Title: SNP-set (Sequence) Kernel Association Test
Description: Kernel based SNP set test
Author: Seunggeun Lee, Larisa Miropolsky and Micheal Wu
Maintainer: Seunggeun (Shawn) Lee
Diff between SKAT versions 0.76 dated 2012-06-27 and 0.77 dated 2012-07-24
DESCRIPTION | 8 +++---- MD5 | 26 +++++++++++------------ R/KMTest_Optimal.R | 46 ++++++++++++++++++++++++++++++++++------- R/KMTest_Optimal_VarMatching.R | 33 ++++++++++++++++++++++++++++- R/Main.R | 3 +- data/SKAT.example.rda |binary data/SKAT.haplotypes.rda |binary inst/doc/SKAT.pdf |binary src/NPsort.cpp | 2 - src/NPsort.h | 4 ++- src/bed_reader.h | 1 src/mwo_reader.h | 2 + src/setid_bim_index.cpp | 1 src/setid_bim_index.h | 1 14 files changed, 99 insertions(+), 28 deletions(-)
Title: spatial and spatio-temporal geostatistical modelling, prediction
and simulation
Description: variogram modelling; simple, ordinary and universal point
or block (co)kriging, sequential Gaussian or indicator
(co)simulation; variogram and variogram map plotting utility
functions.
Author: Edzer Pebesma
Maintainer: Edzer Pebesma
Diff between gstat versions 1.0-12 dated 2012-06-22 and 1.0-13 dated 2012-07-24
DESCRIPTION | 8 ++-- MD5 | 42 +++++++++++------------ data/coalash.rda |binary data/fulmar.rda |binary data/jura.rda |binary data/meuse.all.rda |binary data/meuse.alt.rda |binary data/ncp.grid.rda |binary data/oxford.rda |binary data/pcb.rda |binary data/sic2004.rda |binary data/sic97.rda |binary data/tull.rda |binary data/vv.rda |binary data/walker.rda |binary data/wind.rda |binary demo/lhs.R | 2 - inst/ChangeLog | 86 +++++++++++++++++++++++++++++++++++++++++++++++++ inst/doc/gstat.pdf |binary inst/doc/prs.pdf |binary inst/doc/st.pdf |binary tests/unproj.Rout.save | 20 +++++------ 22 files changed, 122 insertions(+), 36 deletions(-)
Title: Particle Learning of Gaussian Processes
Description: Sequential Monte Carlo inference for fully Bayesian
Gaussian process (GP) regression and classification models by
particle learning (PL). The sequential nature of inference and
the active learning (AL) hooks provided facilitate thrifty
sequential design (by entropy) and optimization (by
improvement) for classification and regression models,
respectively. This package essentially provides a generic PL
interface, and functions (arguments to the interface) which
implement the GP models and AL heuristics. Functions for a
special, linked, regression/classification GP model and an
integrated expected conditional improvement (IECI) statistic is
provides for optimization in the presence of unknown
constraints. Separable and isotropic Gaussian, and
single-index correlation functions are supported. See the
examples section of ?plgp and demo(package="plgp") for an index
of demos
Author: Robert B. Gramacy
Maintainer: Robert B. Gramacy
Diff between plgp versions 1.1-4 dated 2012-01-21 and 1.1-5 dated 2012-07-24
ChangeLog | 6 + DESCRIPTION | 8 +- MD5 | 32 ++++----- NAMESPACE | 2 R/ieci.R | 12 +-- R/plgp.R | 19 ++--- demo/plconstgp_1d_ieci.R | 2 demo/plgp_exp_ei.R | 4 - src/Makevars | 2 src/covar.c | 57 ++++++++++------ src/ieci.c | 139 +++++++++++++++++++++++++++-------------- src/linalg.c | 158 ++++++++++++++++++++++++++--------------------- src/linalg.h | 36 ++++++---- src/matrix.c | 86 +++++++++++++++++++++---- src/matrix.h | 5 + src/rhelp.c | 6 + src/rhelp.h | 7 ++ 17 files changed, 373 insertions(+), 208 deletions(-)
Title: Output analysis and diagnostics for MCMC
Description: Output analysis and diagnostics for Markov Chain Monte
Carlo simulations.
Author: Martyn Plummer [aut, cre, trl], Nicky Best [aut], Kate Cowles
[aut], Karen Vines [aut], Deepayan Sarkar [aut], Russell Almond
[ctb]
Maintainer: Martyn Plummer
Diff between coda versions 0.15-1 dated 2012-07-18 and 0.15-2 dated 2012-07-24
CHANGELOG | 9 ++ DESCRIPTION | 6 - MD5 | 16 ++--- R/output.R | 165 +++++++++++++++++++++++++++++----------------------- R/trellisplots.R | 6 - data/line.rda |binary man/densplot.Rd | 10 ++- man/traceplot.Rd | 8 +- man/trellisplots.Rd | 4 - 9 files changed, 131 insertions(+), 93 deletions(-)
Title: R interface to the OpenBUGS MCMC software
Description: Fully-interactive R interface to the OpenBUGS software for
Bayesian analysis using MCMC sampling. Runs natively and
stably in 32-bit R under Windows. Versions running on Linux
and on 64-bit R under Windows are in "beta" status and less
efficient.
Author: OpenBUGS was developed by Andrew Thomas, Dave Lunn, David
Spiegelhalter and Nicky Best. R interface developed by Uwe
Ligges, Sibylle Sturtz, Andrew Gelman, Gregor Gorjanc and Chris
Jackson. Linux port and most recent developments by Chris
Jackson.
Maintainer: Uwe Ligges
Diff between BRugs versions 0.7-5 dated 2012-01-06 and 0.8-0 dated 2012-07-24
DESCRIPTION | 22 + MD5 | 30 +- NAMESPACE | 2 NEWS | 15 + R/info.modules.R | 2 R/info.node.R | 84 +++---- R/info.updaters.R | 8 R/model.setWD.R | 2 configure | 537 +++++++++++++++++++++++++--------------------- configure.ac | 56 ++-- data/ratsdata.RData |binary data/ratsinits.RData |binary src/Makefile.win | 14 - tests/BRugs.Rout.save | 2 tests/examples.Rout.save | 8 tests/functions.Rout.save | 2 16 files changed, 429 insertions(+), 355 deletions(-)
Title: Generic Reproducible Parallel Backend for foreach Loops
Description: This package provides functions to perform reproducible
parallel foreach loops, using independent random streams as
generated by L'Ecuyer's combined multiple-recursive generator
[L'Ecuyer (1999)]. It enables to easily convert standard
%dopar% loops into fully reproducible loops, independently of
the number of workers, the task scheduling strategy, or the
chosen parallel environment and associated foreach backend.
Author: Renaud Gaujoux
Maintainer: Renaud Gaujoux
Diff between doRNG versions 1.4.1 dated 2012-05-25 and 1.4.5 dated 2012-07-24
doRNG-1.4.1/doRNG/man/write.bib.Rd |only doRNG-1.4.1/doRNG/vignettes/unitTests |only doRNG-1.4.5/doRNG/.Rinstignore |only doRNG-1.4.5/doRNG/DESCRIPTION | 12 + doRNG-1.4.5/doRNG/MD5 | 27 +--- doRNG-1.4.5/doRNG/NAMESPACE | 1 doRNG-1.4.5/doRNG/NEWS | 8 + doRNG-1.4.5/doRNG/R/doRNG-package.R | 141 --------------------- doRNG-1.4.5/doRNG/inst/doc/doRNG-unitTests.Rnw | 36 +---- doRNG-1.4.5/doRNG/inst/doc/doRNG-unitTests.pdf |binary doRNG-1.4.5/doRNG/inst/doc/doRNG.Rnw | 3 doRNG-1.4.5/doRNG/inst/doc/doRNG.pdf |binary doRNG-1.4.5/doRNG/tests |only doRNG-1.4.5/doRNG/vignettes/Makefile | 161 +----------------------- doRNG-1.4.5/doRNG/vignettes/doRNG-unitTests.Rnw | 36 +---- doRNG-1.4.5/doRNG/vignettes/doRNG.Rnw | 3 doRNG-1.4.5/doRNG/vignettes/src/doRNG.Rnw | 59 ++------ 17 files changed, 79 insertions(+), 408 deletions(-)
Title: Estimation of latent class mixed models, joint latent class
mixed models and mixed models for curvilinear outcomes
Description: This package provides functions for the estimation of
various latent class mixed models, joint latent latent class
mixed models and mixed models for curvilinear outcomes using a
maximum likelihood method
Author: Cecile Proust-Lima, Amadou Diakite and Benoit Liquet
Maintainer:
Diff between lcmm versions 1.5.6 dated 2012-07-16 and 1.5.7 dated 2012-07-24
DESCRIPTION | 8 ++++---- MD5 | 20 +++++++++++--------- NEWS | 16 ++++++++++------ R/Jointlcmm.R | 2 +- R/Ordlcmm.R | 10 ++++++---- R/predictY.Jointlcmm.R |only R/predictY.hlme.R |only R/predictY.lcmm.R | 14 +++++++------- man/lcmm-package.Rd | 4 ++-- man/predictY.Rd | 20 ++++++++++---------- src/Jointhet.f90 | 3 +-- src/cvpl.f90 | 3 +++ 12 files changed, 55 insertions(+), 45 deletions(-)
Title: Relative Simulator
Description: A set of tools to explore the behaviour statistics used
for forensic DNA interpretation when close relatives are
involved
Author: James M. Curran
Maintainer: James M. Curran
Diff between relSim versions 0.1-34 dated 2012-03-14 and 0.1-47 dated 2012-07-24
relSim-0.1-34/relSim/.dropbox |only relSim-0.1-47/relSim/DESCRIPTION | 8 - relSim-0.1-47/relSim/MD5 | 28 +++- relSim-0.1-47/relSim/NAMESPACE | 8 + relSim-0.1-47/relSim/R/breedFst.R |only relSim-0.1-47/relSim/R/calcFst.R |only relSim-0.1-47/relSim/R/exclusionPower.R |only relSim-0.1-47/relSim/R/lrMix.R |only relSim-0.1-47/relSim/R/print.population.R |only relSim-0.1-47/relSim/R/readFreqs.R | 160 +++++++++++++++++++++------ relSim-0.1-47/relSim/R/toNexus.R |only relSim-0.1-47/relSim/desktop.ini | 2 relSim-0.1-47/relSim/man/breedFst.Rd |only relSim-0.1-47/relSim/man/calcFst.Rd |only relSim-0.1-47/relSim/man/exclusionPower.Rd |only relSim-0.1-47/relSim/man/lrMix.Rd |only relSim-0.1-47/relSim/man/print.population.Rd |only relSim-0.1-47/relSim/man/randomSibPairs.Rd | 4 relSim-0.1-47/relSim/man/readFreqs.Rd | 37 +++++- relSim-0.1-47/relSim/man/toNexus.Rd |only relSim-0.1-47/relSim/src/breed.cpp |only relSim-0.1-47/relSim/src/calcFst.cpp |only relSim-0.1-47/relSim/src/relSim.cpp | 134 ++++++++++++++++++++++ 23 files changed, 328 insertions(+), 53 deletions(-)
Title: Deprecated 'classic' Rcpp API
Description: The RcppClassic package provides a deprecated C++ library
which facilitates the integration of R and C++. New projects
should use the new Rcpp API in the Rcpp package.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by
David Reiss, and based on code written during 2005 and 2006 by
Dominick Samperi
Maintainer: Dirk Eddelbuettel
Diff between RcppClassic versions 0.9.1 dated 2011-04-07 and 0.9.2 dated 2012-07-24
RcppClassic-0.9.1/RcppClassic/COPYING |only RcppClassic-0.9.1/RcppClassic/inst/doc/Makefile |only RcppClassic-0.9.1/RcppClassic/inst/doc/RcppClassic.Rnw |only RcppClassic-0.9.1/RcppClassic/inst/doc/RcppClassic.pdf |only RcppClassic-0.9.1/RcppClassic/inst/doc/unitTests |only RcppClassic-0.9.1/RcppClassic/inst/doc/unitTests-results |only RcppClassic-0.9.2/RcppClassic/ChangeLog | 21 ++ RcppClassic-0.9.2/RcppClassic/DESCRIPTION | 15 -- RcppClassic-0.9.2/RcppClassic/MD5 |only RcppClassic-0.9.2/RcppClassic/cleanup | 9 - RcppClassic-0.9.2/RcppClassic/inst/doc/RcppClassic-intro.Rnw |only RcppClassic-0.9.2/RcppClassic/inst/doc/RcppClassic-intro.pdf |only RcppClassic-0.9.2/RcppClassic/inst/doc/RcppClassic-unitTests.pdf |binary RcppClassic-0.9.2/RcppClassic/inst/unitTests/runTests.R | 13 - RcppClassic-0.9.2/RcppClassic/inst/unitTests/runit.RcppDate.R | 14 - RcppClassic-0.9.2/RcppClassic/src/Makevars.win | 74 +++++----- RcppClassic-0.9.2/RcppClassic/vignettes |only 17 files changed, 79 insertions(+), 67 deletions(-)
Title: Package development utilities
Description: This package provides some low-level utilities to use for
package development. It currently provides managers for
multiple package specific options and registries, vignette,
unit test and bibtex related utilities. It serves as a base
package for packages like NMF, RcppOctave, doRNG, and as an
incubator package for other general purposes utilities, that
will eventually be packaged separately. It is still under
heavy development and changes in the interface(s) are more than
likely to happen.
Author: Renaud Gaujoux
Maintainer: Renaud Gaujoux
Diff between pkgmaker versions 0.6.5 dated 2012-06-20 and 0.8 dated 2012-07-24
pkgmaker-0.6.5/pkgmaker/README.md |only pkgmaker-0.8/pkgmaker/DESCRIPTION | 12 - pkgmaker-0.8/pkgmaker/MD5 | 44 ++-- pkgmaker-0.8/pkgmaker/NAMESPACE | 11 + pkgmaker-0.8/pkgmaker/R/devutils.R | 232 +++++++++++++++++-------- pkgmaker-0.8/pkgmaker/R/package.R |only pkgmaker-0.8/pkgmaker/R/packages.R |only pkgmaker-0.8/pkgmaker/R/registry.R | 7 pkgmaker-0.8/pkgmaker/R/unitTests.R | 178 ++++++++++++------- pkgmaker-0.8/pkgmaker/R/utils.R | 31 +-- pkgmaker-0.8/pkgmaker/R/vignette.R | 224 +++++++++++++++++------- pkgmaker-0.8/pkgmaker/inst/vignette.mk | 129 +++++++++---- pkgmaker-0.8/pkgmaker/man/R.exec.Rd | 2 pkgmaker-0.8/pkgmaker/man/Rversion.Rd | 2 pkgmaker-0.8/pkgmaker/man/compile_src.Rd | 2 pkgmaker-0.8/pkgmaker/man/devutils.Rd | 49 ++++- pkgmaker-0.8/pkgmaker/man/is_something.Rd | 4 pkgmaker-0.8/pkgmaker/man/latex.Rd | 14 + pkgmaker-0.8/pkgmaker/man/load.Rd |only pkgmaker-0.8/pkgmaker/man/makeUnitVignette.Rd | 15 + pkgmaker-0.8/pkgmaker/man/mirrors.Rd |only pkgmaker-0.8/pkgmaker/man/options.Rd | 2 pkgmaker-0.8/pkgmaker/man/utest.Rd | 14 + pkgmaker-0.8/pkgmaker/man/utestPath.Rd |only pkgmaker-0.8/pkgmaker/man/vignette.Rd | 52 ++++- pkgmaker-0.8/pkgmaker/man/writeUnitVignette.Rd | 11 + 26 files changed, 720 insertions(+), 315 deletions(-)
Title: Desirability functions
Description: Harrington and Derringer-Suich type desirability functions
Author: Heike Trautmann
Maintainer: Olaf Mersmann
Diff between desire versions 1.0.5 dated 2009-09-22 and 1.0.6 dated 2012-07-24
desire-1.0.5/desire/tests |only desire-1.0.6/desire/DESCRIPTION | 6 +++--- desire-1.0.6/desire/MD5 |only desire-1.0.6/desire/man/dsplot.Rd | 1 - 4 files changed, 3 insertions(+), 4 deletions(-)