Title: 3D visualization device system (OpenGL)
Diff between rgl versions 0.92.858 dated 2012-03-20 and 0.92.861 dated 2012-03-26
Description: 3D visualization device (OpenGL)
Author: Daniel Adler
Maintainer: Duncan Murdoch
rgl-0.92.858/rgl/src/AGL |only
rgl-0.92.858/rgl/src/osx/osxgui.o |only
rgl-0.92.858/rgl/src/osx/osxlib.o |only
rgl-0.92.861/rgl/DESCRIPTION | 8 +++---
rgl-0.92.861/rgl/MD5 | 33 ++++++++++++---------------
rgl-0.92.861/rgl/NAMESPACE | 2 -
rgl-0.92.861/rgl/R/enum.R | 2 -
rgl-0.92.861/rgl/R/scene.R | 18 ++++++++++++--
rgl-0.92.861/rgl/R/zzz.R | 1
rgl-0.92.861/rgl/inst/NEWS | 5 +++-
rgl-0.92.861/rgl/man/attributes.Rd | 10 +++++++-
rgl-0.92.861/rgl/src/BBoxDeco.hpp | 2 +
rgl-0.92.861/rgl/src/SceneNode.hpp | 1
rgl-0.92.861/rgl/src/SphereSet.cpp | 25 +++++++++++++-------
rgl-0.92.861/rgl/src/Texture.hpp | 1
rgl-0.92.861/rgl/src/api.cpp | 40 +++++++++++++++++++++++++++++++++
rgl-0.92.861/rgl/src/api.h | 1
rgl-0.92.861/rgl/src/g++.exe.stackdump |only
rgl-0.92.861/rgl/src/win32gui.cpp | 5 +++-
19 files changed, 115 insertions(+), 39 deletions(-)
Title: Package for managing projects with multiple versions derived
from a single source repository.
Diff between makeR versions 1.0.1 dated 2012-03-01 and 1.0.2 dated 2012-03-26
Description: An R package to help manage R projects (e.g. Sweave
reports) where multiple versions are created based upon a
single source repository. For example, a monthly report where
each versions is identitcal with the exception of easily
definable parameters (e.g. date ranges for data extraction,
title, etc.).
Author: Jason Bryer
Maintainer: Jason Bryer
DESCRIPTION | 7
MD5 | 18 -
NAMESPACE | 1
NEWS | 8
R/Project.R | 684 +++++++++++++++++++++++-----------------------
R/buildVersion.R | 3
R/builder.rnw.R | 2
R/builder.rnw.native.R |only
R/builder.tex.R | 4
inst/doc/makeR.pdf |binary
man/builder.rnw.native.Rd |only
11 files changed, 370 insertions(+), 357 deletions(-)
Title: Log-Gaussian Cox Process
Diff between lgcp versions 0.9-2 dated 2012-03-12 and 0.9-3 dated 2012-03-26
Description: Spatial and spatio-temporal modelling of point patterns
using the log-Gaussian Cox process
Author: B. M. Taylor, T. M. Davies, B. S. Rowlingson, P. J. Diggle
Maintainer: Benjamin M. Taylor
lgcp-0.9-2/lgcp/man/computeGradtrunc.Rd |only
lgcp-0.9-2/lgcp/man/diffnorm2.Rd |only
lgcp-0.9-2/lgcp/man/evallogprobY.Rd |only
lgcp-0.9-2/lgcp/man/grad.comp.Rd |only
lgcp-0.9-2/lgcp/man/meanselect.Rd |only
lgcp-0.9-2/lgcp/man/normsq.Rd |only
lgcp-0.9-2/lgcp/man/proposal.means.Rd |only
lgcp-0.9-2/lgcp/man/target.and.grad.Rd |only
lgcp-0.9-3/lgcp/DESCRIPTION | 6
lgcp-0.9-3/lgcp/MD5 | 64 +++----
lgcp-0.9-3/lgcp/NAMESPACE | 1
lgcp-0.9-3/lgcp/R/computeGradtrunc.R | 68 --------
lgcp-0.9-3/lgcp/R/fftgrid.R | 91 +++++------
lgcp-0.9-3/lgcp/R/getCounts.R | 31 +--
lgcp-0.9-3/lgcp/R/gridAverageMethods.R | 38 +---
lgcp-0.9-3/lgcp/R/gridFunctionMethods.R | 25 +--
lgcp-0.9-3/lgcp/R/lgcpInternals.R | 215 --------------------------
lgcp-0.9-3/lgcp/R/lgcpMethods.R | 28 +--
lgcp-0.9-3/lgcp/R/lgcpPredictSpatial.R | 42 ++---
lgcp-0.9-3/lgcp/R/lgcpPredictSpatioTemporal.R | 70 +++-----
lgcp-0.9-3/lgcp/R/lgcpSimSpatioTemporal.R | 4
lgcp-0.9-3/lgcp/R/lgcppars.R | 10 -
lgcp-0.9-3/lgcp/R/selectObsWindow.R | 12 -
lgcp-0.9-3/lgcp/R/spatialOnly.R | 14 +
lgcp-0.9-3/lgcp/R/zzz.R | 2
lgcp-0.9-3/lgcp/inst/doc/lgcp.pdf |binary
lgcp-0.9-3/lgcp/inst/doc/notrot.pdf |binary
lgcp-0.9-3/lgcp/inst/doc/rot.pdf |binary
lgcp-0.9-3/lgcp/man/fftgrid.Rd | 9 -
lgcp-0.9-3/lgcp/man/getCounts.Rd | 9 -
lgcp-0.9-3/lgcp/man/lgcpPredict.Rd | 2
lgcp-0.9-3/lgcp/man/lgcpPredictAggregated.Rd | 2
lgcp-0.9-3/lgcp/man/lgcpPredictSpatial.Rd | 2
lgcp-0.9-3/lgcp/man/lgcpPredictSpatialINLA.Rd | 2
lgcp-0.9-3/lgcp/man/lgcpSimSpatial.Rd | 2
lgcp-0.9-3/lgcp/man/lgcppars.Rd | 3
lgcp-0.9-3/lgcp/tests/gridAverageTest.R | 7
37 files changed, 233 insertions(+), 526 deletions(-)
Title: Joint meta-analysis of diagnostic test sensitivity and
specificity with or without a gold standard reference test
Diff between HSROC versions 1.1.0 dated 2011-10-20 and 2.0.5 dated 2012-03-26
Description: This package implements a model for joint meta-analysis of
sensitivity and specificity of the diagnostic test under
evaluation, while taking into account the possibly imperfect
sensitivity and specificity of the reference test. This
hierarchical model accounts for both within and between study
variability. Estimation is carried out using a Bayesian
approach, implemented via a Gibbs sampler. The model can be
applied in situations where more than one reference test is
used in the selected studies.
Author: Ian Schiller and Nandini Dendukuri
Maintainer:
HSROC-1.1.0/HSROC/HSROC-Ex.R |only
HSROC-1.1.0/HSROC/R/M_H.R |only
HSROC-1.1.0/HSROC/R/M_H2.R |only
HSROC-2.0.5/HSROC/DESCRIPTION | 8
HSROC-2.0.5/HSROC/HSROC.R |only
HSROC-2.0.5/HSROC/MD5 | 31
HSROC-2.0.5/HSROC/NAMESPACE | 1
HSROC-2.0.5/HSROC/NEWS.txt |only
HSROC-2.0.5/HSROC/R/HSROC-internal.R | 143 +-
HSROC-2.0.5/HSROC/R/HSROC.R | 556 +-------
HSROC-2.0.5/HSROC/R/HSROCSummary.R | 2199 +++++++++++---------------------
HSROC-2.0.5/HSROC/R/Initialization.R | 38
HSROC-2.0.5/HSROC/R/M_H2_IND2.R |only
HSROC-2.0.5/HSROC/R/REFSTD_3.R | 2
HSROC-2.0.5/HSROC/R/Restore.R |only
HSROC-2.0.5/HSROC/R/gibbs_sampler_Cpp.R |only
HSROC-2.0.5/HSROC/data/In.house.rda |binary
HSROC-2.0.5/HSROC/data/MRI.rda |binary
HSROC-2.0.5/HSROC/man/HSROC.Rd | 24
HSROC-2.0.5/HSROC/man/simdata.Rd | 2
HSROC-2.0.5/HSROC/src |only
21 files changed, 1075 insertions(+), 1929 deletions(-)
Title: Survival analysis for recurrent event data
Diff between survrec versions 1.1-7 dated 2009-02-06 and 1.2-2 dated 2012-03-26
Description: Estimation of survival function for recurrent event data
using Peña-Strawderman-Hollander, Whang-Chang estimators and
MLE estimation under a Gamma Frailty model.
Author: Juan R González, Edsel A Peña, and Robert L Strawderman
Maintainer: Juan R González
survrec-1.1-7/survrec/data/MMC.R |only
survrec-1.1-7/survrec/data/colon.R |only
survrec-1.1-7/survrec/data/filelist |only
survrec-1.2-2/survrec/DESCRIPTION | 20 +++++++++++---------
survrec-1.2-2/survrec/MD5 |only
survrec-1.2-2/survrec/NAMESPACE |only
survrec-1.2-2/survrec/R/survrec.R | 17 ++++++++++++-----
survrec-1.2-2/survrec/data/MMC.rda |only
survrec-1.2-2/survrec/data/colon.rda |only
survrec-1.2-2/survrec/man/survdiffr.Rd | 10 +++++-----
survrec-1.2-2/survrec/src/bootstrap.f | 14 +++++++-------
survrec-1.2-2/survrec/src/survrec.f | 14 +++++++-------
12 files changed, 42 insertions(+), 33 deletions(-)
Title: Assigning tumor samples to CIT Breast Cancer Molecular Subtypes
from gene expression data
Diff between citbcmst versions 1.0.2 dated 2011-05-24 and 1.0.3 dated 2012-03-26
Description: This package permits to assign tumor gene expression
dataset to one of the 6 CIT Breast Cancer Molecular Subtypes
(Guedj et al. 2011 (submitted))
Author: Laetitia Marisa, Aurelien de Reynies, Mickael Guedj
Maintainer: For any question please contact
citbcmst-1.0.2/citbcmst/inst/doc/Rplots.pdf |only
citbcmst-1.0.3/citbcmst/DESCRIPTION | 9
citbcmst-1.0.3/citbcmst/MD5 |only
citbcmst-1.0.3/citbcmst/NAMESPACE |only
citbcmst-1.0.3/citbcmst/R/cit.bcmst.R | 504 ++++++++---------
citbcmst-1.0.3/citbcmst/R/cit.centroidsFunc.R | 4
citbcmst-1.0.3/citbcmst/data/citbcmst.RData |binary
citbcmst-1.0.3/citbcmst/data/datalist |only
citbcmst-1.0.3/citbcmst/data/exp.norm.bertheau07.RData |binary
citbcmst-1.0.3/citbcmst/data/exp.norm.chanrion08.RData |binary
citbcmst-1.0.3/citbcmst/inst/doc/citbcmstdemo.pdf |binary
11 files changed, 259 insertions(+), 258 deletions(-)
Title: Continuous Optimization using Memetic Algorithms with Local
Search Chains (MA-LS-Chains) in R
Diff between Rmalschains versions 0.1 dated 2012-03-21 and 0.1-2 dated 2012-03-26
Description: This package implements an algorithm family for continuous
optimization called memetic algorithms with local search chains
(MA-LS-Chains). Memetic algorithms are hybridizations of
genetic algorithms with local search methods. They are
especially suited for continuous optimization.
Author: Christoph Bergmeir, Daniel Molina, José M. BenÃtez
Maintainer: Christoph Bergmeir
ChangeLog | 6 ++++--
DESCRIPTION | 8 ++++----
MD5 | 18 +++++++++---------
src/cmaesb.cc | 2 +-
src/jade.cc | 2 +-
src/origcmaes.cc | 4 ++--
src/simplex.cc | 1 +
src/solis.cc | 1 +
src/solisn.cc | 1 +
src/solisn2.cc | 1 +
10 files changed, 25 insertions(+), 19 deletions(-)
Title: Kriging-based Inversion for Deterministic and Noisy Computer
Experiments
Diff between KrigInv versions 1.1 dated 2011-01-03 and 1.2 dated 2012-03-26
Description: Criteria and algorithms for sequentially estimating level
sets of a multivariate numerical function, possibly observed in
tunable noise.
Author: Clement Chevalier, Victor Picheny and David Ginsbourger
Maintainer: Clement Chevalier
KrigInv-1.1/KrigInv/R/real_ind_fundet.R |only
KrigInv-1.1/KrigInv/R/update.km.R |only
KrigInv-1.1/KrigInv/man/real_ind_fundet.Rd |only
KrigInv-1.2/KrigInv/DESCRIPTION | 15
KrigInv-1.2/KrigInv/MD5 |only
KrigInv-1.2/KrigInv/NAMESPACE | 42 +
KrigInv-1.2/KrigInv/R/EGI.R | 66 +--
KrigInv-1.2/KrigInv/R/EGIparallel.R |only
KrigInv-1.2/KrigInv/R/bichon_optim.R | 43 +-
KrigInv-1.2/KrigInv/R/computeAuxVariables_noChol.R | 2
KrigInv-1.2/KrigInv/R/computeAuxVariables_update.R |only
KrigInv-1.2/KrigInv/R/computeQuickKrigcov.R |only
KrigInv-1.2/KrigInv/R/computeRealVolumeConstant.R |only
KrigInv-1.2/KrigInv/R/integration_design.R |only
KrigInv-1.2/KrigInv/R/jn_optim.R |only
KrigInv-1.2/KrigInv/R/lili2D.R | 2
KrigInv-1.2/KrigInv/R/max_infill_criterion.R | 141 +++---
KrigInv-1.2/KrigInv/R/max_sur.R | 189 +++++---
KrigInv-1.2/KrigInv/R/max_sur_parallel.R |only
KrigInv-1.2/KrigInv/R/max_timse.R | 177 ++++----
KrigInv-1.2/KrigInv/R/max_timse_parallel.R |only
KrigInv-1.2/KrigInv/R/precomputeUpdateData.R |only
KrigInv-1.2/KrigInv/R/predict_nobias_km.R |only
KrigInv-1.2/KrigInv/R/predict_update_km.R |only
KrigInv-1.2/KrigInv/R/predict_update_km_parallel.R |only
KrigInv-1.2/KrigInv/R/print_uncertainty.R |only
KrigInv-1.2/KrigInv/R/print_uncertainty_1d.R |only
KrigInv-1.2/KrigInv/R/print_uncertainty_2d.R |only
KrigInv-1.2/KrigInv/R/print_uncertainty_nd.R |only
KrigInv-1.2/KrigInv/R/ranjan_optim.R | 49 +-
KrigInv-1.2/KrigInv/R/sur_optim.R | 107 +---
KrigInv-1.2/KrigInv/R/sur_optim_parallel.R |only
KrigInv-1.2/KrigInv/R/sur_optim_parallel2.R |only
KrigInv-1.2/KrigInv/R/timse_optim.R | 57 +-
KrigInv-1.2/KrigInv/R/timse_optim_parallel.R |only
KrigInv-1.2/KrigInv/R/timse_optim_parallel2.R |only
KrigInv-1.2/KrigInv/R/tmse_optim.R | 15
KrigInv-1.2/KrigInv/R/tsee_optim.R |only
KrigInv-1.2/KrigInv/R/update_km.R |only
KrigInv-1.2/KrigInv/man/EGI.Rd | 386 ++++++++----------
KrigInv-1.2/KrigInv/man/EGIparallel.Rd |only
KrigInv-1.2/KrigInv/man/KrigInv-package.Rd | 135 +++---
KrigInv-1.2/KrigInv/man/bichon_optim.Rd | 175 ++++----
KrigInv-1.2/KrigInv/man/camelback2.Rd | 15
KrigInv-1.2/KrigInv/man/computeAuxVariables_noChol.Rd |only
KrigInv-1.2/KrigInv/man/computeAuxVariables_update.Rd |only
KrigInv-1.2/KrigInv/man/computeQuickKrigcov.Rd |only
KrigInv-1.2/KrigInv/man/computeRealVolumeConstant.Rd |only
KrigInv-1.2/KrigInv/man/fun_test2d_ranjan.Rd | 13
KrigInv-1.2/KrigInv/man/fundet.Rd | 12
KrigInv-1.2/KrigInv/man/integration_design.Rd |only
KrigInv-1.2/KrigInv/man/jn_optim.Rd |only
KrigInv-1.2/KrigInv/man/lili2D.Rd | 13
KrigInv-1.2/KrigInv/man/max_infill_criterion.Rd | 199 ++++-----
KrigInv-1.2/KrigInv/man/max_sur.Rd | 220 +++++-----
KrigInv-1.2/KrigInv/man/max_sur_parallel.Rd |only
KrigInv-1.2/KrigInv/man/max_timse.Rd | 228 +++++-----
KrigInv-1.2/KrigInv/man/max_timse_parallel.Rd |only
KrigInv-1.2/KrigInv/man/precomputeUpdateData.Rd |only
KrigInv-1.2/KrigInv/man/predict_nobias_km.Rd |only
KrigInv-1.2/KrigInv/man/predict_update_km.Rd |only
KrigInv-1.2/KrigInv/man/predict_update_km_parallel.Rd |only
KrigInv-1.2/KrigInv/man/print_uncertainty.Rd |only
KrigInv-1.2/KrigInv/man/print_uncertainty_1d.Rd |only
KrigInv-1.2/KrigInv/man/print_uncertainty_2d.Rd |only
KrigInv-1.2/KrigInv/man/print_uncertainty_nd.Rd |only
KrigInv-1.2/KrigInv/man/ranjan_optim.Rd | 168 ++++---
KrigInv-1.2/KrigInv/man/sur_optim.Rd | 194 +++++----
KrigInv-1.2/KrigInv/man/sur_optim_parallel.Rd |only
KrigInv-1.2/KrigInv/man/sur_optim_parallel2.Rd |only
KrigInv-1.2/KrigInv/man/timse_optim.Rd | 209 +++++----
KrigInv-1.2/KrigInv/man/timse_optim_parallel.Rd |only
KrigInv-1.2/KrigInv/man/timse_optim_parallel2.Rd |only
KrigInv-1.2/KrigInv/man/tmse_optim.Rd | 168 ++++---
KrigInv-1.2/KrigInv/man/tsee_optim.Rd |only
KrigInv-1.2/KrigInv/man/update_km.Rd |only
76 files changed, 1604 insertions(+), 1436 deletions(-)
Title: Kriging-based optimization for computer experiments
Diff between DiceOptim versions 1.2.1 dated 2012-02-06 and 1.3 dated 2012-03-26
Description: Expected Improvement. EGO algorithm. Parallelized versions
of EGO: Constant Liars. Noisy Kriging-based Optimization
criteria and algorithms, including AEI, AKG, EQI, and
EI.plugin.
Author: D. Ginsbourger, V. Picheny, O. Roustant, with contributions by
C. Chevalier and T. Wagner
Maintainer: D. Ginsbourger
DESCRIPTION | 17 ++++----
MD5 | 75 +++++++++++++++++++++++++++++++------
NAMESPACE | 16 ++++---
R/AEI.R |only
R/AEI.grad.R |only
R/AEI.grad_optim.R |only
R/AKG.grad.R |only
R/AKG.grad_optim.R |only
R/AKG.r |only
R/EI.grad.R | 6 --
R/EI.plugin.R |only
R/EI.plugin.grad.R |only
R/EQI.grad.R |only
R/EQI.grad_optim.R |only
R/EQI.r |only
R/branin2.R |only
R/computeAuxVariables_noChol.R |only
R/goldsteinprice.R |only
R/hartman4.R |only
R/kriging.quantile.R |only
R/kriging.quantile.grad.R |only
R/kriging.quantile.grad_optim.R |only
R/max_AEI.R |only
R/max_AKG.R |only
R/max_EI.R | 2
R/max_EI.plugin.R |only
R/max_EQI.R |only
R/min_quantile.R |only
R/noisy.optimizer.R |only
R/rosenbrock4.R |only
R/sphere6.R |only
R/update_km.R |only
man/AEI.Rd |only
man/AEI.grad.Rd |only
man/AEI.grad_optim.Rd |only
man/AKG.Rd |only
man/AKG.grad.Rd |only
man/AKG.grad_optim.Rd |only
man/CL.nsteps.Rd | 2
man/DiceOptim-package.Rd | 31 ++++++++++-----
man/EGO.nsteps.Rd | 4 -
man/EI.Rd | 3 -
man/EI.plugin.Rd |only
man/EI.plugin.grad.Rd |only
man/EQI.Rd |only
man/EQI.grad.Rd |only
man/EQI.grad_optim.Rd |only
man/branin2.Rd |only
man/goldsteinprice.Rd |only
man/hartman4.Rd |only
man/kriging.quantile.Rd |only
man/kriging.quantile.grad.Rd |only
man/kriging.quantile.grad_optim.Rd |only
man/max_AEI.Rd |only
man/max_AKG.Rd |only
man/max_EI.Rd | 8 ++-
man/max_EI.plugin.Rd |only
man/max_EQI.Rd |only
man/max_qEI.CL.Rd | 2
man/min_quantile.Rd |only
man/noisy.optimizer.Rd |only
man/qEI.Rd | 2
man/rosenbrock4.Rd |only
man/sphere6.Rd |only
man/update_km.Rd |only
65 files changed, 121 insertions(+), 47 deletions(-)
Title: Association analysis of CNV data
Diff between CNVassoc versions 1.0 dated 2011-04-26 and 1.2 dated 2012-03-26
Description: This package carries out association analysis of common
copy number variants in population-based studies. This package
includes functions for analysing association under a series of
study designs (case-control, cohort, etc), using several
dependent variables (class status, censored data, counts) as
response, adjusting for covariates and considering various
inheritance models. It also includes functions for inferring
copy number (CNV genotype calling). Various classes and
generic functions (print, summary, plot, anova, ... ) have been
created to facilitate the analysis.
Author: Juan R González, Isaac Subirana
Maintainer: Juan R González
CNVassoc-1.0/CNVassoc/CNVassoc-Ex.R |only
CNVassoc-1.0/CNVassoc/data/A112.RData |only
CNVassoc-1.0/CNVassoc/inst/doc/CNVassoc_vignette.Rnw |only
CNVassoc-1.0/CNVassoc/inst/doc/CNVassoc_vignette.bbl |only
CNVassoc-1.0/CNVassoc/inst/doc/CNVassoc_vignette.bib |only
CNVassoc-1.0/CNVassoc/inst/doc/CNVassoc_vignette.blg |only
CNVassoc-1.0/CNVassoc/inst/doc/Rplots.pdf |only
CNVassoc-1.0/CNVassoc/inst/doc/Sweave.sty |only
CNVassoc-1.0/CNVassoc/inst/doc/figures |only
CNVassoc-1.0/CNVassoc/inst/doc/make_latex.r |only
CNVassoc-1.2/CNVassoc/DESCRIPTION | 13 +++---
CNVassoc-1.2/CNVassoc/MD5 |only
CNVassoc-1.2/CNVassoc/R/CNVtest.r | 2
CNVassoc-1.2/CNVassoc/R/anova.CNVassoc.r | 40 +++++++++----------
CNVassoc-1.2/CNVassoc/data/A112.rda |only
CNVassoc-1.2/CNVassoc/data/NeveCalled.rda |binary
CNVassoc-1.2/CNVassoc/data/NeveData.rda |binary
CNVassoc-1.2/CNVassoc/data/NeveRegions.rda |binary
CNVassoc-1.2/CNVassoc/data/SNPTEST.rda |binary
CNVassoc-1.2/CNVassoc/data/dataMLPA.rda |binary
CNVassoc-1.2/CNVassoc/data/datalist |only
CNVassoc-1.2/CNVassoc/inst/doc/CNVassoc_vignette.pdf |binary
CNVassoc-1.2/CNVassoc/inst/doc/changelog.txt | 5 +-
CNVassoc-1.2/CNVassoc/vignettes |only
24 files changed, 32 insertions(+), 28 deletions(-)
Title: You didn't know you didn't know?
Diff between unknownR versions 0.3 dated 2011-05-26 and 0.4 dated 2012-03-26
Description: Utility to quickly find useful functions in R that you
didn't know you didn't know.
Author: Matthew Dowle
Maintainer: Matthew Dowle
DESCRIPTION | 6 +++---
MD5 |only
NEWS | 13 +++++++++++++
R/funlist.R | 2 +-
R/learn.R | 2 +-
R/onAttach.R | 10 +++++-----
R/popcon.R | 28 ++++++++++++++++++++--------
R/unk.R | 4 ++--
8 files changed, 45 insertions(+), 20 deletions(-)
Title: Continuous Lag Spatial Markov Chains
Diff between spMC versions 0.2.1 dated 2012-03-21 and 0.2.2 dated 2012-03-26
Description: The main goal of this package is to provide a set of
functions for 1) the stratum lengths analysis along a chosen
direction, 2) fast estimation of continuous lag spatial Markov
chains model parameters and probability computing (also for
large data sets), 3) transition probability maps and
transiograms drawing, 4) simulation methods for categorical
random fields.
Author: Luca Sartore
Maintainer: Luca Sartore
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
R/ck.sim.R | 8 +++-----
R/ik.sim.R | 8 +++-----
R/setCores.R | 4 ++--
man/spMC-package.Rd | 4 ++--
src/spMC.c | 8 ++++----
tests/spMC-Ex.R | 16 ++++++++--------
8 files changed, 33 insertions(+), 37 deletions(-)
Title: Computes and compares species richnesses
Diff between rich versions 0.1 dated 2011-01-19 and 0.2 dated 2012-03-26
Description: Computes rarefaction curves, cumulated and mean species
richness. Compares these estimates by means of randomization
tests.
Author: Jean-Pierre Rossi
Maintainer: Jean-Pierre Rossi
rich-0.1/rich/rich.pdf |only
rich-0.2/rich/DESCRIPTION | 12 ++++++------
rich-0.2/rich/MD5 |only
rich-0.2/rich/NAMESPACE |only
rich-0.2/rich/R/raref2.R | 2 +-
rich-0.2/rich/R/rich.R | 6 +++---
rich-0.2/rich/R/zzz.R | 6 +++---
rich-0.2/rich/inst |only
rich-0.2/rich/man/Tomicus.Rd | 2 +-
rich-0.2/rich/man/c2cv.Rd | 4 ++--
rich-0.2/rich/man/c2m.Rd | 12 ++++++------
rich-0.2/rich/man/c2rcv.Rd | 2 +-
rich-0.2/rich/man/efea.Rd | 2 +-
rich-0.2/rich/man/rarc.Rd | 8 ++------
rich-0.2/rich/man/raref.Rd | 5 +----
rich-0.2/rich/man/raref2.Rd | 5 +----
rich-0.2/rich/man/rich.Rd | 4 ++--
17 files changed, 30 insertions(+), 40 deletions(-)
Title: Precipitation Statistics
Diff between PrecipStat versions 1.00 dated 2011-10-14 and 1.03 dated 2012-03-26
Description: The package contains data for the qqplotter package. These
data contain 14 percentiles p in [0.50, 0.55, ... 0.95] and
[0.96,0.97, ... 0.99] for the 24hr precipitation for all days
with amounts greater than 1mm/day.
Author: Rasmus E. Benestad
Maintainer: Rasmus E. Benestad
PrecipStat-1.00/PrecipStat/data/mu.qp.escn.jjas.rda |only
PrecipStat-1.00/PrecipStat/data/mu.qp.escn.rda |only
PrecipStat-1.00/PrecipStat/data/mu.qp.jjas.rda |only
PrecipStat-1.00/PrecipStat/data/mu.qp.lowq.rda |only
PrecipStat-1.00/PrecipStat/data/mu.qp.met.no.jjas.rda |only
PrecipStat-1.00/PrecipStat/data/mu.qp.met.no.rda |only
PrecipStat-1.00/PrecipStat/data/mu.qp.rcm.rda |only
PrecipStat-1.00/PrecipStat/data/mu.qp.res.rda |only
PrecipStat-1.03/PrecipStat/DESCRIPTION | 10 +++---
PrecipStat-1.03/PrecipStat/MD5 | 27 ++++++----------
PrecipStat-1.03/PrecipStat/NAMESPACE |only
PrecipStat-1.03/PrecipStat/R/readGDCN.R | 4 +-
PrecipStat-1.03/PrecipStat/data/f.wet.1990.1999.rda |binary
PrecipStat-1.03/PrecipStat/data/gdcn.inv.rda |binary
PrecipStat-1.03/PrecipStat/data/mu.qp.rda |binary
PrecipStat-1.03/PrecipStat/data/mu.qp.world.jjas.rda |binary
PrecipStat-1.03/PrecipStat/data/mu.qp.world.rda |binary
PrecipStat-1.03/PrecipStat/man/IO.Rd | 4 --
PrecipStat-1.03/PrecipStat/man/data.Rd | 30 +++++++++---------
19 files changed, 33 insertions(+), 42 deletions(-)
Title: FISH Based Normalization and Copy Number inference of SNP
microarray data
Diff between FBN versions 1.5 dated 2010-09-02 and 1.5.1 dated 2012-03-26
Description: Normalizes the data from a file containing the raw values
of the SNP probes of microarrray data by using the FISH probes
and their corresponding CNs.
Author: Adrian Andronache
Maintainer: Luca Agnelli
FBN-1.5.1/FBN/DESCRIPTION | 12 ++++++------
FBN-1.5.1/FBN/MD5 |only
FBN-1.5.1/FBN/NAMESPACE |only
FBN-1.5.1/FBN/data/FISHprobes.txt.gz |only
FBN-1.5.1/FBN/data/datalist |only
FBN-1.5.1/FBN/data/hmcls.rda |binary
FBN-1.5.1/FBN/man/FBN-package.Rd | 6 +++---
FBN-1.5.1/FBN/man/FBN.histogramMaxima.Rd | 2 +-
FBN-1.5.1/FBN/man/FBN.kmeans.Rd | 2 +-
FBN-1.5.1/FBN/man/FBN.valueCenter.Rd | 2 +-
FBN-1.5.1/FBN/man/FBNormalization.Rd | 2 +-
FBN-1.5.1/FBN/man/meanFilter.Rd | 2 +-
FBN-1.5.1/FBN/man/medianFilter.Rd | 2 +-
FBN-1.5/FBN/data/FISHprobes.txt |only
14 files changed, 15 insertions(+), 15 deletions(-)
Title: Distributed Lag Non-linear Models
Diff between dlnm versions 1.5.3 dated 2012-02-21 and 1.6.0 dated 2012-03-26
Description: The package dlnm contains functions to specify and run
distributed lag linear and non-linear models.
Author: Antonio Gasparrini and Ben Armstrong
Maintainer: Antonio Gasparrini
DESCRIPTION | 8 ++---
MD5 | 24 ++++++++---------
R/crossbasis.R | 33 +++++++++++++++++------
R/crosspred.R | 64 +++++++++++++++++++++++++---------------------
R/crossreduce.R | 4 --
R/onebasis.R | 24 +++++++----------
inst/ChangeLog | 45 +++++++++++++++++++++++---------
inst/doc/dlnmOverview.Rnw | 4 +-
inst/doc/dlnmOverview.pdf |binary
man/crossbasis.Rd | 6 ++--
man/crosspred.Rd | 6 ++--
man/dlnm-package.Rd | 4 +-
man/plot.crosspred.Rd | 6 ++--
13 files changed, 131 insertions(+), 97 deletions(-)
Title: Affinity Propagation Clustering
Diff between apcluster versions 1.1.1 dated 2011-09-08 and 1.2.0 dated 2012-03-26
Description: The apcluster package implements Frey's and Dueck's
Affinity Propagation clustering in R. The algorithms are
largely analogous to the Matlab code published by Frey and
Dueck. The package further provides an algorithm for
exemplar-based agglomerative clustering that can also be used
to join clusters obtained from affinity propagation. Various
plotting functions are available for analyzing clustering
results.
Author: Ulrich Bodenhofer, Andreas Kothmeier
Maintainer: Ulrich Bodenhofer
apcluster-1.1.1/apcluster/R/apclusterLM.R |only
apcluster-1.1.1/apcluster/inst/doc/bioinf-article.txi |only
apcluster-1.1.1/apcluster/inst/doc/bioinf-bar.png |only
apcluster-1.1.1/apcluster/inst/doc/bioinf.cls |only
apcluster-1.2.0/apcluster/DESCRIPTION | 18 +-
apcluster-1.2.0/apcluster/MD5 | 25 +--
apcluster-1.2.0/apcluster/NAMESPACE | 4
apcluster-1.2.0/apcluster/NEWS | 6
apcluster-1.2.0/apcluster/R/apcluster.R | 146 ++----------------
apcluster-1.2.0/apcluster/inst/doc/apcluster.Rnw | 80 ++++-----
apcluster-1.2.0/apcluster/inst/doc/apcluster.pdf |binary
apcluster-1.2.0/apcluster/man/apcluster.Rd | 16 -
apcluster-1.2.0/apcluster/src |only
apcluster-1.2.0/apcluster/vignettes |only
14 files changed, 96 insertions(+), 199 deletions(-)
Title: Regularization for semiparametric additive hazards regression
Diff between ahaz versions 1.1 dated 2011-07-05 and 1.11 dated 2012-03-26
Description: Computationally efficient procedures for regularized
estimation with the semiparametric additive hazards regression
model.
Author: Anders Gorst-Rasmussen
Maintainer: Anders Gorst-Rasmussen
DESCRIPTION | 16 ++++++++--------
MD5 |only
data/sorlie.rda |binary
3 files changed, 8 insertions(+), 8 deletions(-)
Title: Design of experiments for detection of linkage disequilibrium
Diff between ldDesign versions 2.0-0 dated 2011-11-18 and 2.0-1 dated 2012-03-26
Description: R package for design of experiments for design of
genome-wide association studies. Version 2 incorporating
quantitative traits and case-control studies. The Bayes factor
should be chosen large enough to give respectable posterior
odds. This requires Bayes factors of the order of 10^6 in
genome-wide association studies where prior odds are low.
Sample sizes needed to get this strength of evidence are
substantially higher than those from traditional power
calculations. The corresponding threshold for p-values is
substantially lower than commonly used. For quantitative
traits ldDesign uses an existing deterministic power
calculation for detection of linkage disequilibrium between a
bi-allelic QTL and a bi-allelic marker, together with the
Spiegelhalter and Smith Bayes factor to generate designs with
power to detect effects with a given Bayes factor. For case-
control studies an asymptotic approximate Bayes factor is used
to derive an analytical power calculation in dominant,
recessive, additive and general genetic models.
Author: Rod Ball
Maintainer: Rod Ball
ldDesign-2.0-0/ldDesign/inst/doc/Makefile |only
ldDesign-2.0-0/ldDesign/inst/doc/Sweave.sty |only
ldDesign-2.0-0/ldDesign/inst/doc/auto |only
ldDesign-2.0-0/ldDesign/inst/doc/ldDesign.Rnw |only
ldDesign-2.0-0/ldDesign/inst/doc/ldDesign.bib |only
ldDesign-2.0-0/ldDesign/inst/doc/ldDesign.tex |only
ldDesign-2.0-1/ldDesign/DESCRIPTION | 38 +++++++++++++++-----------
ldDesign-2.0-1/ldDesign/MD5 | 17 ++++-------
ldDesign-2.0-1/ldDesign/R/ccDesign.R | 26 ++++++++---------
ldDesign-2.0-1/ldDesign/R/ldDesign.R | 34 +++++++++++------------
ldDesign-2.0-1/ldDesign/inst/doc/ldDesign.pdf |binary
ldDesign-2.0-1/ldDesign/vignettes |only
12 files changed, 59 insertions(+), 56 deletions(-)
Title: Data for "Forecasting: principles and practice"
Diff between fpp versions 0.2 dated 2012-02-22 and 0.3 dated 2012-03-26
Description: All data sets required for the examples and exercises in
the book "Forecasting: principles and practice" by Rob J
Hyndman and George Athanasopoulos. All packages required to run
the examples are also loaded.
Author: Rob J Hyndman
Maintainer: Rob J Hyndman
ChangeLog | 3 +++
DESCRIPTION | 8 ++++----
MD5 | 16 +++++++++++++---
data/austourists.rda |only
data/h02.rda |only
data/livestock.rda |only
data/oil.rda |only
data/usmelec.rda |only
man/austa.Rd | 2 +-
man/austourists.Rd |only
man/h02.Rd |only
man/livestock.Rd |only
man/oil.Rd |only
man/usnetelec.Rd |only
14 files changed, 21 insertions(+), 8 deletions(-)
Title: Extension of data.frame for fast indexing, fast ordered joins,
fast assignment, fast grouping and list columns.
Diff between data.table versions 1.7.10 dated 2012-02-07 and 1.8.0 dated 2012-03-26
Description: Enhanced data.frame. Fast indexing, fast ordered joins,
fast assignment, fast grouping and list columns in a short and
flexible syntax. i and j may be expressions of column names
directly, for faster development. Example: X[Y] is a fast join
for large data.
Author: M Dowle, T Short, S Lianoglou
Maintainer: M Dowle
data.table-1.7.10/data.table/R/sortedmatch.R |only
data.table-1.8.0/data.table/DESCRIPTION | 9
data.table-1.8.0/data.table/MD5 | 60 -
data.table-1.8.0/data.table/NAMESPACE | 4
data.table-1.8.0/data.table/NEWS | 156 ++++
data.table-1.8.0/data.table/R/c.factor.R | 6
data.table-1.8.0/data.table/R/data.table.R | 346 +++++-----
data.table-1.8.0/data.table/R/duplicated.R | 6
data.table-1.8.0/data.table/R/like.R | 11
data.table-1.8.0/data.table/R/merge.R | 69 -
data.table-1.8.0/data.table/R/onAttach.R | 10
data.table-1.8.0/data.table/R/setkey.R | 113 +--
data.table-1.8.0/data.table/R/test.data.table.R | 2
data.table-1.8.0/data.table/inst/doc/datatable-faq.Rnw | 3
data.table-1.8.0/data.table/inst/doc/datatable-faq.pdf |binary
data.table-1.8.0/data.table/inst/doc/datatable-intro.Rnw | 10
data.table-1.8.0/data.table/inst/doc/datatable-intro.pdf |binary
data.table-1.8.0/data.table/inst/doc/datatable-timings.pdf |binary
data.table-1.8.0/data.table/inst/tests/test-data.frame-like.R | 43 +
data.table-1.8.0/data.table/inst/tests/tests.Rraw | 340 ++++++---
data.table-1.8.0/data.table/man/IDateTime.Rd | 6
data.table-1.8.0/data.table/man/chmatch.Rd |only
data.table-1.8.0/data.table/man/data.table.Rd | 12
data.table-1.8.0/data.table/man/like.Rd | 7
data.table-1.8.0/data.table/man/merge.Rd | 4
data.table-1.8.0/data.table/man/setkey.Rd | 8
data.table-1.8.0/data.table/man/truelength.Rd | 4
data.table-1.8.0/data.table/src/assign.c | 199 +++--
data.table-1.8.0/data.table/src/countingcharacter.c | 53 +
data.table-1.8.0/data.table/src/dogroups.c | 19
data.table-1.8.0/data.table/src/duplist.c | 45 -
data.table-1.8.0/data.table/src/sortedmatch.c | 183 ++---
32 files changed, 1087 insertions(+), 641 deletions(-)
Title: Core methods and classes used by aroma.* packages part of The
Aroma Framework
Diff between aroma.core versions 2.4.1 dated 2012-01-12 and 2.5.0 dated 2012-03-26
Description: This package contains core methods and classes used by
higher-level aroma.* packages part of the Aroma Project, e.g.
aroma.affymetrix and aroma.cn. Its API should be considered to
be in alpha and beta versions, and is mostly of interest to
developers.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
aroma.core-2.4.1/aroma.core/R/density.EXTS.R |only
aroma.core-2.4.1/aroma.core/inst/annotationData/genomes/Human/Human,cytobands,GLADv2.4.0,HB20100219.txt |only
aroma.core-2.4.1/aroma.core/inst/reports/includes/css/ChromosomeExplorer.css |only
aroma.core-2.4.1/aroma.core/inst/reports/includes/css/ChromosomeExplorer3.1.css |only
aroma.core-2.4.1/aroma.core/inst/reports/includes/css/ChromosomeExplorer4.css |only
aroma.core-2.4.1/aroma.core/inst/reports/includes/js/ArrayExplorer |only
aroma.core-2.4.1/aroma.core/inst/reports/includes/js/ChromosomeExplorer |only
aroma.core-2.4.1/aroma.core/inst/reports/includes/js/ChromosomeExplorer2 |only
aroma.core-2.4.1/aroma.core/inst/reports/includes/js/ChromosomeExplorer3 |only
aroma.core-2.4.1/aroma.core/inst/reports/includes/js/ChromosomeExplorer3.1 |only
aroma.core-2.4.1/aroma.core/inst/reports/includes/js/ChromosomeExplorer4 |only
aroma.core-2.4.1/aroma.core/inst/reports/includes/js/ChromosomeExplorer5 |only
aroma.core-2.4.1/aroma.core/inst/reports/includes/js/aroma |only
aroma.core-2.4.1/aroma.core/inst/reports/templates/rsp/ArrayExplorer/ArrayExplorer.onChipType.js.rsp |only
aroma.core-2.4.1/aroma.core/inst/reports/templates/rsp/ArrayExplorer/ArrayExplorer.onLoad.js.rsp |only
aroma.core-2.4.1/aroma.core/man/updateSamplesFile.ChromosomeExplorer.Rd |only
aroma.core-2.5.0/aroma.core/DESCRIPTION | 18
aroma.core-2.5.0/aroma.core/MD5 | 242 +-
aroma.core-2.5.0/aroma.core/R/006.fixVarArgs.R | 24
aroma.core-2.5.0/aroma.core/R/AbstractCNData.R |only
aroma.core-2.5.0/aroma.core/R/AbstractPSCNData.R |only
aroma.core-2.5.0/aroma.core/R/AromaUnitSignalBinaryFile.R | 10
aroma.core-2.5.0/aroma.core/R/AromaUnitSignalBinaryFile.writeDataFrame.R | 6
aroma.core-2.5.0/aroma.core/R/AromaUnitSignalBinarySet.writeDataFrame.R | 6
aroma.core-2.5.0/aroma.core/R/AromaUnitTabularBinaryFile.writeDataFrame.R | 6
aroma.core-2.5.0/aroma.core/R/AromaUnitTotalCnBinaryFile.R | 3
aroma.core-2.5.0/aroma.core/R/AromaUnitTotalCnBinaryFileList.R | 9
aroma.core-2.5.0/aroma.core/R/ChromosomalModel.drawCytoband.R | 13
aroma.core-2.5.0/aroma.core/R/ChromosomeExplorer.R | 262 +-
aroma.core-2.5.0/aroma.core/R/CopyNumberChromosomalModel.R | 18
aroma.core-2.5.0/aroma.core/R/Explorer.R | 79
aroma.core-2.5.0/aroma.core/R/Image.EXTS.R | 638 ++---
aroma.core-2.5.0/aroma.core/R/NonPairedPSCNData.R |only
aroma.core-2.5.0/aroma.core/R/PairedPSCNData.R |only
aroma.core-2.5.0/aroma.core/R/RasterImage.R | 158 +
aroma.core-2.5.0/aroma.core/R/RawCopyNumbers.R | 29
aroma.core-2.5.0/aroma.core/R/RawGenomicSignals.OPS.R | 20
aroma.core-2.5.0/aroma.core/R/RawGenomicSignals.PLOT.R | 116
aroma.core-2.5.0/aroma.core/R/RawGenomicSignals.R | 1170 +++++++---
aroma.core-2.5.0/aroma.core/R/RawGenomicSignals.SEG.R | 77
aroma.core-2.5.0/aroma.core/R/RawGenomicSignals.append.R | 10
aroma.core-2.5.0/aroma.core/R/RawGenomicSignals.segmentByCBS.R | 4
aroma.core-2.5.0/aroma.core/R/RawGenomicSignals.segmentByGLAD.R | 4
aroma.core-2.5.0/aroma.core/R/RawGenomicSignals.segmentByHaarSeg.R | 4
aroma.core-2.5.0/aroma.core/R/RawGenomicSignals.segmentByMPCBS.R | 4
aroma.core-2.5.0/aroma.core/R/RawMirroredAlleleBFractions.R | 5
aroma.core-2.5.0/aroma.core/R/RawSequenceReads.EXTRAS.R | 6
aroma.core-2.5.0/aroma.core/R/RichDataFrame.R |only
aroma.core-2.5.0/aroma.core/R/SegmentedAlleleBFracions.R | 4
aroma.core-2.5.0/aroma.core/R/SegmentedCopyNumbers.R | 4
aroma.core-2.5.0/aroma.core/R/SegmentedGenomicSignalsInterface.COLS.R | 8
aroma.core-2.5.0/aroma.core/R/SegmentedGenomicSignalsInterface.R | 176 +
aroma.core-2.5.0/aroma.core/R/colBinnedSmoothing.R | 23
aroma.core-2.5.0/aroma.core/R/colGaussianSmoothing.R | 7
aroma.core-2.5.0/aroma.core/R/colKernelSmoothing.R | 7
aroma.core-2.5.0/aroma.core/R/findPngDevice.R | 77
aroma.core-2.5.0/aroma.core/R/weightedMad.R | 126 -
aroma.core-2.5.0/aroma.core/incl/999.missingdocs.txt | 81
aroma.core-2.5.0/aroma.core/incl/SegmentedCopyNumbers.Rex | 4
aroma.core-2.5.0/aroma.core/incl/weightedMad.Rex |only
aroma.core-2.5.0/aroma.core/inst/NEWS | 123 +
aroma.core-2.5.0/aroma.core/inst/annotationData/genomes/Human/Human,cytobands,hg17,GLADv2.4.0,HB20100219.txt |only
aroma.core-2.5.0/aroma.core/inst/archive |only
aroma.core-2.5.0/aroma.core/inst/reports/includes/css/ChromosomeExplorer3.4.css |only
aroma.core-2.5.0/aroma.core/inst/reports/includes/js/ArrayExplorer3.4 |only
aroma.core-2.5.0/aroma.core/inst/reports/includes/js/ChromosomeExplorer3.4 |only
aroma.core-2.5.0/aroma.core/inst/reports/includes/js/ScrollImage2d.js | 191 -
aroma.core-2.5.0/aroma.core/inst/reports/includes/js/Scrollbar2d.js |only
aroma.core-2.5.0/aroma.core/inst/reports/includes/js/Webcuts.js | 63
aroma.core-2.5.0/aroma.core/inst/reports/includes/js/require.js |only
aroma.core-2.5.0/aroma.core/inst/reports/templates/html/ArrayExplorer/ArrayExplorer.html | 49
aroma.core-2.5.0/aroma.core/inst/reports/templates/html/ArrayExplorer/ArrayExplorer1.0 |only
aroma.core-2.5.0/aroma.core/inst/reports/templates/html/ArrayExplorer/ArrayExplorer3.3 |only
aroma.core-2.5.0/aroma.core/inst/reports/templates/html/ArrayExplorer/ArrayExplorer3.4 |only
aroma.core-2.5.0/aroma.core/inst/reports/templates/html/ChromosomeExplorer/ChromosomeExplorer.html | 88
aroma.core-2.5.0/aroma.core/inst/reports/templates/html/ChromosomeExplorer/ChromosomeExplorer3.1/ChromosomeExplorer.html | 11
aroma.core-2.5.0/aroma.core/inst/reports/templates/html/ChromosomeExplorer/ChromosomeExplorer3.2 |only
aroma.core-2.5.0/aroma.core/inst/reports/templates/html/ChromosomeExplorer/ChromosomeExplorer3.3 |only
aroma.core-2.5.0/aroma.core/inst/reports/templates/html/ChromosomeExplorer/ChromosomeExplorer3.4 |only
aroma.core-2.5.0/aroma.core/inst/reports/templates/rsp/ArrayExplorer/setupExplorer.js.rsp |only
aroma.core-2.5.0/aroma.core/inst/reports/templates/rsp/ArrayExplorer1.0 |only
aroma.core-2.5.0/aroma.core/inst/reports/templates/rsp/ArrayExplorer3.3 |only
aroma.core-2.5.0/aroma.core/inst/reports/templates/rsp/ArrayExplorer3.4 |only
aroma.core-2.5.0/aroma.core/inst/reports/templates/rsp/ChromosomeExplorer3.4 |only
aroma.core-2.5.0/aroma.core/inst/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer3.1/ChromosomeExplorer.onLoad.js.rsp | 2
aroma.core-2.5.0/aroma.core/inst/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer3.2 |only
aroma.core-2.5.0/aroma.core/inst/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer3.3 |only
aroma.core-2.5.0/aroma.core/man/AbstractCNData.Rd |only
aroma.core-2.5.0/aroma.core/man/AbstractPSCNData.Rd |only
aroma.core-2.5.0/aroma.core/man/ChromosomeExplorer.Rd | 6
aroma.core-2.5.0/aroma.core/man/Explorer.Rd | 5
aroma.core-2.5.0/aroma.core/man/Non-documented_objects.Rd | 142 +
aroma.core-2.5.0/aroma.core/man/NonPairedPSCNData.Rd |only
aroma.core-2.5.0/aroma.core/man/PairedPSCNData.Rd |only
aroma.core-2.5.0/aroma.core/man/RawAlleleBFractions.Rd | 19
aroma.core-2.5.0/aroma.core/man/RawCopyNumbers.Rd | 21
aroma.core-2.5.0/aroma.core/man/RawGenomicSignals.Rd | 37
aroma.core-2.5.0/aroma.core/man/RawMirroredAlleleBFractions.Rd | 21
aroma.core-2.5.0/aroma.core/man/RawSequenceReads.Rd | 19
aroma.core-2.5.0/aroma.core/man/SegmentedAlleleBFractions.Rd | 25
aroma.core-2.5.0/aroma.core/man/SegmentedCopyNumbers.Rd | 31
aroma.core-2.5.0/aroma.core/man/SegmentedGenomicSignalsInterface.Rd | 2
aroma.core-2.5.0/aroma.core/man/colBinnedSmoothing.matrix.Rd | 2
aroma.core-2.5.0/aroma.core/man/estimateStandardDeviation.RawGenomicSignals.Rd | 3
aroma.core-2.5.0/aroma.core/man/getChromosomes.ChromosomeExplorer.Rd | 2
aroma.core-2.5.0/aroma.core/man/updateSetupExplorerFile.ChromosomeExplorer.Rd |only
aroma.core-2.5.0/aroma.core/man/weightedMad.Rd |only
aroma.core-2.5.0/aroma.core/tests |only
108 files changed, 2860 insertions(+), 1460 deletions(-)
Title: Analysis of large Affymetrix microarray data sets
Diff between aroma.affymetrix versions 2.4.0 dated 2012-01-12 and 2.5.0 dated 2012-03-26
More information about aroma.affymetrix at CRAN
Description: This package implements classes for files and sets of
files for various Affymetrix file formats, e.g.
AffymetrixCdfFile, AffymetrixCelFile, and AffymetrixCelSet.
These are designed to be memory efficient but still being fast.
The idea is to keep all data on file and only read data into
memory when needed. Clever caching mechanisms are used to
minimize the overhead of data IO. All of the above is hidden
in the package API and for the developer (and the end user),
the data is queried as if it lives in memory. With this design
it is only the diskspace that limits the number of arrays that
can be analyzed. To install, do:
source("http://www.aroma-project.org/hbLite.R");
hbInstall("aroma.affymetrix").
Author: Henrik Bengtsson, James Bullard, Kasper Hansen, Pierre Neuvial,
Elizabeth Purdom, Mark Robinson, Ken Simpson
Maintainer: Henrik Bengtsson
DESCRIPTION | 17 -
MD5 | 34 +-
R/AffymetrixCelFile.PLOT.R | 6
R/ArrayExplorer.R | 153 +--------
R/MbeiPlm.R | 18 -
R/MultiArrayUnitModel.R | 35 +-
R/ProbeLevelModel.calculateResiduals.R | 21 +
R/ProbeLevelModel.fit.R | 2
R/RmaPlm.R | 165 +++++++---
R/pdInfo2Cdf.R | 18 -
incl/999.missingdocs.txt | 4
inst/NEWS | 30 +
inst/testScripts/system/chipTypes/HG-U133_Plus_2/test20090428,PLM,priors.R | 25 +
man/AffymetrixCdfFile.Rd | 4
man/ArrayExplorer.Rd | 5
man/DChipCdfBinFile.Rd | 2
man/MultiArrayUnitModel.Rd | 4
man/Non-documented_objects.Rd | 5
18 files changed, 315 insertions(+), 233 deletions(-)
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