Title: Classification and Regression Training
Diff between caret versions 4.58 dated 2010-08-29 and 4.59 dated 2010-09-01
Description: Misc functions for training and plotting classification
and regression models
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer and Allan Engelhardt
Maintainer: Max Kuhn
DESCRIPTION | 8 +-
R/rfe.R | 90 ++++++++++++++++++-------
R/selectByFilter.R | 156 +++++++++++++++++++++++++++++++++++---------
inst/NEWS | 12 +++
inst/doc/caretMisc.pdf |binary
inst/doc/caretSelection.R | 83 ++++++++++++++++++-----
inst/doc/caretSelection.Rnw | 79 ++++++++++++++++++++--
inst/doc/caretSelection.pdf |binary
inst/doc/caretTrain.pdf |binary
inst/doc/caretVarImp.pdf |binary
man/nullModel.Rd | 8 +-
man/trainControl.Rd | 2
12 files changed, 351 insertions(+), 87 deletions(-)
Title: Time wave analysis and graphical representation
Diff between seewave versions 1.5.8 dated 2010-06-15 and 1.5.9 dated 2010-09-01
Description: seewave provides functions for analysing, manipulating,
displaying, editing and synthesizing time waves (particularly
sound). This package processes time analysis (oscillograms and
envelopes), spectral content, resonance quality factor,
entropy, cross correlation and autocorrelation, zero-crossing,
dominant frequency, analytic signal, frequency coherence, 2D
and 3D spectrograms and many other analyses.
Author: Jerome Sueur
Maintainer: Jerome Sueur
DESCRIPTION | 12
NAMESPACE | 2
NEWS | 15 -
R/seewave.r | 602 +++++++++++++++++++++++++++---------------------
inst/doc/seewave_IO.pdf |binary
man/autoc.Rd | 25 +
man/corenv.Rd | 3
man/covspectro.Rd | 3
man/csh.Rd | 7
man/dfreq.Rd | 7
man/dynspec.Rd | 10
man/ffilter.Rd | 5
man/fund.Rd | 3
man/lfs.Rd | 12
man/meanspec.Rd | 17 -
man/oscillo.Rd | 7
man/seewave.package.Rd | 4
man/spec.Rd | 7
man/spectro.Rd | 15 +
man/spectro3D.Rd | 7
man/wf.Rd | 7
21 files changed, 455 insertions(+), 315 deletions(-)
Title: Statistical Catch-at-Age Plotting Environment
Diff between scape versions 1.1-0 dated 2010-08-31 and 1.1-2 dated 2010-09-01
Description: Import and plot results from statistical catch-at-age
models, used in fisheries stock assessments.
Author: Arni Magnusson
Maintainer: Arni Magnusson
DESCRIPTION | 8
NEWS | 6
R/importCol.R | 33
data/x.cod.R | 853 ++++----
data/x.ling.R | 3920 ++++++++++++++++++++---------------------
data/x.oreo.R | 4376 +++++++++++++++++++++++-----------------------
data/x.sbw.R | 785 ++++----
inst/doc/Rplots.pdf | 2937 ++++++++++--------------------
inst/doc/dsc-vignette.pdf |binary
inst/doc/gallery.pdf |binary
inst/doc/mymodel.pdf |binary
man/importCol.Rd | 7
man/x.cod.Rd | 4
man/x.ling.Rd | 4
man/x.oreo.Rd | 5
man/x.sbw.Rd | 4
16 files changed, 6122 insertions(+), 6820 deletions(-)
Title: P2BAT
Diff between pbatR versions 2.2-0 dated 2009-11-23 and 2.2-2 dated 2010-09-01
Description: This package provides data analysis via the pbat program,
and an alternative internal implementation of the power
calculations via simulation only. For analysis, this package
provides a frontend to the PBAT software, automatically reading
in the output from the pbat program and displaying the
corresponding figure when appropriate (i.e. PBAT-logrank). It
includes support for multiple processes and clusters. For
analysis, users must download PBAT (developed by Christoph
Lange) and accept it's license, available on the PBAT webpage.
Both the data analysis and power calculations have command line
and graphical interfaces using tcltk.
Author: Thomas Hoffmann
Maintainer: Thomas Hoffmann
DESCRIPTION | 8 +++----
R/createCommandfile.R | 55 ++++++++++++++++++++++++++++++++++++++++----------
R/pbat.m.R | 2 -
R/pbatGUI.R | 5 ++--
man/pbat.Rd | 8 ++++---
src/kludge.cpp | 25 ++++++++++++----------
src/powerSim.cpp | 20 ++++++++++--------
src/thmalloc.h |only
8 files changed, 83 insertions(+), 40 deletions(-)
Title: Interface between GMT Map-Making Software and R
Diff between gmt versions 1.1-7 dated 2010-08-28 and 1.1-8 dated 2010-09-01
Description: Interface between the GMT map-making software and R,
enabling the user to manipulate geographic data within R and
call GMT commands to draw and annotate maps in postscript
format. The 'gmt' package is about interactive data analysis,
rapidly visualizing subsets and summaries of geographic data,
while performing statistical analysis in the R console.
Author: Arni Magnusson
Maintainer: Arni Magnusson
DESCRIPTION | 8 ++++----
NEWS | 4 ++--
man/gmt-package.Rd | 2 +-
3 files changed, 7 insertions(+), 7 deletions(-)
Title: Efficient selection of undirected graphical models for
high-dimensional datasets
Diff between gRapHD versions 0.1.7 dated 2010-08-17 and 0.1.8 dated 2010-09-01
Description: gRapHD is designed for efficient selection of
high-dimensional undirected graphical models. The package
provides tools for selecting trees, forests and decomposable
models minimizing information criteria such as AIC or BIC, and
for displaying the independence graphs of the models. It has
also some useful tools for analysing graphical structures. It
supports the use of discrete, continuous, or both types of
variables.
Author: Gabriel Coelho Goncalves de Abreu
Maintainer: Gabriel Coelho Goncalves de Abreu
DESCRIPTION | 6 ++---
R/functions.r | 66 +++++++++++++++++++++++++++++++---------------------------
man/fit.rd | 7 ++++--
3 files changed, 44 insertions(+), 35 deletions(-)
Title: Multidimensional Numerical Integration
Diff between R2Cuba versions 1.0-4 dated 2010-02-08 and 1.0-5 dated 2010-09-01
Description: R2Cuba implements four general-purpose multidimensional
integration algorithms: Vegas, Suave, Divonne and Cuhre
Author: The Cuba library has been written by Thomas Hahn
(http://wwwth.mppmu.mpg.de/members/hahn); Interface to R was
written by Annie Bouvier and Kiên Kiêu
Maintainer: Annie Bouvier
DESCRIPTION | 8 ++++----
R/commoncuba.R | 7 +++++--
R/cuhre.R | 3 ++-
R/divonne.R | 3 ++-
R/suave.R | 3 ++-
R/vegas.R | 3 ++-
man/R2Cuba-package.Rd | 4 ++--
man/cuhre.Rd | 1 +
src/cuhre_Cuhre.c | 1 -
src/cuhre_common.c | 2 +-
src/vegas_Vegas.c | 3 ++-
tests/kk.Rout.save | 10 +++++++---
12 files changed, 30 insertions(+), 18 deletions(-)
Title: A package for statistical analysis in epidemiology.
Diff between Epi versions 1.1.15 dated 2010-06-19 and 1.1.17 dated 2010-09-01
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data,
including interval censored data and representation of
multistate data. Also some useful functions for tabulation and
plotting. Contains some epidemiological datasets.
Author: Bendix Carstensen, Martyn Plummer, Esa Laara, Michael Hills et.
al.
Maintainer: Bendix Carstensen
Epi-1.1.15/Epi/inst/doc/Rplots.pdf |only
Epi-1.1.15/Epi/man/mstate.Lexis.Rd |only
Epi-1.1.17/Epi/CHANGES | 20 +
Epi-1.1.17/Epi/DESCRIPTION | 10
Epi-1.1.17/Epi/NAMESPACE | 9
Epi-1.1.17/Epi/R/MS.boxes.R | 7
Epi-1.1.17/Epi/R/lexis.R | 9
Epi-1.1.17/Epi/R/stack.Lexis.R | 68 ++---
Epi-1.1.17/Epi/inst/doc/Follow-up.pdf | 424 ++++++++++++++++------------------
Epi-1.1.17/Epi/man/msdata.Lexis.Rd |only
Epi-1.1.17/Epi/man/plot.Lexis.Rd | 9
Epi-1.1.17/Epi/man/transform.Lexis.Rd | 9
12 files changed, 291 insertions(+), 274 deletions(-)
Title: Wrapper package for design of experiments functionality
Diff between DoE.wrapper versions 0.8 dated 2010-08-10 and 0.8-1 dated 2010-09-01
Description: This package creates various kinds of designs for
(industrial) experiments. It uses, and sometimes enhances,
design generation routines from other packages. Initially,
response surface designs from package rsm and latin hypercube
samples from package lhs have been implemented.
Author: Ulrike Groemping
Maintainer: Ulrike Groemping
DESCRIPTION | 8 ++++----
inst/NEWS | 3 +++
man/Dopt.augment.Rd | 3 +--
man/Dopt.design.Rd | 3 +--
4 files changed, 9 insertions(+), 8 deletions(-)
Title: A software package for annotation and identification of the KEGG
pathways.
Diff between SubpathwayMiner versions 3.0 dated 2010-06-01 and 3.1 dated 2010-09-01
More information about SubpathwayMiner at CRAN
Description: SubpathwayMiner is an R-based software for flexible
pathway identification. (1) SubpathwayMiner can provide users
with sub-pathway annotation and identification of metabolic
pathways based on enzyme commission (EC) numbers. (2)
SubpathwayMiner can provide users with sub-pathway annotation
and identification based on KEGG Orthology (KO) identifiers.
(3) SubpathwayMiner can provide annotation and identification
of entire pathways. (4) SubpathwayMiner can support most of
organisms in the KEGG GENE database. (5) Data can be
automatically updated on demand by the user. (6)
SubpathwayMiner can provide identification of disease related
sub-pathways.(new!) The version 3.1 use a new approach to store
organism-related data (e.g., gene-enzyme relation data), which
make the running time of the function updateOrgAndIdType reduce
significantly compared with the old version. Therefore, the
environment variables of organisms will be provided no longer
for reducing size of the software package. When using this
tool, please cite: Li, C., Li, X., Miao, Y., Wang, Q., Jiang,
W., Xu, C., Li, J., Han, J., Zhang, F., Gong, B. et al. (2009)
SubpathwayMiner: a software package for flexible identification
of pathways. Nucleic Acids Res, 37, e131. Full text:
http://nar.oxfordjournals.org/cgi/content/full/37/19/e131
Author: Chunquan Li
Maintainer: Chunquan Li
SubpathwayMiner-3.0/SubpathwayMiner/R/id.R |only
SubpathwayMiner-3.0/SubpathwayMiner/data/ath_ncbi-geneid.rda |only
SubpathwayMiner-3.0/SubpathwayMiner/data/cel_ncbi-geneid.rda |only
SubpathwayMiner-3.0/SubpathwayMiner/data/dme_ncbi-geneid.rda |only
SubpathwayMiner-3.0/SubpathwayMiner/data/eco_ncbi-geneid.rda |only
SubpathwayMiner-3.0/SubpathwayMiner/data/hsa_ensembl-hsa.rda |only
SubpathwayMiner-3.0/SubpathwayMiner/data/hsa_ncbi-gi.rda |only
SubpathwayMiner-3.0/SubpathwayMiner/data/inData.rda |only
SubpathwayMiner-3.0/SubpathwayMiner/data/mmu_ncbi-geneid.rda |only
SubpathwayMiner-3.0/SubpathwayMiner/data/osa_ncbi-geneid.rda |only
SubpathwayMiner-3.0/SubpathwayMiner/data/pathwayClass.rda |only
SubpathwayMiner-3.0/SubpathwayMiner/data/sce_ncbi-geneid.rda |only
SubpathwayMiner-3.0/SubpathwayMiner/data/sce_ncbi-gi.rda |only
SubpathwayMiner-3.0/SubpathwayMiner/data/sce_sgd-sce.rda |only
SubpathwayMiner-3.0/SubpathwayMiner/man/KO2gene.Rd |only
SubpathwayMiner-3.0/SubpathwayMiner/man/KOuGraph.Rd |only
SubpathwayMiner-3.0/SubpathwayMiner/man/background.Rd |only
SubpathwayMiner-3.0/SubpathwayMiner/man/dGraph.Rd |only
SubpathwayMiner-3.0/SubpathwayMiner/man/ec2gene.Rd |only
SubpathwayMiner-3.0/SubpathwayMiner/man/gene2KO.Rd |only
SubpathwayMiner-3.0/SubpathwayMiner/man/gene2ec.Rd |only
SubpathwayMiner-3.0/SubpathwayMiner/man/gene2path.Rd |only
SubpathwayMiner-3.0/SubpathwayMiner/man/getEnzymeFromGene.Rd |only
SubpathwayMiner-3.0/SubpathwayMiner/man/getGeneFromEnzyme.Rd |only
SubpathwayMiner-3.0/SubpathwayMiner/man/getGeneFromKO.Rd |only
SubpathwayMiner-3.0/SubpathwayMiner/man/getGeneFromPathway.Rd |only
SubpathwayMiner-3.0/SubpathwayMiner/man/getKOFromGene.Rd |only
SubpathwayMiner-3.0/SubpathwayMiner/man/getPathwayFromGene.Rd |only
SubpathwayMiner-3.0/SubpathwayMiner/man/getPathwayNameFromId.Rd |only
SubpathwayMiner-3.0/SubpathwayMiner/man/keggpathid2name.Rd |only
SubpathwayMiner-3.0/SubpathwayMiner/man/kpidList.Rd |only
SubpathwayMiner-3.0/SubpathwayMiner/man/mpidList.Rd |only
SubpathwayMiner-3.0/SubpathwayMiner/man/path2gene.Rd |only
SubpathwayMiner-3.0/SubpathwayMiner/man/uGraph.Rd |only
SubpathwayMiner-3.1/SubpathwayMiner/DESCRIPTION | 24 +
SubpathwayMiner-3.1/SubpathwayMiner/R/D2P.R | 3
SubpathwayMiner-3.1/SubpathwayMiner/R/ann.R | 11
SubpathwayMiner-3.1/SubpathwayMiner/R/go2go.R | 156 ++++++----
SubpathwayMiner-3.1/SubpathwayMiner/R/graph.R | 2
SubpathwayMiner-3.1/SubpathwayMiner/R/initialize.R | 82 ++---
SubpathwayMiner-3.1/SubpathwayMiner/R/ko.R | 4
SubpathwayMiner-3.1/SubpathwayMiner/R/visualize.R | 10
SubpathwayMiner-3.1/SubpathwayMiner/data/hsa_ncbi-geneid.rda |binary
SubpathwayMiner-3.1/SubpathwayMiner/inst/doc/Rplots.pdf | 85 +++--
SubpathwayMiner-3.1/SubpathwayMiner/inst/doc/SubpathwayMiner.Rnw | 38 +-
SubpathwayMiner-3.1/SubpathwayMiner/inst/doc/SubpathwayMiner.pdf |binary
SubpathwayMiner-3.1/SubpathwayMiner/inst/localdata |only
SubpathwayMiner-3.1/SubpathwayMiner/man/Ke2gEnvironment.Rd | 24 -
SubpathwayMiner-3.1/SubpathwayMiner/man/SubpathwayMiner-internal.Rd | 22 -
SubpathwayMiner-3.1/SubpathwayMiner/man/cutoffAnn.Rd | 3
SubpathwayMiner-3.1/SubpathwayMiner/man/generateNetwork.Rd | 18 -
SubpathwayMiner-3.1/SubpathwayMiner/man/getAnn.Rd | 8
SubpathwayMiner-3.1/SubpathwayMiner/man/getDefaultBackground.Rd | 4
SubpathwayMiner-3.1/SubpathwayMiner/man/getDefaultGraph.Rd | 8
SubpathwayMiner-3.1/SubpathwayMiner/man/getDefaultKOPathway.Rd | 2
SubpathwayMiner-3.1/SubpathwayMiner/man/getDefaultKOUndirectedGraph.Rd | 2
SubpathwayMiner-3.1/SubpathwayMiner/man/getDefaultMetabolicPathway.Rd | 2
SubpathwayMiner-3.1/SubpathwayMiner/man/getDefaultUndirectedGraph.Rd | 2
SubpathwayMiner-3.1/SubpathwayMiner/man/getKOAnn.Rd | 16 -
SubpathwayMiner-3.1/SubpathwayMiner/man/getKcSubGraph.Rd | 19 -
SubpathwayMiner-3.1/SubpathwayMiner/man/getKcsmpAnn.Rd | 9
SubpathwayMiner-3.1/SubpathwayMiner/man/getMpAnn.Rd | 9
SubpathwayMiner-3.1/SubpathwayMiner/man/go2go.Rd |only
SubpathwayMiner-3.1/SubpathwayMiner/man/gotoKEGG.Rd | 24 -
SubpathwayMiner-3.1/SubpathwayMiner/man/ke2g.Rd | 17 -
SubpathwayMiner-3.1/SubpathwayMiner/man/plotAnn.Rd | 16 -
SubpathwayMiner-3.1/SubpathwayMiner/man/plotKOAnn.Rd | 16 -
SubpathwayMiner-3.1/SubpathwayMiner/man/printAnn.Rd | 4
SubpathwayMiner-3.1/SubpathwayMiner/man/updateGraphs.Rd | 9
SubpathwayMiner-3.1/SubpathwayMiner/man/updateKOGraphs.Rd | 5
SubpathwayMiner-3.1/SubpathwayMiner/man/updateOrgAndIdType.Rd | 22 -
71 files changed, 397 insertions(+), 279 deletions(-)
Permanent link
Title: Construct time delay gene regulatory network
Diff between GeneReg versions 1.1.1 dated 2009-12-14 and 1.1.2 dated 2010-09-01
Description: GeneReg is an R package for inferring time delay gene
regulatory network using time course gene expression profiles.
The main idea of time delay linear model is to fit a linear
regression model using a set of putative regulators to estimate
the transcription pattern of a specific target gene.
Author: Tao Huang
Maintainer: Tao Huang
DESCRIPTION | 10 +++++++---
R/plot.R | 3 ++-
R/timedelay.lm.R | 3 ++-
data/mut.expr.data.rda |binary
data/tf.list.rda |binary
data/wt.expr.data.rda |binary
man/GeneReg-package.Rd | 8 ++++----
man/plot.GeneReg.Rd | 5 ++++-
man/timedelay.lm.Rd | 5 ++++-
man/timedelay.lm.batch.Rd | 5 ++++-
man/timedelay.univariate.lm.Rd | 4 ++++
11 files changed, 31 insertions(+), 12 deletions(-)