Title: MetaQC: Objective Quality Control and Inclusion/Exclusion
Criteria for Genomic Meta-Analysis
Diff between MetaQC versions 0.1.10-2 dated 2012-05-27 and 0.1.11 dated 2012-08-15
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 inclusion/exclusion decision.
Author: Don Kang
Maintainer: Don Kang
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
R/MetaQC.R | 24 +++++++++++++++---------
man/MetaQC-package.Rd | 4 ++--
4 files changed, 25 insertions(+), 19 deletions(-)
Title: Plot a correlogram
Diff between corrgram versions 1.2 dated 2012-03-28 and 1.3 dated 2012-08-15
Description: Calculates correlation of variables and displays the
results graphically.
Author: Kevin Wright
Maintainer: Kevin Wright
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
NEWS | 10 ++++++----
R/corrgram.r | 36 +++++++++++++++++++++++++++++++-----
man/corrgram.Rd | 7 ++++---
tests/misc.r | 37 ++++++++++++++++++++++++++++++++++++-
6 files changed, 86 insertions(+), 22 deletions(-)
Title: Compound Poisson linear models
Diff between cplm versions 0.6-1 dated 2012-07-17 and 0.6-2 dated 2012-08-15
Description: Likelihood-based and Bayesian methods for various compound
Poisson linear models.
Author: Wayne Zhang
Maintainer: Wayne Zhang
DESCRIPTION | 9 -
MD5 | 32 ++--
NAMESPACE | 4
R/amer.R |only
R/bcplm.R | 368 ++++++++++++++++++++++++++---------------------------
R/cpglmm.R | 370 +++++++++++++++++++++++++++---------------------------
R/spline.R | 50 +++----
inst/doc/cplm.pdf |binary
man/bcplm.Rd | 300 +++++++++++++++++++++----------------------
man/cpglmm.Rd | 6
man/getF.Rd | 46 +++++-
man/tp.Rd |only
src/bcplm.h | 6
src/cpglmm.h | 6
src/init.c | 1
src/mh.c | 15 +-
src/tweedie.c | 1
src/tweedie.h | 6
18 files changed, 640 insertions(+), 580 deletions(-)
Title: Benchmark and frontier analysis using DEA and SFA
Diff between Benchmarking versions 0.20 dated 2011-09-12 and 0.21 dated 2012-08-15
Description: The package contains methods to support frontier analysis.
It covers Data Envelopment Analysis (DEA). DEA is supported
under different technology assumptions (fdh, vrs, drs, crs,
irs, add/frh, and fdh+), and using different efficiency
measures (input based, output based, hyperbolic graph,
additive, super, and directional efficiency). Peers and slacks
are available, partial price information can be included, and
optimal cost, revenue and profit can be calculated. Evaluation
of mergers is also supported. Methods for graphing the
technology sets are also included. The package also support
comparative methods based on Stochastic Frontier Analyses
(SFA). In general, the methods can be used to solve not only
standard models, but also many other model variants. The
package complements the book, Bogetoft and Otto, Benchmarking
with DEA, SFA, and R, Springer-Verlag, 2011, but can of course
also be used as a stand-alone package.
Author: Peter Bogetoft and Lars Otto
Maintainer: Lars Otto
Benchmarking-0.20/Benchmarking/data/charnes1981.csv |only
Benchmarking-0.20/Benchmarking/data/milkProd.csv |only
Benchmarking-0.20/Benchmarking/data/norWood2004.csv |only
Benchmarking-0.20/Benchmarking/data/pigdata.csv |only
Benchmarking-0.20/Benchmarking/data/projekt.csv |only
Benchmarking-0.21/Benchmarking/DESCRIPTION | 10 ++--
Benchmarking-0.21/Benchmarking/MD5 | 32 ++++++-------
Benchmarking-0.21/Benchmarking/NEWS | 14 +++++
Benchmarking-0.21/Benchmarking/R/cost.R | 6 +-
Benchmarking-0.21/Benchmarking/R/dea.R | 3 -
Benchmarking-0.21/Benchmarking/R/dea.dual.R | 20 +++++++-
Benchmarking-0.21/Benchmarking/R/dea.plot.R | 27 +++++++---
Benchmarking-0.21/Benchmarking/R/deaUtil.R | 4 -
Benchmarking-0.21/Benchmarking/data/charnes1981.csv.gz |only
Benchmarking-0.21/Benchmarking/data/milkProd.csv.gz |only
Benchmarking-0.21/Benchmarking/data/norWood2004.csv.gz |only
Benchmarking-0.21/Benchmarking/data/pigdata.csv.gz |only
Benchmarking-0.21/Benchmarking/data/projekt.csv.gz |only
Benchmarking-0.21/Benchmarking/man/Benchmarking-package.Rd | 8 +--
Benchmarking-0.21/Benchmarking/man/dea.Rd | 8 ++-
Benchmarking-0.21/Benchmarking/man/dea.plot.Rd | 16 ++++--
Benchmarking-0.21/Benchmarking/man/slack.Rd | 7 ++
22 files changed, 104 insertions(+), 51 deletions(-)
Title: Automatic Text Classification via Supervised Learning
Diff between RTextTools versions 1.3.8 dated 2012-05-13 and 1.3.9 dated 2012-08-15
Description: RTextTools is a machine learning package for automatic
text classification that makes it simple for novice users to
get started with machine learning, while allowing experienced
users to easily experiment with different settings and
algorithm combinations. The package includes nine algorithms
for ensemble classification (svm, slda, boosting, bagging,
random forests, glmnet, decision trees, neural networks,
maximum entropy), comprehensive analytics, and thorough
documentation.
Author: Timothy P. Jurka, Loren Collingwood, Amber E. Boydstun,
Emiliano Grossman, Wouter van Atteveldt
Maintainer: Timothy P. Jurka
RTextTools-1.3.8/RTextTools/R/create_corpus.R |only
RTextTools-1.3.8/RTextTools/R/wizard_read_data.R |only
RTextTools-1.3.8/RTextTools/R/wizard_train_classify.R |only
RTextTools-1.3.8/RTextTools/data/.Rhistory |only
RTextTools-1.3.8/RTextTools/man/analytics_container-class.Rd |only
RTextTools-1.3.8/RTextTools/man/analytics_container_virgin-class.Rd |only
RTextTools-1.3.8/RTextTools/man/create_corpus.Rd |only
RTextTools-1.3.8/RTextTools/man/wizard_read_data.Rd |only
RTextTools-1.3.8/RTextTools/man/wizard_train_classify.Rd |only
RTextTools-1.3.9/RTextTools/ChangeLog | 8
RTextTools-1.3.9/RTextTools/DESCRIPTION | 7
RTextTools-1.3.9/RTextTools/MD5 | 76 +++---
RTextTools-1.3.9/RTextTools/NAMESPACE | 12 -
RTextTools-1.3.9/RTextTools/R/classify_model.R | 24 +-
RTextTools-1.3.9/RTextTools/R/classify_models.R | 4
RTextTools-1.3.9/RTextTools/R/create_analytics.R | 114 ++--------
RTextTools-1.3.9/RTextTools/R/create_container.R |only
RTextTools-1.3.9/RTextTools/R/create_precisionRecallSummary.R | 6
RTextTools-1.3.9/RTextTools/R/create_scoreSummary.R | 20 +
RTextTools-1.3.9/RTextTools/R/cross_validate.R | 49 +---
RTextTools-1.3.9/RTextTools/R/summary.analytics.R |only
RTextTools-1.3.9/RTextTools/R/summary.analytics_virgin.R |only
RTextTools-1.3.9/RTextTools/R/train_model.R | 24 +-
RTextTools-1.3.9/RTextTools/R/train_models.R | 4
RTextTools-1.3.9/RTextTools/R/zzz.R | 7
RTextTools-1.3.9/RTextTools/data/NYTimes.csv.gz |binary
RTextTools-1.3.9/RTextTools/data/USCongress.csv.gz |binary
RTextTools-1.3.9/RTextTools/demo |only
RTextTools-1.3.9/RTextTools/man/NYTimes.Rd | 3
RTextTools-1.3.9/RTextTools/man/USCongress.Rd | 3
RTextTools-1.3.9/RTextTools/man/analytics-class.Rd |only
RTextTools-1.3.9/RTextTools/man/analytics_virgin-class.Rd |only
RTextTools-1.3.9/RTextTools/man/classify_model.Rd | 20 -
RTextTools-1.3.9/RTextTools/man/classify_models.Rd | 18 -
RTextTools-1.3.9/RTextTools/man/create_analytics.Rd | 22 -
RTextTools-1.3.9/RTextTools/man/create_container.Rd |only
RTextTools-1.3.9/RTextTools/man/create_ensembleSummary.Rd | 17 -
RTextTools-1.3.9/RTextTools/man/create_matrix.Rd | 10
RTextTools-1.3.9/RTextTools/man/create_precisionRecallSummary.Rd | 20 -
RTextTools-1.3.9/RTextTools/man/create_scoreSummary.Rd | 20 -
RTextTools-1.3.9/RTextTools/man/cross_validate.Rd | 18 -
RTextTools-1.3.9/RTextTools/man/matrix_container-class.Rd | 22 -
RTextTools-1.3.9/RTextTools/man/read_data.Rd | 2
RTextTools-1.3.9/RTextTools/man/recall_accuracy.Rd | 14 -
RTextTools-1.3.9/RTextTools/man/summary.analytics.Rd |only
RTextTools-1.3.9/RTextTools/man/summary.analytics_virgin.Rd |only
RTextTools-1.3.9/RTextTools/man/train_model.Rd | 18 -
RTextTools-1.3.9/RTextTools/man/train_models.Rd | 16 -
48 files changed, 256 insertions(+), 322 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-02-20 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-11-13 2.1-1
2010-06-21 2.1-0
2009-09-03 2.0-0
2009-02-26 1.0-0
Title: Ridge Regression with automatic selection of the penalty
parameter
Diff between ridge versions 1.0 dated 2012-06-30 and 2.0 dated 2012-08-15
Description: Linear and logistic ridge regression for small data sets
and genome-wide SNP data
Author: Erika Cule
Maintainer: Erika Cule
ridge-1.0/ridge/man/coef.ridgeLinear.Rd |only
ridge-1.0/ridge/man/coef.ridgeLogistic.Rd |only
ridge-1.0/ridge/man/plot.ridgeLinear.Rd |only
ridge-1.0/ridge/man/plot.ridgeLogistic.Rd |only
ridge-1.0/ridge/man/predict.ridgeLinear.Rd |only
ridge-1.0/ridge/man/predict.ridgeLogistic.Rd |only
ridge-1.0/ridge/man/summary.ridgeLinear.Rd |only
ridge-1.0/ridge/man/summary.ridgeLogistic.Rd |only
ridge-2.0/ridge/ChangeLog |only
ridge-2.0/ridge/DESCRIPTION | 14 +-
ridge-2.0/ridge/MD5 | 87 +++++++++----
ridge-2.0/ridge/NAMESPACE | 12 +
ridge-2.0/ridge/R/coef.ridgeLinear.R | 2
ridge-2.0/ridge/R/coef.ridgeLogistic.R | 1
ridge-2.0/ridge/R/computeRidgeLogistic.R | 2
ridge-2.0/ridge/R/linearRidge.R | 10 +
ridge-2.0/ridge/R/linearRidgeGenotypes.R |only
ridge-2.0/ridge/R/linearRidgeGenotypesPredict.R |only
ridge-2.0/ridge/R/logisticRidge.R | 14 --
ridge-2.0/ridge/R/logisticRidgeGenotypes.R |only
ridge-2.0/ridge/R/logisticRidgeGenotypesPredict.R |only
ridge-2.0/ridge/R/plot.ridgeLinear.R | 2
ridge-2.0/ridge/R/plot.ridgeLogistic.R | 2
ridge-2.0/ridge/R/summary.ridgeLinear.R | 6
ridge-2.0/ridge/R/summary.ridgeLogistic.R | 4
ridge-2.0/ridge/data/GenBin_genotypes.txt.gz |only
ridge-2.0/ridge/data/GenBin_phenotypes.txt.gz |only
ridge-2.0/ridge/data/GenCont_genotypes.txt.gz |only
ridge-2.0/ridge/data/GenCont_phenotypes.txt.gz |only
ridge-2.0/ridge/man/GenBin.Rd | 13 +-
ridge-2.0/ridge/man/GenCont.Rd | 14 +-
ridge-2.0/ridge/man/Gorman.Rd | 17 +-
ridge-2.0/ridge/man/Hald.Rd | 9 +
ridge-2.0/ridge/man/linearRidge.Rd | 119 +++++++++++--------
ridge-2.0/ridge/man/linearRidgeGenotypes.Rd |only
ridge-2.0/ridge/man/linearRidgeGenotypesPredict.Rd |only
ridge-2.0/ridge/man/logisticRidge.Rd | 105 ++++++++++------
ridge-2.0/ridge/man/logisticRidgeGenotypes.Rd |only
ridge-2.0/ridge/man/logisticRidgeGenotypesPredict.Rd |only
ridge-2.0/ridge/man/pvals.Rd | 42 ++----
ridge-2.0/ridge/man/ridge-internal.Rd | 5
ridge-2.0/ridge/man/ridge-package.Rd | 7 -
ridge-2.0/ridge/src |only
43 files changed, 294 insertions(+), 193 deletions(-)
Title: Parallel Analysis for ordinal and numeric data using polychoric
and Pearson correlations with S3 classes.
Diff between pcaPA versions 1.0 dated 2012-05-08 and 1.1 dated 2012-08-15
Description: A set of functions to perform parallel analysis for
principal components analysis intended mainly for large data
sets. It performs a parallel analysis of continuous, ordered
(including dichotomous/binary as a special case) or mixed type
of data associated with a principal components analysis.
Polychoric correlations among ordered variables, Pearson
correlations among continuous variables and polyserial
correlation between mixed type variables (one ordered and one
continuous) are used. Whenever the use of polyserial or
polychoric correlations yields a non positive definite
correlation matrix, the resulting matrix is transformed into
the nearest positive definite matrix. For details on the GSL
installation in windows please visit the following link:
http://wiki.rglab.org/index.php?title=Public:Installation_of_GSL_from_Windows_binary
Author: Carlos A. Arias
Maintainer: Carlos A. Arias
DESCRIPTION | 8 ++++----
MD5 | 26 +++++++++++++-------------
man/CalculatePABinary.Rd | 2 +-
man/CalculatePAContinuous.Rd | 2 +-
man/CalculatePAMixed.Rd | 2 +-
man/CalculatePAOrdered.Rd | 2 +-
man/Check.PA.Rd | 2 +-
man/CountEigen.PA.Rd | 2 +-
man/PA.Rd | 2 +-
man/coef.PA.Rd | 2 +-
man/plot.PA.Rd | 2 +-
man/print.PA.Rd | 2 +-
man/quantile.PA.Rd | 2 +-
src/Cpolychoric.cpp | 22 ++++++++++++++++++----
14 files changed, 46 insertions(+), 32 deletions(-)
Title: Finite Moment Stable Distributions
Diff between FMStable versions 0.1-0 dated 2012-08-14 and 0.1-1 dated 2012-08-15
Description: This package implements some basic procedures for dealing
with log maximally skew stable distributions, which are also
called finite moment log stable distributions.
Author: Geoff Robinson
Maintainer: Geoff Robinson
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
src/FMStable.c | 14 +++-----------
3 files changed, 9 insertions(+), 17 deletions(-)