Title: MultiChIPmixHMM
Diff between MultiChIPmixHMM versions 2.0 dated 2013-01-08 and 3.0 dated 2013-02-04
More information about MultiChIPmixHMM at CRAN
Description: Linear regression mixture model to ChIP-chip data
analysis, taking into account the dependence (HMM), and for
multiple biological samples.
Author: Caroline Berard
Maintainer: Caroline Berard
DESCRIPTION | 6 +++---
MD5 | 12 ++++++------
R/Internal.R | 2 +-
R/multiChIPmix.R | 37 ++++++++++++++++++++++---------------
R/multiChIPmixHMM.R | 22 +++++++++++-----------
man/multiChIPmix.Rd | 18 ++++++++++--------
man/multiChIPmixHMM.Rd | 13 +++++++------
7 files changed, 60 insertions(+), 50 deletions(-)
Permanent link
Title: Network analysis and visualization
Diff between igraph versions 0.6-3 dated 2012-10-17 and 0.6.4 dated 2013-02-04
Description: Routines for simple graphs and network analysis. igraph
can handle large graphs very well and provides functions for
generating random and regular graphs, graph visualization,
centrality indices and much more.
Author: See AUTHORS file.
Maintainer: Gabor Csardi
AUTHORS | 1
DESCRIPTION | 11
MD5 | 256 ++++---
NAMESPACE | 8
NEWS |only
R/attributes.R | 157 ++--
R/auto.R | 120 ++-
R/community.R | 6
R/conversion.R | 44 +
R/fit.R | 16
R/foreign.R | 16
R/games.R | 10
R/indexing.R | 8
R/interface.R | 36 -
R/iterators.R | 28
R/layout.R | 29
R/motifs.R | 8
R/package.R | 4
R/plot.R | 24
R/plot.common.R | 798 ++++++++++++++++++++++-
R/plot.shapes.R | 1191 ++++++++++++++++++-----------------
R/socnet.R | 25
R/structural.properties.R | 17
R/structure.generators.R | 15
configure | 20
configure.in | 4
inst/AUTHORS |only
man/arpack.Rd | 9
man/conversion.Rd | 10
man/degree.sequence.game.Rd | 24
man/evcent.Rd | 6
man/graph.data.frame.Rd | 44 +
man/graph.diversity.Rd | 2
man/graph.motifs.Rd | 10
man/igraph.vertex.shapes.Rd | 218 +++++-
man/is.degree.sequence.Rd |only
man/k.regular.game.Rd |only
man/layout.Rd | 23
man/layout.drl.Rd | 4
man/layout.mds.Rd |only
man/plot.common.Rd | 17
man/plot.graph.Rd | 15
man/power.law.fit.Rd | 111 ++-
man/read.graph.Rd | 9
man/rewire.Rd | 7
man/rglplot.Rd | 2
man/tkplot.Rd | 3
man/transitivity.Rd | 10
src/Color.cpp |only
src/Color.h |only
src/Light.cpp |only
src/Light.h |only
src/Makevars.in | 2
src/Makevars.win | 2
src/Point.cpp |only
src/Point.h |only
src/RIgraphRay.cpp |only
src/Ray.cpp |only
src/Ray.h |only
src/RayTracer.cpp |only
src/RayTracer.h |only
src/RayVector.cpp |only
src/RayVector.h |only
src/Shape.cpp |only
src/Shape.h |only
src/Sphere.cpp |only
src/Sphere.h |only
src/Triangle.cpp |only
src/Triangle.h |only
src/adjlist.c | 58 +
src/arpack.c | 26
src/attributes.c | 8
src/centrality.c | 64 +
src/cliques.c | 7
src/community.c | 17
src/config.h.in | 3
src/distances.c | 28
src/drl_graph.cpp | 3
src/drl_layout.cpp | 15
src/drl_layout_3d.cpp | 4
src/eigen.c | 1
src/error.c | 294 +-------
src/foreign-dl-parser.c | 135 +--
src/foreign-dl-parser.h | 2
src/foreign-gml-parser.c | 57 -
src/foreign-gml-parser.h | 2
src/foreign-lgl-parser.c | 25
src/foreign-lgl-parser.h | 2
src/foreign-ncol-parser.c | 21
src/foreign-ncol-parser.h | 2
src/foreign-pajek-header.h | 2
src/foreign-pajek-parser.c | 865 +++++++++++++------------
src/foreign-pajek-parser.h | 2
src/foreign.c | 30
src/games.c | 436 +++++++++++-
src/gss.c |only
src/hacks.c |only
src/igraph_adjlist.h | 4
src/igraph_constants.h | 6
src/igraph_error.c |only
src/igraph_error.h | 5
src/igraph_games.h | 4
src/igraph_hacks_internal.h |only
src/igraph_nongraph.h | 36 +
src/igraph_topology.h | 15
src/igraph_version.h | 2
src/infomap.cc | 2
src/kolmogorov.c |only
src/layout.c | 68 +
src/lbfgs.c |only
src/motifs.c | 35 -
src/options.c |only
src/other.c | 172 ++++-
src/plfit |only
src/plfit.c |only
src/rinterface.c | 232 ++++++
src/separators.c | 8
src/structural_properties.c | 536 ++++++++++++---
src/sugiyama.c | 8
src/unit_limiter.cpp |only
src/unit_limiter.h |only
src/vector.pmt | 3
src/vector_ptr.c | 5
src/walktrap.cpp | 18
src/walktrap_communities.cpp | 8
src/walktrap_communities.h | 6
src/walktrap_graph.cpp | 21
src/walktrap_graph.h | 6
src/walktrap_heap.cpp | 1
src/walktrap_heap.h | 7
src/zeta.c |only
tests/alpha.centrality.R | 20
tests/alpha.centrality.Rout.save | 37 +
tests/bug-1019624.R |only
tests/bug-1019624.Rout.save |only
tests/bug-1019624.txt |only
tests/bug-1032819.R |only
tests/bug-1032819.Rout.save |only
tests/bug-1033045.R |only
tests/bug-1033045.Rout.save |only
tests/bug-1073705-indexing.R |only
tests/bug-1073705-indexing.Rout.save |only
tests/bug-1073800-clique.R |only
tests/bug-1073800-clique.Rout.save |only
tests/layout.mds.R |only
tests/layout.mds.Rout.save |only
tests/layout.merge.R |only
tests/layout.merge.Rout.save |only
tests/motifs.Rout.save | 16
tests/pajek.Rout.save | 25
150 files changed, 4708 insertions(+), 2087 deletions(-)
Title: A package for downloading files over https
Diff between downloader versions 0.1 dated 2012-11-01 and 0.2 dated 2013-02-04
Description: This package provides a wrapper for the download.file
function, making it possible to download files over https on
Windows, Mac OS X, and other Unix-like platforms. The RCurl
package provides this functionality (and much more) but can be
difficult to install because it must be compiled with external
dependencies. This package has no external dependencies, so it
is much easier to install.
Author: Winston Chang
Maintainer: Winston Chang
DESCRIPTION | 10 ++++++----
MD5 | 12 +++++++++---
NAMESPACE | 1 +
NEWS |only
R/download.r | 22 +++++++++++++---------
R/source_url.r |only
README.md |only
inst |only
man/source_url.Rd |only
tests |only
10 files changed, 29 insertions(+), 16 deletions(-)
Title: Easy profiling of R functions
Diff between timeit versions 0.2.0 dated 2013-01-09 and 0.2.1 dated 2013-02-04
Description: Provides an easy-to-use wrapper to Rprof() and
summaryRprof() in the profiling of both function calls and
whole blocks of code.
Author: Kevin Ushey
Maintainer: Kevin Ushey
DESCRIPTION | 15
MD5 | 12
NEWS | 9
R/timeit.R | 692 +++++++++++++++++++++---------------------
man/determine_replications.Rd | 38 +-
man/do_timeit.Rd | 100 +++---
man/timeit.Rd | 196 ++++++-----
7 files changed, 541 insertions(+), 521 deletions(-)
Title: Functions for phonetics in R.
Diff between phonTools versions 0.1-4 dated 2012-11-08 and 0.1-5 dated 2013-02-04
Description: The functions contained in this package are intended to
facilitate the organization, display, and analysis of the sorts
of data frequently encountered in phonetics research and
experimentation. Some functions also allow for the creation and
manipulation of sounds saved as WAV files.
Author: Santiago Barreda
Maintainer: Santiago Barreda
DESCRIPTION | 8 ++--
MD5 | 35 +++++++++---------
R/Ffilter.R | 63 +++++++++++++++++++-------------
R/normalization.compare.R |only
R/normalize.R | 89 +++++++++++++++++++++++++++++++++-------------
R/plot.template.R |only
R/powertrack.R | 4 --
R/sdellipse.R | 5 +-
R/spectralslice.R | 3 +
R/spectrogram.R | 1
R/vowelplot.R | 8 ++--
R/vowelsynth.R | 74 +++++++++++++++++++++-----------------
man/Ffilter.Rd | 28 ++++++++------
man/PSTM.Rd | 2 -
man/createtemplate.Rd | 9 +++-
man/normalize.Rd | 74 ++++++++++++++++++++------------------
man/normalize.compare.Rd |only
man/sdellipse.Rd | 9 ++--
man/spectralslice.Rd | 2 -
man/vowelsynth.Rd | 37 +++++++++++--------
20 files changed, 268 insertions(+), 183 deletions(-)
Title: Temporal Trend Analysis Graphical Interface
Diff between TTAinterfaceTrendAnalysis versions 1.02 dated 2012-09-03 and 1.03 dated 2013-02-04
More information about TTAinterfaceTrendAnalysis at CRAN
Description: This interface was created to develop a standard procedure
of temporal trend analysis in the framework of the OSPAR
convention. It is based on 4 successive steps : simply
manipulate your database, select the parameters you want to
analyse, build your regulated time series, perform analysis and
read the results all in one easy to use interface. Statistical
analysis call other package function such as Kendall tests (wq
package) or cusum function (Pastec package).
Author: David DEVREKER [aut], Alain LEFEBVRE [aut, cre]
Maintainer: Alain LEFEBVRE
TTAinterfaceTrendAnalysis-1.02/TTAinterfaceTrendAnalysis/R/FULLoption.R |only
TTAinterfaceTrendAnalysis-1.02/TTAinterfaceTrendAnalysis/inst/aide/Logo_Ifremer.gif |only
TTAinterfaceTrendAnalysis-1.02/TTAinterfaceTrendAnalysis/inst/aide/Logo_R.gif |only
TTAinterfaceTrendAnalysis-1.02/TTAinterfaceTrendAnalysis/inst/aide/UserGuide.pdf |only
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/DESCRIPTION | 18
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/MD5 | 39 -
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/R/FULLoption.r |only
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/R/TTAinterface.R | 328 ++++++----
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/R/aide1.r |only
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/R/aide2.r |only
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/R/aide3.r |only
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/R/aide4.r |only
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/R/fixdata.R | 318 +++++----
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/R/selectdirectory.R | 314 +++++----
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/R/zzz.R | 23
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/data |only
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/inst/aide/HELP1.txt | 22
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/inst/aide/HELP2.txt | 30
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/inst/aide/HELP3.txt | 24
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/inst/aide/HELP4.txt | 27
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/inst/aide/Small_Logo_R.gif |only
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/inst/aide/imgArrowleft.gif |only
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/inst/aide/imgArrowright.gif |only
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/inst/aide/imgFixdata.gif |only
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/inst/aide/imgHelp.gif |only
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/inst/aide/imgProcess.gif |only
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/inst/aide/imgShowdata.gif |only
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/inst/aide/imgStart.gif |only
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/inst/aide/imgUserguide.gif |only
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/inst/doc |only
TTAinterfaceTrendAnalysis-1.03/TTAinterfaceTrendAnalysis/man/SRNDunkerque.rd |only
31 files changed, 684 insertions(+), 459 deletions(-)
Permanent link
Title: Create time series BUGS models.
Diff between tsbugs versions 1.0 dated 2013-01-14 and 1.1 dated 2013-02-04
Description: The tsbugs package contains a collection of R functions
that can be used to create time series BUGS models of various
order. Included are function to create BUGS with non-constant
variance such stochastic volatility models and random variance
shift models.
Author: Guy J. Abel
Maintainer: Guy J. Abel
DESCRIPTION | 11 +++++------
MD5 | 29 +++++++++++++++++------------
R/ar.bugs.R | 3 ++-
R/inits.R | 2 +-
R/rv.bugs.R | 3 ++-
R/sv.bugs.R | 3 ++-
R/tsbugs-internal.R |only
data |only
man/ar.bugs.Rd | 15 ++++++++-------
man/ew.Rd |only
man/inits.Rd | 4 ++--
man/nodes.Rd | 4 ++--
man/print.tsbugs.Rd | 4 ++--
man/rv.bugs.Rd | 6 +++---
man/sv.bugs.Rd | 9 +++++----
man/svpdx.Rd |only
man/tsbugs-package.Rd | 1 -
17 files changed, 51 insertions(+), 43 deletions(-)
Title: Statistical inference of vine copulas
Diff between VineCopula versions 1.0 dated 2012-06-28 and 1.1 dated 2013-02-04
Description: This package provides functions for statistical inference
of vine copulas. It contains tools for bivariate exploratory
data analysis, bivariate copula selection and (vine) tree
construction. Models can be estimated either sequentially or by
joint maximum likelihood estimation. Sampling algorithms and
plotting methods are also included. Data is assumed to lie in
the unit hypercube (so-called copula data). For C- and D-vines
links to the package CDVine are provided.
Author: Ulf Schepsmeier, Jakob Stoeber, Eike Christian Brechmann
Maintainer: Ulf Schepsmeier
VineCopula-1.0/VineCopula/R/BiCopGofKendall.r |only
VineCopula-1.0/VineCopula/Thumbs.db |only
VineCopula-1.0/VineCopula/man/BiCopGofKendall.Rd |only
VineCopula-1.0/VineCopula/man/R2CVine.Rd |only
VineCopula-1.0/VineCopula/man/R2DVine.Rd |only
VineCopula-1.1/VineCopula/DESCRIPTION | 8
VineCopula-1.1/VineCopula/MD5 | 129 ++++-----
VineCopula-1.1/VineCopula/NAMESPACE | 5
VineCopula-1.1/VineCopula/R/BiCopCDF.r | 16 -
VineCopula-1.1/VineCopula/R/BiCopEst.r | 91 ++++--
VineCopula-1.1/VineCopula/R/BiCopGofTest.r |only
VineCopula-1.1/VineCopula/R/BiCopSelect.r | 74 +++--
VineCopula-1.1/VineCopula/R/BiCopSim.R | 32 ++
VineCopula-1.1/VineCopula/R/C2RVine.r | 56 ----
VineCopula-1.1/VineCopula/R/D2RVine.r | 54 ----
VineCopula-1.1/VineCopula/R/RVineCopSelect.r | 27 +-
VineCopula-1.1/VineCopula/R/RVineGrad.r | 3
VineCopula-1.1/VineCopula/R/RVineHessian.r | 15 +
VineCopula-1.1/VineCopula/R/RVineSeqEst.R | 6
VineCopula-1.1/VineCopula/R/RVineStdError.r | 2
VineCopula-1.1/VineCopula/R/RVineStructureSelect.r | 39 +-
VineCopula-1.1/VineCopula/R/RVineTreePlot.r | 22 -
VineCopula-1.1/VineCopula/R/TauMatrix.r | 20 +
VineCopula-1.1/VineCopula/R/wrappingCFunctions.r |only
VineCopula-1.1/VineCopula/VineCopula.pdf |binary
VineCopula-1.1/VineCopula/inst |only
VineCopula-1.1/VineCopula/man/BiCopCDF.Rd | 14 -
VineCopula-1.1/VineCopula/man/BiCopEst.Rd | 3
VineCopula-1.1/VineCopula/man/BiCopGofTest.Rd |only
VineCopula-1.1/VineCopula/man/BiCopIndTest.Rd | 2
VineCopula-1.1/VineCopula/man/BiCopKPlot.Rd | 2
VineCopula-1.1/VineCopula/man/BiCopSelect.Rd | 5
VineCopula-1.1/VineCopula/man/BiCopVuongClarke.Rd | 4
VineCopula-1.1/VineCopula/man/C2RVine.Rd | 15 -
VineCopula-1.1/VineCopula/man/D2RVine.Rd | 4
VineCopula-1.1/VineCopula/man/RVineCopSelect.Rd | 16 -
VineCopula-1.1/VineCopula/man/RVineGrad.Rd | 33 +-
VineCopula-1.1/VineCopula/man/RVineHessian.Rd | 33 +-
VineCopula-1.1/VineCopula/man/RVineLogLik.Rd | 7
VineCopula-1.1/VineCopula/man/RVineMLE.Rd | 11
VineCopula-1.1/VineCopula/man/RVineMatrix.Rd | 7
VineCopula-1.1/VineCopula/man/RVineSeqEst.Rd | 3
VineCopula-1.1/VineCopula/man/RVineSim.Rd | 5
VineCopula-1.1/VineCopula/man/RVineStdError.rd | 13
VineCopula-1.1/VineCopula/man/RVineStructureSelect.Rd | 16 -
VineCopula-1.1/VineCopula/man/RVineTreePlot.Rd | 3
VineCopula-1.1/VineCopula/man/TauMatrix.Rd | 5
VineCopula-1.1/VineCopula/man/VineCopula-package.Rd | 35 +-
VineCopula-1.1/VineCopula/src/cdvine.c | 13
VineCopula-1.1/VineCopula/src/hfunc.c | 196 ++++++++++++++-
VineCopula-1.1/VineCopula/src/include/cdvine.h | 5
VineCopula-1.1/VineCopula/src/include/condsim.h | 5
VineCopula-1.1/VineCopula/src/include/deriv.h | 4
VineCopula-1.1/VineCopula/src/include/deriv2.h | 5
VineCopula-1.1/VineCopula/src/include/hfunc.h | 8
VineCopula-1.1/VineCopula/src/include/incompleteBeta.h | 5
VineCopula-1.1/VineCopula/src/include/likelihood.h | 5
VineCopula-1.1/VineCopula/src/include/logderiv.h | 5
VineCopula-1.1/VineCopula/src/include/memoryhandling.h | 5
VineCopula-1.1/VineCopula/src/include/rvine.h | 5
VineCopula-1.1/VineCopula/src/include/rvinederiv.h | 10
VineCopula-1.1/VineCopula/src/include/rvinederiv2.h | 5
VineCopula-1.1/VineCopula/src/include/tcopuladeriv.h | 5
VineCopula-1.1/VineCopula/src/include/tcopuladeriv_new.h | 5
VineCopula-1.1/VineCopula/src/include/tools.h | 8
VineCopula-1.1/VineCopula/src/include/vine.h | 9
VineCopula-1.1/VineCopula/src/likelihood.c | 24 +
VineCopula-1.1/VineCopula/src/rvinederiv.c | 62 +++-
VineCopula-1.1/VineCopula/src/rvinederiv2.c | 76 +++--
VineCopula-1.1/VineCopula/src/tools.c | 41 +++
70 files changed, 893 insertions(+), 448 deletions(-)
Title: Complete Environment for Bayesian Inference
Diff between LaplacesDemon versions 13.01.07 dated 2013-01-08 and 13.02.04 dated 2013-02-04
Description: Laplace's Demon is a complete environment for Bayesian
inference.
Author: Statisticat, LLC
Maintainer: Martina Hall
CHANGELOG | 16
DESCRIPTION | 8
MD5 | 66 +-
R/Combine.R | 48 +
R/Consort.R | 107 ++-
R/Juxtapose.R | 1
R/LML.R | 9
R/LaplaceApproximation.R | 2
R/LaplacesDemon.R | 1059 ++++++++++++++++++++++--------------
R/LaplacesDemon.RAM.R | 30 -
R/LaplacesDemon.hpc.R | 26
R/PMC.R | 16
R/as.covar.R | 30 -
R/as.initial.values.R | 3
R/plot.demonoid.R | 26
R/plot.demonoid.hpc.R | 5
R/plotMatrix.R | 3
R/print.demonoid.R | 8
inst/doc/BayesianInference.Stex | 4
inst/doc/BayesianInference.pdf |binary
inst/doc/Examples.Stex | 205 +++++-
inst/doc/Examples.pdf |binary
inst/doc/LaplacesDemonTutorial.Stex | 59 +-
inst/doc/LaplacesDemonTutorial.pdf |binary
inst/doc/References.bib | 34 +
man/LML.Rd | 4
man/LaplacesDemon-package.Rd | 6
man/LaplacesDemon.RAM.Rd | 50 +
man/LaplacesDemon.Rd | 104 ++-
man/PosteriorChecks.Rd | 4
man/as.covar.Rd | 18
man/as.initial.values.Rd | 17
man/plot.demonoid.Rd | 4
man/plotMatrix.Rd | 11
34 files changed, 1335 insertions(+), 648 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-04-28 1.84
2010-03-04 1.83
2008-12-30 1.70
2008-10-22 1.60
2008-08-22 1.53
2008-07-05 1.52
2008-06-19 1.51
Title: bibtex parser
Diff between bibtex versions 0.3-4 dated 2012-11-28 and 0.3-5 dated 2013-02-04
Description: Utility to parse a bibtex file
Author: Romain Francois [aut], Kurt Hornik [ctb, cre]
Maintainer: Kurt Hornik
bibtex-0.3-4/bibtex/NEWS |only
bibtex-0.3-5/bibtex/DESCRIPTION | 17
bibtex-0.3-5/bibtex/MD5 | 16
bibtex-0.3-5/bibtex/NEWS.Rd |only
bibtex-0.3-5/bibtex/R/bibtex.R | 7
bibtex-0.3-5/bibtex/inst/bibparse.output | 4
bibtex-0.3-5/bibtex/inst/grammar/bibparse.y | 27
bibtex-0.3-5/bibtex/src/biblex.c | 76 -
bibtex-0.3-5/bibtex/src/bibparse.c | 1194 ++++++++++------------------
bibtex-0.3-5/bibtex/src/bibparse.h | 53 -
10 files changed, 558 insertions(+), 836 deletions(-)
Title: Information Decomposition of Two-phase Experiments
Diff between infoDecompuTE versions 0.5.0 dated 2013-02-03 and 0.5.1 dated 2013-02-04
Description: InfoDecompuTE is capable of generating the structure of
the analysis of variance (ANOVA) table of the two-phase
experiments. By inputting the design and the relationships of
the random and fixed factors using the Wilkinson-Rogers'
syntax, infoDecompuTE can generate the structure of the ANOVA
table with the coefficients of the variance components for the
expected mean squares. This package can also study the balanced
incomplete block design and provides the efficiency factors of
the fixed effects.
Author: Kevin Chang and Katya Ruggiero
Maintainer: Kevin Chang
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/toLatexTable.r | 42 ++++++++++++++++++++++++++++--------------
man/infoDecompuTE-package.Rd | 4 ++--
man/summaryAovOnePhase.Rd | 8 +++++++-
man/summaryAovTwoPhase.Rd | 7 ++++++-
6 files changed, 52 insertions(+), 27 deletions(-)
Title: Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
Diff between trio versions 1.7.1 dated 2012-10-03 and 1.9.3 dated 2013-02-04
Description: Testing SNPs and SNP interactions with a genotypic TDT.
This package furthermore contains functions for computing
pairwise values of LD measures and for identifying LD blocks,
as well as functions for setting up matched case pseudo-control
genotype data for case-parent trios in order to run trio logic
regression, for imputing missing genotypes in trios, for
simulating case-parent trios with disease risk dependent on SNP
interaction, and for power and sample size calculation in trio
data.
Author: Holger Schwender, Qing Li, Christoph Neumann, Ingo Ruczinski
Maintainer: Holger Schwender
DESCRIPTION | 8 ++++----
MD5 | 20 ++++++++++----------
NAMESPACE | 2 +-
R/allelicTDT.R | 2 +-
R/fastGxG.R | 2 +-
R/qingInternal.R | 50 +++++++++++++++++++++++++++++++++-----------------
R/read.pedfile.R | 8 ++++++++
R/trio.sim.R | 18 +++++++++++++++---
R/trioFS.R | 4 +---
inst/doc/trio.pdf |binary
man/trio.sim.Rd | 12 ++++++++----
11 files changed, 82 insertions(+), 44 deletions(-)
Title: Rcpp integration for the Eigen templated linear algebra library.
Diff between RcppEigen versions 0.3.1.2 dated 2012-11-29 and 0.3.1.2.1 dated 2013-02-04
Description: R and Eigen integration using Rcpp.
Eigen is a C++ template library for linear algebra: matrices, vectors,
numerical solvers and related algorithms. It supports dense
and sparse matrices on integer, floating point and complex
numbers, decompositions of such matrices, and solutions of
linear systems. Its performance on many algorithms is
comparable with some of the best implementations based on
Lapack and level-3 BLAS.
The RcppEigen package includes the header files from the Eigen C++
template library (currently version 3.1.0). Thus users do not
need to install Eigen itself in order to use RcppEigen.
Eigen is licensed under the GNU LGPL version 3 or later, and also under
the GNU GPL version 2 or later. RcppEigen (the Rcpp
bindings/bridge to Eigen) is licensed under the GNU GPL version
2 or later, as is the rest of Rcpp.
Author: Douglas Bates, Romain Francois and Dirk Eddelbuettel
Maintainer: Douglas Bates
RcppEigen-0.3.1.2.1/RcppEigen/ChangeLog | 17 +++++
RcppEigen-0.3.1.2.1/RcppEigen/DESCRIPTION | 8 +-
RcppEigen-0.3.1.2.1/RcppEigen/MD5 | 17 ++---
RcppEigen-0.3.1.2.1/RcppEigen/NEWS | 33 +++++++---
RcppEigen-0.3.1.2.1/RcppEigen/NEWS.org | 17 ++++-
RcppEigen-0.3.1.2.1/RcppEigen/inst/CITATION |only
RcppEigen-0.3.1.2.1/RcppEigen/inst/doc/RcppEigen-Introduction.pdf |binary
RcppEigen-0.3.1.2.1/RcppEigen/man/RcppEigen-package.Rd | 7 +-
RcppEigen-0.3.1.2.1/RcppEigen/man/fastLm.Rd | 6 +
RcppEigen-0.3.1.2/RcppEigen/vignettes/jss.bst |only
RcppEigen-0.3.1.2/RcppEigen/vignettes/jsslogo.jpg |only
11 files changed, 80 insertions(+), 25 deletions(-)
Title: Collection of functions for orthogonal and orthonormal
polynomials
Diff between orthopolynom versions 1.0-4 dated 2013-01-29 and 1.0-5 dated 2013-02-04
Description: A collection of functions to construct sets of orthogonal
polynomials and their recurrence relations. Additional
functions are provided to calculate the derivative, integral,
value and roots of lists of polynomial objects.
Author: Frederick Novomestky
Maintainer: Frederick Novomestky
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/jacobi.p.recurrences.R | 13 +++++++++++++
3 files changed, 19 insertions(+), 6 deletions(-)
Title: Ozgur-Ozlem Miscellaneous
Diff between OOmisc versions 1.1 dated 2012-08-02 and 1.2 dated 2013-02-04
Description: Includes miscellaneous functions.
Author: Ozgur Asar, Ozlem Ilk
Maintainer: Ozgur Asar
DESCRIPTION | 10 +++++-----
MD5 | 4 ++--
man/OOmisc.Rd | 4 ++--
3 files changed, 9 insertions(+), 9 deletions(-)
Title: Multivariate Marginal Models
Diff between mmm versions 1.1 dated 2012-09-26 and 1.2 dated 2013-02-04
Description: fits multivariate marginal models for multivariate
longitudinal data for both continuous and discrete responses
Author: Ozgur Asar, Ozlem Ilk
Maintainer: Ozgur Asar
DESCRIPTION | 10 +++++-----
MD5 | 4 ++--
man/mmm-package.Rd | 4 ++--
3 files changed, 9 insertions(+), 9 deletions(-)
Title: Citations for knitr markdown files
Diff between knitcitations versions 0.3-1 dated 2013-02-01 and 0.3-2 dated 2013-02-04
Description: While traditional Sweave documents can take advantage of
LaTeX citation tools, knitr also allows users to combine the
much simpler markdown with R code. This package offers
citation tools to make up for this. This package will also
take advantage of the web-based nature of markdown documents to
allow dynamic citations pulled from the web.
Author: Carl Boettiger [aut, cre]
Maintainer: Carl Boettiger
DESCRIPTION | 6 -
MD5 | 33 +++---
NEWS | 16 ++
R/bibliography.R | 37 +++++-
R/cite.R | 4
R/citep.R | 9 -
R/citet.R | 32 +++--
R/newbib.R | 9 +
R/print_rdfa.R | 88 ++++++++++------
README.md | 187 ++++++++++++++++++++++++++--------
inst/examples/README.Rmd | 45 ++++++--
inst/examples/README.html |only
inst/examples/knitcitations.bib | 214 ++--------------------------------------
man/bibliography.Rd | 21 ++-
man/check.Rd |only
man/cite.Rd | 3
man/citep.Rd | 8 +
man/citet.Rd | 19 ++-
man/print_rdfa.Rd |only
19 files changed, 382 insertions(+), 349 deletions(-)
Title: Futile matrix utilities
Diff between futile.matrix versions 1.1.2 dated 2012-02-07 and 1.2.0 dated 2013-02-04
Description: A collection of matrix manipulation functions including
generation of matrix ensembles
Author: Brian Lee Yung Rowe
Maintainer: Brian Lee Yung Rowe
futile.matrix-1.1.2/futile.matrix/man/create.RandomMatrixModel.Rd |only
futile.matrix-1.1.2/futile.matrix/sample-data |only
futile.matrix-1.2.0/futile.matrix/DESCRIPTION | 14 -
futile.matrix-1.2.0/futile.matrix/MD5 | 26 +-
futile.matrix-1.2.0/futile.matrix/R/cutoff.R | 37 +--
futile.matrix-1.2.0/futile.matrix/R/density.R | 27 +-
futile.matrix-1.2.0/futile.matrix/R/ensemble.R | 96 +++++-----
futile.matrix-1.2.0/futile.matrix/R/io.R | 64 ++----
futile.matrix-1.2.0/futile.matrix/inst/sample-data |only
futile.matrix-1.2.0/futile.matrix/inst/unitTests/runit.cutoff.R | 12 -
futile.matrix-1.2.0/futile.matrix/inst/unitTests/runit.ensemble.R | 2
futile.matrix-1.2.0/futile.matrix/man/RandomMatrixModel.Rd |only
futile.matrix-1.2.0/futile.matrix/man/density.Rd | 6
futile.matrix-1.2.0/futile.matrix/man/futile.matrix-package.Rd | 6
futile.matrix-1.2.0/futile.matrix/man/read.matrix.Rd | 7
futile.matrix-1.2.0/futile.matrix/man/rmatrix.Rd | 5
16 files changed, 145 insertions(+), 157 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-04-06 2.0.0
2009-07-18 1.1.1
2009-05-28 1.0.2
2009-04-15 1.0