Author: Stefano Maria Iacus
Title: Simulation and Inference for Stochastic Differential Equations
Description: Companion package to the book Simulation and Inference for
Stochastic Differential Equations With R Examples, ISBN
978-0-387-75838-1, Springer, NY.
Diff between sde versions 2.0.9 dated 2009-07-31 and 2.0.10 dated 2009-08-06
DESCRIPTION | 10 +++++----- R/dcApprox.R | 2 +- inst/doc/changes.txt | 4 ++++ inst/doc/sde.errata.Rnw | 22 ++++++++++++++++++++++ inst/doc/sde.errata.pdf |binary 5 files changed, 32 insertions(+), 6 deletions(-)
Author: Carlos J. Gil Bellosta
Title: Read big text files column by column
Description: This package tries to solve the memory restrictions posed
by large text files by breaking them into its columns, which
are subsequently read individually into R.
Diff between colbycol versions 0.3 dated 2009-07-18 and 0.4 dated 2009-08-06
colbycol-0.3/colbycol/inst/python |only colbycol-0.4/colbycol/DESCRIPTION | 12 ++++----- colbycol-0.4/colbycol/NAMESPACE | 2 + colbycol-0.4/colbycol/R/cbc.read.table.R | 33 +++++++------------------- colbycol-0.4/colbycol/R/onLoad.R |only colbycol-0.4/colbycol/inst/java |only colbycol-0.4/colbycol/inst/java_src |only colbycol-0.4/colbycol/man/colbycol-package.Rd | 4 +-- 8 files changed, 19 insertions(+), 32 deletions(-)
Author: Josef Leydold and Wolfgang H\"ormann
Title: R interface to the UNU.RAN random variate generators
Description: Interface to the UNU.RAN library for Universal Non-Uniform
RANdom variate generators
Diff between Runuran versions 0.10.0 dated 2009-06-24 and 0.10.1 dated 2009-08-06
DESCRIPTION | 8 NEWS | 6 inst/doc/Runuran.pdf | 965 +++++++++++++++--------------- inst/doc/src/version.tex | 2 man/Runuran-package.Rd | 4 man/unuran.packed-methods.Rd | 6 src/unuran-src/distr/discr.c | 2 src/unuran-src/distributions/c_logistic.c | 1 src/unuran-src/methods/arou.c | 8 src/unuran-src/methods/hinv.c | 5 src/unuran-src/methods/itdr.c | 2 src/unuran-src/methods/pinv_prep.ch | 2 src/unuran-src/methods/pinv_sample.ch | 5 src/unuran-src/tests/inverror.c | 2 src/unuran-src/utils/lobatto.c | 12 src/unuran-src/utils/stream.c | 5 tests/test_packed.R | 6 17 files changed, 530 insertions(+), 511 deletions(-)
Author: Yu-Sung Su
Diff between R2jags versions 0.01-23 dated 2009-05-04 and 0.01-24 dated 2009-08-06
Title: A Package for Running jags from R
Description: Using this package to call jags from R.
CHANGELOG | 5 +++++
DESCRIPTION | 8 ++++----
R/as.bugs.array2.R | 2 +-
R/jags.R | 2 +-
R/jags.sims.R | 2 +-
man/jags.Rd | 4 ++--
6 files changed, 14 insertions(+), 9 deletions(-)
Author: Nicholas L. Crookston
Diff between yaImpute versions 1.0-9 dated 2009-04-19 and 1.0-10 dated 2009-08-06
Title: yaImpute: An R Package for k-NN Imputation
Description: Performs popular nearest neighbor routines for imputation
DESCRIPTION | 10
R/asciigridimpute.R | 13 -
R/findFactors.R | 10
R/impute.R | 602 +++++++++++++++++++++++--------------------------
R/newtargets.R | 4
man/asciigridimpute.Rd | 16 -
man/newtargets.Rd | 2
7 files changed, 327 insertions(+), 330 deletions(-)
Author: Han Lin Shang and Rob J Hyndman
Title: Rainbow plots, bagplots and boxplots for functional data
Description: Functions and datasets for functional data display and
outlier detection.
Diff between rainbow versions 1.2 dated 2009-07-28 and 1.3 dated 2009-08-06
rainbow-1.2/rainbow/.fsLockFile |only rainbow-1.2/rainbow/R/fd.R |only rainbow-1.2/rainbow/R/lines.fd.r |only rainbow-1.2/rainbow/R/plot.fd.R |only rainbow-1.2/rainbow/R/points.fd.r |only rainbow-1.2/rainbow/R/print.fd.R |only rainbow-1.2/rainbow/man/fd.Rd |only rainbow-1.2/rainbow/man/plot.fd.Rd |only rainbow-1.3/rainbow/CHANGELOG |only rainbow-1.3/rainbow/DESCRIPTION | 10 +++---- rainbow-1.3/rainbow/NAMESPACE | 23 ++++++++++++------ rainbow-1.3/rainbow/R/fds.R |only rainbow-1.3/rainbow/R/fts.R | 2 - rainbow-1.3/rainbow/R/lines.fds.r |only rainbow-1.3/rainbow/R/lines.sfts.R |only rainbow-1.3/rainbow/R/plot.fdepth.R | 5 ++- rainbow-1.3/rainbow/R/plot.fds.R |only rainbow-1.3/rainbow/R/plot.sfts.R |only rainbow-1.3/rainbow/R/points.fds.r |only rainbow-1.3/rainbow/R/points.sfts.r |only rainbow-1.3/rainbow/R/print.fds.R |only rainbow-1.3/rainbow/R/print.fts.R | 11 ++++++-- rainbow-1.3/rainbow/R/print.sfts.r |only rainbow-1.3/rainbow/R/sfts.R |only rainbow-1.3/rainbow/data/Australiafertility.rda |binary rainbow-1.3/rainbow/data/Australiasmoothfertility.rda |binary rainbow-1.3/rainbow/data/ElNino.rda |binary rainbow-1.3/rainbow/data/Francemortality.rda |binary rainbow-1.3/rainbow/data/Francesmoothmortality.rda |binary rainbow-1.3/rainbow/data/Simulationdata.rda |binary rainbow-1.3/rainbow/man/Australiafertility.Rd | 4 ++- rainbow-1.3/rainbow/man/ElNino.Rd | 20 ++++++++++----- rainbow-1.3/rainbow/man/Francemortality.Rd | 6 +++- rainbow-1.3/rainbow/man/Simulationdata.Rd | 6 ++-- rainbow-1.3/rainbow/man/fboxplot.Rd | 10 ++++--- rainbow-1.3/rainbow/man/fdepth.Rd | 4 +-- rainbow-1.3/rainbow/man/fds.Rd |only rainbow-1.3/rainbow/man/foutliers.Rd | 4 ++- rainbow-1.3/rainbow/man/lines.fds.Rd |only rainbow-1.3/rainbow/man/lines.sfts.Rd |only rainbow-1.3/rainbow/man/plot.fds.Rd |only rainbow-1.3/rainbow/man/plot.sfts.Rd |only rainbow-1.3/rainbow/man/points.fds.Rd |only rainbow-1.3/rainbow/man/points.sfts.Rd |only rainbow-1.3/rainbow/man/rainbow-package.Rd | 6 ++-- rainbow-1.3/rainbow/man/sfts.Rd |only 46 files changed, 70 insertions(+), 41 deletions(-)
Author: Jelle Goeman
Diff between penalized versions 0.9-25 dated 2009-07-18 and 0.9-26 dated 2009-08-06
Title: L1 (lasso) and L2 (ridge) penalized estimation in GLMs and in
the Cox model
Description: A package for fitting possibly high dimensional penalized
regression models. The penalty structure can be any combination
of an L1 penalty (lasso), an L2 penalty (ridge) and a
positivity constraint on the regression coefficients. The
supported regression models are linear, logistic and poisson
regression and the Cox Proportional Hazards model.
Cross-validation routines allow optimization of the tuning
parameters.
DESCRIPTION | 8
R/core.R | 6
R/cvl.R | 35
changelog.txt | 3
inst/doc/Rplots.pdf |14020 ++++++++++++++++++++++++-------------------------
inst/doc/penalized.pdf |binary
6 files changed, 7005 insertions(+), 7067 deletions(-)
Author: Yue Fan, Thomas Brendan Murphy, R. William G. Watson
Title: GUI tool for analyzing 2D DIGE data
Description: An easy to use Graphical User Interfact for spots
correlation analysis, score plot, classification, feature
selection and power analysis for 2D DIGE experiment data.
Diff between digeR versions 1.0 dated 2009-06-24 and 1.1 dated 2009-08-06
digeR-1.0/digeR/inst/digeR_Manual.pdf |only digeR-1.1/digeR/DESCRIPTION | 8 digeR-1.1/digeR/R/digeR.R | 66 ++- digeR-1.1/digeR/inst/Manual_for_digeR_v1.1.pdf |only digeR-1.1/digeR/inst/digeR.pdf | 440 ++++++++++++------------- digeR-1.1/digeR/man/digeR-package.Rd | 4 digeR-1.1/digeR/man/digeR.Rd | 10 7 files changed, 271 insertions(+), 257 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 0.94 dated 2009-08-01 and 1.00 dated 2009-08-06
DESCRIPTION | 8 R/C.score.R | 13 + R/H2fun.R | 46 +++-- R/PAC.r |only R/degreedistr.R | 12 - R/dfun.R | 1 R/networklevel.R | 406 ++++++++++++++++++++++++----------------------- R/specieslevel.R | 148 +++++++++++------ Wishlist.txt | 14 + man/PAC.rd |only man/bipartite-package.Rd | 23 ++ man/degreedistr.Rd | 5 man/networklevel.Rd | 85 +++++---- man/specieslevel.Rd | 44 ++--- 14 files changed, 474 insertions(+), 331 deletions(-)
Author: Alexis Gabadinho
Diff between TraMineR versions 1.2-1 dated 2009-05-13 and 1.4 dated 2009-08-06
Title: Sequences and trajectories mining for social scientists
Description: This package is a toolbox for sequence manipulation,
description, rendering and more generally sequence data mining
in the field of social sciences. Though it is primarily
intended for analyzing state or event sequences that describe
life courses such as family formation histories or professional
careers its features apply indeed also to many other kinds of
categorical sequence data. It accepts as input many different
sequence representations and provides tools for translating
sequences from one format to another. It offers several
statistical functions for describing and rendering sequences,
for computing distances between sequences with different
metrics among which optimal matching, the longest common prefix
and the longest common subsequence, and simple functions for
extracting the most frequent subsequences and identifying the
most discriminating ones among them. A user's guide can be
found on TraMineR's web page.
TraMineR-1.2-1/TraMineR/R/TraMineR-dplot.R |only
TraMineR-1.2-1/TraMineR/R/TraMineR-fplot.R |only
TraMineR-1.2-1/TraMineR/R/TraMineR-iplot.R |only
TraMineR-1.2-1/TraMineR/R/TraMineR-mtplot.R |only
TraMineR-1.2-1/TraMineR/demo/Describing_visualizing.R |only
TraMineR-1.2-1/TraMineR/demo/Event_sequences.R |only
TraMineR-1.2-1/TraMineR/demo/Similarities.R |only
TraMineR-1.2-1/TraMineR/inst/doc |only
TraMineR-1.2-1/TraMineR/man/seqdplot.Rd |only
TraMineR-1.2-1/TraMineR/man/seqfplot.Rd |only
TraMineR-1.2-1/TraMineR/man/seqiplot.Rd |only
TraMineR-1.2-1/TraMineR/man/seqmtplot.Rd |only
TraMineR-1.4/TraMineR/DESCRIPTION | 8
TraMineR-1.4/TraMineR/NAMESPACE | 36 +
TraMineR-1.4/TraMineR/NEWS | 86 +++
TraMineR-1.4/TraMineR/R/BIOSPELL_to_STS.R | 57 +-
TraMineR-1.4/TraMineR/R/DHDdist.R |only
TraMineR-1.4/TraMineR/R/LCSdist.R | 4
TraMineR-1.4/TraMineR/R/TSE_to_STS.R |only
TraMineR-1.4/TraMineR/R/TraMineR-seqdist.R |only
TraMineR-1.4/TraMineR/R/TraMineR-trunc.R | 3
TraMineR-1.4/TraMineR/R/TraMineR.checkupdates.R |only
TraMineR-1.4/TraMineR/R/alphabet-set.R | 5
TraMineR-1.4/TraMineR/R/debuglevel.R |only
TraMineR-1.4/TraMineR/R/disscenter.R | 3
TraMineR-1.4/TraMineR/R/disstree.r | 8
TraMineR-1.4/TraMineR/R/disstree2dot.R | 4
TraMineR-1.4/TraMineR/R/plot.stslist.R | 174 ++-----
TraMineR-1.4/TraMineR/R/plot.stslist.freq.R |only
TraMineR-1.4/TraMineR/R/plot.stslist.meant.R |only
TraMineR-1.4/TraMineR/R/plot.stslist.modst.R |only
TraMineR-1.4/TraMineR/R/plot.stslist.rep.R |only
TraMineR-1.4/TraMineR/R/plot.stslist.statd.R |only
TraMineR-1.4/TraMineR/R/seqHtplot.R |only
TraMineR-1.4/TraMineR/R/seqdecomp.R | 2
TraMineR-1.4/TraMineR/R/seqdef.R | 160 ++++---
TraMineR-1.4/TraMineR/R/seqdist.R | 404 ++++++++----------
TraMineR-1.4/TraMineR/R/seqdistmc.R |only
TraMineR-1.4/TraMineR/R/seqdplot.R | 2
TraMineR-1.4/TraMineR/R/seqdss.R | 5
TraMineR-1.4/TraMineR/R/seqeapplysub.R | 10
TraMineR-1.4/TraMineR/R/seqecmpgroup.R | 97 ++--
TraMineR-1.4/TraMineR/R/seqeconstraint.R | 9
TraMineR-1.4/TraMineR/R/seqecreate.R | 3
TraMineR-1.4/TraMineR/R/seqefsub.R | 4
TraMineR-1.4/TraMineR/R/seqerules.R |only
TraMineR-1.4/TraMineR/R/seqetm.R | 72 +--
TraMineR-1.4/TraMineR/R/seqformat.R | 21
TraMineR-1.4/TraMineR/R/seqfplot.R | 4
TraMineR-1.4/TraMineR/R/seqiplot.R | 4
TraMineR-1.4/TraMineR/R/seqlegend.R | 6
TraMineR-1.4/TraMineR/R/seqlogp.R | 146 ++++--
TraMineR-1.4/TraMineR/R/seqmeant.R |only
TraMineR-1.4/TraMineR/R/seqmodst.R |only
TraMineR-1.4/TraMineR/R/seqmsplot.R |only
TraMineR-1.4/TraMineR/R/seqmtplot.R | 2
TraMineR-1.4/TraMineR/R/seqplot.R |only
TraMineR-1.4/TraMineR/R/seqrep.R |only
TraMineR-1.4/TraMineR/R/seqrplot.R |only
TraMineR-1.4/TraMineR/R/seqstatd.R | 43 +
TraMineR-1.4/TraMineR/R/seqstatf.R |only
TraMineR-1.4/TraMineR/R/seqsubm.R | 105 +++-
TraMineR-1.4/TraMineR/R/seqtab.R | 49 +-
TraMineR-1.4/TraMineR/R/seqtrate.R | 85 ++-
TraMineR-1.4/TraMineR/R/stslist-methods.R | 16
TraMineR-1.4/TraMineR/R/stslist.freq-methods.R |only
TraMineR-1.4/TraMineR/R/stslist.meant-methods.R |only
TraMineR-1.4/TraMineR/R/stslist.modst-methods.R |only
TraMineR-1.4/TraMineR/R/stslist.rep-methods.R |only
TraMineR-1.4/TraMineR/R/stslist.statd-methods.R |only
TraMineR-1.4/TraMineR/data/biofam.RData |binary
TraMineR-1.4/TraMineR/data/ex1.RData |only
TraMineR-1.4/TraMineR/data/famform.R | 8
TraMineR-1.4/TraMineR/demo/00Index | 6
TraMineR-1.4/TraMineR/demo/Events.R |only
TraMineR-1.4/TraMineR/demo/Rendering.R |only
TraMineR-1.4/TraMineR/demo/Seqdist.R |only
TraMineR-1.4/TraMineR/inst/CITATION | 4
TraMineR-1.4/TraMineR/man/TraMineR.checkupdates.Rd |only
TraMineR-1.4/TraMineR/man/biofam.Rd | 9
TraMineR-1.4/TraMineR/man/dissassoc.Rd | 52 +-
TraMineR-1.4/TraMineR/man/disscenter.Rd | 77 +--
TraMineR-1.4/TraMineR/man/dissmfac.Rd | 27 -
TraMineR-1.4/TraMineR/man/disstree.Rd | 37 -
TraMineR-1.4/TraMineR/man/dissvar.Rd | 50 +-
TraMineR-1.4/TraMineR/man/ex1.Rd |only
TraMineR-1.4/TraMineR/man/plot.stslist.Rd | 149 ++----
TraMineR-1.4/TraMineR/man/plot.stslist.freq.Rd |only
TraMineR-1.4/TraMineR/man/plot.stslist.meant.Rd |only
TraMineR-1.4/TraMineR/man/plot.stslist.modst.Rd |only
TraMineR-1.4/TraMineR/man/plot.stslist.rep.Rd |only
TraMineR-1.4/TraMineR/man/plot.stslist.statd.Rd |only
TraMineR-1.4/TraMineR/man/seqST.Rd | 2
TraMineR-1.4/TraMineR/man/seqdef.Rd | 69 ++-
TraMineR-1.4/TraMineR/man/seqdiff.Rd | 13
TraMineR-1.4/TraMineR/man/seqdist.Rd | 51 +-
TraMineR-1.4/TraMineR/man/seqdistmc.Rd |only
TraMineR-1.4/TraMineR/man/seqeapplysub.Rd | 5
TraMineR-1.4/TraMineR/man/seqeconstraint.Rd | 3
TraMineR-1.4/TraMineR/man/seqefsub.Rd | 4
TraMineR-1.4/TraMineR/man/seqfcheck.Rd | 2
TraMineR-1.4/TraMineR/man/seqformat.Rd | 15
TraMineR-1.4/TraMineR/man/seqfpos.Rd | 4
TraMineR-1.4/TraMineR/man/seqlegend.Rd | 6
TraMineR-1.4/TraMineR/man/seqlogp.Rd |only
TraMineR-1.4/TraMineR/man/seqmeant.Rd |only
TraMineR-1.4/TraMineR/man/seqmodst.Rd |only
TraMineR-1.4/TraMineR/man/seqplot.Rd |only
TraMineR-1.4/TraMineR/man/seqrep.Rd |only
TraMineR-1.4/TraMineR/man/seqsep.Rd | 4
TraMineR-1.4/TraMineR/man/seqstatd.Rd | 102 ++--
TraMineR-1.4/TraMineR/man/seqstatf.Rd |only
TraMineR-1.4/TraMineR/man/seqsubm.Rd | 22
TraMineR-1.4/TraMineR/man/seqtab.Rd | 70 ++-
TraMineR-1.4/TraMineR/man/seqtrate.Rd | 15
TraMineR-1.4/TraMineR/src/TraMineR.h |only
TraMineR-1.4/TraMineR/src/alignement.cpp | 14
TraMineR-1.4/TraMineR/src/alignement.h | 8
TraMineR-1.4/TraMineR/src/constraint.cpp |only
TraMineR-1.4/TraMineR/src/constraint.h |only
TraMineR-1.4/TraMineR/src/dist2matrix.c | 5
TraMineR-1.4/TraMineR/src/distancefunctions.cpp | 225 +++++-----
TraMineR-1.4/TraMineR/src/inertiafunctions.c | 37 -
TraMineR-1.4/TraMineR/src/prefixtree.cpp | 17
TraMineR-1.4/TraMineR/src/prefixtree.h | 6
TraMineR-1.4/TraMineR/src/saltt.cpp | 19
TraMineR-1.4/TraMineR/src/salttseq.cpp | 47 +-
TraMineR-1.4/TraMineR/src/salttseq.h | 6
TraMineR-1.4/TraMineR/src/tmrsequence.cpp | 39 +
TraMineR-1.4/TraMineR/src/traminerdebug.cpp |only
TraMineR-1.4/TraMineR/src/treeeventnode.cpp | 27 -
TraMineR-1.4/TraMineR/src/treeeventnode.h | 12
132 files changed, 1717 insertions(+), 1188 deletions(-)