Title: Mokken Scale Analysis in R
Diff between mokken versions 2.7 dated 2011-12-24 and 2.7.1 dated 2012-01-22
Description: mokken contains functions for performing Mokken scale
analysis on test and questionnaire data. It includes an
automated item selection algorithm, and various checks of model
assumptions.
Author: L. Andries van der Ark
Maintainer: L. Andries van der Ark
mokken-2.7.1/mokken/DESCRIPTION | 15 ++++++++-------
mokken-2.7.1/mokken/MD5 | 13 +------------
mokken-2.7/mokken/inst/doc/F1.pdf |only
mokken-2.7/mokken/inst/doc/F2.pdf |only
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mokken-2.7/mokken/inst/doc/F8.pdf |only
mokken-2.7/mokken/inst/doc/Sweave.sty |only
mokken-2.7/mokken/inst/doc/fancyvrb.sty |only
mokken-2.7/mokken/inst/doc/index.html |only
mokken-2.7/mokken/inst/doc/mokken.R |only
mokken-2.7/mokken/inst/doc/try.ps |only
13 files changed, 9 insertions(+), 19 deletions(-)
Title: High-dimensional Undirected Graph Estimation
Diff between huge versions 1.1.2 dated 2011-08-22 and 1.2 dated 2012-01-22
Description: The package "huge" provides a general framework for
high-dimensional undirected graph estimation. It integrates
data preprocessing, neighborhood screening, graph estimation,
and model selection techniques into a pipeline. In
preprocessing stage, the nonparanormal(npn) transformation is
applied to help relax the normality assumption. In the graph
estimation stage, the graph structure is estimated by
Meinshausen-Buhlmann graph estimation or the graphical lasso,
and both methods can be further accelerated by the lossy
screening rule preselecting the neighborhood of each variable
by correlation thresholding. We target on high-dimensional data
analysis usually d >> n, and the computation is
memory-optimized using the sparse matrix output. We also
provide a computationally efficient approach, correlation
thresholding graph estimation. Three
regularization/thresholding parameter selection methods are
included in this package: (1)stability approach for
regularization selection (2) rotation information criterion (3)
extended Bayesian information criterion which is only available
for the graphical lasso.
Author: Tuo Zhao, Han Liu, Kathryn Roeder, John Lafferty, Larry
Wasserman
Maintainer: Tuo Zhao
DESCRIPTION | 10 +++++-----
MD5 | 21 ++++++++++++---------
NAMESPACE | 50 +++++++++++++++++++++++++-------------------------
R/huge.mb.R | 4 ++--
R/huge.select.R | 10 +++++++---
data/stockdata.rda |binary
inst |only
man/huge-package.Rd | 4 ++--
man/huge.Rd | 2 +-
man/huge.generator.Rd | 2 +-
man/huge.select.Rd | 2 +-
11 files changed, 56 insertions(+), 49 deletions(-)
Title: ABCDE_FBA: A-Biologist-Can-Do-Everything of Flux Balance
Analysis with this package.
Diff between abcdeFBA versions 0.1 dated 2011-11-05 and 0.2 dated 2012-01-22
Description: Functions for Constraint Based Simulation using Flux
Balance Analysis and informative analysis of the data generated
during simulation.
Author: Abhilash Gangadharan, Neha Rohatgi
Maintainer: Abhilash Gangadharan
abcdeFBA-0.1/abcdeFBA/data/Ec_iAF1260.rda |only
abcdeFBA-0.1/abcdeFBA/man/Ec_iAF1260.Rd |only
abcdeFBA-0.2/abcdeFBA/DESCRIPTION | 12 -
abcdeFBA-0.2/abcdeFBA/MD5 | 77 ++++-----
abcdeFBA-0.2/abcdeFBA/NAMESPACE | 2
abcdeFBA-0.2/abcdeFBA/R/BFDProcessor.R | 7
abcdeFBA-0.2/abcdeFBA/R/Exhaustive_double_deletion.R | 58 +------
abcdeFBA-0.2/abcdeFBA/R/Exhaustive_single_deletion.R | 109 +++++--------
abcdeFBA-0.2/abcdeFBA/R/FBA_solve.R | 4
abcdeFBA-0.2/abcdeFBA/R/PERTURBATION_analysis.R | 131 ++++++++++++----
abcdeFBA-0.2/abcdeFBA/R/fva_robustness.R | 81 +++++----
abcdeFBA-0.2/abcdeFBA/R/genedel.R |only
abcdeFBA-0.2/abcdeFBA/R/metab_connect.R | 8
abcdeFBA-0.2/abcdeFBA/R/sybil2fba_object.R | 8
abcdeFBA-0.2/abcdeFBA/data/Ec_iAF1260_flux1.rda |only
abcdeFBA-0.2/abcdeFBA/data/Ec_iAF1260_flux2.rda |binary
abcdeFBA-0.2/abcdeFBA/data/Ec_iJR904.rda |binary
abcdeFBA-0.2/abcdeFBA/data/Ecoli_core.rda |binary
abcdeFBA-0.2/abcdeFBA/data/H_pylori_iIT341.rda |binary
abcdeFBA-0.2/abcdeFBA/data/H_sapien_Recon1.rda |binary
abcdeFBA-0.2/abcdeFBA/data/M_barkeri_iAF629.rda |binary
abcdeFBA-0.2/abcdeFBA/data/M_tb_iNJ661.rda |binary
abcdeFBA-0.2/abcdeFBA/data/S_aureus_iSB619.rda |binary
abcdeFBA-0.2/abcdeFBA/data/S_cerevisiae_IND750.rda |binary
abcdeFBA-0.2/abcdeFBA/doc/version_history |only
abcdeFBA-0.2/abcdeFBA/man/BFDProcessor.Rd | 28 +--
abcdeFBA-0.2/abcdeFBA/man/Ec_iAF1260_flux1.Rd |only
abcdeFBA-0.2/abcdeFBA/man/Exhaustive_double_deletion.Rd | 23 +-
abcdeFBA-0.2/abcdeFBA/man/Exhaustive_single_deletion.Rd | 30 ++-
abcdeFBA-0.2/abcdeFBA/man/FBA_solve.Rd | 23 +-
abcdeFBA-0.2/abcdeFBA/man/Gene_del.Rd |only
abcdeFBA-0.2/abcdeFBA/man/PERTURBATION_analysis.Rd | 37 +++-
abcdeFBA-0.2/abcdeFBA/man/PHPP.Rd | 26 +--
abcdeFBA-0.2/abcdeFBA/man/change_obj_function.Rd | 28 ++-
abcdeFBA-0.2/abcdeFBA/man/change_rxn_bounds.Rd | 24 +-
abcdeFBA-0.2/abcdeFBA/man/deg_meas.Rd | 26 +--
abcdeFBA-0.2/abcdeFBA/man/fdiff.Rd | 24 +-
abcdeFBA-0.2/abcdeFBA/man/fva.Rd | 30 ++-
abcdeFBA-0.2/abcdeFBA/man/fva_robustness.Rd | 29 ++-
abcdeFBA-0.2/abcdeFBA/man/metab_connect.Rd | 22 +-
abcdeFBA-0.2/abcdeFBA/man/metab_srch.Rd | 24 +-
abcdeFBA-0.2/abcdeFBA/man/rxn_srch.Rd | 23 +-
abcdeFBA-0.2/abcdeFBA/man/sing_del_flxme.Rd | 22 +-
43 files changed, 528 insertions(+), 388 deletions(-)
Title: Graph Based Multiple Comparison Procedures
Diff between gMCP versions 0.7-3 dated 2012-01-16 and 0.7-4 dated 2012-01-22
Description: This package provides functions and a graphical user
interface for graphical described multiple test procedures.
Author: Kornelius Rohmeyer, Florian Klinglmueller (parametric tests,
adaptive designs), Bjoern Bornkamp (power simulations)
Maintainer: Kornelius Rohmeyer
gMCP-0.7-3/gMCP/R/plotInfiniteCI.R |only
gMCP-0.7-3/gMCP/inst/doc/gMCP/AQuickStart-fake.Rnw |only
gMCP-0.7-3/gMCP/inst/doc/gMCP/AQuickStart.Rnw |only
gMCP-0.7-3/gMCP/inst/doc/gMCP/gMCP.Rnw.backup |only
gMCP-0.7-3/gMCP/inst/doc/gMCP/parametric-fake.Rnw |only
gMCP-0.7-3/gMCP/inst/doc/gMCP/parametric.Rnw |only
gMCP-0.7-3/gMCP/inst/java-src/org/af/gMCP/gui/ResourceBundle.properties |only
gMCP-0.7-3/gMCP/inst/java-src/org/af/gMCP/gui/options/PlotPanel.java |only
gMCP-0.7-4/gMCP/.Rinstignore |only
gMCP-0.7-4/gMCP/DESCRIPTION | 9
gMCP-0.7-4/gMCP/INSTALL | 4
gMCP-0.7-4/gMCP/MD5 | 82 -
gMCP-0.7-4/gMCP/NEWS | 30
gMCP-0.7-4/gMCP/R/gMCP.R | 4
gMCP-0.7-4/gMCP/R/graph2latex.R | 2
gMCP-0.7-4/gMCP/R/graphMCP.R | 18
gMCP-0.7-4/gMCP/R/helperGUI.R | 5
gMCP-0.7-4/gMCP/R/onLoad.R | 5
gMCP-0.7-4/gMCP/R/plotCI.R | 178 +---
gMCP-0.7-4/gMCP/TODO | 113 --
gMCP-0.7-4/gMCP/inst/doc/AQuickStart.Rnw | 115 ++
gMCP-0.7-4/gMCP/inst/doc/AQuickStart.pdf |binary
gMCP-0.7-4/gMCP/inst/doc/Makefile | 11
gMCP-0.7-4/gMCP/inst/doc/gMCP.pdf |binary
gMCP-0.7-4/gMCP/inst/doc/literatur.bib | 3
gMCP-0.7-4/gMCP/inst/doc/parametric.Rnw | 435 +++++++++-
gMCP-0.7-4/gMCP/inst/doc/parametric.pdf |binary
gMCP-0.7-4/gMCP/inst/java-src/org/af/gMCP/config/Configuration.java | 26
gMCP-0.7-4/gMCP/inst/java-src/org/af/gMCP/config/GeneralConfig.java | 1
gMCP-0.7-4/gMCP/inst/java-src/org/af/gMCP/config/JavaConfig.java | 4
gMCP-0.7-4/gMCP/inst/java-src/org/af/gMCP/gui/CreateGraphGUI.java | 59 +
gMCP-0.7-4/gMCP/inst/java-src/org/af/gMCP/gui/MenuBarMGraph.java | 65 -
gMCP-0.7-4/gMCP/inst/java-src/org/af/gMCP/gui/dialogs/ColorChooseDialog.java |only
gMCP-0.7-4/gMCP/inst/java-src/org/af/gMCP/gui/dialogs/DialogConfIntEstVar.java | 11
gMCP-0.7-4/gMCP/inst/java-src/org/af/gMCP/gui/dialogs/VariableNameDialog.java | 16
gMCP-0.7-4/gMCP/inst/java-src/org/af/gMCP/gui/graph/Edge.java | 43
gMCP-0.7-4/gMCP/inst/java-src/org/af/gMCP/gui/graph/GraphMCP.java | 2
gMCP-0.7-4/gMCP/inst/java-src/org/af/gMCP/gui/graph/GraphView.java | 69 +
gMCP-0.7-4/gMCP/inst/java-src/org/af/gMCP/gui/graph/NetList.java | 13
gMCP-0.7-4/gMCP/inst/java-src/org/af/gMCP/gui/graph/PView.java | 12
gMCP-0.7-4/gMCP/inst/java-src/org/af/gMCP/gui/graph/UpdateEdge.java | 75 +
gMCP-0.7-4/gMCP/inst/java-src/org/af/gMCP/gui/options/GeneralPanel.java | 129 +-
gMCP-0.7-4/gMCP/inst/java-src/org/af/gMCP/gui/options/MiscPanel.java | 85 -
gMCP-0.7-4/gMCP/inst/java-src/org/af/gMCP/gui/options/NumericPanel.java |only
gMCP-0.7-4/gMCP/inst/java-src/org/af/gMCP/gui/options/OptionsDialog.java | 25
gMCP-0.7-4/gMCP/inst/java-src/org/mutoss/gui/TransferableImage.java |only
gMCP-0.7-4/gMCP/inst/java/gsrmtp.jar |binary
gMCP-0.7-4/gMCP/inst/unitTests/runit.LaTeX.R |only
gMCP-0.7-4/gMCP/man/graph2latex.Rd | 2
49 files changed, 1090 insertions(+), 561 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-06-06 1.0
Title: Modeling and Inferring Gene Networks
Diff between GeneNet versions 1.2.4 dated 2009-10-11 and 1.2.5 dated 2012-01-22
Description: GeneNet is a package for analyzing gene expression (time
series) data with focus on the inference of gene networks. In
particular, GeneNet implements the methods of Schaefer and
Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
for learning large-scale gene association networks (including
assignment of putative directions).
Author: Juliane Schaefer, Rainer Opgen-Rhein, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 14 +++++++-------
MD5 |only
NAMESPACE |only
NEWS | 10 +++++++++-
4 files changed, 16 insertions(+), 8 deletions(-)
Title: Shrinkage t Statistic and CAT Score
Diff between st versions 1.1.6 dated 2011-07-05 and 1.1.7 dated 2012-01-22
Description: This package implements the "shrinkage t" statistic
introduced in Opgen-Rhein and Strimmer (2007) and a shrinkage
estimate of the "correlation-adjusted t-score" (CAT score)
described in Zuber and Strimmer (2009). It also offers a
convenient interface to a number of other regularized
t-statistics commonly employed in high-dimensional case-control
studies.
Author: Rainer Opgen-Rhein, Verena Zuber, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 10 +++++-----
MD5 |only
NAMESPACE |only
NEWS | 6 ++++++
4 files changed, 11 insertions(+), 5 deletions(-)
Title: Spatial and Space-Time Point Pattern Analysis
Diff between splancs versions 2.01-29 dated 2011-08-20 and 2.01-31 dated 2012-01-22
Description: Spatial and Space-Time Point Pattern Analysis Functions
Author: Barry Rowlingson
Maintainer: Roger Bivand
ChangeLog | 21 +++++++++++++++++++++
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
R/as.points.S | 9 ++++++---
R/kernel2d.S | 12 ++++++++----
inst/ChangeLog | 21 +++++++++++++++++++++
man/kernel2d.Rd | 5 ++++-
src/ptinpoly.c | 2 +-
8 files changed, 72 insertions(+), 20 deletions(-)
Title: Pretty descriptive stats.
Diff between prettyR versions 2.0-3 dated 2012-01-17 and 2.0-4 dated 2012-01-22
Description: Functions for conventionally formatted descriptive stats,
and to format R output as HTML.
Author: Jim Lemon
Maintainer: Jim Lemon
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NEWS | 4 ++++
R/freq.R | 3 ++-
4 files changed, 13 insertions(+), 8 deletions(-)
Title: GAMs with GCV/AIC/REML smoothness estimation and GAMMs by PQL
Diff between mgcv versions 1.7-12 dated 2011-12-12 and 1.7-13 dated 2012-01-22
Description: Routines for GAMs and other generalized ridge regression
with multiple smoothing parameter selection by GCV, REML or
UBRE/AIC. Also GAMMs by REML or PQL. Includes a gam() function.
Author: Simon Wood
Maintainer: Simon Wood
DESCRIPTION | 17 +++---
MD5 | 20 +++----
NAMESPACE | 23 +++++----
R/mgcv.r | 84 +++++++++++++++++++++++++++------
R/smooth.r | 17 +++++-
changeLog | 23 +++++++--
man/bam.Rd | 2
man/gam.side.Rd | 4 +
man/smooth.construct.Rd | 9 ++-
man/smooth.construct.re.smooth.spec.Rd | 5 +
src/mat.c | 55 +++++++--------------
11 files changed, 172 insertions(+), 87 deletions(-)
Title: Analysis of Multiple Time Course Data
Diff between longitudinal versions 1.1.6 dated 2011-03-21 and 1.1.7 dated 2012-01-22
Description: This package contains general data structures and
functions for longitudinal data with multiple variables,
repeated measurements, and irregularly spaced time points. It
also implements a shrinkage estimator of dynamical correlation
and dynamical covariance.
Author: Rainer Opgen-Rhein and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 12 ++++++------
MD5 |only
NAMESPACE |only
NEWS | 13 +++++++++----
4 files changed, 15 insertions(+), 10 deletions(-)
Title: Shrinkage Discriminant Analysis and CAT Score Variable Selection
Diff between sda versions 1.2.0 dated 2011-06-28 and 1.2.1 dated 2012-01-22
Description: This package provides an efficient framework for
high-dimensional linear and diagonal discriminant analysis with
variable selection. The classifier is trained using
James-Stein-type shrinkage estimators and predictor variables
are ranked using CAT scores (correlation-adjusted t-scores).
Variable selection error is controlled using false
non-discovery rates or higher criticism scores.
Author: Miika Ahdesmaki, Verena Zuber, and Korbinian Strimmer
Maintainer: Korbinian Strimmer
DESCRIPTION | 14 +++++++-------
MD5 |only
NAMESPACE |only
NEWS | 9 ++++++++-
4 files changed, 15 insertions(+), 8 deletions(-)
Title: Shape constrained additive models
Diff between scam versions 1.0 dated 2012-01-20 and 1.1 dated 2012-01-22
Description: Routines for generalized additive modelling under shape
constraints on the component functions of the linear predictor.
Models can contain multiple shape constrained (univariate
and/or bivariate) and unconstrained terms. The routines of
mgcv(gam) package are used for setting up the model matrix,
printing and plotting the results. Penalized likelihood
maximization based on Newton-Raphson method is used to fit a
model with multiple smoothing parameter selection by GCV or
UBRE/AIC.
Author: Natalya Pya
Maintainer: Natalya Pya
DESCRIPTION | 13 +++++-----
MD5 | 14 +++++------
R/estimate.scam.R | 47 ++++++++++++++++++++++++++-----------
R/plot.scam.R | 66 ++++++++++++++++++++++++----------------------------
R/predict.scam.R | 3 +-
man/scam-package.Rd | 2 -
man/scam.Rd | 51 ++++++++++++++++++++--------------------
man/summary.scam.Rd | 2 -
8 files changed, 109 insertions(+), 89 deletions(-)
Title: A Package for Running jags from R
Diff between R2jags versions 0.03-02 dated 2012-01-12 and 0.03-03 dated 2012-01-22
Description: Using this package to call jags from R.
Author: Yu-Sung Su
Maintainer: Yu-Sung Su
CHANGELOG | 9 ++++++++-
DESCRIPTION | 10 +++++-----
MD5 | 18 +++++++++---------
NAMESPACE | 3 +++
R/AllClass.R | 5 +++++
R/autojags.R | 2 +-
R/jagsParallel.R | 16 +++++++++-------
R/recompile.R | 8 ++++++++
R/update.R | 20 ++++++++++++++++++++
man/jags.Rd | 21 +++++++++++++++++----
10 files changed, 85 insertions(+), 27 deletions(-)
Title: Simulation of high-dimensional data and parallelized repeated
penalized regression
Diff between pensim versions 1.1.3 dated 2011-07-23 and 1.1.4 dated 2012-01-22
Description: Simulation of continuous, correlated high-dimensional data
with time to event or binary response, and parallelized
functions for Lasso, Ridge, and Elastic Net penalized
regression with repeated starts and two-dimensional tuning of
the Elastic Net.
Author: L. Waldron, M. Pintilie, M.-S. Tsao, F. A. Shepherd, C.
Huttenhower*, I. Jurisica* (*equal contribution)
Maintainer: Levi Waldron
Changelog | 2 +
DESCRIPTION | 6 +--
MD5 |only
NAMESPACE |only
R/opt.nested.crossval.R | 3 +
R/opt.splitval.R | 5 +-
R/opt1D.R | 3 +
R/opt2D.R | 5 +-
R/scan.l1l2.R | 3 +
data/beer.exprs.rda |binary
data/beer.survival.rda |binary
inst |only
man/opt.nested.crossval.Rd | 83 ++++++++++++++++++++++++++++++++++++++-------
man/opt.splitval.Rd | 6 +--
man/opt1D.Rd | 6 +--
man/opt2D.Rd | 6 +--
man/pensim-package.Rd | 13 +++----
man/scan.l1l2.Rd | 6 +--
18 files changed, 106 insertions(+), 41 deletions(-)
Title: Efficient Estimation of Covariance and (Partial) Correlation
Diff between corpcor versions 1.6.1 dated 2012-01-20 and 1.6.2 dated 2012-01-22
Description: This package implements a James-Stein-type shrinkage
estimator for the covariance matrix, with separate shrinkage
for variances and correlations. The details of the method are
explained in Sch\"afer and Strimmer (2005) and Opgen-Rhein and
Strimmer (2007). The approach is both computationally as well
as statistically very efficient, it is applicable to "small n,
large p" data, and always returns a positive definite and
well-conditioned covariance matrix. In addition to inferring
the covariance matrix the package also provides shrinkage
estimators for partial correlations and partial variances. The
inverse of the covariance and correlation matrix can be
efficiently computed, as well as any arbitrary power of the
shrinkage correlation matrix. Furthermore, functions are
available for fast singular value decomposition, for computing
the pseudoinverse, and for checking the rank and positive
definiteness of a matrix.
Author: Juliane Schaefer, Rainer Opgen-Rhein, Verena Zuber, A. Pedro
Duarte Silva, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
corpcor-1.6.1/corpcor/R/cov.shrink.R |only
corpcor-1.6.1/corpcor/R/crossprod.powcor.shrink.R |only
corpcor-1.6.1/corpcor/R/powcor.shrink.R |only
corpcor-1.6.1/corpcor/R/pvt.get.lambda.R |only
corpcor-1.6.1/corpcor/R/shrink.internal.R |only
corpcor-1.6.2/corpcor/DESCRIPTION | 8 +++----
corpcor-1.6.2/corpcor/MD5 | 24 +++++++++++-----------
corpcor-1.6.2/corpcor/NAMESPACE | 2 +
corpcor-1.6.2/corpcor/NEWS | 6 +++++
corpcor-1.6.2/corpcor/R/pvt.cppowscor.R |only
corpcor-1.6.2/corpcor/R/pvt.powscor.R |only
corpcor-1.6.2/corpcor/R/pvt.svar.R |only
corpcor-1.6.2/corpcor/R/shrink.estimates.R |only
corpcor-1.6.2/corpcor/R/shrink.intensity.R |only
corpcor-1.6.2/corpcor/R/shrink.misc.R |only
corpcor-1.6.2/corpcor/R/wt.scale.R | 2 -
corpcor-1.6.2/corpcor/man/corpcor-internal.Rd | 6 -----
corpcor-1.6.2/corpcor/man/cov.shrink.Rd | 17 ++-------------
corpcor-1.6.2/corpcor/man/shrink.intensity.Rd |only
19 files changed, 30 insertions(+), 35 deletions(-)
Title: High-Dimensional Regression and CAR Score Variable Selection
Diff between care versions 1.1.1 dated 2011-07-25 and 1.1.2 dated 2012-01-22
Description: The "care" package implements the regression approach of
Zuber and Strimmer (2011) "High-dimensional regression and
variable selection using CAR scores" SAGMB 10: 34. CAR scores
measure the correlation between the response and the
Mahalanobis-decorrelated predictors. The squared CAR score is
a natural measure of variable importance and provides a
canonical ordering of variables. This package provides
functions for estimating CAR scores, for variable selection
using CAR scores, and for estimating corresponding regression
coefficients. Both shrinkage as well as empirical estimators
are available.
Author: Verena Zuber and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 12 ++++++------
MD5 |only
NAMESPACE |only
NEWS | 6 ++++++
R/carscore.R | 8 +++-----
R/slm.R | 8 +++-----
6 files changed, 18 insertions(+), 16 deletions(-)