Title: For mapping global data : rworldmap
Diff between rworldmap versions 0.106 dated 2010-01-06 and 0.107 dated 2010-02-03
Description: Enables mapping of country level and gridded user
datasets.
Author: Andy South
Maintainer: Andy South
DESCRIPTION | 14
R/addMapLegendBoxes.r | 4
R/mapBubbles.r | 2
R/mapGriddedData.r | 43
inst/doc/Rplots.pdf |56036 --------------------------------------------
inst/doc/cefasLogo.jpg |only
inst/doc/nercLogo.jpg |only
inst/doc/questLogo.png |only
inst/doc/rworldmap.Rnw | 25
inst/doc/rworldmap.pdf | 2538 +
inst/doc/rworldmapFAQ.Rnw | 188
inst/doc/rworldmapFAQ.pdf |58490 +---------------------------------------------
man/addMapLegendBoxes.Rd | 12
man/mapBubbles.Rd | 2
man/mapGriddedData.Rd | 7
15 files changed, 4138 insertions(+), 113223 deletions(-)
Title: Exact or Asymptotic permutation tests
Diff between perm versions 0.9-1.3 dated 2009-07-30 and 0.9-9.5 dated 2010-02-03
Description: Perform Exact or Asymptotic permutation tests
Author: Michael Fay
Maintainer: Michael Fay
DESCRIPTION | 8 ++++----
NEWS |only
R/algorithms.R | 38 ++++++++++++++++++++++++++------------
R/chooseMatrix.R | 4 ++++
R/getcnt.R | 2 ++
R/methodRules.R | 1 +
R/permKS.R | 1 +
R/permTREND.R | 1 +
R/permTS.R | 1 +
man/perm-package.Rd | 2 +-
man/perm.Rd | 11 ++++++++---
tests/perm.coin.check.R |only
tests/precision.problem.R | 4 +++-
13 files changed, 52 insertions(+), 21 deletions(-)
Title: Weighted Logrank Tests and NPMLE for interval censored data
Diff between interval versions 0.7-5.5 dated 2009-08-04 and 0.9-9.5 dated 2010-02-03
Description: Functions to fit nonparametric survival curves, plot them,
and perform logrank or Wilcoxon type tests.
Author: Michael P. Fay
Maintainer: Michael P. Fay
interval-0.7-5.5/interval/ChangeLog |only
interval-0.7-5.5/interval/TODOLIST |only
interval-0.9-9.5/interval/DESCRIPTION | 14
interval-0.9-9.5/interval/NAMESPACE | 4
interval-0.9-9.5/interval/NEWS |only
interval-0.9-9.5/interval/R/SurvLR.R | 2
interval-0.9-9.5/interval/R/getsurv.R | 89
interval-0.9-9.5/interval/R/icScoreTest.R | 5
interval-0.9-9.5/interval/R/icWSR.r | 21
interval-0.9-9.5/interval/R/icfit.R | 258
interval-0.9-9.5/interval/R/icfitControl.R | 4
interval-0.9-9.5/interval/R/ictest.R | 51
interval-0.9-9.5/interval/R/initFuncs.R |only
interval-0.9-9.5/interval/R/methods.icfit.R | 134
interval-0.9-9.5/interval/R/scoresFromFit.R | 37
interval-0.9-9.5/interval/R/wlr_trafo.R | 26
interval-0.9-9.5/interval/demo/00Index | 1
interval-0.9-9.5/interval/demo/check.time.initfit.R |only
interval-0.9-9.5/interval/demo/cosmesis.test.R | 6
interval-0.9-9.5/interval/inst/doc/Rplots.pdf | 193
interval-0.9-9.5/interval/inst/doc/interval.bib | 91
interval-0.9-9.5/interval/inst/doc/intervalPaper.Rnw | 2241 +++---
interval-0.9-9.5/interval/inst/doc/intervalPaper.dvi |only
interval-0.9-9.5/interval/inst/doc/intervalPaper.pdf | 7049 ++++++++++++-------
interval-0.9-9.5/interval/man/Aintmap.Rd | 22
interval-0.9-9.5/interval/man/getsurv.Rd | 14
interval-0.9-9.5/interval/man/icfit.Rd | 38
interval-0.9-9.5/interval/man/icfitControl.Rd | 6
interval-0.9-9.5/interval/man/ictest.Rd | 121
interval-0.9-9.5/interval/man/initcomputeMLE.Rd |only
interval-0.9-9.5/interval/man/interval-internal.Rd | 4
interval-0.9-9.5/interval/man/interval-package.Rd | 4
interval-0.9-9.5/interval/man/plot.icfit.Rd | 42
interval-0.9-9.5/interval/man/summary.icfit.Rd |only
34 files changed, 6753 insertions(+), 3724 deletions(-)
Title: Graphical Independence Networks
Diff between gRain versions 0.8.2 dated 2009-11-22 and 0.8.3 dated 2010-02-03
Description: A package for probability propagation in graphical
independence networks, also known as probabilistic expert
systems (which includes Bayesian networks as a special case).
Author: Søren Højsgaard
Maintainer: Søren Højsgaard
ChangeLog | 6 ++++++
DESCRIPTION | 6 +++---
R/Finding.R | 7 +++++--
R/predict.R | 17 ++++++++---------
inst/doc/gRain-intro.pdf |binary
man/compileCPT.Rd | 2 +-
6 files changed, 23 insertions(+), 15 deletions(-)
Title: Sparse and Dense Matrix Classes and Methods
Diff between Matrix versions 0.999375-33 dated 2009-12-11 and 0.999375-35 dated 2010-02-03
Description: Classes and methods for dense and sparse matrices and
operations on them using Lapack and SuiteSparse.
Author: Douglas Bates
Maintainer: Doug and Martin
ChangeLog | 86 ++++
DESCRIPTION | 8
Done | 10
NAMESPACE | 15
R/AllClass.R | 15
R/AllGeneric.R | 5
R/Auxiliaries.R | 122 +-----
R/Csparse.R | 86 ++++
R/Ops.R | 12
R/SparseM-conv.R | 2
R/Tsparse.R | 244 ------------
R/abIndex.R | 639 +++++++++++++++++++++++++++-----
R/dgeMatrix.R | 4
R/diagMatrix.R | 50 +-
R/nnzero.R |only
R/spModels.R | 4
R/sparseVector.R | 5
R/zzz.R | 5
TODO | 3
inst/doc/Comparisons.pdf | 489 ++++++++++++------------
inst/doc/Design-issues.pdf |binary
inst/doc/Intro2Matrix.pdf | 858 ++++++++++++++++++++-----------------------
inst/doc/Introduction.pdf |binary
inst/doc/sparseModels.pdf | 873 +++++++++++++++++++++-----------------------
inst/include/Matrix_stubs.c | 11
inst/test-tools.R | 21 -
man/CsparseMatrix-class.Rd | 1
man/Diagonal.Rd | 24 +
man/Xtrct-methods.Rd | 3
man/abIndex-class.Rd | 43 +-
man/abIseq.Rd |only
man/all.equal-methods.Rd | 5
man/contrast.Rd | 4
man/nnzero.Rd | 26 +
man/rleDiff-class.Rd | 18
man/sparseMatrix-class.Rd | 1
src/Csparse.c | 7
src/abIndex.c | 63 ---
src/abIndex.h | 3
src/chm_common.c | 8
src/init.c | 4
src/lgCMatrix.c | 4
src/t_Matrix_rle.c |only
tests/Simple.R | 3
tests/abIndex-tsts.R | 60 ++-
tests/base-matrix-fun.R | 2
tests/factorizing.R | 14
tests/indexing.R | 24 -
tests/indexing.Rout.save | 88 +++-
tests/spModel.matrix.R | 8
50 files changed, 2257 insertions(+), 1723 deletions(-)
Title: This package provides some basic methods for meta-analysis
Diff between MADAM versions 1.0-1 dated 2010-02-03 and 1.0-2 dated 2010-02-03
Description: In this package we provide some basic utilities for
performing meta-analysis. We included methods for dealing with
missing values, or measurements with a variance of zero. For
developing or testing meta-analysis methods a mock up data
model is integrated. Additionally did we implement a method for
performing significance based methods proposed by Fisher and
Rhodes. For visualizing the results three methods were added.
Author: Karl Kugler
Maintainer: Karl Kugler
DESCRIPTION | 11 ++++++-----
1 file changed, 6 insertions(+), 5 deletions(-)
Title: LMGene Software for Data Transformation and Identification of
Differentially Expressed Genes in Gene Expression Arrays
Diff between LMGene versions 1.16.0 dated 2009-11-13 and 2.2.0 dated 2010-02-03
Description: LMGene package for analysis of microarray data using a
linear model and glog data transformation
Author: David Rocke, Geun Cheol Lee, John Tillinghast, Blythe
Durbin-Johnson, and Shiquan Wu
Maintainer: Blythe Durbin-Johnson
LMGene-1.16.0/LMGene/inst/doc/Rplots.ps |only
LMGene-1.16.0/LMGene/man/GetLMObj.Rd |only
LMGene-1.16.0/LMGene/man/jggrad2.Rd |only
LMGene-1.16.0/LMGene/man/jglog.Rd |only
LMGene-1.16.0/LMGene/man/mlm2lm.Rd |only
LMGene-1.16.0/LMGene/man/msa.Rd |only
LMGene-1.16.0/LMGene/man/msecalc.Rd |only
LMGene-1.16.0/LMGene/man/msecalcmult.Rd |only
LMGene-1.16.0/LMGene/man/pvadjust.Rd |only
LMGene-1.16.0/LMGene/man/rowlist.Rd |only
LMGene-1.16.0/LMGene/man/tranest2.Rd |only
LMGene-1.16.0/LMGene/man/tranestmult.Rd |only
LMGene-2.2.0/LMGene/DESCRIPTION | 25 -
LMGene-2.2.0/LMGene/NAMESPACE |only
LMGene-2.2.0/LMGene/R/GetLMObj.R | 8
LMGene-2.2.0/LMGene/R/LMGene.R | 26 -
LMGene-2.2.0/LMGene/R/arrayGlogSDStability.R |only
LMGene-2.2.0/LMGene/R/fitFDist.R |only
LMGene-2.2.0/LMGene/R/fitScaledF.R |only
LMGene-2.2.0/LMGene/R/genediff.R | 178 ++++---
LMGene-2.2.0/LMGene/R/glog.R | 3
LMGene-2.2.0/LMGene/R/jggrad2.R | 4
LMGene-2.2.0/LMGene/R/jglog.R | 2
LMGene-2.2.0/LMGene/R/lnorm.R | 6
LMGene-2.2.0/LMGene/R/lnormeS.R | 19
LMGene-2.2.0/LMGene/R/mlm2lm.R | 4
LMGene-2.2.0/LMGene/R/msa.R | 4
LMGene-2.2.0/LMGene/R/msecalc.R | 12
LMGene-2.2.0/LMGene/R/msecalcmult.R | 4
LMGene-2.2.0/LMGene/R/neweS.R | 6
LMGene-2.2.0/LMGene/R/norm.R | 5
LMGene-2.2.0/LMGene/R/plotMeanSD.R |only
LMGene-2.2.0/LMGene/R/psmeans.R | 43 +
LMGene-2.2.0/LMGene/R/pvadjust.R | 4
LMGene-2.2.0/LMGene/R/rowaov.R | 14
LMGene-2.2.0/LMGene/R/rowlist.R | 6
LMGene-2.2.0/LMGene/R/tranest.R | 68 ++
LMGene-2.2.0/LMGene/R/tranest2.R | 75 ++-
LMGene-2.2.0/LMGene/R/tranestAffyProbeLevel.R |only
LMGene-2.2.0/LMGene/R/tranestmult.R | 4
LMGene-2.2.0/LMGene/R/transeS.R | 7
LMGene-2.2.0/LMGene/R/trigammaInverse.R |only
LMGene-2.2.0/LMGene/inst/doc/LMGene.Rnw | 524 +++++++++++------------
LMGene-2.2.0/LMGene/inst/doc/LMGene.pdf |binary
LMGene-2.2.0/LMGene/man/LMGene.Rd | 60 +-
LMGene-2.2.0/LMGene/man/genediff.Rd | 88 ++-
LMGene-2.2.0/LMGene/man/glog.Rd | 31 -
LMGene-2.2.0/LMGene/man/lnorm.Rd | 27 -
LMGene-2.2.0/LMGene/man/lnormeS.Rd | 70 +--
LMGene-2.2.0/LMGene/man/neweS.Rd | 24 -
LMGene-2.2.0/LMGene/man/norm.Rd | 26 -
LMGene-2.2.0/LMGene/man/plotMeanSD.Rd |only
LMGene-2.2.0/LMGene/man/psmeans.Rd | 89 ++-
LMGene-2.2.0/LMGene/man/rowaov.Rd | 32 -
LMGene-2.2.0/LMGene/man/sample.eS.Rd | 10
LMGene-2.2.0/LMGene/man/sample.ind.Rd | 11
LMGene-2.2.0/LMGene/man/sample.mat.Rd | 8
LMGene-2.2.0/LMGene/man/tranest.Rd | 95 +++-
LMGene-2.2.0/LMGene/man/tranestAffyProbeLevel.Rd |only
LMGene-2.2.0/LMGene/man/transeS.Rd | 88 ++-
LMGene-2.2.0/LMGene/man/vlist.Rd | 5
61 files changed, 983 insertions(+), 732 deletions(-)
Title: Processing and Simulating Genotype Data for Trio Logic
Regression
Diff between trio versions 1.0.3 dated 2010-02-01 and 1.0.4 dated 2010-02-03
Description: Set up matched case-pseudo controls genotypes data for
trios in order to run trio logic regreesion, to impute missing
genotypes in trios, or to simulate case-parent trios with
disease risk dependent on SNP-SNP interaction. This package
furthermore contains functions for computing the values of
pairwise LD measures and for identifying LD blocks.
Author: Qing Li, Holger Schwender
Maintainer: Qing Li
DESCRIPTION | 8 ++++----
R/getLD.R | 14 +++++++-------
inst/doc/trio.pdf |binary
3 files changed, 11 insertions(+), 11 deletions(-)
Title: Nonparametric kernel smoothing methods for mixed data types
Diff between np versions 0.30-5 dated 2010-01-29 and 0.30-6 dated 2010-02-03
Description: This package provides a variety of nonparametric (and
semiparametric) kernel methods that seamlessly handle a mix of
continuous, unordered, and ordered factor data types. We would
like to gratefully acknowledge support from the Natural
Sciences and Engineering Research Council of Canada
(NSERC:www.nserc.ca), the Social Sciences and Humanities
Research Council of Canada (SSHRC:www.sshrc.ca), and the Shared
Hierarchical Academic Research Computing Network
(SHARCNET:www.sharcnet.ca).
Author: Tristen Hayfield
Maintainer: Jeffrey S. Racine
np-0.30-5/np/R/np.restest.R |only
np-0.30-6/np/CHANGELOG | 17
np-0.30-6/np/DESCRIPTION | 10
np-0.30-6/np/NAMESPACE | 6
np-0.30-6/np/R/deneqtest.R | 8
np-0.30-6/np/R/deptest.R |only
np-0.30-6/np/R/np.cmstest.R | 12
np-0.30-6/np/R/np.deneqtest.R | 44
np-0.30-6/np/R/np.deptest.R |only
np-0.30-6/np/R/np.plot.R | 11
np-0.30-6/np/R/np.qcmstest.R | 12
np-0.30-6/np/R/np.sdeptest.R |only
np-0.30-6/np/R/np.sigtest.R | 14
np-0.30-6/np/R/np.singleindex.R | 2
np-0.30-6/np/R/np.singleindex.bw.R | 12
np-0.30-6/np/R/np.symtest.R | 100
np-0.30-6/np/R/sdeptest.R |only
np-0.30-6/np/R/zzz.R | 2
np-0.30-6/np/inst/doc/np.Rnw | 1
np-0.30-6/np/inst/doc/np.pdf |27814 ++++++++++++++++++-------------------
np-0.30-6/np/inst/doc/np_faq.pdf | 2476 +--
np-0.30-6/np/man/b.star.Rd | 25
np-0.30-6/np/man/data-wage1.Rd | 2
np-0.30-6/np/man/gradients.Rd | 2
np-0.30-6/np/man/np.cmstest.Rd | 2
np-0.30-6/np/man/np.deneqtest.Rd | 30
np-0.30-6/np/man/np.density.Rd | 58
np-0.30-6/np/man/np.density.bw.Rd | 6
np-0.30-6/np/man/np.deptest.Rd |only
np-0.30-6/np/man/np.plot.Rd | 2
np-0.30-6/np/man/np.qcmstest.Rd | 6
np-0.30-6/np/man/np.sdeptest.Rd |only
np-0.30-6/np/man/np.sigtest.Rd | 16
np-0.30-6/np/man/np.symtest.Rd | 73
np-0.30-6/np/svn-commit.2.tmp |only
35 files changed, 15797 insertions(+), 14966 deletions(-)
Title: Analysis of Mark-Recapture data
Diff between mra versions 2.2 dated 2008-10-09 and 2.3 dated 2010-02-03
Description: Analysis of mark-recapture data using covariates. Models
implemented: CJS open population; Huggin's closed population.
Author: Trent McDonald
Maintainer: Trent McDonald
DESCRIPTION | 23
R/F.cjs.estim.R | 271 +++----
R/F.cr.model.avg.r |only
R/F.fit.table.r |only
R/F.huggins.estim.R | 206 ++---
R/ivar.R | 4
R/mra.control.r |only
R/tvar.r | 4
man/F.cjs.estim.Rd | 47 -
man/F.cr.model.avg.Rd |only
man/F.fit.table.Rd |only
man/F.huggins.estim.Rd | 21
man/ivar.Rd | 22
man/lines.cjs.Rd | 2
man/mra.control.Rd |only
man/residuals.cjs.Rd | 2
man/tvar.Rd | 27
src/Mrawin.f90 | 1777 +++++++++++++++++++++++++------------------------
18 files changed, 1259 insertions(+), 1147 deletions(-)
Title: Batching Routines in Parallel and Passing Command-Line Arguments
to R
Diff between batch versions 1.0-0 dated 2009-12-17 and 1.0-1 dated 2010-02-03
Description: Functions to allow you to easily pass command-line
arguments into R (primary use is linux), and functions to aid
in submitting your R code in parallel on a cluster and joining
the results afterward (e.g. multiple parameter values for
simulations running in parallel, splitting up a permutation
test in parallel, etc.). See `parseCommandArgs(...)' for the
main example of how to use this package.
Author: Thomas Hoffmann
Maintainer: Thomas Hoffmann
DESCRIPTION | 8 ++++----
NAMESPACE | 2 +-
R/batch.R | 3 ++-
R/pasteCsv3.R | 7 ++++++-
4 files changed, 13 insertions(+), 7 deletions(-)
Title: Kalman filter and smoothers for exponential family state space
models.
Diff between KFAS versions 0.5.4 dated 2010-02-02 and 0.5.5 dated 2010-02-03
Description: Package KFAS provides functions for Kalman filtering,
state, disturbance and simulation smoothing, forecasting and
simulation of state space models. All functions can use exact
diffuse initialisation when distributions of some or all
elements of initial state vector are unknown. Filtering, state
smoothing and simulation functions use sequential processing
algorithm, which is faster than standard approach, and it also
allows singularity of prediction error variance matrix. KFAS
also contains function for computing the likelihood of
exponential family state space models and function for state
smoothing of exponential family state space models. These
non-gaussian functions are still under heavy developement.
Author: Jouni Helske
Maintainer: Jouni Helske
DESCRIPTION | 8 ++++----
src/kf.f90 | 2 +-
2 files changed, 5 insertions(+), 5 deletions(-)
Title: An interface for creating GUIs modeled in part after traits UI
module for python.
Diff between traitr versions 0.3 dated 2010-01-22 and 0.4 dated 2010-02-03
Description: An interface for creating GUIs modeled in part after the
traits UI module for python. The basic design takes advantage
of the model-view-controller design pattern. The interface
makes basic dialogs quite easy to produce.
Author: John Verzani
Maintainer: John Verzani
ChangeLog | 11 ++++
DESCRIPTION | 16 +++---
NEWS | 12 ++++
R/base.R | 5 +
R/controller.R | 4 +
R/editor.R | 30 ++++++++---
R/itemgroup.R | 5 -
R/items.R | 135 ++++++++++++++++++++++++++++++++++++++-------------
README | 4 -
TODO.txt | 16 +++++-
inst/doc/traitr.Rnw | 4 -
inst/doc/traitr.pdf |binary
man/buttonItem.Rd | 4 +
man/choiceItem.Rd | 23 ++++++++
man/numericItem.Rd | 9 +++
man/stringItem.Rd | 10 +++
man/trueFalseItem.Rd | 5 +
testing/test-mvc.R | 68 ++++++++++++++++++++++++-
18 files changed, 299 insertions(+), 62 deletions(-)
Title: Tools for Scraping Data from HTML and XML Documents
Diff between scrapeR versions 0.1.5 dated 2010-01-25 and 0.1.6 dated 2010-02-03
Description: Tools for Scraping Data from Web-Based Documents
Author: Ryan M. Acton
Maintainer: Ryan M. Acton
DESCRIPTION | 6 +++---
R/functions.R | 17 +++++------------
man/scrape.Rd | 10 +++++-----
man/scrapeR-package.Rd | 2 +-
4 files changed, 14 insertions(+), 21 deletions(-)
Title: L1 (lasso) and L2 (ridge) penalized estimation in GLMs and in
the Cox model
Diff between penalized versions 0.9-27 dated 2009-10-07 and 0.9-28 dated 2010-02-03
Description: A package for fitting possibly high dimensional penalized
regression models. The penalty structure can be any combination
of an L1 penalty (lasso), an L2 penalty (ridge) and a
positivity constraint on the regression coefficients. The
supported regression models are linear, logistic and poisson
regression and the Cox Proportional Hazards model.
Cross-validation routines allow optimization of the tuning
parameters.
Author: Jelle Goeman
Maintainer: Jelle Goeman
penalized-0.9-27/penalized/inst/doc/penalized.Rnw |only
penalized-0.9-28/penalized/DESCRIPTION | 10 +++++-----
penalized-0.9-28/penalized/R/cvl.R | 4 ++--
penalized-0.9-28/penalized/R/plotpath.R | 2 +-
penalized-0.9-28/penalized/changelog.txt | 8 ++++++++
penalized-0.9-28/penalized/inst/doc/Rplots.pdf | 6 +++---
penalized-0.9-28/penalized/inst/doc/penalized.pdf |binary
penalized-0.9-28/penalized/man/cvl.Rd | 2 +-
penalized-0.9-28/penalized/man/penalized.Rd | 2 +-
9 files changed, 21 insertions(+), 13 deletions(-)
Title: General Polygon Clipping Library for R
Diff between gpclib versions 1.4-4 dated 2009-05-11 and 1.5-1 dated 2010-02-03
Description: General polygon clipping routines for R based on Alan
Murta's C library
Author: Roger D. Peng
Maintainer: Roger D. Peng
DESCRIPTION | 13 ++++---
R/Rgpc.R | 72 ++++++++++++++++---------------------------
man/gpc.poly-class.Rd | 5 ++
man/gpc.poly.nohole-class.Rd | 18 +++++-----
tests/reg-tests.R | 2 -
tests/reg-tests.Rout.save | 7 +---
6 files changed, 51 insertions(+), 66 deletions(-)
Title: Clustering Method Based on Local Shrinking
Diff between clues versions 0.4.0 dated 2009-12-24 and 0.5-0 dated 2010-02-03
Description: The package contains functions for automatically
estimating the number of clusters and getting the final cluster
partition without any input parameter except the stopping rule
for convergence. The package also provides functions to
evaluate and compare the performances of partitions of a data
set both numerically and graphically.
Author: Fang Chang
Maintainer: Fang Chang
clues-0.4.0/clues/inst/doc/clues_intro.Rnw |only
clues-0.4.0/clues/inst/doc/clues_intro.pdf |only
clues-0.5-0/clues/DESCRIPTION | 9 +++++----
clues-0.5-0/clues/inst/CITATION |only
clues-0.5-0/clues/inst/doc/WDBC.dat |only
clues-0.5-0/clues/inst/doc/clues.Rnw |only
clues-0.5-0/clues/inst/doc/clues.bib |only
clues-0.5-0/clues/inst/doc/clues.pdf |only
clues-0.5-0/clues/inst/doc/log_running_time.pdf |only
clues-0.5-0/clues/inst/doc/log_running_time_p.pdf |only
10 files changed, 5 insertions(+), 4 deletions(-)
Title: This package provides some basic methods for meta-analysis
Diff between MADAM versions 1.0 dated 2010-02-02 and 1.0-1 dated 2010-02-03
Description: In this package we provide some basic utilities for
performing meta-analysis. We included methods for dealing with
missing values, or measurements with a variance of zero. For
developing or testing meta-analysis methods a mock up data
model is integrated. Additionally did we implement a method for
performing significance based methods proposed by Fisher and
Rhodes. For visualizing the results three methods were added.
Author: Karl Kugler
Maintainer: Karl Kugler
DESCRIPTION | 9 ++++-----
man/calculateRankProduct.Rd | 2 ++
man/calculateRankSum.Rd | 2 ++
man/doEnsemble.Rd | 4 ++++
4 files changed, 12 insertions(+), 5 deletions(-)
Title: Topographic and Geologic Mapping
Diff between GEOmap versions 1.4-2 dated 2009-06-02 and 1.5-0 dated 2010-02-03
Description: Set of routines for making Map Projections (forward and
inverse), Topographic Maps, Perspective plots, Geological Maps,
geological map symbols, geological databases, interactive
plotting and selection of focus regions.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees
DESCRIPTION | 8 +-
R/GEOTOPO.R | 89 +++++++++++++++++++++++--
R/Gcols.R |only
R/LandSeaCol.R |only
R/SELGEOmap.R | 6 +
R/XSECDEM.R | 65 ++++++++++--------
R/addLLXY.R | 28 ++++++-
R/antipolygon.R | 14 +++
R/mapTeleSeis.R |only
R/rectPERIM.R |only
R/sqrTICXY.R | 178 ++++++++++++++++++++++++++++++++++++++++++++++----
R/subsetTOPO.R | 2
R/targetLL.R |only
inst/doc/GEOmap.pdf |binary
man/GEOmap-package.Rd | 4 -
man/Gcols.Rd |only
man/LandSeaCol.Rd |only
man/Lintersect.Rd | 2
man/antipolygon.Rd | 9 +-
man/mapTeleSeis.Rd |only
man/rectPERIM.Rd |only
man/sqrTICXY.Rd | 6 +
man/targetLL.Rd |only
23 files changed, 343 insertions(+), 68 deletions(-)
Title: Applies GAMbag, GAMrsm and GAMens ensemble classifiers for
binary classification
Diff between GAMens versions 1.0 dated 2010-01-11 and 1.1 dated 2010-02-03
Description: This package implements the GAMbag, GAMrsm and GAMens
ensemble classifiers for binary classification (De Bock et al.,
2010). The ensembles implement Bagging (Breiman, 1996), the
Random Subspace Method (Ho, 1998), or both, and use Hastie and
Tibshirani's (1990) generalized additive models (GAMs) as base
classifiers. Once an ensemble classifier has been trained, it
can be used for predictions on new data. A function for cross
validation is also included.
Author: Koen W. De Bock, Kristof Coussement and Dirk Van den Poel
Maintainer: Koen W. De Bock
DESCRIPTION | 6 +++---
R/predict.GAMens.R | 20 ++++++++------------
man/GAMens.cv.Rd | 14 +++++---------
man/predict.GAMens.Rd | 2 +-
4 files changed, 17 insertions(+), 25 deletions(-)
Title: Integrative Functional Analysis of Transcriptional Networks
Diff between FunNet versions 1.00-7 dated 2009-07-18 and 1.00-8 dated 2010-02-03
Description: FunNet is an integrative tool for analyzing gene
co-expression networks built from microarray expression data.
The analytic model implemented in this library involves two
abstraction layers: transcriptional and functional (biological
roles). A functional profiling technique using Gene Ontology &
KEGG annotations is applied to extract a list of relevant
biological themes from microarray expression profiling data.
Afterwards multiple-instance representations are built to
relate significant themes to their transcriptional instances
(i.e. the two layers of the model). An adapted non-linear
dynamical system model is used to quantify the proximity of
relevant genomic themes based on the similarity of the
expression profiles of their gene instances. Eventually an
unsupervised multiple-instance clustering procedure, relying on
the two abstraction layers, is used to identify the structure
of the co-expression network composed from modules of
functionally related transcripts. Functional and
transcriptional maps of the co-expression network are provided
separately together with detailed information on the network
centrality of related transcripts and genomic themes.
Author: Corneliu Henegar
Maintainer: Corneliu Henegar
DESCRIPTION | 8
R/Annotations.R | 4
R/FunNet.R | 631 ++++++++++++++++++++++++++++++++++++++++++++++++++------
R/sysdata.rda |binary
copying | 2
man/FunNet.Rd | 6
6 files changed, 582 insertions(+), 69 deletions(-)
Title: FISH Based Normalization and Copy Number inference of SNP
microarray data
Diff between FBN versions 1.3 dated 2010-02-01 and 1.4 dated 2010-02-03
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: Adrian Andronache
DESCRIPTION | 8 ++++----
R/FBNormalization.R | 13 +++++++------
2 files changed, 11 insertions(+), 10 deletions(-)