Author: Roger Bivand
Title: Interface between GRASS 6 geographical information system and R
Description: Interpreted interface between GRASS 6 geographical
information system and R, based on starting R from within the
GRASS environment.
Diff between spgrass6 versions 0.6-5 dated 2009-04-30 and 0.6-6 dated 2009-05-27
ChangeLog | 5 +++++ DESCRIPTION | 8 ++++---- R/xml1.R | 11 +++++++++-- inst/ChangeLog | 5 +++++ man/execGRASS.Rd | 5 ++++- 5 files changed, 27 insertions(+), 7 deletions(-)
Author: Wolfgang Lederer
Diff between simex versions 1.2 dated 2006-02-26 and 1.4 dated 2009-05-27
Title: SIMEX- and MCSIMEX-Algorithm for measurement error models
Description: Implementation of the SIMEX-Algorithm by Cook & Stefanski
and MCSIMEX by Küchenhoff, Mwalili & Lesaffre
simex-1.2/simex/R/plot.MCSIMEX.R |only
simex-1.2/simex/R/plot.SIMEX.R |only
simex-1.2/simex/R/predict.MCSIMEX.R |only
simex-1.2/simex/R/predict.SIMEX.R |only
simex-1.2/simex/R/print.MCSIMEX.R |only
simex-1.2/simex/R/print.SIMEX.R |only
simex-1.2/simex/R/print.summary.MCSIMEX.R |only
simex-1.2/simex/R/print.summary.SIMEX.R |only
simex-1.2/simex/R/summary.MCSIMEX.R |only
simex-1.2/simex/R/summary.SIMEX.R |only
simex-1.2/simex/man/check.mc.matrix.Rd |only
simex-1.2/simex/man/construct.s.Rd |only
simex-1.2/simex/man/extract.covmat.Rd |only
simex-1.2/simex/man/fit.logl.Rd |only
simex-1.2/simex/man/fit.nls.Rd |only
simex-1.2/simex/man/overview.Rd |only
simex-1.2/simex/man/plot.SIMEX.Rd |only
simex-1.2/simex/man/predict.MCSIMEX.Rd |only
simex-1.2/simex/man/predict.SIMEX.Rd |only
simex-1.2/simex/man/print.SIMEX.Rd |only
simex-1.2/simex/man/refit.Rd |only
simex-1.2/simex/man/summary.MCSIMEX.Rd |only
simex-1.2/simex/man/summary.SIMEX.Rd |only
simex-1.4/simex/DESCRIPTION | 26 +-
simex-1.4/simex/NAMESPACE |only
simex-1.4/simex/NEWS |only
simex-1.4/simex/R/build.mc.matrix.R | 179 ++++++++--------
simex-1.4/simex/R/check.mc.matrix.R | 18 -
simex-1.4/simex/R/construct.s.R | 75 ++++--
simex-1.4/simex/R/diag.block.R | 27 +-
simex-1.4/simex/R/extract.covmat.R | 20 -
simex-1.4/simex/R/fit.logl.R | 42 ++-
simex-1.4/simex/R/fit.nls.R | 45 ++--
simex-1.4/simex/R/mcsimex.R | 326 +++++++++++++++++-------------
simex-1.4/simex/R/misclass.R | 32 +-
simex-1.4/simex/R/plot.mcsimex.R |only
simex-1.4/simex/R/plot.simex.R |only
simex-1.4/simex/R/predict.mcsimex.R |only
simex-1.4/simex/R/predict.simex.R |only
simex-1.4/simex/R/print.mcsimex.R |only
simex-1.4/simex/R/print.simex.R |only
simex-1.4/simex/R/print.summary.mcsimex.R |only
simex-1.4/simex/R/print.summary.simex.R |only
simex-1.4/simex/R/refit.R | 124 -----------
simex-1.4/simex/R/refit.mcsimex.R |only
simex-1.4/simex/R/refit.simex.R |only
simex-1.4/simex/R/simex-internal.R |only
simex-1.4/simex/R/simex.R | 293 ++++++++++++++------------
simex-1.4/simex/R/summary.mcsimex.R |only
simex-1.4/simex/R/summary.simex.R |only
simex-1.4/simex/man/build.mc.matrix.Rd | 90 +++++---
simex-1.4/simex/man/diag.block.Rd | 36 ++-
simex-1.4/simex/man/mcsimex.Rd | 218 +++++++++++++-------
simex-1.4/simex/man/misclass.Rd | 48 ++--
simex-1.4/simex/man/simex-package.Rd |only
simex-1.4/simex/man/simex.Rd | 156 ++++++++++----
56 files changed, 985 insertions(+), 770 deletions(-)
Author: Ian Dryden
Title: Statistical shape analysis
Description: Routines for the statistical analysis of shapes. In
particular, the package provides routines for procrustes
analysis, displaying shapes and principal components, testing
for mean shape difference, thin-plate spline transformation
grids and edge superimposition methods.
Diff between shapes versions 1.1-2 dated 2009-04-17 and 1.1-3 dated 2009-05-27
DESCRIPTION | 8 - R/shapes.R | 376 ++++++++++++++++++++++++++++++++++--------------- man/procGPA.Rd | 4 man/riemdist.Rd | 5 man/shapes-internal.Rd | 1 man/testmeanshapes.Rd | 2 6 files changed, 277 insertions(+), 119 deletions(-)
Author: Maja Pohar Perme
Title: Relative survival regression
Description: Various functions for regression in relative survival.
Diff between relsurv versions 1.5 dated 2008-11-13 and 1.5.1 dated 2009-05-27
DESCRIPTION | 21 +++++++++++---------- R/Rcode.r | 4 ++-- R/survfitrsadd.r | 32 ++++++++++++++++---------------- man/invtime.Rd | 6 +++--- man/joinrate.Rd | 9 +++------ man/plotrszph.Rd | 10 ++++------ man/rdata.Rd | 2 +- man/resid.Rd | 10 ++++------ man/rsadd.Rd | 10 ++++------ man/rsbr.Rd | 11 +++++------ man/rsmul.Rd | 19 ++++++------------- man/rssurv.Rd | 7 +++---- man/rstrans.Rd | 17 +++++------------ man/rszph.Rd | 11 +++++------ man/survfitrsadd.rd | 30 ++++++++++++------------------ man/transrate.Rd | 7 ++++--- man/transratehld.Rd | 6 +++--- man/transratehmd.Rd | 6 +++--- 18 files changed, 94 insertions(+), 124 deletions(-)
Author: Torsten Hothorn, Frank Bretz and Peter Westfall with
contributions by Richard M. Heiberger
Title: Simultaneous Inference in General Parametric Models
Description: Simultaneous tests and confidence intervals for general
linear hypotheses in parametric models, including linear,
generalized linear, linear mixed effects, and survival models.
Diff between multcomp versions 1.0-7 dated 2009-02-11 and 1.0-8 dated 2009-05-27
multcomp-1.0-7/multcomp/inst/svn-commit.tmp |only multcomp-1.0-8/multcomp/CHANGES | 8 multcomp-1.0-8/multcomp/DESCRIPTION | 19 multcomp-1.0-8/multcomp/cleanup | 3 multcomp-1.0-8/multcomp/inst/CHANGES | 8 multcomp-1.0-8/multcomp/inst/doc/chfls1.Rnw |only multcomp-1.0-8/multcomp/inst/doc/chfls1.bbl |only multcomp-1.0-8/multcomp/inst/doc/chfls1.bib |only multcomp-1.0-8/multcomp/inst/doc/chfls1.blg |only multcomp-1.0-8/multcomp/inst/doc/chfls1.pdf |only multcomp-1.0-8/multcomp/inst/doc/generalsiminf.pdf | 1096 ++++++++--------- multcomp-1.0-8/multcomp/inst/doc/multcomp-examples.pdf |binary multcomp-1.0-8/multcomp/man/glht.Rd | 2 multcomp-1.0-8/multcomp/man/methods.Rd | 2 multcomp-1.0-8/multcomp/man/trees513.Rd | 2 15 files changed, 581 insertions(+), 559 deletions(-)
Author: Luc Wouters
Diff between mpm versions 1.0-13 dated 2009-04-14 and 1.0-15 dated 2009-05-27
Title: Multivariate Projection Methods
Description: Exploratory graphical analysis of multivariate data,
specifically gene expression data with different projection
methods: principal component analysis, correspondence analysis,
spectral map analysis.
DESCRIPTION | 8 ++++----
R/plot.mpm.R | 30 +++++++++++++++++++++++++-----
inst/NEWS | 6 ++++++
man/plot.mpm.Rd | 6 ++++++
tests/tests.R | 6 ++++++
5 files changed, 47 insertions(+), 9 deletions(-)
Author: Robert B. Gramacy
Diff between monomvn versions 1.7 dated 2009-04-15 and 1.7-1 dated 2009-05-27
Title: Estimation for multivariate normal and Student-t data with
monotone missingness
Description: Estimation of multivariate normal and student-t 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 a nearly arbitrary amount of
missing data. The current version supports maximum likelihood
inference and a full Bayesian approach employing scale-mixtures
for the lasso (double-exponential) prior and Student-t errors.
Monotone data augmentation extends this Bayesian approach to
arbitrary missingness patterns. A fully functional standalone
interface to the Bayesian lasso (from Park & Casella) and ridge
regression with model selection via Reversible Jump, and
student-t errors (from Geweke) is also provided
.Rbuildindex.20799 |only
ChangeLog | 15 +++
DESCRIPTION | 8 -
R/blasso.R | 65 ++++++++++---
R/blasso.s3.R | 11 +-
R/bmonomvn.R | 11 +-
R/bmonomvn.traces.R | 14 ++
R/randmvn.R | 15 ++-
man/blasso.Rd | 51 +++++++---
man/bmonomvn.Rd | 12 +-
man/monomvn-internal.Rd | 1
man/randmvn.Rd | 6 +
src/blasso.cc | 226 +++++++++++++++++++++++++++++-------------------
src/blasso.h | 29 +++---
src/bmonomvn.cc | 45 +++++----
src/bmonomvn.h | 14 +-
src/hshoe.c |only
src/hshoe.h |only
src/nu.c | 1
19 files changed, 341 insertions(+), 183 deletions(-)
Author: Nicholas J. Lewin-Koh and Roger Bivand, contributions by Edzer
J. Pebesma, Eric Archer, Adrian Baddeley, Hans-Jörg Bibiko,
Stéphane Dray, David Forrest, Patrick Giraudoux, Duncan
Golicher, Virgilio Gómez Rubio, Patrick Hausmann, Thomas
Jagger, Sebastian P. Luque, Don MacQueen, Andrew Niccolai and
Tom Short
Title: Tools for reading and handling spatial objects
Description: Set of tools for manipulating and reading geographic data,
in particular ESRI shapefiles; C code used from shapelib. It
includes binary access to GSHHS shoreline files. The package
also provides interface wrappers for exchanging spatial objects
with packages such as PBSmapping, spatstat, maps, RArcInfo,
Stata tmap, WinBUGS, Mondrian, and others.
Diff between maptools versions 0.7-22 dated 2009-04-14 and 0.7-23 dated 2009-05-27
ChangeLog | 6 ++++++ DESCRIPTION | 8 ++++---- R/sp_spat1.R | 4 ++++ R/spatstat1.R | 40 +++++++++++++++++++++++++++++++++++++++- inst/ChangeLog | 6 ++++++ man/as.ppp.Rd | 20 ++++++++++++++++---- 6 files changed, 75 insertions(+), 9 deletions(-)
Author: Giovanni Petris
Diff between dlm versions 1.0-0 dated 2009-04-15 and 1.0-1 dated 2009-05-27
Title: Bayesian and Likelihood Analysis of Dynamic Linear Models
Description: Maximum likelihood, Kalman filtering and smoothing, and
Bayesian analysis of Normal linear State Space models, also
known as Dynamic Linear Models
CITATION |only
DESCRIPTION | 8 ++++----
R/arms.R | 4 ++--
inst/doc/dlm.pdf |binary
man/rwishart.Rd | 2 +-
5 files changed, 7 insertions(+), 7 deletions(-)
Author: Rasmus E. Benestad
Diff between clim.pact versions 2.2-34 dated 2009-04-17 and 2.2-35 dated 2009-05-27
Title: Climate analysis and empirical-statistical downscaling (ESD)
package for monthly and daily data.
Description: The package contains R functions for retrieving data,
making climate analysis and downscaling of monthly mean and
daily mean global climate scenarios. (Windows-users may need to
obtain the 'ncdf' package from URL
'http://www.stats.ox.ac.uk/pub/RWin/' to get clim.pact to
work). The package is also described in the book
'Empirical-Statistical Downscaling
(http://www.worldscibooks.com/environsci/6908.html)
DESCRIPTION | 8 ++++----
R/ds.R | 2 +-
R/eof.R | 6 +++---
R/getnordklim.R | 2 +-
R/retrieve.nc.R | 24 ++++++++++++------------
5 files changed, 21 insertions(+), 21 deletions(-)
Author: Sundar Dorai-Raj
Diff between binom versions 1.0-4 dated 2008-10-05 and 1.0-5 dated 2009-05-27
Title: Binomial Confidence Intervals For Several Parameterizations
Description: Constructs confidence intervals on the probability of
success in a binomial experiment via several parameterizations
DESCRIPTION | 24 ++++++++++++++----------
man/binom.optim.Rd | 2 --
2 files changed, 14 insertions(+), 12 deletions(-)
Author: Miguel A. R. Manese
Title: Stores data frames & matrices in SQLite tables
Description: Transparently stores data frames & matrices into SQLite
tables.
Diff between SQLiteDF versions 0.1.32 dated 2009-02-17 and 0.1.34 dated 2009-05-27
SQLiteDF-0.1.32/SQLiteDF/src/sqliteInt.h |only SQLiteDF-0.1.34/SQLiteDF/.gitignore |only SQLiteDF-0.1.34/SQLiteDF/ChangeLog | 8 + SQLiteDF-0.1.34/SQLiteDF/DESCRIPTION | 15 +-- SQLiteDF-0.1.34/SQLiteDF/NAMESPACE | 10 -- SQLiteDF-0.1.34/SQLiteDF/R/All.R | 32 +++--- SQLiteDF-0.1.34/SQLiteDF/src/sqlite_dataframe.c | 115 +++++++++++++++++++----- SQLiteDF-0.1.34/SQLiteDF/src/sqlite_dataframe.h | 17 +++ SQLiteDF-0.1.34/SQLiteDF/src/sqlite_vector.c | 39 ++++---- SQLiteDF-0.1.34/SQLiteDF/src/sqlite_workspace.c | 5 - SQLiteDF-0.1.34/SQLiteDF/src/utils.c | 25 +++-- SQLiteDF-0.1.34/SQLiteDF/tests/tests.R | 11 ++ 12 files changed, 197 insertions(+), 80 deletions(-)
Author: Markus Loecher
Diff between ReadImages versions 0.1.1 dated 2009-05-19 and 0.1.2 dated 2009-05-27
Title: Image Reading Module for R
Description: This package provides functions for reading JPEG and PNG
files. This package requires libjpeg
ReadImages-0.1.1/ReadImages/R/.AppleDouble |only
ReadImages-0.1.1/ReadImages/src/jpeglib.h |only
ReadImages-0.1.2/ReadImages/DESCRIPTION | 6 +++---
ReadImages-0.1.2/ReadImages/configure.win |only
ReadImages-0.1.2/ReadImages/man/ReadImages-package.Rd | 2 +-
ReadImages-0.1.2/ReadImages/man/plot.imagematrix.Rd | 3 ++-
ReadImages-0.1.2/ReadImages/man/print.imagematrix.Rd | 3 ++-
ReadImages-0.1.2/ReadImages/src/Makevars.win |only
8 files changed, 8 insertions(+), 6 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 1.0-3 dated 2009-04-22 and 1.0-4 dated 2009-05-27
DESCRIPTION | 8 ++++---- NAMESPACE | 3 ++- R/HP1.shape.R | 2 ++ R/HR.Mest.R | 4 +++- R/duembgen.shape.R | 2 +- R/duembgen.shape.wt.R |only R/hl.loc.R |only R/ind.ictest.R | 41 ++++++++++++++++++++++++++++------------- R/spatial.sign.R | 1 + R/symm.huber.R |only R/symm.huber.wt.R |only R/tyler.shape.R | 2 ++ R/vdw.loc.R |only inst/CHANGES | 6 ++++++ man/ICSNP-package.Rd | 4 ++-- man/duembgen.shape.Rd | 4 ++-- man/duembgen.shape.wt.Rd |only man/hl.loc.Rd |only man/ind.ictest.Rd | 8 ++++---- man/symm.huber.Rd |only man/symm.huber.wt.Rd |only man/vdw.loc.Rd |only 22 files changed, 57 insertions(+), 28 deletions(-)
Author: Ulrike Groemping
Title: Full factorials, orthogonal arrays and base utilities for DoE
packages
Description: This package creates full factorial experiments and
experiments based on orthogonal arrays for (industrial)
experiments. Additionally, it provides some utility functions
used also by other DoE packages.
Diff between DoE.base versions 0.1 dated 2009-05-25 and 0.2 dated 2009-05-27
DESCRIPTION | 8 ++++---- R/export.design.R | 27 ++++++++++++++++++++++----- R/html.data.frame.R | 3 ++- inst |only man/export.design.Rd | 12 ++++++++++-- man/oa.design.Rd | 4 +--- man/utitlities.Rd | 9 +++++++++ 7 files changed, 48 insertions(+), 15 deletions(-)
Author: Ramon Diaz-Uriarte
Diff between ADaCGH versions 1.3-10 dated 2009-01-11 and 1.3-13 dated 2009-05-27
Title: Analysis of data from aCGH experiments
Description: Analysis and plotting of array CGH data. Allows usage of
Circular Binary Segementation, wavelet-based smoothing (both as
in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), , ACE
method (CGH Explorer), HMM, BioHMM, GLAD, CGHseg, and Price's
modification of Smith & Waterman's algorith. Most computations
are parallelized. Figures are imagemaps with links to IDClight
(http://idclight.bioinfo.cnio.es).
Changes | 17 +
DESCRIPTION | 34 +-
NAMESPACE | 8
R/ADaCGH.R | 774 ++++++++++++++++++++++++++++++++++++------------
R/HaarSeg.R |only
man/SegmentPlotWrite.Rd | 43 ++
man/mpiInit.Rd | 3
man/pSegment.Rd | 125 ++++++-
man/segmentPlot.Rd | 134 --------
man/tempdir2.Rd |only
src/HaarSeg.h |only
src/r_haarseg.c |only
12 files changed, 792 insertions(+), 346 deletions(-)