 files changed, 571 insertions(+), 333 deletions(-)
Title: A Package for Running jags from R
Diff between R2jags versions 0.02-15 dated 2011-03-30 and 0.02-16 dated 2011-07-23
Description: Using this package to call jags from R.
Author: Yu-Sung Su
Maintainer: Yu-Sung Su
CHANGELOG | 4 ++++
DESCRIPTION | 8 ++++----
R/print.R | 7 ++++---
3 files changed, 12 insertions(+), 7 deletions(-)
Title: Statistical Methods for Quality Science
Diff between qualityTools versions 1.44 dated 2011-06-01 and 1.45 dated 2011-07-23
Description: This is a package for teaching statistical methods in the
field of Quality Science. It covers distribution fitting,
process capability, Gage R&R, factorial, fractional factorial
design as well as response surface methods including the use of
desirability functions. Define - Pareto Chart; Measure -
Probability and Quantile-Quantile Plots, Process Capability
Ratios for various distributions and Gage RR Analyze i.e.
Pareto Chart, Multi-Vari Chart, Dot Plot; Improve - Full and
fractional factorial, response surface and mixture designs as
well as the desirability approach for simultaneous optimization
of more than one response variable. Normal, Pareto and Lenth
Plot of effects as well as Interaction Plots; Control - Quality
Control Charts can be found in the qcc package. The focus is on
teaching the statistical methodology used in the Quality
Sciences.
Author: Thomas Roth
Maintainer: Thomas Roth
DESCRIPTION | 8
R/COM_P.R | 36 +--
R/cg._g.r | 41 ++-
R/des_e.r | 23 +-
R/dis_t.r | 80 +++----
R/dot_t.r | 3
R/eff_t.r | 60 +++--
R/gag_n.r | 64 +++--
R/int_t.r | 36 +--
R/min_s.r | 34 +--
R/mix_n.r | 16 -
R/mul_t.r | 55 ++--
R/myA_r.r | 8
R/nor_t.r | 120 +++++-----
R/ort_s.r | 492 ++++++++++++++++++++++++--------------------
R/par_l.r | 17 -
R/par_t.r | 8
R/pcr_r.r | 247 ++++++++++++++--------
R/rsm_n.r | 9
R/sim_c.r | 12 -
R/tag_e.r | 17 -
R/vis_2.r | 28 +-
R/vis_n.r | 35 +--
Rplots.pdf |only
inst/CITATION | 8
inst/NEWS.Rd | 13 +
inst/doc/qualityTools.pdf |binary
inst/doc/qualityTools.rnw | 16 -
inst/doc/vignette.bib | 81 ++++++-
man/normalPlot.Rd | 9
man/pcr.Rd | 48 +++-
man/ppPlot.Rd | 6
man/qqPlot.Rd | 15 +
man/qualityTools-package.Rd | 4
man/taguchiDesign.Rd | 25 ++
35 files changed, 1025 insertions(+), 649 deletions(-)
Title: Profile Dirichlet Process Mixtures
Diff between profdpm versions 2.0 dated 2010-05-25 and 3.0 dated 2011-07-23
Description: This package facilitates profile inference (inference at
the posterior mode) for a class of product partition models
(PPM). The Dirichlet process mixture is currently the only
available member of this class. These methods search for the
maximum posterior (MAP) estimate for the data partition in a
PPM.
Author: Matt Shotwell
Maintainer: Matt Shotwell
DESCRIPTION | 18 -
NAMESPACE |only
R/profBinary.R | 171 +++++-----
R/profLinear.R | 218 ++++++-------
R/summary.profBinary.R |only
R/summary.profLinear.R |only
TODO | 7
inst |only
man/pci.Rd | 4
man/profBinary.Rd | 17 -
man/profLinear.Rd | 30 -
man/summary.profBinary.Rd |only
man/summary.profLinear.Rd |only
src/methods.c | 744 ++++++++++++++++++++++++++++------------------
src/pci.c | 97 ++---
src/pdpmbm.c | 127 +++----
src/pdpmlm.c | 335 +++++++++-----------
src/profBinary.c | 288 ++++++++---------
src/profLinear.c | 450 +++++++++++++--------------
src/profdpm.h | 188 +++++++----
src/util.c | 64 +--
21 files changed, 1468 insertions(+), 1290 deletions(-)
Title: Practical Numerical Math Functions
Diff between pracma versions 0.6-3 dated 2011-06-29 and 0.7-3 dated 2011-07-23
Description: This package provides R implementations of functions in
numerical analysis, with a special view on on optimization and
time series routines. Uses Matlab/Octave function names where
appropriate to simplify porting.
Author: Hans W Borchers
Maintainer: HwB
pracma-0.6-3/pracma/man/diffmat.Rd |only
pracma-0.7-3/pracma/DESCRIPTION | 20 +++----
pracma-0.7-3/pracma/NEWS | 70 +++++++++++++++++++++++++-
pracma-0.7-3/pracma/R/abm3.R |only
pracma-0.7-3/pracma/R/broyden.R |only
pracma-0.7-3/pracma/R/charpoly.R |only
pracma-0.7-3/pracma/R/complexstep.R | 2
pracma-0.7-3/pracma/R/cotes.R |only
pracma-0.7-3/pracma/R/cross.R | 27 +++-------
pracma-0.7-3/pracma/R/droplet.R |only
pracma-0.7-3/pracma/R/einsteinF.R |only
pracma-0.7-3/pracma/R/erf.R |only
pracma-0.7-3/pracma/R/froots.R |only
pracma-0.7-3/pracma/R/mdiag.R | 23 --------
pracma-0.7-3/pracma/R/neville.R |only
pracma-0.7-3/pracma/R/newtonsys.R | 6 +-
pracma-0.7-3/pracma/R/numderiv.R | 2
pracma-0.7-3/pracma/R/rkf54.R |only
pracma-0.7-3/pracma/R/sigmoid.R |only
pracma-0.7-3/pracma/R/tri.R |only
pracma-0.7-3/pracma/R/triquad.R |only
pracma-0.7-3/pracma/doc/NEWS.Rd | 80 ++++++++++++++++++++++++++++--
pracma-0.7-3/pracma/inst/NEWS.pdf |binary
pracma-0.7-3/pracma/man/abm3.Rd |only
pracma-0.7-3/pracma/man/broyden.Rd |only
pracma-0.7-3/pracma/man/charpoly.Rd |only
pracma-0.7-3/pracma/man/complexstep.Rd | 8 +--
pracma-0.7-3/pracma/man/cotes.Rd |only
pracma-0.7-3/pracma/man/cross.Rd | 4 -
pracma-0.7-3/pracma/man/distmat.Rd | 3 -
pracma-0.7-3/pracma/man/droplet_e.Rd |only
pracma-0.7-3/pracma/man/einsteinF.Rd |only
pracma-0.7-3/pracma/man/erfz.Rd |only
pracma-0.7-3/pracma/man/fmins.Rd |only
pracma-0.7-3/pracma/man/froots.Rd |only
pracma-0.7-3/pracma/man/neville.Rd |only
pracma-0.7-3/pracma/man/newtonInterp.Rd |only
pracma-0.7-3/pracma/man/newtonsys.Rd | 2
pracma-0.7-3/pracma/man/pracma-package.Rd | 65 ++++++++++++++++++++----
pracma-0.7-3/pracma/man/rkf54.Rd |only
pracma-0.7-3/pracma/man/sigmoid.Rd |only
pracma-0.7-3/pracma/man/tri.Rd |only
pracma-0.7-3/pracma/man/triquad.Rd |only
43 files changed, 232 insertions(+), 80 deletions(-)
Title: Construction and analysis of matrix population models
Diff between popbio versions 2.2 dated 2011-03-23 and 2.3.1 dated 2011-07-23
Description: Construct and analyze projection matrix models from a
demography study of marked individuals classified by age or
stage. The package covers methods described in Matrix
Population Models by Caswell (2001) and Quantitative
Conservation Biology by Morris and Doak (2002).
Author: Chris Stubben, Brook Milligan, Patrick Nantel
Maintainer: Chris Stubben
DESCRIPTION | 8 +-
R/image2.R | 22 +++++---
R/matrix2.R |only
R/vitalsens.R | 5 +
inst/ChangeLog | 9 +++
inst/doc/load_matrix.Rnw | 129 ++++++++++++++++++-----------------------------
inst/doc/load_matrix.pdf |binary
man/matrix2.Rd |only
8 files changed, 82 insertions(+), 91 deletions(-)
Title: Phylogenetic tools for Eco-phylogenetics
Diff between phylotools versions 0.0.7.4 dated 2010-11-03 and 0.1.1 dated 2011-07-23
Description: Building supermatrix for DNA barcodes using different
genes, calculating the inequality among lineages and
phylogenetic similarity for very large dataset using slicing
methods by invoking Phylocom.
Author: Jinlong Zhang, Nancai Pei, Xiangcheng Mi
Maintainer: Jinlong Zhang
DESCRIPTION | 22 +++++----
R/RMPD.R |only
R/del.tree.tip.R |only
R/dimension.R |only
R/edgesub.R | 8 +--
R/formatXY.R |only
R/framsub.R | 2
R/gini.R |only
R/hcreorder.R |only
R/imagevect.R |only
R/inequality.R |only
R/meangini.R |only
R/phylocom.comdist.R |only
R/phylocom.comstruct.R |only
R/phylocom.pd.R |only
R/phylocom.phylosor.R |only
R/phyloshuffle.R |only
R/plotcut.R |only
R/plotscale.R |only
R/resid.tree.R |only
R/rh.R |only
R/rm.col.R |only
man/RMPD.Rd |only
man/add.mat.Rd | 8 +--
man/aln2dat.Rd | 3 -
man/dat2phy.Rd | 2
man/del.tree.tip.Rd |only
man/dimension.Rd |only
man/edgesub.Rd | 12 ++---
man/fasta.split.Rd | 6 +-
man/fmatch.Rd | 2
man/formatXY.Rd |only
man/framsub.Rd | 4 -
man/gini.Rd |only
man/hcreorder.Rd |only
man/imagevect.Rd |only
man/inequality.Rd |only
man/meangini.Rd |only
man/phy2dat.Rd | 4 -
man/phylocom.comdist.Rd |only
man/phylocom.comstruct.Rd |only
man/phylocom.pd.Rd |only
man/phylocom.phylosor.Rd |only
man/phyloshuffle.Rd |only
man/phylotools-package.Rd | 105 ++++++++++++++++++++++++++++++++++++++++++++--
man/plotcut.Rd |only
man/plotscale.Rd |only
man/rename.fasta.Rd | 9 +--
man/resid.tree.Rd |only
man/reverse.Rd | 9 +--
man/rh.Rd |only
man/rm.col.Rd |only
52 files changed, 147 insertions(+), 49 deletions(-)
Title: Population and Evolutionary Genetics Analysis System
Diff between pegas versions 0.3-4 dated 2011-04-01 and 0.4 dated 2011-07-23
Description: pegas provides functions for reading, writing, plotting,
analysing, and manipulating allelic and haplotypic data, and
for the analysis of population nucleotide sequences including
coalescence analyses.
Author: Emmanuel Paradis, Alastair Potts
Maintainer: Emmanuel Paradis
DESCRIPTION | 10 +++++-----
NEWS | 22 ++++++++++++++++++++++
R/haplotype.R | 32 ++++++++++++++++++++++++++------
R/rr.test.R |only
inst/doc/ReadingFiles.pdf |binary
man/haploNet.Rd | 32 +++++++++++++++++++++++++++-----
man/pegas-package.Rd | 2 +-
man/rr.test.Rd |only
8 files changed, 81 insertions(+), 17 deletions(-)
Title: Analysis of Oceanographic data
Diff between oce versions 0.3-1 dated 2011-06-22 and 0.4-1 dated 2011-07-23
Description: Supports the analysis of Oceanographic data, including ADP
measurements, CTD measurements, sectional data, sea-level time
series, coastline files, etc. Provides functions for
calculating seawater properties such as potential temperature
and density, as well as derived properties such as buoyancy
frequency and dynamic height.
Author: Dan Kelley
Maintainer: Dan Kelley
oce-0.3-1/oce/tests/ctd.R |only
oce-0.3-1/oce/tests/ctd.cnv |only
oce-0.3-1/oce/tests/ctd01.cnv |only
oce-0.4-1/oce/.gitignore | 2
oce-0.4-1/oce/DESCRIPTION | 8
oce-0.4-1/oce/NAMESPACE | 2
oce-0.4-1/oce/NEWS | 8
oce-0.4-1/oce/R/accessors.R | 31 ++
oce-0.4-1/oce/R/adp.R | 1
oce-0.4-1/oce/R/adp.nortek.R | 22 +
oce-0.4-1/oce/R/adp.rdi.R | 2
oce-0.4-1/oce/R/adv.R | 14 +
oce-0.4-1/oce/R/adv.nortek.R | 21 +
oce-0.4-1/oce/R/ctd.R | 215 +++++++++-------
oce-0.4-1/oce/R/imagep.R | 47 ++-
oce-0.4-1/oce/R/oce.R | 25 -
oce-0.4-1/oce/R/processingLog.R | 14 -
oce-0.4-1/oce/R/sealevel.R | 16 -
oce-0.4-1/oce/R/sw.R | 4
oce-0.4-1/oce/R/tidem.R | 2
oce-0.4-1/oce/R/zzz.R | 2
oce-0.4-1/oce/data/RRprofile.rda |binary
oce-0.4-1/oce/data/a03.rda |binary
oce-0.4-1/oce/data/adp.rda |binary
oce-0.4-1/oce/data/airHalifax.rda |binary
oce-0.4-1/oce/data/coastlineHalifax.rda |binary
oce-0.4-1/oce/data/coastlineMaritimes.rda |binary
oce-0.4-1/oce/data/coastlineSLE.rda |binary
oce-0.4-1/oce/data/coastlineWorld.rda |binary
oce-0.4-1/oce/data/ctd.rda |binary
oce-0.4-1/oce/data/ctdRaw.rda |binary
oce-0.4-1/oce/data/datalist | 1
oce-0.4-1/oce/data/lobo.rda |binary
oce-0.4-1/oce/data/munk.rda |binary
oce-0.4-1/oce/data/ptr.rda |binary
oce-0.4-1/oce/data/redfieldNC.rda |binary
oce-0.4-1/oce/data/redfieldNP.rda |binary
oce-0.4-1/oce/data/redfieldPlankton.rda |binary
oce-0.4-1/oce/data/riley.rda |binary
oce-0.4-1/oce/data/sealevelHalifax.rda |binary
oce-0.4-1/oce/data/sealevelTuktoyaktuk.rda |binary
oce-0.4-1/oce/data/section.rda |binary
oce-0.4-1/oce/data/soi.rda |only
oce-0.4-1/oce/data/tidedata.rda |binary
oce-0.4-1/oce/data/topoMaritimes.rda |binary
oce-0.4-1/oce/data/topoWorld.rda |binary
oce-0.4-1/oce/data/wilson.rda |binary
oce-0.4-1/oce/data/wind.rda |binary
oce-0.4-1/oce/inst/doc/oce.Rnw | 8
oce-0.4-1/oce/inst/doc/oce.pdf |binary
oce-0.4-1/oce/inst/extdata/ctd.cnv | 388 ++++++++++++++++-------------
oce-0.4-1/oce/man/ctd.Rd | 4
oce-0.4-1/oce/man/ctdTrim.Rd | 31 +-
oce-0.4-1/oce/man/imagep.Rd | 32 +-
oce-0.4-1/oce/man/interpBarnes.Rd | 2
oce-0.4-1/oce/man/oce.plot.ts.Rd | 26 -
oce-0.4-1/oce/man/plot.adv.Rd | 25 +
oce-0.4-1/oce/man/plot.ctd.Rd | 12
oce-0.4-1/oce/man/plot.sealevel.Rd | 13
oce-0.4-1/oce/man/pressure.Rd | 6
oce-0.4-1/oce/man/processingLog.Rd | 20 -
oce-0.4-1/oce/man/read.adv.Rd | 7
oce-0.4-1/oce/man/read.ctd.Rd | 3
oce-0.4-1/oce/man/soi.Rd |only
oce-0.4-1/oce/man/wind.Rd | 2
oce-0.4-1/oce/src/bitwise.c | 2
oce-0.4-1/oce/src/sontek_adp.c | 2
67 files changed, 654 insertions(+), 366 deletions(-)
Title: (non)linear time series analysis
Diff between nlts versions 0.1-7 dated 2010-09-27 and 0.1-8 dated 2011-07-23
Description: R functions for (non)linear time series analysis. A core
topic is order estimation through cross-validation.
Author: Ottar N. Bjornstad
Maintainer: Ottar N. Bjornstad
CHANGES | 3 ++
DESCRIPTION | 8 ++---
NAMESPACE | 1
R/nlts.R | 65 ++++++++++++++++++++++++++++++++++++++++++++++--
man/predict.ll.order.Rd |only
5 files changed, 71 insertions(+), 6 deletions(-)
Title: Classes for Relational Data
Diff between network versions 1.6 dated 2011-01-29 and 1.7 dated 2011-07-23
Description: Tools to create and modify network objects. The network
class can represent a range of relational data types, and
supports arbitrary vertex/edge/graph attributes.
Author: Carter T. Butts
Maintainer: Carter T. Butts
ChangeLog | 23 +++++++++++++++++++++++
DESCRIPTION | 10 +++++-----
R/coercion.R | 20 +++++++++++++++-----
R/constructors.R | 19 +++++++++----------
R/printsum.R | 46 +++++++++++++++++++++++++++-------------------
data/emon.RData |binary
data/flo.RData |binary
man/as.matrix.network.Rd | 10 ++++++----
man/network-operators.Rd | 2 +-
9 files changed, 86 insertions(+), 44 deletions(-)
Title: Rcpp integration for Armadillo templated linear algebra library
Diff between RcppArmadillo versions 0.2.26 dated 2011-07-23 and 0.2.27 dated 2011-07-23
Description: R and Armadillo integration using Rcpp Armadillo is a
templated C++ linear algebra library (by Conrad Sanderson) that
aims towards a good balance between speed and ease of use.
Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions.
Various matrix decompositions are provided through optional
integration with LAPACK and ATLAS libraries.
A delayed evaluation approach is employed (during compile time) to
combine several operations into one, and to reduce (or
eliminate) the need for temporaries. This is accomplished
through recursive templates and template meta-programming.
This library is useful if C++ has been decided as the language of
choice (due to speed and/or integration capabilities), rather
than another language.
The RcppArmadillo package includes the header files from the templated
Armadillo library (currently version 2.1.91). Thus users do not
need to install Armadillo itself in order to use RcppArmadillo.
This Armadillo integration provides a nice illustration of the
capabilities of the Rcpp package for seamless R and C++
integration.
Armadillo is licensed under the GNU LGPL version 3 or later, while
RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is
licenses under the GNU GPL version 2 or later, as is the rest
of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Romain Francois, Dirk Eddelbuettel and Doug Bates
ChangeLog | 6
DESCRIPTION | 10
inst/NEWS | 11
inst/include/armadillo_bits/Col_bones.hpp | 6
inst/include/armadillo_bits/Col_meat.hpp | 72 ++
inst/include/armadillo_bits/Mat_bones.hpp | 7
inst/include/armadillo_bits/Mat_meat.hpp | 34 +
inst/include/armadillo_bits/Row_bones.hpp | 6
inst/include/armadillo_bits/Row_meat.hpp | 72 ++
inst/include/armadillo_bits/arma_static_assert.hpp | 16
inst/include/armadillo_bits/arma_version.hpp | 8
inst/include/armadillo_bits/auxlib_bones.hpp | 6
inst/include/armadillo_bits/auxlib_meat.hpp | 291 +++++++++++
inst/include/armadillo_bits/config.hpp | 16
inst/include/armadillo_bits/diskio_meat.hpp | 4
inst/include/armadillo_bits/fn_as_scalar.hpp | 8
inst/include/armadillo_bits/fn_norm.hpp | 186 +++++--
inst/include/armadillo_bits/fn_svd.hpp | 47 +
inst/include/armadillo_bits/fn_toeplitz.hpp | 18
inst/include/armadillo_bits/glue_relational_meat.hpp | 345 ++++----------
inst/include/armadillo_bits/glue_times_meat.hpp | 8
inst/include/armadillo_bits/glue_toeplitz_bones.hpp | 15
inst/include/armadillo_bits/glue_toeplitz_meat.hpp | 82 +++
inst/include/armadillo_bits/op_strans_meat.hpp | 44 +
inst/include/armadillo_bits/promote_type.hpp | 241 +++++----
inst/include/armadillo_bits/span.hpp | 107 ++--
inst/include/armadillo_bits/strip.hpp | 36 -
inst/include/armadillo_bits/subview_bones.hpp | 13
inst/include/armadillo_bits/subview_cube_bones.hpp | 8
inst/include/armadillo_bits/subview_cube_meat.hpp | 8
inst/include/armadillo_bits/subview_meat.hpp | 96 +++
inst/include/armadillo_bits/traits.hpp | 13
inst/include/armadillo_bits/unwrap.hpp | 463 ++++++++++---------
33 files changed, 1566 insertions(+), 737 deletions(-)
Title: statistical methods for analysing multivariate abundance data
Diff between mvabund versions 2.2-5.3 dated 2011-07-06 and 2.2-5.6 dated 2011-07-23
Description: A set of tools for displaying, modeling and analysing
multivariate abundance data in community ecology. See
mvabund-package.Rd for details of overall package organization.
The package is implemented with the Gnu Scientific Library
(http://www.gnu.org/software/gsl/) and Rcpp
(http://dirk.eddelbuettel.com/code/rcpp.html) R / C++ classes.
Author: Yi Wang, Ulrike Naumann, Stephen Wright and David Warton
Maintainer: Yi Wang
DESCRIPTION | 8 +--
R/anova.manyglm.R | 37 ++++++++------
R/anova.manylm.R | 52 ++++++++++++--------
R/default.plot.manyglm.R | 98 ++++++++++++++++++--------------------
R/default.plot.manylm.R | 97 +++++++++++++++++--------------------
R/default.plot.mvabund.R | 12 ++--
R/default.plotMvaFactor.R | 1
R/default.print.anova.manyglm.R | 8 +--
R/default.print.summary.manyglm.R | 10 +--
R/is.wholenumber.R |only
R/manyglm.R | 24 ++++++---
R/manylm.R | 2
R/print.anova.manylm.R | 2
R/print.manyglm.R | 10 +--
R/print.summary.manylm.R | 10 +--
R/summary.manylm.R | 18 +++---
man/anova.manyglm.Rd | 7 +-
man/anova.manylm.Rd | 2
man/manyglm.Rd | 2
man/manylm.Rd | 2
man/summary.manylm.Rd | 6 +-
src/RtoAnovaCpp.cpp | 2
src/RtoGlm.cpp | 12 +++-
src/RtoGlmAnova.cpp | 8 +--
src/RtoGlmSmry.cpp | 8 +--
src/RtoSmryCpp.cpp | 4 -
src/glm.cpp | 55 ++-------------------
src/resampTest.h | 18 +-----
28 files changed, 246 insertions(+), 269 deletions(-)
Title: Simultaneous Inference in General Parametric Models
Diff between multcomp versions 1.2-6 dated 2011-05-02 and 1.2-7 dated 2011-07-23
Description: Simultaneous tests and confidence intervals for general
linear hypotheses in parametric models, including linear,
generalized linear, linear mixed effects, and survival models.
The package includes demos reproducing analyzes presented in
the book "Multiple Comparisons Using R" (Bretz, Hothorn,
Westfall, 2010, CRC Press).
Author: Torsten Hothorn, Frank Bretz and Peter Westfall and Richard M.
Heiberger and Andre Schuetzenmeister
Maintainer: Torsten Hothorn
DESCRIPTION | 8 ++--
NEWS | 6 +++
inst/CHANGES | 6 +++
inst/doc/chfls1.pdf |binary
inst/doc/generalsiminf.pdf |binary
inst/doc/multcomp-examples.Rnw | 66 +++++++++++++++++++++++++++++++++++++++++
inst/doc/multcomp-examples.pdf |binary
7 files changed, 82 insertions(+), 4 deletions(-)
Title: Estimation for multivariate normal and Student-t data with
monotone missingness
Diff between monomvn versions 1.8-5 dated 2011-03-08 and 1.8-6 dated 2011-07-23
Description: Estimation of multivariate normal and student-t data of
arbitrary dimension where the pattern of missing data is
monotone. Through the use of parsimonious/shrinkage regressions
(plsr, pcr, lasso, ridge, etc.), where standard regressions
fail, the package can handle a nearly arbitrary amount of
missing data. The current version supports maximum likelihood
inference and a full Bayesian approach employing scale-mixtures
for the lasso (double-exponential) and Normal-Gamma priors, and
Student-t errors. Monotone data augmentation extends this
Bayesian approach to arbitrary missingness patterns. A fully
functional standalone interface to the Bayesian lasso (from
Park & Casella), Normal-Gamma (from Griffin & Brown), and ridge
regression with model selection via Reversible Jump, and
student-t errors (from Geweke) is also provided
Author: Robert B. Gramacy
Maintainer: Robert B. Gramacy
ChangeLog | 7 ++++
DESCRIPTION | 8 ++---
R/blasso.R | 9 +++--
man/blasso.Rd | 6 ++-
src/blasso.cc | 19 +++++++-----
src/matrix.c | 89 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
src/matrix.h | 7 +++-
7 files changed, 128 insertions(+), 17 deletions(-)
Title: Forensic Genetics DNA Mixture Separation
Diff between mixsep versions 0.1-5 dated 2011-05-26 and 0.1-6 dated 2011-07-23
Description: Separates DNA mixtures using a statistical model within a
greedy algorithm.
Author: Torben Tvedebrink
Maintainer: Torben Tvedebrink
DESCRIPTION | 8 ++++----
R/gui.R | 43 ++++++++++++++++++++++++++++---------------
inst/doc |only
vignettegraphics |only
4 files changed, 32 insertions(+), 19 deletions(-)
Title: Multidimensional Item Response Theory
Diff between mirt versions 0.1-13 dated 2011-07-02 and 0.1-14 dated 2011-07-23
Description: Analysis of dichotomous and polychotomous response data
using latent trait models under the Item Response Theory
paradigm. Includes the multivariate two- and three-parameter
logistic models, confirmatory bifactor analysis, and polytomous
confirmatory and exploratory item response models.
Author: Phil Chalmers
Maintainer: Phil Chalmers
mirt-0.1-13/mirt/ChangeLog |only
mirt-0.1-14/mirt/DESCRIPTION | 10 +-
mirt-0.1-14/mirt/R/bfactor.R | 26 +++---
mirt-0.1-14/mirt/R/confmirt.R | 135 ++++++++++++++++++++---------------
mirt-0.1-14/mirt/R/mirt.R | 31 +++-----
mirt-0.1-14/mirt/R/misc.R | 14 +--
mirt-0.1-14/mirt/R/polymirt.R | 82 +++++++++++++--------
mirt-0.1-14/mirt/ToDo | 9 +-
mirt-0.1-14/mirt/data/LSAT7.RData |binary
mirt-0.1-14/mirt/data/SAT12.RData |binary
mirt-0.1-14/mirt/data/Science.RData |binary
mirt-0.1-14/mirt/inst |only
mirt-0.1-14/mirt/man/LSAT7.Rd | 2
mirt-0.1-14/mirt/man/SAT12.Rd | 8 +-
mirt-0.1-14/mirt/man/Science.Rd | 2
mirt-0.1-14/mirt/man/bfactor.Rd | 51 +++----------
mirt-0.1-14/mirt/man/confmirt.Rd | 36 ++-------
mirt-0.1-14/mirt/man/expand.table.Rd | 2
mirt-0.1-14/mirt/man/fscores.Rd | 4 -
mirt-0.1-14/mirt/man/itemplot.Rd | 2
mirt-0.1-14/mirt/man/logLik.Rd | 10 +-
mirt-0.1-14/mirt/man/mirt.Rd | 41 ++--------
mirt-0.1-14/mirt/man/polymirt.Rd | 40 ++--------
mirt-0.1-14/mirt/man/simdata.Rd | 10 +-
mirt-0.1-14/mirt/src/dgroup.c | 28 +++++++
25 files changed, 266 insertions(+), 277 deletions(-)
Title: Multivariate Data Handling with S4 Classes and Sparse Matrices
Diff between mefa4 versions 0.2-1 dated 2011-05-15 and 0.2-2 dated 2011-07-23
Description: An S4 update of the 'mefa' package using sparse matrices
for enhanced efficiency. Sparse array-like obejects are
supported via lists of sparse matrices.
Author: Peter Solymos
Maintainer: Peter Solymos
mefa4-0.2-1/mefa4/tests |only
mefa4-0.2-2/mefa4/DESCRIPTION | 8
mefa4-0.2-2/mefa4/R/mefa4classes.R | 445 ---------------------------------
mefa4-0.2-2/mefa4/R/mefa4extras.R |only
mefa4-0.2-2/mefa4/R/mefa4methods.R |only
mefa4-0.2-2/mefa4/R/mefa4utilities.R | 5
mefa4-0.2-2/mefa4/inst/ChangeLog | 4
mefa4-0.2-2/mefa4/inst/doc/mefa4.pdf |binary
mefa4-0.2-2/mefa4/man/Mefa.Rd | 6
mefa4-0.2-2/mefa4/man/nonDuplicated.Rd | 5
10 files changed, 23 insertions(+), 450 deletions(-)
Title: Tools for Two-Dimensional Monte-Carlo Simulations
Diff between mc2d versions 0.1-9 dated 2010-12-17 and 0.1-10 dated 2011-07-23
Description: Various distributions and utilities to ease the use of R
to build and study Two-Dimensional Monte-Carlo simulations
Author: Regis Pouillot
Maintainer: Regis Pouillot
mc2d-0.1-10/mc2d/DESCRIPTION | 12 -
mc2d-0.1-10/mc2d/R/betagen.R | 54 +++-
mc2d-0.1-10/mc2d/R/empiricalC.R | 313 ++++++++++++++++++++--------
mc2d-0.1-10/mc2d/R/empiricalD.R | 35 ++-
mc2d-0.1-10/mc2d/R/extractvar.R | 2
mc2d-0.1-10/mc2d/R/mcapply.R | 30 +-
mc2d-0.1-10/mc2d/R/pert.R | 53 ++--
mc2d-0.1-10/mc2d/R/plot.mc.R | 9
mc2d-0.1-10/mc2d/R/rdirichlet.R | 27 +-
mc2d-0.1-10/mc2d/R/rmultinomial.R | 9
mc2d-0.1-10/mc2d/R/triang.R | 62 ++++-
mc2d-0.1-10/mc2d/data/ec.rda |only
mc2d-0.1-10/mc2d/data/total.RData |binary
mc2d-0.1-10/mc2d/inst/CITATION | 2
mc2d-0.1-10/mc2d/inst/NEWS | 17 +
mc2d-0.1-10/mc2d/inst/doc/docmcEnglish.pdf |binary
mc2d-0.1-10/mc2d/inst/doc/mc2dLmEnglish.pdf |binary
mc2d-0.1-10/mc2d/man/empiricalC.Rd | 38 ++-
mc2d-0.1-10/mc2d/man/empiricalD.Rd | 13 +
mc2d-0.1-10/mc2d/man/mcapply.Rd | 3
mc2d-0.1-10/mc2d/man/plot.mc.Rd | 6
mc2d-0.1-10/mc2d/man/triangular.Rd | 7
mc2d-0.1-9/mc2d/data/ec.r |only
23 files changed, 491 insertions(+), 201 deletions(-)
Title: MATLAB emulation package
Diff between matlab versions 0.8.6 dated 2011-04-24 and 0.8.7 dated 2011-07-23
Description: Emulate MATLAB code using R
Author: P. Roebuck
Maintainer: P. Roebuck
matlab-0.8.6/matlab/.hide |only
matlab-0.8.6/matlab/NEWS.real |only
matlab-0.8.7/matlab/DESCRIPTION | 8 ++++----
matlab-0.8.7/matlab/NAMESPACE | 5 +++++
matlab-0.8.7/matlab/NEWS | 16 ++++++++++++++++
matlab-0.8.7/matlab/R/factors.R |only
matlab-0.8.7/matlab/R/hilb.R |only
matlab-0.8.7/matlab/R/isprime.R |only
matlab-0.8.7/matlab/R/primes.R |only
matlab-0.8.7/matlab/R/rosser.R |only
matlab-0.8.7/matlab/man/colorbar.Rd | 7 ++++---
matlab-0.8.7/matlab/man/factors.Rd |only
matlab-0.8.7/matlab/man/hilb.Rd |only
matlab-0.8.7/matlab/man/isprime.Rd |only
matlab-0.8.7/matlab/man/matlab-package.Rd | 4 ++--
matlab-0.8.7/matlab/man/primes.Rd |only
matlab-0.8.7/matlab/man/rosser.Rd |only
matlab-0.8.7/matlab/tests/factors.R |only
matlab-0.8.7/matlab/tests/hilb.R |only
matlab-0.8.7/matlab/tests/isprime.R |only
matlab-0.8.7/matlab/tests/primes.R |only
21 files changed, 31 insertions(+), 9 deletions(-)
Title: L-moments, Censored L-moments, Trimmed L-moments, L-comoments,
and Many Distributions
Diff between lmomco versions 1.3.6 dated 2011-06-25 and 1.4.2 dated 2011-07-23
Description: The package implements the statistical theory of L-moments
in R including L-moment estimation, probability-weighted moment
estimation, parameter estimation for numerous familiar and
not-so-familiar distributions, and L-moment estimation for the
same distributions from the parameters. L-moments are derived
from the expectations of order statistics and are linear with
respect to the probability-weighted moments; choice of either
can be made by mathematical convenience. L-moments are directly
analogous to the well-known product moments; however, L-moments
have many advantages including unbiasedness, robustness, and
consistency with respect to the product moments. The method of
L-moments can out perform the method of maximum likelihood. The
lmomco package historically is oriented around canonical
FORTRAN algorithms of J.R.M. Hosking, and the nomenclature for
many of the functions parallels that of the Hosking library,
which later became available in the lmom package. However, vast
arrays of various extensions and curiosities are added by the
author to aid and expand the breadth of L-moment application.
Such extensions include venerable statistics as Sen weighted
mean, Gini mean difference, plotting positions, and conditional
probability adjustment. The plotting of L-moment ratio diagrams
is directly supported in this package. Computations of
L-moments for right-tail and left-tail censoring by known or
unknown censoring threshold and also by indicator variable also
are available. E.A.H. Elamir and A.H. Seheult have developed
the trimmed L-moments, which are implemented in this package,
and numerical integration of quantile functions is used to
dynamically compute trajectories of select TL-moment ratios for
the construction of TL-moment ratio diagrams. Robert Serfling
and Peng Xiao have extended L-moments into multivariate space;
the so-called sample L-comoments are implemented here and might
have considerable application in copula theory because they
measure asymmetric correlation and higher co-moments. The
supported distributions with moment type shown as "L"
(L-moments) or "TL" (trimmed L-moments) and additional support
for right-tail censoring ([RC]) include: Cauchy (TL),
Exponential (L), Gamma (L), Generalized Extreme Value (L),
Generalized Lambda (L & TL), Generalized Logistic (L),
Generalized Normal (L), Generalized Pareto (L[RC] & TL), Gumbel
(L), Kappa (L), Kumaraswamy (L), Normal (L), 3-parameter
log-Normal (L), Pearson Type III (L), Rayleigh (L), Reverse
Gumbel (L[RC]), Rice/Rician (L), Truncated Exponential (L),
Wakeby (L), and Weibull (L).
Author: William H. Asquith
Maintainer: William H. Asquith
ChangeLog | 32 +++++++++++++++++++++++
DESCRIPTION | 43 +++++++++++++++++--------------
NAMESPACE | 11 ++++++++
R/par2qua.R | 38 ++++++++++++++--------------
R/pwm.pp.R | 66 +++++++++++++++++++++++++++++++------------------
R/quacau.R | 7 ++---
R/quaexp.R | 6 ++--
R/quagam.R | 6 ++--
R/quagev.R | 6 ++--
R/quaglo.R | 6 ++--
R/quagno.R | 6 ++--
R/quagpa.R | 6 ++--
R/quagum.R | 6 ++--
R/quakap.R | 7 ++---
R/quakur.R | 6 ++--
R/qualn3.R | 9 +++---
R/quanor.R | 7 +++--
R/quape3.R | 7 ++---
R/quaray.R | 6 ++--
R/quarevgum.R | 6 ++--
R/quarice.R | 13 +++++----
R/quatexp.R | 8 +++--
R/quawak.R | 7 ++---
R/quawei.R | 8 +++--
R/tlmrcau.R |only
R/tlmrexp.R |only
R/tlmrgev.R |only
R/tlmrglo.R |only
R/tlmrgno.R |only
R/tlmrgpa.R |only
R/tlmrgum.R |only
R/tlmrln3.R |only
R/tlmrnor.R |only
R/tlmrpe3.R |only
R/tlmrray.R |only
R/vec2par.R | 5 ++-
README | 2 -
inst/legacy/tlmrwei.R |only
inst/legacy/tlmrwei.Rd |only
man/pwm.pp.Rd | 9 +++++-
man/quacau.Rd | 3 +-
man/quaexp.Rd | 3 +-
man/quagam.Rd | 3 +-
man/quagev.Rd | 3 +-
man/quagld.Rd | 4 +-
man/quaglo.Rd | 3 +-
man/quagno.Rd | 3 +-
man/quagpa.Rd | 3 +-
man/quagum.Rd | 3 +-
man/quakap.Rd | 3 +-
man/quakur.Rd | 3 +-
man/qualn3.Rd | 3 +-
man/quanor.Rd | 3 +-
man/quape3.Rd | 3 +-
man/quaray.Rd | 3 +-
man/quarevgum.Rd | 3 +-
man/quarice.Rd | 3 +-
man/quatexp.Rd | 3 +-
man/quawak.Rd | 3 +-
man/quawei.Rd | 3 +-
man/rlmomco.Rd | 6 +---
man/tlmrcau.Rd |only
man/tlmrexp.Rd |only
man/tlmrgev.Rd |only
man/tlmrglo.Rd |only
man/tlmrgno.Rd |only
man/tlmrgpa.Rd |only
man/tlmrgum.Rd |only
man/tlmrln3.Rd |only
man/tlmrnor.Rd |only
man/tlmrpe3.Rd |only
man/tlmrray.Rd |only
man/vec2par.Rd | 3 +-
73 files changed, 267 insertions(+), 142 deletions(-)
Title: Linear mixed-effects models using S4 classes
Diff between lme4 versions 0.999375-39 dated 2011-03-08 and 0.999375-40 dated 2011-07-23
Description: Fit linear and generalized linear mixed-effects models.
Author: Douglas Bates
Maintainer:
ChangeLog | 42 ++++++++++++++++++++++++++++
DESCRIPTION | 8 ++---
NAMESPACE | 6 ++++
R/AllGeneric.R | 11 -------
R/carryOver.R | 65 +++++++++++++++++++-------------------------
R/drop1-etc.R |only
inst/doc/Implementation.Rnw | 2 -
inst/doc/Implementation.pdf |binary
inst/doc/PLSvGLS.Rnw | 8 ++---
inst/doc/PLSvGLS.pdf |binary
inst/doc/Theory.Rnw | 40 +++++++++++++--------------
inst/doc/Theory.pdf |binary
tests/drop.R |only
tests/lmer-1.Rout.save | 18 ++++++------
tests/nlmer.Rout.save | 28 +++++++++---------
15 files changed, 130 insertions(+), 98 deletions(-)
Title: Tools for Generating, Visualizing, and Analysing Link
Communities in Networks
Diff between linkcomm versions 1.0-2 dated 2011-05-29 and 1.0-3 dated 2011-07-23
Description: Link communities reveal the nested and overlapping
structure in networks, and uncover the key nodes that form
connections to multiple communities. linkcomm provides a set of
tools for generating, visualizing, and analysing link
communities in networks of arbitrary size and type.
Author: Alex T. Kalinka
Maintainer: Alex T. Kalinka
DESCRIPTION | 6 +++---
NEWS | 12 ++++++++++++
R/linkcomm_plotting.R | 6 +++---
inst/CITATION | 4 +++-
inst/doc/fig1_vignette.pdf |binary
inst/doc/linkcomm.Rnw | 2 +-
inst/doc/linkcomm.pdf |binary
man/corLinkcommCentrality.Rd | 2 +-
man/cutDendrogramAt.Rd | 2 +-
man/getAllNestedComm.Rd | 2 +-
man/getClusterRelatedness.Rd | 2 +-
man/getCommunityCentrality.Rd | 4 ++--
man/getCommunityConnectedness.Rd | 2 +-
man/getCommunityMatrix.Rd | 2 +-
man/getLinkCommDensities.Rd | 5 +++--
man/getLinkCommunities.Rd | 5 +++--
man/getNestedHierarchies.Rd | 2 +-
man/getNodesIn.Rd | 2 +-
man/karate.Rd | 2 +-
man/layout.spencer.circle.Rd | 3 ++-
man/lesmiserables.Rd | 2 +-
man/linkcomm-package.Rd | 6 ++++--
man/linkcomm2cytoscape.Rd | 5 +++--
man/newLinkCommsAt.Rd | 2 +-
man/orderCommunities.Rd | 2 +-
man/plot.linkcomm.Rd | 2 +-
man/plotLinkCommDend.Rd | 2 +-
man/plotLinkCommGraph.Rd | 2 +-
man/plotLinkCommMembers.Rd | 2 +-
man/plotLinkCommSumm.Rd | 2 +-
man/plotLinkCommSummComm.Rd | 2 +-
man/pp_rnapol.Rd | 2 +-
man/print.linkcomm.Rd | 2 +-
man/weighted.Rd | 2 +-
34 files changed, 60 insertions(+), 40 deletions(-)
Title: Less Code, More Results
Diff between lessR versions 1.9.8 dated 2011-06-30 and 2.0 dated 2011-07-23
Description: Each function accomplishes the work of several or more
standard R functions. For example, two function calls, rad()
and full(), together read the csv data and generate descriptive
statistics for all variables in the data frame, plus histograms
and bar charts for all respective numerical and non-numerical
variables. The function smd.t.test introduces the ODDSMD plot,
which displays the Overlapping Density Distributions of two
independent groups as well as a visual display of the mean
difference and standardized mean difference. Other functions
provide for descriptive statistics, the t-test from descriptive
statistics, a comprehensive regression analysis, color
plotting, color bar chart, color histogram, color box plot,
density curves, a calibrated power curve plotted with colors,
and the reading and display of csv formatted data. The function
help.me provides a help system that suggests specific analyses
and functions.
Author: David W. Gerbing, School of Business Administration, Portland
State University
Maintainer: David W. Gerbing
DESCRIPTION | 12 -
R/color.barchart.default.R | 22 +-
R/color.density.R | 4
R/color.plot.R | 3
R/reg.R | 384 +++++++++++++++++++++++++++++++++++----------
man/color.barchart.Rd | 12 +
man/color.boxplot.Rd | 2
man/color.density.Rd | 6
man/color.hist.Rd | 2
man/color.plot.Rd | 10 -
man/color.show.Rd | 2
man/describe.Rd | 2
man/full.Rd | 2
man/help.me.Rd | 2
man/out.Rd | 2
man/powercurve.t.test.Rd | 2
man/prob.norm.Rd | 2
man/rad.Rd | 2
man/reg.Rd | 119 ++++++++-----
man/smd.t.test.Rd | 2
man/stats.t.test.Rd | 2
21 files changed, 429 insertions(+), 167 deletions(-)
Title: Time series analysis package for students
Diff between itsmr versions 1.0 dated 2011-06-15 and 1.1 dated 2011-07-23
Description: This package provides a subset of the functionality found
in the Windows-based program ITSM. The intended audience is
students using the textbook "Introduction to Time Series and
Forecasting" by Peter J. Brockwell and Richard A. Davis.
Author: George Weigt
Maintainer: George Weigt
DESCRIPTION | 15 -
R/itsmr.R | 493 ++++++++++++++++++++++++++++++++++++------------------------
2 files changed, 310 insertions(+), 198 deletions(-)
Title: Iterator construct for R
Diff between iterators versions 1.0.4 dated 2011-05-20 and 1.0.5 dated 2011-07-23
Description: Support for iterators, which allow a programmer to
traverse through all the elements of a vector, list, or other
collection of data.
Author: Revolution Analytics
Maintainer: Revolution Analytics
DESCRIPTION | 8 ++++----
R/iterators.R | 3 ++-
inst/doc/iterators.pdf |binary
inst/doc/writing.pdf |binary
4 files changed, 6 insertions(+), 5 deletions(-)
Title: Provides datasets for Introduction to Statistical Data Analysis
for the Life Sciences
Diff between isdals versions 1.0-2 dated 2011-02-22 and 1.0-4 dated 2011-07-23
Description: Provides datasets for Introduction to Statistical Data
Analysis for the Life Sciences
Author: Claus Ekstrom
Maintainer: Claus Ekstrom
DESCRIPTION | 10 +++++-----
R/residualplot.R | 4 ++++
data/herring.rda |binary
3 files changed, 9 insertions(+), 5 deletions(-)
Title: iPlots - interactive graphics for R
Diff between iplots versions 1.1-3 dated 2009-02-07 and 1.1-4 dated 2011-07-23
Description: Interactive plots for R
Author: Simon Urbanek
Maintainer: Simon Urbanek
DESCRIPTION | 11 +++++++----
NAMESPACE |only
NEWS | 5 +++++
R/iplots.R | 24 +++++++++++++++---------
inst/java/iplots.jar |binary
5 files changed, 27 insertions(+), 13 deletions(-)
Title: Irreproducible discovery rate
Diff between idr versions 1.0 dated 2011-06-15 and 1.1 dated 2011-07-23
Description: This is a package for estimating the copula mixture model
and plotting correspondence curves in "Measuring
reproducibility of high-throughput experiments" (2011), Annals
of Applied Statistics, by Li, Brown, Huang, and Bickel
Author: Qunhua Li
Maintainer: Qunhua Li
DESCRIPTION | 6 +++---
man/idr-package.Rd | 2 +-
2 files changed, 4 insertions(+), 4 deletions(-)
Title: High-dimensional Undirected Graph Estimation
Diff between huge versions 1.0.3 dated 2011-06-17 and 1.1.0 dated 2011-07-23
Description: The package "huge" provides a general framework for
high-dimensional undirected graph estimation. It integrates
data preprocessing, neighborhood screening, graph estimation,
and model selection techniques into a pipeline. In
preprocessing stage, the nonparanormal(npn) transformation is
applied to help relax the normality assumption. In the graph
estimation stage, the graph structure is estimated by
Meinshausen-Buhlmann graph estimation or the graphical lasso,
and both methods can be further accelerated by the lossy
screening rule preselecting the neighborhood of each variable
by correlation thresholding. We target on high-dimensional data
analysis usually d >> n, and the computation is
memory-optimized using the sparse matrix output. We also
provide a computationally efficient approach, correlation
thresholding graph estimation. Three
regularization/thresholding parameter selection methods are
included in this package: (1)stability approach for
regularization selection (2) rotation information criterion (3)
extended Bayesian information criterion which is only available
for the graphical lasso.
Author: Tuo Zhao, Han Liu, Kathryn Roeder, John Lafferty, Larry
Wasserman
Maintainer: Tuo Zhao
huge-1.0.3/huge/.Rapp.history |only
huge-1.0.3/huge/R/huge.gect.R |only
huge-1.0.3/huge/R/huge.mbgel.R |only
huge-1.1.0/huge/DESCRIPTION | 48 +++----
huge-1.1.0/huge/NAMESPACE | 2
huge-1.1.0/huge/R/huge.R | 52 +++----
huge-1.1.0/huge/R/huge.ct.R |only
huge-1.1.0/huge/R/huge.generator.R | 17 +-
huge-1.1.0/huge/R/huge.glasso.R | 120 ++++++++++--------
huge-1.1.0/huge/R/huge.mb.R |only
huge-1.1.0/huge/R/huge.npn.R | 14 +-
huge-1.1.0/huge/R/huge.plot.R | 8 -
huge-1.1.0/huge/R/huge.roc.R | 10 -
huge-1.1.0/huge/R/huge.select.R | 127 ++++++++++---------
huge-1.1.0/huge/R/zzz.R | 2
huge-1.1.0/huge/data |only
huge-1.1.0/huge/man/huge-internal.Rd | 6
huge-1.1.0/huge/man/huge-package.Rd | 34 ++---
huge-1.1.0/huge/man/huge.Rd | 51 +++----
huge-1.1.0/huge/man/huge.generator.Rd | 12 +
huge-1.1.0/huge/man/huge.npn.Rd | 10 -
huge-1.1.0/huge/man/huge.plot.Rd | 2
huge-1.1.0/huge/man/huge.roc.Rd | 2
huge-1.1.0/huge/man/huge.select.Rd | 46 +++---
huge-1.1.0/huge/man/plot.huge.Rd | 4
huge-1.1.0/huge/man/plot.roc.Rd | 2
huge-1.1.0/huge/man/plot.select.Rd | 2
huge-1.1.0/huge/man/plot.sim.Rd | 2
huge-1.1.0/huge/man/print.huge.Rd | 2
huge-1.1.0/huge/man/print.roc.Rd | 2
huge-1.1.0/huge/man/print.select.Rd | 2
huge-1.1.0/huge/man/print.sim.Rd | 2
huge-1.1.0/huge/man/stockdata.Rd |only
huge-1.1.0/huge/src/RIC.c | 76 +++++------
huge-1.1.0/huge/src/SFGen.c |only
huge-1.1.0/huge/src/SPMBgraph.c | 226 +++++++++++++++-------------------
huge-1.1.0/huge/src/SPMBscr.c | 189 ++++++++++++----------------
huge-1.1.0/huge/src/hugeglasso.c |only
huge-1.1.0/huge/src/hugeglassoscr.c |only
39 files changed, 541 insertions(+), 531 deletions(-)
Title: Interface between R and the Google Visualisation API
Diff between googleVis versions 0.2.6 dated 2011-06-15 and 0.2.7 dated 2011-07-23
Description: googleVis provides an interface between R and the Google
Visualisation API to create interactive charts for web pages.
The functions of the package allow the user to visualise data
stored in R data frames with the Google Visualisation API
without uploading their data to Google. The output of a
googleVis function is html code that contains the data and
references to JavaScript functions hosted by Google and can be
displayed locally with the R HTTP help server. A browser with
Flash and Internet connection is required. Please visit the
project web site for more information and examples.
Author: Markus Gesmann, Diego de Castillo
Maintainer: Markus Gesmann
googleVis-0.2.6/googleVis/inst/doc/prv_googleVis.Rnw.log |only
googleVis-0.2.7/googleVis/DESCRIPTION | 10
googleVis-0.2.7/googleVis/LICENSE |only
googleVis-0.2.7/googleVis/NEWS | 29
googleVis-0.2.7/googleVis/R/gvis.R | 21
googleVis-0.2.7/googleVis/R/gvisGeoMap.R | 2
googleVis-0.2.7/googleVis/demo/00Index | 5
googleVis-0.2.7/googleVis/demo/AnimatedGeoMap.R | 3
googleVis-0.2.7/googleVis/demo/EventListner.R |only
googleVis-0.2.7/googleVis/demo/googleVis.R | 12
googleVis-0.2.7/googleVis/inst/doc/CreatePost.png |only
googleVis-0.2.7/googleVis/inst/doc/googleVis.Rnw | 254 ++-
googleVis-0.2.7/googleVis/inst/doc/googleVis.bib | 2
googleVis-0.2.7/googleVis/inst/doc/googleVis.pdf |binary
googleVis-0.2.7/googleVis/inst/gadgets/.Rhistory | 1255 ++++++---------
googleVis-0.2.7/googleVis/inst/gadgets/gadgets.R | 11
googleVis-0.2.7/googleVis/inst/gadgets/geochart.xml |only
googleVis-0.2.7/googleVis/inst/gadgets/scatterchart.xml | 27
googleVis-0.2.7/googleVis/inst/tests |only
googleVis-0.2.7/googleVis/man/googleVis-package.Rd | 6
googleVis-0.2.7/googleVis/man/gvisAnnotatedTimeLine.Rd | 14
googleVis-0.2.7/googleVis/man/gvisGeoMap.Rd | 27
googleVis-0.2.7/googleVis/man/gvisMethods.Rd | 2
googleVis-0.2.7/googleVis/man/gvisMotionChart.Rd | 11
googleVis-0.2.7/googleVis/man/gvisScatterChart.Rd | 9
googleVis-0.2.7/googleVis/man/gvisTable.Rd | 5
26 files changed, 901 insertions(+), 804 deletions(-)
Title: Fit a penalized continuation ratio model for predicting an
ordinal response.
Diff between glmpathcr versions 1.0.1 dated 2011-03-16 and 1.0.2 dated 2011-07-23
Description: Provides a function for fitting a penalized constrained
continuation ratio model using the glmpath algorithm and
methods for extracting coefficient estimates, predicted class,
class probabilities, and plots.
Author: Kellie J. Archer
Maintainer: Kellie J. Archer
glmpathcr |only
1 file changed
Title: Fit a penalized constrained continuation ratio model for
predicting an ordinal response
Diff between glmnetcr versions 1.0 dated 2011-03-16 and 1.0.1 dated 2011-07-23
Description: This packages includes functions for restructuring an
ordinal response dataset for fitting continuation ratio models
for datasets where the number of covariates exceeds the sample
size or when there is collinearity among the covariates. This
package uses the glmnet package fitting algorithm.
Author: Kellie J. Archer
Maintainer: Kellie J. Archer
glmnetcr-1.0.1/glmnetcr/DESCRIPTION | 8 ++++----
glmnetcr-1.0.1/glmnetcr/R/predict.glmnet.cr.R | 4 ++--
glmnetcr-1.0.1/glmnetcr/inst/doc/.Rapp.history |only
glmnetcr-1.0.1/glmnetcr/inst/doc/Sweave.sty |only
glmnetcr-1.0.1/glmnetcr/inst/doc/glmnetRefs.bib |only
glmnetcr-1.0.1/glmnetcr/inst/doc/glmnetcr.Rnw |only
glmnetcr-1.0.1/glmnetcr/inst/doc/glmnetcr.bbl |only
glmnetcr-1.0.1/glmnetcr/inst/doc/glmnetcr.blg |only
glmnetcr-1.0.1/glmnetcr/inst/doc/glmnetcr.pdf |binary
glmnetcr-1.0.1/glmnetcr/inst/doc/jss.bst |only
glmnetcr-1.0.1/glmnetcr/inst/doc/jss.cls |only
glmnetcr-1.0/glmnetcr/inst/doc/.build.timestamp |only
12 files changed, 6 insertions(+), 6 deletions(-)
Title: Geophysics, Continuum Mechanics, Mogi Model
Diff between geophys versions 1.1-0 dated 2010-11-24 and 1.2-0 dated 2011-07-23
Description: Geophysics, Continuum Mechanics, Mogi Model, Okada Model
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees
DESCRIPTION | 8 ++++----
R/okada85.R |only
man/geophys-package.Rd | 4 ++--
man/okada85.Rd |only
4 files changed, 6 insertions(+), 6 deletions(-)
Title: Generalized additive mixed models using mgcv and lme4
Diff between gamm4 versions 0.1-2 dated 2011-03-02 and 0.1-3 dated 2011-07-23
Description: Fit generalized additive mixed models via a version of
mgcv's gamm function, using lme4 for estimation via Fabian
Scheipl's trick.
Author: Simon Wood
Maintainer: Simon Wood
DESCRIPTION | 6 ++---
R/gamm4.r | 63 +++++++++++++++++++-----------------------------------------
changeLog | 20 +++++++++++++++++++
3 files changed, 43 insertions(+), 46 deletions(-)
Title: Toolkit implementation of gWidgets for tcltk package
Diff between gWidgetstcltk versions 0.0-43 dated 2011-04-30 and 0.0-44 dated 2011-07-23
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
ChangeLog | 75 +++++++++++++++++
DESCRIPTION | 10 --
NAMESPACE | 3
NEWS | 10 ++
R/aaaGenerics.R | 75 +++++++++++++----
R/aaaR5classes.R | 59 +++++++++++++-
R/common.R | 4
R/gcalendar.R | 51 ++++++++----
R/gcheckbox.R | 20 +++-
R/gdialogs.R | 5 -
R/gdroplist.R | 23 +++--
R/gedit.R | 2
R/gexpandgroup.R | 4
R/gfile.R | 24 ++++-
R/ggraphics.R | 8 +
R/ggroup.R | 10 +-
R/ghtml.R |only
R/gimage.R | 6 -
R/gnotebook.R | 2
R/gpanedgroup.R | 2
R/gradio.R | 2
R/gspinbutton.R | 159 ++++++++++++++++++++++++--------------
R/gstatusbar.R | 2
R/gtable.R | 6 -
R/gtext.R | 2
R/gtoolbar.R | 2
R/gtree.R | 2
R/gwindow.R | 25 +++++
R/zzz.R | 2
TODO.txt | 8 +
man/gWidgetstcltk-package.Rd | 48 ++++++++---
man/gWidgetstcltk-undocumented.Rd | 13 ++-
32 files changed, 508 insertions(+), 156 deletions(-)
Title: Toolkit implementation of gWidgets for RGtk2
Diff between gWidgetsRGtk2 versions 0.0-74 dated 2011-05-08 and 0.0-75 dated 2011-07-23
Description: Port of gWidgets API to RGtk2
Author: Michael Lawrence, John Verzani
Maintainer: John Verzani
ChangeLog | 15 +++++
DESCRIPTION | 10 +--
NAMESPACE | 37 +++++++------
NEWS | 15 ++++-
R/aaaGenerics.R | 28 +++++++++
R/aacR5Classes.R | 2
R/gedit.R | 27 +++++++--
R/gexpandgroup.R | 7 ++
R/ghtml.R |only
R/gtext.R | 108 ++++++++++++++++++++++++++++----------
R/gwindow.R | 22 +++++++
TODO.txt | 3 -
man/gWidgetsRGtk2-undocumented.Rd | 36 ++++++++++++
13 files changed, 251 insertions(+), 59 deletions(-)
Title: gWidgets API for building toolkit-independent, interactive GUIs
Diff between gWidgets versions 0.0-44 dated 2011-04-30 and 0.0-45 dated 2011-07-23
Description: gWidgets provides a toolkit-independent API for building
interactive GUIs. Atleast 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 | 8 +----
NEWS | 4 ++
R/common.R | 2 -
R/gcheckbox.R | 2 +
R/guiComponent.R | 4 +-
R/handlers.R | 71 ++++++++++++++++++++++++++++++++++++++++++---
TODO.txt | 1
inst/doc/addingToolkit.pdf |binary
inst/doc/gWidgets.pdf |binary
inst/images/Rplots.ps |only
man/gWidgets-methods.Rd | 1
man/gradio.Rd | 8 +----
12 files changed, 84 insertions(+), 17 deletions(-)
Title: A package for graphical modelling in R
Diff between gRbase versions 1.3.9 dated 2011-01-18 and 1.4.0 dated 2011-07-23
Description: The gRbase package provides certain general constructs
which are used by other graphical modelling packages. This
includes 1) the concept of gmData (graphical meta data), 2)
several graph algorithms 3) facilities for table operations, 4)
functions for testing for conditional independence. gRbase also
illustrates how hierarchical log-linear models (hllm) may be
implemented.
Author: Søren Højsgaard
Maintainer: Søren Højsgaard
gRbase-1.3.9/gRbase/R/GraphSH2.R |only
gRbase-1.3.9/gRbase/R/ptable.R |only
gRbase-1.3.9/gRbase/data/BodyFat.txt |only
gRbase-1.3.9/gRbase/data/cad1.txt |only
gRbase-1.3.9/gRbase/data/cad2.txt |only
gRbase-1.3.9/gRbase/data/carcass.txt |only
gRbase-1.3.9/gRbase/data/carcassall.txt |only
gRbase-1.3.9/gRbase/data/dietox.txt |only
gRbase-1.3.9/gRbase/data/math.txt |only
gRbase-1.3.9/gRbase/data/mathmark.txt |only
gRbase-1.3.9/gRbase/data/milkcomp.txt |only
gRbase-1.3.9/gRbase/data/milkcomp1.txt |only
gRbase-1.3.9/gRbase/data/rats.txt |only
gRbase-1.3.9/gRbase/man/GraphAlgo-operations2.Rd |only
gRbase-1.3.9/gRbase/man/ptable.Rd |only
gRbase-1.4.0/gRbase/ChangeLog | 15
gRbase-1.4.0/gRbase/DESCRIPTION | 10
gRbase-1.4.0/gRbase/R/FIX-formulae.R | 100 ++-
gRbase-1.4.0/gRbase/R/Generics.R | 5
gRbase-1.4.0/gRbase/R/GraphAlgo-JunctionTree.R |only
gRbase-1.4.0/gRbase/R/GraphAlgo-coerce.R |only
gRbase-1.4.0/gRbase/R/GraphAlgo-edgeList.R | 6
gRbase-1.4.0/gRbase/R/GraphAlgo-glist2adjmat.R |only
gRbase-1.4.0/gRbase/R/GraphAlgo-isGSD.R |only
gRbase-1.4.0/gRbase/R/GraphAlgo-mcs.R | 211 +++++---
gRbase-1.4.0/gRbase/R/GraphAlgo-mcsmarked.R |only
gRbase-1.4.0/gRbase/R/GraphAlgo-moralize.R | 46 +
gRbase-1.4.0/gRbase/R/GraphAlgo-querygraph.R | 293 ++++-------
gRbase-1.4.0/gRbase/R/GraphAlgo-rip.R | 42 +
gRbase-1.4.0/gRbase/R/GraphAlgo-triangulate.R | 334 ++++++++-----
gRbase-1.4.0/gRbase/R/GraphAlgo-ugdag.R |only
gRbase-1.4.0/gRbase/R/arrayCombine.R |only
gRbase-1.4.0/gRbase/R/iplot.R | 5
gRbase-1.4.0/gRbase/R/names2pairs.R | 183 ++++---
gRbase-1.4.0/gRbase/R/parray.R |only
gRbase-1.4.0/gRbase/R/table-operations.R | 533 ++++-----------------
gRbase-1.4.0/gRbase/R/utilities.R | 91 ++-
gRbase-1.4.0/gRbase/R/xxxPrim.R | 10
gRbase-1.4.0/gRbase/R/yyyPrim.R | 47 -
gRbase-1.4.0/gRbase/data/BodyFat.txt.gz |only
gRbase-1.4.0/gRbase/data/Nutrimouse.RData |only
gRbase-1.4.0/gRbase/data/cad1.txt.gz |only
gRbase-1.4.0/gRbase/data/cad2.txt.gz |only
gRbase-1.4.0/gRbase/data/carcass.txt.gz |only
gRbase-1.4.0/gRbase/data/carcassall.txt.gz |only
gRbase-1.4.0/gRbase/data/datalist |only
gRbase-1.4.0/gRbase/data/dietox.txt.gz |only
gRbase-1.4.0/gRbase/data/dumping.RData |only
gRbase-1.4.0/gRbase/data/lizardAGG.txt.gz |only
gRbase-1.4.0/gRbase/data/lizardRAW.txt.gz |only
gRbase-1.4.0/gRbase/data/math.txt.gz |only
gRbase-1.4.0/gRbase/data/mathmark.txt.gz |only
gRbase-1.4.0/gRbase/data/milkcomp.txt.gz |only
gRbase-1.4.0/gRbase/data/milkcomp1.txt.gz |only
gRbase-1.4.0/gRbase/data/rats.txt.gz |only
gRbase-1.4.0/gRbase/data/wine.txt.gz |only
gRbase-1.4.0/gRbase/gRbase-Ex.R | 323 ++++++++++--
gRbase-1.4.0/gRbase/inst/doc/ArrayOps.Rnw | 163 +++---
gRbase-1.4.0/gRbase/inst/doc/ArrayOps.pdf |binary
gRbase-1.4.0/gRbase/inst/doc/ArrayOpsPrim.Rnw | 103 ++--
gRbase-1.4.0/gRbase/inst/doc/ArrayOpsPrim.pdf |binary
gRbase-1.4.0/gRbase/inst/doc/Graphs.Rnw | 241 ++++++---
gRbase-1.4.0/gRbase/inst/doc/Graphs.pdf |binary
gRbase-1.4.0/gRbase/inst/doc/fig |only
gRbase-1.4.0/gRbase/inst/doc/gRbase.pdf |binary
gRbase-1.4.0/gRbase/man/DATA-Nutrimouse.Rd |only
gRbase-1.4.0/gRbase/man/DATA-dumping.Rd |only
gRbase-1.4.0/gRbase/man/DATA-lizard.Rd | 13
gRbase-1.4.0/gRbase/man/DATA-wine.Rd |only
gRbase-1.4.0/gRbase/man/GraphAlgo-glist2adjMAT.Rd |only
gRbase-1.4.0/gRbase/man/GraphAlgo-mcs.Rd |only
gRbase-1.4.0/gRbase/man/GraphAlgo-minimalTriang.Rd | 2
gRbase-1.4.0/gRbase/man/GraphAlgo-moralize.Rd |only
gRbase-1.4.0/gRbase/man/GraphAlgo-mpd.Rd | 2
gRbase-1.4.0/gRbase/man/GraphAlgo-operations1.Rd | 33 -
gRbase-1.4.0/gRbase/man/GraphAlgo-querygraph.Rd | 6
gRbase-1.4.0/gRbase/man/GraphAlgo-rip.Rd |only
gRbase-1.4.0/gRbase/man/GraphAlgo-triangulate.Rd | 49 +
gRbase-1.4.0/gRbase/man/arrayCombine.Rd |only
gRbase-1.4.0/gRbase/man/compareModels.Rd |only
gRbase-1.4.0/gRbase/man/compile-propagate.Rd | 2
gRbase-1.4.0/gRbase/man/gRbase-internal.Rd | 24
gRbase-1.4.0/gRbase/man/gRbase-utilities.Rd | 27 -
gRbase-1.4.0/gRbase/man/parray.Rd |only
gRbase-1.4.0/gRbase/man/table-operations.Rd | 11
gRbase-1.4.0/gRbase/man/ugdag.Rd | 34 -
gRbase-1.4.0/gRbase/src/Makevars | 2
gRbase-1.4.0/gRbase/src/xxxPrim.c | 2
88 files changed, 1628 insertions(+), 1340 deletions(-)
Title: Graphical Independence Networks
Diff between gRain versions 0.8.7 dated 2011-01-18 and 0.8.8 dated 2011-07-23
Description: A package for probability propagation in graphical
independence networks, also known as probabilistic expert
systems (which includes Bayesian networks as a special case).
Author: Søren Højsgaard
Maintainer: Søren Højsgaard
ChangeLog | 10 +
DESCRIPTION | 8 -
R/Finding.R | 25 ++--
R/SimulateArray.R | 4
R/compile-grain.R | 268 ++++++++++++++++++++++-------------------------
R/compileCPT.R | 45 +++++--
R/cptable.R | 4
R/display.R | 43 +++----
R/extractCPT.R | 77 ++++++-------
R/grain-main.R | 35 +++---
R/potentialList.R | 22 +--
R/propagate.R | 41 +++----
R/querygrain.R | 50 ++++----
R/summary.R | 4
R/update.R |only
R/utilities.R | 4
inst/doc/gRain-intro.Rnw | 24 +---
inst/doc/gRain-intro.pdf |binary
man/compile.grain.Rd | 2
man/internal-gRain.Rd | 5
man/propagate.grain.Rd | 2
21 files changed, 354 insertions(+), 319 deletions(-)
Title: Simple key-value database
Diff between filehash versions 2.1-1 dated 2010-10-05 and 2.2 dated 2011-07-23
Description: Simple key-value database
Author: Roger D. Peng
Maintainer: Roger D. Peng
DESCRIPTION | 10 +++++-----
NAMESPACE | 4 +++-
R/filehash.R | 19 +++++++++++++++++++
inst/doc/filehash.pdf |binary
man/db2env.Rd | 2 ++
man/filehash-class.Rd | 5 +++++
6 files changed, 34 insertions(+), 6 deletions(-)
Title: Extreme value toolkit.
Diff between extRemes versions 1.62 dated 2010-04-25 and 1.63 dated 2011-07-23
Description: Uses Stuart Coles' (Coles, Stewart, "An introduction to
statistical modeling of extreme values", Springer-Verlag,
London 2001) S-plus functions as ported to the R programming
language (ismev) by Alec Stephenson
(http://www.maths.lancs.ac.uk/~stephena/). This toolkit
provides a Graphical User Interface (GUI) to ismev for
pedagogical purposes.
Author: Eric Gilleland, Rick Katz, Greg Young
Maintainer: Eric Gilleland
DESCRIPTION | 6 +++---
R/eiAnalyze.R | 4 ++++
R/extremes.gui.R | 12 ++++++------
R/quantiles.R |only
inst |only
man/extRemes-internal.Rd | 2 ++
man/qqnorm.Rd |only
man/qqplot.Rd |only
man/shiftplot.Rd |only
9 files changed, 15 insertions(+), 9 deletions(-)
Title: Data sets from "Forecasting with exponential smoothing"
Diff between expsmooth versions 2.00 dated 2009-09-07 and 2.01 dated 2011-07-23
Description: Data sets from the book "Forecasting with exponential
smoothing: the state space approach" by Hyndman, Koehler, Ord
and Snyder (Springer, 2008).
Author: Rob J Hyndman
Maintainer: Rob J Hyndman
ChangeLog | 3 +++
DESCRIPTION | 14 +++++++-------
data/jewelry.rda |binary
3 files changed, 10 insertions(+), 7 deletions(-)
Title: Epidemiological calculator
Diff between epicalc versions 2.12.2.3 dated 2011-04-11 and 2.13.1.0 dated 2011-07-23
Description: Functions making R easy for epidemiological calculation.
Author: Virasakdi Chongsuvivatwong
Maintainer: Virasakdi Chongsuvivatwong
epicalc-2.12.2.3/epicalc/data/ANCtable.txt |only
epicalc-2.12.2.3/epicalc/data/Bang.txt |only
epicalc-2.12.2.3/epicalc/data/Hakimi.txt |only
epicalc-2.12.2.3/epicalc/data/Montana.txt |only
epicalc-2.13.1.0/epicalc/DESCRIPTION | 8 ++--
epicalc-2.13.1.0/epicalc/R/epicalc.R | 45 ++++++++++++--------------
epicalc-2.13.1.0/epicalc/data/ANCtable.txt.gz |only
epicalc-2.13.1.0/epicalc/data/Bang.txt.gz |only
epicalc-2.13.1.0/epicalc/data/Hakimi.txt.gz |only
epicalc-2.13.1.0/epicalc/data/Montana.txt.gz |only
10 files changed, 26 insertions(+), 27 deletions(-)
Title: R package for parsing and manipulating edit rules
Diff between editrules versions 0.8 dated 2011-07-06 and 0.9-0 dated 2011-07-23
Description: Facilitates reading and manipulation of linear
(in)equalities, converting them into matrix format (and vice
versa) and checking if data are valid according to these rules.
Sets of linear edits can be manipulated using Fourier-Motzkin
elimination and variable substitution and solving error
localization problems based on the generalized principle of
Felligi and Holt.
Author: Edwin de Jonge, Mark van der Loo
Maintainer: Edwin de Jonge
editrules-0.8/editrules/R/findBlocks.R |only
editrules-0.8/editrules/inst/doc/editrules-categorical.tex |only
editrules-0.8/editrules/inst/doc/editrules-linear-008.pdf |only
editrules-0.8/editrules/inst/doc/editrules-linear.bbl |only
editrules-0.8/editrules/inst/doc/editrules-linear.blg |only
editrules-0.8/editrules/inst/doc/editrules-linear.dvi |only
editrules-0.8/editrules/inst/doc/texput.log |only
editrules-0.8/editrules/inst/doc/tree.tex.aux |only
editrules-0.8/editrules/inst/doc/x.log |only
editrules-0.8/editrules/man/cp.editmatrix.Rd |only
editrules-0.8/editrules/man/errorLocalizer.editmatrix.Rd |only
editrules-0.8/editrules/man/findBlocks.Rd |only
editrules-0.9-0/editrules/DESCRIPTION | 12
editrules-0.9-0/editrules/NAMESPACE | 94 -
editrules-0.9-0/editrules/NEWS | 13
editrules-0.9-0/editrules/R/backtracker.R | 46
editrules-0.9-0/editrules/R/blocks.R |only
editrules-0.9-0/editrules/R/editmatrix.R | 9
editrules-0.9-0/editrules/R/editmatrixAttr.R | 35
editrules-0.9-0/editrules/R/eliminate.R | 11
editrules-0.9-0/editrules/R/errorLocalizer.R | 63 -
editrules-0.9-0/editrules/R/reduce.R | 24
editrules-0.9-0/editrules/data/edits.RData |binary
editrules-0.9-0/editrules/inst/doc/editrules-categorical.Snw | 2
editrules-0.9-0/editrules/inst/doc/editrules-categorical.pdf |binary
editrules-0.9-0/editrules/inst/doc/editrules-linear.Snw | 472 +++++-----
editrules-0.9-0/editrules/inst/doc/editrules-linear.pdf |binary
editrules-0.9-0/editrules/inst/doc/editrules.bib | 25
editrules-0.9-0/editrules/inst/doc/tree.tex | 2
editrules-0.9-0/editrules/inst/tests/testErrorLocalizer.R |only
editrules-0.9-0/editrules/inst/tests/testFourierMotzkin.R | 35
editrules-0.9-0/editrules/inst/tests/testIsFeasible.R |only
editrules-0.9-0/editrules/man/as.character.editmatrix.Rd | 22
editrules-0.9-0/editrules/man/as.data.frame.editmatrix.Rd | 24
editrules-0.9-0/editrules/man/as.editmatrix.Rd | 40
editrules-0.9-0/editrules/man/as.expression.editmatrix.Rd | 22
editrules-0.9-0/editrules/man/as.matrix.editmatrix.Rd | 28
editrules-0.9-0/editrules/man/backtracker.Rd | 125 +-
editrules-0.9-0/editrules/man/blocks.Rd |only
editrules-0.9-0/editrules/man/checkRows.Rd | 108 +-
editrules-0.9-0/editrules/man/duplicated.editmatrix.Rd | 22
editrules-0.9-0/editrules/man/echelon.Rd | 30
editrules-0.9-0/editrules/man/editmatrix-subscript.Rd | 24
editrules-0.9-0/editrules/man/editmatrix.Rd | 132 +-
editrules-0.9-0/editrules/man/editrules-package.Rd | 112 +-
editrules-0.9-0/editrules/man/editrules.Rd | 102 +-
editrules-0.9-0/editrules/man/edits.Rd | 18
editrules-0.9-0/editrules/man/eliminateFM.Rd | 139 +-
editrules-0.9-0/editrules/man/errorLocalizer.Rd | 204 ++--
editrules-0.9-0/editrules/man/getA.Rd | 88 -
editrules-0.9-0/editrules/man/getAb.Rd | 86 -
editrules-0.9-0/editrules/man/getOps.Rd | 86 -
editrules-0.9-0/editrules/man/getVars.Rd | 86 -
editrules-0.9-0/editrules/man/getb.Rd | 87 -
editrules-0.9-0/editrules/man/geth.Rd |only
editrules-0.9-0/editrules/man/is.editmatrix.Rd | 22
editrules-0.9-0/editrules/man/isFeasible.Rd | 30
editrules-0.9-0/editrules/man/isNormalized.Rd | 86 -
editrules-0.9-0/editrules/man/isObviouslyInfeasible.Rd | 26
editrules-0.9-0/editrules/man/isObviouslyRedundant.Rd | 44
editrules-0.9-0/editrules/man/isObviouslyRedundant.editmatrix.Rd | 22
editrules-0.9-0/editrules/man/isObviouslyRedundant.matrix.Rd | 32
editrules-0.9-0/editrules/man/iter.backtracker.Rd | 30
editrules-0.9-0/editrules/man/listViolatedEdits.Rd | 50 -
editrules-0.9-0/editrules/man/neweditmatrix.Rd | 28
editrules-0.9-0/editrules/man/normalize.Rd | 92 -
editrules-0.9-0/editrules/man/parseEdits.Rd | 26
editrules-0.9-0/editrules/man/print.backtracker.Rd | 22
editrules-0.9-0/editrules/man/print.editmatrix.Rd | 20
editrules-0.9-0/editrules/man/str.editmatrix.Rd | 20
editrules-0.9-0/editrules/man/substValue.Rd | 41
editrules-0.9-0/editrules/man/violatedEdits.Rd | 74 -
72 files changed, 1653 insertions(+), 1440 deletions(-)
Title: Multivariate Adaptive Regression Spline Models
Diff between earth versions 3.2-0 dated 2011-06-19 and 3.2-1 dated 2011-07-23
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines". (The term "MARS" is copyrighted and thus not used in
the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and
Rob Tibshirani.
Maintainer: Stephen Milborrow
DESCRIPTION | 6 -
NEWS | 3
inst/doc/earth-notes.Rnw | 115 ++++++++++++++++++++----------------
inst/doc/earth-notes.bib | 6 +
inst/doc/earth-notes.pdf |binary
src/earth.c | 7 +-
src/tests/earth.times.bat | 2
src/tests/test.earth.full.Rout.save | 6 -
src/tests/test.earthc.bat | 12 +--
src/tests/test.earthc.mak | 4 -
src/tests/test.earthc.out.save | 10 +--
src/tests/test.earthmain.bat | 16 ++---
src/tests/test.earthmain.gcc.bat | 18 ++---
13 files changed, 114 insertions(+), 91 deletions(-)
Title: delftfews R extensions
Diff between delftfews versions 0.3-38 dated 2010-08-27 and 0.3-67 dated 2011-07-23
Description: a collection of timeseries sets handling functions used
here at work (Nelen en Schuurmans), initially for the Lizard
Scripter.
Author: Mario Frasca
Maintainer: Mario Frasca
delftfews-0.3-38/delftfews/inst/RUnit |only
delftfews-0.3-38/delftfews/man/teardown.fewsdiagnostics.Rd |only
delftfews-0.3-38/delftfews/tests/doRUnit.R |only
delftfews-0.3-67/delftfews/DESCRIPTION | 15 +-
delftfews-0.3-67/delftfews/NAMESPACE | 33 ++++-
delftfews-0.3-67/delftfews/R/augment.R | 5
delftfews-0.3-67/delftfews/R/diagnostics.R | 16 ++
delftfews-0.3-67/delftfews/R/rezoo.R | 26 ++--
delftfews-0.3-67/delftfews/R/select.R | 4
delftfews-0.3-67/delftfews/R/timeseries-io.R | 18 ++-
delftfews-0.3-67/delftfews/R/utils.R | 56 +++++++++-
delftfews-0.3-67/delftfews/inst/unitTest |only
delftfews-0.3-67/delftfews/man/cumulate.Rd | 12 +-
delftfews-0.3-67/delftfews/man/findLocalExtremes.Rd |only
delftfews-0.3-67/delftfews/man/get.step.Rd |only
delftfews-0.3-67/delftfews/man/read.BfG.Rd | 2
delftfews-0.3-67/delftfews/man/read.PI.Rd | 13 +-
delftfews-0.3-67/delftfews/man/read.dcf.parsed.Rd | 32 ++++-
delftfews-0.3-67/delftfews/man/setup.fewsdiagnostics.Rd | 19 ++-
delftfews-0.3-67/delftfews/tests/data/test.write.PI.na.1.xml.target | 2
delftfews-0.3-67/delftfews/tests/data/test.write.PI.na.2.xml.target | 4
delftfews-0.3-67/delftfews/tests/data/test.write.PI.na.3.xml.target | 4
delftfews-0.3-67/delftfews/tests/data/test.write.PI.na.4.xml.target | 8 -
delftfews-0.3-67/delftfews/tests/data/test.write.PI.nan.na.xml.target | 2
delftfews-0.3-67/delftfews/tests/data/test.write.PI.no.events.target | 4
delftfews-0.3-67/delftfews/tests/data/test.write.PI.one.event.target |only
delftfews-0.3-67/delftfews/tests/data/write.PI.missing.columns.target | 2
delftfews-0.3-67/delftfews/tests/data/write.PI.na.missing.elements.target | 2
delftfews-0.3-67/delftfews/tests/doSvUnit.R |only
29 files changed, 206 insertions(+), 73 deletions(-)
Title: Dynamic Deterministic Effects Propagation Networks: Infer
signalling networks for timecourse RPPA data.
Diff between ddepn versions 1.8 dated 2011-06-17 and 1.9 dated 2011-07-23
Description: DDEPN (Dynamic Deterministic Effects Propagation
Networks): Infer signalling networks for timecourse data. Given
a matrix of high-throughput genomic or proteomic timecourse
data, generated after external perturbation of the biological
system, DDEPN models the time-dependent propagation of active
and passive states depending on a network structure. Optimal
network structures given the experimental data are
reconstructed. Two network inference algorithms can be used:
inhibMCMC, a Markov Chain Monte Carlo sampling approach and GA,
a Genetic Algorithm network optimisation. Inclusion of prior
biological knowledge can be done using different network prior
models.
Author: Christian Bender
Maintainer: Christian Bender
DESCRIPTION | 16 +-
R/addstimuli.R |only
R/ddepn.R | 243 +++++++++++++++++++++++++++++++++-----------
R/gelman_diag.R |only
R/getfirstphi.R | 8 -
R/likl.R | 31 +++--
R/mcmc_accept.R | 35 +++---
R/mcmc_ddepn.R | 147 ++++++++++++++++----------
R/mcmc_move.R | 12 +-
R/netga.R | 104 +++++++++++++-----
R/perform.hmmsearch.R | 15 +-
R/plot_edgeconfidences.R | 8 -
R/plot_profiles.R | 54 +++++----
R/propagate.effect.R | 100 ++++--------------
R/samplephi.R | 23 +---
R/signalnetwork.R | 87 ++++++++-------
R/simulatedata.R | 4
data/hcc1954.RData |binary
data/hcc1954raw.RData |binary
data/kegggraphs.RData |binary
inst/doc/ddepn.Rnw | 104 +++++++++++++++++-
inst/doc/ddepn.pdf |binary
inst/doc/mcmcedgeconf.pdf |only
inst/doc/mcmcprofiles.pdf |only
inst/doc/references.bib | 23 +++-
inst/doc/scorenetgatest.pdf |binary
man/addstimuli.Rd |only
man/create_signetwork.Rd | 4
man/ddepn-package.Rd | 3
man/ddepn.Rd | 46 +++++++-
man/gelman_diag.Rd |only
man/getfirstphi.Rd | 4
man/mcmc_accept.Rd | 3
man/mcmc_ddepn.Rd | 14 ++
man/netga.Rd | 10 +
man/plot_edgeconfidences.Rd | 6 -
man/plot_profiles.Rd | 7 -
man/propagate.effect.Rd | 7 -
man/samplephi.Rd | 5
man/signalnetwork.Rd | 6 -
man/simulatedata.Rd | 4
41 files changed, 748 insertions(+), 385 deletions(-)
Title: Data Cloning and MCMC Tools for Maximum Likelihood Methods
Diff between dclone versions 1.3-2 dated 2011-05-15 and 1.3-3 dated 2011-07-23
Description: Low level functions for implementing maximum likelihood
estimating procedures for complex models using data cloning and
Bayesian Markov chain Monte Carlo methods with support for
JAGS, WinBUGS and OpenBUGS. With some functions for parallel
MCMC computations.
Author: Peter Solymos
Maintainer: Peter Solymos
DESCRIPTION | 8 ++++----
R/dc.parfit.R | 12 +++++++++---
R/jags.parfit.R | 12 +++++++++---
R/mcmcapply.R | 23 +++--------------------
R/snowWrapper.R | 9 ++++++---
inst/ChangeLog | 10 ++++++++++
man/jags.parfit.Rd | 2 ++
man/mcmcapply.Rd | 3 +++
man/snowWrapper.Rd | 9 ++++++---
9 files changed, 52 insertions(+), 36 deletions(-)
Title: Continuous Time Autoregressive Models
Diff between cts versions 1.0-1 dated 2006-09-29 and 1.0-4 dated 2011-07-23
Description: Continuous Time Autoregressive Models and the Kalman
Filter
Author: Fortran original by G. Tunnicliffe-Wilson and Zhu Wang, R port
by Zhu Wang.
Maintainer: Zhu Wang
cts-1.0-1/cts/R/ctsdiag.R |only
cts-1.0-1/cts/R/predict.car.R |only
cts-1.0-1/cts/R/print.car.R |only
cts-1.0-1/cts/R/spec.car.R |only
cts-1.0-1/cts/man/aic.Rd |only
cts-1.0-1/cts/man/ctsdiag.Rd |only
cts-1.0-1/cts/man/kalsmo.car.Rd |only
cts-1.0-1/cts/man/plotpredict.car.Rd |only
cts-1.0-1/cts/man/predict.car.Rd |only
cts-1.0-1/cts/man/print.car.Rd |only
cts-1.0-1/cts/man/print.factab.Rd |only
cts-1.0-1/cts/man/spec.car.Rd |only
cts-1.0-4/cts/DESCRIPTION | 16 ++-
cts-1.0-4/cts/NAMESPACE | 15 +++
cts-1.0-4/cts/R/aic.R | 19 ++--
cts-1.0-4/cts/R/car.R | 160 +++++++++++++++++++++++++----------
cts-1.0-4/cts/R/factab.R | 28 +++---
cts-1.0-4/cts/R/kalsmo.car.R | 18 ++-
cts-1.0-4/cts/R/kalsmo.comp.R | 14 +--
cts-1.0-4/cts/R/plot.car.R |only
cts-1.0-4/cts/R/plot.spec.car.R | 8 -
cts-1.0-4/cts/R/plot.spec.ls.R | 24 ++++-
cts-1.0-4/cts/R/spec.ls.R | 4
cts-1.0-4/cts/R/spectrum.car.R |only
cts-1.0-4/cts/cleanup |only
cts-1.0-4/cts/inst |only
cts-1.0-4/cts/man/asth.Rd | 3
cts-1.0-4/cts/man/car.Rd | 126 +++++++++++++++++----------
cts-1.0-4/cts/man/control.Rd |only
cts-1.0-4/cts/man/cts-internal.Rd |only
cts-1.0-4/cts/man/factab.Rd | 6 -
cts-1.0-4/cts/man/kalsmo.comp.Rd | 21 ++--
cts-1.0-4/cts/man/plot.spec.car.Rd | 9 +
cts-1.0-4/cts/man/spec.ls.Rd | 9 -
cts-1.0-4/cts/src/cinvert.f | 6 +
cts-1.0-4/cts/src/complete.f | 138 +++++++++++++++++-------------
cts-1.0-4/cts/src/cspec.f | 7 +
cts-1.0-4/cts/src/display.f | 86 +++++++++---------
cts-1.0-4/cts/src/dpca.f | 3
cts-1.0-4/cts/src/envirn.f | 4
cts-1.0-4/cts/src/envron.f | 9 +
cts-1.0-4/cts/src/erm0.f | 2
cts-1.0-4/cts/src/erm1.f | 3
cts-1.0-4/cts/src/erm2.f | 3
cts-1.0-4/cts/src/erm3.f | 3
cts-1.0-4/cts/src/erm4.f | 3
cts-1.0-4/cts/src/forecast.f | 67 ++++++++------
cts-1.0-4/cts/src/kfilsm.f | 74 ++++++++--------
cts-1.0-4/cts/src/kfilsm1.f | 11 +-
cts-1.0-4/cts/src/loop.f | 49 +++++++---
cts-1.0-4/cts/src/lybsc.f | 1
cts-1.0-4/cts/src/mutil.f | 9 +
cts-1.0-4/cts/src/newline.f | 2
cts-1.0-4/cts/src/rejuce.f | 1
cts-1.0-4/cts/src/repar.f | 8 +
cts-1.0-4/cts/src/resg0.f | 4
cts-1.0-4/cts/src/resg0new.f | 4
cts-1.0-4/cts/src/resg1d.f | 10 +-
cts-1.0-4/cts/src/resg1dpre.f | 10 +-
cts-1.0-4/cts/src/resg1dpre1.f | 8 +
cts-1.0-4/cts/src/resgen.f | 12 ++
cts-1.0-4/cts/src/revg1.f | 13 +-
cts-1.0-4/cts/src/roots.f | 3
cts-1.0-4/cts/src/search.f | 1
cts-1.0-4/cts/src/setcom.f | 6 -
cts-1.0-4/cts/src/setfor.f | 4
cts-1.0-4/cts/src/setkfilsm.f | 3
cts-1.0-4/cts/src/setup1.f | 12 +-
cts-1.0-4/cts/src/setupdate.f | 12 +-
cts-1.0-4/cts/src/simi.f | 1
cts-1.0-4/cts/src/update.f | 43 +++++----
71 files changed, 716 insertions(+), 399 deletions(-)
Title: Circular Statistics
Diff between circular versions 0.4-2 dated 2011-03-19 and 0.4-3 dated 2011-07-23
Description: Circular Statistics, from "Topics in circular Statistics"
(2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific.
Author: Ulric Lund
Maintainer: Claudio Agostinelli
circular-0.4-2/circular/R/cross_validation.R |only
circular-0.4-2/circular/data/coope.R |only
circular-0.4-2/circular/data/fisherB1.R |only
circular-0.4-2/circular/data/fisherB10.R |only
circular-0.4-2/circular/data/fisherB11.R |only
circular-0.4-2/circular/data/fisherB12.R |only
circular-0.4-2/circular/data/fisherB13.R |only
circular-0.4-2/circular/data/fisherB2.R |only
circular-0.4-2/circular/data/fisherB3.R |only
circular-0.4-2/circular/data/fisherB4.R |only
circular-0.4-2/circular/data/fisherB5.R |only
circular-0.4-2/circular/data/fisherB6.R |only
circular-0.4-2/circular/data/fisherB7.R |only
circular-0.4-2/circular/data/fisherB8.R |only
circular-0.4-2/circular/data/fisherB9.R |only
circular-0.4-2/circular/data/ncfrog.R |only
circular-0.4-2/circular/data/rao.table.R |only
circular-0.4-3/circular/DESCRIPTION | 12 -
circular-0.4-3/circular/NAMESPACE | 38 +++
circular-0.4-3/circular/R/angular.deviation.R |only
circular-0.4-3/circular/R/angular.variance.R |only
circular-0.4-3/circular/R/axis.circular.R | 211 +++++++++----------
circular-0.4-3/circular/R/bw.circular.R |only
circular-0.4-3/circular/R/circular.R | 10
circular-0.4-3/circular/R/density.circular.R | 97 ++++++--
circular-0.4-3/circular/R/modal.region.R |only
circular-0.4-3/circular/R/onAttach.R |only
circular-0.4-3/circular/R/plot.circular.R | 25 +-
circular-0.4-3/circular/R/quantile.circular.R |only
circular-0.4-3/circular/R/range.circular.R | 12 -
circular-0.4-3/circular/R/sd.circular.R |only
circular-0.4-3/circular/R/totalvariation.R |only
circular-0.4-3/circular/R/var.circular.R | 44 +--
circular-0.4-3/circular/R/vonmises.R | 87 ++++++-
circular-0.4-3/circular/R/wallraff.test.R |only
circular-0.4-3/circular/R/watson.williams.test.R | 159 ++++++++------
circular-0.4-3/circular/R/windrose.R | 57 +++--
circular-0.4-3/circular/R/zzz.R | 4
circular-0.4-3/circular/README | 2
circular-0.4-3/circular/STATUS | 18 +
circular-0.4-3/circular/TODO | 2
circular-0.4-3/circular/data/coope.rda |only
circular-0.4-3/circular/data/fisherB1.rda |only
circular-0.4-3/circular/data/fisherB10.rda |only
circular-0.4-3/circular/data/fisherB10c.rda |binary
circular-0.4-3/circular/data/fisherB11.rda |only
circular-0.4-3/circular/data/fisherB11c.rda |binary
circular-0.4-3/circular/data/fisherB12.rda |only
circular-0.4-3/circular/data/fisherB12c.rda |binary
circular-0.4-3/circular/data/fisherB13.rda |only
circular-0.4-3/circular/data/fisherB13c.rda |binary
circular-0.4-3/circular/data/fisherB1c.rda |binary
circular-0.4-3/circular/data/fisherB2.rda |only
circular-0.4-3/circular/data/fisherB2c.rda |binary
circular-0.4-3/circular/data/fisherB3.rda |only
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circular-0.4-3/circular/data/fisherB6.rda |only
circular-0.4-3/circular/data/fisherB6c.rda |binary
circular-0.4-3/circular/data/fisherB7.rda |only
circular-0.4-3/circular/data/fisherB7c.rda |binary
circular-0.4-3/circular/data/fisherB8.rda |only
circular-0.4-3/circular/data/fisherB8c.rda |binary
circular-0.4-3/circular/data/fisherB9.rda |only
circular-0.4-3/circular/data/fisherB9c.rda |binary
circular-0.4-3/circular/data/ncfrog.rda |only
circular-0.4-3/circular/data/pigeons.rda |binary
circular-0.4-3/circular/data/rao.table.rda |only
circular-0.4-3/circular/data/swallows.rda |binary
circular-0.4-3/circular/data/turtles.rda |binary
circular-0.4-3/circular/data/wind.rda |binary
circular-0.4-3/circular/inst |only
circular-0.4-3/circular/man/A1.Rd | 4
circular-0.4-3/circular/man/A1inv.Rd | 2
circular-0.4-3/circular/man/I.0.Rd | 2
circular-0.4-3/circular/man/I.1.Rd | 2
circular-0.4-3/circular/man/I.p.Rd | 2
circular-0.4-3/circular/man/angular.deviation.Rd |only
circular-0.4-3/circular/man/angular.variance.Rd |only
circular-0.4-3/circular/man/aov.circular.Rd | 2
circular-0.4-3/circular/man/bw.circular.Rd |only
circular-0.4-3/circular/man/circular-package.Rd |only
circular-0.4-3/circular/man/equal.kappa.test.Rd | 2
circular-0.4-3/circular/man/lm.circular.Rd | 4
circular-0.4-3/circular/man/lsfit.circle.Rd | 2
circular-0.4-3/circular/man/mixedvonmises.Rd | 31 +-
circular-0.4-3/circular/man/mle.vonmises.Rd | 2
circular-0.4-3/circular/man/mle.wrappedcauchy.Rd | 2
circular-0.4-3/circular/man/mle.wrappednormal.Rd | 2
circular-0.4-3/circular/man/plot.density.circular.Rd | 2
circular-0.4-3/circular/man/quantile.circular.Rd |only
circular-0.4-3/circular/man/sd.circular.Rd |only
circular-0.4-3/circular/man/standarddeviation.Rd |only
circular-0.4-3/circular/man/var.circular.Rd | 17 -
circular-0.4-3/circular/man/wallraff.test.Rd |only
circular-0.4-3/circular/man/watson.williams.test.Rd |only
circular-0.4-3/circular/man/windrose.Rd | 65 +++--
circular-0.4-3/circular/tests |only
101 files changed, 556 insertions(+), 365 deletions(-)
Title: High-Dimensional Regression and CAR Score Variable Selection
Diff between care versions 1.0.0 dated 2010-08-08 and 1.1.0 dated 2011-07-23
Description: The "care" package implements the CAR regression approach
described in Zuber and Strimmer (2011). CAR scores measure the
correlations between the response and the
Mahalanobis-decorrelated predictors. The squared CAR score is
a natural measure of variable importance and provides a
canonical ordering of variables - see Zuber and Strimmer (2011)
for details. This package provides functions for estimating CAR
scores, for variable selection using CAR scores, and for
estimating corresponding regression coefficients. Both
shrinkage as well as empirical estimators are available.
Author: Verena Zuber and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
care-1.0.0/care/R/care.R |only
care-1.0.0/care/R/fitlm.R |only
care-1.0.0/care/man/care.Rd |only
care-1.0.0/care/man/fitlm.Rd |only
care-1.1.0/care/DESCRIPTION | 25 +++++------
care-1.1.0/care/NEWS | 12 +++++
care-1.1.0/care/R/car.models.R |only
care-1.1.0/care/R/carscore.R | 63 +++++++++++-----------------
care-1.1.0/care/R/predict.slm.R |only
care-1.1.0/care/R/slm.R |only
care-1.1.0/care/data/efron2004.rda |binary
care-1.1.0/care/data/lu2004.rda |binary
care-1.1.0/care/man/car.models.Rd |only
care-1.1.0/care/man/care.package.Rd | 33 ++++++++------
care-1.1.0/care/man/carscore.Rd | 80 ++++++++++++++++++++++++------------
care-1.1.0/care/man/lu2004.Rd | 5 +-
care-1.1.0/care/man/slm.Rd |only
17 files changed, 126 insertions(+), 92 deletions(-)
Title: Tools for caching Sweave computations
Diff between cacheSweave versions 0.5 dated 2011-06-30 and 0.6 dated 2011-07-23
Description: Tools for caching Sweave computations and storing them in
key-value databases
Author: Roger D. Peng
Maintainer: Roger D. Peng
DESCRIPTION | 11 +-
NAMESPACE | 3
R/SweaveCache.R | 183 ++++++++++++++++++++++++++++++++++++++--------
inst/doc/cacheSweave.pdf |binary
man/cacheSweave.Rd | 26 ++++++
tests/reg-tests.R | 2
tests/reg-tests.Rout.save | 17 ++--
7 files changed, 200 insertions(+), 42 deletions(-)
Title: From BIOlogical Sequences to MultiDimensional Scaling
Diff between bios2mds versions 1.0 dated 2011-07-05 and 1.1 dated 2011-07-23
Description: Bios2mds is primarily dedicated to the analysis of
biological sequences by metric MultiDimensional Scaling with
projection of supplementary data. It contains functions for
reading multiple sequence alignment files, calculating distance
matrices, performing metric multidimensional scaling and
visualizing results.
Author: Julien Pele with Jean-Michel Becu, Herve Abdi, and Marie
Chabbert
Maintainer: Marie Chabbert
ChangeLog |only
DESCRIPTION | 13 +++++-----
NAMESPACE | 3 +-
R/dis.R | 2 -
R/extract.cluster.R |only
R/kmeans.run.R | 2 -
R/mat.dis.R | 2 -
R/mmds.2D.plot.R | 9 ++++---
R/mmds.3D.plot.R |only
R/read.fasta.R | 2 -
R/read.msf.R | 2 -
R/write.fasta.r |only
R/write.mmds.pdb.R | 57 +++++++++++++++++++++++-------------------------
inst/doc/bios2mds.pdf |binary
man/bios2mds-package.Rd | 4 +--
man/extract.cluster.Rd |only
man/kmeans.run.Rd | 4 +--
man/mmds.2D.plot.Rd | 19 +++++++++-------
man/mmds.3D.plot.Rd |only
man/mmds.plot.Rd | 4 +--
man/read.fasta.Rd | 2 -
man/read.msf.Rd | 2 -
man/sil.score.Rd | 3 +-
man/write.fasta.Rd |only
24 files changed, 68 insertions(+), 62 deletions(-)
Title: A Package to Recover a Basic Space from Issue Scales
Diff between basicspace versions 0.02 dated 2011-01-26 and 0.03 dated 2011-07-23
Description: Conducts Aldrich-McKelvey and Blackbox Scaling (SVD
generalization with missing values)
Author: Keith Poole
Maintainer: Keith Poole
DESCRIPTION | 8
HISTORY | 11
R/basicspace.R | 72 +-
data/.Rapp.history |only
data/colombia.rda |only
inst/basicspace.Rnw |only
inst/basicspace.bib |only
inst/doc/Sweave.sty | 22
inst/doc/basicspace-aldmck_plot.eps |only
inst/doc/basicspace-aldmck_plot.pdf |only
inst/doc/basicspace-bbt.eps |only
inst/doc/basicspace-bbt.pdf |only
inst/doc/basicspace-eight.eps |only
inst/doc/basicspace-eight.pdf |only
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inst/doc/basicspace-seven.pdf |only
inst/doc/basicspace-six.eps |only
inst/doc/basicspace-six.pdf |only
inst/doc/basicspace.Rnw | 1292 ++++++++++++++++++------------------
inst/doc/basicspace.aux |only
inst/doc/basicspace.bbl |only
inst/doc/basicspace.bib |only
inst/doc/basicspace.log |only
inst/doc/basicspace.out |only
inst/doc/basicspace.pdf |binary
inst/doc/basicspace.synctex.gz |only
inst/doc/basicspace.tex |only
inst/doc/jss.bst |only
inst/doc/jss.cls |only
inst/doc/jss.dbj |only
inst/doc/jss.drv |only
inst/doc/jss.dtx |only
inst/doc/jss.ins |only
inst/doc/jss.pdf |only
inst/doc/jsslogo.jpg |only
man/aldmck.Rd | 18
man/blackbox.Rd | 5
man/blackbox_transpose.Rd | 5
man/colombia.Rd |only
man/plot.AM.Rd | 3
man/plot.aldmck.Rd | 3
man/plot.aldmck_negative.Rd | 4
man/plot.aldmck_positive.Rd | 3
man/plot.cdf.Rd | 3
src/Makevars.win | 4
49 files changed, 780 insertions(+), 673 deletions(-)
Title: bounded memory linear and generalized linear models
Diff between biglm versions 0.7 dated 2009-05-05 and 0.8 dated 2011-07-23
Description: Regression for data too large to fit in memory
Author: Thomas Lumley
Maintainer: Thomas Lumley
DESCRIPTION | 6 +++---
NEWS | 2 ++
R/bigglm.R | 9 +++++----
R/biglm.R | 5 +++--
R/update.biglm.R | 5 +++--
R/update.bigqr.R | 2 +-
man/bigglm.Rd | 8 ++++++--
man/biglm.Rd | 2 +-
8 files changed, 24 insertions(+), 15 deletions(-)
Title: Automatic interpolation package
Diff between automap versions 1.0-10 dated 2011-05-30 and 1.0-11 dated 2011-07-23
Description: This package performs an automatic interpolation by
automatically estimating the variogram and then calling gstat.
Author: Paul Hiemstra
Maintainer: Paul Hiemstra
.hgtags | 1 +
DESCRIPTION | 8 ++++----
HgLog | 27 ++++++++++++++++++++++++++-
R/autofitVariogram.r | 3 +++
man/autofitVariogram.rd | 12 +++++++++++-
5 files changed, 45 insertions(+), 6 deletions(-)
Title: Copy-number analysis of large microarray data sets
Diff between aroma.cn versions 0.7.3 dated 2011-06-25 and 0.8.0 dated 2011-07-23
Description: Package for analysis of copy-number estimates obtained
from various platforms.
Author: Henrik Bengtsson and Pierre Neuvial
Maintainer: Henrik Bengtsson
DESCRIPTION | 10 -
R/PairedPSCBS.BOOT.R | 86 +++++-----
R/PairedPSCBS.EXTS2.R | 28 +--
R/PairedPSCBS.NORM.R | 14 -
R/PairedPSCBS.calibrateC1C2.R | 10 -
R/PairedPSCBS.deShearC1C2.R | 26 +--
R/PruneCNA.PLOT.R | 8
R/callXXorXY.numeric.R | 2
R/findCopyNumberNeutralState.R | 10 -
incl/bootstrap.PairedPSCBS.Rex | 6
incl/calibrateC1C2.PairedPSCBS.Rex | 6
incl/callAllelicBalanceByBAFs.PairedPSCBS.Rex | 6
incl/callCopyNeutralRegions.PairedPSCBS.Rex | 6
incl/deShearC1C2.PairedPSCBS.Rex | 10 -
incl/normalizeBAFsByRegions.PairedPSCBS.Rex | 6
incl/orthogonalizeC1C2.PairedPSCBS.Rex | 6
inst/NEWS | 8
inst/testScripts/system/ortho/calibrateC1C2.PairedPSCBS.Rex | 2
inst/testScripts/system/ortho/deShearC1C2.PairedPSCBS.Rex | 10 -
inst/testScripts/system/ortho/normalizeLoess2D.PairedPSCBS.Rex | 2
inst/testScripts/system/ortho/orthogonalizeC1C2.PairedPSCBS.Rex | 2
inst/testScripts/system/ortho/tcga.Rex | 2
man/calibrateC1C2.PairedPSCBS.Rd | 6
man/callAllelicBalanceByBAFs.PairedPSCBS.Rd | 6
man/callCopyNeutralRegions.PairedPSCBS.Rd | 6
man/callXXorXY.numeric.Rd | 2
man/deShearC1C2.PairedPSCBS.Rd | 10 -
man/findNeutralCopyNumberState.Rd | 6
man/normalizeBAFsByRegions.PairedPSCBS.Rd | 6
man/testAllelicBalanceByBAFs.Rd | 6
30 files changed, 170 insertions(+), 144 deletions(-)
Title: A Gallery of Animations in Statistics and Utilities to Create
Animations
Diff between animation versions 2.0-4 dated 2011-04-28 and 2.0-5 dated 2011-07-23
Description: This package contains various functions for animations in
statistics, covering many areas such as probability theory,
mathematical statistics, multivariate statistics, nonparametric
statistics, sampling survey, linear models, time series,
computational statistics, data mining and machine learning.
These functions might be of help in teaching statistics and
data analysis. Also provided in this package are several
approaches to save animations to various formats, e.g. Flash,
GIF, HTML pages, PDF and videos (saveSWF(), saveGIF(),
saveHTML(), saveLatex(), and saveVideo() respectively). PDF
animations can be inserted into Sweave easily.
Author: Yihui Xie
Maintainer: Yihui Xie
DESCRIPTION | 15 ++++++-------
R/animation-package.R | 4 ---
R/im.convert.R | 12 +++++-----
R/pdftk.R | 2 -
R/price.ani.R | 5 +---
R/qpdf.R | 2 -
R/saveHTML.R | 2 +
R/saveLatex.R | 2 -
R/saveSWF.R | 6 ++---
R/saveVideo.R | 11 ++-------
R/zzz.R | 1
inst/NEWS | 15 +++++++++++++
man/BM.circle.Rd | 3 +-
man/CLELAL09.Rd | 2 -
man/MC.hitormiss.Rd | 8 ++++--
man/MC.samplemean.Rd | 12 ++++++----
man/Rosling.bubbles.Rd | 20 +++++++++--------
man/ani.options.Rd | 28 +++++++++++++-----------
man/ani.pause.Rd | 3 +-
man/ani.record.Rd | 15 ++++++-------
man/animation-package.Rd | 36 ++++++++++++++++++-------------
man/bisection.method.Rd | 7 +++---
man/boot.iid.Rd | 10 +++++---
man/brownian.motion.Rd | 7 +++---
man/buffon.needle.Rd | 21 ++++++++++--------
man/clt.ani.Rd | 14 ++++++------
man/conf.int.Rd | 3 +-
man/cv.ani.Rd | 4 +--
man/cv.nfeaturesLDA.Rd | 10 +++++---
man/ecol.death.sim.Rd | 11 ++++++---
man/flip.coin.Rd | 10 +++++---
man/g.brownian.motion.Rd | 5 ++--
man/grad.desc.Rd | 22 ++++++++++---------
man/kmeans.ani.Rd | 9 ++++---
man/knn.ani.Rd | 17 +++++++-------
man/least.squares.Rd | 16 +++++++------
man/lln.ani.Rd | 7 +++---
man/moving.block.Rd | 54 +++++++++++++++++++++++++----------------------
man/mwar.ani.Rd | 11 ++++++---
man/newton.method.Rd | 28 +++++++++++++-----------
man/pollen.Rd | 2 -
man/price.ani.Rd | 3 +-
man/quincunx.Rd | 12 ++++++----
man/sample.cluster.Rd | 7 +++---
man/sample.ratio.Rd | 25 ++++++++++++---------
man/sample.simple.Rd | 3 +-
man/sample.strat.Rd | 10 +++++---
man/sample.system.Rd | 6 +++--
man/saveGIF.Rd | 10 ++++----
man/saveHTML.Rd | 41 ++++++++++++++++++++---------------
man/saveLatex.Rd | 26 ++++++++++++----------
man/saveSWF.Rd | 7 +++---
man/saveVideo.Rd | 7 ++----
man/sim.qqnorm.Rd | 6 +++--
man/vanke1127.Rd | 20 +++++++----------
man/vi.grid.illusion.Rd | 4 +--
man/vi.lilac.chaser.Rd | 4 +--
57 files changed, 372 insertions(+), 291 deletions(-)
Title: Applies Adaboost.M1 and Bagging
Diff between adabag versions 1.1 dated 2007-10-25 and 2.0 dated 2011-07-23
Description: This package implements Freund and Schapire's Adaboost.M1
algorithm and Breiman's Bagging algorithm using classification
trees as individual classifiers. Once these classifiers have
been trained, they can be used to predict on new data. Also,
cross validation predictions can be done. This version 2.0 adds
a new function "margins" to calculate the margins for these
classifiers. Also a higher flexibility is achieved giving
access to the "rpart.control" argument of "rpart".
Author: Esteban Alfaro Cortes, Matias Gamez Martinez and Noelia Garcia
Rubio
Maintainer: Esteban Alfaro Cortes
adabag-1.1/adabag/README |only
adabag-2.0/adabag/DESCRIPTION | 33 +++--
adabag-2.0/adabag/R/adabag-internal.R |only
adabag-2.0/adabag/R/adaboost.M1.R | 188 +++++++++++++++---------------
adabag-2.0/adabag/R/bagging.R | 108 ++++++++---------
adabag-2.0/adabag/R/bagging.cv.R | 33 ++---
adabag-2.0/adabag/R/boosting.cv.R | 33 ++---
adabag-2.0/adabag/R/margins.R |only
adabag-2.0/adabag/R/predict.bagging.R | 61 +++++----
adabag-2.0/adabag/R/predict.boosting.R | 62 +++++----
adabag-2.0/adabag/man/adabag-package.Rd |only
adabag-2.0/adabag/man/adaboost.M1.Rd | 22 +--
adabag-2.0/adabag/man/bagging.Rd | 22 +--
adabag-2.0/adabag/man/bagging.cv.Rd | 14 --
adabag-2.0/adabag/man/boosting.cv.Rd | 20 +--
adabag-2.0/adabag/man/margins.Rd |only
adabag-2.0/adabag/man/predict.bagging.Rd | 14 +-
adabag-2.0/adabag/man/predict.boosting.Rd | 20 +--
18 files changed, 324 insertions(+), 306 deletions(-)
Title: S3 Infrastructure for Regular and Irregular Time Series (Z's
ordered observations)
Diff between zoo versions 1.7-1 dated 2011-07-18 and 1.7-2 dated 2011-07-23
Description: An S3 class with methods for totally ordered indexed
observations. It is particularly aimed at irregular time series
of numeric vectors/matrices and factors. zoo's key design goals
are independence of a particular index/date/time class and
consistency with ts and base R by providing methods to extend
standard generics.
Author: Achim Zeileis [aut, cre], Gabor Grothendieck [aut], Jeffrey A.
Ryan [aut], Felix Andrews [ctb]
Maintainer: Achim Zeileis
zoo-1.7-1/zoo/R/zzz.R |only
zoo-1.7-2/zoo/DESCRIPTION | 10 +++++-----
zoo-1.7-2/zoo/NAMESPACE | 6 +++++-
zoo-1.7-2/zoo/NEWS | 14 ++++++++++++--
zoo-1.7-2/zoo/R/as.Date.R |only
zoo-1.7-2/zoo/R/yearmon.R | 2 +-
zoo-1.7-2/zoo/inst/doc/zoo-design.pdf |binary
zoo-1.7-2/zoo/inst/doc/zoo-faq.pdf |binary
zoo-1.7-2/zoo/inst/doc/zoo-quickref.pdf |binary
zoo-1.7-2/zoo/inst/doc/zoo-read.pdf |binary
zoo-1.7-2/zoo/inst/doc/zoo.pdf |binary
zoo-1.7-2/zoo/man/yearmon.Rd | 2 ++
zoo-1.7-2/zoo/tests/vignette-zoo-quickref.Rout.save | 9 ++++++++-
zoo-1.7-2/zoo/tests/vignette-zoo.Rout.save | 9 ++++++++-
14 files changed, 41 insertions(+), 11 deletions(-)
Title: Visualization and Imputation of Missing Values
Diff between VIM versions 2.0.2 dated 2011-07-02 and 2.0.3 dated 2011-07-23
Description: This package introduces new tools for the visualization of
missing values in R, which can be used for exploring the data
and the structure of the missing values. Depending on this
structure, they may help to identify the mechanism generating
the missings. A graphical user interface allows an easy
handling of the implemented plot methods.
Author: Matthias Templ, Andreas Alfons, Alexander Kowarik
Maintainer: Matthias Templ
VIM-2.0.2/VIM/.project |only
VIM-2.0.2/VIM/inst/doc/.directory |only
VIM-2.0.2/VIM/inst/doc/fig-aggr.eps |only
VIM-2.0.2/VIM/inst/doc/fig-margin.eps |only
VIM-2.0.2/VIM/inst/doc/fig-matrix.eps |only
VIM-2.0.2/VIM/inst/doc/fig-parallel.eps |only
VIM-2.0.2/VIM/inst/doc/fig-spine.eps |only
VIM-2.0.2/VIM/inst/doc/screenshot1.eps |only
VIM-2.0.2/VIM/inst/doc/screenshot2.eps |only
VIM-2.0.2/VIM/inst/doc/screenshot3.eps |only
VIM-2.0.2/VIM/inst/doc/screenshot4.eps |only
VIM-2.0.2/VIM/inst/doc/screenshot5.eps |only
VIM-2.0.2/VIM/inst/doc/screenshot6.eps |only
VIM-2.0.2/VIM/inst/doc/screenshot7.eps |only
VIM-2.0.2/VIM/inst/doc/screenshot8.eps |only
VIM-2.0.3/VIM/DESCRIPTION | 8 +++---
VIM-2.0.3/VIM/R/aggr.R | 40 +++++++++++++++++++++++++++-----
VIM-2.0.3/VIM/inst/doc/VIM-EU-SILC.pdf |binary
VIM-2.0.3/VIM/inst/doc/fig-aggr.pdf |binary
VIM-2.0.3/VIM/inst/doc/fig-margin.pdf |binary
VIM-2.0.3/VIM/inst/doc/fig-matrix.pdf |binary
VIM-2.0.3/VIM/inst/doc/fig-parallel.pdf |binary
VIM-2.0.3/VIM/inst/doc/fig-spine.pdf |binary
VIM-2.0.3/VIM/inst/doc/screenshot1.pdf |binary
VIM-2.0.3/VIM/inst/doc/screenshot2.pdf |binary
VIM-2.0.3/VIM/inst/doc/screenshot3.pdf |binary
VIM-2.0.3/VIM/inst/doc/screenshot4.pdf |binary
VIM-2.0.3/VIM/inst/doc/screenshot5.pdf |binary
VIM-2.0.3/VIM/inst/doc/screenshot6.pdf |binary
VIM-2.0.3/VIM/inst/doc/screenshot7.pdf |binary
VIM-2.0.3/VIM/inst/doc/screenshot8.pdf |binary
VIM-2.0.3/VIM/man/VIM-package.Rd | 12 +++++----
VIM-2.0.3/VIM/man/aggr.Rd | 15 ++++++++----
VIM-2.0.3/VIM/src/Makevars | 4 +--
34 files changed, 58 insertions(+), 21 deletions(-)
Title: Estimating speciation and extinction rates based on phylogenies
Diff between TreePar versions 1.4 dated 2011-05-10 and 2.1 dated 2011-07-23
Description: For a given species phylogeny on present day data which is
calibrated to calendar-time, a method for estimating maximum
likelihood speciation and extinction processes is provided. The
method allows for non-constant rates. Rates may change (i) as a
function of time, i.e. rate shifts at specified times or mass
extinction events (implemented as bd.shifts.optim) or (ii) as a
function of the number of species, i.e. density-dependence
(implemented as bd.densdep.optim). Note that the method takes
into account the whole phylogeny, in particular it accounts for
the "pull of the present" effect. For a given phylogeny on
higher taxa, but where the number of species is known within
each higher taxa, speciation and extinction rates can be
estimated, under the assumption that these rates remained
constant (implemented as bd.groups.optim).
Author: Tanja Stadler
Maintainer: Tanja Stadler
DESCRIPTION | 25 +++++++++++++++----------
NAMESPACE | 2 +-
R/bd.densdep.optim.R | 1 +
R/bd.groups.conf.R |only
R/bd.groups.optim.R |only
R/bd.shifts.optim.R | 8 +++++---
R/treemrca.R | 12 ++++++------
man/TreePar-package.Rd | 12 +++++++++---
man/bd.densdep.optim.Rd | 7 ++++---
man/bd.groups.optim.Rd |only
man/bd.shifts.optim.Rd | 3 +--
man/treemrca.Rd |only
12 files changed, 42 insertions(+), 28 deletions(-)
Title: Optimal stratification of sampling frames for multipurpose
sampling surveys
Diff between SamplingStrata versions 0.9 dated 2011-04-29 and 0.9-1 dated 2011-07-23
More information about SamplingStrata at CRAN
Description: In the field of sampling design (in particular for
stratified sampling), this package offers an approach for the
determination of the best stratification of a sampling frame,
the one that ensures the minimum sample size under the
condition to satisfy precision constraints in a multivariate
and multidomain case. This approach is based on the use of the
genetic algorithm: each solution (i.e. a particular partition
in strata of the sampling frame) is considered as an individual
in a population; the fitness of all individuals is evaluated by
calculating (using the Bethel-Chromy algorithm) the sampling
size satisfying accuracy constraints on the target estimates.
Functions in the package allows to: (a) analyse the obtained
results of the optimisation step; (b) assign the new strata
labels to the sampling frame; (c) select a sample from the new
frame accordingly to the best allocation. There is also a
function that allows to build the most important input to the
optimisation step, i.e. the "strata" dataframe, containing
information (means and standard errors) regarding the
distributions of the target variables in the different strata,
using the sampling frame or using data from previous rounds of
the same survey.
Author: Giulio Barcaroli
Maintainer: Giulio Barcaroli
DESCRIPTION | 8 +++---
R/aggrStrata.r | 4 +++
R/buildStrataDF.R | 24 ++++++++++++++-----
R/checkInput.R | 4 +--
R/optimizeStrata.R | 45 ++++++++++++++++++++++++++++--------
R/selectSample.R | 4 +--
R/summary.rbga.R | 7 +++--
R/updateStrata.r | 2 +
R/verify.R | 6 ++--
inst/doc/SamplingStrataVignette.Rnw |only
inst/doc/SamplingStrataVignette.pdf |binary
inst/doc/distributionplot.pdf |only
inst/doc/executionplot.pdf |only
inst/doc/fancyvrb.sty |only
inst/doc/natbib.sty |only
inst/doc/sweave.sty |only
man/optimizeStrata.Rd | 20 +++++++++++++---
17 files changed, 92 insertions(+), 32 deletions(-)
Permanent link
Title: SYNCSA - Analysis of functional and phylogenetic patterns in
metacommunities.
Diff between SYNCSA versions 1.0 dated 2011-05-25 and 1.1 dated 2011-07-23
Description: Analysis of metacommunities based on functional traits and
phylogeny of the community components. The functions that are
offered here implement for the R environment methods that have
been available in the SYNCSA application written in C++ (by
Valerio Pillar, available at
http://ecoqua.ecologia.ufrgs.br/ecoqua/SYNCSA.html).
Author: Vanderlei Julio Debastiani
Maintainer: Vanderlei Julio Debastiani
DESCRIPTION | 6 +++---
R/matrix.x.R | 2 +-
man/SYNCSA-package.Rd | 2 +-
3 files changed, 5 insertions(+), 5 deletions(-)
Title: Sequential Parameter Optimization
Diff between SPOT versions 0.1.1375 dated 2011-05-03 and 0.1.1550 dated 2011-07-23
Description: R-Package for Sequential Parameter Optimization Toolbox
Author: T. Bartz-Beielstein with contributions from: J. Ziegenhirt, W.
Konen, O. Flasch, P. Koch, M. Zaefferer
Maintainer: M. Zaefferer
SPOT-0.1.1375/SPOT/man/spotMetaCreateSubProject.Rd |only
SPOT-0.1.1375/SPOT/man/spotMetaGetAssignmentOp.Rd |only
SPOT-0.1.1375/SPOT/man/spotMetaGetMetaVarNames.Rd |only
SPOT-0.1.1375/SPOT/man/spotMetaRead.Rd |only
SPOT-0.1.1550/SPOT/DESCRIPTION | 20
SPOT-0.1.1550/SPOT/R/spot.R | 1424 ++++++-------
SPOT-0.1.1550/SPOT/R/spotGenerateSequentialDesign.R | 9
SPOT-0.1.1550/SPOT/R/spotGenerateSequentialDesignOcba.R | 12
SPOT-0.1.1550/SPOT/R/spotGetOptions.R | 33
SPOT-0.1.1550/SPOT/R/spotHelpFunctions.R | 22
SPOT-0.1.1550/SPOT/R/spotMeta.R | 244 +-
SPOT-0.1.1550/SPOT/R/spotPredictMlegp.R | 9
SPOT-0.1.1550/SPOT/R/spotPredictOptMultiNew.R |only
SPOT-0.1.1550/SPOT/R/spotPredictTgp.R | 12
SPOT-0.1.1550/SPOT/R/spotReportMetaDefault.R | 66
SPOT-0.1.1550/SPOT/R/spotReportSens.R | 1
SPOT-0.1.1550/SPOT/inst/ReleaseNotesSPOT.txt | 12
SPOT-0.1.1550/SPOT/inst/doc/SPOT.pdf |binary
SPOT-0.1.1550/SPOT/inst/doc/SPOTmanual.pdf |binary
SPOT-0.1.1550/SPOT/man/SPOT-package.Rd | 54
SPOT-0.1.1550/SPOT/man/spot.Rd | 64
SPOT-0.1.1550/SPOT/man/spotAlgEs.Rd | 86
SPOT-0.1.1550/SPOT/man/spotAlgEsBanana.Rd | 22
SPOT-0.1.1550/SPOT/man/spotAlgEsBananaGradient.Rd | 20
SPOT-0.1.1550/SPOT/man/spotAlgEsDominantReco.Rd | 26
SPOT-0.1.1550/SPOT/man/spotAlgEsF.Rd | 24
SPOT-0.1.1550/SPOT/man/spotAlgEsGetSuccessRate.Rd | 22
SPOT-0.1.1550/SPOT/man/spotAlgEsHps.Rd | 22
SPOT-0.1.1550/SPOT/man/spotAlgEsIndividualInitial.Rd | 38
SPOT-0.1.1550/SPOT/man/spotAlgEsInitParentPop.Rd | 38
SPOT-0.1.1550/SPOT/man/spotAlgEsInterReco.Rd | 24
SPOT-0.1.1550/SPOT/man/spotAlgEsInterRecoBeSw02.Rd | 22
SPOT-0.1.1550/SPOT/man/spotAlgEsMarriage.Rd | 22
SPOT-0.1.1550/SPOT/man/spotAlgEsMarriageWithReplace.Rd | 22
SPOT-0.1.1550/SPOT/man/spotAlgEsObjMutation.Rd | 16
SPOT-0.1.1550/SPOT/man/spotAlgEsQuickTest.Rd | 20
SPOT-0.1.1550/SPOT/man/spotAlgEsRastrigin.Rd | 20
SPOT-0.1.1550/SPOT/man/spotAlgEsSelection.Rd | 24
SPOT-0.1.1550/SPOT/man/spotAlgEsSphere.Rd | 20
SPOT-0.1.1550/SPOT/man/spotAlgEsSphere1.Rd | 20
SPOT-0.1.1550/SPOT/man/spotAlgEsStratMutation.Rd | 26
SPOT-0.1.1550/SPOT/man/spotAlgEsTermination.Rd | 36
SPOT-0.1.1550/SPOT/man/spotAlgEsWild.Rd | 22
SPOT-0.1.1550/SPOT/man/spotAlgStartAlg....Rd | 30
SPOT-0.1.1550/SPOT/man/spotAlgStartEs.Rd | 38
SPOT-0.1.1550/SPOT/man/spotAlgStartSann.Rd | 42
SPOT-0.1.1550/SPOT/man/spotBraninFunction.Rd | 22
SPOT-0.1.1550/SPOT/man/spotCalcNoise.Rd | 28
SPOT-0.1.1550/SPOT/man/spotCompare.Rd | 26
SPOT-0.1.1550/SPOT/man/spotCreate....Rd | 50
SPOT-0.1.1550/SPOT/man/spotCreateDesignBasicDoe.Rd | 36
SPOT-0.1.1550/SPOT/man/spotCreateDesignDoeR3.Rd | 28
SPOT-0.1.1550/SPOT/man/spotCreateDesignFrF2.Rd | 30
SPOT-0.1.1550/SPOT/man/spotCreateDesignLhd.Rd | 28
SPOT-0.1.1550/SPOT/man/spotCreateDesignLhs.Rd | 36
SPOT-0.1.1550/SPOT/man/spotFuncStartBranin.Rd | 34
SPOT-0.1.1550/SPOT/man/spotFuncStartMexicanHat.Rd | 34
SPOT-0.1.1550/SPOT/man/spotFuncStartRastrigin.Rd | 34
SPOT-0.1.1550/SPOT/man/spotFuncStartRosenbrock.Rd | 34
SPOT-0.1.1550/SPOT/man/spotFuncStartSixHump.Rd | 34
SPOT-0.1.1550/SPOT/man/spotFuncStartSphere.Rd | 34
SPOT-0.1.1550/SPOT/man/spotGenerateSequentialDesign.Rd | 34
SPOT-0.1.1550/SPOT/man/spotGenerateSequentialDesignOcba.Rd | 34
SPOT-0.1.1550/SPOT/man/spotGetAllRepeats.Rd | 18
SPOT-0.1.1550/SPOT/man/spotGetMergedDataMatrixB.Rd | 32
SPOT-0.1.1550/SPOT/man/spotGetOptions.Rd | 201 -
SPOT-0.1.1550/SPOT/man/spotGetRawDataMatrixB.Rd | 34
SPOT-0.1.1550/SPOT/man/spotGetRawResData.Rd | 30
SPOT-0.1.1550/SPOT/man/spotGetRepeats.Rd | 22
SPOT-0.1.1550/SPOT/man/spotGui.Rd | 20
SPOT-0.1.1550/SPOT/man/spotHlpF.norm.Rd | 18
SPOT-0.1.1550/SPOT/man/spotHlpF.norminv.Rd | 20
SPOT-0.1.1550/SPOT/man/spotInstAndLoadPackages.Rd | 36
SPOT-0.1.1550/SPOT/man/spotInterface....Rd | 18
SPOT-0.1.1550/SPOT/man/spotMetaFlattenFbsRow.Rd | 22
SPOT-0.1.1550/SPOT/man/spotMexicanHatFunction.Rd | 22
SPOT-0.1.1550/SPOT/man/spotNormDesign.Rd | 32
SPOT-0.1.1550/SPOT/man/spotOcba.Rd | 28
SPOT-0.1.1550/SPOT/man/spotOcbaTest.Rd | 12
SPOT-0.1.1550/SPOT/man/spotOptim.Rd | 70
SPOT-0.1.1550/SPOT/man/spotOptimInterface.Rd | 42
SPOT-0.1.1550/SPOT/man/spotPlotBst.Rd | 20
SPOT-0.1.1550/SPOT/man/spotPlotPower.Rd | 34
SPOT-0.1.1550/SPOT/man/spotPlotSeverity.Rd | 32
SPOT-0.1.1550/SPOT/man/spotPower.Rd | 32
SPOT-0.1.1550/SPOT/man/spotPredict....Rd | 40
SPOT-0.1.1550/SPOT/man/spotPredictKrig.Rd | 26
SPOT-0.1.1550/SPOT/man/spotPredictLm.Rd | 36
SPOT-0.1.1550/SPOT/man/spotPredictLmOptim.Rd | 32
SPOT-0.1.1550/SPOT/man/spotPredictMlegp.Rd | 28
SPOT-0.1.1550/SPOT/man/spotPredictOptMulti.Rd | 54
SPOT-0.1.1550/SPOT/man/spotPredictOptMultiNew.Rd |only
SPOT-0.1.1550/SPOT/man/spotPredictRandomForest.Rd | 28
SPOT-0.1.1550/SPOT/man/spotPredictRandomForestMlegp.Rd | 28
SPOT-0.1.1550/SPOT/man/spotPredictTgp.Rd | 28
SPOT-0.1.1550/SPOT/man/spotPredictTree.Rd | 28
SPOT-0.1.1550/SPOT/man/spotPrepare.Rd | 34
SPOT-0.1.1550/SPOT/man/spotPrepareData.Rd | 54
SPOT-0.1.1550/SPOT/man/spotPrepareDataAsMatrixC.Rd | 32
SPOT-0.1.1550/SPOT/man/spotPrepareSystem.Rd | 18
SPOT-0.1.1550/SPOT/man/spotPrint.Rd | 22
SPOT-0.1.1550/SPOT/man/spotRastriginFunction.Rd | 24
SPOT-0.1.1550/SPOT/man/spotReadAroi.Rd | 22
SPOT-0.1.1550/SPOT/man/spotReadBstFile.Rd | 28
SPOT-0.1.1550/SPOT/man/spotReadRoi.Rd |only
SPOT-0.1.1550/SPOT/man/spotReportDefault.Rd | 30
SPOT-0.1.1550/SPOT/man/spotReportMetaDefault.Rd | 30
SPOT-0.1.1550/SPOT/man/spotReportSens.Rd | 26
SPOT-0.1.1550/SPOT/man/spotReportSensY.Rd | 22
SPOT-0.1.1550/SPOT/man/spotRosenbrockFunction.Rd | 30
SPOT-0.1.1550/SPOT/man/spotRsm.Rd | 22
SPOT-0.1.1550/SPOT/man/spotSafelyAddSource.Rd | 58
SPOT-0.1.1550/SPOT/man/spotSeqDesignIncreaseMultTwo.Rd | 22
SPOT-0.1.1550/SPOT/man/spotSeqDesignIncreasePlusOne.Rd | 22
SPOT-0.1.1550/SPOT/man/spotSeverity.Rd | 30
SPOT-0.1.1550/SPOT/man/spotSixHumpFunction.Rd | 24
SPOT-0.1.1550/SPOT/man/spotSphereFunction.Rd | 22
SPOT-0.1.1550/SPOT/man/spotStepAutoOpt.Rd | 34
SPOT-0.1.1550/SPOT/man/spotStepInitial.Rd | 44
SPOT-0.1.1550/SPOT/man/spotStepMetaOpt.Rd | 51
SPOT-0.1.1550/SPOT/man/spotStepReport.Rd | 28
SPOT-0.1.1550/SPOT/man/spotStepRunAlg.Rd | 60
SPOT-0.1.1550/SPOT/man/spotStepSequential.Rd | 32
SPOT-0.1.1550/SPOT/man/spotVersion.Rd | 16
SPOT-0.1.1550/SPOT/man/spotWriteAroi.Rd | 26
SPOT-0.1.1550/SPOT/man/spotWriteBest.Rd | 26
SPOT-0.1.1550/SPOT/man/spotWriteDes.Rd | 28
SPOT-0.1.1550/SPOT/man/spotWriteLines.Rd | 24
SPOT-0.1.1550/SPOT/man/writeRoiFileForRepeats.Rd | 22
129 files changed, 2665 insertions(+), 2661 deletions(-)
Title: SPARQL client
Diff between SPARQL versions 1.1 dated 2011-06-22 and 1.2 dated 2011-07-23
Description: Load SPARQL result table from an end-point as a data.frame
Author: Willem Robert van Hage
Maintainer: Willem Robert van Hage
DESCRIPTION | 12 ++++++-----
R/SPARQL.R | 52 +++++++++++++++++++++++++++-----------------------
man/SPARQL-package.Rd | 8 +++----
3 files changed, 40 insertions(+), 32 deletions(-)
Title: Resource Selection (Probability) Functions for Use-Availability
Data
Diff between ResourceSelection versions 0.1-0 dated 2011-06-04 and 0.1-1 dated 2011-07-23
More information about ResourceSelection at CRAN
Description: Resource Selection (Probability) Functions for
use-availability wildlife data as described in Lele and Keim
(2006, Ecology 87, 3021--3028), and Lele (2009, J. Wildlife
Management 73, 122--127).
Author: Subhash R. Lele, Jonah L. Keim, Peter Solymos
Maintainer: Peter Solymos
DESCRIPTION | 8 ++++----
R/hoslem.test.R | 4 ++--
R/kdepairs.default.R | 6 ++----
inst/ChangeLog | 4 ++++
4 files changed, 12 insertions(+), 10 deletions(-)
Permanent link
Title: Rcpp integration for Armadillo templated linear algebra library
Diff between RcppArmadillo versions 0.2.25 dated 2011-06-30 and 0.2.26 dated 2011-07-23
Description: R and Armadillo integration using Rcpp Armadillo is a
templated C++ linear algebra library (by Conrad Sanderson) that
aims towards a good balance between speed and ease of use.
Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions.
Various matrix decompositions are provided through optional
integration with LAPACK and ATLAS libraries.
A delayed evaluation approach is employed (during compile time) to
combine several operations into one, and to reduce (or
eliminate) the need for temporaries. This is accomplished
through recursive templates and template meta-programming.
This library is useful if C++ has been decided as the language of
choice (due to speed and/or integration capabilities), rather
than another language.
The RcppArmadillo package includes the header files from the templated
Armadillo library (currently version 2.0.2). Thus users do not
need to install Armadillo itself in order to use RcppArmadillo.
This Armadillo integration provides a nice illustration of the
capabilities of the Rcpp package for seamless R and C++
integration.
Armadillo is licensed under the GNU LGPL version 3 or later, while
RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is
licenses under the GNU GPL version 2 or later, as is the rest
of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Romain Francois, Dirk Eddelbuettel and Doug Bates
ChangeLog | 6 ++++
DESCRIPTION | 10 +++----
inst/NEWS | 8 ++++++
inst/include/armadillo_bits/arma_version.hpp | 2 -
inst/include/armadillo_bits/fn_as_scalar.hpp | 7 +++--
inst/include/armadillo_bits/glue_times_meat.hpp | 8 +++---
inst/include/armadillo_bits/op_diagmat_meat.hpp | 32 +++++++++++++++++++-----
inst/include/armadillo_bits/op_symmat_meat.hpp | 4 +--
8 files changed, 56 insertions(+), 21 deletions(-)
Title: R Commander Plugin for (industrial) Design of Experiments
Diff between RcmdrPlugin.DoE versions 0.10-2 dated 2011-02-21 and 0.10-4 dated 2011-07-23
More information about RcmdrPlugin.DoE at CRAN
Description: WARNING: This package is currently in beta status! The
package provides a platform-independent GUI for design of
experiments. It is implemented as a plugin to the R-Commander,
which is a more general graphical user interface for statistics
in R based on tcl/tk. DoE functionality can be accessed through
the menu Design that is added to the R-Commander menus.
Author: Ulrike Groemping
Maintainer: Ulrike Groemping
DESCRIPTION | 15 +++-----
NAMESPACE |only
R/Menu.FrF2level.R | 8 +++-
R/Menu.rsm.R | 5 +-
R/Menu.rsmmodel.R | 21 ++++++++---
R/Menu.steepest.R | 10 +++++
R/aaa.R | 2 -
R/menushelp.R | 50 ++--------------------------
inst/NEWS | 16 ++++++++
man/Menu.rsmmodel.Rd | 3 +
man/RcmdrPlugin.DoEUndocumentedFunctions.Rd | 2 -
11 files changed, 65 insertions(+), 67 deletions(-)
Permanent link
Title: Diverse basic statistical and graphical functions accompanying
the french book 'Aide-memoire de statistique appliquee a la
biologie'
Diff between RVAideMemoire versions 0.9.1 dated 2011-03-14 and 0.9-5 dated 2011-07-23
Description: This package contains diverse more or less complicated
functions, written to simplify beginners' life: simplifications
of existing functions, basic but not implemented tests,
easy-to-use tools... All functions are presented in the french
book 'Aide-memoire de statistique appliquee a la biologie',
written by the same author and available on CRAN.
Author: Maxime Hervé
Maintainer: Maxime Hervé
RVAideMemoire-0.9-5/RVAideMemoire/DESCRIPTION | 28
RVAideMemoire-0.9-5/RVAideMemoire/R/adjust.esticon.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/bootstrap.R | 8
RVAideMemoire-0.9-5/RVAideMemoire/R/chisq.exp.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/chisq.gof.multcomp.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/cochran.qtest.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/cor.2comp.R | 32
RVAideMemoire-0.9-5/RVAideMemoire/R/cor.conf.R | 15
RVAideMemoire-0.9-5/RVAideMemoire/R/cor.multcomp.R | 57 -
RVAideMemoire-0.9-5/RVAideMemoire/R/cox.resid.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/cramer.cor.R | 28
RVAideMemoire-0.9-5/RVAideMemoire/R/cv.R | 10
RVAideMemoire-0.9-5/RVAideMemoire/R/fisher.medtest.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/fisher.multcomp.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/ind.contrib.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/least.rect.R | 49
RVAideMemoire-0.9-5/RVAideMemoire/R/logis.fit.R | 7
RVAideMemoire-0.9-5/RVAideMemoire/R/logis.noise.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/lr.multcomp.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/mod.R | 7
RVAideMemoire-0.9-5/RVAideMemoire/R/plot.resid.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/plot.survivors.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/print.adjust.esticon.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/print.bootstrap.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/print.chisq.exp.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/print.chisq.gof.multcomp.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/print.cochran.qtest.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/print.cor.2comp.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/print.cor.conf.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/print.cor.multcomp.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/print.cramer.cor.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/print.fisher.medtest.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/print.fisher.multcomp.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/print.ind.contrib.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/print.least.rect.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/print.lr.multcomp.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/print.plotsurvivors.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/print.prop.multcomp.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/print.reg.intcomp.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/print.reg.slpcomp.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/print.spearman.ci.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/print.surv.multcomp.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/print.wilcox.paired.multcomp.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/print.wilcox.sign.test.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/prop.multcomp.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/psignif.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/reg.ci.R | 13
RVAideMemoire-0.9-5/RVAideMemoire/R/reg.intcomp.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/reg.slpcomp.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/scat.mix.categorical.R | 3
RVAideMemoire-0.9-5/RVAideMemoire/R/se.R | 5
RVAideMemoire-0.9-5/RVAideMemoire/R/seq2.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/spearman.ci.R | 11
RVAideMemoire-0.9-5/RVAideMemoire/R/surv.multcomp.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/wilcox.paired.multcomp.R |only
RVAideMemoire-0.9-5/RVAideMemoire/R/wilcox.sign.test.R |only
RVAideMemoire-0.9-5/RVAideMemoire/RVAideMemoire-Ex.R | 507 ++++++----
RVAideMemoire-0.9-5/RVAideMemoire/man/RVAideMemoire-package.Rd | 17
RVAideMemoire-0.9-5/RVAideMemoire/man/adjust.esticon.Rd |only
RVAideMemoire-0.9-5/RVAideMemoire/man/bootstrap.Rd | 44
RVAideMemoire-0.9-5/RVAideMemoire/man/chisq.exp.Rd |only
RVAideMemoire-0.9-5/RVAideMemoire/man/chisq.gof.multcomp.Rd |only
RVAideMemoire-0.9-5/RVAideMemoire/man/cochran.qtest.Rd |only
RVAideMemoire-0.9-5/RVAideMemoire/man/cor.2comp.Rd | 50
RVAideMemoire-0.9-5/RVAideMemoire/man/cor.conf.Rd | 29
RVAideMemoire-0.9-5/RVAideMemoire/man/cor.multcomp.Rd | 57 -
RVAideMemoire-0.9-5/RVAideMemoire/man/cox.resid.Rd |only
RVAideMemoire-0.9-5/RVAideMemoire/man/cramer.cor.Rd | 34
RVAideMemoire-0.9-5/RVAideMemoire/man/cv.Rd | 28
RVAideMemoire-0.9-5/RVAideMemoire/man/fisher.medtest.Rd |only
RVAideMemoire-0.9-5/RVAideMemoire/man/fisher.multcomp.Rd |only
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RVAideMemoire-0.9-5/RVAideMemoire/man/least.rect.Rd | 52 -
RVAideMemoire-0.9-5/RVAideMemoire/man/logis.fit.Rd | 26
RVAideMemoire-0.9-5/RVAideMemoire/man/logis.noise.Rd |only
RVAideMemoire-0.9-5/RVAideMemoire/man/lr.multcomp.Rd |only
RVAideMemoire-0.9-5/RVAideMemoire/man/mod.Rd | 13
RVAideMemoire-0.9-5/RVAideMemoire/man/plotresid.Rd |only
RVAideMemoire-0.9-5/RVAideMemoire/man/plotsurvivors.Rd |only
RVAideMemoire-0.9-5/RVAideMemoire/man/print.bootstrap.Rd |only
RVAideMemoire-0.9-5/RVAideMemoire/man/prop.multcomp.Rd |only
RVAideMemoire-0.9-5/RVAideMemoire/man/psignif.Rd |only
RVAideMemoire-0.9-5/RVAideMemoire/man/reg.ci.Rd | 30
RVAideMemoire-0.9-5/RVAideMemoire/man/reg.intcomp.Rd |only
RVAideMemoire-0.9-5/RVAideMemoire/man/reg.slpcomp.Rd |only
RVAideMemoire-0.9-5/RVAideMemoire/man/scat.mix.categorical.Rd | 34
RVAideMemoire-0.9-5/RVAideMemoire/man/scat.mix.numeric.Rd | 36
RVAideMemoire-0.9-5/RVAideMemoire/man/se.Rd | 19
RVAideMemoire-0.9-5/RVAideMemoire/man/seq2.Rd |only
RVAideMemoire-0.9-5/RVAideMemoire/man/spearman.ci.Rd | 32
RVAideMemoire-0.9-5/RVAideMemoire/man/surv.multcomp.Rd |only
RVAideMemoire-0.9-5/RVAideMemoire/man/wilcox.paired.multcomp.Rd |only
RVAideMemoire-0.9-5/RVAideMemoire/man/wilcox.sign.test.Rd |only
RVAideMemoire-0.9.1/RVAideMemoire/R/cook.dist.R |only
RVAideMemoire-0.9.1/RVAideMemoire/R/eff.theo.R |only
RVAideMemoire-0.9.1/RVAideMemoire/R/rect.line.R |only
RVAideMemoire-0.9.1/RVAideMemoire/R/reg.dircomp.R |only
RVAideMemoire-0.9.1/RVAideMemoire/R/reg.ordcomp.R |only
RVAideMemoire-0.9.1/RVAideMemoire/R/tend.curve.R |only
RVAideMemoire-0.9.1/RVAideMemoire/R/val.resid.R |only
RVAideMemoire-0.9.1/RVAideMemoire/man/cook.dist.Rd |only
RVAideMemoire-0.9.1/RVAideMemoire/man/eff.theo.Rd |only
RVAideMemoire-0.9.1/RVAideMemoire/man/rect.line.Rd |only
RVAideMemoire-0.9.1/RVAideMemoire/man/reg.dircomp.Rd |only
RVAideMemoire-0.9.1/RVAideMemoire/man/reg.ordcomp.Rd |only
RVAideMemoire-0.9.1/RVAideMemoire/man/tend.curve.Rd |only
RVAideMemoire-0.9.1/RVAideMemoire/man/val.resid.Rd |only
107 files changed, 726 insertions(+), 555 deletions(-)
Title: Graphical User Interface (GUI) for interactive R analysis
sessions
Diff between RPMG versions 2.0-5 dated 2010-11-24 and 2.0-6 dated 2011-07-23
Description: Poor Man's Gui: create interactive R analysis sessions
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees
DESCRIPTION | 6 +++---
R/jpng.R |only
R/jpostscript.R | 22 +++++++++++++++-------
R/pickcolors.R | 11 +++++++++++
R/see.pal.R | 2 +-
man/RPMG-package.Rd | 2 +-
man/jpostscript.Rd | 27 +++++++++++++++++++++++----
7 files changed, 54 insertions(+), 16 deletions(-)
Title: DBI/RJDBC interface to h2 Database
Diff between RH2 versions 0.1-2.3 dated 2011-03-08 and 0.1-2.5 dated 2011-07-23
Description: DBI/RJDBC interface to h2 database. h2 version 1.3.155 is
included.
Author: G. Grothendieck. Author of h2 is Thomas Mueller.
Maintainer: G. Grothendieck
RH2-0.1-2.3/RH2/inst/java/h2-1.2.128.jar |only
RH2-0.1-2.5/RH2/DESCRIPTION | 10 +++++-----
RH2-0.1-2.5/RH2/NEWS | 19 +++++++++++++++++++
RH2-0.1-2.5/RH2/R/class.R | 16 ++++++++++++----
RH2-0.1-2.5/RH2/inst/INSTALL |only
RH2-0.1-2.5/RH2/inst/java/h2-1.3.158.jar |only
RH2-0.1-2.5/RH2/man/H2.Rd | 14 +++++++++++---
7 files changed, 47 insertions(+), 12 deletions(-)
Title: R object-oriented programming with or without references
Diff between R.oo versions 1.8.0 dated 2011-04-04 and 1.8.1 dated 2011-07-23
Description: Methods and classes for object-oriented programming in R
with or without references. Large effort has been made on
making definition of methods as simple as possible with a
minimum of maintenance for package developers. The package has
been developed since 2001 and is now considered very stable.
This is a cross-platform package implemented in pure R that
defines standard S3 classes without any tricks.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
DESCRIPTION | 8 ++++----
R/Exception.R | 8 +++++++-
inst/NEWS | 5 +++++
3 files changed, 16 insertions(+), 5 deletions(-)
Title: Fast and light-weight caching (memoization) of objects
Diff between R.cache versions 0.4.2 dated 2011-05-21 and 0.4.3 dated 2011-07-23
Description: Methods for memoization, that is, caching arbitrary R
objects in persistent memory. Objects can be loaded and saved
stratified on a set of hashing objects.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
DESCRIPTION | 10 ++++------
R/getCachePath.R | 7 ++++---
R/loadCache.R | 4 +++-
R/saveCache.R | 4 +++-
inst/NEWS | 6 ++++++
man/getCachePath.Rd | 5 +++--
man/loadCache.Rd | 4 +++-
man/saveCache.Rd | 4 +++-
8 files changed, 29 insertions(+), 15 deletions(-)
Title: Tools for mapping of quantitative traits of genetically related
individuals and calculating identity coefficients from a
pedigree
Diff between QTLRel versions 0.2-8 dated 2011-06-28 and 0.2-9 dated 2011-07-23
Description: This software provides tools for quantitative trait
mapping in populations such as advanced intercross lines where
relatedness among individuals should not be ignored. It can
estimate background genetic variance components, impute missing
genotypes, simulate genotypes, perform a genome scan for
putative quantitative trait loci (QTL), and plot mapping
results. It also has functions to calculate identity
coefficients from pedigrees, especially suitable for pedigrees
that consist of a large number of generations, or estimate
identity coefficients from genotypic data in certain
circumstances.
Author: Riyan Cheng
Maintainer: Riyan Cheng
ChangeLog | 6 +-
DESCRIPTION | 8 +--
R/ibsFn.R | 2
R/scan.R | 140 ++++++++++++++++++++++++++++++++++++++++++++++++++----
inst |only
man/aicVC.Rd | 2
man/blup.Rd | 3 +
man/cic.Rd | 7 ++
man/estVC.Rd | 2
man/genMatrix.Rd | 6 +-
man/genoImpute.Rd | 9 +++
man/genoProb.Rd | 3 +
man/genoSim.Rd | 7 ++
man/hapSim.Rd | 6 +-
man/ibs.Rd | 2
man/lodci.Rd | 7 ++
man/mAIC.Rd | 12 +++-
man/plots.Rd | 8 +++
man/qqplot.Rd | 2
man/qtlVar.Rd | 7 ++
man/rem.Rd | 2
man/scanOne.Rd | 17 +++++-
22 files changed, 230 insertions(+), 28 deletions(-)
Title: Automates the creation of new statistical analysis projects.
Diff between ProjectTemplate versions 0.3-4 dated 2011-07-04 and 0.3-5 dated 2011-07-23
More information about ProjectTemplate at CRAN
Description: ProjectTemplate provides functions to automatically build
a directory structure for a new R project. Using this
structure, ProjectTemplate automates data loading,
preprocessing, library importing and unit testing.
Author: John Myles White
Maintainer: John Myles White
ProjectTemplate-0.3-4/ProjectTemplate/data_examples |only
ProjectTemplate-0.3-4/ProjectTemplate/ideas/dewar |only
ProjectTemplate-0.3-4/ProjectTemplate/man/ProjectTemplate-package.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/ChangeLog | 11
ProjectTemplate-0.3-5/ProjectTemplate/DESCRIPTION | 29
ProjectTemplate-0.3-5/ProjectTemplate/NAMESPACE | 17
ProjectTemplate-0.3-5/ProjectTemplate/R/arff.reader.R | 13
ProjectTemplate-0.3-5/ProjectTemplate/R/cache.R | 24
ProjectTemplate-0.3-5/ProjectTemplate/R/cache.name.R | 13
ProjectTemplate-0.3-5/ProjectTemplate/R/cache.project.R |only
ProjectTemplate-0.3-5/ProjectTemplate/R/clean.variable.name.R | 16
ProjectTemplate-0.3-5/ProjectTemplate/R/create.project.R | 41 +
ProjectTemplate-0.3-5/ProjectTemplate/R/csv.reader.R | 24
ProjectTemplate-0.3-5/ProjectTemplate/R/db.reader.R | 18
ProjectTemplate-0.3-5/ProjectTemplate/R/dbf.reader.R | 15
ProjectTemplate-0.3-5/ProjectTemplate/R/epiinfo.reader.R | 15
ProjectTemplate-0.3-5/ProjectTemplate/R/extensions.dispatch.table.R | 10
ProjectTemplate-0.3-5/ProjectTemplate/R/file.reader.R | 30
ProjectTemplate-0.3-5/ProjectTemplate/R/help.R |only
ProjectTemplate-0.3-5/ProjectTemplate/R/load.project.R | 49 +
ProjectTemplate-0.3-5/ProjectTemplate/R/mp3.reader.R |only
ProjectTemplate-0.3-5/ProjectTemplate/R/mtp.reader.R | 15
ProjectTemplate-0.3-5/ProjectTemplate/R/octave.reader.R | 14
ProjectTemplate-0.3-5/ProjectTemplate/R/ppm.reader.R |only
ProjectTemplate-0.3-5/ProjectTemplate/R/r.reader.R | 16
ProjectTemplate-0.3-5/ProjectTemplate/R/rdata.reader.R | 16
ProjectTemplate-0.3-5/ProjectTemplate/R/reload.project.R | 16
ProjectTemplate-0.3-5/ProjectTemplate/R/run.project.R | 15
ProjectTemplate-0.3-5/ProjectTemplate/R/show.project.R | 20
ProjectTemplate-0.3-5/ProjectTemplate/R/spss.reader.R | 16
ProjectTemplate-0.3-5/ProjectTemplate/R/sql.reader.R | 63 +
ProjectTemplate-0.3-5/ProjectTemplate/R/stata.reader.R | 14
ProjectTemplate-0.3-5/ProjectTemplate/R/stub.tests.R | 16
ProjectTemplate-0.3-5/ProjectTemplate/R/systat.reader.R | 14
ProjectTemplate-0.3-5/ProjectTemplate/R/test.project.R | 18
ProjectTemplate-0.3-5/ProjectTemplate/R/translate.dcf.R | 15
ProjectTemplate-0.3-5/ProjectTemplate/R/tsv.reader.R | 24
ProjectTemplate-0.3-5/ProjectTemplate/R/url.reader.R | 32
ProjectTemplate-0.3-5/ProjectTemplate/R/wsv.reader.R | 24
ProjectTemplate-0.3-5/ProjectTemplate/R/xls.reader.R | 16
ProjectTemplate-0.3-5/ProjectTemplate/R/xlsx.reader.R | 16
ProjectTemplate-0.3-5/ProjectTemplate/R/xport.reader.R | 14
ProjectTemplate-0.3-5/ProjectTemplate/TODO.markdown | 32
ProjectTemplate-0.3-5/ProjectTemplate/build_script.R |only
ProjectTemplate-0.3-5/ProjectTemplate/build_script.sh | 1
ProjectTemplate-0.3-5/ProjectTemplate/ideas/Allen |only
ProjectTemplate-0.3-5/ProjectTemplate/ideas/NOTES | 366 ----------
ProjectTemplate-0.3-5/ProjectTemplate/inst/defaults/full/config/global.dcf | 2
ProjectTemplate-0.3-5/ProjectTemplate/inst/defaults/minimal/config/global.dcf | 2
ProjectTemplate-0.3-5/ProjectTemplate/inst/example_data/example_35.ppm |only
ProjectTemplate-0.3-5/ProjectTemplate/inst/example_data/example_36.dbf |only
ProjectTemplate-0.3-5/ProjectTemplate/inst/example_data/example_37.sav |only
ProjectTemplate-0.3-5/ProjectTemplate/inst/example_data/example_38.sav |only
ProjectTemplate-0.3-5/ProjectTemplate/inst/example_data/example_39.dta |only
ProjectTemplate-0.3-5/ProjectTemplate/inst/example_data/example_40.dta |only
ProjectTemplate-0.3-5/ProjectTemplate/inst/example_data/example_41.xport |only
ProjectTemplate-0.3-5/ProjectTemplate/inst/example_data/example_42.xpt |only
ProjectTemplate-0.3-5/ProjectTemplate/man/ProjectTemplate.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/arff.reader.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/cache.Rd | 39 -
ProjectTemplate-0.3-5/ProjectTemplate/man/cache.name.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/cache.project.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/clean.variable.name.Rd | 32
ProjectTemplate-0.3-5/ProjectTemplate/man/create.project.Rd | 51 -
ProjectTemplate-0.3-5/ProjectTemplate/man/csv.reader.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/db.reader.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/dbf.reader.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/epiinfo.reader.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/extensions.dispatch.table.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/file.reader.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/load.project.Rd | 27
ProjectTemplate-0.3-5/ProjectTemplate/man/mp3.reader.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/mtp.reader.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/octave.reader.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/ppm.reader.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/r.reader.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/rdata.reader.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/reload.project.Rd | 28
ProjectTemplate-0.3-5/ProjectTemplate/man/run.project.Rd | 30
ProjectTemplate-0.3-5/ProjectTemplate/man/show.project.Rd | 33
ProjectTemplate-0.3-5/ProjectTemplate/man/spss.reader.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/sql.reader.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/stata.reader.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/stub.tests.Rd | 32
ProjectTemplate-0.3-5/ProjectTemplate/man/systat.reader.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/test.project.Rd | 33
ProjectTemplate-0.3-5/ProjectTemplate/man/translate.dcf.Rd | 32
ProjectTemplate-0.3-5/ProjectTemplate/man/tsv.reader.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/url.reader.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/wsv.reader.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/xls.reader.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/xlsx.reader.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/man/xport.reader.Rd |only
ProjectTemplate-0.3-5/ProjectTemplate/tests/3.R | 271 ++++++-
ProjectTemplate-0.3-5/ProjectTemplate/website/TODO.html | 36
ProjectTemplate-0.3-5/ProjectTemplate/website/TODO.markdown | 28
ProjectTemplate-0.3-5/ProjectTemplate/website/configuring.html | 2
ProjectTemplate-0.3-5/ProjectTemplate/website/configuring.markdown | 2
ProjectTemplate-0.3-5/ProjectTemplate/website/file_formats.html | 5
ProjectTemplate-0.3-5/ProjectTemplate/website/file_formats.markdown | 5
ProjectTemplate-0.3-5/ProjectTemplate/website/index.html | 1
ProjectTemplate-0.3-5/ProjectTemplate/website/index.markdown | 1
ProjectTemplate-0.3-5/ProjectTemplate/website/mastering.html |only
ProjectTemplate-0.3-5/ProjectTemplate/website/mastering.markdown |only
ProjectTemplate-0.3-5/ProjectTemplate/website/updating.html | 8
ProjectTemplate-0.3-5/ProjectTemplate/website/updating.markdown | 6
106 files changed, 1185 insertions(+), 639 deletions(-)
Permanent link
Title: Estimation of the peak-to-trough ratio of a seasonal variation
component
Diff between Peak2Trough versions 1.0 dated 2011-04-28 and 1.1 dated 2011-07-23
Description: Estimation of the peak-to-trough ratio of a seasonal
variation component.
Author: Anette Luther Christensen
Maintainer: Anette Luther Christensen
CHANGES |only
DESCRIPTION | 10 ++--
R/rr1.R | 62 +++++++++++++++++++++++----
R/rr2.R | 84 ++++++++++++++++++++++++++++++-------
R/rr3.R | 100 ++++++++++++++++++++++++++++++++++++---------
man/Peak2Trough-package.Rd | 4 -
man/rr1.Rd | 23 +++++++---
man/rr2.Rd | 29 +++++++++----
man/rr3.Rd | 39 ++++++++++++-----
9 files changed, 274 insertions(+), 77 deletions(-)
Title: Analysis of Parent-Specific DNA Copy Numbers
Diff between PSCBS versions 0.11.3 dated 2011-07-07 and 0.11.7 dated 2011-07-23
Description: Segments allele-specific DNA copy number data to detect
regions with abnormal copy number within each parental
chromosome
Author: A.B. Olshen, H. Bengtsson, P. Neuvial, P.T. Spellman, R.A.
Olshen, V.E. Seshan
Maintainer: Henrik Bengtsson
DESCRIPTION | 8 +--
R/999.package.R | 6 --
R/PairedPSCBS.BOOT.R | 6 ++
R/PairedPSCBS.PLOT.R | 24 ++++++++--
R/PairedPSCBS.callAB.R | 6 ++
R/PairedPSCBS.callLOH.R | 6 +-
R/PairedPSCBS.estimateDeltaLOH.R | 50 +++++++++++++--------
R/segmentByPairedPSCBS.R | 37 +++++++++++++--
incl/segmentByPairedPSCBS,allLOH.Rex |only
inst/NEWS | 39 ++++++++++++++++
man/PSCBS-package.Rd | 4 -
man/estimateDeltaLOH.PairedPSCBS.Rd | 4 +
man/estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS.Rd | 4 +
man/segmentByPairedPSCBS.Rd | 18 +++++--
14 files changed, 167 insertions(+), 45 deletions(-)
Title: MultiPhen, a package for the genetic association testing of
multiple phenotypes
Diff between MultiPhen versions 0.1 dated 2011-07-06 and 0.2 dated 2011-07-23
Description: Performs genetic association tests between SNPs
(one-at-a-time) and multiple phenotypes (separately or in joint
model)
Author: Lachlan Coin, Paul O'Reilly, Yotsawat Pompyen, Clive Hoggart
and Federico Calboli
Maintainer: Federico Calboli
MultiPhen-0.1/MultiPhen/data/snp.rda |only
MultiPhen-0.1/MultiPhen/man/snp.Rd |only
MultiPhen-0.2/MultiPhen/DESCRIPTION | 18
MultiPhen-0.2/MultiPhen/R/MultiPhen-internal.R | 499 +++++++++++++++++------
MultiPhen-0.2/MultiPhen/R/mPhen.R | 240 -----------
MultiPhen-0.2/MultiPhen/data/pheno.rda |binary
MultiPhen-0.2/MultiPhen/data/snps.imputed.rda |only
MultiPhen-0.2/MultiPhen/data/snps.rda |only
MultiPhen-0.2/MultiPhen/man/MultiPhen-package.Rd | 24 -
MultiPhen-0.2/MultiPhen/man/mPhen.Rd | 88 ++--
MultiPhen-0.2/MultiPhen/man/pheno.Rd | 18
MultiPhen-0.2/MultiPhen/man/snps.Rd |only
MultiPhen-0.2/MultiPhen/man/snps.imputed.Rd |only
13 files changed, 473 insertions(+), 414 deletions(-)
Title: Detect gene-gene interactions using multifactor dimensionality
reduction
Diff between MDR versions 1.0 dated 2010-12-13 and 1.1 dated 2011-07-23
Description: Performs multifactor dimensionality reduction (MDR) to
detect potential gene-gene interactions in case-control
studies.
Author: Stacey Winham
Maintainer: Stacey Winham
DESCRIPTION | 8 ++--
R/mdr.r | 100 ++++++++++++++++++++++++++++++++++++++++-------------
man/MDR-package.Rd | 6 ++-
man/permute.mdr.Rd | 13 +++++-
4 files changed, 95 insertions(+), 32 deletions(-)
Title: Markov chain Monte Carlo (MCMC) Package
Diff between MCMCpack versions 1.0-11 dated 2011-04-26 and 1.1-1 dated 2011-07-23
Description: This package contains functions to perform Bayesian
inference using posterior simulation for a number of
statistical models. Most simulation is done in compiled C++
written in the Scythe Statistical Library Version 1.0.2. All
models return coda mcmc objects that can then be summarized
using the coda package. MCMCpack also contains some useful
utility functions, including some additional density functions
and pseudo-random number generators for statistical
distributions, a general purpose Metropolis sampling algorithm,
and tools for visualization.
Author: Andrew D. Martin, Kevin M. Quinn, and Jong Hee Park
Maintainer: Andrew D. Martin
DESCRIPTION | 8 ++++----
NAMESPACE | 4 ++++
R/MCMChierBetaBinom.R |only
R/MCMChlogit.R |only
R/MCMChpoisson.R |only
R/MCMChregress.R |only
R/hidden-hmodels.R |only
data/PErisk.rda |binary
data/SupremeCourt.rda |binary
man/MCMChlogit.Rd |only
man/MCMChpoisson.Rd |only
man/MCMChregress.Rd |only
src/MCMChierBetaBinom.cc |only
src/MCMChlogit.cc |only
src/MCMChpoisson.cc |only
src/MCMChregress.cc |only
16 files changed, 8 insertions(+), 4 deletions(-)
Title: Hybrid Markov chain Monte Carlo using Gaussian Processes
Diff between MCMChybridGP versions 3.1 dated 2010-09-30 and 4.2 dated 2011-07-23
Description: Hybrid Markov chain Monte Carlo (MCMC) to simulate from a
multimodal target distribution. A Gaussian process
approximation makes this possible when derivatives are unknown.
The Package serves to minimize the number of function
evaluations in Bayesian calibration of computer models using
parallel tempering. It allows replacement of the true target
distribution in high temperature chains, or complete
replacement of the target. Methods used are described in,
"Efficient MCMC schemes for Bayesian calibration of computer
models", Fielding, Mark, Nott, David J. and Liong Shie-Yui,
Technometrics (2010). The authors gratefully acknowledge the
support & contributions of the Singapore-Delft Water Alliance
(SDWA). The research presented in this work was carried out as
part of the SDWA's Multi-Objective Multi-Reservoir Management
research programme (R-264-001-272).
Author: Mark J. Fielding
Maintainer: Mark J. Fielding
DESCRIPTION | 10 +++++-----
R/MCMChybridGP-internal.R | 11 ++++++++---
R/hybrid.sample.R | 2 +-
3 files changed, 14 insertions(+), 9 deletions(-)
Title: Software for Bayesian Inference
Diff between LaplacesDemon versions 11.07.05 dated 2011-07-05 and 11.07.15 dated 2011-07-23
Description: Laplace's Demon is software for Bayesian inference.
Author: Byron Hall
Maintainer: Byron Hall
CHANGELOG | 18
DESCRIPTION | 8
R/BayesFactor.R | 4
R/CenterScale.R | 4
R/Consort.R | 310 -
R/Cov2Cor.R | 2
R/ESS.R | 4
R/Geweke.Diagnostic.R | 16
R/HPD.R | 2
R/LML.R | 6
R/LaplaceApproximation.R | 43
R/LaplacesDemon.R | 121
R/Mode.R | 4
R/caterpillar.plot.R | 51
R/distributions.R | 245 -
R/interval.R | 9
R/joint.density.plot.R | 2
R/logit.R | 6
R/parm.names.R | 14
R/plot.demonoid.R | 36
R/plot.demonoid.ppc.R | 6
R/plot.laplace.R | 19
R/plot.laplace.ppc.R | 2
R/predict.demonoid.R | 6
R/predict.laplace.R | 6
R/summary.demonoid.ppc.R | 117
R/summary.laplace.ppc.R | 173
inst/CITATION | 2
inst/doc/BayesianInference.pdf |binary
inst/doc/Examples.Stex | 576 +-
inst/doc/Examples.pdf | 8736 +++++++++++++++++++++-------------------
inst/doc/LaplacesDemon.Stex | 12
inst/doc/LaplacesDemon.pdf |binary
inst/doc/References.bib | 2
man/BayesFactor.Rd | 6
man/LaplaceApproximation.Rd | 2
man/LaplacesDemon.Rd | 2
man/caterpillar.plot.Rd | 17
man/dist.Multivariate.Normal.Rd | 8
man/plot.demonoid.Rd | 5
man/plot.laplace.Rd | 5
man/summary.demonoid.ppc.Rd | 42
man/summary.laplace.ppc.Rd | 44
43 files changed, 5856 insertions(+), 4837 deletions(-)
Title: A suite of functions to back-fit fixed effects and forward-fit
random effects, as well as other miscellaneous functions.
Diff between LMERConvenienceFunctions versions 1.6.2 dated 2011-06-29 and 1.6.3 dated 2011-07-23
More information about LMERConvenienceFunctions at CRAN
Description: Functions to back-fit fixed effects (on F or t values and,
potentially, log-likelihood ratio testing) and to forward-fit
random effects (using log-likelihood ratio testing). Note that
the back- and forward-fitting of generalized linear
mixed-effects regression (\code{glmer}s) models is not yet
supported. The package also includes a function to compute
ANOVAs with upper- and lower-bound p-values (anti-conservative
and conservative, respectively), a function to graph model
criticism plots, functions to trim data on model residuals or
on a response variable (per subject), a function to perform
posthoc analyses, a function to generate (dynamic) 3d plots of
(i) predicted values of an LMER model for interactions between
two numeric variables,(ii) the raw data as a function of two
numeric variable, and (iii) kernel density estimates
(densities) of two numeric variables.
Author: Antoine Tremblay
Maintainer: Antoine Tremblay, IWK Health Center
DESCRIPTION | 15 +--
NEWS | 16 +++
R/plotDensity3d.fnc.R |only
R/plotLMER3d.fnc.R | 118 +++++++++++++++++++-----
R/plotRaw3d.fnc.R |only
data |only
man/LMERConvenienceFunctions-package.Rd | 155 +-------------------------------
man/erpFz.Rd |only
man/mcp.fnc.Rd | 1
man/plotDensity3d.fnc.Rd |only
man/plotLMER3d.fnc.Rd | 27 +++--
man/plotRaw3d.fnc.Rd |only
12 files changed, 144 insertions(+), 188 deletions(-)
Permanent link
Title: Fractional Factorial designs with 2-level factors
Diff between FrF2 versions 1.2-2 dated 2011-02-07 and 1.2-4 dated 2011-07-23
Description: This package creates regular and non-regular Fractional
Factorial designs. Furthermore, analysis tools for Fractional
Factorial designs with 2-level factors are offered (main
effects and interaction plots for all factors simultaneously,
cube plot for looking at the simultaneous effects of three
factors, full or half normal plot, alias structure in a more
readable format than with the built-in function alias). The
package is currently subject to intensive development. While
much of the intended functionality is already available, some
changes and improvements are still to be expected. Suggestions
are welcome.
Author: Ulrike Groemping
Maintainer: Ulrike Groemping
DESCRIPTION | 8 +--
NAMESPACE | 4 -
R/CIG.catlg.R |only
R/DanielPlot.R | 56 +++++++++++++++++++--
R/FrF2.R | 1
R/add.center.R | 2
R/estimable2fis.R | 10 +++
R/utilperm.R | 4 -
inst/NEWS | 21 ++++++++
man/CIG.catlg.Rd |only
man/DanielPlot.Rd | 28 +++++++++-
man/FrF2.Rd | 4 +
man/add.center.Rd | 4 +
tests/generators.summary.test.R | 5 -
tests/generators.summary.test.Rout.save | 83 +++++++++++---------------------
15 files changed, 150 insertions(+), 80 deletions(-)
Title: Wrapper package for design of experiments functionality
Diff between DoE.wrapper versions 0.8-2 dated 2011-01-31 and 0.8-3 dated 2011-07-23
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
DESCRIPTION | 10 ++---
NAMESPACE | 2 -
R/code.design.R | 25 +++++++++++++
inst/NEWS | 103 ++++++++++++++++++++++++++++--------------------------
man/rsmformula.Rd | 19 ++++++---
5 files changed, 98 insertions(+), 61 deletions(-)
Title: Bayesian Association Model for Genomic Data with Missing
Covariates
Diff between BAMD versions 3.4 dated 2011-02-19 and 3.5 dated 2011-07-23
Description: This package fits a linear mixed model where the
covariates for the random effects have missing values.
Author: Gopal, V. and Li, Z. and Casella, G.
Maintainer: Gopal, V.
DESCRIPTION | 9 +++++----
NAMESPACE | 1 +
R/variableSelector.R | 4 ++--
R/variableSelectorBatchP.R |only
R/variableSelectorInteractP.R |only
README | 28 +++++++++++++++++++++++++++-
demo |only
inst |only
man/BAMD-package.Rd | 4 ++--
man/variableSelectorBatchP.Rd |only
man/variableSelectorInteractP.Rd |only
src/computeLoop.c | 6 +++---
src/gibbs.c | 2 +-
13 files changed, 41 insertions(+), 13 deletions(-)
Title: Full factorials, orthogonal arrays and base utilities for DoE
packages
Diff between DoE.base versions 0.21-1 dated 2011-04-27 and 0.21-2 dated 2011-07-22
Description: This package creates full factorial experimental designs
and designs based on orthogonal arrays for (industrial)
experiments. Additionally, it provides some utility functions
used also by other DoE packages.
Author: Ulrike Groemping, with contributions by Boyko Amarov
Maintainer: Ulrike Groemping
DESCRIPTION | 10 +++++-----
R/utilities.R | 6 +++++-
inst/NEWS | 5 +++++
3 files changed, 15 insertions(+), 6 deletions(-)
Title: Tools for analysing forensic genetic DNA data
Diff between DNAtools versions 0.1-2 dated 2011-06-25 and 0.1-3 dated 2011-07-22
Description: Functions for making a database comparison exercise where
each DNA profile is compared to any other in the database. Also
has functions for optimising parameters of the population
genetic model and for simulating DNA databases.
Author: Torben Tvedebrink and James Curran
Maintainer: Torben Tvedebrink
DESCRIPTION | 8 ++++----
R/dbcompare.R | 3 ++-
src/compare.cpp | 3 ++-
3 files changed, 8 insertions(+), 6 deletions(-)
Title: Data Analysis And Graphics data and functions
Diff between DAAG versions 1.06 dated 2011-03-09 and 1.07 dated 2011-07-22
Description: various data sets used in examples and exercises in the
book Maindonald, J.H. and Braun, W.J. (2003, 2007, 2010) "Data
Analysis and Graphics Using R".
Author: John Maindonald and W. John Braun
Maintainer: W. John Braun
DAAG-1.06/DAAG/R/leaftemp.all.R |only
DAAG-1.06/DAAG/data/ACF1.R |only
DAAG-1.06/DAAG/data/Cars93.summary.R |only
DAAG-1.06/DAAG/data/DAAGxdb.R |only
DAAG-1.06/DAAG/data/Lottario.R |only
DAAG-1.06/DAAG/data/Manitoba.lakes.R |only
DAAG-1.06/DAAG/data/SP500W90.R |only
DAAG-1.06/DAAG/data/SP500close.R |only
DAAG-1.06/DAAG/data/ais.R |only
DAAG-1.06/DAAG/data/allbacks.R |only
DAAG-1.06/DAAG/data/anesthetic.R |only
DAAG-1.06/DAAG/data/ant111b.R |only
DAAG-1.06/DAAG/data/antigua.R |only
DAAG-1.06/DAAG/data/appletaste.R |only
DAAG-1.06/DAAG/data/austpop.R |only
DAAG-1.06/DAAG/data/biomass.R |only
DAAG-1.06/DAAG/data/bomsoi.R |only
DAAG-1.06/DAAG/data/bomsoi2001.R |only
DAAG-1.06/DAAG/data/bostonc.R |only
DAAG-1.06/DAAG/data/carprice.R |only
DAAG-1.06/DAAG/data/cerealsugar.R |only
DAAG-1.06/DAAG/data/cfseal.R |only
DAAG-1.06/DAAG/data/cities.R |only
DAAG-1.06/DAAG/data/codling.R |only
DAAG-1.06/DAAG/data/cottonworkers.R |only
DAAG-1.06/DAAG/data/cuckoohosts.R |only
DAAG-1.06/DAAG/data/cuckoos.R |only
DAAG-1.06/DAAG/data/dengue.R |only
DAAG-1.06/DAAG/data/dewpoint.R |only
DAAG-1.06/DAAG/data/droughts.R |only
DAAG-1.06/DAAG/data/dumpdata.R |only
DAAG-1.06/DAAG/data/elastic1.R |only
DAAG-1.06/DAAG/data/elastic2.R |only
DAAG-1.06/DAAG/data/elasticband.R |only
DAAG-1.06/DAAG/data/fossilfuel.R |only
DAAG-1.06/DAAG/data/fossum.R |only
DAAG-1.06/DAAG/data/frogs.R |only
DAAG-1.06/DAAG/data/frostedflakes.R |only
DAAG-1.06/DAAG/data/fruitohms.R |only
DAAG-1.06/DAAG/data/geophones.R |only
DAAG-1.06/DAAG/data/head.injury.R |only
DAAG-1.06/DAAG/data/headInjury.R |only
DAAG-1.06/DAAG/data/hills.R |only
DAAG-1.06/DAAG/data/hills2000.R |only
DAAG-1.06/DAAG/data/houseprices.R |only
DAAG-1.06/DAAG/data/humanpower1.R |only
DAAG-1.06/DAAG/data/humanpower2.R |only
DAAG-1.06/DAAG/data/ironslag.R |only
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DAAG-1.06/DAAG/data/kiwishade.R |only
DAAG-1.06/DAAG/data/leafshape.R |only
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DAAG-1.06/DAAG/data/leaftemp.all.R |only
DAAG-1.06/DAAG/data/litters.R |only
DAAG-1.06/DAAG/data/lung.R |only
DAAG-1.06/DAAG/data/medExpenses.R |only
DAAG-1.06/DAAG/data/mifem.R |only
DAAG-1.06/DAAG/data/mignonette.R |only
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DAAG-1.06/DAAG/data/nsw74psid3.R |only
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DAAG-1.06/DAAG/data/sorption.R |only
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DAAG-1.06/DAAG/data/tinting.R |only
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DAAG-1.06/DAAG/data/vince111b.R |only
DAAG-1.06/DAAG/data/vlt.R |only
DAAG-1.06/DAAG/data/wages1833.R |only
DAAG-1.06/DAAG/data/whoops.R |only
DAAG-1.06/DAAG/data/zzDAAGxdb.R |only
DAAG-1.07/DAAG/DESCRIPTION | 6 +++---
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DAAG-1.07/DAAG/data/Cars93.summary.rda |only
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DAAG-1.07/DAAG/data/spam7.rda |only
DAAG-1.07/DAAG/data/stVincent.rda |only
DAAG-1.07/DAAG/data/sugar.rda |only
DAAG-1.07/DAAG/data/tinting.rda |only
DAAG-1.07/DAAG/data/toycars.rda |only
DAAG-1.07/DAAG/data/two65.rda |only
DAAG-1.07/DAAG/data/vince111b.rda |only
DAAG-1.07/DAAG/data/vlt.rda |only
DAAG-1.07/DAAG/data/wages1833.rda |only
DAAG-1.07/DAAG/data/whoops.rda |only
DAAG-1.07/DAAG/data/zzDAAGxdb.rda |only
194 files changed, 3 insertions(+), 3 deletions(-)
Title: Distributed Lag Non-linear Models
Diff between dlnm versions 1.4.0 dated 2011-06-27 and 1.4.1 dated 2011-07-21
Description: The package dlnm contains functions to specify basis and
cross-basis matrices in order to run distributed lag models and
their non-linear extension, then to predict and graph the
results for a fitted model.
Author: Antonio Gasparrini and Ben Armstrong
Maintainer: Antonio Gasparrini
DESCRIPTION | 8 ++++----
inst/CITATION | 37 +++++++++++++++++++++++--------------
inst/ChangeLog | 10 ++++++++++
inst/doc/biblioVignette.bib | 11 +++++++++++
inst/doc/dlnmOverview.Rnw | 14 +++++++-------
inst/doc/dlnmOverview.pdf |binary
man/crossbasis.Rd | 2 ++
man/crosspred.Rd | 2 ++
man/dlnm-internal.Rd | 2 ++
man/dlnm-package.Rd | 2 ++
man/plot.crosspred.Rd | 2 ++
11 files changed, 65 insertions(+), 25 deletions(-)
Title: TK Rplot
Diff between tkrplot versions 0.0-21 dated 2011-07-19 and 0.0-22 dated 2011-07-21
Description: simple mechanism for placing R graphics in a Tk widget
Author: Luke Tierney
Maintainer: Luke Tierney
DESCRIPTION | 6 +++---
R/tkrplot.R | 3 ++-
2 files changed, 5 insertions(+), 4 deletions(-)
Title: Simple Network of Workstations
Diff between snow versions 0.3-5 dated 2011-05-16 and 0.3-6 dated 2011-07-20
Description: Support for simple parallel computing in R.
Author: Luke Tierney, A. J. Rossini, Na Li, H. Sevcikova
Maintainer: Luke Tierney
snow-0.3-5/snow/INDEX |only
snow-0.3-6/snow/DESCRIPTION | 6 +-
snow-0.3-6/snow/NAMESPACE |only
snow-0.3-6/snow/R/snow.R | 88 +++++++++++++++++------------------
snow-0.3-6/snow/R/timing.R | 2
snow-0.3-6/snow/man/snow-internal.Rd | 2
6 files changed, 48 insertions(+), 50 deletions(-)
Title: Radiometric and topographic correction of satellite imagery
Diff between landsat versions 1.0.3 dated 2011-04-30 and 1.0.4 dated 2011-07-19
Description: Processing of Landsat or other multispectral satellite
imagery. Includes relative normalization, image-based
radiometric correction, and topographic correction options.
Author: Sarah Goslee
Maintainer: Sarah Goslee
DESCRIPTION | 8 ++++----
R/topocorr.R | 24 +++++++++++++++++++++---
inst |only
man/topocorr.Rd | 5 ++++-
4 files changed, 29 insertions(+), 8 deletions(-)
Title: TK Rplot
Diff between tkrplot versions 0.0-20 dated 2011-05-05 and 0.0-21 dated 2011-07-19
Description: simple mechanism for placing R graphics in a Tk widget
Author: Luke Tierney
Maintainer: Luke Tierney
tkrplot-0.0-20/tkrplot/INDEX |only
tkrplot-0.0-21/tkrplot/DESCRIPTION | 8 +++---
tkrplot-0.0-21/tkrplot/NAMESPACE |only
tkrplot-0.0-21/tkrplot/R/tkrplot.R | 49 +++++++++++++++----------------------
4 files changed, 24 insertions(+), 33 deletions(-)
Title: Bitmap Images (``Pixel Maps'')
Diff between pixmap versions 0.4-10 dated 2009-11-13 and 0.4-11 dated 2011-07-19
Description: Functions for import, export, plotting and other
manipulations of bitmapped images.
Author: Roger Bivand, Friedrich Leisch and Martin Maechler
Maintainer: Friedrich Leisch
pixmap-0.4-10/pixmap/COPYING |only
pixmap-0.4-11/pixmap/DESCRIPTION | 9 +++-----
pixmap-0.4-11/pixmap/NAMESPACE |only
pixmap-0.4-11/pixmap/NEWS | 9 +++++++-
pixmap-0.4-11/pixmap/R/AAA-classes.R |only
pixmap-0.4-11/pixmap/R/pixmap.R | 36 -----------------------------------
6 files changed, 12 insertions(+), 42 deletions(-)
Title: Bayesian Two-Zone Model
Diff between B2Z versions 1.3 dated 2011-05-02 and 1.4 dated 2011-07-18
Description: This package fits the Bayesian two-Zone Models.
Author: Joao Vitor Dias Monteiro
Maintainer: Joao Vitor Dias Monteiro
DESCRIPTION | 8 ++++----
inst |only
man/B2Z-package.Rd | 10 +++++++---
man/B2ZM.Rd | 7 +++++--
man/B2ZM_BCLT.Rd | 5 +++--
man/B2ZM_IMIS.Rd | 8 +++++---
man/B2ZM_MCMC.Rd | 5 +++--
man/B2ZM_SIR.Rd | 5 +++--
8 files changed, 30 insertions(+), 18 deletions(-)
Title: Multivariate Nonparametric Methods. An Approach Based on Spatial
Signs and Ranks
Diff between MNM versions 0.95-3 dated 2011-06-15 and 1.0-0 dated 2011-07-18
Description: The package provides multivariate tests, estimates and
methods based on the identity score, spatial sign score and
spatial rank score. The methods include one and c-sample
problems, shape estimation and testing, linear regression and
principal components.
Author: Klaus Nordhausen, Jyrki Mottonen, Hannu Oja
Maintainer: Klaus Nordhausen
DESCRIPTION | 8 ++++----
data/beans.rda |binary
inst/CITATION |only
inst/ChangeLog | 4 ++++
man/MNM-package.Rd | 7 +++++--
man/anova.mvl1lm.Rd | 4 +++-
man/mv.1sample.est.Rd | 4 +++-
man/mv.1sample.test.Rd | 5 ++++-
man/mv.2sample.est.Rd | 5 ++++-
man/mv.Csample.test.Rd | 5 ++++-
man/mv.ind.test.Rd | 5 ++++-
man/mv.l1lm.Rd | 4 +++-
man/mv.shape.est.Rd | 5 ++++-
man/mv.shape.test.Rd | 5 ++++-
14 files changed, 46 insertions(+), 15 deletions(-)
Title: S3 Infrastructure for Regular and Irregular Time Series (Z's
ordered observations)
Diff between zoo versions 1.7-0 dated 2011-07-12 and 1.7-1 dated 2011-07-18
Description: An S3 class with methods for totally ordered indexed
observations. It is particularly aimed at irregular time series
of numeric vectors/matrices and factors. zoo's key design goals
are independence of a particular index/date/time class and
consistency with ts and base R by providing methods to extend
standard generics.
Author: Achim Zeileis [aut, cre], Gabor Grothendieck [aut], Jeffrey A.
Ryan [aut], Felix Andrews [ctb]
Maintainer: Achim Zeileis
DESCRIPTION | 8 ++++----
NEWS | 9 +++++++++
R/rollapply.R | 4 ++--
R/rollmean.R | 6 +++---
R/zzz.R | 3 ++-
inst/doc/zoo-design.pdf |binary
inst/doc/zoo-faq.pdf |binary
inst/doc/zoo-quickref.pdf |binary
inst/doc/zoo-read.pdf |binary
inst/doc/zoo.pdf |binary
10 files changed, 20 insertions(+), 10 deletions(-)
Title: Bayesian Fertility Projection
Diff between bayesTFR versions 1.4-0 dated 2011-05-08 and 1.4-1 dated 2011-07-18
Description: Making probabilistic projections of total fertility rate
for all countries of the world, using a Bayesian hierarchical
model.
Author: Hana Sevcikova
Maintainer: Hana Sevcikova
ChangeLog | 4 ++++
DESCRIPTION | 8 ++++----
inst/CITATION |only
man/bayesTFR-package.Rd | 9 +++++++--
4 files changed, 15 insertions(+), 6 deletions(-)
Title: Graphical User Interface for bayesTFR and bayesLife
Diff between bayesDem versions 1.3-0 dated 2011-05-08 and 1.3-1 dated 2011-07-18
Description: Provides Graphical user interface for the packages
bayesTFR and bayesLife
Author: Hana Sevcikova
Maintainer: Hana Sevcikova
ChangeLog | 4 ++++
DESCRIPTION | 8 ++++----
man/bayesDem-package.Rd | 14 +++++++++-----
3 files changed, 17 insertions(+), 9 deletions(-)
Title: S3 Infrastructure for Regular and Irregular Time Series (Z's
ordered observations)
Diff between zoo versions 1.6-5 dated 2011-04-08 and 1.7-0 dated 2011-07-12
Description: An S3 class with methods for totally ordered indexed
observations. It is particularly aimed at irregular time series
of numeric vectors/matrices and factors. zoo's key design goals
are independence of a particular index/date/time class and
consistency with ts and base R by providing methods to extend
standard generics.
Author: Achim Zeileis [aut, cre], Gabor Grothendieck [aut], Jeffrey A.
Ryan [aut], Felix Andrews [ctb]
Maintainer: Achim Zeileis
DESCRIPTION | 24 +++-
NAMESPACE | 20 +++
NEWS | 83 ++++++++++++++-
R/aggregate.zoo.R | 2
R/as.zoo.R | 43 +++++---
R/as.zoo.tis.R | 4
R/barplot.zoo.R | 6 -
R/coredata.R | 9 +
R/merge.zoo.R | 5
R/na.StructTS.R |only
R/na.aggregate.R | 2
R/na.approx.R | 15 +-
R/na.fill.R |only
R/na.locf.R | 2
R/na.spline.R | 4
R/na.trim.R | 2
R/plot.zoo.R | 24 ++--
R/read.zoo.R | 88 ++++++++++++----
R/rollapply.R | 228 +++++++++++++++++++++++++++++-------------
R/rollmean.R | 245 ++++++++++++++++++++++++----------------------
R/zoo.R | 99 +++++++++++++++---
R/zooreg.R | 6 -
THANKS | 3
inst/doc/zoo-design.Rnw |only
inst/doc/zoo-design.pdf |only
inst/doc/zoo-faq.Rnw | 122 +++++++++++++++-------
inst/doc/zoo-faq.pdf |binary
inst/doc/zoo-quickref.Rnw | 5
inst/doc/zoo-quickref.pdf |binary
inst/doc/zoo-read.Rnw |only
inst/doc/zoo-read.pdf |only
inst/doc/zoo.Rnw | 21 ++-
inst/doc/zoo.bib | 28 +++--
inst/doc/zoo.pdf |binary
man/as.zoo.Rd | 2
man/merge.zoo.Rd | 2
man/na.StructTS.Rd |only
man/na.fill.Rd |only
man/na.locf.Rd | 27 +++--
man/plot.zoo.Rd | 18 +++
man/read.zoo.Rd | 50 ++++++---
man/rollapply.Rd | 209 ++++++++++++++++++++++++++++++++++-----
man/rollmean.Rd | 24 +++-
man/xyplot.zoo.Rd | 14 +-
man/yearmon.Rd | 7 +
man/zoo.Rd | 26 +++-
src |only
tests |only
48 files changed, 1048 insertions(+), 421 deletions(-)
Title: The Multifactor Dimensionality Reduction (MDR) Analysis for
Imcomplete Data
Diff between imputeMDR versions 1.1 dated 2010-05-22 and 1.1.1 dated 2011-07-07
Description: This package provides various approaches to handling
missing values for the MDR analysis to identify gene-gene
interactions using biallelic marker data in genetic association
studies
Author: Junghyun Namkung, Taeyoung Hwang, MinSeok Kwon, Sunggon Yi and
Wonil Chung
Maintainer: Junghyun Namkung
DESCRIPTION | 8 ++++----
R/impute.mdr.R | 6 +++---
data/incomplete.rda |binary
man/imputeMDR-package.Rd | 4 ++--
4 files changed, 9 insertions(+), 9 deletions(-)
Title: JAR dependencies for the XLConnect package
Diff between XLConnectJars versions 0.1-1 dated 2011-05-26 and 0.1-2 dated 2011-07-07
Description: This package provides external JAR dependencies for the
XLConnect package
Author: Mirai Solutions GmbH
Maintainer: Mirai Solutions GmbH
XLConnectJars-0.1-1/XLConnectJars/inst/java/poi-3.8-beta2.jar |only
XLConnectJars-0.1-1/XLConnectJars/inst/java/poi-ooxml-3.8-beta2.jar |only
XLConnectJars-0.1-2/XLConnectJars/DESCRIPTION | 6 +++---
XLConnectJars-0.1-2/XLConnectJars/NEWS |only
XLConnectJars-0.1-2/XLConnectJars/inst/java/commons-codec-1.5.jar |only
XLConnectJars-0.1-2/XLConnectJars/inst/java/poi-3.8-beta3.jar |only
XLConnectJars-0.1-2/XLConnectJars/inst/java/poi-ooxml-3.8-beta3.jar |only
XLConnectJars-0.1-2/XLConnectJars/man/XLConnectJars-package.Rd | 4 ++--
8 files changed, 5 insertions(+), 5 deletions(-)
Title: Excel Connector for R
Diff between XLConnect versions 0.1-4 dated 2011-05-26 and 0.1-5 dated 2011-07-07
Description: Manipulate Excel files from R
Author: Mirai Solutions GmbH
Maintainer: Mirai Solutions GmbH
XLConnect-0.1-4/XLConnect/inst/java/XLConnect-0.1-4-sources.jar |only
XLConnect-0.1-4/XLConnect/inst/java/XLConnect-0.1-4.jar |only
XLConnect-0.1-5/XLConnect/DESCRIPTION | 12 +++++-----
XLConnect-0.1-5/XLConnect/NAMESPACE | 11 ++++++++-
XLConnect-0.1-5/XLConnect/NEWS |only
XLConnect-0.1-5/XLConnect/R/aref.R |only
XLConnect-0.1-5/XLConnect/R/aref2idx.R |only
XLConnect-0.1-5/XLConnect/R/idx2aref.R |only
XLConnect-0.1-5/XLConnect/R/with.workbook.R | 2 -
XLConnect-0.1-5/XLConnect/R/workbook.getCellFormula.R |only
XLConnect-0.1-5/XLConnect/R/workbook.getForceFormulaRecalculation.R |only
XLConnect-0.1-5/XLConnect/R/workbook.getReferenceCoordinates.R |only
XLConnect-0.1-5/XLConnect/R/workbook.setAutoFilter.R |only
XLConnect-0.1-5/XLConnect/R/workbook.setCellFormula.R |only
XLConnect-0.1-5/XLConnect/R/workbook.setForceFormulaRecalculation.R |only
XLConnect-0.1-5/XLConnect/inst/java/XLConnect-0.1-5-sources.jar |only
XLConnect-0.1-5/XLConnect/inst/java/XLConnect-0.1-5.jar |only
XLConnect-0.1-5/XLConnect/inst/unitTests/resources/testWorkbookCellFormula.xls |only
XLConnect-0.1-5/XLConnect/inst/unitTests/resources/testWorkbookCellFormula.xlsx |only
XLConnect-0.1-5/XLConnect/inst/unitTests/resources/testWorkbookForceRecalc.xls |only
XLConnect-0.1-5/XLConnect/inst/unitTests/resources/testWorkbookForceRecalc.xlsx |only
XLConnect-0.1-5/XLConnect/inst/unitTests/runit.arefidx.R |only
XLConnect-0.1-5/XLConnect/inst/unitTests/runit.workbook.getReferenceCoordinates.R |only
XLConnect-0.1-5/XLConnect/inst/unitTests/workbook.setForceFormulaRecalculation.R |only
XLConnect-0.1-5/XLConnect/man/XLConnect-package.Rd | 6 ++---
XLConnect-0.1-5/XLConnect/man/addImage-methods.Rd | 8 ++++++
XLConnect-0.1-5/XLConnect/man/aref.Rd |only
XLConnect-0.1-5/XLConnect/man/aref2idx.Rd |only
XLConnect-0.1-5/XLConnect/man/col2idx.Rd | 3 +-
XLConnect-0.1-5/XLConnect/man/cref2idx.Rd | 5 ++--
XLConnect-0.1-5/XLConnect/man/getCellFormula-methods.Rd |only
XLConnect-0.1-5/XLConnect/man/getForceFormulaRecalculation-methods.Rd |only
XLConnect-0.1-5/XLConnect/man/getReferenceCoordinates-methods.Rd |only
XLConnect-0.1-5/XLConnect/man/idx2aref.Rd |only
XLConnect-0.1-5/XLConnect/man/idx2col.Rd | 3 +-
XLConnect-0.1-5/XLConnect/man/idx2cref.Rd | 3 +-
XLConnect-0.1-5/XLConnect/man/onErrorCell-methods.Rd | 2 -
XLConnect-0.1-5/XLConnect/man/setAutoFilter-methods.Rd |only
XLConnect-0.1-5/XLConnect/man/setCellFormula-methods.Rd |only
XLConnect-0.1-5/XLConnect/man/setForceFormulaRecalculation-methods.Rd |only
XLConnect-0.1-5/XLConnect/man/setStyleAction-methods.Rd | 4 ++-
XLConnect-0.1-5/XLConnect/man/workbook-class.Rd | 2 -
42 files changed, 42 insertions(+), 19 deletions(-)
Title: Implement tour methods in pure R code
Diff between tourr versions 0.4 dated 2011-04-05 and 0.4.1 dated 2011-07-07
Description: Implements geodesic interpolation and basis generation
functions that allow you to create new tour methods from R.
Author: Dianne Cook
Maintainer: Hadley Wickham
DESCRIPTION | 6 +-
NAMESPACE | 101 ++++++++++++++++++++---------------
NEWS | 7 ++
R/interesting-indices.r | 118 ++++++++++++++++++++++--------------------
R/search-frozen-geodesic.r | 2
R/search-geodesic.r | 2
man/anaglyph.Rd | 14 +++-
man/andrews.Rd | 23 ++++----
man/animate.Rd | 74 ++++++++++++++++----------
man/bases_little.Rd | 13 ++--
man/basis_init.Rd | 14 ++--
man/basis_nearby.Rd | 6 +-
man/basis_random.Rd | 13 ++--
man/blank_plot.Rd | 6 +-
man/center.Rd | 10 ++-
man/check_freezer_safe.Rd | 12 ++--
man/cm.Rd | 13 ++--
man/dependence_tour.Rd | 22 ++++---
man/display_andrews.Rd | 31 ++++++-----
man/display_depth.Rd | 39 ++++++++-----
man/display_dist.Rd | 54 ++++++++++++-------
man/display_faces.Rd | 31 ++++++-----
man/display_ggobi.Rd | 20 +++----
man/display_image.Rd | 35 ++++++++----
man/display_pcp.Rd | 29 ++++++----
man/display_scatmat.Rd | 29 ++++++----
man/display_stars.Rd | 33 +++++++----
man/display_stereo.Rd | 26 +++++----
man/display_trails.Rd | 48 ++++++++++-------
man/display_xy.Rd | 49 ++++++++++-------
man/draw_tour_axes.Rd | 6 +-
man/find_best_dir.Rd | 22 ++++---
man/find_best_frozen_dir.Rd | 8 +-
man/find_frozen_path_peak.Rd | 8 +-
man/find_path_peak.Rd | 23 ++++----
man/find_platform.Rd | 2
man/freeze.Rd | 19 +++---
man/frozen_guided_tour.Rd | 35 ++++++++----
man/frozen_tour.Rd | 22 ++++---
man/geodesic_info.Rd | 21 ++++---
man/geodesic_path.Rd | 46 ++++++++--------
man/grand_tour.Rd | 19 +++---
man/guided_tour.Rd | 59 +++++++++++++--------
man/holes.Rd | 13 ++--
man/interpolate.Rd | 22 ++++---
man/is_orthonormal.Rd | 16 +++--
man/lda_pp.Rd | 13 ++--
man/little_tour.Rd | 19 +++---
man/local_tour.Rd | 20 ++++---
man/new_geodesic_path.Rd | 19 +++---
man/new_tour.Rd | 46 +++++++++-------
man/normalise.Rd | 15 ++---
man/orthonormalise.Rd | 14 ++--
man/orthonormalise_by.Rd | 16 +++--
man/path_curves.Rd | 30 ++++++----
man/path_dist.Rd | 26 +++++----
man/path_index.Rd | 29 ++++++----
man/paths_index.Rd | 26 +++++----
man/pda_pp.Rd | 15 +++--
man/planned_tour.Rd | 34 +++++++-----
man/plot.path_curve.Rd | 7 +-
man/plot.path_index.Rd | 8 +-
man/proj_dist.Rd | 14 ++--
man/project3d.Rd | 21 ++++---
man/render.Rd | 58 +++++++++++++-------
man/rescale.Rd | 13 ++--
man/save_history.Rd | 59 +++++++++++++--------
man/search_better.Rd | 8 +-
man/search_better_random.Rd | 8 +-
man/search_frozen_geodesic.Rd | 13 ++--
man/search_geodesic.Rd | 27 ++++++---
man/sphere.Rd | 13 ++--
man/step_angle.Rd | 13 ++--
man/step_fraction.Rd | 14 +++-
man/to_stop.Rd | 3 -
man/xnul.Rd | 13 ++--
76 files changed, 1107 insertions(+), 728 deletions(-)
Title: Estimation of various latent class mixed models and joint latent
class mixed models
Diff between lcmm versions 1.4 dated 2011-06-06 and 1.4-1 dated 2011-07-07
Description: This package provides functions for the estimation of
various latent class mixed models and joint latent latent class
mixed models using a maximum likelihood method
Author: Cecile Proust-Lima, Amadou Diakite and Benoit Liquet
Maintainer:
DESCRIPTION | 10
R/Contlcmm.R | 18 -
R/Jointlcmm.R | 212 +++++++++---------
R/Ordlcmm.R | 417 +++++++++++++++++++++++++++++++++++++
R/hlme.R | 7
R/lcmm.R | 16 +
R/plot.Jointlcmm.R | 4
R/plot.hlme.R | 4
R/plot.lcmm.R | 13 -
R/plot.linkfunction.lcmm.R | 17 +
R/plot.postprob.Jointlcmm.R | 33 +-
R/plot.postprob.hlme.R | 24 +-
R/plot.postprob.lcmm.R | 14 -
R/plot.predict.Jointlcmm.R | 1
R/plot.predict.hlme.R | 1
R/plot.predict.lcmm.R | 3
R/postprob.Jointlcmm.R | 7
R/postprob.hlme.R | 8
R/postprob.lcmm.R | 7
R/print.lcmm.R | 2
R/summary.Jointlcmm.R | 9
R/summary.hlme.R | 7
R/summary.lcmm.R | 25 +-
man/Jointlcmm.Rd | 491 +++++++++++++++++++++++---------------------
man/data_Jointlcmm.Rd | 2
man/data_hlme.Rd | 2
man/hlme.Rd | 28 +-
man/lcmm-package.Rd | 24 +-
man/lcmm.Rd | 153 +++++++++----
man/plot.baselinerisk.Rd | 10
man/plot.lcmm.Rd | 3
man/plot.linkfunction.Rd | 31 +-
man/plot.postprob.Rd | 3
man/plot.predict.Rd | 17 -
man/plot.survival.Rd | 17 -
man/postprob.Rd | 3
man/print.lcmm.Rd | 2
man/summary.lcmm.Rd | 2
src/hetmixCont.f90 | 28 +-
src/hetmixOrd.f90 |only
40 files changed, 1140 insertions(+), 535 deletions(-)
Title: Weighted Gene Co-Expression Network Analysis
Diff between WGCNA versions 1.11-2 dated 2011-06-06 and 1.11-3 dated 2011-07-07
Description: Functions necessary to perform Weighted Gene Co-Expression
Network Analysis
Author: Peter Langfelder
Maintainer: Peter Langfelder
Changelog | 7 +++++++
DESCRIPTION | 8 ++++----
R/Functions-modColor.R | 2 +-
R/modulePreservation.R | 30 +++++++++++++++++++++---------
R/votingLinearPredictor.R | 11 ++++++++++-
man/WGCNA-package.Rd | 4 ++--
man/votingLinearPredictor.Rd | 8 +++-----
7 files changed, 48 insertions(+), 22 deletions(-)
Title: Analysis of Parent-Specific DNA Copy Numbers
Diff between PSCBS versions 0.11.0 dated 2011-06-17 and 0.11.3 dated 2011-07-07
Description: Segments allele-specific DNA copy number data to detect
regions with abnormal copy number within each parental
chromosome
Author: A.B. Olshen, H. Bengtsson, P. Neuvial, P.T. Spellman, R.A.
Olshen, V.E. Seshan
Maintainer: Henrik Bengtsson
DESCRIPTION | 12 +++++-------
R/PairedPSCBS.R | 27 +++++++++++++++++++++++++++
R/PairedPSCBS.estimateDeltaLOH.R | 14 +++++++++++++-
R/segmentByCBS.R | 2 +-
R/segmentByPairedPSCBS.R | 28 ++++++++++++++++++++--------
incl/999.missingdocs.txt | 2 +-
incl/OlshenA_etal_2011.Rd | 2 +-
inst/NEWS | 21 +++++++++++++++++++++
man/Non-documented_objects.Rd | 1 -
man/PSCBS-package.Rd | 4 ++--
man/PairedPSCBS.Rd | 2 +-
man/as.data.frame.PairedPSCBS.Rd |only
man/segmentByCBS.Rd | 2 +-
man/segmentByPairedPSCBS.Rd | 17 +++++++++--------
14 files changed, 102 insertions(+), 32 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining with R
Diff between FactoMineR versions 1.14 dated 2010-05-10 and 1.16 dated 2011-07-07
Description: an R package for exploratory data analysis
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson
DESCRIPTION | 8
FactoMineR-Ex.R |only
R/CA.R | 37 ++--
R/HCPC.R | 9 -
R/MCA.R | 2
R/MFA.R | 207 ++++++++++++++++++-----
R/PCA.R | 327 ++++++++++++++++++++----------------
R/coeffRV.R | 6
R/dimdesc.r | 4
R/estim_ncp.r | 61 +++++-
R/plot.HCPC.R | 12 -
R/plot.MFA.R | 180 +++++++++++++-------
R/plot.catdes.R | 24 +-
R/plotellipses.r | 462 ++++++++++++++++++++++++++++------------------------
R/print.MFA.R | 11 +
R/reconst.R | 2
R/svd.triplet.R | 64 ++++---
R/write.infile.R | 24 +-
inst |only
man/MCA.Rd | 3
man/MFA.Rd | 28 +--
man/PCA.Rd | 2
man/catdes.Rd | 4
man/condes.Rd | 4
man/dimdesc.Rd | 2
man/estim_ncp.Rd | 6
man/plot.MFA.Rd | 19 +-
man/plotellipses.Rd | 20 +-
man/svd.triplet.Rd | 3
man/tea.Rd | 2
man/wine.Rd | 4
31 files changed, 943 insertions(+), 594 deletions(-)
Title: sos
Diff between sos versions 1.3-0 dated 2010-06-23 and 1.3-1 dated 2011-07-06
Description: R related Search Engines
Author: Spencer Graves, Sundar Dorai-Raj, and Romain Francois
Maintainer: Spencer Graves
DESCRIPTION | 8 +++----
R/Extract.findFn.R |only
R/findFn.R | 54 +++++++++++++++++++++++++++-----------------------
R/writeFindFn2xls.R | 2 -
inst/doc/sos.pdf |binary
man/Extract.findFn.Rd |only
man/findFn.Rd | 7 +++++-
7 files changed, 41 insertions(+), 30 deletions(-)
Title: RVM Binary Classification
Diff between rvmbinary versions 0.1 dated 2011-04-11 and 0.1.2 dated 2011-07-06
Description: Performs binary classification of data using a Relevance
Vector Machine
Author: Robert Lowe
Maintainer: Robert Lowe
DESCRIPTION | 6 ++--
R/gaus.R | 4 +-
R/gauspredict.R | 71 +++++++++++++++++++++++++++++++++++--------------
man/aa.Rd | 5 ++-
man/aapredict.Rd | 5 ++-
man/gaus.Rd | 5 ++-
man/gauspredict.Rd | 5 ++-
man/rvmbinary.Rd | 5 ++-
src/fullstatistics.cpp | 11 ++++---
src/fullstatistics.h | 9 ++----
src/main.cpp | 24 +++++++++++-----
11 files changed, 104 insertions(+), 46 deletions(-)
Title: statistical methods for analysing multivariate abundance data
Diff between mvabund versions 2.2-4 dated 2011-06-30 and 2.2-5.3 dated 2011-07-06
Description: A set of tools for displaying, modeling and analysing
multivariate abundance data in community ecology. See
mvabund-package.Rd for details of overall package organization.
The package is implemented with the Gnu Scientific Library
(http://www.gnu.org/software/gsl/) and Rcpp
(http://dirk.eddelbuettel.com/code/rcpp.html) R / C++ classes.
Author: Yi Wang, Ulrike Naumann, Stephen Wright and David Warton
Maintainer: Yi Wang
DESCRIPTION | 12 -
R/anova.manyglm.R | 121 +++++------
R/anova.manylm.R | 396 ++++++++++++++++----------------------
R/cooks.distance.manylm.R | 4
R/default.plot.manyglm.R | 4
R/default.plot.manylm.R | 17 -
R/default.print.summary.manyglm.R | 4
R/deviance.manylm.R | 6
R/manyglm.R | 2
R/manylm.R | 7
R/predict.manylm.R | 2
R/print.summary.manylm.R | 2
src/Makevars.win | 9
src/RtoAnovaCpp.cpp | 51 ++--
src/RtoGlm.cpp | 32 +--
src/RtoGlmAnova.cpp | 65 +++---
src/RtoGlmSmry.cpp | 72 +++---
src/RtoSmryCpp.cpp | 71 +++---
src/anova.cpp | 38 +--
src/calctest.cpp | 119 +++++------
src/glm.cpp | 26 +-
src/glmtest.cpp | 94 ++++-----
src/io.cpp | 12 -
src/resampTest.h | 87 ++++----
src/rmv.h | 12 -
src/rnd.cpp | 20 -
src/simutility.cpp | 52 ++--
src/summary.cpp | 85 ++++----
tests |only
29 files changed, 692 insertions(+), 730 deletions(-)
Title: Inferences for ratios of coefficients in the general linear
model
Diff between mratios versions 1.3.15 dated 2011-03-24 and 1.3.16 dated 2011-07-06
Description: With this package, it is possible to perform
(simultaneous) inferences for ratios of linear combinations of
coefficients in the general linear model. In particular, tests
and confidence interval estimations for ratios of treatment
means in the normal one-way layout and confidence interval
estimations like in (multiple) slope ratio and parallel line
assays can be carried out. Moreover, it is possible to
calculate the sample sizes required in comparisons with a
control based on relative margins. For the simple two-sample
problem, functions for a t-test for ratio-formatted hypotheses
and the corresponding Fieller-type confidence interval are
provided assuming homogeneous or heterogeneous group variances.
Author: Gemechis Dilba Djira, Mario Hasler, Daniel Gerhard, Frank
Schaarschmidt
Maintainer: Frank Schaarschmidt
DESCRIPTION | 8 ++++----
R/ratioVH.R | 16 ++++++++--------
R/simtest.ratioI.R | 6 +++---
3 files changed, 15 insertions(+), 15 deletions(-)
Title: Jitter/CI Plot with Ordered Points Below the Limit of Detection
Diff between limitplot versions 1.0 dated 2010-04-15 and 1.2 dated 2011-07-06
Description: Values below a specified limit of detection are stacked in
rows in order to reduce overplotting and create a clear
graphical representation of your data.
Author: Omar E. Olmedo
Maintainer: Omar E. Olmedo
DESCRIPTION | 11 +--
NAMESPACE |only
R/limitplot.R | 169 +++++++++++--------------------------------------------
R/plotBox.R |only
R/plotInit.R |only
R/plotStack.R |only
README |only
man/limitplot.Rd | 33 ++++++----
8 files changed, 60 insertions(+), 153 deletions(-)
Title: Regularization paths for regression models with grouped
covariates
Diff between grpreg versions 1.2-0 dated 2011-06-22 and 1.2-1 dated 2011-07-06
Description: Efficient algorithms for fitting the regularization path
for linear or logistic regression models penalized by the group
lasso, group bridge, or group MCP methods. The algorithm is
based on the idea of a locally approximated coordinate descent.
Author: Patrick Breheny
Maintainer: Patrick Breheny
DESCRIPTION | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
Title: R package for parsing and manipulating edit rules
Diff between editrules versions 0.7-1 dated 2011-06-29 and 0.8 dated 2011-07-06
Description: Facilitates reading and manipulation of linear
(in)equalities, converting them into matrix format (and vice
versa) and checking if data are valid according to these rules.
Sets of linear edits can be manipulated using Fourier-Motzkin
elimination and variable substitution and solving error
localization problems based on the generalized principle of
Felligi and Holt.
Author: Edwin de Jonge, Mark van der Loo
Maintainer: Edwin de Jonge
editrules-0.7-1/editrules/R/choicepoint.R |only
editrules-0.7-1/editrules/man/choicepoint.Rd |only
editrules-0.7-1/editrules/man/iter.choicepoint.Rd |only
editrules-0.7-1/editrules/man/print.choicepoint.Rd |only
editrules-0.8/editrules/DESCRIPTION | 8
editrules-0.8/editrules/NAMESPACE | 10
editrules-0.8/editrules/NEWS | 12
editrules-0.8/editrules/R/backtracker.R |only
editrules-0.8/editrules/R/editmatrix.R | 38
editrules-0.8/editrules/R/editmatrixAttr.R | 14
editrules-0.8/editrules/R/eliminate.R | 23
editrules-0.8/editrules/R/errorLocalizer.R | 36
editrules-0.8/editrules/R/pkg.R | 34
editrules-0.8/editrules/R/reduce.R | 29
editrules-0.8/editrules/inst/doc/Sweave.sty | 6
editrules-0.8/editrules/inst/doc/editrules-categorical.pdf |binary
editrules-0.8/editrules/inst/doc/editrules-linear.Snw | 771 +++++-----
editrules-0.8/editrules/inst/doc/editrules-linear.bbl | 31
editrules-0.8/editrules/inst/doc/editrules-linear.blg | 68
editrules-0.8/editrules/inst/doc/editrules-linear.dvi |binary
editrules-0.8/editrules/inst/doc/editrules-linear.pdf |binary
editrules-0.8/editrules/inst/doc/editrules.bib | 46
editrules-0.8/editrules/inst/doc/texput.log |only
editrules-0.8/editrules/inst/doc/tree.tex |only
editrules-0.8/editrules/inst/doc/tree.tex.aux |only
editrules-0.8/editrules/inst/doc/x.log |only
editrules-0.8/editrules/inst/tests/testFourierMotzkin.R | 18
editrules-0.8/editrules/inst/tests/testIsObviouslyInfeasible.R |only
editrules-0.8/editrules/inst/tests/testIsObviouslyRedundant.R |only
editrules-0.8/editrules/inst/tests/testeditmatrix.R | 1
editrules-0.8/editrules/man/as.character.editmatrix.Rd | 5
editrules-0.8/editrules/man/as.editmatrix.Rd | 8
editrules-0.8/editrules/man/as.expression.editmatrix.Rd | 5
editrules-0.8/editrules/man/backtracker.Rd |only
editrules-0.8/editrules/man/editmatrix.Rd | 4
editrules-0.8/editrules/man/editrules-package.Rd | 24
editrules-0.8/editrules/man/errorLocalizer.Rd | 16
editrules-0.8/editrules/man/getA.Rd | 1
editrules-0.8/editrules/man/getb.Rd | 1
editrules-0.8/editrules/man/isObviouslyInfeasible.Rd | 2
editrules-0.8/editrules/man/iter.backtracker.Rd |only
editrules-0.8/editrules/man/print.backtracker.Rd |only
editrules-0.8/editrules/man/substValue.Rd | 7
43 files changed, 670 insertions(+), 548 deletions(-)
Title: Classification and Regression Training
Diff between caret versions 4.91 dated 2011-06-09 and 4.92 dated 2011-07-06
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
DESCRIPTION | 11 +-
R/createGrid.R | 1
R/createModel.R | 21 ++++
R/misc.R | 26 +++++
R/modelLookup.R | 54 ++++++++++--
R/plot.train.R | 11 ++
R/preProcess.R | 1
R/predictionFunction.R | 83 ++++++++++++------
R/resamples.R | 193 ++++++++++++++++++++++++++++++++++++--------
R/rfe.R | 43 +++++----
R/selectByFilter.R | 35 ++++---
R/selection.R | 3
R/train.default.R | 26 ++++-
R/trainControl.R | 2
inst/NEWS | 35 +++++++
inst/doc/caretMisc.pdf |binary
inst/doc/caretSelection.pdf |binary
inst/doc/caretTrain.Rnw | 17 +++
inst/doc/caretTrain.pdf |binary
inst/doc/caretVarImp.pdf |binary
man/lattice.resamples.Rd | 9 +-
man/rfeControl.Rd | 2
man/sbfControl.Rd | 2
man/train.Rd | 13 ++
man/trainControl.Rd | 2
25 files changed, 467 insertions(+), 123 deletions(-)
Title: Six Sigma Tools for Quality and Process Improvement
Diff between SixSigma versions 0.2.1 dated 2011-04-01 and 0.3.0 dated 2011-07-06
Description: This package contains functions and utilities to perform
Statistical Analysis for Six Sigma methodology. Through its
outline DMAIC (Define, Measure, Analyze, Improve, Control), you
can manage several Quality Management studies. The current
version includes Capability Analysis, Gage R&R Study,
Confidence Interval, Cause-and-effect diagram and Process Map.
There will be new functions very soon for Capability Analysis,
Control Charts, Reliability, OC Curves, Regression and Design
of Experiments. See ?SixSigma for an Introduction.
Author: Emilio Lopez, Andres Redchuk, Javier M.Moguerza
Maintainer: Emilio Lopez
DESCRIPTION | 21 +++++++++++----------
INDEX | 9 +++++++--
R/SixSigma.R |only
R/ss.ca.R |only
R/ss.heli.R |only
R/ss.rr.R | 2 +-
data/ss.data.ca.RData |only
inst/doc |only
man/ss.ca.indices.Rd |only
man/ss.ca.yield.Rd |only
man/ss.data.ca.Rd |only
man/ss.heli.Rd |only
man/ss.study.ca.Rd |only
13 files changed, 19 insertions(+), 13 deletions(-)
Title: Seamless R and C++ Integration
Diff between Rcpp versions 0.9.4 dated 2011-04-12 and 0.9.5 dated 2011-07-06
Description: The Rcpp package provides a C++ library which facilitates
the integration of R and C++.
R data types (SEXP) are matched to C++ objects in a class hierarchy.
All R types are supported (vectors, functions, environment, etc
...) and each type is mapped to a dedicated class. For
example, numeric vectors are represented as instances of the
Rcpp::NumericVector class, environments are represented as
instances of Rcpp::Environment, functions are represented as
Rcpp::Function, etc ... The "Rcpp-introduction" vignette
provides a good entry point to Rcpp.
Conversion from C++ to R and back is driven by the templates Rcpp::wrap
and Rcpp::as which are highly flexible and extensible, as
documented in the "Rcpp-extending" vignette.
Rcpp also provides Rcpp modules, a framework that allows exposing C++
functions and classes to the R level. The "Rcpp-modules"
vignette details the current set of features of Rcpp-modules.
Rcpp includes a concept called Rcpp sugar that brings many R functions
into C++. Sugar takes advantage of lazy evaluation and
expression templates to achieve great performance while
exposing a syntax that is much nicer to use than the equivalent
low-level loop code. The "Rcpp-sugar" vignette gives an
overview of the feature.
Several examples are included, and 753 unit tests in 338 unit test
functions provide additional usage examples.
An earlier version of Rcpp, containing what we now call the 'classic
Rcpp API' was written during 2005 and 2006 by Dominick Samperi.
This code has been factored out of Rcpp into the package
RcppClassic and it is still available for code relying on this
interface. New development should use this package instead.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by
Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel and Romain Francois
ChangeLog | 74
DESCRIPTION | 10
R/00_classes.R | 3
R/Module.R | 16
R/loadRcppModules.R | 10
R/populate.R | 10
R/tools.R | 13
R/zzz.R | 3
cleanup | 2
inst/NEWS | 21
inst/doc/Rcpp-FAQ.pdf |binary
inst/doc/Rcpp-FAQ/Rcpp-FAQ.Rnw | 62
inst/doc/Rcpp-extending.pdf |binary
inst/doc/Rcpp-introduction.pdf |binary
inst/doc/Rcpp-modules.pdf |binary
inst/doc/Rcpp-modules/Rcpp-modules.Rnw | 7
inst/doc/Rcpp-package.pdf |binary
inst/doc/Rcpp-quickref.pdf |binary
inst/doc/Rcpp-quickref/Rcpp-quickref.Rnw | 59
inst/doc/Rcpp-sugar.pdf |binary
inst/doc/Rcpp-unitTests.pdf |binary
inst/doc/Rcpp.bib | 4
inst/doc/unitTests-results/Rcpp-unitTests.html | 18
inst/doc/unitTests-results/Rcpp-unitTests.txt | 49
inst/examples/OpenMP |only
inst/include/Rcpp/Module.h | 33
inst/include/Rcpp/config.h | 2
inst/include/Rcpp/internal/wrap.h | 5
inst/include/Rcpp/module/Module_generated_CppMethod.h | 2902 +++++++++++++++++-
inst/include/Rcpp/stats/random/rlnorm.h | 14
inst/include/Rcpp/stats/random/rnorm.h | 4
inst/include/Rcpp/sugar/functions/functions.h | 3
inst/include/Rcpp/sugar/functions/mean.h |only
inst/include/Rcpp/sugar/functions/sd.h |only
inst/include/Rcpp/sugar/functions/sum.h | 4
inst/include/Rcpp/sugar/functions/var.h |only
inst/include/Rcpp/vector/Vector.h | 4
inst/skeleton/zzz.R | 1
inst/unitTests/runit.wrap.R | 25
man/CppClass-class.Rd | 2
man/loadRcppModules.Rd | 6
src/Module.cpp | 1
42 files changed, 3252 insertions(+), 115 deletions(-)
Title: Joint Optimization Plot
Diff between JOP versions 2.0.2 dated 2011-06-15 and 2.0.3 dated 2011-07-06
Description: JOP is a tool for simultanous optimization of multiple
responses and visualization of the results. The visualization
is done by the joint optimization plot introduced by Kuhnt and
Erbruegge (2004).
Author: Sonja Kuhnt and Nikolaus Rudak
Maintainer: Nikolaus Rudak
DESCRIPTION | 8 ++++----
R/locate.R | 30 +++++++++++++++---------------
R/oplot.R | 18 +++++++++---------
man/JOP-package.Rd | 4 ++--
4 files changed, 30 insertions(+), 30 deletions(-)
Title: gpseq: Using the generalized Poisson distribution to model
sequence read counts from high throughput sequencing
experiments
Diff between GPseq versions 0.4 dated 2011-01-11 and 0.5 dated 2011-07-06
Description: Some functions for modeling sequence read counts as a
generalized poisson model and to use this model for detecting
differentially expressed genes in different conditions and
differentially spliced exons.
Author: Sudeep Srivastava, Liang Chen
Maintainer: Sudeep Srivastava
DESCRIPTION | 6 +++---
R/wrapper2.R | 9 +++------
2 files changed, 6 insertions(+), 9 deletions(-)
Title: Find biomarkers in two-class discrimination problems
Diff between BioMark versions 0.2.6 dated 2011-02-08 and 0.3.0 dated 2011-07-06
Description: The package implements PCLDA, PLSDA, and several t-tests
to find those variables that allow for adequate discrimination
between two classes. Apart from the usual approaches based on
the size of model coefficients, a set of functions is provided
that assess the stability of the potential biomarkers under
crossvalidation.
Author: Ron Wehrens, Pietro Franceschi
Maintainer: Ron Wehrens
CHANGES |only
DESCRIPTION | 10 +-
R/biom.HC.R |only
R/biom.coef.R | 32 ++----
R/biom.options.R |only
R/biom.stab.R | 14 +-
R/gen.data.R | 2
R/get.biom.R | 247 +++++++++++++++++++++++++++++++++++++++-------------
R/roc.R | 12 +-
TODO |only
data/SpikeNeg.RData |only
data/SpikePos.RData |only
man/HCthresh.Rd |only
man/ROC.Rd | 96 ++++++++------------
man/SpikedApple.Rd |only
man/auxBiom.Rd |only
man/biom.options.Rd |only
man/gen.data.Rd | 9 +
man/get.biom.Rd | 169 ++++++++++++++---------------------
man/get.segments.Rd | 6 -
man/scalefun.Rd | 3
man/spikedApples.Rd | 7 +
22 files changed, 349 insertions(+), 258 deletions(-)
Title: R Fortunes
Diff between fortunes versions 1.4-1 dated 2011-03-30 and 1.4-2 dated 2011-07-05
Description: R Fortunes
Author: Achim Zeileis (R code) and the R community (fortunes).
Contributions (fortunes and/or code) by Torsten Hothorn, Peter
Dalgaard, Uwe Ligges, Kevin Wright, Martin Maechler, Kjetil
Brinchmann Halvorsen, Kurt Hornik, Duncan Murdoch, Andy Bunn,
Ray Brownrigg, Roger Bivand, Spencer Graves, Jim Lemon,
Christian Kleiber, David L. Reiner, Berton Gunter, Roger
Koenker, Charles Berry, Marc Schwartz, Michael Dewey, Ben
Bolker, Peter Dunn, Sarah Goslee, Simon Blomberg, Bill
Venables, Roland Rau, Thomas Petzoldt, Rolf Turner, Mark Leeds,
Emmanuel Charpentier, Chris Evans, Paolo Sonego, Peter Ehlers,
Detlef Steuer, Tal Galili, Greg Snow, Brian D. Ripley, Michael
Sumner, David Winsemius, Liviu Andronic, Brian Diggs, Matthieu
Stigler, Michael Friendly, Dirk Eddelbuettel.
Maintainer: Achim Zeileis
DESCRIPTION | 11 +++++------
inst/doc/fortunes.pdf |binary
inst/fortunes/fortunes.csv | 12 +++++++++++-
3 files changed, 16 insertions(+), 7 deletions(-)
Title: GUI implementing Bayesian working memory models
Diff between WMCapacity versions 0.9.6.4 dated 2011-06-29 and 0.9.6.5 dated 2011-07-05
Description: A GUI R implementation of hierarchical Bayesian models of
working memory, used for analyzing change detection data.
Author: R. D. Morey
Maintainer: R. D. Morey
DESCRIPTION | 8 ++---
R/analysistab.R | 15 ++++++---
R/modeltab.R | 74 +++++++++++++++++++++++++++++++++----------------
R/resultstab.R | 2 -
data/VisualArray.RData |binary
5 files changed, 66 insertions(+), 33 deletions(-)
Title: Segmented relationships in regression models
Diff between segmented versions 0.2-8.1 dated 2011-06-20 and 0.2-8.2 dated 2011-07-05
Description: Given a (generalized) linear model, segmented `updates'
the model by adding one or more segmented relationships.
Several variables with multiple breakpoints are allowed.
Author: Vito M.R. Muggeo
Maintainer: Vito M.R. Muggeo
DESCRIPTION | 8 ++++----
NEWS | 12 ++++++++++--
R/confint.segmented.R | 2 +-
R/intercept.r | 2 +-
R/segmented.glm.R | 2 ++
R/segmented.lm.R | 2 ++
man/intercept.Rd | 11 ++++++++---
man/segmented-package.Rd | 4 ++--
8 files changed, 30 insertions(+), 13 deletions(-)
Title: Shrinkage t Statistic and CAT Score
Diff between st versions 1.1.5 dated 2011-06-28 and 1.1.6 dated 2011-07-05
Description: This package implements the "shrinkage t" statistic
introduced in Opgen-Rhein and Strimmer (2007) and a shrinkage
estimate of the "correlation-adjusted t-score" (CAT score)
described in Zuber and Strimmer (2009). It also offers a
convenient interface to a number of other regularized
t-statistics commonly employed in high-dimensional case-control
studies.
Author: Rainer Opgen-Rhein, Verena Zuber, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 8 ++++----
NEWS | 5 +++++
R/studentt.R | 6 +++---
data/choedata.rda |binary
4 files changed, 12 insertions(+), 7 deletions(-)
Title: simexaft
Diff between simexaft versions 1.0.4 dated 2011-06-01 and 1.0.5 dated 2011-07-05
Description: Implement of the Simulation-Extrapolation (SIMEX)
algorithm for the accelerated failure time (AFT) with
covariates subject to measurement error.
Author: Juan Xiong
Maintainer: Juan Xiong
DESCRIPTION | 8 ++++----
R/plotsimexaft.R | 9 +++++++--
man/simexaft-package.Rd | 4 ++--
3 files changed, 13 insertions(+), 8 deletions(-)
Title: Geographic analysis and modeling with raster data
Diff between raster versions 1.8-38 dated 2011-06-18 and 1.8-39 dated 2011-07-05
Description: Reading, writing, manipulating, analyzing and modeling of
gridded spatial data. The package implements basic and
high-level functions, as well as map algebra. Processing of
very large files is supported.
Author: Robert J. Hijmans & Jacob van Etten
Maintainer: Robert J. Hijmans
ChangeLog | 4 ++++
DESCRIPTION | 13 ++++++-------
R/Geary.R | 2 +-
R/coverBrick.R | 4 ++--
R/kml.R | 23 ++++++++++++++---------
R/levelplot.R | 7 ++++---
R/moran.R | 2 +-
R/plot.R | 6 ++----
R/setCV.R | 2 +-
R/stack.R | 11 ++++++-----
R/subset.R | 30 +++++++++++++++++++++++++-----
inst/doc/Raster.pdf |binary
inst/doc/functions.pdf |binary
inst/doc/rasterfile.pdf |binary
man/KML.Rd | 4 ++--
man/spplot.Rd | 9 ++-------
16 files changed, 70 insertions(+), 47 deletions(-)
Title: GRAPH Interaction from pathway Topological Environment
Diff between graphite versions 1.0 dated 2011-05-30 and 1.1 dated 2011-07-05
Description: Graph objects from pathway topology derived from NCI,
KEGG, Biocarta and Reactome databases.
Author: Gabriele Sales
Maintainer: Gabriele Sales
graphite-1.0/graphite/R/pathway.graph.R |only
graphite-1.0/graphite/R/pathway.names.R |only
graphite-1.0/graphite/data/datalist |only
graphite-1.0/graphite/man/biocarta.pathways.Rd |only
graphite-1.0/graphite/man/kegg.pathways.Rd |only
graphite-1.0/graphite/man/nci.pathways.Rd |only
graphite-1.0/graphite/man/pathway.graph.Rd |only
graphite-1.0/graphite/man/pathway.names.Rd |only
graphite-1.0/graphite/man/reactome.pathways.Rd |only
graphite-1.1/graphite/DESCRIPTION | 11 ++++++-----
graphite-1.1/graphite/NAMESPACE | 12 +++++++++++-
graphite-1.1/graphite/R/conversion.R |only
graphite-1.1/graphite/R/cytoscapePlot.R |only
graphite-1.1/graphite/R/degraph.R |only
graphite-1.1/graphite/R/graph.R |only
graphite-1.1/graphite/R/pathway.R |only
graphite-1.1/graphite/R/spia.R |only
graphite-1.1/graphite/R/tables.R |only
graphite-1.1/graphite/R/topologygsa.R |only
graphite-1.1/graphite/R/utils.R |only
graphite-1.1/graphite/data/pathways.RData |binary
graphite-1.1/graphite/inst |only
graphite-1.1/graphite/man/biocarta.Rd |only
graphite-1.1/graphite/man/convertIdentifiers.Rd |only
graphite-1.1/graphite/man/cytoscapePlot.Rd |only
graphite-1.1/graphite/man/kegg.Rd |only
graphite-1.1/graphite/man/nci.Rd |only
graphite-1.1/graphite/man/pathway-class.Rd |only
graphite-1.1/graphite/man/pathwayGraph.Rd |only
graphite-1.1/graphite/man/prepareSPIA.Rd |only
graphite-1.1/graphite/man/reactome.Rd |only
graphite-1.1/graphite/man/runDEGraph.Rd |only
graphite-1.1/graphite/man/runSPIA.Rd |only
graphite-1.1/graphite/man/topologyGSA.Rd |only
34 files changed, 17 insertions(+), 6 deletions(-)
Title: Regularization for semiparametric additive hazards regression
Diff between ahaz versions 1.0 dated 2011-05-17 and 1.1 dated 2011-07-05
Description: Computationally efficient procedures for regularized
estimation with the semiparametric additive hazards regression
model.
Author: Anders Gorst-Rasmussen
Maintainer: Anders Gorst-Rasmussen
ahaz-1.0/ahaz/R/ahaz.mse.R |only
ahaz-1.0/ahaz/R/ahazpartial.R |only
ahaz-1.0/ahaz/R/coef.ahaz.R |only
ahaz-1.0/ahaz/R/coef.ahazpen.R |only
ahaz-1.1/ahaz/DESCRIPTION | 11
ahaz-1.1/ahaz/NAMESPACE | 5
ahaz-1.1/ahaz/R/ahaz.R | 106 --
ahaz-1.1/ahaz/R/ahaz.adjust.R | 24
ahaz-1.1/ahaz/R/ahaz.partial.R | 96 --
ahaz-1.1/ahaz/R/ahaz.tune.control.R | 1
ahaz-1.1/ahaz/R/ahazisis.R | 44 -
ahaz-1.1/ahaz/R/ahazpen.R | 306 ++++----
ahaz-1.1/ahaz/R/ahazpen.fit.control.R | 2
ahaz-1.1/ahaz/R/ahazpen.pen.control.R | 29
ahaz-1.1/ahaz/R/helpers.R | 263 ++++---
ahaz-1.1/ahaz/R/plot.ahazpen.R | 57 -
ahaz-1.1/ahaz/R/plot.cumahaz.R | 11
ahaz-1.1/ahaz/R/plot.tune.ahazpen.R | 64 -
ahaz-1.1/ahaz/R/predict.ahaz.R | 36
ahaz-1.1/ahaz/R/predict.ahazpen.R | 58 -
ahaz-1.1/ahaz/R/predict.tune.ahazpen.R |only
ahaz-1.1/ahaz/R/print.ahaz.R | 2
ahaz-1.1/ahaz/R/print.ahazpen.R | 1
ahaz-1.1/ahaz/R/print.tune.ahazpen.R | 10
ahaz-1.1/ahaz/R/summary.ahaz.R | 6
ahaz-1.1/ahaz/R/tune.ahazpen.R | 71 +
ahaz-1.1/ahaz/man/ahaz.Rd | 12
ahaz-1.1/ahaz/man/ahaz.adjust.Rd | 14
ahaz-1.1/ahaz/man/ahaz.partial.Rd | 12
ahaz-1.1/ahaz/man/ahaz.tune.control.Rd | 23
ahaz-1.1/ahaz/man/ahazisis.Rd | 23
ahaz-1.1/ahaz/man/ahazpen.Rd | 89 +-
ahaz-1.1/ahaz/man/ahazpen.fit.control.Rd | 11
ahaz-1.1/ahaz/man/ahazpen.pen.control.Rd | 41 -
ahaz-1.1/ahaz/man/plot.ahazpen.Rd | 20
ahaz-1.1/ahaz/man/plot.tune.ahazpen.Rd | 6
ahaz-1.1/ahaz/man/predict.ahaz.Rd | 15
ahaz-1.1/ahaz/man/predict.ahazpen.Rd | 37
ahaz-1.1/ahaz/man/predict.tune.ahazpen.Rd |only
ahaz-1.1/ahaz/man/summary.ahaz.Rd | 4
ahaz-1.1/ahaz/man/tune.ahazpen.Rd | 23
ahaz-1.1/ahaz/src/Makevars |only
ahaz-1.1/ahaz/src/ahaz.c | 1127 ++++++++++++++++++++----------
43 files changed, 1522 insertions(+), 1138 deletions(-)
Title: Modelling Spatial Extremes
Diff between SpatialExtremes versions 1.8-0 dated 2011-03-23 and 1.8-1 dated 2011-07-05
More information about SpatialExtremes at CRAN
Description: This package proposes several approaches for spatial
extremes modelling.
Author: Mathieu Ribatet
Maintainer: Mathieu Ribatet
SpatialExtremes-1.8-0/SpatialExtremes/src/nsgeomgauss.c |only
SpatialExtremes-1.8-1/SpatialExtremes/ChangeLog | 74 +
SpatialExtremes-1.8-1/SpatialExtremes/DESCRIPTION | 10
SpatialExtremes-1.8-1/SpatialExtremes/NEWS | 24
SpatialExtremes-1.8-1/SpatialExtremes/R/conditionalSim.R | 4
SpatialExtremes-1.8-1/SpatialExtremes/R/copula.R | 329 ++++---
SpatialExtremes-1.8-1/SpatialExtremes/R/covariance.R | 60 +
SpatialExtremes-1.8-1/SpatialExtremes/R/extremalt.R | 16
SpatialExtremes-1.8-1/SpatialExtremes/R/fitcovmat.R | 46 -
SpatialExtremes-1.8-1/SpatialExtremes/R/geomgauss.R | 16
SpatialExtremes-1.8-1/SpatialExtremes/R/kriging.R | 2
SpatialExtremes-1.8-1/SpatialExtremes/R/madogram.R | 4
SpatialExtremes-1.8-1/SpatialExtremes/R/methods.R | 76 -
SpatialExtremes-1.8-1/SpatialExtremes/R/modelChecking.R | 117 ++
SpatialExtremes-1.8-1/SpatialExtremes/R/plots.R | 14
SpatialExtremes-1.8-1/SpatialExtremes/R/predict.R | 84 +
SpatialExtremes-1.8-1/SpatialExtremes/R/schlather.R | 16
SpatialExtremes-1.8-1/SpatialExtremes/R/schlatherind.R | 16
SpatialExtremes-1.8-1/SpatialExtremes/R/simmaxstab.R | 42
SpatialExtremes-1.8-1/SpatialExtremes/R/standardErrors.R | 18
SpatialExtremes-1.8-1/SpatialExtremes/R/starting.values.R | 10
SpatialExtremes-1.8-1/SpatialExtremes/inst/doc/Figures/Schlather2Sim.png |binary
SpatialExtremes-1.8-1/SpatialExtremes/inst/doc/Figures/Smith2Sim.png |binary
SpatialExtremes-1.8-1/SpatialExtremes/inst/doc/Figures/rmaxstabSmith.png |binary
SpatialExtremes-1.8-1/SpatialExtremes/inst/doc/Figures/tbm.png |binary
SpatialExtremes-1.8-1/SpatialExtremes/inst/doc/SpatialExtremesGuide.Rnw | 97 +-
SpatialExtremes-1.8-1/SpatialExtremes/inst/doc/SpatialExtremesGuide.pdf |binary
SpatialExtremes-1.8-1/SpatialExtremes/inst/doc/layout.sty | 1
SpatialExtremes-1.8-1/SpatialExtremes/man/TIC.Rd | 2
SpatialExtremes-1.8-1/SpatialExtremes/man/condmap.Rd | 4
SpatialExtremes-1.8-1/SpatialExtremes/man/condrgp.Rd | 6
SpatialExtremes-1.8-1/SpatialExtremes/man/covariance.Rd | 14
SpatialExtremes-1.8-1/SpatialExtremes/man/extcoeff.Rd | 6
SpatialExtremes-1.8-1/SpatialExtremes/man/fitcopula.Rd | 13
SpatialExtremes-1.8-1/SpatialExtremes/man/fitcovariance.Rd | 2
SpatialExtremes-1.8-1/SpatialExtremes/man/fitmaxstab.Rd | 2
SpatialExtremes-1.8-1/SpatialExtremes/man/fitspatgev.Rd | 2
SpatialExtremes-1.8-1/SpatialExtremes/man/fmadogram.Rd | 4
SpatialExtremes-1.8-1/SpatialExtremes/man/lmadogram.Rd | 2
SpatialExtremes-1.8-1/SpatialExtremes/man/logLik.maxstab.Rd | 2
SpatialExtremes-1.8-1/SpatialExtremes/man/madogram.Rd | 4
SpatialExtremes-1.8-1/SpatialExtremes/man/map.Rd | 6
SpatialExtremes-1.8-1/SpatialExtremes/man/plot.copula.Rd |only
SpatialExtremes-1.8-1/SpatialExtremes/man/plot.maxstab.Rd | 4
SpatialExtremes-1.8-1/SpatialExtremes/man/predict.copula.Rd |only
SpatialExtremes-1.8-1/SpatialExtremes/man/predict.maxstab.Rd | 2
SpatialExtremes-1.8-1/SpatialExtremes/man/predict.spatgev.Rd | 2
SpatialExtremes-1.8-1/SpatialExtremes/man/print.copula.Rd | 13
SpatialExtremes-1.8-1/SpatialExtremes/man/print.maxstab.Rd | 2
SpatialExtremes-1.8-1/SpatialExtremes/man/print.spatgev.Rd | 2
SpatialExtremes-1.8-1/SpatialExtremes/man/profile2d.maxstab.Rd | 2
SpatialExtremes-1.8-1/SpatialExtremes/man/rcopula.Rd |only
SpatialExtremes-1.8-1/SpatialExtremes/man/simmaxstab.Rd | 10
SpatialExtremes-1.8-1/SpatialExtremes/src/Makevars | 3
SpatialExtremes-1.8-1/SpatialExtremes/src/brownResnick.c | 3
SpatialExtremes-1.8-1/SpatialExtremes/src/circulant.c | 13
SpatialExtremes-1.8-1/SpatialExtremes/src/copula.c | 94 +-
SpatialExtremes-1.8-1/SpatialExtremes/src/covariance.c | 155 +--
SpatialExtremes-1.8-1/SpatialExtremes/src/direct.c | 10
SpatialExtremes-1.8-1/SpatialExtremes/src/extremalt.c | 35
SpatialExtremes-1.8-1/SpatialExtremes/src/fitcovmat.c | 148 +--
SpatialExtremes-1.8-1/SpatialExtremes/src/geomgauss.c | 19
SpatialExtremes-1.8-1/SpatialExtremes/src/gpdproc.c |only
SpatialExtremes-1.8-1/SpatialExtremes/src/header.h | 86 -
SpatialExtremes-1.8-1/SpatialExtremes/src/kriging.c | 14
SpatialExtremes-1.8-1/SpatialExtremes/src/latentVariable.c | 52 -
SpatialExtremes-1.8-1/SpatialExtremes/src/maxLinear.c | 5
SpatialExtremes-1.8-1/SpatialExtremes/src/pairwiselik.c | 448 +++++-----
SpatialExtremes-1.8-1/SpatialExtremes/src/schlather.c | 35
SpatialExtremes-1.8-1/SpatialExtremes/src/schlatherind.c | 35
SpatialExtremes-1.8-1/SpatialExtremes/src/simextremalt.c | 41
SpatialExtremes-1.8-1/SpatialExtremes/src/simgeometric.c | 44
SpatialExtremes-1.8-1/SpatialExtremes/src/simschlather.c | 48 -
SpatialExtremes-1.8-1/SpatialExtremes/src/smith.c | 3
SpatialExtremes-1.8-1/SpatialExtremes/src/smith3d.c | 3
SpatialExtremes-1.8-1/SpatialExtremes/src/standardErrors.c | 117 +-
SpatialExtremes-1.8-1/SpatialExtremes/src/turningbands.c | 3
SpatialExtremes-1.8-1/SpatialExtremes/src/utils.c | 61 -
78 files changed, 1551 insertions(+), 1106 deletions(-)
Permanent link
More information about RcmdrPlugin.coin at CRAN
Permanent link
Title: Software for Bayesian Inference
Diff between LaplacesDemon versions 11.06.27 dated 2011-06-27 and 11.07.05 dated 2011-07-05
Description: Laplace's Demon is software for Bayesian inference.
Author: Byron Hall
Maintainer: Byron Hall
CHANGELOG | 7
DESCRIPTION | 8
NAMESPACE | 1
R/Geweke.Diagnostic.R | 2
R/LaplacesDemon.R | 4
R/distributions.R | 31
R/predict.demonoid.R | 8
R/summary.demonoid.ppc.R | 3
R/summary.laplace.ppc.R | 2
inst/CITATION | 2
inst/doc/BayesianInference.Stex | 136
inst/doc/BayesianInference.pdf |binary
inst/doc/Examples.Stex | 476 +-
inst/doc/Examples.pdf | 8763 ++++++++++++++++++++++------------------
inst/doc/LaplacesDemon.Stex | 29
inst/doc/LaplacesDemon.pdf |binary
inst/doc/References.bib | 2
man/dist.Categorical.Rd |only
man/predict.demonoid.Rd | 11
19 files changed, 5358 insertions(+), 4127 deletions(-)
Title: Dendrochronology Program Library in R
Diff between dplR versions 1.4.3 dated 2011-07-02 and 1.4.4 dated 2011-07-04
Description: This package contains functions for performing tree-ring
analyses, IO, and graphics.
Author: Andy Bunn with major additions from Mikko Korpela and other
significant contributions from Franco Biondi and Christian Zang
Maintainer: Andy Bunn
ChangeLog | 107 ++++++++
DESCRIPTION | 12
R/bai.in.R | 9
R/bai.out.R | 4
R/ccf.series.rwl.R | 55 ++--
R/chron.R | 10
R/cms.R | 13 -
R/corr.series.seg.R | 60 ++--
R/crn.plot.R | 5
R/detrend.R | 16 -
R/detrend.series.R | 49 +--
R/exactmean.R | 4
R/ffcsaps.R | 87 +++---
R/gini.coef.R | 4
R/glk.R | 37 +-
R/hanning.R | 11
R/helpers.R | 20 -
R/i.detrend.R | 4
R/i.detrend.series.R | 12
R/morlet.R | 68 ++---
R/normalize.xdate.R | 8
R/rcs.R | 16 -
R/read.rwl.R | 3
R/read.tridas.R | 230 +++++++++--------
R/read.tucson.R | 5
R/rwi.stats.R | 25 +
R/rwi.stats.running.R | 85 +++---
R/rwl.stats.R | 7
R/sea.R | 26 +-
R/sens1.R | 4
R/sens2.R | 4
R/series.rwl.plot.R | 51 ++-
R/simpleXML.R | 224 ++++++++---------
R/skel.plot.R | 68 ++---
R/spag.plot.R | 18 -
R/tbrm.R | 4
R/tridas.vocabulary.R | 3
R/wavelet.plot.R | 18 -
R/write.compact.R | 4
R/write.crn.R | 52 ++--
R/write.rwl.R | 3
R/write.tridas.R | 502 ++++++++++++++++++++-------------------
R/write.tucson.R | 49 +--
data/ca533.rda |binary
data/cana157.rda |binary
data/co021.rda |binary
data/gp.d2pith.rda |binary
data/gp.dbh.rda |binary
data/gp.po.rda |binary
data/gp.rwl.rda |binary
inst/po/fi/LC_MESSAGES/R-dplR.mo |binary
man/ccf.series.rwl.Rd | 18 -
man/chron.Rd | 12
man/corr.series.seg.Rd | 17 -
man/detrend.Rd | 4
man/detrend.series.Rd | 6
man/glk.Rd | 11
man/hanning.Rd | 20 -
man/i.detrend.Rd | 4
man/i.detrend.series.Rd | 6
man/morlet.Rd | 13 -
po/R-dplR.pot | 7
po/R-fi.po | 16 -
63 files changed, 1156 insertions(+), 974 deletions(-)
Title: Flux rate calculation from dynamic closed chamber measurements
Diff between flux versions 0.1-2 dated 2011-04-11 and 0.1-3 dated 2011-07-04
Description: Functions for the calculation of greenhouse gas flux rates
from closed chamber concentration measurements. The package
follows a modular concept: Fluxes can be calculated in just two
simple steps or in several steps if more control in details is
wanted. Additionaly plot and preparation functions are
provided.
Author: Gerald Jurasinski, Franziska Koebsch
Maintainer: Gerald Jurasinski
DESCRIPTION | 8 ++++----
R/CO2.control.R |only
R/flux.R | 29 ++++++++++++++++++++++++++++-
R/flux.calib.R | 2 +-
R/print.fluss.R |only
inst/ChangeLog | 11 +++++++++++
man/CO2.control.Rd |only
man/flux-internal.Rd |only
man/flux.Rd | 44 +++++++++++++++++++++++++++++++++++++-------
9 files changed, 81 insertions(+), 13 deletions(-)
Title: Detection of disease-associated SNP interactions in case-parent
trio data
Diff between trio versions 1.2.0 dated 2011-04-24 and 1.2.1 dated 2011-07-04
Description: Testing SNPs and SNP interactions with a genotypic TDT.
This package furthermore contains functions for computing
pairwise values of LD measures and for identifying LD blocks,
as well as functions for setting up matched case pseudo-control
genotype data for case-parent trios in order to run trio logic
regreesion, to impute missing genotypes in trios, or to
simulate case-parent trios with disease risk dependent on SNP
interaction.
Author: Holger Schwender, Qing Li
Maintainer: Holger Schwender
DESCRIPTION | 8 ++++----
R/colGxE.R | 32 ++++++++++++++------------------
R/colTDTsam.R | 4 ++--
R/fastTDT.R | 29 ++++++++++++++++++++++-------
R/tdt.R | 22 ++++++++--------------
inst/doc/trio.pdf |binary
man/colGxE.Rd | 1 +
man/tdt.Rd | 1 +
8 files changed, 52 insertions(+), 45 deletions(-)
Title: Pretty Heatmaps
Diff between pheatmap versions 0.5 dated 2011-06-15 and 0.5.1 dated 2011-07-04
Description: The package for drawing pretty heatmaps in R. The ordinary
heatmap function in R has several drawbacks, when it comes to
producing publication quality heatmaps. It is hard to produce
pictures with consistent text, cell and overall sizes and
shapes. The function pheatmap tries to alleviate the problems
by offering more fine grained control over heatmap dimensions
and appearance.
Author: Raivo Kolde
Maintainer: Raivo Kolde
DESCRIPTION | 6 +++---
R/pheatmap.r | 54 +++++++++++++++++++++++++++++++++++-------------------
man/pheatmap.Rd | 9 ++++++---
run_roxygen.r |only
4 files changed, 44 insertions(+), 25 deletions(-)
Title: A graphical approach to sequentially rejective multiple test
procedures
Diff between gMCP versions 0.6-5 dated 2011-05-26 and 0.6-6 dated 2011-07-04
Description: This package provides functions and a graphical user
interface for graphical described multiple test procedures.
Author: Kornelius Rohmeyer, Florian Klinglmueller
Maintainer: Kornelius Rohmeyer
DESCRIPTION | 8
INSTALL | 39 +-
NAMESPACE | 2
NEWS | 21 +
R/closure.R | 4
R/convertFromOldClassDefinition.R |only
R/gACT-internal.R | 42 ++
R/gMCP.R | 54 +--
R/generatePvals.R |only
R/graphMCP.R | 27 +
R/matrix2graph.R | 18 -
R/misc.R | 12
R/onLoad.R | 21 -
R/subVariables.R |only
TODO | 7
inst/doc/AQuickStart.Rnw | 1
inst/doc/AQuickStart.pdf |binary
inst/doc/Makefile | 2
inst/doc/gMCP.Rnw | 1
inst/doc/gMCP.pdf |binary
inst/doc/gMCP/AQuickStart-fake.Rnw | 1
inst/doc/gMCP/AQuickStart.Rnw | 4
inst/doc/gMCP/gMCP-fake.Rnw | 1
inst/doc/gMCP/gMCP.Rnw | 168 +++++++---
inst/doc/gMCP/parametric-fake.Rnw | 1
inst/doc/parametric.Rnw | 1
inst/doc/parametric.pdf |binary
inst/java-src/org/af/gMCP/config/Configuration.java | 8
inst/java-src/org/af/gMCP/config/GeneralConfig.java | 47 ++
inst/java-src/org/af/gMCP/config/VersionComparator.java | 76 +++-
inst/java-src/org/af/gMCP/gui/CreateGraphGUI.java | 67 ++-
inst/java-src/org/af/gMCP/gui/JSplitPaneBugWorkAround.java |only
inst/java-src/org/af/gMCP/gui/MenuBarMGraph.java | 2
inst/java-src/org/af/gMCP/gui/RControl.java | 11
inst/java-src/org/af/gMCP/gui/dialogs/DialogConfIntEstVar.java | 1
inst/java-src/org/af/gMCP/gui/dialogs/GraphSendToArchiveDialog.java | 4
inst/java-src/org/af/gMCP/gui/dialogs/NewVersionDialog.java |only
inst/java-src/org/af/gMCP/gui/graph/Edge.java | 102 ++----
inst/java-src/org/af/gMCP/gui/graph/GraphView.java | 10
inst/java-src/org/af/gMCP/gui/graph/NetList.java | 1
inst/java-src/org/af/gMCP/gui/graph/PView.java | 19 -
inst/java-src/org/af/gMCP/tests/FormatTest.java | 1
inst/java/gsrmtp.jar |binary
inst/unitTests/runit.fastgMCP.R | 11
inst/unitTests/runit.misc.R | 10
man/gMCP.Rd | 8
man/generatePvals.Rd |only
src/gMCP.c | 25 +
48 files changed, 559 insertions(+), 279 deletions(-)
Title: Species distribution modeling
Diff between dismo versions 0.6-12 dated 2011-06-15 and 0.7-1 dated 2011-07-04
Description: Functions for species distribution modeling, that is,
predicting entire geographic distributions form occurences at
specific sites.
Author: Robert J. Hijmans, Steven Phillips, John Leathwick and Jane
Elith
Maintainer:
ChangeLog | 4 ++++
DESCRIPTION | 17 ++++++++---------
NAMESPACE | 1 -
R/Mahalanobis.R | 2 +-
R/Mahalanobis.predict.R | 5 +++--
R/maxent.R | 19 +++++++++++++++++--
R/maxent.predict.R | 7 ++++---
R/onLoad.R | 3 +--
data/Anguilla_grids.RData |binary
data/Anguilla_test.RData |binary
data/Anguilla_train.RData |binary
data/ECOcrops.RData |binary
data/acaule.RData |binary
inst/doc/brt.pdf |binary
inst/doc/sdm.pdf |binary
man/mahal.Rd | 15 ++++++++++++++-
man/maxent.Rd | 4 ++--
17 files changed, 54 insertions(+), 23 deletions(-)
Title: Deductive correction of simple rounding, typing and sign errors
Diff between deducorrect versions 1.0-0 dated 2011-07-02 and 1.0-1 dated 2011-07-04
Description: Deductive correction of simple rounding, typing and sign
errors
Author: Mark van der Loo, Edwin de Jonge, and Sander Scholtus
Maintainer: Mark van der Loo
deducorrect-1.0-0/deducorrect/inst/doc/deducorrect-vignette.ps |only
deducorrect-1.0-0/deducorrect/inst/doc/deducorrect-vignette.tex |only
deducorrect-1.0-1/deducorrect/DESCRIPTION | 6 +++---
deducorrect-1.0-1/deducorrect/NEWS | 3 +++
deducorrect-1.0-1/deducorrect/R/correctSigns.R | 8 ++++----
deducorrect-1.0-1/deducorrect/inst/doc/buildVignette.bash | 4 +---
deducorrect-1.0-1/deducorrect/inst/doc/deducorrect-vignette.Snw.edited |only
deducorrect-1.0-1/deducorrect/inst/doc/deducorrect-vignette.dvi |binary
deducorrect-1.0-1/deducorrect/inst/doc/deducorrect-vignette.pdf |binary
deducorrect-1.0-1/deducorrect/inst/doc/sweave.r | 1 +
deducorrect-1.0-1/deducorrect/inst/tests/testCorrectSigns.R |only
11 files changed, 12 insertions(+), 10 deletions(-)
Title: Statistical Matching
Diff between StatMatch versions 1.0.1 dated 2011-03-12 and 1.0.2 dated 2011-07-04
Description: This package provides some R functions to perform
statistical matching between two data sources sharing a number
of common variables. Some functions can also be used to impute
missing values in data sets through hot deck imputation
methods. Methods to perform statistical atching when dealing
with data from complex sample surveys are available too.
Author: Marcello D'Orazio
Maintainer: Marcello D'Orazio
StatMatch-1.0.1/StatMatch/R/maximum.dist.r |only
StatMatch-1.0.1/StatMatch/chm |only
StatMatch-1.0.2/StatMatch/DESCRIPTION | 14 +++----
StatMatch-1.0.2/StatMatch/NEWS | 8 ++++
StatMatch-1.0.2/StatMatch/R/NND.hotdeck.R | 40 ++++++++++----------
StatMatch-1.0.2/StatMatch/R/RANDwNND.hotdeck.R | 23 +++++++----
StatMatch-1.0.2/StatMatch/R/mahalanobis.dist.R |only
StatMatch-1.0.2/StatMatch/R/maximum.dist.R |only
StatMatch-1.0.2/StatMatch/R/mixed.mtc.R | 24 +++++++-----
StatMatch-1.0.2/StatMatch/man/Fbwidths.by.x.Rd | 6 +--
StatMatch-1.0.2/StatMatch/man/Frechet.bounds.cat.Rd | 12 +++---
StatMatch-1.0.2/StatMatch/man/NND.hotdeck.Rd | 21 +++++-----
StatMatch-1.0.2/StatMatch/man/RANDwNND.hotdeck.Rd | 18 ++++-----
StatMatch-1.0.2/StatMatch/man/comb.samples.Rd | 34 ++++++++---------
StatMatch-1.0.2/StatMatch/man/create.fused.Rd | 10 ++---
StatMatch-1.0.2/StatMatch/man/fact2dummy.Rd | 2 -
StatMatch-1.0.2/StatMatch/man/gower.dist.Rd | 2 -
StatMatch-1.0.2/StatMatch/man/harmonize.x.Rd | 13 +++---
StatMatch-1.0.2/StatMatch/man/mahalanobis.dist.Rd |only
StatMatch-1.0.2/StatMatch/man/maximum.dist.Rd | 8 ++--
StatMatch-1.0.2/StatMatch/man/mixed.mtc.Rd | 34 ++++++++---------
StatMatch-1.0.2/StatMatch/man/rankNND.hotdeck.Rd | 10 ++---
22 files changed, 146 insertions(+), 133 deletions(-)
Title: Automates the creation of new statistical analysis projects.
Diff between ProjectTemplate versions 0.3-3 dated 2011-07-02 and 0.3-4 dated 2011-07-04
More information about ProjectTemplate at CRAN
Description: ProjectTemplate provides functions to automatically build
a directory structure for a new R project. Using this
structure, ProjectTemplate automates data loading,
preprocessing, library importing and unit testing.
Author: John Myles White
Maintainer: John Myles White
ProjectTemplate-0.3-3/ProjectTemplate/R/run.tests.R |only
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70 files changed, 381 insertions(+), 222 deletions(-)
Permanent link
Title: Bindings for the Geospatial Data Abstraction Library
Diff between rgdal versions 0.6-33 dated 2010-12-16 and 0.7-1 dated 2011-07-04
Description: Provides bindings to Frank Warmerdam's Geospatial Data
Abstraction Library (GDAL) (>= 1.3.1) and access to
projection/transformation operations from the PROJ.4 library.
The GDAL and PROJ.4 libraries are external to the package, and,
when installing the package from source, must be correctly
installed first. Both GDAL raster and OGR vector map data can
be imported into R, and GDAL raster data and OGR vector data
exported. Use is made of classes defined in the sp package.
rgdal binaries for OSX are available from the CRAN (extras)
repository.
Author: Timothy H. Keitt
Maintainer: Roger Bivand
ChangeLog | 80
DESCRIPTION | 8
R/AAA.R | 1
R/SGDF2RGB.R | 4
R/gdal.R | 30
R/ogr.R | 6
R/ogr_sp.R | 18
R/ogr_write.R | 2
R/project.R | 6
R/sgdf_gdal.R | 2
R/sp_gdal.R | 24
R/subs.R | 6
configure | 5064 +++++++++++++++++++++++++++-----------------------
configure.in | 56
inst/ChangeLog | 80
man/readGDAL.Rd | 3
man/readOGR.Rd | 3
src/OGR_write.cpp | 53
src/gdal-bindings.cpp | 336 ++-
src/local_stubs.c | 1
src/ogr_geom.cpp | 48
src/ogr_proj.cpp | 19
src/ogrdrivers.cpp | 5
src/ogrsource.cpp | 52
src/projectit.cpp | 48
src/rgdal.h | 17
tests |only
27 files changed, 3636 insertions(+), 2336 deletions(-)
Title: Tools for mapping multiple complex traits
Diff between qtlmt versions 0.1-1 dated 2011-06-27 and 0.1-2 dated 2011-07-04
Description: This software provides tools for simultaneous analysis of
multiple traits in a backcross (BC) or recombinant inbred lines
(RIL) population. It can be used to select an optimal subset of
traits for multiple-trait mapping, analyze multiple traits via
the SURE model and perform multiple-trait composite
multiple-interval mapping.
Author: Riyan Cheng
Maintainer: Riyan Cheng
ChangeLog | 4
DESCRIPTION | 8
NAMESPACE | 13 +
R/misc.R | 61 +++---
R/mstep.R |only
R/mtcmim.R | 207 +++++++++++-----------
R/sure.R | 492 +++++++++++-------------------------------------------
R/varSel.R | 107 ++++++-----
man/gv2mpos.Rd | 16 -
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man/mtcmim.Rd | 23 +-
man/mtcmimStep.Rd | 34 +--
man/sureEps.Rd | 13 -
man/sureEst.Rd | 23 --
man/sureStep.Rd | 42 ++--
man/varGroups.Rd | 13 -
man/varSelect.Rd | 11 -
man/varStep.Rd | 19 --
man/varT2.Rd | 11 -
21 files changed, 408 insertions(+), 689 deletions(-)
Title: Analysis with the Constant Elasticity of Scale (CES) function
Diff between micEconCES versions 0.9-2 dated 2011-06-05 and 0.9-4 dated 2011-07-04
Description: Tools for economic analysis and economic modelling with a
Constant Elasticity of Scale (CES) function
Author: Arne Henningsen and Geraldine Henningsen
Maintainer: Arne Henningsen
micEconCES-0.9-2/micEconCES/inst/doc/Kemfert |only
micEconCES-0.9-4/micEconCES/DESCRIPTION | 10
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micEconCES-0.9-4/micEconCES/inst/doc/CES.Rnw | 396 ++++++------
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micEconCES-0.9-4/micEconCES/inst/doc/references.bib | 74 +-
8 files changed, 292 insertions(+), 210 deletions(-)
Title: Hierarchical Generalized Linear Models
Diff between hglm versions 1.2-1 dated 2011-06-24 and 1.2-2 dated 2011-07-04
Description: The hglm package is used to fit hierarchical generalized
linear models. It can be used for linear mixed models and
generalized linear mixed models with random effects for a
variety of links and a variety of distributions for both the
outcomes and the random effects. Fixed effects can also be
fitted in the dispersion part of the mean model.
Author: Moudud Alam, Xia Shen, Lars Ronnegard
Maintainer: Lars Ronnegard
hglm-1.2-1/hglm/R/GAMMA.R |only
hglm-1.2-2/hglm/DESCRIPTION | 10 ++++----
hglm-1.2-2/hglm/NAMESPACE | 2 -
hglm-1.2-2/hglm/R/hglm.R | 2 -
hglm-1.2-2/hglm/R/hglm.default.R | 41 ++++++++++++++++++++++++++++++++++-
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hglm-1.2-2/hglm/man/hglm-package.Rd | 8 +++---
11 files changed, 52 insertions(+), 13 deletions(-)
Title: Search Pubmed, Make bibliographic content analyzable
Diff between RISmed versions 1.2.1 dated 2011-04-08 and 1.2.3 dated 2011-07-04
Description: Pubmed search through R, creating analyzable object from
Pubmed results and RIS files. This package replaces ris.
Author: S. A. Kovalchik
Maintainer: S. A. Kovalchik
DESCRIPTION | 8 ++++----
R/cite.R | 1 +
2 files changed, 5 insertions(+), 4 deletions(-)
Title: Functions to access vegetation databases (Turboveg and VegetWeb)
and prepare data for analysis
Diff between vegdata versions 0.3.1 dated 2011-06-30 and 0.3.2 dated 2011-07-02
Description: Handling of vegetation data sets from personal Turboveg or
online VegetWeb Databases. Taxonomic harmonization of datasets
with the help of the German taxonomical standard list
"GermanSL".
Author: Florian Jansen
Maintainer: Florian Jansen
DESCRIPTION | 6 +++---
R/child.r | 4 ++--
inst/ChangeLog | 12 ++++++++----
inst/doc/vegdata.pdf |binary
4 files changed, 13 insertions(+), 9 deletions(-)
Title: classes and methods for spatio-temporal data
Diff between spacetime versions 0.4-4 dated 2011-06-21 and 0.5-0 dated 2011-07-02
Description: A package with classes and methods for spatio-temporal
data.
Author: Edzer Pebesma
Maintainer: Edzer Pebesma
spacetime-0.4-4/spacetime/TODO |only
spacetime-0.5-0/spacetime/DESCRIPTION | 8
spacetime-0.5-0/spacetime/R/STFDF-methods.R | 12
spacetime-0.5-0/spacetime/R/apply.R | 3
spacetime-0.5-0/spacetime/R/over.R | 59
spacetime-0.5-0/spacetime/R/stplot.R | 3
spacetime-0.5-0/spacetime/demo/CressieWikle.R | 16
spacetime-0.5-0/spacetime/inst/doc/spacetime.Rnw | 51
spacetime-0.5-0/spacetime/inst/doc/spacetime.pdf | 2575 +++++++++++------------
spacetime-0.5-0/spacetime/inst/doc/sto.Rnw | 119 -
spacetime-0.5-0/spacetime/inst/doc/sto.pdf | 1583 +++++++-------
spacetime-0.5-0/spacetime/man/over.Rd | 2
spacetime-0.5-0/spacetime/tests/basic.Rout.save | 36
13 files changed, 2348 insertions(+), 2119 deletions(-)
Title: Visualisation of hexagonal Kohonen maps
Diff between somplot versions 1.04 dated 2011-05-19 and 1.05 dated 2011-07-02
Description: The package provides the plot function som.plot() to
create high quality visualisations of hexagonal Kohonen maps
(self-organising maps).
Author: Benjamin Schulz, Andreas Dominik
Maintainer: Andreas Dominik
DESCRIPTION | 6 +++---
R/somplot.R | 2 +-
man/somplot-package.Rd | 4 ++--
3 files changed, 6 insertions(+), 6 deletions(-)
Title: Stochastic Approximation Expectation Maximization (SAEM)
algorithm
Diff between saemix versions 0.95 dated 2011-06-30 and 0.96 dated 2011-07-02
Description: The SAEM package implements the Stochastic Approximation
EM algorithm for parameter estimation in (non)linear mixed
effects models. The SAEM algorithm: - computes the maximum
likelihood estimator of the population parameters, without any
approximation of the model (linearization, quadrature
approximation,...), using the Stochastic Approximation
Expectation Maximization (SAEM) algorithm, - provides standard
errors for the maximum likelihood estimator - estimates the
conditional modes, the conditional means and the conditional
standard deviations of the individual parameters, using the
Hastings-Metropolis algorithm. Several applications of SAEM in
agronomy, animal breeding and PKPD analysis have been published
by members of the Monolix group (http://software.monolix.org/).
Author: Emmanuelle Comets, Audrey Lavenu, Marc Lavielle.
Maintainer: Emmanuelle Comets
saemix-0.95/saemix/inst/saemix.pdf |only
saemix-0.95/saemix/inst/userguide_saemix.pdf |only
saemix-0.96/saemix/DESCRIPTION | 6 +-
saemix-0.96/saemix/R/main.R | 66 +++++++++++++------------
saemix-0.96/saemix/R/zzz.R | 5 +
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saemix-0.96/saemix/man/PD1.saemix.Rd | 5 +
saemix-0.96/saemix/man/conddist.saemix.Rd | 2
saemix-0.96/saemix/man/default.saemix.plots.Rd | 2
saemix-0.96/saemix/man/fim.saemix.Rd | 2
saemix-0.96/saemix/man/llgq.saemix.Rd | 2
saemix-0.96/saemix/man/llis.saemix.Rd | 2
saemix-0.96/saemix/man/map.saemix.Rd | 3 -
saemix-0.96/saemix/man/oxboys.saemix.Rd | 3 -
saemix-0.96/saemix/man/psi.Rd | 2
saemix-0.96/saemix/man/saemix-package.Rd | 2
saemix-0.96/saemix/man/saemix.Rd | 3 -
saemix-0.96/saemix/man/saemix.plot.data.Rd | 2
saemix-0.96/saemix/man/saemix.plot.select.Rd | 2
saemix-0.96/saemix/man/saemix.plots.Rd | 2
saemix-0.96/saemix/man/theo.saemix.Rd | 6 +-
saemix-0.96/saemix/man/yield.saemix.Rd | 3 -
22 files changed, 67 insertions(+), 53 deletions(-)
Title: Random name generating function and data set
Diff between randomNames versions 0.0-2 dated 2011-06-15 and 0.0-3 dated 2011-07-02
Description: Function to generate random gender and ethnicity correct
first and/or last names. Names are chosen proportionally based
upon their probability of appearing in a large scale data base
of real names.
Author: Damian W. Betebenner
Maintainer: Damian W. Betebenner
DESCRIPTION | 10 +++++-----
R/randomNames.R | 8 ++++++--
inst/CITATION | 4 ++--
inst/NEWS | 4 ++++
man/randomNames-package.Rd | 4 ++--
5 files changed, 19 insertions(+), 11 deletions(-)
Title: Flexible Copula Density Estimation with Penalized Hierarchical
B-Splines
Diff between pencopula versions 0.3 dated 2011-06-28 and 0.3.1 dated 2011-07-02
Description: Flexible copula density estimation with penalized
hierarchical B-Splines.
Author: Christian Schellhase
Maintainer: Christian Schellhase
DESCRIPTION | 8 ++--
R/Derv2.R | 7 ++-
R/hierarch.bs.R | 2 -
R/knots.start.R | 55 ++++++++++++++++++-------------
R/my.IC.r | 6 +--
R/new.weights.R | 1
R/pencopula.R | 83 ++++++++++++++++++++++++++++++-----------------
R/plot.pencopula.R | 13 +++++--
R/print.pencopula.R | 5 +-
R/start.valgrid.R | 2 -
man/pencopula-package.Rd | 4 +-
11 files changed, 113 insertions(+), 73 deletions(-)
Title: Dendrochronology Program Library in R
Diff between dplR versions 1.4.2 dated 2011-06-04 and 1.4.3 dated 2011-07-02
Description: This package contains functions for performing tree-ring
analyses, IO, and graphics.
Author: Andy Bunn with major additions from Mikko Korpela and other
significant contributions from Franco Biondi and Christian Zang
Maintainer: Andy Bunn
ChangeLog | 156 ++++++++++++++++-
DESCRIPTION | 11 -
R/bai.in.R | 2
R/bai.out.R | 3
R/ccf.series.rwl.R | 14 -
R/cms.R | 133 ++++++--------
R/combine.rwl.R | 6
R/corr.rwl.seg.R | 43 ++--
R/corr.series.seg.R | 15 -
R/crn.plot.R | 9
R/detrend.series.R | 25 +-
R/ffcsaps.R | 6
R/glk.R | 2
R/helpers.R | 3
R/i.detrend.R | 6
R/i.detrend.series.R | 9
R/rcs.R | 23 +-
R/read.compact.R | 8
R/read.crn.R | 32 ++-
R/read.fh.R | 8
R/read.rwl.R | 15 +
R/read.tridas.R | 427 ++++++++++++++++++++++++-----------------------
R/read.tucson.R | 27 +-
R/rwi.stats.R | 2
R/rwi.stats.running.R | 6
R/rwl.stats.R | 3
R/sea.R | 19 +-
R/seg.plot.R | 4
R/series.rwl.plot.R | 43 ++--
R/skel.plot.R | 6
R/spag.plot.R | 6
R/wavelet.plot.R | 10 -
R/write.compact.R | 5
R/write.crn.R | 16 -
R/write.tridas.R | 57 ++----
R/write.tucson.R | 12 -
inst/po |only
man/ccf.series.rwl.Rd | 12 -
man/corr.rwl.seg.Rd | 6
man/crn.plot.Rd | 24 +-
man/detrend.Rd | 23 +-
man/glk.Rd | 3
man/po.to.wc.Rd | 5
man/rwi.stats.running.Rd | 68 ++++---
man/series.rwl.plot.Rd | 2
man/skel.plot.Rd | 46 ++---
man/tbrm.Rd | 16 -
man/wavelet.plot.Rd | 4
po |only
src/dplR.h |only
src/rcompact.c | 88 ++++-----
51 files changed, 834 insertions(+), 635 deletions(-)
Title: Deductive correction of simple rounding, typing and sign errors
Diff between deducorrect versions 0.9-6 dated 2011-06-29 and 1.0-0 dated 2011-07-02
Description: Deductive correction of simple rounding, typing and sign
errors
Author: Mark van der Loo, Edwin de Jonge, and Sander Scholtus
Maintainer: Mark van der Loo
DESCRIPTION | 6 +++---
NEWS | 3 +++
inst/doc/deducorrect-vignette.Snw | 4 ++--
inst/doc/deducorrect-vignette.pdf |binary
inst/doc/deducorrect-vignette.tex | 8 ++++----
inst/doc/index.html | 3 +++
inst/doc/vanderlooDeJongeScholtus2011.pdf |only
7 files changed, 15 insertions(+), 9 deletions(-)
Title: Extension of data.frame for fast indexing, fast ordered joins
and fast grouping.
Diff between data.table versions 1.6.1 dated 2011-06-29 and 1.6.2 dated 2011-07-02
Description: Enhanced data.frame. Fast indexing, fast ordered joins and
fast grouping in a short and flexible syntax. i and j may be
expressions of column names directly, for faster development.
Example: X[Y] is a fast join for large data.
Author: M Dowle, T Short, S Lianoglou
Maintainer: M Dowle
DESCRIPTION | 6
NEWS | 20
R/IDateTime.R | 1
R/data.table.R | 3
R/setkey.R | 19
inst/doc/datatable-faq.pdf | 905 ++++++++++++++++++++---------------------
inst/doc/datatable-intro.pdf |binary
inst/doc/datatable-timings.pdf |binary
inst/tests/tests.R | 11
man/data.table.Rd | 7
man/setkey.Rd | 3
src/dogroups.c | 7
src/readfile.c | 2
src/reorder.c |only
14 files changed, 507 insertions(+), 477 deletions(-)
Title: Plot a correlogram
Diff between corrgram versions 0.1 dated 2006-12-01 and 1.0 dated 2011-07-02
Description: Calculates correlation of variables and displays the
results graphically.
Author: Kevin Wright
Maintainer: Kevin Wright
corrgram-0.1/corrgram/data/auto.R |only
corrgram-0.1/corrgram/data/baseball.R |only
corrgram-1.0/corrgram/DESCRIPTION | 26 -
corrgram-1.0/corrgram/NEWS |only
corrgram-1.0/corrgram/R/corrgram.r | 572 ++++++++++++++------------------
corrgram-1.0/corrgram/data/auto.rda |only
corrgram-1.0/corrgram/data/baseball.rda |only
corrgram-1.0/corrgram/data/vote.rda |only
corrgram-1.0/corrgram/man/auto.Rd | 4
corrgram-1.0/corrgram/man/baseball.Rd | 15
corrgram-1.0/corrgram/man/corrgram.Rd | 39 +-
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13 files changed, 298 insertions(+), 358 deletions(-)
Title: Visualization and Imputation of Missing Values
Diff between VIM versions 2.0.1 dated 2011-05-05 and 2.0.2 dated 2011-07-02
Description: This package introduces new tools for the visualization of
missing values in R, which can be used for exploring the data
and the structure of the missing values. Depending on this
structure, they may help to identify the mechanism generating
the missings. A graphical user interface allows an easy
handling of the implemented plot methods.
Author: Matthias Templ, Andreas Alfons, Alexander Kowarik
Maintainer: Matthias Templ
VIM-2.0.1/VIM/inst/tklibs/BWidget-1.9.0/images/Thumbs.db |only
VIM-2.0.2/VIM/DESCRIPTION | 8
VIM-2.0.2/VIM/R/aggr.R | 516 ++++++++-------
VIM-2.0.2/VIM/inst/doc/.directory |only
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VIM-2.0.2/VIM/inst/doc/screenshot8.eps |only
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VIM-2.0.2/VIM/man/aggr.Rd | 53 +
VIM-2.0.2/VIM/src/gowerD.cpp | 2
34 files changed, 318 insertions(+), 261 deletions(-)
Title: Record Linkage in R
Diff between RecordLinkage versions 0.3-2 dated 2011-05-11 and 0.3-3 dated 2011-07-02
Description: Provides functions for linking and deduplicating data
sets. Methods based on a stochastical approach are implemented
as well as classification algorithms from the machine learning
domain.
Author: Andreas Borg
Maintainer: Murat Sariyar
RecordLinkage-0.3-2/RecordLinkage/R/firstlib.r |only
RecordLinkage-0.3-3/RecordLinkage/DESCRIPTION | 20 +--
RecordLinkage-0.3-3/RecordLinkage/NAMESPACE |only
RecordLinkage-0.3-3/RecordLinkage/NEWS | 12 ++
RecordLinkage-0.3-3/RecordLinkage/R/classify.r | 30 +++++
RecordLinkage-0.3-3/RecordLinkage/R/compare.r | 33 +++---
RecordLinkage-0.3-3/RecordLinkage/R/em-methods.r | 12 +-
RecordLinkage-0.3-3/RecordLinkage/R/epilink-methods.r | 54 +++++-----
RecordLinkage-0.3-3/RecordLinkage/R/getPairs-methods.r | 14 +-
RecordLinkage-0.3-3/RecordLinkage/R/onAttach.r |only
RecordLinkage-0.3-3/RecordLinkage/R/stochastic.r |only
RecordLinkage-0.3-3/RecordLinkage/R/strcmp.r | 6 -
RecordLinkage-0.3-3/RecordLinkage/inst/doc/BigData.pdf |binary
RecordLinkage-0.3-3/RecordLinkage/inst/doc/EVT.pdf |binary
RecordLinkage-0.3-3/RecordLinkage/inst/doc/Supervised.pdf |binary
RecordLinkage-0.3-3/RecordLinkage/inst/doc/WeightBased.pdf |binary
RecordLinkage-0.3-3/RecordLinkage/inst/doc/WeightBased.rnw | 4
RecordLinkage-0.3-3/RecordLinkage/inst/unitTests/data1.fsWeights.txt |only
RecordLinkage-0.3-3/RecordLinkage/inst/unitTests/runit.getPairs.r | 9 +
RecordLinkage-0.3-3/RecordLinkage/inst/unitTests/runit.stochastic.r |only
RecordLinkage-0.3-3/RecordLinkage/inst/unitTests/runit.various.r | 13 ++
RecordLinkage-0.3-3/RecordLinkage/man/stochastic.rd |only
RecordLinkage-0.3-3/RecordLinkage/man/trainSupv.Rd | 17 +++
23 files changed, 155 insertions(+), 69 deletions(-)
Title: R Code for MARK Analysis
Diff between RMark versions 2.0.5 dated 2011-06-30 and 2.0.6 dated 2011-07-02
Description: This package provides an interface to the software package
MARK developed by Gary White. MARK is freely available at
(http://www.phidot.org/software/mark/download/) but is not open
source.
Author: Jeff Laake
Maintainer: Jeff Laake
DESCRIPTION | 8 ++++----
man/IELogitNormalMR.Rd | 3 ++-
man/LogitNormalMR.Rd | 4 ++--
man/PoissonMR.Rd | 4 ++--
man/Poisson_twoMR.Rd | 3 ++-
man/Whatsnew.Rd | 5 +++++
6 files changed, 17 insertions(+), 10 deletions(-)
Title: Automates the creation of new statistical analysis projects.
Diff between ProjectTemplate versions 0.1-3 dated 2010-10-03 and 0.3-3 dated 2011-07-02
More information about ProjectTemplate at CRAN
Description: ProjectTemplate provides functions to automatically build
a directory structure for a new R project. Using this
structure, ProjectTemplate automates data loading,
preprocessing, library importing and unit testing.
Author: John Myles White
Maintainer: John Myles White
ProjectTemplate-0.1-3/ProjectTemplate/R/show.updates.R |only
ProjectTemplate-0.1-3/ProjectTemplate/data_examples/a.csv |only
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ProjectTemplate-0.1-3/ProjectTemplate/data_examples/p.sql |only
ProjectTemplate-0.1-3/ProjectTemplate/file_formats.markdown |only
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ProjectTemplate-0.1-3/ProjectTemplate/man/show.updates.Rd |only
ProjectTemplate-0.3-3/ProjectTemplate/.gitignore | 2
ProjectTemplate-0.3-3/ProjectTemplate/ChangeLog | 41 ++
ProjectTemplate-0.3-3/ProjectTemplate/DESCRIPTION | 24 -
ProjectTemplate-0.3-3/ProjectTemplate/NAMESPACE |only
ProjectTemplate-0.3-3/ProjectTemplate/R/arff.reader.R |only
ProjectTemplate-0.3-3/ProjectTemplate/R/cache.R |only
ProjectTemplate-0.3-3/ProjectTemplate/R/cache.name.R |only
ProjectTemplate-0.3-3/ProjectTemplate/R/clean.variable.name.R |only
ProjectTemplate-0.3-3/ProjectTemplate/R/create.project.R | 33 +
ProjectTemplate-0.3-3/ProjectTemplate/R/csv.reader.R |only
ProjectTemplate-0.3-3/ProjectTemplate/R/dbf.reader.R |only
ProjectTemplate-0.3-3/ProjectTemplate/R/epiinfo.reader.R |only
ProjectTemplate-0.3-3/ProjectTemplate/R/extensions.dispatch.table.R |only
ProjectTemplate-0.3-3/ProjectTemplate/R/load.project.R | 176 +++++++++-
ProjectTemplate-0.3-3/ProjectTemplate/R/mtp.reader.R |only
ProjectTemplate-0.3-3/ProjectTemplate/R/octave.reader.R |only
ProjectTemplate-0.3-3/ProjectTemplate/R/r.reader.R |only
ProjectTemplate-0.3-3/ProjectTemplate/R/rdata.reader.R |only
ProjectTemplate-0.3-3/ProjectTemplate/R/reload.project.R |only
ProjectTemplate-0.3-3/ProjectTemplate/R/run.project.R |only
ProjectTemplate-0.3-3/ProjectTemplate/R/run.tests.R | 4
ProjectTemplate-0.3-3/ProjectTemplate/R/spss.reader.R |only
ProjectTemplate-0.3-3/ProjectTemplate/R/sql.reader.R |only
ProjectTemplate-0.3-3/ProjectTemplate/R/stata.reader.R |only
ProjectTemplate-0.3-3/ProjectTemplate/R/systat.reader.R |only
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ProjectTemplate-0.3-3/ProjectTemplate/R/tsv.reader.R |only
ProjectTemplate-0.3-3/ProjectTemplate/R/url.reader.R |only
ProjectTemplate-0.3-3/ProjectTemplate/R/wsv.reader.R |only
ProjectTemplate-0.3-3/ProjectTemplate/R/xls.reader.R |only
ProjectTemplate-0.3-3/ProjectTemplate/R/xlsx.reader.R |only
ProjectTemplate-0.3-3/ProjectTemplate/R/xport.reader.R |only
ProjectTemplate-0.3-3/ProjectTemplate/README.markdown | 88 -----
ProjectTemplate-0.3-3/ProjectTemplate/TODO | 41 +-
ProjectTemplate-0.3-3/ProjectTemplate/data_examples/q.sav |only
ProjectTemplate-0.3-3/ProjectTemplate/ideas |only
ProjectTemplate-0.3-3/ProjectTemplate/inst/defaults/full |only
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ProjectTemplate-0.3-3/ProjectTemplate/man/ProjectTemplate-package.Rd | 6
ProjectTemplate-0.3-3/ProjectTemplate/man/cache.Rd |only
ProjectTemplate-0.3-3/ProjectTemplate/man/clean.variable.name.Rd |only
ProjectTemplate-0.3-3/ProjectTemplate/man/create.project.Rd | 10
ProjectTemplate-0.3-3/ProjectTemplate/man/reload.project.Rd |only
ProjectTemplate-0.3-3/ProjectTemplate/man/run.project.Rd |only
ProjectTemplate-0.3-3/ProjectTemplate/man/translate.dcf.Rd |only
ProjectTemplate-0.3-3/ProjectTemplate/tests/1.R | 45 ++
ProjectTemplate-0.3-3/ProjectTemplate/tests/2.R |only
ProjectTemplate-0.3-3/ProjectTemplate/tests/3.R |only
ProjectTemplate-0.3-3/ProjectTemplate/website |only
ProjectTemplate-0.3-3/ProjectTemplate/workflows.dot |only
81 files changed, 343 insertions(+), 127 deletions(-)
Permanent link
Title: Pharmacometric tools for data preparation, modeling, simulation,
and reporting
Diff between MIfuns versions 4.3.2 dated 2011-06-05 and 4.3.7 dated 2011-07-02
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
MIfuns-4.3.2/MIfuns/inst/sample/script/.Rhistory |only
MIfuns-4.3.2/MIfuns/inst/sample/script/wikitab.Rnw |only
MIfuns-4.3.2/MIfuns/wikimath |only
MIfuns-4.3.7/MIfuns/DESCRIPTION | 8
MIfuns-4.3.7/MIfuns/NAMESPACE | 2
MIfuns-4.3.7/MIfuns/R/latex.R |only
MIfuns-4.3.7/MIfuns/R/omegacor.R | 14
MIfuns-4.3.7/MIfuns/R/parens.R |only
MIfuns-4.3.7/MIfuns/R/runCommand.R | 3
MIfuns-4.3.7/MIfuns/R/wikimath.R | 6
MIfuns-4.3.7/MIfuns/inst/sample/nonmem/1005.boot/CombRunLog.csv | 1200
MIfuns-4.3.7/MIfuns/inst/sample/nonmem/1005.boot/log.csv |23400 ++++++----
MIfuns-4.3.7/MIfuns/inst/sample/nonmem/1005/1005.ctl | 9
MIfuns-4.3.7/MIfuns/inst/sample/nonmem/1005/1005.lst | 35
MIfuns-4.3.7/MIfuns/inst/sample/nonmem/1005/diagnostics.pdf | 2448 -
MIfuns-4.3.7/MIfuns/inst/sample/nonmem/1105/1105.ctl | 7
MIfuns-4.3.7/MIfuns/inst/sample/nonmem/1105/1105.lst | 21
MIfuns-4.3.7/MIfuns/inst/sample/nonmem/ctl/1005.ctl | 9
MIfuns-4.3.7/MIfuns/inst/sample/nonmem/ctl/1105.ctl | 9
MIfuns-4.3.7/MIfuns/inst/sample/script/assemble.pdf |binary
MIfuns-4.3.7/MIfuns/inst/sample/script/assemble.tex | 4
MIfuns-4.3.7/MIfuns/inst/sample/script/covplot-covplot.pdf |only
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MIfuns-4.3.7/MIfuns/inst/sample/script/covplot.pdf |only
MIfuns-4.3.7/MIfuns/inst/sample/script/covplot.tex |only
MIfuns-4.3.7/MIfuns/inst/sample/script/model-qq.pdf | 4
MIfuns-4.3.7/MIfuns/inst/sample/script/model-qqdensity.pdf | 2990 -
MIfuns-4.3.7/MIfuns/inst/sample/script/model-qqdetail.pdf | 4
MIfuns-4.3.7/MIfuns/inst/sample/script/model.Rnw | 215
MIfuns-4.3.7/MIfuns/inst/sample/script/model.pdf |binary
MIfuns-4.3.7/MIfuns/inst/sample/script/model.tex | 615
MIfuns-4.3.7/MIfuns/inst/sample/script/parameters.Rnw |only
MIfuns-4.3.7/MIfuns/inst/sample/script/parameters.pdf |only
MIfuns-4.3.7/MIfuns/inst/sample/script/parameters.tex |only
MIfuns-4.3.7/MIfuns/inst/sample/script/settings.sty | 2
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MIfuns-4.3.7/MIfuns/man/MIfuns-package.Rd | 4
MIfuns-4.3.7/MIfuns/man/NONR.Rd | 2
MIfuns-4.3.7/MIfuns/man/align.decimal.Rd |only
MIfuns-4.3.7/MIfuns/man/breaks.Rd |only
MIfuns-4.3.7/MIfuns/man/colname.Rd | 30
MIfuns-4.3.7/MIfuns/man/command.Rd |only
MIfuns-4.3.7/MIfuns/man/helpList.Rd | 22
MIfuns-4.3.7/MIfuns/man/helpReport.Rd | 3
MIfuns-4.3.7/MIfuns/man/is.alpha.Rd |only
MIfuns-4.3.7/MIfuns/man/is.latex.token.Rd |only
MIfuns-4.3.7/MIfuns/man/is.one.nonalpha.Rd |only
MIfuns-4.3.7/MIfuns/man/latex.args.Rd |only
MIfuns-4.3.7/MIfuns/man/latex.options.Rd |only
MIfuns-4.3.7/MIfuns/man/ltable.Rd |only
MIfuns-4.3.7/MIfuns/man/ltable.data.frame.Rd |only
MIfuns-4.3.7/MIfuns/man/nm.pl.Rd | 20
MIfuns-4.3.7/MIfuns/man/omegacor.Rd | 23
MIfuns-4.3.7/MIfuns/man/parens.Rd |only
MIfuns-4.3.7/MIfuns/man/partab.Rd | 30
MIfuns-4.3.7/MIfuns/man/row2tabular.Rd |only
MIfuns-4.3.7/MIfuns/man/spaces.Rd |only
MIfuns-4.3.7/MIfuns/man/tabular.Rd |only
MIfuns-4.3.7/MIfuns/man/tabular.data.frame.Rd |only
MIfuns-4.3.7/MIfuns/man/tabularformat.Rd |only
MIfuns-4.3.7/MIfuns/man/tagvalue.Rd |only
MIfuns-4.3.7/MIfuns/man/wikiparse.Rd | 25
MIfuns-4.3.7/MIfuns/man/wrap.Rd |only
64 files changed, 18779 insertions(+), 12385 deletions(-)
Title: Joint Modelling of Longitudinal and Survival Data
Diff between JM versions 0.8-3 dated 2011-04-23 and 0.8-4 dated 2011-07-02
Description: Shared parameter models for the joint modelling of
longitudinal and time-to-event data.
Author: Dimitris Rizopoulos
Maintainer: Dimitris Rizopoulos
DESCRIPTION | 8 +-
R/MI.fixed.times.R | 18 +++--
R/MI.random.times.R | 14 ++--
R/S.b.R | 2
R/anova.jointModel.R | 146 ++++++++++++++++++++++++++++++++++---------
R/jointModel.R | 9 ++
R/log.posterior.b.R | 2
R/log.posterior.b2.R |only
R/piecewisePHGH.fit.R | 5 +
R/plot.jointModel.R | 8 +-
R/plot.survfitJM.R | 59 ++++++++++++-----
R/posterior.b.R | 38 ++++++++++-
R/print.aov.jointModel.R | 50 +++++++++++---
R/print.summary.jointModel.R | 2
R/ranef.jointModel.R | 31 +++++----
R/residuals.jointModel.R | 4 +
R/survfitJM.R | 5 -
R/wald.strata.R | 2
data/prothros.rda |binary
inst/NEWS | 23 +++++-
man/JM.Rd | 4 -
man/anova.Rd | 14 +++-
man/jointModel.Rd | 10 +-
man/plot-survfitJM.Rd | 7 +-
man/ranef.Rd | 16 +---
25 files changed, 355 insertions(+), 122 deletions(-)
Title: Extension to ggplot2.
Diff between GGally versions 0.2.3 dated 2011-01-20 and 0.3.0 dated 2011-07-02
Description: Package contains templates for different plots to be
combined into a plot matrix, as well as a parallel coordinate
plot function.
Author: Barret Schloerke
Maintainer: Jason Crowley
GGally-0.2.3/GGally/Testing/aes.r |only
GGally-0.3.0/GGally/DESCRIPTION | 29
GGally-0.3.0/GGally/NAMESPACE | 2
GGally-0.3.0/GGally/R/find-combo.r | 148 -
GGally-0.3.0/GGally/R/gg-plots.r | 1853 ++++++++++----------
GGally-0.3.0/GGally/R/ggpairs.r | 1833 ++++++++++---------
GGally-0.3.0/GGally/R/ggparcoord.R |only
GGally-0.3.0/GGally/TODO | 24
GGally-0.3.0/GGally/Testing/gparis.r | 1490 ++++++++--------
GGally-0.3.0/GGally/Testing/plotmatrix2.r | 70
GGally-0.3.0/GGally/Testing/violin.r | 30
GGally-0.3.0/GGally/load.r | 18
GGally-0.3.0/GGally/man/addAndOverwriteAes.Rd | 36
GGally-0.3.0/GGally/man/eval_ggpair.Rd | 18
GGally-0.3.0/GGally/man/find_plot_type.Rd | 22
GGally-0.3.0/GGally/man/get.VarTypes.Rd |only
GGally-0.3.0/GGally/man/getPlot.Rd | 26
GGally-0.3.0/GGally/man/get_plot_type.Rd | 20
GGally-0.3.0/GGally/man/ggally_barDiag.Rd | 28
GGally-0.3.0/GGally/man/ggally_blank.Rd | 20
GGally-0.3.0/GGally/man/ggally_box.Rd | 28
GGally-0.3.0/GGally/man/ggally_cor.Rd | 32
GGally-0.3.0/GGally/man/ggally_density.Rd | 32
GGally-0.3.0/GGally/man/ggally_densityDiag.Rd | 28
GGally-0.3.0/GGally/man/ggally_denstrip.Rd | 28
GGally-0.3.0/GGally/man/ggally_diagAxis.Rd |only
GGally-0.3.0/GGally/man/ggally_dot.Rd | 30
GGally-0.3.0/GGally/man/ggally_dotAndBox.Rd | 28
GGally-0.3.0/GGally/man/ggally_facetbar.Rd | 26
GGally-0.3.0/GGally/man/ggally_facetdensity.Rd | 26
GGally-0.3.0/GGally/man/ggally_facetdensitystrip.Rd | 28
GGally-0.3.0/GGally/man/ggally_facethist.Rd | 26
GGally-0.3.0/GGally/man/ggally_points.Rd | 28
GGally-0.3.0/GGally/man/ggally_ratio.Rd | 26
GGally-0.3.0/GGally/man/ggally_smooth.Rd | 28
GGally-0.3.0/GGally/man/ggally_text.Rd | 36
GGally-0.3.0/GGally/man/ggfluctuation2.Rd | 36
GGally-0.3.0/GGally/man/ggpairs.Rd | 318 +--
GGally-0.3.0/GGally/man/ggparcoord.Rd |only
GGally-0.3.0/GGally/man/is_blank_plot.Rd | 18
GGally-0.3.0/GGally/man/make_ggpair_text.Rd | 22
GGally-0.3.0/GGally/man/mapping_color_fill.Rd | 14
GGally-0.3.0/GGally/man/plot_types.Rd | 18
GGally-0.3.0/GGally/man/print.ggpairs.Rd | 22
GGally-0.3.0/GGally/man/putPlot.Rd | 38
GGally-0.3.0/GGally/man/scagOrder.Rd |only
GGally-0.3.0/GGally/man/singleClassOrder.Rd |only
GGally-0.3.0/GGally/man/skewness.Rd |only
GGally-0.3.0/GGally/man/vplayout.Rd | 20
49 files changed, 3384 insertions(+), 3219 deletions(-)