Author: Eric Aldrich
Diff between wavelets versions 0.2-3 dated 2007-08-02 and 0.2-4 dated 2009-04-22
Title: A package of funtions for computing wavelet filters, wavelet
transforms and multiresolution analyses
Description: This package contains functions for computing and plotting
discrete wavelet transforms (DWT) and maximal overlap discrete
wavelet transforms (MODWT), as well as their inverses.
Additionally, it contains functionality for computing and
plotting wavelet transform filters that are used in the above
decompositions as well as multiresolution analyses.
DESCRIPTION | 29 ++++++++++++------------
R/dwt.R | 2 -
R/plot.dwt.R | 5 +++-
R/plot.modwt.R | 2 -
R/wt.filter.R | 54 ++++++++++++++++++++++++----------------------
R/wt.filter.shift.R | 12 +++++++---
man/figure98.wt.filter.Rd | 2 -
man/plot.dwt.multiple.Rd | 2 -
man/plot.modwt.Rd | 2 -
9 files changed, 62 insertions(+), 48 deletions(-)
Author: Benjamin Haibe-Kains, Christos Sotiriou, Gianluca Bontempi
Title: Performance Assessment and Comparison for Survival Analysis
Description: R package providing functions to assess and to compare the
performance of risk prediction (survival) models.
Diff between survcomp versions 1.0 dated 2009-02-09 and 1.1.0 dated 2009-04-22
DESCRIPTION | 16 ++++++++++------ man/getsurv2.Rd | 2 +- man/survcomp-package.Rd | 6 +++--- 3 files changed, 14 insertions(+), 10 deletions(-)
Author: Heloise Lavigne and Aurelien Proye and Jean-Pierre Gattuso.
Portions of code and/or corrections were contributed by
Jean-Marie Epitalon, Andreas Hofmann, Bernard Gentili, Jim Orr
and Karline Soetaert
Title: Calculates parameters of the seawater carbonate system
Description: Calculates parameters of the seawater carbonate system
Diff between seacarb versions 2.0.8 dated 2009-04-17 and 2.1 dated 2009-04-22
ChangeLog | 20 ++++++- DESCRIPTION | 10 +-- R/K1.R | 18 +++++-- R/K1p.R | 18 +++++-- R/K2.R | 17 +++++- R/K2p.R | 19 +++++-- R/K3p.R | 18 +++++-- R/Kb.R | 20 ++++++- R/Kf.R | 16 +++++- R/Khs.R | 18 +++++-- R/Kn.R | 18 +++++-- R/Ksi.R | 19 ++++++- R/Kw.R | 19 ++++++- R/buffer.R | 38 ++++++++++---- R/carb.R | 132 ++++++++-------------------------------------------- R/kconv.R | 4 - R/pCa.R | 4 - R/pHconv.R | 53 ++++++++++++++------ R/pTA.R | 12 ++-- R/pgas.R | 6 +- R/phinsi.R | 6 +- R/pmix.R | 8 +-- R/ppH.R | 116 ++------------------------------------------- R/psi.R |only man/K1.Rd | 9 +-- man/K1p.Rd | 5 + man/K2.Rd | 8 +-- man/K2p.Rd | 3 - man/K3p.Rd | 5 + man/Kb.Rd | 7 +- man/Kf.Rd | 10 ++- man/Khs.Rd | 9 +-- man/Kn.Rd | 9 +-- man/Ks.Rd | 2 man/Ksi.Rd | 9 +-- man/Kw.Rd | 7 +- man/buffer.Rd | 21 +++++--- man/carb.Rd | 19 +++++-- man/pCa.Rd | 21 ++++---- man/pHconv.Rd | 43 +++++++++++----- man/pTA.Rd | 9 ++- man/pgas.Rd | 7 +- man/phinsi.Rd | 6 +- man/pmix.Rd | 7 +- man/ppH.Rd | 13 +++-- man/psi.Rd |only man/seacarb_test.Rd | 19 ++++--- 47 files changed, 457 insertions(+), 400 deletions(-)
Author: Kaspar Rufibach
Title: Generate LaTeX tables of descriptive statistics
Description: The functions in this package are especially helpful when
writing reports of data analysis using Sweave.
Diff between reporttools versions 1.0.2 dated 2009-03-04 and 1.0.3 dated 2009-04-22
CHANGES | 5 +++ DESCRIPTION | 26 ++++++++++-------- R/tableContinuous.R | 59 +++++++++++++++++++++++++++++++----------- R/tableDate.R | 62 ++++++++++++++++++++++++++++++++++----------- R/tableNominal.R | 42 +++++++++++++++++++++++------- man/NAtoCategory.Rd | 2 - man/checkDateSuccession.Rd | 2 - man/disp.Rd | 2 - man/displayCI.Rd | 2 - man/displayKbyC.Rd | 2 - man/eliminateNA.Rd | 2 - man/reporttools-package.Rd | 8 ++--- man/tableContinuous.Rd | 49 ++++++++++++++++++++++------------- man/tableDate.Rd | 35 ++++++++++++++++--------- man/tableNominal.Rd | 28 +++++++++++++------- man/transformVarNames.Rd | 2 - man/varNamesToChar.Rd | 2 - 17 files changed, 228 insertions(+), 102 deletions(-)
Author: Berend Hasselman
Title: Solve systems of non linear equations
Description: Solve a system of non linear equations using a Broyden or
a Newton method with a choice of global strategies such as
linesearch and trust region. There are options for using a
numerical or an analytical jacobian and fixed or automatic
scaling of parameters.
Diff between nleqslv versions 1.3 dated 2009-03-22 and 1.4 dated 2009-04-22
DESCRIPTION | 10 +++++----- NEWS | 5 +++++ src/nleqslv.c | 3 ++- src/nwnleq.f | 2 +- src/nwnwtn.f | 4 ++-- 5 files changed, 15 insertions(+), 9 deletions(-)
Author: Simon Wood
Diff between mgcv versions 1.5-2 dated 2009-03-26 and 1.5-3 dated 2009-04-22
Title: GAMs with GCV/AIC/REML smoothness estimation and GAMMs by PQL
Description: Routines for GAMs and other generalized ridge regression
with multiple smoothing parameter selection by GCV, REML or
UBRE/AIC. Also GAMMs by REML or PQL. Includes a gam() function.
DESCRIPTION | 8 ++++----
R/gam.fit3.r | 2 +-
R/mgcv.r | 13 +++++++++----
changeLog | 14 +++++++++++---
4 files changed, 25 insertions(+), 12 deletions(-)
Author: Torsten Hothorn, Peter Buhlmann, Thomas Kneib, Matthias Schmid
and Benjamin Hofner
Title: Model-Based Boosting
Description: Functional gradient descent algorithms (boosting) for
optimizing general loss functions utilizing componentwise least
squares, either of parametric linear form or smoothing splines,
or regression trees as base learners for fitting generalized
linear, additive and interaction models to potentially
high-dimensional data.
Diff between mboost versions 1.1-0 dated 2009-03-27 and 1.1-1 dated 2009-04-22
DESCRIPTION | 6 ++-- R/family.R | 18 ++++++++++++ R/xsp.R | 18 ++++-------- inst/CHANGES | 6 ++++ inst/India_quantiles.R |only inst/analysis.R |only inst/doc/SurvivalEnsembles.pdf |binary inst/doc/mboost_illustrations.pdf |binary inst/india.Rdata |only inst/india.raw |only inst/india_fit.R |only inst/india_helpfunc.R |only inst/india_preproc.R |only man/Family.Rd | 15 ++++++++++ tests/bugfixes.R | 11 ++++++- tests/bugfixes.Rout.save | 51 ++++++++++++++++++++++++++++++++--- tests/codetools-checks.Rout.save | 2 - tests/mboost_illustrations.Rout.save | 2 - tests/regtest-blackboost.Rout.save | 2 - tests/regtest-gamboost.Rout.save | 2 - tests/regtest-glmboost.Rout.save | 2 - tests/regtest-hatmatrix.Rout.save | 2 - tests/setup.Rout.save |only to_do_list.txt | 2 + 24 files changed, 114 insertions(+), 25 deletions(-)
Author: Holger Froehlich
Diff between gene2pathway versions 1.0.5.3 dated 2008-12-08 and 1.0.5.4 dated 2009-04-22
Title: Prediction of KEGG pathway membership for individual genes based
on InterPro domain signatures
Description: The package takes a list of genes and predicts to which
KEGG pathway each gene maps to. This is done by looking at the
InterPro domains of each gene. Each prediction is assigned a
confidence score. The package also allows to predict connected
component membership of genes within signaling pathways.
Separate models for each organism supported by KEGG can be
trained.
DESCRIPTION | 33 ++++++++++++++++++++++++---------
R/gene2pathway.signaltrans.R | 9 +++++----
inst/doc/gene2pathway.Rnw | 2 +-
inst/doc/gene2pathway.pdf |binary
man/classificationModel.Rd | 18 ++++++++++--------
man/classificationModelSignalTrans.Rd | 22 +++++++++++++---------
6 files changed, 53 insertions(+), 31 deletions(-)
Author: Seija Sirkia, Klaus Nordhausen, Hannu Oja
Title: Multivariate nonparametric methods based on spatial signs and
ranks
Description: This package contains test and estimates of location,
tests of independence, tests of sphericity and several
estimates of shape all based on spatial signs, symmetrized
signs, ranks and signed ranks.
Diff between SpatialNP versions 0.9.1 dated 2009-02-23 and 1.00 dated 2009-04-22
SpatialNP-0.9.1/SpatialNP/R/sr.regression.R |only SpatialNP-0.9.1/SpatialNP/man/sr.regression.Rd |only SpatialNP-1.00/SpatialNP/DESCRIPTION | 22 + SpatialNP-1.00/SpatialNP/NAMESPACE | 43 +-- SpatialNP-1.00/SpatialNP/R/signrankinternals.R | 236 ++++++++---------- SpatialNP-1.00/SpatialNP/R/spatial.signrank.R | 5 SpatialNP-1.00/SpatialNP/R/sr.loc.test.R | 275 +++++++++++----------- SpatialNP-1.00/SpatialNP/man/SRCov.Rd | 2 SpatialNP-1.00/SpatialNP/man/SpatialNP-package.Rd | 21 - SpatialNP-1.00/SpatialNP/man/independencetests.Rd | 2 SpatialNP-1.00/SpatialNP/man/locationtests.Rd | 2 SpatialNP-1.00/SpatialNP/man/shapematrices.Rd | 10 SpatialNP-1.00/SpatialNP/man/spatial.location.Rd | 4 SpatialNP-1.00/SpatialNP/man/spatialsignsranks.Rd | 6 SpatialNP-1.00/SpatialNP/man/sphericitytests.Rd | 2 SpatialNP-1.00/SpatialNP/man/to.shape.Rd | 12 16 files changed, 312 insertions(+), 330 deletions(-)
Author: Cyril Piou
Title: Pattern Oriented Modelling Information Criterion
Description: This package propose calculations of an information
criterion to check the quality of simulations results of
ABM/IBM or other non-linear rule-based models. The POMDEV
measure is based on the KL divergence and likelihood theory. It
basically indicates the deviance of simulation results from
field observations. Once POMDEV scores and metropolis-hasting
sampling on different model versions are effectuated, POMIC
scores can be calculated. This method is still under
development and further work are needed for the incorporation
of multiple patterns assessment.
Diff between Pomic versions 0.9.1 dated 2008-08-22 and 0.9.2 dated 2009-04-22
Pomic-0.9.1/Pomic/R/analyse.pomics.R |only Pomic-0.9.1/Pomic/R/pomic.R |only Pomic-0.9.1/Pomic/R/pomic.corrected.r |only Pomic-0.9.1/Pomic/R/pomic.simple.r |only Pomic-0.9.1/Pomic/R/pomic.timeseries.r |only Pomic-0.9.1/Pomic/R/summarize.parameters.R |only Pomic-0.9.1/Pomic/R/summarize.pomics.r |only Pomic-0.9.1/Pomic/man/analyse.pomics.Rd |only Pomic-0.9.1/Pomic/man/pomic.Rd |only Pomic-0.9.1/Pomic/man/pomic.corrected.rd |only Pomic-0.9.1/Pomic/man/pomic.simple.rd |only Pomic-0.9.1/Pomic/man/pomic.timeseries.rd |only Pomic-0.9.1/Pomic/man/summarize.parameters.Rd |only Pomic-0.9.1/Pomic/man/summarize.pomics.Rd |only Pomic-0.9.2/Pomic/DESCRIPTION | 33 ++++++++----- Pomic-0.9.2/Pomic/INDEX |only Pomic-0.9.2/Pomic/NEWS | 8 +++ Pomic-0.9.2/Pomic/R/pomdev.corrected.r |only Pomic-0.9.2/Pomic/R/pomdev.extra.R |only Pomic-0.9.2/Pomic/R/pomdev.r |only Pomic-0.9.2/Pomic/demo |only Pomic-0.9.2/Pomic/inst |only Pomic-0.9.2/Pomic/man/Pomic-package.Rd | 65 +++++++++++--------------- Pomic-0.9.2/Pomic/man/pomdev.corrected.rd |only Pomic-0.9.2/Pomic/man/pomdev.extra.Rd |only Pomic-0.9.2/Pomic/man/pomdev.rd |only 26 files changed, 58 insertions(+), 48 deletions(-)
Author: Klaus Nordhausen, Jean-Francois Cardoso, Hannu Oja, Esa Ollila
Title: JADE and ICA performance criteria
Description: The package ports JF Cardoso's JADE algorithm as well as
his function for joint diagonalization. There are also several
criteria for performance evaluation of ICA algorithms.
Diff between JADE versions 1.0-1 dated 2008-03-29 and 1.0-2 dated 2009-04-22
DESCRIPTION | 24 ++++++++++++++---------- inst/CHANGES | 3 +++ man/JADE-package.Rd | 4 ++-- man/JADE.Rd | 3 ++- 4 files changed, 21 insertions(+), 13 deletions(-)
Author: Klaus Nordhausen, Seija Sirkia, Hannu Oja, David E. Tyler
Title: Tools for Multivariate Nonparametrics
Description: Tools for multivariate nonparametrics, as location tests
based on marginal ranks, spatial median and spatial signs
computation, Hotelling's T-test, estimates of shape
Diff between ICSNP versions 1.0-2 dated 2007-12-31 and 1.0-3 dated 2009-04-22
DESCRIPTION | 28 ++++++++++++++++------------ NAMESPACE | 2 +- R/HR.Mest.R | 2 +- R/center.step.R | 3 +-- R/pair.diff.R | 2 -- R/pair.prod.R |only R/pair.sum.R |only inst/CHANGES | 6 ++++++ man/HP1.shape.Rd | 3 ++- man/HR.Mest.Rd | 23 ++++++++++++----------- man/ICSNP-package.Rd | 4 ++-- man/duembgen.shape.Rd | 2 +- man/pair.diff.Rd |only man/pair.prod.Rd |only man/pair.sum.Rd |only man/rank.ictest.Rd | 2 +- man/spatial.median.Rd | 2 +- man/spatial.sign.Rd | 2 +- man/tyler.shape.Rd | 2 +- src/icsnp.cpp | 15 +++++++++++++++ 20 files changed, 61 insertions(+), 37 deletions(-)
Author: Klaus Nordhausen, Hannu Oja, David E. Tyler
Title: Tools for Exploring Multivariate Data via ICS/ICA
Description: The package implements Tyler et al.'s and Oja et al.'s
method of two different scatter matrices to obtain an invariant
coordinate system or independent components, depending on the
underlying assumptions.
Diff between ICS versions 1.2-0 dated 2008-10-30 and 1.2-1 dated 2009-04-22
DESCRIPTION | 35 NAMESPACE | 2 R/cov4.wt.R |only inst/CHANGES | 5 inst/CITATION | 2 inst/doc/ICS.pdf |12953 ++++++++++++++++++++++++++++++++++++++++++++++++---- inst/doc/Rplots.pdf |11645 +++++++++++++++++++++++++++++++++++++++++++++- man/ICS-package.Rd | 4 man/cov4.wt.Rd |only man/covAxis.Rd | 2 man/ics.Rd | 4 11 files changed, 23533 insertions(+), 1119 deletions(-)