Author: Nicola Lama
Diff between vbmp versions 1.3.0 dated 2007-07-24 and 1.12.0 dated 2009-05-10
Title: Variational Bayesian Multinomial Probit Regression
Description: Variational Bayesian Multinomial Probit Regression with
Gaussian Process Priors. It estimates class membership
posterior probability employing variational and sparse
approximation to the full posterior. This software also
incorporates feature weighting by means of Automatic Relevance
Determination.
DESCRIPTION | 38 +++++++++++++++++++++++---------------
NAMESPACE | 2 +-
R/computeKernel.R | 6 +++---
R/gaussQuad.R |only
R/genCPP.classic.R |only
R/genCPP.quad.R |only
R/plotDiagnostics.R | 6 +++---
R/predictCPP.R |only
R/tmean.classic.R |only
R/tmean.quad.R |only
R/vbmp.R | 37 ++++++++++++++++++-------------------
data |only
inst |only
man/BRCA12.Rd |only
man/covParams.Rd | 2 +-
man/lowerBound.Rd | 2 +-
man/predLik.Rd | 2 +-
man/predictCPP.rd |only
man/vbmp.Rd | 33 +++++++++++++++++++++++++--------
19 files changed, 76 insertions(+), 52 deletions(-)
Author: Rainer Opgen-Rhein, Verena Zuber, and Korbinian Strimmer.
Title: Shrinkage t Statistic and Correlation-Adjusted t Score
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.
Diff between st versions 1.1.2 dated 2009-04-26 and 1.1.3 dated 2009-05-10
DESCRIPTION | 8 ++++---- NEWS | 6 ++++++ R/shrinkcat.R | 37 ++++++++++++++++++++++++++++++++----- man/shrinkcat.stat.Rd | 27 ++++++++++++++++++--------- man/st-internal.Rd | 1 + 5 files changed, 61 insertions(+), 18 deletions(-)
Author: Duncan Temple Lang
Diff between rggobi versions 2.1.13 dated 2009-05-05 and 2.1.14 dated 2009-05-10
Title: Interface between R and GGobi
Description: The rggobi package provides a command-line interface to
GGobi, an interactive and dynamic graphics package. Rggobi
complements GGobi's graphical user interface, providing a way
to fluidly transition between analysis and exploration, as well
as automating common tasks.
DESCRIPTION | 8 ++++----
R/gtk.r | 3 ++-
aclocal.m4 | 4 ++--
src/Makevars | 4 ++--
4 files changed, 10 insertions(+), 9 deletions(-)
Author: Alan Dabney
Diff between qvalue versions 1.1.1 dated 2009-02-24 and 1.18.0 dated 2009-05-10
Title: Q-value estimation for false discovery rate control
Description: This package takes a list of p-values resulting from the
simultaneous testing of many hypotheses and estimates their
q-values. The q-value of a test measures the proportion of
false positives incurred (called the false discovery rate) when
that particular test is called significant. Various plots are
automatically generated, allowing one to make sensible
significance cut-offs. Several mathematical results have
recently been shown on the conservative accuracy of the
estimated q-values from this software. The software can be
applied to problems in genomics, brain imaging, astrophysics,
and data mining.
qvalue-1.1.1/qvalue/INDEX |only
qvalue-1.1.1/qvalue/inst/doc/qvalue.log |only
qvalue-1.18.0/qvalue/DESCRIPTION | 46
qvalue-1.18.0/qvalue/R/qvalue.R | 2
qvalue-1.18.0/qvalue/inst/doc/my-qvalue-results.txt | 6342 ++++++++++----------
qvalue-1.18.0/qvalue/inst/doc/qvalue-002.eps | 62
qvalue-1.18.0/qvalue/inst/doc/qvalue-002.pdf | 207
qvalue-1.18.0/qvalue/inst/doc/qvalue-004.eps | 103
qvalue-1.18.0/qvalue/inst/doc/qvalue-004.pdf | 253
qvalue-1.18.0/qvalue/inst/doc/qvalue-006.eps | 545 -
qvalue-1.18.0/qvalue/inst/doc/qvalue-006.pdf | 967 +--
qvalue-1.18.0/qvalue/inst/doc/qvalue.pdf |binary
qvalue-1.18.0/qvalue/inst/doc/qvalue.tex | 4
qvalue-1.18.0/qvalue/man/qplot.rd | 4
qvalue-1.18.0/qvalue/man/qvalue.rd | 4
15 files changed, 4311 insertions(+), 4228 deletions(-)
Author: Aaron A. King, Edward L. Ionides, Carles Martinez Breto, Steve
Ellner, Bruce Kendall
Title: Statistical inference for partially observed Markov processes
Description: Inference methods for partially-observed Markov processes
Diff between pomp versions 0.23-5 dated 2009-05-04 and 0.23-6 dated 2009-05-10
DESCRIPTION | 10 +++++----- R/init.state-pomp.R | 4 ++-- inst/ChangeLog | 24 ++++++++++++++++++++++++ inst/doc/Rplots.pdf | 4 ++-- inst/doc/compiled_code_in_pomp.pdf |binary inst/doc/intro_to_pomp.pdf |binary inst/include/pomp.h | 11 +---------- src/eulermultinom.c | 8 ++++---- src/pomp.h | 11 +---------- tests/sir.R | 2 +- tests/sir.Rout.save | 10 +++++----- 11 files changed, 45 insertions(+), 39 deletions(-)
Author: Gaston Sanchez
Diff between plspm versions 0.1-1 dated 2009-05-04 and 0.1-2 dated 2009-05-10
Title: Partial Least Squares data analysis methods
Description: Partial Least Squares (PLS) methods with emphasis on
structural equation models with latent variables.
plspm-0.1-1/plspm/R/nipals.default.R |only
plspm-0.1-1/plspm/R/plsca.default.R |only
plspm-0.1-1/plspm/R/plspm.default.R |only
plspm-0.1-1/plspm/R/plsreg1.default.R |only
plspm-0.1-1/plspm/R/plsreg2.default.R |only
plspm-0.1-2/plspm/DESCRIPTION | 9
plspm-0.1-2/plspm/R/nipals.R | 101 +++++
plspm-0.1-2/plspm/R/plot.plspm.groups.R |only
plspm-0.1-2/plspm/R/plsca.R | 98 ++++-
plspm-0.1-2/plspm/R/plspm.R | 547 +++++++++++++++++++++++++++-
plspm-0.1-2/plspm/R/plspm.groups.R |only
plspm-0.1-2/plspm/R/plsreg1.R | 175 ++++++++
plspm-0.1-2/plspm/R/plsreg2.R | 142 +++++++
plspm-0.1-2/plspm/R/print.plspm.groups.R |only
plspm-0.1-2/plspm/data/satisfaction.rda |binary
plspm-0.1-2/plspm/man/nipals.Rd | 2
plspm-0.1-2/plspm/man/plot.plspm.groups.Rd |only
plspm-0.1-2/plspm/man/plsca.Rd | 2
plspm-0.1-2/plspm/man/plspm-package.Rd | 10
plspm-0.1-2/plspm/man/plspm.Rd | 3
plspm-0.1-2/plspm/man/plspm.groups.Rd |only
plspm-0.1-2/plspm/man/plsreg1.Rd | 2
plspm-0.1-2/plspm/man/plsreg2.Rd | 2
plspm-0.1-2/plspm/man/print.plspm.groups.Rd |only
plspm-0.1-2/plspm/man/satisfaction.Rd | 2
25 files changed, 1070 insertions(+), 25 deletions(-)
Author: T. Hastie, R. Tibshirani, Balasubramanian Narasimhan, Gil Chu
Title: Pam: prediction analysis for microarrays
Description: Some functions for sample classification in microarrays
Diff between pamr versions 1.33 dated 2009-04-15 and 1.42.0 dated 2009-05-10
pamr-1.33/pamr/INDEX |only pamr-1.42.0/pamr/DESCRIPTION | 9 ++-- pamr-1.42.0/pamr/R/pamr.fdr.R | 3 - pamr-1.42.0/pamr/R/pamr.listgenes.R | 5 -- pamr-1.42.0/pamr/R/pamr.makeclasses.R | 1 pamr-1.42.0/pamr/R/pamr.plotstrata.R | 1 pamr-1.42.0/pamr/R/pamr.survfuns.R | 39 +++++++----------- pamr-1.42.0/pamr/R/pamr.xlfuns.R | 3 - pamr-1.42.0/pamr/inst |only pamr-1.42.0/pamr/man/pamr.confusion.survival.Rd | 13 +++--- pamr-1.42.0/pamr/man/pamr.cv.Rd | 8 +-- pamr-1.42.0/pamr/man/pamr.fdr.Rd | 3 - pamr-1.42.0/pamr/man/pamr.from.excel.Rd | 6 +- pamr-1.42.0/pamr/man/pamr.listgenes.Rd | 6 +- pamr-1.42.0/pamr/man/pamr.makeclasses.Rd | 4 + pamr-1.42.0/pamr/man/pamr.plotcen.Rd | 2 pamr-1.42.0/pamr/man/pamr.plotstrata.Rd | 6 +- pamr-1.42.0/pamr/man/pamr.plotsurvival.Rd | 4 - pamr-1.42.0/pamr/man/pamr.predict.Rd | 2 pamr-1.42.0/pamr/man/pamr.surv.to.class2.Rd | 6 +- pamr-1.42.0/pamr/man/pamr.test.errors.surv.compute.Rd | 6 +- pamr-1.42.0/pamr/man/pamr.to.excel.Rd | 2 pamr-1.42.0/pamr/man/pamr.train.Rd | 3 - pamr-1.42.0/pamr/src/cox_func.c |only 24 files changed, 63 insertions(+), 69 deletions(-)
Author: Katherine S. Pollard, Houston N. Gilbert, Yongchao Ge, Sandra
Taylor, Sandrine Dudoit
Title: Resampling-based multiple hypothesis testing
Description: Non-parametric bootstrap and permutation resampling-based
multiple testing procedures (including empirical Bayes methods)
for controlling the family-wise error rate (FWER), generalized
family-wise error rate (gFWER), tail probability of the
proportion of false positives (TPPFP), and false discovery rate
(FDR). Several choices of bootstrap-based null distribution
are implemented (centered, centered and scaled,
quantile-transformed). Single-step and step-wise methods are
available. Tests based on a variety of t- and F-statistics
(including t-statistics based on regression parameters from
linear and survival models as well as those based on
correlation parameters) are included. When probing hypotheses
with t-statistics, users may also select a potentially faster
null distribution which is multivariate normal with mean zero
and variance covariance matrix derived from the vector
influence function. Results are reported in terms of adjusted
p-values, confidence regions and test statistic cutoffs. The
procedures are directly applicable to identifying
differentially expressed genes in DNA microarray experiments.
Diff between multtest versions 1.23.3 dated 2009-02-15 and 2.0.0 dated 2009-05-10
DESCRIPTION | 42 ++++--- NAMESPACE | 17 ++ R/EBMTP.R |only R/EBzzz.R |only R/ICQTNullDist.R |only R/mt.basic.R | 59 +++++++++ R/nulldistn_c.R | 175 +++++++++++++++++++---------- R/statistics.R | 17 +- R/test.R | 175 ++++++++++++++++++++++++----- R/zzz.R | 311 ++++++++++++++++++++++++++++++++++++++++++---------- man/EBMTP-class.Rd |only man/EBMTP.Rd |only man/Hsets.Rd |only man/MTP-class.Rd | 60 +++++++--- man/MTP-methods.Rd | 66 ++++++++--- man/MTP.Rd | 131 ++++++++++++++++----- man/boot.null.Rd | 86 +++++++++++--- man/corr.null.Rd |only man/meanX.Rd | 24 +++- man/mt.internal.Rd | 13 ++ man/mt.rawp2adjp.Rd | 112 +++++++++++------- src/VScount.c |only 22 files changed, 989 insertions(+), 299 deletions(-)
Author: Patrick E. Meyer, Frederic Lafitte, Gianluca Bontempi
Title: Mutual Information Network Inference
Description: This package implements various algorithms for inferring
mutual information networks from data. All the algorithms
compute the mutual information matrix in order to infer a
network. Several mutual information estimators are implemented.
Diff between minet versions 1.1.7 dated 2009-01-05 and 1.4.0 dated 2009-05-10
CHANGES | 11 DESCRIPTION | 14 R/build.mim.R | 5 R/disc.R | 6 demo/demo.R | 2 inst/doc/minet.Rnw | 187 +--- inst/doc/minet.bib |only inst/doc/minet.pdf | 2324 +++++++++++++++++++++++++++-------------------------- man/build.mim.Rd | 14 man/disc.Rd | 7 man/minet.Rd | 4 man/mr.net.Rd | 27 man/syn.data.Rd | 5 man/vis.res.Rd | 7 src/disc.cpp | 2 15 files changed, 1316 insertions(+), 1299 deletions(-)
Author: Andrew Gelman
Diff between mi versions 0.07-1 dated 2009-04-29 and 0.07-2 dated 2009-05-10
Title: Missing Data Imputation and Model Checking
Description: Missing-data imputation and model checking
CHANGELOG | 5 ++++
DESCRIPTION | 8 +++----
NAMESPACE | 4 +--
R/write.mi.R |only
man/mi.Rd | 57 ++++++++++++++++++++++++++------------------------------
man/write.mi.Rd |only
6 files changed, 38 insertions(+), 36 deletions(-)
Author: Hao Wu, modified by Hyuna Yang and Keith Sheppard with ideas
from Gary Churchill, Katie Kerr and Xiangqin Cui.
Title: Tools for analyzing Micro Array experiments
Description: Analysis of N-dye Micro Array experiment using mixed model
effect. Containing anlysis of variance, permutation and
bootstrap, cluster and consensus tree.
Diff between maanova versions 1.13.3 dated 2009-02-13 and 1.14.0 dated 2009-05-10
DESCRIPTION | 16 inst/doc/maanova.pdf | 946 +++++++++++++++++++++++++-------------------------- 2 files changed, 482 insertions(+), 480 deletions(-)
Author: Trevor Hastie, Robert Tibshirani, Balasubramanian Narasimhan,
Gilbert Chu
Title: impute: Imputation for microarray data
Description: Imputation for microarray data (currently KNN only)
Diff between impute versions 1.0-5 dated 2006-04-18 and 1.16.0 dated 2009-05-10
impute-1.0-5/impute/INDEX |only impute-1.16.0/impute/DESCRIPTION | 12 + impute-1.16.0/impute/R/allknnimp.R | 66 ++++------ impute-1.16.0/impute/man/impute.knn.Rd | 60 ++++----- impute-1.16.0/impute/man/khanmiss.Rd | 30 ++-- impute-1.16.0/impute/src/knnimpute.f | 214 +++++++++++++++------------------ 6 files changed, 182 insertions(+), 200 deletions(-)
Author: Katherine S. Pollard, with Mark J. van der Laan
Diff between hopach versions 2.3.0 dated 2009-02-15 and 2.4.0 dated 2009-05-10
Title: Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
Description: The HOPACH clustering algorithm builds a hierarchical tree
of clusters by recursively partitioning a data set, while
ordering and possibly collapsing clusters at each level. The
algorithm uses the Mean/Median Split Silhouette (MSS) criteria
to identify the level of the tree with maximally homogeneous
clusters. It also runs the tree down to produce a final ordered
list of the elements. The non-parametric bootstrap allows one
to estimate the probability that each element belongs to each
cluster (fuzzy clustering).
DESCRIPTION | 23 -
inst/doc/hopach.pdf | 688 ++++++++++++++++++++++++----------------------------
2 files changed, 343 insertions(+), 368 deletions(-)
Author: Dan Carr
Diff between hexbin versions 1.17.0 dated 2008-12-04 and 1.18.0 dated 2009-05-10
Title: Hexagonal Binning Routines
Description: Binning and plotting functions for hexagonal bins. Now
uses and relies on grid graphics and formal (S4) classes and
methods.
DESCRIPTION | 14
R/grid.hexagons.R | 1
inst/doc/hexagon_binning.pdf |66939 +++++++++++++++++++++----------------------
man/hexbinplot.Rd | 2
4 files changed, 33057 insertions(+), 33899 deletions(-)
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by Ben Bolker and Thomas Lumley
Title: Various R programming tools
Description: Various R programming tools
Diff between gtools versions 2.5.0-1 dated 2009-02-19 and 2.6.1 dated 2009-05-10
ChangeLog | 987 +++++++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 22 - NAMESPACE | 1 NEWS | 18 R/keywords.R |only R/newVersionAvailable.R |only inst |only man/addLast.Rd | 2 man/binsearch.Rd | 4 man/capture.Rd | 7 man/combinations.Rd | 4 man/defmacro.Rd | 4 man/dirichlet.Rd | 4 man/foldchange.Rd | 4 man/gtools-deprecated.Rd | 2 man/invalid.Rd | 4 man/keywords.Rd |only man/logit.Rd | 4 man/mixedsort.Rd | 4 man/oddeven.Rd | 4 man/permute.Rd | 4 man/quantcut.Rd | 6 man/running.Rd | 4 man/scat.Rd | 4 man/setTCPNoDelay.Rd | 4 man/smartbind.Rd | 2 src/Makevars.win | 2 27 files changed, 1055 insertions(+), 46 deletions(-)
Author: R. Gentleman, Elizabeth Whalen, W. Huber, S. Falcon
Title: graph: A package to handle graph data structures
Description: A package that implements some simple graph handling
capabilities.
Diff between graph versions 1.20.0 dated 2008-11-28 and 1.22.2 dated 2009-05-10
DESCRIPTION | 22 +- NAMESPACE | 20 +- R/AllGenerics.R | 2 R/attrData.R | 4 R/edgefunctions.R | 2 R/graphNEL.R | 68 +++----- R/methods-graph.R | 7 R/settings.R | 66 ++++++-- inst/doc/GraphClass.pdf | 334 ++++++++++++++++++++++--------------------- inst/doc/clusterGraph.pdf |binary inst/doc/graph.pdf |binary inst/doc/graphAttributes.pdf |binary man/combineNodes.Rd | 13 + man/graphNEL-class.Rd | 1 man/renderInfo-class.Rd | 127 +++++++++++++--- src/Makevars |only src/Makevars.win |only src/graph.c | 2 18 files changed, 398 insertions(+), 270 deletions(-)
Author: Beiying Ding
Title: Classification using generalized partial least squares
Description: Classification using generalized partial least squares for
two-group and multi-group (more than 2 group) classification.
Diff between gpls versions 1.3.1 dated 2006-04-15 and 1.16.0 dated 2009-05-10
gpls-1.16.0/gpls/DESCRIPTION | 18 +++++++++++------- gpls-1.16.0/gpls/NAMESPACE | 4 ++-- gpls-1.16.0/gpls/R/glpls1a.R | 6 ------ gpls-1.16.0/gpls/inst/doc/gpls.pdf |binary gpls-1.16.0/gpls/man/glpls1a.Rd | 9 +++++++-- gpls-1.16.0/gpls/man/glpls1a.cv.error.Rd | 9 +++++++-- gpls-1.16.0/gpls/man/glpls1a.logit.all.Rd | 9 +++++++-- gpls-1.16.0/gpls/man/glpls1a.mlogit.Rd | 9 +++++++-- gpls-1.16.0/gpls/man/glpls1a.mlogit.cv.error.Rd | 8 ++++++-- gpls-1.16.0/gpls/man/glpls1a.train.test.error.Rd | 9 +++++++-- gpls-1.16.0/gpls/man/gpls.Rd | 17 +++++++++++------ gpls-1.16.0/gpls/man/predict.gpls.Rd | 17 +++++++---------- gpls-1.3.1/gpls/INDEX |only 13 files changed, 72 insertions(+), 43 deletions(-)
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by Ben Bolker, Thomas Lumley, and Randall C
Johnson. Contributions from Randall C. Johnson are Copyright
(2005) SAIC-Frederick, Inc. Funded by the Intramural Research
Program, of the NIH, National Cancer Institute, Center for
Cancer Research under NCI Contract NO1-CO-12400.
Title: Various R programming tools for model fitting
Description: Various R programming tools for model fitting
Diff between gmodels versions 2.14.1 dated 2007-12-08 and 2.15.0 dated 2009-05-10
ChangeLog | 61 +++++++++++++++++++++ DESCRIPTION | 27 ++++----- NAMESPACE | 6 +- NEWS | 14 ++++ R/ci.R | 12 ++-- R/est.lmer.R | 4 - R/est.mer.R |only R/estimable.R | 142 ++++++++++++++++++++++++++------------------------ R/fit.contrast.R | 32 +++++------ R/to.est.R | 12 ++-- inst |only man/CrossTable.Rd | 7 +- man/ci.Rd | 18 +++--- man/estimable.Rd | 16 ++--- man/fast.prcomp.Rd | 4 - man/fit.contrast.Rd | 14 ++-- man/glh.test.Rd | 8 +- man/make.contrasts.Rd | 4 - test |only 19 files changed, 230 insertions(+), 151 deletions(-)
Author: Holger Froehlich
Diff between gene2pathway versions 1.0.5.4 dated 2009-04-22 and 1.2.0 dated 2009-05-10
Title: Prediction of KEGG pathway membership for individual genes based
on InterPro domain signatures
Description: The package takes a list of genes and predicts to which
KEGG pathway each gene maps to. This is done by looking at the
InterPro domains of each gene. Each prediction is assigned a
confidence score. The package also allows to predict connected
component membership of genes within signaling pathways.
Separate models for each organism supported by KEGG can be
trained.
DESCRIPTION | 8 ++++----
R/gene2pathway.signaltrans.R | 9 ++++-----
inst/doc/gene2pathway.pdf |binary
3 files changed, 8 insertions(+), 9 deletions(-)
Author: Gregory R. Warnes
Diff between fork versions 1.2.1 dated 2007-11-27 and 1.2.2 dated 2009-05-10
Title: R functions for handling multiple processes.
Description: These functions provides simple wrappers around the Unix
process management API calls: fork, signal, wait, waitpid,
kill, and _exit. This enables construction of programs that
utilize and mange multiple concurrent processes. Commercial
support for this package available from Random Technologies,
LLC
ChangeLog | 167 +++++++++++++++++++++++++++++++++++++-----------------------
DESCRIPTION | 26 +++++----
inst |only
man/wait.Rd | 9 +--
4 files changed, 125 insertions(+), 77 deletions(-)
Author: Chris Fraley, Adrian E. Raftery, J. McLean Sloughter, Tilmann
Gneiting, University of Washington With contributions from
Bobby Yuen and Michael Polokowski
Title: Probabilistic Forecasting using Ensembles and Bayesian Model
Averaging
Description: Bayesian Model Averaging to create probabilistic forecasts
from ensemble forecasts and weather observations.
Diff between ensembleBMA versions 4.2 dated 2009-04-01 and 4.2.1 dated 2009-05-10
CHANGELOG | 4 +++- DESCRIPTION | 8 ++++---- R/cdf.ensembleBMAgamma.R | 2 +- R/ensembleBMAgamma.R | 2 +- R/ensembleBMAgamma0.R | 2 +- R/ensembleBMAnormal.R | 2 +- R/ensembleData.R | 7 ++++--- R/trainingData.R | 3 +-- 8 files changed, 16 insertions(+), 14 deletions(-)
Author: John Fox
Diff between effects versions 2.0-6 dated 2009-04-23 and 2.0-7 dated 2009-05-10
Title: Effect Displays for Linear, Generalized Linear,
Multinomial-Logit, and Proportional-Odds Logit Models
Description: Graphical and tabular effect displays, e.g., of
interactions, for linear generalized linear, multinomial-logit,
and proportional-odds logit models.
DESCRIPTION | 10 +++++-----
R/utilities.R | 6 ++++--
inst/CHANGES | 4 ++++
man/effects-package.Rd | 4 ++--
4 files changed, 15 insertions(+), 9 deletions(-)
Author: Joseph Richards
Diff between diffusionMap versions 0.0-1 dated 2009-05-08 and 0.0-2 dated 2009-05-10
Title: Diffusion map
Description: Implements diffusion map method of data parametrization,
including creation and visualization of diffusion map and
course-graining using diffusion K-means.
DESCRIPTION | 6 +++---
man/diffusionKmeans.Rd | 2 +-
2 files changed, 4 insertions(+), 4 deletions(-)
Author: Michael Malecki
Title: apsrtable model-output formatter for social science
Description: Formats latex tables from one or more model objects
side-by-side with standard errors below, not unlike tables
found in such journals as the American Political Science
Review.
Diff between apsrtable versions 0.7-2 dated 2009-02-26 and 0.7-3 dated 2009-05-10
DESCRIPTION | 17 +++++-- NAMESPACE | 5 +- R/apsrtable.R | 104 ++++++++++++++++++++++++++++++++++++------------ inst |only man/apsrtable.Rd | 12 ++++- man/apsrtableSummary.Rd |only man/modelInfo.Rd | 2 7 files changed, 105 insertions(+), 35 deletions(-)
Author: Nusrat Rabbee
Diff between RLMM versions 0.7 dated 2005-09-05 and 1.6.0 dated 2009-05-10
Title: A Genotype Calling Algorithm for Affymetrix SNP Arrays
Description: A classification algorithm, based on a multi-chip,
multi-SNP approach for Affymetrix SNP arrays. Using a large
training sample where the genotype labels are known, this
aglorithm will obtain more accurate classification results on
new data. RLMM is based on a robust, linear model and uses the
Mahalanobis distance for classification. The chip-to-chip
non-biological variation is removed through normalization. This
model-based algorithm captures the similarities across genotype
groups and probes, as well as thousands other SNPs for accurate
classification. NOTE: 100K-Xba only at for now.
RLMM-0.7/RLMM/inst/Xba.CQV |only
RLMM-0.7/RLMM/inst/Xba.regions |only
RLMM-0.7/RLMM/inst/doc/RLMM.tex |only
RLMM-1.6.0/RLMM/DESCRIPTION | 30
RLMM-1.6.0/RLMM/R/create_Thetafile.R | 289 ++-
RLMM-1.6.0/RLMM/inst/doc/RLMM.Rnw | 242 ++-
RLMM-1.6.0/RLMM/inst/doc/RLMM.pdf | 2536 ++++++++++++++++++++++++-----------
RLMM-1.6.0/RLMM/inst/doc/Xba.rlmm |only
RLMM-1.6.0/RLMM/inst/doc/Xba.theta |only
RLMM-1.6.0/RLMM/inst/doc/snps.lst |only
10 files changed, 2103 insertions(+), 994 deletions(-)
Author: Vince Carey
Diff between RBGL versions 1.18.0 dated 2008-11-28 and 1.20.0 dated 2009-05-10
Title: An interface to the BOOST graph library
Description: A fairly extensive and comprehensive interface to the
graph algorithms contained in the BOOST library.
DESCRIPTION | 12
inst/doc/RBGL.pdf | 2729 +++++++++++++++++++++++++-------------------------
man/clusteringCoef.Rd | 11
man/coloring.Rd | 2
man/kCores.Rd | 2
man/layout.Rd | 2
man/transitivity.Rd | 7
7 files changed, 1401 insertions(+), 1364 deletions(-)
Author: David Rocke, Geun Cheol Lee, and John Tillinghast.
Title: LMGene Software for Date Transformation and Identification of
Differentially Expressed Genes in Gene Expression Arrays
Description: LMGene package for analysis of microarray data using a
linear model and glog data transformation in the R statistical
package.
Diff between LMGene versions 1.9.1 dated 2007-12-15 and 1.14.0 dated 2009-05-10
LMGene-1.14.0/LMGene/DESCRIPTION | 32 LMGene-1.14.0/LMGene/R/GetLMObj.R | 15 LMGene-1.14.0/LMGene/R/LMGene.R |only LMGene-1.14.0/LMGene/R/genediff.R | 14 LMGene-1.14.0/LMGene/R/jggrad2.R | 2 LMGene-1.14.0/LMGene/R/lnormeS.R | 20 LMGene-1.14.0/LMGene/R/mlm2lm.R | 2 LMGene-1.14.0/LMGene/R/msa.R | 2 LMGene-1.14.0/LMGene/R/msecalc.R | 19 LMGene-1.14.0/LMGene/R/msecalcmult.R | 35 LMGene-1.14.0/LMGene/R/neweS.R | 18 LMGene-1.14.0/LMGene/R/norm.R | 2 LMGene-1.14.0/LMGene/R/psmeans.R | 38 LMGene-1.14.0/LMGene/R/pvadjust.R | 2 LMGene-1.14.0/LMGene/R/rowaov.R | 26 LMGene-1.14.0/LMGene/R/tranest.R | 15 LMGene-1.14.0/LMGene/R/tranest2.R | 31 LMGene-1.14.0/LMGene/R/tranestmult.R | 56 LMGene-1.14.0/LMGene/R/transeS.R | 3 LMGene-1.14.0/LMGene/data/sample.eS.RData |binary LMGene-1.14.0/LMGene/inst/doc/LMGene.Rnw | 515 LMGene-1.14.0/LMGene/inst/doc/LMGene.pdf |binary LMGene-1.14.0/LMGene/inst/doc/Rplots.ps |43884 +++++++++++++++--------------- LMGene-1.14.0/LMGene/man/GetLMObj.Rd | 63 LMGene-1.14.0/LMGene/man/LMGene.Rd | 49 LMGene-1.14.0/LMGene/man/genediff.Rd | 54 LMGene-1.14.0/LMGene/man/lnormeS.Rd | 70 LMGene-1.14.0/LMGene/man/mlm2lm.Rd | 43 LMGene-1.14.0/LMGene/man/msa.Rd | 36 LMGene-1.14.0/LMGene/man/msecalc.Rd | 44 LMGene-1.14.0/LMGene/man/msecalcmult.Rd | 45 LMGene-1.14.0/LMGene/man/neweS.Rd | 29 LMGene-1.14.0/LMGene/man/psmeans.Rd | 84 LMGene-1.14.0/LMGene/man/rowaov.Rd | 46 LMGene-1.14.0/LMGene/man/rowlist.Rd | 51 LMGene-1.14.0/LMGene/man/sample.eS.Rd | 13 LMGene-1.14.0/LMGene/man/tranest.Rd | 54 LMGene-1.14.0/LMGene/man/tranest2.Rd | 54 LMGene-1.14.0/LMGene/man/tranestmult.Rd | 56 LMGene-1.14.0/LMGene/man/transeS.Rd | 72 LMGene-1.9.1/LMGene/R/LMGene.r |only 41 files changed, 22735 insertions(+), 22859 deletions(-)
Author: R. Gentleman and Alain Vandal .
Title: NPMLE for Censored and Truncated Data
Description: Many functions for computing the NPMLE for censored and
truncated data.
Diff between Icens versions 1.2.0 dated 2005-11-04 and 1.16.0 dated 2009-05-10
Icens-1.16.0/Icens/DESCRIPTION | 12 ++++++++---- Icens-1.16.0/Icens/NAMESPACE |only Icens-1.16.0/Icens/man/icsurv.Rd | 25 ++++++++++++++----------- Icens-1.2.0/Icens/INDEX |only 4 files changed, 22 insertions(+), 15 deletions(-)
Author: Dongxiao Zhu and Youjuan Li
Title: Multivariate Correlation Estimator and Statistical Inference
Procedures.
Description: Multivariate correlation estimation and statistical
inference. See package vignette.
Diff between CORREP versions 1.0.1 dated 2007-03-31 and 1.10.0 dated 2009-05-10
CORREP-1.0.1/CORREP/R/cor.LRtest1.R |only CORREP-1.0.1/CORREP/R/cor.LRtest2.R |only CORREP-1.0.1/CORREP/inst/doc/CORREP-002.eps |only CORREP-1.0.1/CORREP/inst/doc/CORREP.aux |only CORREP-1.0.1/CORREP/inst/doc/CORREP.log |only CORREP-1.0.1/CORREP/inst/doc/CORREP.rnw |only CORREP-1.0.1/CORREP/inst/doc/CORREP.tex |only CORREP-1.0.1/CORREP/inst/doc/Rplots.ps |only CORREP-1.0.1/CORREP/inst/doc/gal_all.rda |only CORREP-1.0.1/CORREP/inst/doc/true.member.rda |only CORREP-1.0.1/CORREP/man/cor.LRtest1.Rd |only CORREP-1.0.1/CORREP/man/cor.LRtest2.Rd |only CORREP-1.10.0/CORREP/DESCRIPTION | 27 +++++++++++++++++---------- CORREP-1.10.0/CORREP/R/cor.LRtest.R |only CORREP-1.10.0/CORREP/R/cor.LRtest.std.R |only CORREP-1.10.0/CORREP/inst/doc/CORREP.Rnw |only CORREP-1.10.0/CORREP/inst/doc/CORREP.pdf |binary CORREP-1.10.0/CORREP/man/CORREP-package.Rd | 11 ++++++++--- CORREP-1.10.0/CORREP/man/cor.LRtest.Rd |only CORREP-1.10.0/CORREP/man/cor.LRtest.std.Rd |only CORREP-1.10.0/CORREP/man/cor.balance.Rd | 2 +- CORREP-1.10.0/CORREP/man/cor.bootci.Rd | 10 +++++----- CORREP-1.10.0/CORREP/man/cor.unbalance.Rd | 2 +- CORREP-1.10.0/CORREP/man/gal_all.Rd | 6 +++--- CORREP-1.10.0/CORREP/man/permutest.Rd | 4 ++-- 25 files changed, 37 insertions(+), 25 deletions(-)