Title: SNP-set (Sequence) Kernel Association Test
Diff between SKAT versions 0.76 dated 2012-06-27 and 0.77 dated 2012-07-24
Description: Kernel based SNP set test
Author: Seunggeun Lee, Larisa Miropolsky and Micheal Wu
Maintainer: Seunggeun (Shawn) Lee
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
Diff between gstat versions 1.0-12 dated 2012-06-22 and 1.0-13 dated 2012-07-24
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
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
Diff between plgp versions 1.1-4 dated 2012-01-21 and 1.1-5 dated 2012-07-24
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
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
Diff between coda versions 0.15-1 dated 2012-07-18 and 0.15-2 dated 2012-07-24
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
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
Diff between BRugs versions 0.7-5 dated 2012-01-06 and 0.8-0 dated 2012-07-24
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
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
Diff between doRNG versions 1.4.1 dated 2012-05-25 and 1.4.5 dated 2012-07-24
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
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
Diff between lcmm versions 1.5.6 dated 2012-07-16 and 1.5.7 dated 2012-07-24
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:
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
Diff between relSim versions 0.1-34 dated 2012-03-14 and 0.1-47 dated 2012-07-24
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
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
Diff between RcppClassic versions 0.9.1 dated 2011-04-07 and 0.9.2 dated 2012-07-24
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
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
Diff between pkgmaker versions 0.6.5 dated 2012-06-20 and 0.8 dated 2012-07-24
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
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
Diff between desire versions 1.0.5 dated 2009-09-22 and 1.0.6 dated 2012-07-24
Description: Harrington and Derringer-Suich type desirability functions
Author: Heike Trautmann
Maintainer: Olaf Mersmann
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(-)