Title: Bayesian Inference for Zero-Inflated Count Models
Diff between zic versions 0.5-3 dated 2010-01-28 and 0.5-4 dated 2010-08-25
Description: This package provides MCMC algorithms for the analysis of
zero-inflated count models. The case of stochastic search
variable selection (SSVS) is also considered. All MCMC samplers
are coded in C++ for improved efficiency. A data set
considering the demand for health care is also provided.
Author: Markus Jochmann
Maintainer: Markus Jochmann
DESCRIPTION | 8 ++++----
src/cvm.h | 8 ++++----
src/zic.cc | 4 ++--
3 files changed, 10 insertions(+), 10 deletions(-)
Title: Zero-coupon Yield Curve Estimation
Diff between termstrc versions 1.3.2 dated 2010-07-28 and 1.3.3 dated 2010-08-25
Description: The package offers a wide range of functions for term
structure estimation based on static and dynamic coupon bond
and yield data sets. The implementation focuses on the cubic
splines approach of McCulloch (1971, 1975) and the Nelson and
Siegel (1987) method with extensions by Svensson (1994),
Diebold and Li (2006) and De Pooter (2007). We propose a
weighted constrained optimization procedure with analytical
gradients and a globally optimal start parameter search
algorithm. Extensive summary statistics and plots are provided
to compare the results of the different estimation methods.
Several demos are available using data from European government
bonds and yields.
Author: Robert Ferstl, Josef Hayden
Maintainer: Josef Hayden
termstrc-1.3.2/termstrc/data/GermanBonds.RData |only
termstrc-1.3.2/termstrc/man/GermanBonds.Rd |only
termstrc-1.3.3/termstrc/DESCRIPTION | 10 ++++++----
termstrc-1.3.3/termstrc/data/datadyncouponbonds.RData |only
termstrc-1.3.3/termstrc/demo/nss_dynamic.R | 2 +-
termstrc-1.3.3/termstrc/man/datadyncouponbonds.Rd |only
termstrc-1.3.3/termstrc/man/rm_bond.dyncouponbonds.Rd | 2 +-
7 files changed, 8 insertions(+), 6 deletions(-)
Title: R genetic programming framework
Diff between rgp versions 0.1-0 dated 2010-05-22 and 0.2-1 dated 2010-08-25
Description: RGP is a simple modular Genetic Programming (GP) system
build in pure R. In addition to general GP tasks, the system
supports Symbolic Regression by GP through the familiar R model
formula interface. GP individuals are represented as R
expressions, an (optional) type system enables domain-specific
function sets containing functions of diverse domain- and range
types. A basic set of genetic operators for variation (mutation
and crossover) and selection is provided.
Author: Oliver Flasch, Olaf Mersmann, Thomas Bartz-Beielstein, Joerg
Stork
Maintainer: Oliver Flasch
DESCRIPTION | 12 -
NAMESPACE | 21 +++
R/creation.r | 74 +++++++++++
R/evolution.r | 92 ++++++++++++--
R/list_utils.r | 29 ++++
R/population.r | 6
R/rgp.r |only
R/search_space.r | 31 +++-
R/selection.r | 202 ++++++++++++++++++++++++++------
R/similarity.r | 117 +++++++++++++++++-
R/test_utils.r |only
demo |only
man/customDist.Rd |only
man/defaultGPFunctionAndConstantSets.Rd | 25 +++
man/exprChildrenOrEmptyList.Rd |only
man/exprLabel.Rd |only
man/expressionSimilarityMeasures.Rd | 34 ++++-
man/geneticProgramming.Rd | 7 -
man/inversePermutation.Rd |only
man/nondeterministicRanking.Rd |only
man/orderByParetoMeasure.Rd |only
man/paretoSorting.Rd |only
man/randomCall.Rd |only
man/rgp-package.Rd |only
man/rgpTestingAndBenchmarking.Rd |only
man/searchSpaceDefinition.Rd | 4
man/selectionFunctions.Rd | 67 +++++++---
man/sortByRange.Rd | 6
man/sortByRanking.Rd |only
man/sortByType.Rd |only
man/symbolicRegression.Rd | 10 -
src |only
32 files changed, 628 insertions(+), 109 deletions(-)
Title: Gifi Methods for Optimal Scaling
Diff between homals versions 1.0-0 dated 2009-08-01 and 1.0-3 dated 2010-08-25
Description: This package performs a homogeneity analysis and various
extensions. Rank restrictions on the category quantifications
can be imposed (nonlinear PCA). The categories are transformed
by means of optimal scaling with options for nominal, ordinal,
and numerical scale levels (for rank-1 restrictions). Variables
can be grouped into sets, in order to emulate regression
analysis and canonical correlation analysis.
Author: Jan de Leeuw, Patrick Mair
Maintainer: Jan de Leeuw
DESCRIPTION | 10 ++++++----
R/homals.R | 26 +++++++++++++-------------
R/normX.R | 5 +++--
inst/doc/homals.Rnw | 5 +++++
inst/doc/homals.pdf |binary
inst/doc/jsslogo.jpg |only
man/senate07.Rd | 6 +++---
7 files changed, 30 insertions(+), 22 deletions(-)
Title: Functions for medical statistics book with some demographic data
Diff between fmsb versions 0.1.1 dated 2010-08-25 and 0.2 dated 2010-08-25
Description: Several utility functions for the book entitled "Practices
of Medical and Health Data Analysis using R" (Pearson Education
Japan, 2007)
Author: Minato Nakazawa
Maintainer: Minato Nakazawa
fmsb |only
1 file changed
Title: A Program to Estimate Animal Abundance and Density using
Spatially-Explicit Capture-Recapture
Diff between SPACECAP versions 1.0 dated 2010-02-16 and 1.0.1 dated 2010-08-25
Description: SPACECAP is a user-friendly software package for
estimating animal densities using closed model
capture-recapture sampling based on photographic captures using
Bayesian spatially-explicit capture-recapture models. This
approach offers advantage such as: substantially dealing with
problems posed by individual heterogeneity in capture
probabilities in conventional capture-recapture analyses. It
also offers non-asymptotic inferences which are more
appropriate for small samples of capture data typical of
photo-capture studies.
Author: Pallavi Singh, Arjun M. Gopalaswamy, Andrew J. Royle, N. Samba
Kumar and K. Ullas Karanth with contributions from Sumanta
Mukherjee, Vatsaraj & Dipti Bharadwaj
Maintainer: Jim Hines
SPACECAP-1.0.1/SPACECAP/DESCRIPTION | 8 ++++----
SPACECAP-1.0.1/SPACECAP/R/SPACECAP.R | 4 ++--
SPACECAP-1.0.1/SPACECAP/inst/doc/SPACECAP_Manual.pdf |binary
SPACECAP-1.0.1/SPACECAP/man/SPACECAP-package.Rd | 6 +++---
SPACECAP-1.0.1/SPACECAP/man/SPACECAP.Rd | 8 ++++----
SPACECAP-1.0/SPACECAP/data |only
6 files changed, 13 insertions(+), 13 deletions(-)
Title: Siena - Simulation Investigation for Empirical Network Analysis
Diff between RSiena versions 1.0.11.110 dated 2010-07-03 and 1.0.11.119 dated 2010-08-25
Description: Fits models to longitudinal networks
Author: Various
Maintainer: Ruth Ripley
DESCRIPTION | 10
R/RSienaRDocumentation.r | 4
R/maxlike.r | 4
R/phase1.r | 4
R/print01Report.r | 2
R/print07Report.r | 12
R/siena08.r | 2
R/sienaDataCreate.r | 102
R/sienaModelCreate.r | 11
R/sienaprint.r | 14
R/sienautils.r | 5
R/simstatsc.r | 50
changeLog | 83
inst/doc/s_man400.pdf | 5267 ++++++++++++++++----------------
man/RSiena-package.Rd | 4
man/sienaModelCreate.Rd | 65
src/model/Model.cpp | 52
src/model/Model.h | 18
src/model/ml/Chain.cpp | 37
src/model/ml/MLSimulation.cpp | 372 ++
src/model/ml/MLSimulation.h | 24
src/model/ml/NetworkChange.cpp | 13
src/model/ml/Option.cpp | 9
src/model/ml/Option.h | 1
src/model/variables/NetworkVariable.cpp | 114
src/siena07.cpp | 26
26 files changed, 3503 insertions(+), 2802 deletions(-)
Title: Algorithms and framework for Nonnegative Matrix Factorization
(NMF).
Diff between NMF versions 0.5 dated 2010-08-20 and 0.5.02 dated 2010-08-25
Description: This package provides a framework to perform Non-negative
Matrix Factorization (NMF). It implements a set of already
published algorithms and seeding methods, and provides a
framework to test, develop and plug new/custom algorithms. Most
of the built-in algorithms have been optimized in C++, and the
main interface function provides an easy way of performing
parallel computations on multicore machines.
Author: Renaud Gaujoux
Maintainer: Renaud Gaujoux
DESCRIPTION | 6 +++---
NEWS | 12 ++++++++++++
R/NMF-class.R | 3 ++-
R/nmf.R | 12 +++++++-----
man/NMFList.Rd | 2 +-
5 files changed, 25 insertions(+), 10 deletions(-)
Title: Identification of Family Relations using linked markers
Diff between FEST versions 0.07 dated 2010-04-12 and 0.08 dated 2010-08-25
Description: Identification of Family Relations using linked markers.
Author: Øivind Skare
Maintainer: Øivind Skare
DESCRIPTION | 11 ++++++-----
R/zzz.R | 15 +++++++--------
2 files changed, 13 insertions(+), 13 deletions(-)
Title: Calculate the consensus clustering result from re-sampled
clustering experiments with the option of using multiple
algorithms and parameter
Diff between clusterCons versions 0.4 dated 2010-03-09 and 0.5 dated 2010-08-25
Description: clusterCons is a package containing functions that
generate robustness measures for clusters and cluster
membership based on generating consensus matrices from
bootstrapped clustering experiments in which a random
proportion of rows of the data set are used in each individual
clustering. This allows the user to prioritise clusters and the
members of clusters based on their consistency in this regime.
The functions allow the user to select several algorithms to
use in the re-sampling scheme and with any of the parameters
that the algorithm would normally take.
Author: Dr. T. Ian Simpson, University of Edinburgh
Maintainer: Dr. T. Ian Simpson
clusterCons-0.4/clusterCons/scripts |only
clusterCons-0.5/clusterCons/.project |only
clusterCons-0.5/clusterCons/DESCRIPTION | 12
clusterCons-0.5/clusterCons/INDEX |only
clusterCons-0.5/clusterCons/R/algorithms.R | 39 +-
clusterCons-0.5/clusterCons/R/functions.R | 232 ++++++++++++++---
clusterCons-0.5/clusterCons/data/testcmr.rda |only
clusterCons-0.5/clusterCons/man/auc-class.Rd |only
clusterCons-0.5/clusterCons/man/auc.Rd |only
clusterCons-0.5/clusterCons/man/aucplot.Rd |only
clusterCons-0.5/clusterCons/man/checks.Rd |only
clusterCons-0.5/clusterCons/man/clrob.Rd |only
clusterCons-0.5/clusterCons/man/cluscomp.Rd | 144 ++++++++--
clusterCons-0.5/clusterCons/man/clusterCons-package.Rd | 63 +++-
clusterCons-0.5/clusterCons/man/consmatrix-class.Rd |only
clusterCons-0.5/clusterCons/man/data.Rd |only
clusterCons-0.5/clusterCons/man/deltak.Rd |only
clusterCons-0.5/clusterCons/man/dk-class.Rd |only
clusterCons-0.5/clusterCons/man/dkplot.Rd |only
clusterCons-0.5/clusterCons/man/memrob.Rd |only
clusterCons-0.5/clusterCons/man/memroblist-class.Rd |only
clusterCons-0.5/clusterCons/man/memrobmatrix-class.Rd |only
clusterCons-0.5/clusterCons/man/mergematrix-class.Rd |only
clusterCons-0.5/clusterCons/man/wrappers.Rd |only
clusterCons-0.5/clusterCons/tests |only
25 files changed, 383 insertions(+), 107 deletions(-)
More information about ProjectTemplate at CRAN
Permanent link
Title: Multi-model inference
Diff between MuMIn versions 0.13.8 dated 2010-08-05 and 0.13.9 dated 2010-08-25
Description: Model selection and model averaging based on information
criteria (AICc and alikes).
Author: Kamil Bartoń
Maintainer: Kamil Bartoń
ChangeLog | 3 +++
DESCRIPTION | 10 +++++-----
R/dredge.R | 16 ++++++++++------
3 files changed, 18 insertions(+), 11 deletions(-)
Title: Gaussian Graphs Models selection
Diff between GGMselect versions 0.1-0 dated 2009-09-03 and 0.1-2 dated 2010-08-25
Description: GGMselect is a package dedicated to graph estimation in
Gaussian Graphical Models. The main functions return the
adjacency matrix of an undirected graph estimated from a data
matrix.
Author: Annie Bouvier, Christophe Giraud, Sylvie Huet, Verzelen N.
Maintainer: Annie Bouvier
DESCRIPTION | 10 +++++-----
NEWS |only
R/GGMselect.R | 4 ++--
inst/doc/Notice.pdf |binary
man/GGMselect-package.Rd | 4 ++--
src/scr.c | 7 ++++++-
6 files changed, 15 insertions(+), 10 deletions(-)
Title: Performance Assessment and Comparison for Survival Analysis
Diff between survcomp versions 1.1.3 dated 2009-11-13 and 1.1.6 dated 2010-08-25
Description: R package providing functions to assess and to compare the
performance of risk prediction (survival) models.
Author: Benjamin Haibe-Kains, Christos Sotiriou, Gianluca Bontempi
Maintainer: Benjamin Haibe-Kains
DESCRIPTION | 8 ++--
R/cindex.comp.R | 5 ++
R/cindex.comp.meta.R | 5 +-
R/cvpl.R | 68 ++++++++++++++++++++++++++++-------
R/ibsc.comp.R | 2 -
R/logpl.R | 89 +++++++++++++++++++++++------------------------
man/cindex.comp.Rd | 4 +-
man/concordance.index.Rd | 2 -
man/cvpl.Rd | 31 ++++++++++++----
man/hazard.ratio.Rd | 2 -
man/logpl.Rd | 6 +--
man/survcomp-package.Rd | 29 ++++++++++++---
12 files changed, 164 insertions(+), 87 deletions(-)
Title: Importing Vector Graphics
Diff between grImport versions 0.6-1 dated 2010-05-25 and 0.6-3 dated 2010-08-25
Description: Functions for converting, importing, and drawing
PostScript pictures in R plots.
Author: Paul Murrell and Richard Walton.
Maintainer: Paul Murrell
DESCRIPTION | 6 +++---
R/AllClasses.R | 3 ++-
R/PostScript2RGML.R | 13 ++++++++++++-
R/RGML2picture.R | 16 ++++++++++++++--
R/util.R | 17 +++++++++++++++++
inst/doc/changes.txt | 15 +++++++++++++++
inst/doc/import.pdf |binary
inst/doc/importText.pdf |binary
man/PictureFill-class.Rd | 3 +++
man/readPicture.Rd | 6 +++++-
10 files changed, 71 insertions(+), 8 deletions(-)
Title: Relevant Functions for Gene Expression Analysis, Especially in
Breast Cancer.
Diff between genefu versions 1.0.8 dated 2010-07-26 and 1.0.9 dated 2010-08-25
Description: R package providing various functions relevant for gene
expression analysis with emphasis on breast cancer.
Author: Benjamin Haibe-Kains, Gianluca Bontempi, John Quackenbush,
Christos Sotiriou
Maintainer: Benjamin Haibe-Kains
DESCRIPTION | 6 +-
R/gene70.R | 63 ++++++++++++++++++++++++++-----
R/gene76.R | 6 --
R/ggi.R | 9 ++--
R/intrinsic.cluster.R | 3 -
R/intrinsic.cluster.predict.R | 5 --
R/oncotypedx.R |only
R/subtype.cluster.predict.R | 10 +++-
data/nki.rda |binary
data/sig.oncotypedx.rda |only
inst/extdata/paik2004_sig_oncotypedx.csv |only
man/gene70.Rd | 23 +++++++++--
man/gene76.Rd | 5 --
man/genefu-package.Rd | 4 -
man/ggi.Rd | 6 +-
man/intrinsic.cluster.Rd | 5 --
man/intrinsic.cluster.predict.Rd | 7 ---
man/nki.Rd | 2
man/oncotypedx.Rd |only
man/pam50.Rd | 6 +-
man/sig.oncotypedx.Rd |only
man/ssp2003.Rd | 6 +-
man/ssp2006.Rd | 6 +-
man/subtype.cluster.predict.Rd | 1
24 files changed, 116 insertions(+), 57 deletions(-)
Title: Modelling and estimation of the yield curve
Diff between YieldCurve versions 3.0 dated 2010-07-24 and 3.1 dated 2010-08-25
Description: Modelling the yield curve with some parametric models. The
models implemented are: Nelson-Siegel, Diebold-Li and Svensson.
The package also includes the data of the term structure of
interest rate of Federal Reserve Bank and European Central
Bank.
Author: Sergio Salvino Guirreri
Maintainer: Sergio Salvino Guirreri
YieldCurve-3.0/YieldCurve/CITATION |only
YieldCurve-3.1/YieldCurve/DESCRIPTION | 8 ++++----
YieldCurve-3.1/YieldCurve/inst |only
3 files changed, 4 insertions(+), 4 deletions(-)
Title: Symmetric discrete triangular distributions
Diff between TRIANG versions 1.1 dated 2009-03-14 and 1.2 dated 2010-08-25
Description: This is a package for symmetric discrete triangular
distributions
Author: Tristan Senga Kiess\'{e}, Silvio S. Zocchi, C\'{e}lestin C.
Kokonendji
Maintainer: Tristan Senga Kiess\'{e}
TRIANG-1.1/TRIANG/Read-and-delete-me |only
TRIANG-1.1/TRIANG/man/PackageTRIANG-package.Rd |only
TRIANG-1.2/TRIANG/DESCRIPTION | 18 +++----
TRIANG-1.2/TRIANG/R/dtrg.R | 19 +++-----
TRIANG-1.2/TRIANG/man/dtrg.Rd | 58 ++++++++++++++-----------
5 files changed, 52 insertions(+), 43 deletions(-)
Title: Integrative Functional Analysis of Transcriptional Networks
Diff between FunNet versions 1.00-9 dated 2010-06-27 and 1.00-10 dated 2010-08-25
Description: FunNet is an integrative tool for analyzing gene
co-expression networks built 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.
Author: Corneliu Henegar
Maintainer: Corneliu Henegar
DESCRIPTION | 8 ++++----
R/Annotations.R | 29 +++++++++++++++++++++++++++--
R/FunNet.R | 4 ++--
R/sysdata.rda |binary
man/Annotations.Rd | 11 ++++++-----
man/FunNet.Rd | 5 +++--
6 files changed, 42 insertions(+), 15 deletions(-)
Title: Global optimization by differential evolution
Diff between DEoptim versions 2.0-5 dated 2010-04-19 and 2.0-6 dated 2010-08-25
Description: This package provides the DEoptim function which performs
global optimization by differential evolution.
Author: David Ardia and Katharine Mullen
Maintainer: Katharine Mullen
DESCRIPTION | 6 +++---
NEWS | 2 ++
man/SMI.Rd |only
man/xrrData.Rd |only
4 files changed, 5 insertions(+), 3 deletions(-)