Author: Jan de Leeuw, Patrick Mair
Title: SMACOF for Multidimensional Scaling.
Description: This package provides the following approaches of
multidimensional scaling (MDS) based on stress minimization by
means of majorization (smacof): Simple smacof on symmetric
dissimilarity matrices, smacof for rectangular matrices
(unfolding models), smacof with constraints on the
configuration, three-way smacof for individual differences
(including constraints for idioscal, indscal, and identity),
and spherical smacof (primal and dual algorithm). Each of these
approaches is implemented in a metric and nonmetric manner
including primary, secondary, and tertiary approaches for tie
handling.
Diff between smacof versions 0.9-6 dated 2009-05-17 and 1.0-0 dated 2009-08-01
smacof-0.9-6/smacof/inst/doc/Rplots.pdf |only smacof-0.9-6/smacof/inst/doc/jss1.bst |only smacof-0.9-6/smacof/inst/doc/jss1.cls |only smacof-1.0-0/smacof/DESCRIPTION | 10 smacof-1.0-0/smacof/inst/CITATION |only smacof-1.0-0/smacof/inst/doc/ekmanbasic.pdf | 135 smacof-1.0-0/smacof/inst/doc/ekmansphere.pdf | 338 smacof-1.0-0/smacof/inst/doc/inddiffconfid.pdf | 115 smacof-1.0-0/smacof/inst/doc/inddiffconfuc.pdf | 114 smacof-1.0-0/smacof/inst/doc/inddiffresid.pdf | 203 smacof-1.0-0/smacof/inst/doc/inddiffresuc.pdf | 203 smacof-1.0-0/smacof/inst/doc/jconfbfast.pdf | 205 smacof-1.0-0/smacof/inst/doc/jss.cls | 190 smacof-1.0-0/smacof/inst/doc/kinshipconstr.pdf | 144 smacof-1.0-0/smacof/inst/doc/kinshipstressr.pdf | 201 smacof-1.0-0/smacof/inst/doc/kinshipstressu.pdf | 200 smacof-1.0-0/smacof/inst/doc/kinshipsym.pdf | 144 smacof-1.0-0/smacof/inst/doc/shepbfast.pdf | 1373 +-- smacof-1.0-0/smacof/inst/doc/smacof.Rnw | 55 smacof-1.0-0/smacof/inst/doc/smacof.bib | 532 - smacof-1.0-0/smacof/inst/doc/smacof.pdf | 9741 ++++++++++++------------ smacof-1.0-0/smacof/inst/doc/spectrum.gif |only smacof-1.0-0/smacof/man/smacof-package.Rd | 8 smacof-1.0-0/smacof/man/smacofConstraint.rd | 3 smacof-1.0-0/smacof/man/smacofIndDiff.Rd | 4 smacof-1.0-0/smacof/man/smacofRect.Rd | 4 smacof-1.0-0/smacof/man/smacofSym.Rd | 4 27 files changed, 6832 insertions(+), 7094 deletions(-)
Author: Jan de Leeuw, Patrick Mair
Title: Gifi Methods for Optimal Scaling
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.
Diff between homals versions 0.9-11 dated 2009-07-27 and 1.0-0 dated 2009-08-01
homals-0.9-11/homals/inst/doc/Sweave.sty |only homals-0.9-11/homals/inst/doc/Z.cls |only homals-0.9-11/homals/inst/doc/galoAdvice.pdf |only homals-0.9-11/homals/inst/doc/galoIQ.pdf |only homals-0.9-11/homals/inst/doc/galoStar.pdf |only homals-0.9-11/homals/inst/doc/homalsR.Rnw |only homals-0.9-11/homals/inst/doc/homalsR.bbl |only homals-0.9-11/homals/inst/doc/homalsR.blg |only homals-0.9-11/homals/inst/doc/homalsR.pdf |only homals-0.9-11/homals/inst/doc/jss1.bst |only homals-0.9-11/homals/inst/doc/jss1.cls |only homals-0.9-11/homals/inst/doc/mammalsgraph.pdf |only homals-0.9-11/homals/inst/doc/mammalsstar.pdf |only homals-1.0-0/homals/DESCRIPTION | 12 homals-1.0-0/homals/R/plot.homals.R | 36 homals-1.0-0/homals/inst/CITATION |only homals-1.0-0/homals/inst/doc/galoLab.pdf | 2666 ++++++++++++------------ homals-1.0-0/homals/inst/doc/galoVor.pdf | 2716 ++++++++++++------------- homals-1.0-0/homals/inst/doc/homals.Rnw |only homals-1.0-0/homals/inst/doc/homals.pdf |only homals-1.0-0/homals/inst/doc/homalsR.bib | 29 homals-1.0-0/homals/inst/doc/irisHull.pdf | 1398 ++++++------ homals-1.0-0/homals/inst/doc/irisLab.pdf | 402 +-- homals-1.0-0/homals/inst/doc/irisLoss1.pdf | 678 ++---- homals-1.0-0/homals/inst/doc/irisLoss2.pdf | 488 ++-- homals-1.0-0/homals/inst/doc/irisLoss3.pdf | 808 +++---- homals-1.0-0/homals/inst/doc/irisLoss4.pdf | 472 ++-- homals-1.0-0/homals/inst/doc/jss.cls | 190 + homals-1.0-0/homals/inst/doc/listings.sty |only homals-1.0-0/homals/inst/doc/neuloadlin.pdf | 119 - homals-1.0-0/homals/inst/doc/neuloadmon.pdf | 119 - homals-1.0-0/homals/inst/doc/neutrfdens.pdf | 316 +- homals-1.0-0/homals/inst/doc/neutrfpres.pdf | 502 ++-- homals-1.0-0/homals/inst/doc/neutrftemp.pdf | 223 +- homals-1.0-0/homals/inst/doc/roskamobj.pdf | 113 - homals-1.0-0/homals/inst/doc/roskamvec.pdf | 194 - homals-1.0-0/homals/inst/doc/senatespan12.pdf | 1116 +++++----- homals-1.0-0/homals/inst/doc/senatespan13.pdf | 1116 +++++----- homals-1.0-0/homals/inst/doc/senatespan23.pdf | 1117 +++++----- homals-1.0-0/homals/man/homals.Rd | 3 40 files changed, 7426 insertions(+), 7407 deletions(-)
Author: Stefan Funke, Patrick Mair, and Alexander von Eye
Title: Analysis of configuration frequencies (CFA)
Description: Analysis of configuration frequencies for simple and
repeated measures, more sample CFa, hierarchical CFA,
bootstrap-CFA, functional CFA, Kieser-Victor CFA and various
plots
Diff between cfa versions 0.8-4 dated 2008-11-02 and 0.8-5 dated 2009-08-01
DESCRIPTION | 25 +++++++++++++++---------- R/fCFA.R | 2 +- R/kvCFA.R | 2 +- man/fCFA.Rd | 3 --- 4 files changed, 17 insertions(+), 15 deletions(-)
Author: Carsten F. Dormann and Bernd Gruber, with additional code from
Mariano Devoto, Jochen Fruend, Jose Iriondo and Diego Vazquez,
also based on C-code developed by Nils Bluethgen and by Miguel
Rodriguez-Girones.
Title: Visualising bipartite networks and calculating some ecological
indices.
Description: Bipartite provides functions to viualise webs and
calculate a series of indices commonly used to describe pattern
in ecological webs. It focusses on webs consisting of only two
trophic levels, e.g. pollination webs or predator-prey-webs.
Visualisation is important to get an idea of what we are
actually looking at, while the indices summarise different
aspects of the webs topology.
Diff between bipartite versions 0.93 dated 2009-06-25 and 0.94 dated 2009-08-01
DESCRIPTION | 8 ++++---- R/networklevel.R | 20 +++++++++++++++----- R/nullmodel.r |only R/slope.bipartite.R | 2 +- Wishlist.txt | 2 ++ man/bipartite-package.Rd | 10 ++++++++-- man/networklevel.Rd | 5 +++-- man/nullmodel.rd |only matrix.cpp |only 9 files changed, 33 insertions(+), 14 deletions(-)
Author: Jan de Leeuw, Patrick Mair
Title: Simple and Canonical Correspondence Analysis.
Description: This package performs simple and canonical CA (covariates
on rows/columns) on a two-way frequency table (with missings)
by means of SVD. Different scaling methods (standard, centroid,
Benzecri, Goodman) as well as various plots including
confidence ellipsoids are provided.
Diff between anacor versions 0.9-8 dated 2009-03-05 and 1.0-0 dated 2009-08-01
anacor-0.9-8/anacor/inst/doc/Sweave.sty |only anacor-0.9-8/anacor/inst/doc/Z.cls |only anacor-0.9-8/anacor/inst/doc/jss1.bst |only anacor-0.9-8/anacor/inst/doc/jss1.cls |only anacor-0.9-8/anacor/inst/doc/maxcol.pdf |only anacor-1.0-0/anacor/DESCRIPTION | 17 anacor-1.0-0/anacor/R/plot.anacor.R | 4 anacor-1.0-0/anacor/inst/CITATION |only anacor-1.0-0/anacor/inst/doc/Rplots.pdf |only anacor-1.0-0/anacor/inst/doc/Rplots1.pdf |only anacor-1.0-0/anacor/inst/doc/Rplots2.pdf |only anacor-1.0-0/anacor/inst/doc/anacor.Rnw | 66 - anacor-1.0-0/anacor/inst/doc/anacor.bib | 99 -- anacor-1.0-0/anacor/inst/doc/anacor.pdf |binary anacor-1.0-0/anacor/inst/doc/bit2dcols.pdf | 970 +++++++++++++++-------- anacor-1.0-0/anacor/inst/doc/bit2drows.pdf | 970 +++++++++++++++-------- anacor-1.0-0/anacor/inst/doc/bit5dcols.pdf | 970 +++++++++++++++-------- anacor-1.0-0/anacor/inst/doc/bit5drows.pdf | 970 +++++++++++++++-------- anacor-1.0-0/anacor/inst/doc/glassreg1.pdf | 461 +++++++---- anacor-1.0-0/anacor/inst/doc/glassreg2.pdf | 334 ++++---- anacor-1.0-0/anacor/inst/doc/jss.cls | 190 +++- anacor-1.0-0/anacor/inst/doc/maxord.pdf | 236 ++--- anacor-1.0-0/anacor/inst/doc/maxtrans.pdf | 444 ++++++---- anacor-1.0-0/anacor/inst/doc/tochergraph.pdf | 235 ++--- anacor-1.0-0/anacor/inst/doc/tocherjoint.pdf | 1106 +++++++++++++-------------- anacor-1.0-0/anacor/man/anacor-package.Rd | 7 anacor-1.0-0/anacor/man/anacor.Rd | 5 27 files changed, 4235 insertions(+), 2849 deletions(-)
Author: Patrick Mair, Eric Wu
Title: R/EQS Interface
Description: This package contains the function run.eqs() which calls
an EQS script file, executes the EQS estimation, and, finally,
imports the results as R objects. These two steps can be
performed separately: call.eqs() calls and executes EQS,
whereas read.eqs() imports existing EQS outputs as objects into
R.
Diff between REQS versions 0.7-2 dated 2008-11-02 and 0.8-1 dated 2009-08-01
DESCRIPTION | 33 ++++++++++++++++++++------------- R/call.eqs.R | 9 ++++++--- man/call.eqs.rd | 4 ++-- man/run.eqs.rd | 5 +++-- 4 files changed, 31 insertions(+), 20 deletions(-)
Author: Michael Lawrence, John Verzani
Title: Toolkit implementation of gWidgets for RGtk2
Description: Port of gWidgets API to RGtk2
Diff between gWidgetsRGtk2 versions 0.0-52 dated 2009-06-14 and 0.0-53 dated 2009-08-01
ChangeLog | 21 ++++++++ DESCRIPTION | 6 +- NEWS | 11 ++++ R/aaaGenerics.R | 7 ++ R/gbutton.R | 6 ++ R/ggrid.R | 11 ++-- R/glayout.R | 2 R/gtree.R | 95 ++++++++++++++++++++------------------ R/gvarbrowser.R | 6 +- R/gwindow.R | 4 - man/gWidgetsRGtk2-undocumented.Rd | 2 11 files changed, 111 insertions(+), 60 deletions(-)
Author: Søren Højsgaard
Diff between gRain versions 0.8.0 dated 2009-04-26 and 0.8.1 dated 2009-08-01
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).
gRain-0.8.0/gRain/inst/doc/fig/chest-007.eps |only
gRain-0.8.0/gRain/inst/doc/fig/chest-007.pdf |only
gRain-0.8.0/gRain/inst/doc/fig/chest-LS2tm.eps |only
gRain-0.8.0/gRain/inst/doc/fig/chest-LS2tm.pdf |only
gRain-0.8.0/gRain/inst/doc/gRain-intro.q |only
gRain-0.8.1/gRain/ChangeLog | 8 +++
gRain-0.8.1/gRain/DESCRIPTION | 6 +-
gRain-0.8.1/gRain/R/grain-main2.R | 2
gRain-0.8.1/gRain/R/propagate.R | 12 +++-
gRain-0.8.1/gRain/R/querygrain.R | 27 ++++++-----
gRain-0.8.1/gRain/inst/doc/R-current.lnk |only
gRain-0.8.1/gRain/inst/doc/fig/chest-LS2.pdf |binary
gRain-0.8.1/gRain/inst/doc/gRain-intro.Rnw | 61 +++++++++++++++++--------
gRain-0.8.1/gRain/inst/doc/gRain-intro.pdf |binary
gRain-0.8.1/gRain/man/compileCPT.Rd | 2
gRain-0.8.1/gRain/man/extractCPT.Rd | 2
gRain-0.8.1/gRain/man/grain.Rd | 25 ++++------
gRain-0.8.1/gRain/man/internal-gRain.Rd | 6 +-
gRain-0.8.1/gRain/man/loadSaveHuginNet.Rd | 6 +-
gRain-0.8.1/gRain/man/querygrain.Rd | 8 +--
20 files changed, 102 insertions(+), 63 deletions(-)
Author: Veronica Andrea Gonzalez-Lopez
Diff between fgac versions 0.6-0 dated 2006-02-08 and 0.6-1 dated 2009-08-01
Title: Generalized Archimedean Copula
Description: Bi-variate data fitting is done by two stochastic
components: the marginal distributions and the dependency
structure. The dependency structure is modeled through a
copula. An algorithm was implemented considering seven families
of copulas (Generalized Archimedean Copulas), the best fitting
can be obtained looking all copula's options (totally positive
of order 2 and stochastically increasing models).
DESCRIPTION | 22 +++++++++++++++-------
man/KGalambos.Rd | 1 -
man/OptimCBB.Rd | 2 +-
man/dirac1.Rd | 2 +-
man/dirac2.Rd | 2 +-
man/diracS1.Rd | 2 +-
man/diracS2.Rd | 2 +-
man/fitCBB.Rd | 2 +-
man/ivphiBB1.Rd | 2 +-
man/ivphiBB2.Rd | 2 +-
man/ivphiBB3.Rd | 4 ++--
man/ivphiBB6.Rd | 2 +-
man/ivphiBB7.Rd | 2 +-
man/ivpsiGumbel.Rd | 2 +-
man/ivpsiKS.Rd | 2 +-
man/pCBB1.Rd | 2 +-
man/pCBB2.Rd | 2 +-
man/pCBB4.Rd | 2 +-
man/pCBB6.Rd | 2 +-
man/pCBB7.Rd | 2 +-
man/pCMax.Rd | 2 +-
man/pCMin.Rd | 2 +-
man/pcopula1.Rd | 2 +-
man/pcopula2.Rd | 2 +-
man/phiBB1.Rd | 2 +-
man/phiBB2.Rd | 2 +-
man/phiBB3.Rd | 2 +-
man/phiBB6.Rd | 2 +-
man/phiBB7.Rd | 2 +-
man/psiGumbel.Rd | 2 +-
man/psiKS.Rd | 2 +-
31 files changed, 45 insertions(+), 38 deletions(-)
Author: Longhai Li
Diff between BPHO versions 1.2-5 dated 2008-04-08 and 1.3-0 dated 2009-08-01
Title: Bayesian Prediction with High-order Interactions
Description: This software can be used in two situations. The first is
to predict the next outcome based on the previous states of a
discrete sequence. The second is to classify a discrete
response based on a number of discreate covariates. In both
situations, we use Bayesian logistic regression models that
consider the high-order interactions. The models are trained
with slice sampling method, a variant of Markov chain Monte
Carlo. The time arising from using high-order interactions is
reduced greatly by our compression technique that represents a
group of original parameters as a single one in MCMC step.
BPHO-1.2-5/BPHO/note |only
BPHO-1.3-0/BPHO/DESCRIPTION | 23 +-
BPHO-1.3-0/BPHO/R/compress.r | 87 ++++---
BPHO-1.3-0/BPHO/R/firstlib.r | 2
BPHO-1.3-0/BPHO/R/gendata.r | 4
BPHO-1.3-0/BPHO/R/pred.r | 47 ++--
BPHO-1.3-0/BPHO/R/training.r | 174 +++++++--------
BPHO-1.3-0/BPHO/R/user.r | 254 ++++++++++++----------
BPHO-1.3-0/BPHO/man/a-user.Rd | 335 +++++++++++++++++-------------
BPHO-1.3-0/BPHO/man/b-compression.Rd | 34 +--
BPHO-1.3-0/BPHO/man/c-training.Rd | 56 ++---
BPHO-1.3-0/BPHO/man/d-prediction.Rd | 7
BPHO-1.3-0/BPHO/src/ccodes/compress.c | 10
BPHO-1.3-0/BPHO/src/ccodes/compress_int.c | 67 +++---
BPHO-1.3-0/BPHO/src/ccodes/display_mc_g.c | 2
BPHO-1.3-0/BPHO/src/ccodes/display_mc_g.h | 2
BPHO-1.3-0/BPHO/src/ccodes/int_list.c | 10
BPHO-1.3-0/BPHO/src/ccodes/int_list.h | 1
BPHO-1.3-0/BPHO/src/ccodes/pred_int.c | 72 +++---
BPHO-1.3-0/BPHO/src/ccodes/pred_int.h | 3
BPHO-1.3-0/BPHO/src/ccodes/training_int.c | 95 +-------
BPHO-1.3-0/BPHO/src/ccodes/util.c | 1
22 files changed, 670 insertions(+), 616 deletions(-)