Title: Constrained L1-minimization for Inverse (covariance) Matrix
Estimation
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
Diff between clime versions 0.2 dated 2011-02-03 and 0.3 dated 2011-07-23
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
Description: Great utilities that you won't be able to live without.
Author: David M. Schruth
Maintainer: David M. Schruth
Diff between caroline versions 0.5.1 dated 2011-06-07 and 0.5.4 dated 2011-07-23
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
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"
Diff between RgoogleMaps versions 1.1.9.8 dated 2011-06-29 and 1.1.9.11 dated 2011-07-23
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
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
Diff between pensim versions 1.0.3 dated 2011-06-30 and 1.1.3 dated 2011-07-23
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
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
Diff between rcdklibs versions 1.3.11 dated 2011-06-19 and 1.4.1 dated 2011-07-23
DESCRIPTION | 8 ++++---- NEWS | 1 + inst/cont/cdk.jar |binary 3 files changed, 5 insertions(+), 4 deletions(-)
Title: rcdk - Interface to the CDK Libraries
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
Diff between rcdk versions 3.1.1 dated 2011-06-19 and 3.1.2 dated 2011-07-23
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
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
Diff between nlme versions 3.1-101 dated 2011-05-06 and 3.1-102 dated 2011-07-23
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,
...
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
Diff between foreign versions 0.8-44 dated 2011-04-13 and 0.8-45 dated 2011-07-23
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
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
Diff between RghcnV3 versions 1.1 dated 2011-06-28 and 1.5 dated 2011-07-23
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
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
Diff between MASS versions 7.3-13 dated 2011-04-13 and 7.3-14 dated 2011-07-23
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.
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
Diff between wnominate versions 0.95 dated 2011-05-26 and 0.96 dated 2011-07-23
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.
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
Diff between visualizationTools versions 0.2.01 dated 2011-05-23 and 0.2.02 dated 2011-07-23
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(-)
More information about visualizationTools at CRAN
Permanent link
Title: Perform SQL Selects on R Data Frames
Description: Manipulate R data frames using SQL.
Author: G. Grothendieck
Maintainer: G. Grothendieck
Diff between sqldf versions 0.4-1 dated 2011-06-29 and 0.4-1.2 dated 2011-07-23
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
Description: A Set of Tools for Administering SHared Repositories
Author: Sandy Eckel, Roger D. Peng
Maintainer: Roger D. Peng
Diff between stashR versions 0.3-3 dated 2009-03-27 and 0.3-4 dated 2011-07-23
DESCRIPTION | 10 +++++----- tests/tests.Rout.save | 11 ++++++----- 2 files changed, 11 insertions(+), 10 deletions(-)
Title: Sparklines and graphical tables for tex and html
Description: Create Sparklines and graphical tables for documents and
websites
Author: Alexander Kowarik, Bernhard Meindl, Stefan Zechner
Maintainer: Alexander Kowarik
Diff between sparkTable versions 0.1.3 dated 2010-09-13 and 0.9.1 dated 2011-07-23
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
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
Diff between spacetime versions 0.5-0 dated 2011-07-02 and 0.5-1 dated 2011-07-23
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
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
Diff between sp versions 0.9-83 dated 2011-06-15 and 0.9-84 dated 2011-07-23
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
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
Diff between sn versions 0.4-16 dated 2010-08-30 and 0.4-17 dated 2011-07-23
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
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
Diff between smatr versions 3.2.0 dated 2011-04-27 and 3.2.2 dated 2011-07-23
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
Description: A general framework for statistical simulation.
Author: Andreas Alfons
Maintainer: Andreas Alfons
Diff between simFrame versions 0.4.1 dated 2011-03-21 and 0.4.2 dated 2011-07-23
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
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
Diff between siar versions 4.1 dated 2011-03-31 and 4.1.1 dated 2011-07-23
DESCRIPTION | 11 ++++++----- R/standard.ellipse.r | 4 +++- 2 files changed, 9 insertions(+), 6 deletions(-)
Title: Regression with Functional Data
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
Diff between refund versions 0.1-3 dated 2011-05-15 and 0.1-4 dated 2011-07-23
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)
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
Diff between rdyncall versions 0.7.2 dated 2011-04-27 and 0.7.3 dated 2011-07-23
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Title: Graphical user interface for data mining in R
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
Diff between rattle versions 2.6.6 dated 2011-04-10 and 2.6.7 dated 2011-07-23
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
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
Diff between rasterVis versions 0.10-2 dated 2011-07-06 and 0.10-3 dated 2011-07-23
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
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
Diff between raster versions 1.8-39 dated 2011-07-05 and 1.9-1 dated 2011-07-23
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
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
Diff between gstat versions 0.9-82 dated 2011-06-27 and 1.0-0 dated 2011-07-23
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
Description: Collection of package development tools
Author: Hadley Wickham
Maintainer: Hadley Wickham
Diff between devtools versions 0.3 dated 2011-06-30 and 0.4 dated 2011-07-23
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
Description: Using this package to call jags from R.
Author: Yu-Sung Su
Maintainer: Yu-Sung Su
Diff between R2jags versions 0.02-15 dated 2011-03-30 and 0.02-16 dated 2011-07-23
CHANGELOG | 4 ++++ DESCRIPTION | 8 ++++---- R/print.R | 7 ++++--- 3 files changed, 12 insertions(+), 7 deletions(-)
Title: Statistical Methods for Quality Science
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
Diff between qualityTools versions 1.44 dated 2011-06-01 and 1.45 dated 2011-07-23
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
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
Diff between profdpm versions 2.0 dated 2010-05-25 and 3.0 dated 2011-07-23
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
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
Diff between pracma versions 0.6-3 dated 2011-06-29 and 0.7-3 dated 2011-07-23
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
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
Diff between popbio versions 2.2 dated 2011-03-23 and 2.3.1 dated 2011-07-23
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
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
Diff between phylotools versions 0.0.7.4 dated 2010-11-03 and 0.1.1 dated 2011-07-23
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
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
Diff between pegas versions 0.3-4 dated 2011-04-01 and 0.4 dated 2011-07-23
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
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
Diff between oce versions 0.3-1 dated 2011-06-22 and 0.4-1 dated 2011-07-23
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
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
Diff between nlts versions 0.1-7 dated 2010-09-27 and 0.1-8 dated 2011-07-23
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
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
Diff between network versions 1.6 dated 2011-01-29 and 1.7 dated 2011-07-23
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
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
Diff between RcppArmadillo versions 0.2.26 dated 2011-07-23 and 0.2.27 dated 2011-07-23
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
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
Diff between mvabund versions 2.2-5.3 dated 2011-07-06 and 2.2-5.6 dated 2011-07-23
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
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
Diff between multcomp versions 1.2-6 dated 2011-05-02 and 1.2-7 dated 2011-07-23
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
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
Diff between monomvn versions 1.8-5 dated 2011-03-08 and 1.8-6 dated 2011-07-23
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
Description: Separates DNA mixtures using a statistical model within a
greedy algorithm.
Author: Torben Tvedebrink
Maintainer: Torben Tvedebrink
Diff between mixsep versions 0.1-5 dated 2011-05-26 and 0.1-6 dated 2011-07-23
DESCRIPTION | 8 ++++---- R/gui.R | 43 ++++++++++++++++++++++++++++--------------- inst/doc |only vignettegraphics |only 4 files changed, 32 insertions(+), 19 deletions(-)
Title: Multidimensional Item Response Theory
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
Diff between mirt versions 0.1-13 dated 2011-07-02 and 0.1-14 dated 2011-07-23
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
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
Diff between mefa4 versions 0.2-1 dated 2011-05-15 and 0.2-2 dated 2011-07-23
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
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
Diff between mc2d versions 0.1-9 dated 2010-12-17 and 0.1-10 dated 2011-07-23
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
Description: Emulate MATLAB code using R
Author: P. Roebuck
Maintainer: P. Roebuck
Diff between matlab versions 0.8.6 dated 2011-04-24 and 0.8.7 dated 2011-07-23
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
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
Diff between lmomco versions 1.3.6 dated 2011-06-25 and 1.4.2 dated 2011-07-23
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
Description: Fit linear and generalized linear mixed-effects models.
Author: Douglas Bates
Maintainer:
Diff between lme4 versions 0.999375-39 dated 2011-03-08 and 0.999375-40 dated 2011-07-23
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
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
Diff between linkcomm versions 1.0-2 dated 2011-05-29 and 1.0-3 dated 2011-07-23
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
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
Diff between lessR versions 1.9.8 dated 2011-06-30 and 2.0 dated 2011-07-23
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
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
Diff between itsmr versions 1.0 dated 2011-06-15 and 1.1 dated 2011-07-23
DESCRIPTION | 15 - R/itsmr.R | 493 ++++++++++++++++++++++++++++++++++++------------------------ 2 files changed, 310 insertions(+), 198 deletions(-)
Title: Iterator construct for R
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
Diff between iterators versions 1.0.4 dated 2011-05-20 and 1.0.5 dated 2011-07-23
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
Description: Provides datasets for Introduction to Statistical Data
Analysis for the Life Sciences
Author: Claus Ekstrom
Maintainer: Claus Ekstrom
Diff between isdals versions 1.0-2 dated 2011-02-22 and 1.0-4 dated 2011-07-23
DESCRIPTION | 10 +++++----- R/residualplot.R | 4 ++++ data/herring.rda |binary 3 files changed, 9 insertions(+), 5 deletions(-)
Title: iPlots - interactive graphics for R
Description: Interactive plots for R
Author: Simon Urbanek
Maintainer: Simon Urbanek
Diff between iplots versions 1.1-3 dated 2009-02-07 and 1.1-4 dated 2011-07-23
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
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
Diff between idr versions 1.0 dated 2011-06-15 and 1.1 dated 2011-07-23
DESCRIPTION | 6 +++--- man/idr-package.Rd | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Title: High-dimensional Undirected Graph Estimation
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
Diff between huge versions 1.0.3 dated 2011-06-17 and 1.1.0 dated 2011-07-23
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
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
Diff between googleVis versions 0.2.6 dated 2011-06-15 and 0.2.7 dated 2011-07-23
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.
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
Diff between glmpathcr versions 1.0.1 dated 2011-03-16 and 1.0.2 dated 2011-07-23
glmpathcr |only 1 file changed
Title: Fit a penalized constrained continuation ratio model for
predicting an ordinal response
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
Diff between glmnetcr versions 1.0 dated 2011-03-16 and 1.0.1 dated 2011-07-23
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
Description: Geophysics, Continuum Mechanics, Mogi Model, Okada Model
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees
Diff between geophys versions 1.1-0 dated 2010-11-24 and 1.2-0 dated 2011-07-23
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
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
Diff between gamm4 versions 0.1-2 dated 2011-03-02 and 0.1-3 dated 2011-07-23
DESCRIPTION | 6 ++--- R/gamm4.r | 63 +++++++++++++++++++----------------------------------------- changeLog | 20 +++++++++++++++++++ 3 files changed, 43 insertions(+), 46 deletions(-)
Title: Toolkit implementation of gWidgets for tcltk package
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
Diff between gWidgetstcltk versions 0.0-43 dated 2011-04-30 and 0.0-44 dated 2011-07-23
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
Description: Port of gWidgets API to RGtk2
Author: Michael Lawrence, John Verzani
Maintainer: John Verzani
Diff between gWidgetsRGtk2 versions 0.0-74 dated 2011-05-08 and 0.0-75 dated 2011-07-23
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
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
Diff between gWidgets versions 0.0-44 dated 2011-04-30 and 0.0-45 dated 2011-07-23
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
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: S�ren H�jsgaard
Maintainer: S�ren H�jsgaard
Diff between gRbase versions 1.3.9 dated 2011-01-18 and 1.4.0 dated 2011-07-23
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
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: S�ren H�jsgaard
Maintainer: S�ren H�jsgaard
Diff between gRain versions 0.8.7 dated 2011-01-18 and 0.8.8 dated 2011-07-23
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
Description: Simple key-value database
Author: Roger D. Peng
Maintainer: Roger D. Peng
Diff between filehash versions 2.1-1 dated 2010-10-05 and 2.2 dated 2011-07-23
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.
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
Diff between extRemes versions 1.62 dated 2010-04-25 and 1.63 dated 2011-07-23
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"
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
Diff between expsmooth versions 2.00 dated 2009-09-07 and 2.01 dated 2011-07-23
ChangeLog | 3 +++ DESCRIPTION | 14 +++++++------- data/jewelry.rda |binary 3 files changed, 10 insertions(+), 7 deletions(-)
Title: Epidemiological calculator
Description: Functions making R easy for epidemiological calculation.
Author: Virasakdi Chongsuvivatwong
Maintainer: Virasakdi Chongsuvivatwong
Diff between epicalc versions 2.12.2.3 dated 2011-04-11 and 2.13.1.0 dated 2011-07-23
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
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
Diff between editrules versions 0.8 dated 2011-07-06 and 0.9-0 dated 2011-07-23
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
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
Diff between earth versions 3.2-0 dated 2011-06-19 and 3.2-1 dated 2011-07-23
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
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
Diff between delftfews versions 0.3-38 dated 2010-08-27 and 0.3-67 dated 2011-07-23
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.
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
Diff between ddepn versions 1.8 dated 2011-06-17 and 1.9 dated 2011-07-23
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
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
Diff between dclone versions 1.3-2 dated 2011-05-15 and 1.3-3 dated 2011-07-23
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
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
Diff between cts versions 1.0-1 dated 2006-09-29 and 1.0-4 dated 2011-07-23
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
Description: Circular Statistics, from "Topics in circular Statistics"
(2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific.
Author: Ulric Lund
Maintainer: Claudio Agostinelli
Diff between circular versions 0.4-2 dated 2011-03-19 and 0.4-3 dated 2011-07-23
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 circular-0.4-3/circular/data/fisherB3c.rda |binary circular-0.4-3/circular/data/fisherB4.rda |only circular-0.4-3/circular/data/fisherB4c.rda |binary circular-0.4-3/circular/data/fisherB5.rda |only circular-0.4-3/circular/data/fisherB5c.rda |binary 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
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
Diff between care versions 1.0.0 dated 2010-08-08 and 1.1.0 dated 2011-07-23
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
Description: Tools for caching Sweave computations and storing them in
key-value databases
Author: Roger D. Peng
Maintainer: Roger D. Peng
Diff between cacheSweave versions 0.5 dated 2011-06-30 and 0.6 dated 2011-07-23
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
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
Diff between bios2mds versions 1.0 dated 2011-07-05 and 1.1 dated 2011-07-23
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
Description: Conducts Aldrich-McKelvey and Blackbox Scaling (SVD
generalization with missing values)
Author: Keith Poole
Maintainer: Keith Poole
Diff between basicspace versions 0.02 dated 2011-01-26 and 0.03 dated 2011-07-23
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 inst/doc/basicspace-four.eps |only inst/doc/basicspace-four.pdf |only inst/doc/basicspace-nine.eps |only inst/doc/basicspace-nine.pdf |only inst/doc/basicspace-seven.eps |only 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
Description: Regression for data too large to fit in memory
Author: Thomas Lumley
Maintainer: Thomas Lumley
Diff between biglm versions 0.7 dated 2009-05-05 and 0.8 dated 2011-07-23
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
Description: This package performs an automatic interpolation by
automatically estimating the variogram and then calling gstat.
Author: Paul Hiemstra
Maintainer: Paul Hiemstra
Diff between automap versions 1.0-10 dated 2011-05-30 and 1.0-11 dated 2011-07-23
.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
Description: Package for analysis of copy-number estimates obtained
from various platforms.
Author: Henrik Bengtsson and Pierre Neuvial
Maintainer: Henrik Bengtsson
Diff between aroma.cn versions 0.7.3 dated 2011-06-25 and 0.8.0 dated 2011-07-23
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
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
Diff between animation versions 2.0-4 dated 2011-04-28 and 2.0-5 dated 2011-07-23
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
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
Diff between adabag versions 1.1 dated 2007-10-25 and 2.0 dated 2011-07-23
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)
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
Diff between zoo versions 1.7-1 dated 2011-07-18 and 1.7-2 dated 2011-07-23
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
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
Diff between VIM versions 2.0.2 dated 2011-07-02 and 2.0.3 dated 2011-07-23
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
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
Diff between TreePar versions 1.4 dated 2011-05-10 and 2.1 dated 2011-07-23
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
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
Diff between SamplingStrata versions 0.9 dated 2011-04-29 and 0.9-1 dated 2011-07-23
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(-)
More information about SamplingStrata at CRAN
Permanent link
Title: SYNCSA - Analysis of functional and phylogenetic patterns in
metacommunities.
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
Diff between SYNCSA versions 1.0 dated 2011-05-25 and 1.1 dated 2011-07-23
DESCRIPTION | 6 +++--- R/matrix.x.R | 2 +- man/SYNCSA-package.Rd | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-)
Title: Sequential Parameter Optimization
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
Diff between SPOT versions 0.1.1375 dated 2011-05-03 and 0.1.1550 dated 2011-07-23
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
Description: Load SPARQL result table from an end-point as a data.frame
Author: Willem Robert van Hage
Maintainer: Willem Robert van Hage
Diff between SPARQL versions 1.1 dated 2011-06-22 and 1.2 dated 2011-07-23
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
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
Diff between ResourceSelection versions 0.1-0 dated 2011-06-04 and 0.1-1 dated 2011-07-23
DESCRIPTION | 8 ++++---- R/hoslem.test.R | 4 ++-- R/kdepairs.default.R | 6 ++---- inst/ChangeLog | 4 ++++ 4 files changed, 12 insertions(+), 10 deletions(-)
More information about ResourceSelection at CRAN
Permanent link
Title: Rcpp integration for Armadillo templated linear algebra library
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
Diff between RcppArmadillo versions 0.2.25 dated 2011-06-30 and 0.2.26 dated 2011-07-23
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
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
Diff between RcmdrPlugin.DoE versions 0.10-2 dated 2011-02-21 and 0.10-4 dated 2011-07-23
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(-)
More information about RcmdrPlugin.DoE at CRAN
Permanent link
Title: Diverse basic statistical and graphical functions accompanying
the french book 'Aide-memoire de statistique appliquee a la
biologie'
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 Herv�
Maintainer: Maxime Herv�
Diff between RVAideMemoire versions 0.9.1 dated 2011-03-14 and 0.9-5 dated 2011-07-23
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 RVAideMemoire-0.9-5/RVAideMemoire/man/ind.contrib.Rd |only 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
Description: Poor Man's Gui: create interactive R analysis sessions
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees
Diff between RPMG versions 2.0-5 dated 2010-11-24 and 2.0-6 dated 2011-07-23
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
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
Diff between RH2 versions 0.1-2.3 dated 2011-03-08 and 0.1-2.5 dated 2011-07-23
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
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
Diff between R.oo versions 1.8.0 dated 2011-04-04 and 1.8.1 dated 2011-07-23
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
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
Diff between R.cache versions 0.4.2 dated 2011-05-21 and 0.4.3 dated 2011-07-23
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
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
Diff between QTLRel versions 0.2-8 dated 2011-06-28 and 0.2-9 dated 2011-07-23
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.
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
Diff between ProjectTemplate versions 0.3-4 dated 2011-07-04 and 0.3-5 dated 2011-07-23
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(-)
More information about ProjectTemplate at CRAN
Permanent link
Title: Estimation of the peak-to-trough ratio of a seasonal variation
component
Description: Estimation of the peak-to-trough ratio of a seasonal
variation component.
Author: Anette Luther Christensen
Maintainer: Anette Luther Christensen
Diff between Peak2Trough versions 1.0 dated 2011-04-28 and 1.1 dated 2011-07-23
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
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
Diff between PSCBS versions 0.11.3 dated 2011-07-07 and 0.11.7 dated 2011-07-23
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
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
Diff between MultiPhen versions 0.1 dated 2011-07-06 and 0.2 dated 2011-07-23
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
Description: Performs multifactor dimensionality reduction (MDR) to
detect potential gene-gene interactions in case-control
studies.
Author: Stacey Winham
Maintainer: Stacey Winham
Diff between MDR versions 1.0 dated 2010-12-13 and 1.1 dated 2011-07-23
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
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
Diff between MCMCpack versions 1.0-11 dated 2011-04-26 and 1.1-1 dated 2011-07-23
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
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
Diff between MCMChybridGP versions 3.1 dated 2010-09-30 and 4.2 dated 2011-07-23
DESCRIPTION | 10 +++++----- R/MCMChybridGP-internal.R | 11 ++++++++--- R/hybrid.sample.R | 2 +- 3 files changed, 14 insertions(+), 9 deletions(-)
Title: Software for Bayesian Inference
Description: Laplace's Demon is software for Bayesian inference.
Author: Byron Hall
Maintainer: Byron Hall
Diff between LaplacesDemon versions 11.07.05 dated 2011-07-05 and 11.07.15 dated 2011-07-23
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.
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
Diff between LMERConvenienceFunctions versions 1.6.2 dated 2011-06-29 and 1.6.3 dated 2011-07-23
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(-)
More information about LMERConvenienceFunctions at CRAN
Permanent link
Title: Fractional Factorial designs with 2-level factors
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
Diff between FrF2 versions 1.2-2 dated 2011-02-07 and 1.2-4 dated 2011-07-23
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
Description: This package creates various kinds of designs for
(industrial) experiments. It uses, and sometimes enhances,
design generation routines from other packages. Initially,
response surface designs from package rsm and latin hypercube
samples from package lhs have been implemented.
Author: Ulrike Groemping
Maintainer: Ulrike Groemping
Diff between DoE.wrapper versions 0.8-2 dated 2011-01-31 and 0.8-3 dated 2011-07-23
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
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.
Diff between BAMD versions 3.4 dated 2011-02-19 and 3.5 dated 2011-07-23
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(-)