Title: Computational routines for proton and ion radiotherapy
Diff between libamtrack versions 0.5.2 dated 2011-12-22 and 0.5.3 dated 2012-04-27
Description: This package is the R interface to the open-source, ANSI C
library libamtrack (http://libamtrack.dkfz.org). libamtrack
provides computational routines for the prediction of detector
response and radiobiological efficiency in heavy charged
particle beams. It is designed for research in proton and ion
dosimetry and radiotherapy. libamtrack also provides many
auxiliary physics routines for proton and ion beams. Original
package and C-to-R autoconversion routines developed by Felix
A. Klein.
Author: Steffen Greilich and the libamtrack team
Maintainer: Steffen Greilich
DESCRIPTION | 18 -
MD5 | 167 +++++----
NAMESPACE | 10
R/hardcoded_wrapper.R | 31 -
R/initial.R | 2
R/libamtrack.R | 281 +++++++++++++++
configure | 121 ++++--
man/AT.A.from.particle.no.Rd | 2
man/AT.CSDA.energy.after.slab.E.MeV.u.Rd | 2
man/AT.CSDA.range.Bethe.g.cm2.Rd | 2
man/AT.CSDA.range.g.cm2.Rd | 2
man/AT.CSDA.range.m.Rd | 2
man/AT.D.RDD.Gy.Rd | 2
man/AT.E.MeV.u.from.momentum.MeV.c.u.Rd | 2
man/AT.E.from.beta.Rd | 2
man/AT.Highland.angle.Rd |only
man/AT.I.eV.from.composition.Rd | 2
man/AT.I.eV.from.element.acronym.Rd | 2
man/AT.Moliere.function.f0.Rd |only
man/AT.Moliere.function.f1.Rd |only
man/AT.Moliere.function.f2.Rd |only
man/AT.Rutherford.SDCS.Rd | 2
man/AT.Stopping.Power.Mass.Bethe.MeV.cm2.g.Rd | 2
man/AT.Stopping.Power.MeV.cm2.g.Rd | 2
man/AT.Stopping.Power.keV.um.Rd | 2
man/AT.WEPL.Bethe.Rd | 2
man/AT.Z.from.element.acronym.Rd | 2
man/AT.Z.from.particle.no.Rd | 2
man/AT.atomic.weight.from.Z.Rd | 2
man/AT.atomic.weight.from.element.acronym.Rd | 6
man/AT.average.A.from.composition.Rd | 2
man/AT.average.Z.from.composition.Rd | 2
man/AT.beam.par.physical.to.technical.Rd | 2
man/AT.beam.par.technical.to.physical.Rd | 2
man/AT.beta.from.E.Rd | 2
man/AT.characteristic.single.scattering.angle.Rd |only
man/AT.characteristicple.scattering.angle.Rd |only
man/AT.density.g.cm3.from.element.acronym.Rd | 2
man/AT.dose.Gy.from.fluence.cm2.Rd | 2
man/AT.dose.weighted.E.MeV.u.Rd | 2
man/AT.dose.weighted.LET.MeV.cm2.g.Rd | 2
man/AT.effective.Z.from.composition.Rd | 2
man/AT.effective.charge.from.E.MeV.u.Rd | 2
man/AT.effective.collision.number.Rd |only
man/AT.electron.density.m3.Rd | 2
man/AT.electron.density.m3.from.composition.Rd | 2
man/AT.electron.density.m3.from.material.no.Rd | 2
man/AT.element.acronym.from.Z.Rd | 2
man/AT.energy.straggling.MeV2.cm2.g.Rd | 2
man/AT.energy.straggling.after.slab.E.MeV.u.Rd | 2
man/AT.fluence.cm2.from.dose.Gy.Rd | 2
man/AT.fluence.weighted.E.MeV.u.Rd | 2
man/AT.fluence.weighted.LET.MeV.cm2.g.Rd | 2
man/AT.gamma.from.E.Rd | 2
man/AT.get.materials.data.Rd | 2
man/AT.material.name.from.material.no.Rd | 2
man/AT.max.E.transfer.MeV.Rd | 2
man/AT.max.electron.ranges.m.Rd | 2
man/AT.mean.number.of.tracks.contrib.Rd | 2
man/AT.momentum.MeV.c.u.from.E.MeV.u.Rd | 2
man/AT.nuclear.spin.from.particle.no.Rd | 2
man/AT.particle.no.from.Z.and.A.Rd | 2
man/AT.r.RDD.m.Rd | 2
man/AT.reduced.target.thickness.Rd |only
man/AT.run.CPPSC.method.Rd | 2
man/AT.run.GSM.method.Rd | 2
man/AT.run.IGK.method.Rd | 2
man/AT.scattering.angle.distribution.Rd |only
man/AT.screening.angle.Rd |only
man/AT.set.user.material.Rd | 2
man/AT.set.user.material.from.composition.Rd | 2
man/AT.stopping.power.ratio.Rd | 2
man/AT.total.D.Gy.Rd | 2
man/AT.total.fluence.cm2.Rd | 2
man/libamtrack-package.Rd | 4
src/AT.h | 6
src/AT_Constants.h | 12
src/AT_DataParticle.c | 7
src/AT_DataParticle.h | 42 +-
src/AT_KatzModel.c | 16
src/AT_KatzModel.h | 4
src/AT_MultipleCoulombScattering.c |only
src/AT_MultipleCoulombScattering.h |only
src/AT_PhysicsRoutines.c | 2
src/AT_R_Wrapper.c | 410 ++++++++++++++++++++++-
src/AT_R_Wrapper.h | 87 ++++
src/AT_SPC.c | 255 ++++++++++++++
src/AT_SPC.h | 58 +++
src/config.h |only
src/hardcoded_wrapper.c | 54 +--
src/hardcoded_wrapper.h | 13
91 files changed, 1430 insertions(+), 288 deletions(-)
Title: Mixed Effects Cox Models.
Diff between coxme versions 2.2-1 dated 2011-12-31 and 2.2-2 dated 2012-04-27
Description: Cox proportional hazards models containing Gaussian random
effects, also known as frailty models.
Author: Terry Therneau
Maintainer: Terry Therneau
DESCRIPTION | 12 +-
MD5 | 85 +++++++++----------
R/coxme.R | 18 ++--
R/coxme.control.R | 6 -
R/coxme.fit.R | 210 ++++++++++++++++++++++++++----------------------
R/lmekin.R | 65 ++++++++------
inst/NEWS.Rd | 18 ++++
inst/doc/coxme.pdf |binary
inst/doc/laplace.Rnw | 13 +-
inst/doc/laplace.pdf |binary
inst/doc/lmekin.Rnw | 74 ++++++++++++++++
inst/doc/lmekin.pdf |binary
inst/doc/variance.pdf |binary
man/coxme.control.Rd | 5 -
noweb/all.nw | 191 +++++++++++++++++++++++++------------------
noweb/build.Rnw | 26 +++--
noweb/fit.Rnw | 132 +++++++++++++++++-------------
noweb/lmekin.Rnw | 12 +-
noweb/main.Rnw | 21 ++--
tests/bdstest.Rout.save | 18 +---
tests/lmekin1.Rout.save | 18 +---
tests/nest1.Rout.save | 18 +---
tests/nest2.Rout.save | 18 +---
tests/refine.R | 3
tests/refine.Rout.save | 21 +---
tests/refine1.Rout.save | 18 +---
tests/refine2.R | 4
tests/refine2.Rout.save | 24 ++---
tests/refine3.Rout.save | 18 +---
tests/shrink.Rout.save | 18 +---
tests/slope1.Rout.save | 18 +---
tests/slope2.Rout.save | 18 +---
tests/slope3.Rout.save | 18 +---
tests/slope4.Rout.save | 18 +---
tests/strata1.Rout.save | 18 +---
tests/test0.Rout.save | 18 +---
tests/test1.Rout.save | 18 +---
tests/test2.Rout.save | 18 +---
tests/test3.Rout.save | 18 +---
tests/test4.Rout.save | 18 +---
tests/twoterm.Rout.save | 20 +---
vignettes/gaw.rda |only
vignettes/laplace.Rnw | 13 +-
vignettes/lmekin.Rnw | 74 ++++++++++++++++
44 files changed, 759 insertions(+), 594 deletions(-)
Title: Bayesian Model Averaging
Diff between BMA versions 3.15 dated 2012-02-11 and 3.15.1 dated 2012-04-27
Description: Package for Bayesian model averaging for linear models,
generalizable linear models and survival models (cox
regression).
Author: Adrian Raftery
Maintainer: Chris Fraley (interim)
CHANGELOG | 2 ++
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/bicreg.R | 8 ++++----
man/summary.iBMA.Rd | 3 ---
5 files changed, 14 insertions(+), 15 deletions(-)
Title: Basic statistical functions for package ff
Diff between ffbase versions 0.2-1 dated 2011-07-25 and 0.4 dated 2012-04-27
Description: Basic (statistical) functionality for package ff
Author: Edwin de Jonge, Jan Wijffels
Maintainer: Edwin de Jonge
ffbase-0.2-1/ffbase/man/mean.ffdf.Rd |only
ffbase-0.4/ffbase/DESCRIPTION | 19 +++--
ffbase-0.4/ffbase/MD5 |only
ffbase-0.4/ffbase/NAMESPACE | 52 +++++++++++-----
ffbase-0.4/ffbase/NEWS | 11 +++
ffbase-0.4/ffbase/R/Summary_ff.R | 3
ffbase-0.4/ffbase/R/auxilary.R | 27 +++++++-
ffbase-0.4/ffbase/R/chunkify.R | 23 ++++++-
ffbase-0.4/ffbase/R/compact.R | 1
ffbase-0.4/ffbase/R/cumsum.R |only
ffbase-0.4/ffbase/R/cut_ff.R | 2
ffbase-0.4/ffbase/R/diff_ff.R | 2
ffbase-0.4/ffbase/R/ffappend.R | 35 ++++++----
ffbase-0.4/ffbase/R/ffdfdply.R |only
ffbase-0.4/ffbase/R/ffdfsave.R | 35 ++++++++--
ffbase-0.4/ffbase/R/ffdfwith.R |only
ffbase-0.4/ffbase/R/ffordered.R |only
ffbase-0.4/ffbase/R/ffwhich.R |only
ffbase-0.4/ffbase/R/hist_ff.R |only
ffbase-0.4/ffbase/R/laf_to_ffdf.R |only
ffbase-0.4/ffbase/R/mean.R | 17 -----
ffbase-0.4/ffbase/R/merge.R |only
ffbase-0.4/ffbase/R/pkg.R | 53 ++++++++++++----
ffbase-0.4/ffbase/R/quantile_ff.R |only
ffbase-0.4/ffbase/R/risplit.R | 15 ++--
ffbase-0.4/ffbase/R/subset.R | 4 -
ffbase-0.4/ffbase/R/tabulate_ff.R | 2
ffbase-0.4/ffbase/R/transform.R | 2
ffbase-0.4/ffbase/R/unique.R | 10 ++-
ffbase-0.4/ffbase/R/with.R | 39 +++++++++---
ffbase-0.4/ffbase/R/zzz.R |only
ffbase-0.4/ffbase/inst/tests/testSummary.R | 2
ffbase-0.4/ffbase/inst/tests/testchunkify.R | 2
ffbase-0.4/ffbase/inst/tests/testcut_ff.R | 2
ffbase-0.4/ffbase/inst/tests/testdroplevels.R | 2
ffbase-0.4/ffbase/inst/tests/testffappend.R | 2
ffbase-0.4/ffbase/inst/tests/testmean.ff.R | 1
ffbase-0.4/ffbase/inst/tests/testmin.ff.R | 2
ffbase-0.4/ffbase/inst/tests/testrange_ff.R | 2
ffbase-0.4/ffbase/inst/tests/testsubset.R | 2
ffbase-0.4/ffbase/inst/tests/testsum_ff.R | 2
ffbase-0.4/ffbase/inst/tests/testtable_ff.R | 18 +++--
ffbase-0.4/ffbase/inst/tests/testtabulate_ff.R | 2
ffbase-0.4/ffbase/inst/tests/testtransform.R | 2
ffbase-0.4/ffbase/inst/tests/testwith.R | 42 ++++++++++++-
ffbase-0.4/ffbase/inst/tests/testwithin.R | 8 +-
ffbase-0.4/ffbase/man/all.ff.Rd | 27 +++++---
ffbase-0.4/ffbase/man/any.ff.Rd | 27 +++++---
ffbase-0.4/ffbase/man/c.ff.Rd | 20 ++++--
ffbase-0.4/ffbase/man/chunkexpr.Rd |only
ffbase-0.4/ffbase/man/chunkify.Rd | 24 +++++--
ffbase-0.4/ffbase/man/compact.Rd | 29 +++++----
ffbase-0.4/ffbase/man/cumsum.ff.Rd |only
ffbase-0.4/ffbase/man/cut.ff.Rd | 35 ++++++++--
ffbase-0.4/ffbase/man/droplevels.ff.Rd | 33 +++++++---
ffbase-0.4/ffbase/man/droplevels.ffdf.Rd | 36 ++++++++---
ffbase-0.4/ffbase/man/ffappend.Rd | 31 ++++++---
ffbase-0.4/ffbase/man/ffbase-package.Rd | 80 +++++++++++++++++++------
ffbase-0.4/ffbase/man/ffdfappend.Rd | 38 ++++++++---
ffbase-0.4/ffbase/man/ffdfdply.Rd |only
ffbase-0.4/ffbase/man/ffdfsave.Rd |only
ffbase-0.4/ffbase/man/ffdfwith.Rd |only
ffbase-0.4/ffbase/man/ffordered.Rd |only
ffbase-0.4/ffbase/man/ffwhich.Rd |only
ffbase-0.4/ffbase/man/grouprunningcumsum.Rd |only
ffbase-0.4/ffbase/man/hist.ff.Rd |only
ffbase-0.4/ffbase/man/laf_to_ffdf.Rd |only
ffbase-0.4/ffbase/man/mean.ff.Rd | 33 +++++++---
ffbase-0.4/ffbase/man/merge.ffdf.Rd |only
ffbase-0.4/ffbase/man/min.ff.Rd | 44 ++++++++-----
ffbase-0.4/ffbase/man/quantile.ff.Rd |only
ffbase-0.4/ffbase/man/risplit.Rd |only
ffbase-0.4/ffbase/man/subset.ff.Rd | 28 +++++---
ffbase-0.4/ffbase/man/sum.ff.Rd | 26 +++++---
ffbase-0.4/ffbase/man/table.ff.Rd | 38 +++++++----
ffbase-0.4/ffbase/man/tabulate.ff.Rd | 30 ++++++---
ffbase-0.4/ffbase/man/transform.ffdf.Rd | 36 +++++++----
ffbase-0.4/ffbase/man/unique.ff.Rd | 33 +++++++---
ffbase-0.4/ffbase/man/with.ffdf.Rd | 43 +++++++++----
ffbase-0.4/ffbase/man/within.ffdf.Rd | 36 +++++++----
ffbase-0.4/ffbase/src |only
ffbase-0.4/ffbase/tests/test_all.R | 12 +--
82 files changed, 849 insertions(+), 333 deletions(-)
Title: Multivariate Adaptive Regression Spline Models
Diff between earth versions 3.2-2 dated 2012-03-14 and 3.2-3 dated 2012-04-27
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines". (The term "MARS" is copyrighted and thus not used in
the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and
Rob Tibshirani.
Maintainer: Stephen Milborrow
earth-3.2-2/earth/src/tests/Rblas.lib |only
earth-3.2-2/earth/src/tests/Rdll.lib |only
earth-3.2-3/earth/.Rinstignore |only
earth-3.2-3/earth/DESCRIPTION | 6
earth-3.2-3/earth/MD5 | 82 ++----
earth-3.2-3/earth/NEWS | 8
earth-3.2-3/earth/R/earth.R | 4
earth-3.2-3/earth/R/mars.to.earth.R | 1
earth-3.2-3/earth/R/predict.earth.R | 6
earth-3.2-3/earth/inst/doc/earth-notes.Rnw | 30 +-
earth-3.2-3/earth/inst/doc/earth-notes.bib | 2
earth-3.2-3/earth/inst/doc/earth-notes.pdf |binary
earth-3.2-3/earth/inst/doc/figs/cube-transform.pdf |binary
earth-3.2-3/earth/inst/doc/figs/cv-detailed.pdf |binary
earth-3.2-3/earth/inst/doc/figs/cv-example.pdf |binary
earth-3.2-3/earth/inst/doc/figs/cv-plot-earth.pdf |binary
earth-3.2-3/earth/inst/doc/figs/cv-variation.pdf |binary
earth-3.2-3/earth/inst/doc/figs/cv.pdf |binary
earth-3.2-3/earth/inst/doc/figs/fda-earth.pdf |binary
earth-3.2-3/earth/inst/doc/figs/fda-lm.pdf |binary
earth-3.2-3/earth/inst/doc/figs/fda-plotmo.pdf |binary
earth-3.2-3/earth/inst/doc/figs/fda.pdf |binary
earth-3.2-3/earth/inst/doc/figs/learning-curve.pdf |binary
earth-3.2-3/earth/inst/doc/figs/ncross.pdf |binary
earth-3.2-3/earth/inst/doc/figs/negative-grsq.pdf |binary
earth-3.2-3/earth/inst/doc/figs/plot-earth.pdf |binary
earth-3.2-3/earth/inst/doc/figs/trees.pdf |binary
earth-3.2-3/earth/man/format.earth.Rd | 6
earth-3.2-3/earth/src/earth.c | 9
earth-3.2-3/earth/src/tests/earth.times.bat | 2
earth-3.2-3/earth/src/tests/fast.postscript.R | 2
earth-3.2-3/earth/src/tests/test.earth.big.bat | 2
earth-3.2-3/earth/src/tests/test.earth.cv.bat | 2
earth-3.2-3/earth/src/tests/test.earth.full.R | 10
earth-3.2-3/earth/src/tests/test.earth.full.Rout.save | 232 +++++++----------
earth-3.2-3/earth/src/tests/test.earth.full.bat | 2
earth-3.2-3/earth/src/tests/test.earth.glm.bat | 2
earth-3.2-3/earth/src/tests/test.earthc.bat | 14 -
earth-3.2-3/earth/src/tests/test.earthc.out.save | 10
earth-3.2-3/earth/src/tests/test.earthmain.bat | 12
earth-3.2-3/earth/src/tests/test.earthmain.gcc.bat | 12
earth-3.2-3/earth/src/tests/test.plotd.bat | 2
earth-3.2-3/earth/tests/test.earth.R | 32 +-
earth-3.2-3/earth/tests/test.earth.Rout.save | 244 +++++++-----------
44 files changed, 340 insertions(+), 394 deletions(-)
Title: Simple Parallel R INTerface
Diff between sprint versions 1.0.1 dated 2012-04-19 and 1.0.2 dated 2012-04-27
Description: SPRINT (Simple Parallel R INTerface) is a parallel
framework for R. It provides a High Performance Computing (HPC)
harness which allow R scripts to run on HPC clusters. SPRINT
contains a library of selected R functions that have been
parallelized. Functions are named after the original R function
with the added prefix 'p', i.e. the parallel version of cor()
in SPRINT is called pcor(). Call to the parallel R functions
are included directly in standard R scripts.
Author: University of Edinburgh SPRINT Team
Maintainer: University of Edinburgh SPRINT Team
sprint-1.0.1/sprint/inst |only
sprint-1.0.1/sprint/test_suite |only
sprint-1.0.2/sprint/DESCRIPTION | 6 -
sprint-1.0.2/sprint/MD5 | 28 +-------
sprint-1.0.2/sprint/NEWS | 5 +
sprint-1.0.2/sprint/src/algorithms/ppam/implementation/cstat.c | 3
sprint-1.0.2/sprint/src/algorithms/ppam/implementation/pamedoids.c | 34 +++++-----
7 files changed, 30 insertions(+), 46 deletions(-)
Title: R functions for Generalized Simulated Annealing
Diff between GenSA versions 1.0.2 dated 2011-12-22 and 1.0.3 dated 2012-04-27
Description: This package searches for global minimum of a very complex
non-linear objective function with a very large number of
optima.
Author: Sylvain Gubian, Yang Xiang, Brian Suomela, Julia Hoeng, PMP SA.
Maintainer: Sylvain Gubian
DESCRIPTION | 12 +++++++-----
MD5 | 16 ++++++++--------
NEWS | 4 ++++
R/GenSA.R | 3 +++
inst/CITATION | 4 ++--
man/GenSA-package.Rd | 4 ++--
man/GenSA.Rd | 3 +--
src/Engine.cpp | 17 ++++++++++-------
src/Engine.h | 1 -
9 files changed, 37 insertions(+), 27 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-11-20 1.0.5
2011-09-07 1.0.4
2011-08-04 1.0.3
2011-07-24 1.0.2
2011-06-15 1.0.0
More information about weightedKmeans at CRAN
Permanent link
Title: R binding for cppbugs
Diff between rcppbugs versions 0.0.2 dated 2012-04-23 and 0.0.8 dated 2012-04-27
Description: R binding for cppbugs
Author: Whit Armstrong
Maintainer: Whit Armstrong
DESCRIPTION | 9 +++++----
MD5 | 16 +++++++++-------
src/Makevars.win |only
src/cppbugs/cppbugs/mcmc.jump.hpp | 2 +-
src/cppbugs/cppbugs/mcmc.math.hpp | 4 ----
src/cppbugs/cppbugs/mcmc.object.hpp | 2 +-
src/cppbugs/cppbugs/mcmc.rng.base.hpp |only
src/cppbugs/cppbugs/mcmc.rng.hpp | 10 +---------
src/interface.cpp | 6 +-----
src/mcmc.rng.h | 2 +-
10 files changed, 19 insertions(+), 32 deletions(-)
Title: Utilities and kinship information for Behavior Genetics and
Developmental research using the NLSY.
Diff between NlsyLinks versions 0.19 dated 2012-03-10 and 1.0 dated 2012-04-27
Description: Utilities and kinship information for Behavioral Genetics
and Developmental research using the NLSY.
Author: Will Beasley, Joe Rodgers, David Bard, and Kelly Meredith
Maintainer: Will Beasley
NlsyLinks-0.19/NlsyLinks/inst/tests/DFFixture.R |only
NlsyLinks-0.19/NlsyLinks/inst/tests/UtilitiesFixture.R |only
NlsyLinks-1.0/NlsyLinks/DESCRIPTION | 14 +
NlsyLinks-1.0/NlsyLinks/MD5 | 82 +++++++----
NlsyLinks-1.0/NlsyLinks/NAMESPACE | 7
NlsyLinks-1.0/NlsyLinks/NEWS |only
NlsyLinks-1.0/NlsyLinks/R/AceEstimate.R |only
NlsyLinks-1.0/NlsyLinks/R/AceLavaanGroup.R |only
NlsyLinks-1.0/NlsyLinks/R/AceUnivariate.R | 8 -
NlsyLinks-1.0/NlsyLinks/R/CleanSemAceDataset.R |only
NlsyLinks-1.0/NlsyLinks/R/CreateAceEstimate.R |only
NlsyLinks-1.0/NlsyLinks/R/DeFriesFulkerMethod1.R | 14 +
NlsyLinks-1.0/NlsyLinks/R/DeFriesFulkerMethod3.R | 18 +-
NlsyLinks-1.0/NlsyLinks/R/RGroupSummary.R |only
NlsyLinks-1.0/NlsyLinks/R/ReadCsvNlsy79Gen2.R |only
NlsyLinks-1.0/NlsyLinks/R/RenameColumn.R |only
NlsyLinks-1.0/NlsyLinks/R/RenameNlsyColumn.R |only
NlsyLinks-1.0/NlsyLinks/R/ValidatePairLinksAreSymmetric.R | 3
NlsyLinks-1.0/NlsyLinks/R/VerifyColumnExists.R |only
NlsyLinks-1.0/NlsyLinks/data/ExtraOutcomes79.rda |binary
NlsyLinks-1.0/NlsyLinks/data/Links79Pair.rda |binary
NlsyLinks-1.0/NlsyLinks/data/Links79PairExpanded.rda |binary
NlsyLinks-1.0/NlsyLinks/data/SubjectDetails79.rda |only
NlsyLinks-1.0/NlsyLinks/inst/doc/NlsInvestigator.Rnw | 2
NlsyLinks-1.0/NlsyLinks/inst/doc/NlsInvestigator.pdf |binary
NlsyLinks-1.0/NlsyLinks/inst/doc/NlsyAce.Rnw | 2
NlsyLinks-1.0/NlsyLinks/inst/doc/NlsyAce.pdf |binary
NlsyLinks-1.0/NlsyLinks/inst/extdata |only
NlsyLinks-1.0/NlsyLinks/inst/tests/AceDFFixture.R |only
NlsyLinks-1.0/NlsyLinks/inst/tests/AceEstimationFixture.R |only
NlsyLinks-1.0/NlsyLinks/inst/tests/AceLavaanGroupFixture.R |only
NlsyLinks-1.0/NlsyLinks/inst/tests/AcePreparationFixture.R |only
NlsyLinks-1.0/NlsyLinks/inst/tests/AceWrapperExceptions.R | 8 -
NlsyLinks-1.0/NlsyLinks/inst/tests/ColumnUtilitiesFixture.R |only
NlsyLinks-1.0/NlsyLinks/inst/tests/MasterTestRunner.R | 60 +++++---
NlsyLinks-1.0/NlsyLinks/inst/tests/OutcomeDatasetFixture.R | 8 -
NlsyLinks-1.0/NlsyLinks/inst/tests/ReadCsvFixture.R |only
NlsyLinks-1.0/NlsyLinks/man/Ace.Rd | 45 +++---
NlsyLinks-1.0/NlsyLinks/man/AceEstimate-class.Rd |only
NlsyLinks-1.0/NlsyLinks/man/AceLavaanGroup.Rd |only
NlsyLinks-1.0/NlsyLinks/man/CleanSemAceDataset.Rd |only
NlsyLinks-1.0/NlsyLinks/man/ColumnUtilities.Rd |only
NlsyLinks-1.0/NlsyLinks/man/CreateAceEstimate.Rd |only
NlsyLinks-1.0/NlsyLinks/man/CreatePairLinks.Rd | 12 -
NlsyLinks-1.0/NlsyLinks/man/CreateSpatialNeighbours.Rd | 4
NlsyLinks-1.0/NlsyLinks/man/CreateSubjectTag.Rd | 15 +-
NlsyLinks-1.0/NlsyLinks/man/ExtraOutcomes79.Rd | 3
NlsyLinks-1.0/NlsyLinks/man/GetDetails.Rd |only
NlsyLinks-1.0/NlsyLinks/man/GetEstimate.Rd |only
NlsyLinks-1.0/NlsyLinks/man/Links79Pair.Rd | 2
NlsyLinks-1.0/NlsyLinks/man/Links79PairExpanded.Rd | 6
NlsyLinks-1.0/NlsyLinks/man/NlsyLinks-package.Rd | 10 -
NlsyLinks-1.0/NlsyLinks/man/RGroupSummary.Rd |only
NlsyLinks-1.0/NlsyLinks/man/ReadCsvNlsy79Gen2.Rd |only
NlsyLinks-1.0/NlsyLinks/man/SubjectDetails79.Rd |only
NlsyLinks-1.0/NlsyLinks/man/ValidateOutcomeDataset.Rd | 12 -
NlsyLinks-1.0/NlsyLinks/man/ValidatePairLinksAreSymmetric.Rd | 19 +-
57 files changed, 224 insertions(+), 130 deletions(-)
Title: Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness
estimation
Diff between mgcv versions 1.7-13 dated 2012-01-22 and 1.7-14 dated 2012-04-27
Description: Routines for GAMs and other generalized ridge regression
with multiple smoothing parameter selection by GCV, REML or
UBRE/AIC. Also GAMMs. Includes a gam() function.
Author: Simon Wood
Maintainer: Simon Wood
mgcv-1.7-13/mgcv/man/mgcv.Rd |only
mgcv-1.7-13/mgcv/man/mgcv.control.Rd |only
mgcv-1.7-13/mgcv/src/gcv.c |only
mgcv-1.7-13/mgcv/src/gcv.h |only
mgcv-1.7-14/mgcv/DESCRIPTION | 11
mgcv-1.7-14/mgcv/MD5 | 86 -
mgcv-1.7-14/mgcv/NAMESPACE | 2
mgcv-1.7-14/mgcv/R/bam.r | 478 ++++++++--
mgcv-1.7-14/mgcv/R/fast-REML.r |only
mgcv-1.7-14/mgcv/R/gamm.r | 2
mgcv-1.7-14/mgcv/R/mgcv.r | 486 ++++------
mgcv-1.7-14/mgcv/R/plots.r | 81 +
mgcv-1.7-14/mgcv/R/smooth.r | 154 ++-
mgcv-1.7-14/mgcv/R/sparse.r | 13
mgcv-1.7-14/mgcv/changeLog | 55 +
mgcv-1.7-14/mgcv/man/bam.Rd | 39
mgcv-1.7-14/mgcv/man/choose.k.Rd | 30
mgcv-1.7-14/mgcv/man/formula.gam.Rd | 8
mgcv-1.7-14/mgcv/man/gam.Rd | 24
mgcv-1.7-14/mgcv/man/gam.check.Rd | 27
mgcv-1.7-14/mgcv/man/gam.control.Rd | 3
mgcv-1.7-14/mgcv/man/gam.fit3.Rd | 2
mgcv-1.7-14/mgcv/man/gam.outer.Rd | 2
mgcv-1.7-14/mgcv/man/gam.selection.Rd | 4
mgcv-1.7-14/mgcv/man/gam2objective.Rd | 2
mgcv-1.7-14/mgcv/man/magic.Rd | 26
mgcv-1.7-14/mgcv/man/mgcv-FAQ.Rd | 3
mgcv-1.7-14/mgcv/man/mgcv-package.Rd | 5
mgcv-1.7-14/mgcv/man/mono.con.Rd | 2
mgcv-1.7-14/mgcv/man/pcls.Rd | 2
mgcv-1.7-14/mgcv/man/plot.gam.Rd | 10
mgcv-1.7-14/mgcv/man/predict.bam.Rd |only
mgcv-1.7-14/mgcv/man/predict.gam.Rd | 3
mgcv-1.7-14/mgcv/man/qq.gam.Rd | 5
mgcv-1.7-14/mgcv/man/smoothCon.Rd | 6
mgcv-1.7-14/mgcv/man/step.gam.Rd | 6
mgcv-1.7-14/mgcv/man/t2.Rd | 6
mgcv-1.7-14/mgcv/src/gdi.c | 353 -------
mgcv-1.7-14/mgcv/src/init.c | 3
mgcv-1.7-14/mgcv/src/magic.c | 26
mgcv-1.7-14/mgcv/src/matrix.c | 1518 ----------------------------------
mgcv-1.7-14/mgcv/src/matrix.h | 44
mgcv-1.7-14/mgcv/src/mgcv.c | 792 ++---------------
mgcv-1.7-14/mgcv/src/mgcv.h | 12
mgcv-1.7-14/mgcv/src/misc.c | 1
mgcv-1.7-14/mgcv/src/tprs.c | 257 +++--
mgcv-1.7-14/mgcv/src/tprs.h | 2
47 files changed, 1332 insertions(+), 3259 deletions(-)
Title: MetaQC: Objective Quality Control and Inclusion/Exclusion
Criteria for Genomic Meta-Analysis
Diff between MetaQC versions 0.1.9 dated 2012-02-26 and 0.1.10-1 dated 2012-04-27
Description: MetaQC implements our proposed quantitative quality
control measures: (1) internal homogeneity of co-expression
structure among studies (internal quality control; IQC); (2)
external consistency of co-expression structure correlating
with pathway database (external quality control; EQC); (3)
accuracy of differentially expressed gene detection (accuracy
quality control; AQCg) or pathway identification (AQCp); (4)
consistency of differential expression ranking in genes
(consistency quality control; CQCg) or pathways (CQCp). (See
the reference for detailed explanation.) For each quality
control index, the p-values from statistical hypothesis testing
are minus log transformed and PCA biplots were applied to
assist visualization and decision. Results generate systematic
suggestions to exclude problematic studies in microarray
meta-analysis and potentially can be extended to GWAS or other
types of genomic meta-analysis. The identified problematic
studies can be scrutinized to identify technical and biological
causes (e.g. sample size, platform, tissue collection,
preprocessing etc) of their bad quality or irreproducibility
for final inclustion/exclusion decision.
Author: Don Kang
Maintainer: Don Kang
DESCRIPTION | 13 ++++---
MD5 | 22 ++++++-------
R/MetaQC.R | 84 +++++++++++++++++++++++++++++++++-----------------
R/functions.R | 79 +++++++++++++++++++++++++----------------------
R/requireAll.R | 3 +
man/MetaQC-package.Rd | 15 ++++++--
man/MetaQC.Rd | 22 ++++++++-----
man/cleanup.Rd | 7 ----
man/plot.proto.Rd | 6 ---
man/print.proto.Rd | 6 ---
man/requireAll.Rd | 12 -------
man/runQC.Rd | 15 +++++---
12 files changed, 152 insertions(+), 132 deletions(-)
Title: Lasso and elastic-net regularized generalized linear models
Diff between glmnet versions 1.7.3 dated 2012-02-19 and 1.7.4 dated 2012-04-27
Description: Extremely efficient procedures for fitting the entire
lasso or elastic-net regularization path for linear regression,
logistic and multinomial regression models, poisson regression
and the Cox model. The algorithm uses cyclical coordinate
descent in a pathwise fashion, as described in the paper listed
below.
Author: Jerome Friedman, Trevor Hastie, Rob Tibshirani
Maintainer: Trevor Hastie
glmnet-1.7.3/glmnet/inst/doc/.Rhistory |only
glmnet-1.7.3/glmnet/inst/doc/VignetteExample.rdata |only
glmnet-1.7.4/glmnet/ChangeLog | 3 ++
glmnet-1.7.4/glmnet/DESCRIPTION | 10 ++++----
glmnet-1.7.4/glmnet/MD5 | 25 ++++++++++-----------
glmnet-1.7.4/glmnet/R/getcoef.R | 8 +++++-
glmnet-1.7.4/glmnet/R/getcoef.multinomial.R | 2 -
glmnet-1.7.4/glmnet/R/glmnet.R | 5 ++++
glmnet-1.7.4/glmnet/R/jerr.elnet.R | 2 -
glmnet-1.7.4/glmnet/R/predict.glmnet.R | 2 +
glmnet-1.7.4/glmnet/inst/doc/Coxnet.pdf |binary
glmnet-1.7.4/glmnet/inst/doc/Coxnet.rnw | 2 -
glmnet-1.7.4/glmnet/man/cv.glmnet.Rd | 9 ++++++-
glmnet-1.7.4/glmnet/src/newGLMnet.f90 | 5 ++--
glmnet-1.7.4/glmnet/vignettes |only
15 files changed, 48 insertions(+), 25 deletions(-)
Title: Fraction Proliferation via a quiescent growth model
Diff between fracprolif versions 1.0.1 dated 2012-04-24 and 1.0.2 dated 2012-04-27
Description: Functions for fitting data to a quiescent growth model,
i.e. a growth process that involves members of the population
who stop dividing or propagating.
Author: Shawn Garbett, Darren Tyson
Maintainer: Shawn Garbett
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
man/fracprolif-package.Rd | 22 +++++++++++-----------
3 files changed, 17 insertions(+), 17 deletions(-)
Title: Functions for medical statistics book with some demographic data
Diff between fmsb versions 0.3.3 dated 2012-03-15 and 0.3.4 dated 2012-04-27
Description: Several utility functions for the book entitled "Practices
of Medical and Health Data Analysis using R" (Pearson Education
Japan, 2007) with Japanese demographic data and some
demographic analysis related functions.
Author: Minato Nakazawa
Maintainer: Minato Nakazawa
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
NEWS | 4 ++++
R/fmsb.R | 4 +++-
man/radarchart.Rd | 2 +-
5 files changed, 16 insertions(+), 10 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2004-12-10 1.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2004-12-10 1.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-12-13 0.2-7
2009-11-08 0.2-6
2009-01-27 0.2-5
2008-09-09 0.2-4
2008-08-21 0.2-3
2008-07-05 0.2-2
2008-05-08 0.2-1
2007-12-24 0.2-0