Author: Aaron A. King, Edward L. Ionides, Carles Martinez Breto
Title: Partially-observed Markov processes
Description: Inference methods for partially-observed Markov processes
Diff between pomp versions 0.18-1 dated 2008-05-02 and 0.18-2 dated 2008-05-05
pomp-0.18-1/pomp/R/simulate-mif.R |only pomp-0.18-2/pomp/DESCRIPTION | 6 - pomp-0.18-2/pomp/R/aaa.R | 8 - pomp-0.18-2/pomp/R/mif-methods.R | 55 ----------- pomp-0.18-2/pomp/R/mif.R | 15 ++- pomp-0.18-2/pomp/R/pfilter-mif.R | 14 +-- pomp-0.18-2/pomp/R/pfilter.R | 7 + pomp-0.18-2/pomp/R/plot-pomp.R | 28 ++++-- pomp-0.18-2/pomp/R/pomp-methods.R | 66 ++++++++++++++ pomp-0.18-2/pomp/R/pomp.R | 2 pomp-0.18-2/pomp/R/simulate-pomp.R | 34 +++---- pomp-0.18-2/pomp/data/ou2.rda |binary pomp-0.18-2/pomp/inst/doc/random_walk.Rnw | 14 ++- pomp-0.18-2/pomp/inst/doc/random_walk.pdf |binary pomp-0.18-2/pomp/inst/examples/sir.R | 6 - pomp-0.18-2/pomp/man/mif-class.Rd | 140 ++++++++++++++++++------------ pomp-0.18-2/pomp/man/mif-methods.Rd | 108 ++++++++++++----------- pomp-0.18-2/pomp/man/mif.Rd | 2 pomp-0.18-2/pomp/man/pfilter.Rd | 6 - pomp-0.18-2/pomp/man/pomp-class.Rd | 129 +++++++++++++++++---------- pomp-0.18-2/pomp/man/pomp-package.Rd | 43 +++++---- pomp-0.18-2/pomp/man/simulate-pomp.Rd | 11 +- pomp-0.18-2/pomp/tests/ou2-mif.R | 45 ++++----- pomp-0.18-2/pomp/tests/ou2-simulate.R | 7 + 24 files changed, 433 insertions(+), 313 deletions(-)
Author: Max Kuhn, Steve Weaston
Title: Sweave processing of Open Document Format (ODF) files
Description: Sweave processing of Open Document Format (ODF) files
Diff between odfWeave versions 0.7.3 dated 2008-02-13 and 0.7.4 dated 2008-05-05
DESCRIPTION | 6 +- R/adjustImageSize.R | 2 R/getExt.R | 50 +++++++++++------------ R/getStyles.R | 105 +++++++++++++++++++++++--------------------------- R/pkgVersions.R | 4 + inst/doc/odfWeave.pdf |binary inst/doc/odfWeave.tex | 10 ++-- man/announce.Rd | 2 man/odfCat.Rd | 2 9 files changed, 89 insertions(+), 92 deletions(-)
Author: Juan R González, Lluís Armengol, Elisabet Guinó, Xavier Solé, and Víctor Moreno
Title: SNPs-based whole genome association studies
Description: This package carries out most common analysis when performing whole genome association studies. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented.
Diff between SNPassoc versions 1.5-2 dated 2008-04-22 and 1.5-3 dated 2008-05-05
DESCRIPTION | 10 +++---- NAMESPACE | 3 +- R/Bonferroni.sig.R | 4 +-- R/LD.R | 61 ++++++++++++++++++++++++++++++++++++++++++++++++ R/firstlib.R | 3 +- R/intervals.haplo.glm.R | 4 ++- inst/docs/changelog.txt | 7 +++++ 7 files changed, 82 insertions(+), 10 deletions(-)
Author: Corneliu Henegar
Diff between FunNet versions 1.00 dated 2008-04-03 and 1.00-1 dated 2008-05-05
Title: Functional Analysis of Gene Co-expression Networks
Description: FunNet is an integrative tool for analyzing gene co-expression networks from
microarray expression data. The analytic model implemented in this library
involves two abstraction layers: transcriptional and functional (biological roles).
A functional profiling technique using Gene Ontology & KEGG annotations is
applied to extract a list of relevant biological themes from
microarray expression profiling data. Afterwards multiple-instance
representations are built to relate significant themes to their
transcriptional instances (i.e. the two layers of the model). An adapted
non-linear dynamical system model is used to quantify the proximity of relevant
genomic themes based on the similarity of the expression profiles of their gene instances.
Eventually an unsupervised multiple-instance clustering procedure, relying on
the two abstraction layers, is used to identify the structure of the co-expression
network composed from modules of functionally related transcripts. Functional
and transcriptional maps of the co-expression network are provided separately
together with detailed information on the network centrality of related transcripts
and genomic themes.
DESCRIPTION | 9
R/Annotations.R | 35
R/FunNet.R |12660 ++++++++++++++++++++---------------------
R/sysdata.rda |binary
copying | 3
man/Annotations.Rd | 2
man/FunNet.R-package.Rd | 203
man/FunNet.Rd | 130
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man/RN.GO.DIR.CC.file.annot.Rd |only
man/RN.GO.DIR.MF.file.annot.Rd |only
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man/RN.locus.name.Rd |only
13 files changed, 6545 insertions(+), 6497 deletions(-)
Author: Martin Maechler and many others.
Title: Utilities from Seminar fuer Statistik ETH Zurich
Description: Useful utilities ['goodies'] from Seminar fuer Statistik ETH
Zurich, many ported from S-plus times.
Diff between sfsmisc versions 1.0-1 dated 2008-02-11 and 1.0-2 dated 2008-05-05
ChangeLog | 4 ++++ DESCRIPTION | 7 ++++--- inst/ChangeLog | 4 ++++ 3 files changed, 12 insertions(+), 3 deletions(-)
Author: R. Gentleman, Elizabeth Whalen, W. Huber, S. Falcon
Title: graph: A package to handle graph data structures
Description: A package that implements some simple graph handling
capabilities.
Diff between graph versions 1.17.15 dated 2008-04-22 and 1.18.0 dated 2008-05-05
DESCRIPTION | 4 R/settings.R | 4 data/pancrCaIni.rda |only inst/doc/GraphClass.pdf | 423 ++++++++++++------------- inst/doc/clusterGraph.pdf |binary inst/doc/graph.pdf | 707 ++++++++++++++++++++----------------------- inst/doc/graphAttributes.pdf |binary man/pancrCaIni.Rd |only 8 files changed, 559 insertions(+), 579 deletions(-)
Author: S original
Diff between boot versions 1.2-32 dated 2008-03-30 and 1.2-33 dated 2008-05-05
Title: Bootstrap R (S-Plus) Functions (Canty)
Description: functions and datasets for bootstrapping from the
book "Bootstrap Methods and Their Applications" by A. C. Davison and
D. V. Hinkley (1997, CUP).
ChangeLog | 5 +++++
DESCRIPTION | 6 +++---
R/bootfuns.q | 2 +-
man/cv.glm.Rd | 2 +-
4 files changed, 10 insertions(+), 5 deletions(-)
Author: S original by Venables & Ripley.
R port by Brian Ripley
Diff between VR versions 7.2-41 dated 2008-02-18 and 7.2-42 dated 2008-05-05
Bundle: VR
Contains: MASS class nnet spatial
DESCRIPTION | 6 +++---
MASS/R/polr.R | 19 +++++++++++++------
MASS/R/stdres.R | 2 +-
MASS/inst/NEWS | 4 +++-
WHATS.NEW | 4 +++-
5 files changed, 23 insertions(+), 12 deletions(-)
Author: Jeff Gentry
Diff between Rgraphviz versions 1.16.0 dated 2008-01-24 and 1.18.0 dated 2008-05-05
Title: Provides plotting capabilities for R graph objects
Description: Interfaces R with the AT&T GraphViz library to provide
the ability for plotting R graph objects from the graph
package
Rgraphviz-1.16.0/Rgraphviz/.BBSoptions |only
Rgraphviz-1.16.0/Rgraphviz/graphviz-win32 |only
Rgraphviz-1.16.0/Rgraphviz/src/Makevars.win |only
Rgraphviz-1.18.0/Rgraphviz/DESCRIPTION | 9
Rgraphviz-1.18.0/Rgraphviz/NAMESPACE | 11
Rgraphviz-1.18.0/Rgraphviz/R/Ragraph.R | 2
Rgraphviz-1.18.0/Rgraphviz/R/Rgraphviz.R | 10
Rgraphviz-1.18.0/Rgraphviz/R/defaultAttrs.R | 150
Rgraphviz-1.18.0/Rgraphviz/R/graph.R | 8
Rgraphviz-1.18.0/Rgraphviz/R/layoutGraph.R |only
Rgraphviz-1.18.0/Rgraphviz/R/renderGraph.R |only
Rgraphviz-1.18.0/Rgraphviz/R/zzz.R | 27
Rgraphviz-1.18.0/Rgraphviz/README | 38
Rgraphviz-1.18.0/Rgraphviz/configure.win |only
Rgraphviz-1.18.0/Rgraphviz/inst/doc/Rgraphviz.Rnw | 48
Rgraphviz-1.18.0/Rgraphviz/inst/doc/Rgraphviz.pdf |12010 +++++-----
Rgraphviz-1.18.0/Rgraphviz/inst/doc/newRgraphvizInterface.Rnw |only
Rgraphviz-1.18.0/Rgraphviz/inst/doc/newRgraphvizInterface.pdf |only
Rgraphviz-1.18.0/Rgraphviz/man/agopen.Rd | 2
Rgraphviz-1.18.0/Rgraphviz/man/agopenSimple.Rd | 2
Rgraphviz-1.18.0/Rgraphviz/man/graphLayout.Rd |only
Rgraphviz-1.18.0/Rgraphviz/man/layoutGraph.Rd | 81
Rgraphviz-1.18.0/Rgraphviz/man/renderGraph.Rd |only
Rgraphviz-1.18.0/Rgraphviz/src/Makevars.win.in |only
Rgraphviz-1.18.0/Rgraphviz/src/graphvizVersion.c | 6
25 files changed, 6246 insertions(+), 6158 deletions(-)
Author: Vince Carey
Diff between RBGL versions 1.14.0 dated 2008-01-24 and 1.16.0 dated 2008-05-05
Title: An interface to the BOOST graph library
Description: A fairly extensive and comprehensive interface to the graph
algorithms contained in the BOOST library.
DESCRIPTION | 9
NAMESPACE | 4
R/interfaces.R | 101
inst/XML/dominator.gxl |only
inst/doc/RBGL.Rnw | 21
inst/doc/RBGL.pdf | 5159 +++++++++++++++++++++----------------------
man/dominatorTree.Rd |only
man/layout.Rd | 60
src/boostIncl.tar.gz |binary
src/dominatorTree.cpp |only
src/fruchterman_reingold.hpp |only
src/incrConnComp.cpp | 3
src/layout.cpp | 253 +-
13 files changed, 2865 insertions(+), 2745 deletions(-)
Author: Torsten Hothorn, Kurt Hornik, Mark A. van de Wiel and Achim Zeileis
Title: Conditional Inference Procedures in a Permutation Test Framework
Description: Conditional inference procedures for the general independence
problem including two-sample, K-sample, correlation, censored, ordered and
multivariate problems.
Diff between coin versions 0.6-7 dated 2007-10-09 and 0.6-9 dated 2008-05-05
coin-0.6-7/coin/inst/doc/Rplots.ps |only coin-0.6-7/coin/inst/doc/coin_implementation-js-plot.pdf |only coin-0.6-7/coin/inst/doc/coin_implementation.tex |only coin-0.6-7/coin/inst/doc/coin_implementation.tpt |only coin-0.6-7/coin/inst/documentation/html/dir_ffcd7fcaa547dc02c1b00308358d1322.html |only coin-0.6-7/coin/inst/documentation/html/dir_ffcd7fcaa547dc02c1b00308358d1322_dep.map |only coin-0.6-7/coin/inst/documentation/html/dir_ffcd7fcaa547dc02c1b00308358d1322_dep.png |only coin-0.6-7/coin/inst/documentation/html/globals_defs.html |only coin-0.6-7/coin/inst/documentation/html/hierarchy.html |only coin-0.6-7/coin/inst/documentation/html/inherit__graph__0.map |only coin-0.6-7/coin/inst/documentation/html/inherit__graph__0.md5 |only coin-0.6-7/coin/inst/documentation/html/inherit__graph__0.png |only coin-0.6-7/coin/inst/documentation/html/inherits.html |only coin-0.6-7/coin/inst/documentation/latex/Helvetica.ttf |only 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coin-0.6-9/coin/inst/documentation/man/man3/vandeWiel.c.3 | 26 coin-0.6-9/coin/tests/Examples/coin-Ex.Rout.save | 34 coin-0.6-9/coin/tests/bugfixes.R | 8 coin-0.6-9/coin/tests/bugfixes.Rout.save | 28 coin-0.6-9/coin/tests/codetools-checks.Rout.save | 13 coin-0.6-9/coin/tests/comparisons.Rout.save | 12 coin-0.6-9/coin/tests/regtest_2sample.Rout.save | 12 coin-0.6-9/coin/tests/regtest_Ksample.Rout.save | 12 coin-0.6-9/coin/tests/regtest_MTP.Rout.save | 12 coin-0.6-9/coin/tests/regtest_contingency.Rout.save | 12 coin-0.6-9/coin/tests/regtest_correlation.Rout.save | 12 251 files changed, 7557 insertions(+), 8674 deletions(-)
Author: Carsten F. Dormann and Bernd Gruber, with additional code from Jochen Fruend, based on the C-code developed by Nils Bluethgen.
Title: Visualises bipartite networks and calculates some ecological indices.
Description: See bipartite-package for more details.
Diff between bipartite versions 0.5 dated 2008-03-06 and 0.6 dated 2008-05-05
DESCRIPTION | 8 ++++---- R/as.one.mode.r |only R/dfun.R | 18 ++++++++++++------ R/functspec.r |only R/networklevel.R | 28 ++++++++++++++++------------ R/specieslevel.R | 10 +++++++++- R/swap.web.R |only Wishlist.txt |only data/barrett1987.rda |binary man/C.score.Rd | 6 ++++++ man/as.one.mode.Rd |only man/bipartite-package.Rd | 12 +++++++++--- man/functspec.Rd |only man/networklevel.Rd | 6 +++--- man/null.t.test.Rd | 2 +- man/shuffle.web.Rd | 10 +++++++--- man/specieslevel.Rd | 9 ++++++--- man/swap.web.Rd |only 18 files changed, 73 insertions(+), 36 deletions(-)
Author: Andrew Gelman
Diff between arm versions 1.1-4 dated 2008-04-14 and 1.1-5 dated 2008-05-05
Title: Data Analysis Using Regression and Multilevel/Hierarchical Models
Description: R functions for processing lm, glm, mer and polr outputs.
CHANGELOG | 9 +++++++++
DESCRIPTION | 6 +++---
R/bayesglm.h.R | 5 ++++-
R/coefplot.R | 8 ++++++++
man/bayesglm.Rd | 1 +
man/coefplot.Rd | 3 ++-
6 files changed, 27 insertions(+), 5 deletions(-)