Title: Variable metric nonlinear function minimization with bounds
constraints
Diff between Rvmmin versions 0.96 dated 2010-11-15 and 2011-2.11 dated 2011-02-23
Description: Variable metric nonlinear function minimization with
bounds constraints
Author: John C. Nash
Maintainer: John C. Nash
Rvmmin-0.96/Rvmmin/tests |only
Rvmmin-2011-2.11/Rvmmin/DESCRIPTION | 10 ++++-----
Rvmmin-2011-2.11/Rvmmin/R/Rvmmin.R | 35 ++++++++++++++++++++++------------
Rvmmin-2011-2.11/Rvmmin/man/Rvmmin.Rd | 13 +++++++++++-
4 files changed, 40 insertions(+), 18 deletions(-)
Title: Conjugate gradient minimization of nonlinear functions with box
constraints
Diff between Rcgmin versions 0.82 dated 2010-11-15 and 2011-2.10 dated 2011-02-23
Description: Conjugate gradient minimization of nonlinear functions
with box constraints incorporating Dai/Yuan update
Author: John C. Nash
Maintainer: John C. Nash
Rcgmin-0.82/Rcgmin/tests |only
Rcgmin-2011-2.10/Rcgmin/DESCRIPTION | 10 +++++-----
Rcgmin-2011-2.10/Rcgmin/R/Rcgmin.R | 6 ++++--
3 files changed, 9 insertions(+), 7 deletions(-)
Title: Inverse Regression for Text Analysis
Diff between textir versions 1.2.1 dated 2011-02-22 and 1.2.2 dated 2011-02-23
Description: A set of tools for inference about text and associated
speaker/document sentiment. This includes the mnlm function
for map estimation in Laplace regularized multinomial logistic
regression, which can be used for inverse regression analysis
of sentiment in text. Feel free to send questions/comments!
Author: Matt Taddy
Maintainer: Matt Taddy
ChangeLog | 4 ++++
DESCRIPTION | 8 ++++----
R/pls.R | 29 ++++++++---------------------
3 files changed, 16 insertions(+), 25 deletions(-)
Title: Flexible Copula Density Estimation with Penalized Hierarchical
B-Splines
Diff between pencopula versions 0.2.0 dated 2011-02-22 and 0.2.1 dated 2011-02-23
Description: Flexible copula density estimation with penalized
hierarchical B-Splines.
Author: Christian Schellhase
Maintainer: Christian Schellhase
DESCRIPTION | 8 ++++----
R/pencopula.R | 12 ++++++------
man/pencopula-package.Rd | 4 ++--
3 files changed, 12 insertions(+), 12 deletions(-)
Title: Estimation of various latent class mixed models and joint latent
class mixed models
Diff between lcmm versions 1.2 dated 2011-02-21 and 1.3-1 dated 2011-02-23
Description: This package provides functions for the estimation of
various latent class mixed models and joint latent latent class
mixed models using a maximum likelihood method
Author: Cecile Proust-Lima, Amadou Diakite and Benoit Liquet
Maintainer:
lcmm-1.2/lcmm/src/hetmixlin.f |only
lcmm-1.3-1/lcmm/DESCRIPTION | 8 ++++----
lcmm-1.3-1/lcmm/src/hetmixlin_with_optim2011.f90 |only
3 files changed, 4 insertions(+), 4 deletions(-)
Title: R interface to the QuantLib library
Diff between RQuantLib versions 0.3.5 dated 2010-11-30 and 0.3.6 dated 2011-02-23
Description: The RQuantLib package makes parts of QuantLib visible to
the R user. Currently a number option pricing functions are
included, both vanilla and exotic, as well as a broad range of
fixed-income functions. Also included are general calendaring
and holiday utilities. 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 uses 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).
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
RQuantLib-0.3.5/RQuantLib/configure.win |only
RQuantLib-0.3.6/RQuantLib/ChangeLog | 7 +++++++
RQuantLib-0.3.6/RQuantLib/DESCRIPTION | 8 ++++----
RQuantLib-0.3.6/RQuantLib/src/bermudan.cpp | 8 ++++----
RQuantLib-0.3.6/RQuantLib/src/utils.cpp | 8 ++++----
5 files changed, 19 insertions(+), 12 deletions(-)
Title: Kalman filter and smoothers for exponential family state space
models.
Diff between KFAS versions 0.6.0 dated 2010-04-15 and 0.6.1 dated 2011-02-23
Description: Package KFAS provides functions for Kalman filtering,
state, disturbance and simulation smoothing, forecasting and
simulation of state space models. All functions can use exact
diffuse initialisation when distributions of some or all
elements of initial state vector are unknown. Filtering, state
smoothing and simulation functions use sequential processing
algorithm, which is faster than standard approach, and it also
allows singularity of prediction error variance matrix. KFAS
also contains function for computing the likelihood of
exponential family state space models and function for state
smoothing of exponential family state space models.
Author: Jouni Helske
Maintainer: Jouni Helske
DESCRIPTION | 8 ++++----
data |only
man/GlobalTemp.Rd |only
man/kf.Rd | 12 +++++++-----
man/ks.Rd | 11 +++++------
5 files changed, 16 insertions(+), 15 deletions(-)
Title: classes and methods for spatial data
Diff between sp versions 0.9-77 dated 2011-02-21 and 0.9-78 dated 2011-02-23
Description: A package that provides classes and methods for spatial
data. The classes document where the spatial location
information resides, for 2D or 3D data. Utility functions are
provided, e.g. for plotting data as maps, spatial selection, as
well as methods for retrieving coordinates, for subsetting,
print, summary, etc.
Author: Edzer Pebesma
Maintainer: Edzer Pebesma
sp-0.9-77/sp/.Rbuildindex.19095 |only
sp-0.9-77/sp/grob.R |only
sp-0.9-77/sp/inst/doc/over-004.eps |only
sp-0.9-77/sp/inst/doc/over-004.pdf |only
sp-0.9-78/sp/ChangeLog | 4055 +++++++++--------------
sp-0.9-78/sp/DESCRIPTION | 8
sp-0.9-78/sp/NAMESPACE | 2
sp-0.9-78/sp/R/GridTopology-methods.R | 5
sp-0.9-78/sp/R/SpatialGrid-methods.R | 4
sp-0.9-78/sp/R/SpatialGridDataFrame-methods.R | 5
sp-0.9-78/sp/R/SpatialPolygons-methods.R | 9
sp-0.9-78/sp/inst/ChangeLog | 4055 +++++++++--------------
sp-0.9-78/sp/inst/doc/over.pdf |binary
sp-0.9-78/sp/inst/doc/sp.pdf |binary
sp-0.9-78/sp/man/GridTopology-class.Rd | 2
sp-0.9-78/sp/man/SpatialGrid-class.Rd | 2
sp-0.9-78/sp/man/SpatialGrid.Rd | 5
sp-0.9-78/sp/man/SpatialGridDataFrame.Rd | 3
sp-0.9-78/sp/man/SpatialPixels-class.Rd | 2
sp-0.9-78/sp/man/SpatialPixelsDataFrame-class.Rd | 2
sp-0.9-78/sp/man/SpatialPoints-class.Rd | 2
sp-0.9-78/sp/man/SpatialPolygons-class.Rd | 2
sp-0.9-78/sp/oChangeLog |only
sp-0.9-78/sp/svn2cl.xsl |only
sp-0.9-78/sp/tests/fail1.R | 2
sp-0.9-78/sp/tests/fail1.Rout.save | 34
sp-0.9-78/sp/tests/grid.Rout.save | 7
sp-0.9-78/sp/tests/spplot.Rout.save | 17
28 files changed, 3260 insertions(+), 4963 deletions(-)
Title: Time-of-flight mass spectra signal processing
Diff between rTOFsPRO versions 1.2 dated 2010-08-18 and 1.3 dated 2011-02-23
Description: rTOFsPRO provides functions for signal processing of the
linear TOF spectra to produce aligned peak intensity matrix
(and peak positions)
Author: Dariya Malyarenko, Maureen Tracy and William Cooke
Maintainer: Dariya Malyarenko
DESCRIPTION | 9 +++++----
inst/Examples/alignedPeaksTrain.Rdat |binary
inst/Examples/tofListMetaDataPCAqc11.Rdat |binary
inst/Examples/tofListPCAqc11.Rdat |binary
4 files changed, 5 insertions(+), 4 deletions(-)
Title: Tools for analyzing QTL experiments
Diff between qtl versions 1.19-20 dated 2010-11-30 and 1.20-15 dated 2011-02-23
Description: Analysis of experimental crosses to identify genes (called
quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Author: Karl W Broman
Maintainer: Karl W Broman
DESCRIPTION | 8 +-
R/addqtl.R | 12 +--
R/argmax.geno.R | 6 -
R/calc.genoprob.R | 6 -
R/est.map.R | 45 ++++++++++++
R/makeqtl.R | 9 +-
R/mqmcircleplot.R | 6 -
R/mqmplots.R | 81 +++++++++++------------
R/mqmscan.R | 65 +++++++++++++-----
R/plot.R | 14 ++--
R/refineqtl.R | 19 ++++-
R/replacemap.R | 40 ++++++++++-
R/scanone.R | 14 ++--
R/scanqtl.R | 10 +-
R/scantwo.R | 15 ++--
R/sim.geno.R | 6 -
R/stepwiseqtl.R | 4 -
R/summary.scantwo.R | 2
R/util.R | 142 ++++++++++++++++++++++++++++++++++++-----
R/xchr.R | 11 ++-
inst/README.txt | 16 ++--
inst/STATUS.txt | 55 +++++++++++++++
inst/TODO.txt | 9 ++
man/addpair.Rd | 2
man/addqtl.Rd | 2
man/argmax.geno.Rd | 12 ++-
man/calc.genoprob.Rd | 12 ++-
man/chrnames.Rd | 2
man/est.map.Rd | 5 +
man/mapthis.Rd | 7 ++
man/markernames.Rd | 2
man/mqmplotclusteredheatmap.Rd | 5 +
man/mqmplotheatmap.Rd | 8 +-
man/phenames.Rd |only
man/qtl-internal.Rd | 4 -
man/replace.map.Rd | 5 +
man/scanone.Rd | 2
man/scanqtl.Rd | 4 -
man/scantwo.Rd | 2
man/sim.geno.Rd | 10 +-
src/mqm.h | 6 -
src/mqmaugment.cpp | 8 +-
src/mqmprob.cpp | 10 ++
tests/test_qtl.R | 2
44 files changed, 513 insertions(+), 192 deletions(-)
Title: qgraph
Diff between qgraph versions 0.4.6 dated 2011-02-18 and 0.4.7 dated 2011-02-23
Description: The qgraph package can be used to visualize psychometric
data by using networks. (see URL).
Author: Sacha Epskamp, Angelique O. J. Cramer, Lourens J. Waldorp,
Verena D. Schmittmann and Denny Borsboom
Maintainer: Sacha Epskamp
DESCRIPTION | 12 ++++----
NAMESPACE | 2 -
NEWS | 8 +++++
R/qgraph.R | 73 ++++++++++++++++++++++++++++++++++---------------
R/qgraph_cfa.R |only
R/qgraph_loadings.R | 2 -
R/qgraph_sem.R | 69 ++++++++++++++++++++++++++--------------------
R/qgraph_semModel.R | 55 ++++++++++++++++++++++--------------
man/qgraph.Rd | 1
man/qgraph.cfa.Rd |only
man/qgraph.semModel.Rd | 4 +-
man/qgraph_sem.Rd | 13 +++++---
12 files changed, 151 insertions(+), 88 deletions(-)
Title: Computes local false discovery rates
Diff between locfdr versions 1.1-6 dated 2007-11-03 and 1.1-7 dated 2011-02-23
Description: Computation of local false discovery rates
Author: Bradley Efron, Brit B. Turnbull and Balasubramanian Narasimhan
Maintainer: Bradley Efron
DESCRIPTION | 8 +-
inst/doc/locfdr-example-Compute-local-fdr.pdf | 89 ++++++++++++++------------
inst/doc/locfdr-example.pdf |binary
man/locfdr.Rd | 2
4 files changed, 57 insertions(+), 42 deletions(-)
Title: Generalized Estimating Equation Package
Diff between geepack versions 1.0-17 dated 2010-01-28 and 1.0-18 dated 2011-02-23
Description: Generalized estimating equations solver for parameters in
mean, scale, and correlation structures, through mean link,
scale link, and correlation link. Can also handle clustered
categorical responses.
Author: Jun Yan
Maintainer: Søren Højsgaard
geepack-1.0-17/geepack/INDEX |only
geepack-1.0-18/geepack/ChangeLog | 11 +++++++++++
geepack-1.0-18/geepack/DESCRIPTION | 6 +++---
geepack-1.0-18/geepack/R/geeglm-anova.R | 6 +++++-
geepack-1.0-18/geepack/R/geeglm.R | 19 ++++++++++++++++++-
geepack-1.0-18/geepack/geepack-Ex.R |only
geepack-1.0-18/geepack/inst/doc/geepack-manual.pdf |binary
7 files changed, 37 insertions(+), 5 deletions(-)
Title: Simulation and Analysis of Random Fields
Diff between RandomFields versions 2.0.42 dated 2011-02-21 and 2.0.43 dated 2011-02-23
Description: Simulation of6 Gaussian and extreme value random fields;
conditional simulation; kriging
Author: Martin Schlather
Maintainer: Martin Schlather
DESCRIPTION | 6 +-
R/MLE.R | 140 +++++--------------------------------------------------
src/basic.h | 1
src/circulant.cc | 2
4 files changed, 19 insertions(+), 130 deletions(-)
Title: Data from the M-competitions
Diff between Mcomp versions 2.01 dated 2009-10-19 and 2.02 dated 2011-02-23
Description: The 1001 time series from the M-competition (Makridakis et
al. 1982) and the 3003 time series from the IJF-M3 competition
(Makridakis and Hibon, 2000).
Author: Rob J Hyndman
Maintainer: Rob J Hyndman
ChangeLog | 9 +++++++--
DESCRIPTION | 10 +++++-----
man/Mcomp-package.Rd | 6 +++---
3 files changed, 15 insertions(+), 10 deletions(-)
Title: Chemical Thermodynamics and Activity Diagrams
Diff between CHNOSZ versions 0.9-3 dated 2010-12-22 and 0.9-4 dated 2011-02-23
Description: This package includes functions and data sets to support
chemical thermodynamic modeling in biochemistry and
low-temperature geochemistry. The features include calculation
of the standard molal thermodynamic properties and chemical
affinities of reactions involving minerals and/or biomolecules;
a database of thermodynamic properties of aqueous, crystalline
and gaseous species; amino acid group additivity for the
standard molal thermodynamic properties of neutral and ionized
proteins; use of the revised Helgeson-Kirkham-Flowers equations
of state for aqueous species; construction of equilibrium
activity diagrams as a function of temperature, pressure, and
chemical activities or fugacities of basis species.
Author: Jeffrey M. Dick
Maintainer: Jeffrey M. Dick
CHNOSZ-0.9-3/CHNOSZ/data/ECO.csv.old |only
CHNOSZ-0.9-3/CHNOSZ/data/EF-Tu.aln |only
CHNOSZ-0.9-3/CHNOSZ/data/HTCC1062.faa |only
CHNOSZ-0.9-3/CHNOSZ/data/bisonN_vs_refseq39.blastp |only
CHNOSZ-0.9-3/CHNOSZ/data/bisonP_vs_refseq39.blastp |only
CHNOSZ-0.9-3/CHNOSZ/data/bisonR_vs_refseq39.blastp |only
CHNOSZ-0.9-3/CHNOSZ/data/gi.taxid.txt |only
CHNOSZ-0.9-3/CHNOSZ/data/names.dmp |only
CHNOSZ-0.9-3/CHNOSZ/data/nodes.dmp |only
CHNOSZ-0.9-3/CHNOSZ/inst/doc/.build.timestamp |only
CHNOSZ-0.9-4/CHNOSZ/DESCRIPTION | 8 -
CHNOSZ-0.9-4/CHNOSZ/R/affinity.R | 14 ++
CHNOSZ-0.9-4/CHNOSZ/R/anim.TCA.R |only
CHNOSZ-0.9-4/CHNOSZ/R/diagram.R | 13 +-
CHNOSZ-0.9-4/CHNOSZ/R/examples.R | 2
CHNOSZ-0.9-4/CHNOSZ/R/hkf.R | 2
CHNOSZ-0.9-4/CHNOSZ/R/info.R | 6 -
CHNOSZ-0.9-4/CHNOSZ/R/subcrt.R | 110 ++++++++++----------
CHNOSZ-0.9-4/CHNOSZ/R/taxonomy.R | 4
CHNOSZ-0.9-4/CHNOSZ/R/util.args.R | 4
CHNOSZ-0.9-4/CHNOSZ/R/util.blast.R | 35 ++++--
CHNOSZ-0.9-4/CHNOSZ/R/util.character.R | 69 ++++--------
CHNOSZ-0.9-4/CHNOSZ/R/util.data.R | 24 +---
CHNOSZ-0.9-4/CHNOSZ/R/water.R | 2
CHNOSZ-0.9-4/CHNOSZ/data/OBIGT.csv | 1
CHNOSZ-0.9-4/CHNOSZ/data/protein_refseq.csv |only
CHNOSZ-0.9-4/CHNOSZ/data/source.csv | 1
CHNOSZ-0.9-4/CHNOSZ/inst/NEWS | 13 ++
CHNOSZ-0.9-4/CHNOSZ/inst/doc/CHNOSZ-formation.Rnw | 4
CHNOSZ-0.9-4/CHNOSZ/inst/doc/CHNOSZ-formation.lyx | 4
CHNOSZ-0.9-4/CHNOSZ/inst/doc/CHNOSZ-formation.pdf |binary
CHNOSZ-0.9-4/CHNOSZ/inst/doc/CHNOSZ-intro.Rnw | 2
CHNOSZ-0.9-4/CHNOSZ/inst/doc/CHNOSZ-intro.lyx | 2
CHNOSZ-0.9-4/CHNOSZ/inst/doc/CHNOSZ-temperature.Rnw | 2
CHNOSZ-0.9-4/CHNOSZ/inst/doc/CHNOSZ-temperature.lyx | 34 +++---
CHNOSZ-0.9-4/CHNOSZ/inst/doc/CHNOSZ-temperature.pdf |binary
CHNOSZ-0.9-4/CHNOSZ/inst/extdata |only
CHNOSZ-0.9-4/CHNOSZ/inst/refseq |only
CHNOSZ-0.9-4/CHNOSZ/man/anim.TCA.Rd |only
CHNOSZ-0.9-4/CHNOSZ/man/basis.Rd | 13 +-
CHNOSZ-0.9-4/CHNOSZ/man/data.Rd | 10 +
CHNOSZ-0.9-4/CHNOSZ/man/diagram.Rd | 12 +-
CHNOSZ-0.9-4/CHNOSZ/man/findit.Rd | 12 --
CHNOSZ-0.9-4/CHNOSZ/man/protein.Rd | 2
CHNOSZ-0.9-4/CHNOSZ/man/revisit.Rd | 2
CHNOSZ-0.9-4/CHNOSZ/man/subcrt.Rd | 2
CHNOSZ-0.9-4/CHNOSZ/man/taxonomy.Rd | 6 -
CHNOSZ-0.9-4/CHNOSZ/man/util.array.Rd | 15 ++
CHNOSZ-0.9-4/CHNOSZ/man/util.blast.Rd | 4
CHNOSZ-0.9-4/CHNOSZ/man/util.character.Rd | 7 -
CHNOSZ-0.9-4/CHNOSZ/man/util.data.Rd | 8 -
CHNOSZ-0.9-4/CHNOSZ/man/util.fasta.Rd | 2
CHNOSZ-0.9-4/CHNOSZ/man/util.formula.Rd | 42 ++++++-
53 files changed, 284 insertions(+), 209 deletions(-)