Author: Diethelm Wuertz and Yohan Chalabi
Title: Rmetrics - Financial Time Series Objects
Description: Environment for teaching "Financial Engineering and
Computational Finance"
Diff between timeSeries versions 280.78 dated 2008-10-27 and 290.79 dated 2008-12-04
DESCRIPTION | 16 +++++++++------- R/time.R | 5 +++-- 2 files changed, 12 insertions(+), 9 deletions(-)
Author: Søren Højsgaard
Diff between gRbase versions 0.6.0 dated 2008-10-13 and 0.6.4 dated 2008-12-04
Title: A package for graphical modelling in R
Description: This package defines S3-classes gmData (graphical meta data), gModel (graphical model). Several other graphical modelling packages rely on these fundamental constructs. gRbase illustrates how hierarchical log-linear models (hllm) may be implemented.
gRbase-0.6.0/gRbase/man/DATA-cad1.Rd |only
gRbase-0.6.0/gRbase/man/graph-operations.Rd |only
gRbase-0.6.4/gRbase/ChangeLog | 22 +++
gRbase-0.6.4/gRbase/DESCRIPTION | 6
gRbase-0.6.4/gRbase/INDEX | 8 -
gRbase-0.6.4/gRbase/R/GraphSH2.R | 31 ----
gRbase-0.6.4/gRbase/R/Graphsh-mcs-moral-rip.R | 18 +-
gRbase-0.6.4/gRbase/R/Graphsh-querygSH2.R | 178 +++++++++++++++-----------
gRbase-0.6.4/gRbase/R/formulae.R | 58 --------
gRbase-0.6.4/gRbase/R/hllm.R | 34 ++++
gRbase-0.6.4/gRbase/R/processFormula.R |only
gRbase-0.6.4/gRbase/R/processFormula2.R |only
gRbase-0.6.4/gRbase/R/setopsR.R | 7 +
gRbase-0.6.4/gRbase/R/utilities.R |only
gRbase-0.6.4/gRbase/R/utility.R | 3
gRbase-0.6.4/gRbase/data/breastcancer.RData |only
gRbase-0.6.4/gRbase/data/carcassall.txt |only
gRbase-0.6.4/gRbase/inst/doc/gRbase.pdf |binary
gRbase-0.6.4/gRbase/man/DATA-breastcancer.Rd |only
gRbase-0.6.4/gRbase/man/DATA-cad.Rd |only
gRbase-0.6.4/gRbase/man/DATA-carcass.Rd | 45 ++++--
gRbase-0.6.4/gRbase/man/gRbase-internal.Rd | 3
gRbase-0.6.4/gRbase/man/gRbase-utilities.Rd | 2
gRbase-0.6.4/gRbase/man/graph-operations1.Rd |only
gRbase-0.6.4/gRbase/man/graph-operations2.Rd |only
gRbase-0.6.4/gRbase/man/newUG.Rd | 60 +++++---
gRbase-0.6.4/gRbase/man/querygraph.Rd | 13 -
gRbase-0.6.4/gRbase/src/Makevars |only
28 files changed, 279 insertions(+), 209 deletions(-)
Author: Søren Højsgaard
Diff between gRain versions 0.4.0 dated 2008-10-28 and 0.4.1 dated 2008-12-04
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).
ChangeLog | 7 +++++++
DESCRIPTION | 4 ++--
R/gmInstance.R | 2 +-
inst/doc/gRain-intro.pdf |binary
4 files changed, 10 insertions(+), 3 deletions(-)
Author: Karsten Tabelow
Diff between dti versions 0.5-4 dated 2008-05-21 and 0.6-0 dated 2008-12-04
Title: DTI Analysis
Description: Diffusion Weighted Imaging is a Magnetic Resonance Imaging
modality, that measures diffusion of water in tissues like the human brain.
The package contains R-functions to process diffusion-weighted data in the
context of the diffusion tensor model (DTI). This includes the calculation
of anisotropy measures and, most important, the implementation of our structural
adaptive smoothing algorithm as described in K. Tabelow, J. Polzehl, V. Spokoiny,
and H.U. Voss, Diffusion Tensor Imaging: Structural Adaptive Smoothing,
Neuroimage 39(4), 1763-1773 (2008).
dti-0.5-4/dti/R/awsvar.r |only
dti-0.5-4/dti/R/propagation.r |only
dti-0.5-4/dti/man/dti.smooth.Rd |only
dti-0.5-4/dti/man/dtiData-class.Rd |only
dti-0.5-4/dti/man/dtiData.Rd |only
dti-0.5-4/dti/man/dtiIndices-class.Rd |only
dti-0.5-4/dti/man/dtiIndices.Rd |only
dti-0.5-4/dti/man/dtiTensor-class.Rd |only
dti-0.5-4/dti/man/dtiTensor.Rd |only
dti-0.5-4/dti/man/medinria2tensor.Rd |only
dti-0.5-4/dti/man/plot.Rd |only
dti-0.5-4/dti/man/print.Rd |only
dti-0.5-4/dti/man/summary.Rd |only
dti-0.5-4/dti/man/tensor2medinria.Rd |only
dti-0.5-4/dti/src/dtinraws.f |only
dti-0.5-4/dti/src/nlrdti.f |only
dti-0.5-4/dti/src/riemann.f |only
dti-0.6-0/dti/DESCRIPTION | 8
dti-0.6-0/dti/HISTORY | 10
dti-0.6-0/dti/NAMESPACE | 7
dti-0.6-0/dti/R/Classes.r | 25
dti-0.6-0/dti/R/aws.r | 256 +------
dti-0.6-0/dti/R/aws2.r | 188 +++--
dti-0.6-0/dti/R/dti.r | 1039 +++++++++++++++++++++++++++++---
dti-0.6-0/dti/R/misc.r | 69 +-
dti-0.6-0/dti/R/varest.r |only
dti-0.6-0/dti/README | 59 +
dti-0.6-0/dti/demo/dti_art.r | 254 ++-----
dti-0.6-0/dti/inst/rcode |only
dti-0.6-0/dti/man/dti-class.Rd | 113 ++-
dti-0.6-0/dti/man/dti-package.Rd |only
dti-0.6-0/dti/man/dti.smooth-methods.Rd |only
dti-0.6-0/dti/man/dtiIndices-methods.Rd |only
dti-0.6-0/dti/man/dtiTensor-methods.Rd |only
dti-0.6-0/dti/man/extract-methods.Rd |only
dti-0.6-0/dti/man/medinria.Rd |only
dti-0.6-0/dti/man/plot-methods.Rd |only
dti-0.6-0/dti/man/print-methods.Rd |only
dti-0.6-0/dti/man/readDWIdata.Rd |only
dti-0.6-0/dti/man/sdpar-methods.Rd |only
dti-0.6-0/dti/man/show-methods.Rd |only
dti-0.6-0/dti/man/show3d-methods.Rd |only
dti-0.6-0/dti/man/summary-methods.Rd |only
dti-0.6-0/dti/src/aniso.f | 381 ++++++-----
dti-0.6-0/dti/src/awsvar.f | 233 +++++--
dti-0.6-0/dti/src/dtinraw2.f | 588 ++++++------------
dti-0.6-0/dti/src/misc.f | 124 +++
dti-0.6-0/dti/src/nlrdtirg.f | 129 +--
dti-0.6-0/dti/src/rice.f |only
49 files changed, 2148 insertions(+), 1335 deletions(-)
Author: Susanne Gammelgaard Bottcher
Diff between deal versions 1.2-30 dated 2007-04-20 and 1.2-31 dated 2008-12-04
Title: Learning Bayesian Networks with Mixed Variables
Description: Bayesian networks with continuous and/or discrete variables can be learned and compared from data.
deal-1.2-30/deal/CHANGES.txt |only
deal-1.2-31/deal/CHANGELOG |only
deal-1.2-31/deal/DESCRIPTION | 8 ++++----
deal-1.2-31/deal/R/autosearch.R | 6 +++---
deal-1.2-31/deal/R/heuristic.R | 6 +++---
deal-1.2-31/deal/R/jointdisc.R | 9 ++++++---
deal-1.2-31/deal/man/autosearch.Rd | 8 +++++---
deal-1.2-31/deal/man/deal-internal.Rd | 6 +++---
deal-1.2-31/deal/man/drawnetwork.Rd | 8 +++++---
deal-1.2-31/deal/man/genlatex.Rd | 30 +++++++++++++++---------------
deal-1.2-31/deal/man/insert.Rd | 8 ++++----
deal-1.2-31/deal/man/jointprior.Rd | 12 ++++++------
deal-1.2-31/deal/man/learn.Rd | 12 ++++++------
deal-1.2-31/deal/man/makesimprob.Rd | 8 ++++----
deal-1.2-31/deal/man/maketrylist.Rd | 8 ++++----
deal-1.2-31/deal/man/network.Rd | 8 ++++----
deal-1.2-31/deal/man/networkfamily.Rd | 8 ++++----
deal-1.2-31/deal/man/node.Rd | 8 ++++----
deal-1.2-31/deal/man/numbermixed.Rd | 12 ++++++------
deal-1.2-31/deal/man/nwfsort.Rd | 7 ++++---
deal-1.2-31/deal/man/nwfunique.Rd | 8 ++++----
deal-1.2-31/deal/man/perturb.Rd | 8 ++++----
deal-1.2-31/deal/man/prob.Rd | 8 ++++----
deal-1.2-31/deal/man/readnet.Rd | 3 ++-
deal-1.2-31/deal/man/rnetwork.Rd | 8 ++++----
deal-1.2-31/deal/man/score.Rd | 11 +++++++----
26 files changed, 115 insertions(+), 103 deletions(-)
Author: Dirk Eddelbuettel
Diff between RQuantLib versions 0.2.9 dated 2008-08-11 and 0.2.10 dated 2008-12-04
Title: R interface to the QuantLib library
Description: The RQuantLib package makes selected parts of QuantLib
visible to the R user. Currently some basic option pricing
functions are included, as well as fixed-income functions that
can be used for interest rate curve construction and Bermuda
swaption pricing. Further software contributions are welcome.
The QuantLib project aims to provide a comprehensive software
framework for quantitative finance. The goal is to provide a
standard open source library for quantitative analysis,
modeling, trading, and risk management of financial
assets.
The Windows binary version is self-contained and does not require
a QuantLib (or Boost) installation.
RQuantLib use the Rcpp R/C++ interface class library. See the Rcpp
package on CRAN (or R-Forge) for more information on Rcpp.
Note that while RQuantLib's code is licensed under the GPL (v2 or
later), QuantLib itself is released under a somewhat less
restrictive Open Source license (see QuantLib-License.txt).
RQuantLib-0.2.10/RQuantLib/DESCRIPTION | 53 +-
RQuantLib-0.2.10/RQuantLib/INDEX | 1
RQuantLib-0.2.10/RQuantLib/configure | 676 +++++++++++----------------
RQuantLib-0.2.10/RQuantLib/configure.in | 93 ++-
RQuantLib-0.2.10/RQuantLib/configure.win | 13
RQuantLib-0.2.10/RQuantLib/inst/ChangeLog | 22
RQuantLib-0.2.10/RQuantLib/src/Makefile.win | 23
RQuantLib-0.2.10/RQuantLib/src/bermudan.cpp | 14
RQuantLib-0.2.10/RQuantLib/src/discount.cpp | 10
RQuantLib-0.2.10/RQuantLib/src/rquantlib.hpp | 13
RQuantLib-0.2.10/RQuantLib/src/utils.cpp | 6
RQuantLib-0.2.9/RQuantLib/R/RcppVersion.R |only
RQuantLib-0.2.9/RQuantLib/RcppSrc |only
RQuantLib-0.2.9/RQuantLib/man/RcppVersion.Rd |only
14 files changed, 442 insertions(+), 482 deletions(-)
Author: Korbinian Strimmer
Title: Shrinkage Discriminant Analysis
Description: This package performs linear and diagonal discriminant analysis
where the classifier is trained using Stein-type shrinkage estimators.
This approach is particularly suited for high-dimensional classification.
Diff between sda versions 1.0.1 dated 2008-11-22 and 1.0.2 dated 2008-12-04
DESCRIPTION | 8 ++--- NEWS | 15 ++++++++- R/centroids.R | 57 +++++++++++++++++++++++------------ R/predict.sda.R | 51 +++++++++++++------------------- R/sda.R | 84 +++++++++++++++++++++++++++++++++++------------------ data |only man/centroids.Rd | 33 +++++++++++++------- man/khan2001.Rd |only man/sda.Rd | 82 +++++++++++++++++++++++++-------------------------- man/sda.package.Rd | 2 - 10 files changed, 194 insertions(+), 138 deletions(-)
Author: Alberto Viglione
Title: Non-supervised Regional Frequency Analysis
Description: A collection of statistical tools for objective (non-supervised) applications
of the Regional Frequency Analysis methods in hydrology.
The package refers to the index-value method and, more precisely, helps the
hydrologist to: (1) regionalize the index-value; (2) form homogeneous regions
with similar growth curves; (3) fit distribution functions to the
empirical regional growth curves.
Diff between nsRFA versions 0.6-2 dated 2008-09-19 and 0.6-4 dated 2008-12-04
nsRFA-0.6-2/nsRFA/inst/doc/.build.timestamp |only nsRFA-0.6-4/nsRFA/DESCRIPTION | 6 nsRFA-0.6-4/nsRFA/R/BayesianMCMC.R | 324 ++++++++++++++++++++++- nsRFA-0.6-4/nsRFA/inst/doc/Fig1ElamirSeheult.pdf |binary nsRFA-0.6-4/nsRFA/inst/doc/MSClaio2008.pdf |binary nsRFA-0.6-4/nsRFA/inst/doc/nsRFA_ex01.pdf |binary nsRFA-0.6-4/nsRFA/inst/doc/nsRFA_ex02.pdf |binary nsRFA-0.6-4/nsRFA/man/BayesianMCMC.Rd | 4 nsRFA-0.6-4/nsRFA/man/nsRFA-package.Rd | 1 9 files changed, 321 insertions(+), 14 deletions(-)
Author: Robert B. Gramacy
Diff between monomvn versions 1.5 dated 2008-11-13 and 1.6 dated 2008-12-04
Title: Estimation for multivariate normal data with monotone missingness
Description: Estimation of multivariate normal 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 an
(almost) arbitrary amount of missing data. The current version
supports maximum likelihood inference and implementation
of a Bayesian version employing a Bayesian lasso. A fully
functional standalone interface to the Bayesian lasso
(from Park & Casella) and ridge regression with model selection
via Reversible Jump is also provided
monomvn-1.5/monomvn/INDEX |only
monomvn-1.6/monomvn/ChangeLog | 32 +
monomvn-1.6/monomvn/DESCRIPTION | 6
monomvn-1.6/monomvn/R/bmonomvn.R | 319 ++++++----------
monomvn-1.6/monomvn/R/bmonomvn.traces.R |only
monomvn-1.6/monomvn/R/default.QP.R | 178 ++++++++
monomvn-1.6/monomvn/R/monomvn.R | 4
monomvn-1.6/monomvn/R/monomvn.s3.R | 53 ++
monomvn-1.6/monomvn/R/regress.fact.R | 1
monomvn-1.6/monomvn/R/util.R | 50 ++
monomvn-1.6/monomvn/data/market.rda |only
monomvn-1.6/monomvn/data/market.test.rda |only
monomvn-1.6/monomvn/data/returns.rda |only
monomvn-1.6/monomvn/data/returns.test.rda |only
monomvn-1.6/monomvn/man/blasso.Rd | 1
monomvn-1.6/monomvn/man/bmonomvn.Rd | 102 +++--
monomvn-1.6/monomvn/man/default.QP.Rd | 30 +
monomvn-1.6/monomvn/man/monomvn-internal.Rd | 7
monomvn-1.6/monomvn/man/monomvn.Rd | 16
monomvn-1.6/monomvn/man/monomvn.solve.QP.Rd |only
monomvn-1.6/monomvn/man/returns.Rd |only
monomvn-1.6/monomvn/src/blasso.cc | 555 +++++++++++++++++++++-------
monomvn-1.6/monomvn/src/blasso.h | 76 ++-
monomvn-1.6/monomvn/src/bmonomvn.cc | 526 +++++++-------------------
monomvn-1.6/monomvn/src/bmonomvn.h | 77 ---
monomvn-1.6/monomvn/src/matrix.c | 66 +++
monomvn-1.6/monomvn/src/matrix.h | 3
monomvn-1.6/monomvn/src/ustructs.cc |only
monomvn-1.6/monomvn/src/ustructs.h |only
29 files changed, 1233 insertions(+), 869 deletions(-)
Author: Venkatraman E. Seshan
Title: Clinical Trial Design and Data Analysis Functions
Description: Utilities to make your clinical collaborations easier if not fun.
Diff between clinfun versions 0.8.3 dated 2008-11-18 and 0.8.4 dated 2008-12-04
CHANGES | 7 ++++++ DESCRIPTION | 4 +-- R/pselect.R | 64 ++++++++++++++++++++++++++++++++++++++++++++++----------- man/pselect.Rd | 30 ++++++++++++++++---------- 4 files changed, 79 insertions(+), 26 deletions(-)
Author: David Ardia
Diff between bayesGARCH versions 1-00.01 dated 2008-06-03 and 1-00.02 dated 2008-12-04
Title: Bayesian Estimation of the GARCH(1,1) Model with Student-t Innovations
Description: This package provides the bayesGARCH function which performs the
Bayesian estimation of the GARCH(1,1) model with Student's t innovations.
DESCRIPTION | 8 ++++----
R/onload.R | 4 ++--
README | 1 +
man/addPriorConditions.Rd | 5 ++++-
man/bayesGARCH.Rd | 12 +++++++-----
man/formSmpl.Rd | 5 ++++-
6 files changed, 22 insertions(+), 13 deletions(-)
Author: Vinzenz Erhardt
Title: Zero Inflated Generalized Poisson (ZIGP) regression models
Description: Adapt and analyze and compare GP, ZIP and ZIGP regression models
Diff between ZIGP versions 2.7 dated 2008-11-14 and 3.0 dated 2008-12-04
ZIGP-2.7/ZIGP/R/wald.test.r |only ZIGP-2.7/ZIGP/man/wald.test.rd |only ZIGP-3.0/ZIGP/DESCRIPTION | 6 +- ZIGP-3.0/ZIGP/NAMESPACE | 2 ZIGP-3.0/ZIGP/R/eda.od.r |only ZIGP-3.0/ZIGP/R/eda.zi.r |only ZIGP-3.0/ZIGP/R/est.zigp.r |only ZIGP-3.0/ZIGP/R/fit.zigp1.r | 2 ZIGP-3.0/ZIGP/R/gradient.r | 12 ++--- ZIGP-3.0/ZIGP/R/gradient1.r | 14 +++--- ZIGP-3.0/ZIGP/R/loglikelihood.zigp.full.r | 26 ++++++------ ZIGP-3.0/ZIGP/R/loglikelihood.zigp.r | 14 +++--- ZIGP-3.0/ZIGP/R/loglikelihood.zigp.vuong.r | 14 +++--- ZIGP-3.0/ZIGP/R/mle.zigp.full.like.r | 50 ++++++++++++------------ ZIGP-3.0/ZIGP/R/mle.zigp.r | 27 +++++++++---- ZIGP-3.0/ZIGP/R/optimized.run.r | 16 +++---- ZIGP-3.0/ZIGP/man/ZIGP-package.rd | 9 ++-- ZIGP-3.0/ZIGP/man/clarke.rd | 39 ++++++++++--------- ZIGP-3.0/ZIGP/man/eda.od.rd |only ZIGP-3.0/ZIGP/man/eda.zi.rd |only ZIGP-3.0/ZIGP/man/est.zigp.rd |only ZIGP-3.0/ZIGP/man/gradient.rd | 3 - ZIGP-3.0/ZIGP/man/loglikelihood.zigp.rd | 3 - ZIGP-3.0/ZIGP/man/mle.zigp.rd | 45 +++++++++------------- ZIGP-3.0/ZIGP/man/vuong.rd | 59 +++++++++++++++-------------- 25 files changed, 179 insertions(+), 162 deletions(-)
Author: Dominick Samperi and Dirk Eddelbuettel
Title: Rcpp R/C++ interface library and package template
Description: R/C++ interface class library and package template.
The Rcpp library maps data types betweeen R and C++,
and includes support for R types real, integer, character,
vector, matrix, Date, datetime (i.e. POSIXct) data frame,
and function. It supports calling R functions from C++.
See the package documentation file doc/RcppAPI.pdf for more
information, including details on building binary R packages
for Windows.
Diff between Rcpp versions 0.6.1 dated 2008-11-30 and 0.6.2 dated 2008-12-04
DESCRIPTION | 6 +++--- R/RcppLdpath.R | 2 +- inst/ChangeLog | 12 +++++++++--- inst/doc/RcppAPI.pdf |binary 4 files changed, 13 insertions(+), 7 deletions(-)
Author: David Harte
Title: Time Dependent Point Process Modelling
Description: This package fits and analyses time dependent marked point process models with an emphasis on earthquake modelling. For a more detailed introduction to the package, see the topic "PtProcess". A list of recent changes can be found in the topic "Changes".
Diff between PtProcess versions 3.1-1 dated 2008-11-18 and 3.1-2 dated 2008-12-04
DESCRIPTION | 6 +++--- data/Phuket.R |only data/Phuket.txt |only man/Changes.Rd | 4 ++++ man/Phuket.Rd |only man/mpp.Rd | 4 ++-- 6 files changed, 9 insertions(+), 5 deletions(-)
Author: Jarrod Hadfield
Title: ML and MCMC Methods for Pedigree Reconstruction and Analysis
Description: The primary aim of MasterBayes is to use MCMC techniques to integrate over uncertainty in pedigree configurations estimated from molecular markers and phenotypic data. Emphasis is put on the marginal distribution of parameters that relate the phenotypic data to the pedigree. All simulation is done in compiled C++ for efficency.
Diff between MasterBayes versions 2.4 dated 2008-09-05 and 2.41 dated 2008-12-04
DESCRIPTION | 6 R/ErrorCheck.R | 4 R/MCMCped.R | 2 R/getXlist.R | 96 ++-- R/getsPandtP.R | 9 inst/doc/Tutorial.pdf | 1065 ++++++++++++++++++++++++-------------------------- src/SampP.cc | 12 7 files changed, 602 insertions(+), 592 deletions(-)
Author: Holger Froehlich
Diff between GOSim versions 1.1.5.3 dated 2008-12-01 and 1.1.5.4 dated 2008-12-04
Title: Computation of functional similarities between GO terms and gene products; GO enrichement analysis
Description: This package implements several functions useful for
computing similarities between GO terms and gene products based on their GO annotation. Moreover it allows for computing a GO enrichment analysis
DESCRIPTION | 6
R/GOenrichment.R | 36 +
inst/doc/GOSim.pdf | 1254 +++++++++++++++++++++++++---------------------------
man/GOenrichment.Rd | 12
man/internal.Rd | 2
5 files changed, 663 insertions(+), 647 deletions(-)
Author: David Ardia
Diff between DEoptim versions 1.2-1 dated 2007-09-12 and 1.3-0 dated 2008-12-04
Title: Differential Evolution Optimization
Description: This package provides the DEoptim function which performs
Differential Evolution Optimization (evolutionary algorithm).
CHANGES | 5 ++++
DESCRIPTION | 6 ++---
R/DEoptim.R | 57 +++++++++++++++++++++++++++++++++++++++--------------
XEmacs-21.4.20.lnk |only
man/DEoptim.Rd | 10 ++++++++-
5 files changed, 60 insertions(+), 18 deletions(-)