Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-02-08 1.0.3
2009-01-21 1.0.2
2008-06-01 1.0.1
Title: Iterated Racing Procedures
Diff between irace versions 1.01 dated 2012-03-19 and 1.02 dated 2012-10-12
Description: Iterated racing for automatic algorithm configuration
Author: Manuel López-Ibáñez, Jérémie Dubois-Lacoste, Thomas Stützle,
Mauro Birattari, Eric Yuan and Prasanna Balaprakash
Maintainer: Manuel López-Ibáñez
DESCRIPTION | 13 --
MD5 | 48 +++----
NEWS | 14 ++
R/cluster.R | 4
R/generation.R | 2
R/irace.R | 197 +++++++++++++++++++++++++++-----
R/main.R | 72 ++++++-----
R/race-wrapper.R | 48 +++----
R/race.R | 46 +++----
R/readConfiguration.R | 98 ++++++++++-----
R/readParameters.R | 37 ++----
R/utils.R | 46 +++++--
R/version.R | 2
README | 19 ++-
inst/examples/acotsp/tune-conf | 16 --
inst/examples/mpi/tune-main-cluster-mpi | 9 -
inst/examples/tune-main-cluster | 19 ++-
inst/templates/tune-conf.tmpl | 28 +---
man/checkConfiguration.Rd | 35 ++---
man/defaultConfiguration.Rd | 22 ++-
man/irace-package.Rd | 15 +-
man/irace.main.Rd | 23 ++-
man/printConfiguration.Rd | 14 +-
man/readConfiguration.Rd | 18 +-
svn_version | 2
25 files changed, 534 insertions(+), 313 deletions(-)
Title: Chemometrics with R - Multivariate Data Analysis in the Natural
Sciences and Life Sciences
Diff between ChemometricsWithR versions 0.1.5 dated 2012-01-04 and 0.1.7 dated 2012-10-12
More information about ChemometricsWithR at CRAN
Description: The package provides functions and scripts used in the
book "Chemometrics with R - Multivariate Data Analysis in the
Natural Sciences and Life Sciences" by Ron Wehrens, Springer
(2011).
Author: Ron Wehrens
Maintainer: Ron Wehrens
CHANGES |only
DESCRIPTION | 21 -
MD5 | 53 ++-
NAMESPACE | 29 --
R/PCA.R | 48 +--
R/classvec2classmat.R |only
R/optim.R | 17 -
demo/chapter10.R | 219 +++++++++-------
demo/chapter11.R | 496 +++++++++++++++++++------------------
demo/chapter2.R | 10
demo/chapter3.R | 276 +++++++++++---------
demo/chapter4.R | 51 ++-
demo/chapter5.R | 15 -
demo/chapter6.R | 137 ++++++----
demo/chapter7.R | 519 +++++++++++++++++++++------------------
demo/chapter8.R | 94 ++++---
demo/chapter9.R | 415 ++++++++++++++++---------------
man/AdjRkl.Rd | 18 -
man/ChemometricsWithR-package.Rd | 4
man/Error.Rd | 4
man/Evaluation.Rd | 4
man/GA.Rd | 20 +
man/MCR.Rd | 12
man/PCA.Rd | 7
man/PCA.plot.Rd | 9
man/SA.Rd | 8
man/classvec2classmat.Rd |only
man/gini.Rd | 4
man/pick.peaks.Rd | 4
29 files changed, 1397 insertions(+), 1097 deletions(-)
Permanent link
Title: Package development utilities
Diff between pkgmaker versions 0.8 dated 2012-07-24 and 0.8.5 dated 2012-10-12
Description: This package provides some low-level utilities to use for
package development. It currently provides managers for
multiple package specific options and registries, vignette,
unit test and bibtex related utilities. It serves as a base
package for packages like NMF, RcppOctave, doRNG, and as an
incubator package for other general purposes utilities, that
will eventually be packaged separately. It is still under
heavy development and changes in the interface(s) are more than
likely to happen.
Author: Renaud Gaujoux
Maintainer: Renaud Gaujoux
DESCRIPTION | 10 +--
MD5 | 31 ++++++----
NAMESPACE | 4 +
R/bibtex.R | 13 ++--
R/devutils.R | 46 ++++++++++++++-
R/unitTests.R | 38 +++++++++++++
R/utils.R | 36 ++++++++++++
R/vignette.R | 140 +++++++++++++++++++++++++++++++-----------------
inst/cleveref.sty |only
inst/doc |only
inst/vignette.mk | 2
man/R.exec.Rd | 3 -
man/orderVersion.Rd |only
man/packageReference.Rd | 5 +
man/quickinstall.Rd |only
man/vignette.Rd | 11 ---
man/write.bib.Rd | 6 +-
vignettes |only
18 files changed, 252 insertions(+), 93 deletions(-)
Title: Data for package ChemometricsWithR
Diff between ChemometricsWithRData versions 0.1.2 dated 2012-01-04 and 0.1.3 dated 2012-10-12
More information about ChemometricsWithRData at CRAN
Description: The package provides data sets used in the book
"Chemometrics with R - Multivariate Data Analysis in the
Natural Sciences and Life Sciences" by Ron Wehrens, Springer
(2011).
Author: Ron Wehrens
Maintainer: Ron Wehrens
DESCRIPTION | 13 ++++++++-----
MD5 | 14 +++++++++-----
data/Prostate2000Raw.rda |only
data/datalist | 2 ++
data/wines.rda |only
man/Prostate2000Raw.Rd |only
man/bdata.Rd | 5 ++++-
man/prostate.Rd | 18 ++++++++++++------
man/shootout.Rd | 4 ++++
man/wines.Rd |only
10 files changed, 39 insertions(+), 17 deletions(-)
Permanent link
Title: Bootstrap Functions (originally by Angelo Canty for S)
Diff between boot versions 1.3-6 dated 2012-10-08 and 1.3-7 dated 2012-10-12
Description: functions and datasets for bootstrapping from the book
"Bootstrap Methods and Their Applications" by A. C. Davison and
D. V. Hinkley (1997, CUP).
Author: S original
Maintainer: Brian Ripley
ChangeLog | 4 +
DESCRIPTION | 10 +-
MD5 | 26 +++----
R/bootfuns.q | 4 -
inst/po/de/LC_MESSAGES/R-boot.mo |binary
inst/po/en@quot/LC_MESSAGES/R-boot.mo |binary
inst/po/fr/LC_MESSAGES/R-boot.mo |binary
inst/po/pl/LC_MESSAGES/R-boot.mo |binary
inst/po/ru/LC_MESSAGES/R-boot.mo |binary
po/R-boot.pot | 6 -
po/R-de.po | 123 ++++++++++++----------------------
po/R-fr.po | 6 -
po/R-pl.po | 7 +
po/R-ru.po | 6 -
14 files changed, 82 insertions(+), 110 deletions(-)
Title: QuACN: Quantitative Analysis of Complex Networks
Diff between QuACN versions 1.7.3 dated 2012-10-04 and 1.7.4 dated 2012-10-12
Description: Quantitative Analysis of Complex Networks. This package
offers a set of topological network measures to analyze complex
Networks structurally.
Author: Laurin Mueller, Michael Schutte, Karl Kugler, Matthias Dehmer
Maintainer: Laurin Mueller
DESCRIPTION | 12 ++++++------
MD5 | 8 ++++----
R/distanceMatrix.R | 3 +--
R/utilities.R | 4 ++--
inst/doc/QuACN.pdf |binary
5 files changed, 13 insertions(+), 14 deletions(-)
Title: Maximally Selected Rank Statistics
Diff between maxstat versions 0.7-14 dated 2011-08-23 and 0.7-15 dated 2012-10-12
Description: Maximally selected rank statistics with several p-value
approximations.
Author: Torsten Hothorn
Maintainer: Torsten Hothorn
maxstat-0.7-14/maxstat/tests/maxstat-Ex.R |only
maxstat-0.7-14/maxstat/tests/maxstat-Ex.Rout.save |only
maxstat-0.7-15/maxstat/CHANGES | 6 +++
maxstat-0.7-15/maxstat/DESCRIPTION | 11 +++---
maxstat-0.7-15/maxstat/MD5 | 35 ++++++++++------------
maxstat-0.7-15/maxstat/R/maxstat.R | 15 +--------
maxstat-0.7-15/maxstat/data/sphase.rda |binary
maxstat-0.7-15/maxstat/data/treepipit.rda |binary
maxstat-0.7-15/maxstat/inst/doc/maxstat.pdf |binary
maxstat-0.7-15/maxstat/inst/doc/maxstatlit.bib | 13 +++++---
maxstat-0.7-15/maxstat/man/DLBCL.Rd | 7 +---
maxstat-0.7-15/maxstat/man/corrmsrs.Rd | 12 +++----
maxstat-0.7-15/maxstat/man/hohnloser.Rd | 5 +--
maxstat-0.7-15/maxstat/man/maxstat.test.Rd | 13 +++-----
maxstat-0.7-15/maxstat/man/pexactgauss.Rd | 2 +
maxstat-0.7-15/maxstat/man/plot.maxtest.Rd | 2 +
maxstat-0.7-15/maxstat/man/pmaxstat.Rd | 2 -
maxstat-0.7-15/maxstat/man/sphase.Rd | 20 ++++++++----
maxstat-0.7-15/maxstat/man/treepipit.Rd | 11 +++---
maxstat-0.7-15/maxstat/tests/Examples |only
20 files changed, 80 insertions(+), 74 deletions(-)
Title: Spatial Survey Design and Analysis
Diff between spsurvey versions 2.4 dated 2012-05-30 and 2.5 dated 2012-10-12
Description: This group of functions implements algorithms for design
and analysis of probability surveys. The functions are
tailored for Generalized Random Tesselation Stratified (GRTS)
survey designs.
Author: Tom Kincaid
Maintainer: Tom Kincaid
spsurvey-2.4/spsurvey/inst/doc/reg1_lakes.dbf |only
spsurvey-2.4/spsurvey/inst/doc/reg1_lakes.shp |only
spsurvey-2.4/spsurvey/inst/doc/reg1_lakes.shx |only
spsurvey-2.4/spsurvey/vignettes/reg1_lakes.dbf |only
spsurvey-2.4/spsurvey/vignettes/reg1_lakes.shp |only
spsurvey-2.4/spsurvey/vignettes/reg1_lakes.shx |only
spsurvey-2.5/spsurvey/DESCRIPTION | 10
spsurvey-2.5/spsurvey/MD5 | 122 +++++-----
spsurvey-2.5/spsurvey/NAMESPACE | 8
spsurvey-2.5/spsurvey/R/attrisk.analysis.r | 3
spsurvey-2.5/spsurvey/R/cat.analysis.s | 3
spsurvey-2.5/spsurvey/R/cdf.decon.s | 12 -
spsurvey-2.5/spsurvey/R/cdf.est.s | 16 -
spsurvey-2.5/spsurvey/R/cdf.test.s | 13 -
spsurvey-2.5/spsurvey/R/change.analysis.r | 6
spsurvey-2.5/spsurvey/R/cont.analysis.s | 3
spsurvey-2.5/spsurvey/R/cont.cdftest.s | 10
spsurvey-2.5/spsurvey/R/dframe.check.s | 71 ++----
spsurvey-2.5/spsurvey/R/grtspts.r | 12 -
spsurvey-2.5/spsurvey/R/localmean.weight.s | 7
spsurvey-2.5/spsurvey/R/onAttach.r | 2
spsurvey-2.5/spsurvey/R/relrisk.analysis.s | 3
spsurvey-2.5/spsurvey/R/spbalance.r | 17 -
spsurvey-2.5/spsurvey/inst/CITATION | 4
spsurvey-2.5/spsurvey/inst/NEWS | 29 ++
spsurvey-2.5/spsurvey/inst/NEWS.pdf |binary
spsurvey-2.5/spsurvey/inst/doc/Area_Analysis.Rnw | 54 +---
spsurvey-2.5/spsurvey/inst/doc/Area_Analysis.pdf |binary
spsurvey-2.5/spsurvey/inst/doc/Area_Design.Rnw | 18 -
spsurvey-2.5/spsurvey/inst/doc/Area_Design.pdf |binary
spsurvey-2.5/spsurvey/inst/doc/CDF_Analysis.Rnw | 3
spsurvey-2.5/spsurvey/inst/doc/CDF_Analysis.pdf |binary
spsurvey-2.5/spsurvey/inst/doc/CDF_Deconvolution.Rnw |only
spsurvey-2.5/spsurvey/inst/doc/CDF_Deconvolution.pdf |only
spsurvey-2.5/spsurvey/inst/doc/CHANGES.pdf |binary
spsurvey-2.5/spsurvey/inst/doc/Finite_Analysis.Rnw | 48 +---
spsurvey-2.5/spsurvey/inst/doc/Finite_Analysis.pdf |binary
spsurvey-2.5/spsurvey/inst/doc/Finite_Design.Rnw | 72 ++----
spsurvey-2.5/spsurvey/inst/doc/Finite_Design.pdf |binary
spsurvey-2.5/spsurvey/inst/doc/IN_streams.tab | 200 +++++++++---------
spsurvey-2.5/spsurvey/inst/doc/Linear_Analysis.Rnw | 58 ++---
spsurvey-2.5/spsurvey/inst/doc/Linear_Analysis.pdf |binary
spsurvey-2.5/spsurvey/inst/doc/Linear_Design.Rnw | 27 --
spsurvey-2.5/spsurvey/inst/doc/Linear_Design.pdf |binary
spsurvey-2.5/spsurvey/inst/doc/NE_lakes.dbf |only
spsurvey-2.5/spsurvey/inst/doc/NE_lakes.shp |only
spsurvey-2.5/spsurvey/inst/doc/NE_lakes.shx |only
spsurvey-2.5/spsurvey/inst/doc/README.pdf |binary
spsurvey-2.5/spsurvey/inst/doc/UserGuide.pdf |binary
spsurvey-2.5/spsurvey/inst/doc/decon_data.tab |only
spsurvey-2.5/spsurvey/man/adjwgt.Rd | 2
spsurvey-2.5/spsurvey/man/cdf.plot.Rd | 6
spsurvey-2.5/spsurvey/man/cdf.test.Rd | 8
spsurvey-2.5/spsurvey/man/cont.cdftest.Rd | 7
spsurvey-2.5/spsurvey/man/spbalance.Rd | 4
spsurvey-2.5/spsurvey/man/spsurvey-internal.Rd | 2
spsurvey-2.5/spsurvey/man/uniqueID.Rd |only
spsurvey-2.5/spsurvey/src/grts.c | 12 -
spsurvey-2.5/spsurvey/vignettes/Area_Analysis.Rnw | 54 +---
spsurvey-2.5/spsurvey/vignettes/Area_Design.Rnw | 18 -
spsurvey-2.5/spsurvey/vignettes/CDF_Analysis.Rnw | 3
spsurvey-2.5/spsurvey/vignettes/CDF_Deconvolution.Rnw |only
spsurvey-2.5/spsurvey/vignettes/Finite_Analysis.Rnw | 48 +---
spsurvey-2.5/spsurvey/vignettes/Finite_Design.Rnw | 72 ++----
spsurvey-2.5/spsurvey/vignettes/IN_streams.tab | 200 +++++++++---------
spsurvey-2.5/spsurvey/vignettes/Linear_Analysis.Rnw | 58 ++---
spsurvey-2.5/spsurvey/vignettes/Linear_Design.Rnw | 27 --
spsurvey-2.5/spsurvey/vignettes/NE_lakes.dbf |only
spsurvey-2.5/spsurvey/vignettes/NE_lakes.shp |only
spsurvey-2.5/spsurvey/vignettes/NE_lakes.shx |only
spsurvey-2.5/spsurvey/vignettes/decon_data.tab |only
71 files changed, 656 insertions(+), 696 deletions(-)
Title: rChoiceDialogs collection
Diff between rChoiceDialogs versions 1.0.3 dated 2012-08-10 and 1.0.4 dated 2012-10-12
More information about rChoiceDialogs at CRAN
Description: Collection of portable choice dialog widgets
Author: Alex Lisovich, Roger Day
Maintainer: Alex Lisovich
DESCRIPTION | 13 -
MD5 | 37 ++--
NAMESPACE | 25 +-
R/rChoiceDialogs-package.R | 36 ++--
R/rFileChooser.R | 164 ++++++++++++++++++-
inst/doc/rChoiceDialogs.Rnw | 352 ++++++++++++++++++++++--------------------
inst/doc/rChoiceDialogs.pdf |binary
man/canUseJava.Rd | 22 +-
man/canUseJavaModal.Rd | 23 ++
man/canUseTclTk.Rd | 22 +-
man/cmdchoose.files.Rd |only
man/getDefaultFilters.Rd | 28 ++-
man/jchoose.dir.Rd | 74 ++++++--
man/jchoose.files.Rd | 89 +++++++---
man/jselect.list.Rd | 98 +++++++----
man/rChoiceDialogs-package.Rd | 30 +--
man/rchoose.dir.Rd | 53 ++++--
man/rchoose.files.Rd | 67 +++++--
man/rselect.list.Rd | 87 +++++++---
man/tkchoose.files.Rd | 76 ++++++---
20 files changed, 859 insertions(+), 437 deletions(-)
Permanent link
Title: Power in a Group Sequential Design
Description: Tools the evaluation of interim analysis plans for
sequentially monitored trials on a survival endpoint; tools to
construct efficacy and futility boundaries, for deriving power
of a sequential design at a specified alternative, template for
evaluating the performance of candidate plans at a set of time
varying alternatives.
Author: Grant Izmirlian
Maintainer: ORPHANED
Diff between PwrGSD versions 1.16 dated 2010-03-13 and 1.16.1 dated 2012-10-12
DESCRIPTION | 9 +++++---- MD5 |only R/PwrGSD.R | 25 ++++++++++++------------- inst/doc/GrpSeqBnds-vignette-1.pdf |binary inst/doc/cpd-PwrGSD-vignette-1.pdf |binary 5 files changed, 17 insertions(+), 17 deletions(-)
Title: Protein (identification and) quantification based on peptide
evidence
Diff between protiq versions 1.0-1 dated 2012-10-08 and 1.1 dated 2012-10-12
Description: Method for protein quantification based on identified and
quantified peptides. protiq can be used for absolute and
relative protein quantification. Input peptide abundance scores
can come from various sources, including SRM transition areas
and intensities or spectral counts derived from shotgun
experiments. The package is still being extended to also
include the model for protein identification, MIPGEM, presented
in Gerster, S., Qeli, E., Ahrens, C.H. and Buehlmann, P.
(2010). Protein and gene model inference based on statistical
modeling in k-partite graphs. Proceedings of the National
Academy of Sciences 107(27):12101-12106.
Author: Sarah Gerster and Peter Buehlmann
Maintainer: Sarah Gerster
DESCRIPTION | 9 +++++----
MD5 | 24 ++++++++++++------------
R/protiq.R | 26 +++++++++++++++-----------
data/leptoSRM.rda |binary
man/checkInputData.Rd | 3 ++-
man/checkInputData.scampi.Rd | 10 ++++++++--
man/estimateModelParameters.Rd | 5 +++--
man/getCovU.Rd | 5 +++--
man/preprocessInputData.Rd | 5 +++--
man/preprocessInputData.scampi.Rd | 12 ++++--------
man/quantifyPeptide.Rd | 5 +++--
man/quantifyProtein.Rd | 5 +++--
man/quantifyProteins.Rd | 5 +++--
13 files changed, 64 insertions(+), 50 deletions(-)
Title: NCBI2R-An R package to navigate and annotate genes and SNPs
Diff between NCBI2R versions 1.4.3 dated 2012-09-29 and 1.4.4 dated 2012-10-12
Description: NCBI2R is an R package that annotates lists of SNPs and/or
genes, with current information from NCBI, including LD
information. Functions are provided that with one command will
provide annotation of the results from genome wide association
studies to provide a broader context of their meaning. Other
functions enable comparisons between a user's GWA results, and
candidate snp/gene lists that are created from keywords, such
as specific diseases, phenotypes or gene ontology terms.
Commands are simple to follow and designed to work with R
objects to integrate into existing workflows. The output
produces text fields and weblinks to more information for items
such as: gene descriptions, nucleotide positions, OMIM,
pathways, phenotypes, and lists of interacting and neighboring
genes. Annotation can then be used in R for further analysis,
or the objects can be customized for use in spreadsheet
programs or web browsers. The NCBI2R package wasdesigned to
allow those performing genome analysis to produce output that
could easily be understood by a person not familiar with R.
Please see the website at http://NCBI2R.wordpress.com for more
information. The internet is required for almost all of these
functions. Use the function PrintNCBI2RInfo() for information.
Author: Scott Melville
Maintainer: Scott Melville
DESCRIPTION | 8 +++---
MD5 | 12 ++++-----
R/AnnotateDataframe.r | 34 ++++++++++++---------------
R/GetSNPFlankSeq.r | 56 ++++++++++++++++++++++++++++-----------------
R/MakeHTML.r | 4 ++-
R/check.package.r | 4 +--
R/order.to.original.list.r | 10 ++++++--
7 files changed, 74 insertions(+), 54 deletions(-)
Title: Delaunay Triangulation and Dirichlet (Voronoi) Tessellation.
Diff between deldir versions 0.0-20 dated 2012-09-08 and 0.0-21 dated 2012-10-12
Description: Calculates the Delaunay triangulation and the Dirichlet or
Voronoi tessellation (with respect to the entire plane) of a
planar point set.
Author: Rolf Turner
Maintainer: Rolf Turner
ChangeLog | 20 ++++++++++++++------
DESCRIPTION | 8 ++++----
MD5 | 8 +++++---
R/deldir.R | 2 +-
R/duplicatedxy.R |only
man/duplicatedxy.Rd |only
6 files changed, 24 insertions(+), 14 deletions(-)
Title: Visualization of a correlation matrix
Diff between corrplot versions 0.66 dated 2012-09-12 and 0.70 dated 2012-10-12
Description: The corrplot package is a graphical display of a
correlation matrix, confidence interval. It also contains some
algorithms to do matrix reordering.
Author: Taiyun Wei
Maintainer: Taiyun Wei
DESCRIPTION | 8
MD5 | 14
NEWS | 7
R/corrplot.R | 12
inst/doc/index.Rmd | 4
inst/doc/index.html | 985 ++++++++++++++++++++++++------------------------
man/corrplot-package.Rd | 6
man/corrplot.Rd | 9
8 files changed, 540 insertions(+), 505 deletions(-)
Title: Censored Regression (Tobit) Models
Diff between censReg versions 0.5-14 dated 2012-06-29 and 0.5-16 dated 2012-10-12
Description: Estimation of censored regression (Tobit) models with
cross-section and panel data
Author: Arne Henningsen
Maintainer: Arne Henningsen
DESCRIPTION | 8
MD5 | 15 -
NAMESPACE | 1
NEWS | 9 +
R/margEff.censReg.R | 2
R/print.margEff.censReg.R |only
inst/doc/censReg.pdf |binary
tests/censRegTest.R | 11 +
tests/censRegTest.Rout.save | 381 +++++++++++++++++++++++++++-----------------
9 files changed, 274 insertions(+), 153 deletions(-)
Title: Computation of Bayes factors for simple designs
Diff between BayesFactor versions 0.8.2 dated 2012-10-11 and 0.8.3 dated 2012-10-12
Description: The BayesFactor package is a suite of functions for
computing various Bayes factors for simple designs, including
the one- and two-sample designs, one-way designs, general ANOVA
designs, and linear regression.
Author: Richard D. Morey, Jeffrey N. Rouder
Maintainer: Richard D. Morey
BayesFactor-0.8.2/BayesFactor/configure |only
BayesFactor-0.8.3/BayesFactor/DESCRIPTION | 15
BayesFactor-0.8.3/BayesFactor/MD5 | 19 -
BayesFactor-0.8.3/BayesFactor/R/allNways.R | 104 +++++-
BayesFactor-0.8.3/BayesFactor/R/common.R | 2
BayesFactor-0.8.3/BayesFactor/inst/SVN_VERSION | 2
BayesFactor-0.8.3/BayesFactor/man/BayesFactor-package.Rd | 104 +++---
BayesFactor-0.8.3/BayesFactor/man/allNways.Rd | 194 ++++++------
BayesFactor-0.8.3/BayesFactor/man/nWayAOV.Rd | 2
BayesFactor-0.8.3/BayesFactor/man/puzzles.Rd | 2
BayesFactor-0.8.3/BayesFactor/man/ttest.Gibbs.Rd | 242 +++++++--------
11 files changed, 388 insertions(+), 298 deletions(-)