Title: Map filenames to MIME types
Diff between mime versions 0.1.2 dated 2014-07-25 and 0.2 dated 2014-09-26
Description: This package guesses the MIME type from a filename extension using
the data derived from /etc/mime.types in UNIX-type systems.
Author: Jeffrey Horner [ctb],
Yihui Xie [aut, cre]
Maintainer: Yihui Xie
DESCRIPTION | 15 +++++++++------
MD5 | 11 +++++++----
NAMESPACE | 2 ++
NEWS | 7 +++++++
R/parse.R |only
README.md | 6 ++++--
man/parse_multipart.Rd |only
src |only
8 files changed, 29 insertions(+), 12 deletions(-)
Title: Data to accompany Applied Linear Regression 4rd edition
Diff between alr4 versions 1.0.3 dated 2013-10-11 and 1.0.5 dated 2014-09-26
Description: This package is a companion to the textbook S. Weisberg (2014),
"Applied Linear Regression," 4rd edition, Wiley. It includes all the
data sets discussed in the book and one function to access the textbook's
website.
This package depends on the car package. Many data files in this package
are included in the alr3 package as well, so only one of them should be
loaded.
Author: Sanford Weisberg
Maintainer: Sanford Weisberg
alr4-1.0.3/alr4/data/bgs.rda |only
alr4-1.0.3/alr4/data/blowdown.rda |only
alr4-1.0.3/alr4/data/challeng.rda |only
alr4-1.0.3/alr4/data/donner.rda |only
alr4-1.0.3/alr4/data/downer.rda |only
alr4-1.0.3/alr4/data/forbes.rda |only
alr4-1.0.3/alr4/data/heights.rda |only
alr4-1.0.3/alr4/data/htwt.rda |only
alr4-1.0.3/alr4/man/forbes.Rd |only
alr4-1.0.3/alr4/man/heights.Rd |only
alr4-1.0.5/alr4/DESCRIPTION | 10 -
alr4-1.0.5/alr4/MD5 | 167 ++++++++++++++++-----------------
alr4-1.0.5/alr4/NAMESPACE | 2
alr4-1.0.5/alr4/NEWS |only
alr4-1.0.5/alr4/R/alr4.R | 5
alr4-1.0.5/alr4/data/BGSall.rda |only
alr4-1.0.5/alr4/data/BGSboys.rda |only
alr4-1.0.5/alr4/data/BGSgirls.rda |only
alr4-1.0.5/alr4/data/BigMac2003.rda |binary
alr4-1.0.5/alr4/data/BlowBS.rda |only
alr4-1.0.5/alr4/data/Blowdown.rda |only
alr4-1.0.5/alr4/data/Challeng.rda |only
alr4-1.0.5/alr4/data/Donner.rda |only
alr4-1.0.5/alr4/data/Downer.rda |only
alr4-1.0.5/alr4/data/Forbes.rda |only
alr4-1.0.5/alr4/data/Heights.rda |only
alr4-1.0.5/alr4/data/Highway.rda |binary
alr4-1.0.5/alr4/data/Hooker.rda |only
alr4-1.0.5/alr4/data/Htwt.rda |only
alr4-1.0.5/alr4/data/MWwords.rda |binary
alr4-1.0.5/alr4/data/MinnLand.rda |binary
alr4-1.0.5/alr4/data/MinnWater.rda |binary
alr4-1.0.5/alr4/data/Mitchell.rda |binary
alr4-1.0.5/alr4/data/Rateprof.rda |binary
alr4-1.0.5/alr4/data/Rpdata.rda |binary
alr4-1.0.5/alr4/data/Stevens.rda |binary
alr4-1.0.5/alr4/data/UBSprices.rda |binary
alr4-1.0.5/alr4/data/UN1.rda |binary
alr4-1.0.5/alr4/data/UN11.rda |binary
alr4-1.0.5/alr4/data/Whitestar.rda |binary
alr4-1.0.5/alr4/data/ais.rda |binary
alr4-1.0.5/alr4/data/allshoots.rda |binary
alr4-1.0.5/alr4/data/baeskel.rda |binary
alr4-1.0.5/alr4/data/brains.rda |binary
alr4-1.0.5/alr4/data/cakes.rda |binary
alr4-1.0.5/alr4/data/cathedral.rda |binary
alr4-1.0.5/alr4/data/caution.rda |binary
alr4-1.0.5/alr4/data/cloud.rda |binary
alr4-1.0.5/alr4/data/domedata.rda |binary
alr4-1.0.5/alr4/data/domedata1.rda |binary
alr4-1.0.5/alr4/data/drugcost.rda |binary
alr4-1.0.5/alr4/data/dwaste.rda |binary
alr4-1.0.5/alr4/data/florida.rda |binary
alr4-1.0.5/alr4/data/ftcollinssnow.rda |binary
alr4-1.0.5/alr4/data/ftcollinstemp.rda |binary
alr4-1.0.5/alr4/data/fuel2001.rda |binary
alr4-1.0.5/alr4/data/galapagos.rda |binary
alr4-1.0.5/alr4/data/galtonpeas.rda |binary
alr4-1.0.5/alr4/data/jevons.rda |binary
alr4-1.0.5/alr4/data/lakemary.rda |binary
alr4-1.0.5/alr4/data/lakes.rda |binary
alr4-1.0.5/alr4/data/landrent.rda |binary
alr4-1.0.5/alr4/data/lathe1.rda |binary
alr4-1.0.5/alr4/data/longshoots.rda |binary
alr4-1.0.5/alr4/data/mantel.rda |binary
alr4-1.0.5/alr4/data/mile.rda |binary
alr4-1.0.5/alr4/data/npdata.rda |binary
alr4-1.0.5/alr4/data/oldfaith.rda |binary
alr4-1.0.5/alr4/data/physics.rda |binary
alr4-1.0.5/alr4/data/physics1.rda |binary
alr4-1.0.5/alr4/data/pipeline.rda |binary
alr4-1.0.5/alr4/data/prodscore.rda |binary
alr4-1.0.5/alr4/data/rat.rda |binary
alr4-1.0.5/alr4/data/salary.rda |binary
alr4-1.0.5/alr4/data/salarygov.rda |binary
alr4-1.0.5/alr4/data/segreg.rda |binary
alr4-1.0.5/alr4/data/shocks.rda |binary
alr4-1.0.5/alr4/data/shortshoots.rda |binary
alr4-1.0.5/alr4/data/sleep1.rda |binary
alr4-1.0.5/alr4/data/snake.rda |binary
alr4-1.0.5/alr4/data/sniffer.rda |binary
alr4-1.0.5/alr4/data/stopping.rda |binary
alr4-1.0.5/alr4/data/swan96.rda |binary
alr4-1.0.5/alr4/data/turk0.rda |binary
alr4-1.0.5/alr4/data/turkey.rda |binary
alr4-1.0.5/alr4/data/twins.rda |binary
alr4-1.0.5/alr4/data/ufc.rda |binary
alr4-1.0.5/alr4/data/ufcdf.rda |binary
alr4-1.0.5/alr4/data/ufcgf.rda |binary
alr4-1.0.5/alr4/data/ufcwc.rda |binary
alr4-1.0.5/alr4/data/walleye.rda |binary
alr4-1.0.5/alr4/data/water.rda |binary
alr4-1.0.5/alr4/data/wblake.rda |binary
alr4-1.0.5/alr4/data/wm1.rda |binary
alr4-1.0.5/alr4/data/wm2.rda |binary
alr4-1.0.5/alr4/man/Forbes.Rd |only
alr4-1.0.5/alr4/man/Heights.Rd |only
97 files changed, 98 insertions(+), 86 deletions(-)
Title: Support for Linear Models
Diff between lmSupport versions 2.09 dated 2014-09-04 and 2.9.1 dated 2014-09-26
Description: Accompanies Markus Brauer, Bas Rokers, and John Curtin's two-course graduate series in
General, Generalized, and Multi-level Linear Models (PSY 610/710).
Author: John Curtin
Maintainer: John Curtin
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
R/modelEffectSizes.R | 2 +-
R/varDescribeBy.R | 11 ++---------
man/varDescribeBy.Rd | 15 ++++++++-------
5 files changed, 20 insertions(+), 26 deletions(-)
Title: jSonar Analytics Platform API for R
Diff between jSonarR versions 1.1 dated 2014-09-03 and 1.1.1 dated 2014-09-26
Description: This package enables users to access MongoDB by running queries
and returning their results in R data frames. Usually, data in MongoDB is
only available in the form of a JSON document. jSonarR uses data
processing and conversion capabilities in the jSonar Analytics Platform
and the JSON Studio Gateway (http://www.jsonstudio.com), to convert it to
a tabular format which is easy to use with existing R packages.
Author: jSonar Inc.
Maintainer: Dylan McCall
DESCRIPTION | 6 +--
MD5 | 5 +-
NEWS |only
R/exampleData.R | 101 --------------------------------------------------------
4 files changed, 7 insertions(+), 105 deletions(-)
Title: Calculate textures from grey-level co-occurrence matrices
(GLCMs) in R
Diff between glcm versions 0.3.2 dated 2014-07-30 and 1.0 dated 2014-09-26
Description: Enables calculation of image textures derived from grey-level
co-occurrence matrices (GLCMs) in R. Supports processing images that cannot
fit in memory.
Author: Alex Zvoleff [aut, cre]
Maintainer: Alex Zvoleff
DESCRIPTION | 12 -
MD5 | 34 ++---
NAMESPACE | 2
NEWS | 12 +
R/RcppExports.R | 5
R/glcm.R | 226 ++++++++++++++++++++++++++++++-------
README.md | 30 +++-
man/L5TSR_1986.Rd | 2
man/calc_texture.Rd | 7 -
man/expected_textures_3x3_1x1.Rd | 2
man/expected_textures_5x3_n1xn2.Rd | 2
man/expected_textures_5x7_2x3.Rd | 2
man/glcm-package.Rd | 2
man/glcm.Rd | 40 +++++-
man/test_raster.Rd | 2
src/RcppExports.cpp | 6
src/calc_texture.cpp | 211 +++++++++++++++++++---------------
tests/testthat/test-glcm.R | 62 ++++++++++
18 files changed, 474 insertions(+), 185 deletions(-)
Title: Combined analysis of pleiotropy and epistasis
Diff between cape versions 1.2 dated 2013-08-03 and 1.3 dated 2014-09-26
Description: This package combines complementary information across multiple related phenotypes to infer directed epistatic interactions between genetic markers. The analysis in this package can be applied to a variety of engineered and natural populations.
Author: Anna L. Tyler, Wei Lu, Justin J. Hendrick, Vivek M. Philip, and Greg W. Carter
Maintainer: Anna L. Tyler
cape-1.2/cape/R/linkage.blocks.R |only
cape-1.2/cape/man/linkage.blocks.Rd |only
cape-1.3/cape/DESCRIPTION | 10
cape-1.3/cape/MD5 | 159 ++++---
cape-1.3/cape/NAMESPACE | 5
cape-1.3/cape/R/calc.p.R | 71 ++-
cape-1.3/cape/R/create.covar.R | 4
cape-1.3/cape/R/direct.influence.R | 93 +++-
cape-1.3/cape/R/genome.wide.threshold.1D.R | 79 ++-
cape-1.3/cape/R/get.network.R | 128 +++---
cape-1.3/cape/R/get.pairs.for.pairscan.R | 6
cape-1.3/cape/R/linkage.blocks.stepwise.R |only
cape-1.3/cape/R/myImagePlot.R | 142 +++++-
cape-1.3/cape/R/one.pairscan.R | 21 -
cape-1.3/cape/R/one.singlescan.R |only
cape-1.3/cape/R/pairscan.R | 36 -
cape-1.3/cape/R/pairscan.null.R |only
cape-1.3/cape/R/plotCollapsedVarInf.R | 59 ++
cape-1.3/cape/R/plotNetwork.R | 436 ++++++++++++++-------
cape-1.3/cape/R/plotPairscan.R | 41 -
cape-1.3/cape/R/plotSinglescan.R | 131 +++---
cape-1.3/cape/R/plotSinglescan.heat.R |only
cape-1.3/cape/R/plotVariantInfluences.R | 281 ++++++++++++-
cape-1.3/cape/R/read.population.R | 30 +
cape-1.3/cape/R/select.by.chr.R | 1
cape-1.3/cape/R/select.markers.for.pairscan.R | 268 ++++++++++--
cape-1.3/cape/R/set.pairscan.thresh.R | 8
cape-1.3/cape/R/singlescan.R | 31 -
cape-1.3/cape/R/writePopulation.R |only
cape-1.3/cape/R/writeVariantInfluences.R | 6
cape-1.3/cape/build |only
cape-1.3/cape/data/obesity.cross.rda |binary
cape-1.3/cape/inst/doc/cape.R | 18
cape-1.3/cape/inst/doc/cape.Rnw | 315 ++++++++-------
cape-1.3/cape/inst/doc/cape.pdf |binary
cape-1.3/cape/man/calc.delta.errors.Rd | 3
cape-1.3/cape/man/calc.p.Rd | 9
cape-1.3/cape/man/cape-package.Rd | 4
cape-1.3/cape/man/consec.pairs.Rd | 4
cape-1.3/cape/man/create.covar.Rd | 3
cape-1.3/cape/man/delete.pheno.Rd | 3
cape-1.3/cape/man/direct.influence.Rd | 10
cape-1.3/cape/man/error.prop.Rd | 7
cape-1.3/cape/man/genome.wide.threshold.1D.Rd | 22 -
cape-1.3/cape/man/get.col.num.Rd | 3
cape-1.3/cape/man/get.covar.Rd | 7
cape-1.3/cape/man/get.eigentraits.Rd | 7
cape-1.3/cape/man/get.layout.mat.Rd | 3
cape-1.3/cape/man/get.linearly.independent.Rd | 8
cape-1.3/cape/man/get.network.Rd | 31 -
cape-1.3/cape/man/get.pairs.for.pairscan.Rd | 3
cape-1.3/cape/man/linkage.blocks.stepwise.Rd |only
cape-1.3/cape/man/myImagePlot.Rd | 3
cape-1.3/cape/man/norm.pheno.Rd | 6
cape-1.3/cape/man/one.pairscan.Rd | 3
cape-1.3/cape/man/one.singlescan.Rd |only
cape-1.3/cape/man/pair.matrix.Rd | 3
cape-1.3/cape/man/pairscan.Rd | 9
cape-1.3/cape/man/pairscan.null.Rd |only
cape-1.3/cape/man/plotCollapsedVarInf.Rd | 17
cape-1.3/cape/man/plotNetwork.Rd | 51 +-
cape-1.3/cape/man/plotPairscan.Rd | 9
cape-1.3/cape/man/plotSVD.Rd | 7
cape-1.3/cape/man/plotSinglescan.Rd | 19
cape-1.3/cape/man/plotSinglescan.heat.Rd |only
cape-1.3/cape/man/plotVariantInfluences.Rd | 41 +
cape-1.3/cape/man/read.population.Rd | 9
cape-1.3/cape/man/remove.ind.with.missing.pheno.Rd | 3
cape-1.3/cape/man/report.progress.Rd | 3
cape-1.3/cape/man/rotate.mat.Rd | 3
cape-1.3/cape/man/rz.transform.Rd | 3
cape-1.3/cape/man/segment.region.Rd | 3
cape-1.3/cape/man/select.by.chr.Rd | 3
cape-1.3/cape/man/select.by.ind.Rd | 3
cape-1.3/cape/man/select.eigentraits.Rd | 7
cape-1.3/cape/man/select.markers.for.pairscan.Rd | 31 +
cape-1.3/cape/man/select.pheno.Rd | 3
cape-1.3/cape/man/set.covar.Rd | 11
cape-1.3/cape/man/set.pairscan.thresh.Rd | 8
cape-1.3/cape/man/singlescan.Rd | 27 -
cape-1.3/cape/man/writePopulation.Rd |only
cape-1.3/cape/man/writeVariantInfluences.Rd | 12
cape-1.3/cape/vignettes/Network_Collapsed.pdf |binary
cape-1.3/cape/vignettes/Network_Full.pdf |binary
cape-1.3/cape/vignettes/cape.Rnw | 315 ++++++++-------
cape-1.3/cape/vignettes/pair_regression.pdf |binary
cape-1.3/cape/vignettes/variant_influences.pdf |binary
87 files changed, 2032 insertions(+), 1086 deletions(-)
Title: Another Plot PACKage: stem.leaf, bagplot, faces, spin3R,
plotsummary, plothulls, and some slider functions
Diff between aplpack versions 1.2.9 dated 2013-11-05 and 1.3.0 dated 2014-09-26
Description: set of functions for drawing some special plots:
stem.leaf plots a stem and leaf plot,
stem.leaf.backback plots back-to-back versions of stem and leafs,
bagplot plots a bagplot,
skyline.hist plots several histgramm in one plot of a one dimensional data set,
plotsummary plots a graphical summary of a data set with one or more variables,
plothulls plots sequentially hulls of a bivariate data set,
faces plots chernoff faces,
spin3R for an inspection of a 3-dim point cloud,
slider functions for interactive graphics.
Author: Hans Peter Wolf, Uni Bielefeld
Maintainer: Hans Peter Wolf
aplpack-1.2.9/aplpack/inst/doc/sliderfns.R |only
aplpack-1.3.0/aplpack/DESCRIPTION | 12 +--
aplpack-1.3.0/aplpack/MD5 | 45 ++++++------
aplpack-1.3.0/aplpack/NAMESPACE | 1
aplpack-1.3.0/aplpack/R/bagplot.R | 2
aplpack-1.3.0/aplpack/R/slider.R | 6 -
aplpack-1.3.0/aplpack/R/slider.brush.pairs.R | 10 +-
aplpack-1.3.0/aplpack/R/slider.density.R | 3
aplpack-1.3.0/aplpack/R/slider.stem.leaf.R | 13 +--
aplpack-1.3.0/aplpack/TODO |only
aplpack-1.3.0/aplpack/build |only
aplpack-1.3.0/aplpack/inst/doc/bagplot.pdf |binary
aplpack-1.3.0/aplpack/inst/doc/faces.pdf |binary
aplpack-1.3.0/aplpack/inst/doc/ms.pdf |binary
aplpack-1.3.0/aplpack/inst/doc/sc.pdf |binary
aplpack-1.3.0/aplpack/inst/doc/slider-make.pdf |binary
aplpack-1.3.0/aplpack/inst/doc/sliderfns.Snw | 22 ++++-
aplpack-1.3.0/aplpack/inst/doc/spin3R.pdf |binary
aplpack-1.3.0/aplpack/inst/src/bagplot.rev | 18 +++-
aplpack-1.3.0/aplpack/inst/src/sc.rev | 93 +++++++++++++------------
aplpack-1.3.0/aplpack/inst/src/sliderfns.rev | 20 ++++-
aplpack-1.3.0/aplpack/man/boxplot2D.Rd | 2
aplpack-1.3.0/aplpack/man/plothulls.Rd | 6 -
aplpack-1.3.0/aplpack/man/slider.Rd | 2
aplpack-1.3.0/aplpack/vignettes/sliderfns.Snw | 22 ++++-
25 files changed, 164 insertions(+), 113 deletions(-)
Title: Genealogical Data Analysis
Diff between GENLIB versions 1.0 dated 2014-09-22 and 1.0.1 dated 2014-09-26
Description: Genealogical data analysis including descriptive statistics (e.g., kinship and inbreeding coefficients) and gene-dropping simulations.
Author: Louis Houde [aut],
Jean-Francois Lefebvre [aut],
Valery Roy-Lagace [aut],
Sebastien Lemieux [aut],
Michael J. Fromberger [ctb],
Marie-Helene Roy-Gagnon [cre]
Maintainer: Marie-Helene Roy-Gagnon
GENLIB-1.0.1/GENLIB/DESCRIPTION | 27 +++++++----
GENLIB-1.0.1/GENLIB/MD5 | 71 +++++++++++++----------------
GENLIB-1.0.1/GENLIB/R/fonctionsBase.R | 2
GENLIB-1.0.1/GENLIB/data/geneaJi.rda |binary
GENLIB-1.0.1/GENLIB/data/pop140.rda |binary
GENLIB-1.0.1/GENLIB/man/GenlibR-package.Rd | 2
GENLIB-1.0.1/GENLIB/man/gen.f.Rd | 10 ++--
GENLIB-1.0.1/GENLIB/man/gen.fCI.Rd | 3 -
GENLIB-1.0.1/GENLIB/man/gen.findMRCA.Rd | 26 +++-------
GENLIB-1.0.1/GENLIB/man/gen.phi.Rd | 12 ----
GENLIB-1.0.1/GENLIB/man/gen.phiCI.Rd | 12 ++--
GENLIB-1.0.1/GENLIB/man/gen.phiMean.Rd | 9 ++-
GENLIB-1.0.1/GENLIB/man/gen.phiOver.Rd | 10 ++--
GENLIB-1.0.1/GENLIB/src/apparentement.cpp | 10 ++--
GENLIB-1.0.1/GENLIB/src/apparentement.h | 2
GENLIB-1.0.1/GENLIB/src/base.h | 2
GENLIB-1.0.1/GENLIB/src/congen.cpp | 4 -
GENLIB-1.0.1/GENLIB/src/consanguinite.cpp | 14 ++---
GENLIB-1.0.1/GENLIB/src/fondateur.cpp | 47 +++++++++----------
GENLIB-1.0.1/GENLIB/src/fondateur.h | 2
GENLIB-1.0.1/GENLIB/src/genphi.cpp | 21 ++++----
GENLIB-1.0.1/GENLIB/src/hal.cpp | 8 +--
GENLIB-1.0.1/GENLIB/src/hal.h | 4 +
GENLIB-1.0.1/GENLIB/src/hashtable.h | 4 -
GENLIB-1.0.1/GENLIB/src/interface.cpp | 26 ++++------
GENLIB-1.0.1/GENLIB/src/md5.cpp | 2
GENLIB-1.0.1/GENLIB/src/mpi-types.h | 2
GENLIB-1.0.1/GENLIB/src/mpi.c | 6 +-
GENLIB-1.0.1/GENLIB/src/outilanal.cpp | 2
GENLIB-1.0.1/GENLIB/src/outils.cpp | 7 +-
GENLIB-1.0.1/GENLIB/src/outilsalloc.h | 7 +-
GENLIB-1.0.1/GENLIB/src/probsimul.cpp | 18 ++++---
GENLIB-1.0.1/GENLIB/src/userInterface.cpp | 10 ++--
GENLIB-1.0/GENLIB/src/RInside.h |only
GENLIB-1.0/GENLIB/src/RInsideAutoloads.h |only
GENLIB-1.0/GENLIB/src/RInsideCommon.h |only
GENLIB-1.0/GENLIB/src/RInsideConfig.h |only
GENLIB-1.0/GENLIB/src/RInsideEnvVars.h |only
GENLIB-1.0/GENLIB/src/crtdbg.h |only
GENLIB-1.0/GENLIB/src/crtdbg_s.h |only
40 files changed, 186 insertions(+), 196 deletions(-)
Title: Basic Theoretical Copula, Empirical Copula, and Various Utility
Functions
Diff between copBasic versions 1.5.4 dated 2013-05-10 and 1.6.0 dated 2014-09-26
Description: The package implements extensive functions for copula computations and related mathematical operations oriented around the oft cited and fundamental copula theory described by Nelson (2006). The lower (W), upper (M), product (P), PSP, and Plackett (with parameter estimation) copulas are provided. Individual copula functional support is intentionally limited to keep the package focused on an API to general copula theory. Expressions available for an arbitrary copula include the diagonal of a copula, the survival copula, the dual of a copula, and co-copula. Level curves (sets) are available. Horizontal and vertical copula sections and derivatives of such sections also are supported. The numerical derivatives of a copula are provided as well as inverses, and thus functions for copula simulation also are supported. Composition of copulas is provided: (1) composition of a single copula using two composition parameters, (2) composition of two copulas using two composition parameters, (3) composition of two copulas using four composition parameters, and (4) composite copula random variates. Characteristics of copulas include Kendall Tau, Spearman Rho, Gini Gamma, Blomqvist Beta, and Schweizer-Wolff Sigma. Logical evaluators of positively/negatively quadrant dependency, left-tail decreasing, and right-tail increasing also are available. Quantile and median regression for V with respect to U and U with respect to V is available. Empirical copulas (EC) are supported. ECs are dependent on gridded data structures for which generation capability is provided. The derivatives of the EC grid are computable. Also, the inverses of the derivatives, which are the conditional QDFs of copula sections also are computable. Median and quantile regression of an EC also is supported along with support for EC simulation of V conditional on U.
Author: William Asquith
Maintainer: William Asquith
ChangeLog | 55 +++++-
DESCRIPTION | 60 +------
MD5 | 217 +++++++++++++------------
NAMESPACE | 9 +
R/COP.R | 4
R/EMPIRcop.R | 62 +++++--
R/EMPIRgrid.R | 25 +-
R/EMPIRgridderinv.R | 6
R/EMPIRgridderinv2.R | 6
R/EMPIRqua.regress.R | 12 -
R/EMPIRqua.regress2.R | 12 -
R/EMPIRsim.R | 6
R/M.R | 15 +
R/P.R | 17 +
R/PSP.R | 16 +
R/W.R | 17 +
R/asCOP.R |only
R/coCOP.R | 5
R/derCOP.R | 38 +++-
R/derCOP2.R | 37 +++-
R/diagCOP.R | 8
R/duCOP.R | 4
R/giniCOP.R | 16 -
R/gridCOP.R |only
R/hoefCOP.R |only
R/isCOP.LTD.R | 30 +--
R/isCOP.PQD.R |only
R/isCOP.RTI.R | 30 +--
R/isCOP.radsym.R |only
R/level.curvesCOP.R | 52 +++++-
R/level.curvesCOP2.R |only
R/level.setCOP.R |only
R/level.setCOP2.R |only
R/med.regressCOP.R | 5
R/med.regressCOP2.R | 5
R/qua.regressCOP.R | 28 +--
R/qua.regressCOP.draw.R | 18 --
R/qua.regressCOP2.R | 28 +--
R/rhoCOP.R | 50 ++++-
R/sectionCOP.R | 54 +-----
R/simCOP.R | 36 ++--
R/simCOPmicro.R | 8
R/simcomposite3COP.R | 6
R/simcompositeCOP.R | 8
R/surCOP.R | 4
R/surfuncCOP.R |only
R/taildepCOP.R | 45 ++---
R/tauCOP.R | 54 ++++--
R/wolfCOP.R | 30 ++-
man/COP.Rd | 43 +----
man/COPinv.Rd | 45 +----
man/COPinv2.Rd | 27 +--
man/EMPIRcop.Rd | 119 +++++++------
man/EMPIRcopdf.Rd | 41 +---
man/EMPIRgrid.Rd | 197 ++++++++++++-----------
man/EMPIRgridder.Rd | 47 ++---
man/EMPIRgridder2.Rd | 65 -------
man/EMPIRgridderinv.Rd | 123 ++++++--------
man/EMPIRgridderinv2.Rd | 14 -
man/EMPIRmed.regress.Rd | 13 -
man/EMPIRmed.regress2.Rd | 11 -
man/EMPIRqua.regress.Rd | 324 ++++++++++++++++----------------------
man/EMPIRqua.regress2.Rd | 24 +-
man/EMPIRsim.Rd | 48 ++---
man/EMPIRsimv.Rd | 78 +++++----
man/M.Rd | 23 +-
man/N4212cop.Rd | 31 +--
man/P.Rd | 19 +-
man/PLACKETTcop.Rd | 33 +--
man/PLACKETTpar.Rd | 39 +---
man/PLACKETTsim.Rd | 25 +-
man/PSP.Rd | 21 +-
man/PlackettPlackettABKGtest.Rd | 83 +++------
man/PlackettPlackettNP.Rd | 118 +++++--------
man/ReineckeWell266.Rd | 14 -
man/ReineckeWells.Rd | 12 -
man/W.Rd | 23 +-
man/asCOP.Rd |only
man/blomCOP.Rd | 24 +-
man/coCOP.Rd | 64 +++----
man/composite1COP.Rd | 49 ++---
man/composite2COP.Rd | 93 ++++++----
man/composite3COP.Rd | 98 +++++------
man/copBasic-package.Rd |only
man/derCOP.Rd | 82 ++++-----
man/derCOP2.Rd | 74 ++++----
man/derCOPinv.Rd | 69 +++-----
man/derCOPinv2.Rd | 68 +++----
man/diagCOP.Rd | 30 +--
man/duCOP.Rd | 48 +++--
man/giniCOP.Rd | 62 ++++---
man/gridCOP.Rd |only
man/hoefCOP.Rd |only
man/isCOP.LTD.Rd | 53 ++----
man/isCOP.PQD.Rd |only
man/isCOP.RTI.Rd | 57 ++----
man/isCOP.radsym.Rd |only
man/lcomoms2.ABKGcop2parameter.Rd | 60 +++----
man/lcomoms2.ABcop2parameter.Rd | 62 +++----
man/level.curvesCOP.Rd | 32 ++-
man/level.curvesCOP2.Rd |only
man/level.setCOP.Rd |only
man/level.setCOP2.Rd |only
man/med.regressCOP.Rd | 63 +++----
man/med.regressCOP2.Rd | 34 +--
man/qua.regressCOP.Rd | 109 ++++--------
man/qua.regressCOP.draw.Rd | 24 +-
man/qua.regressCOP2.Rd | 58 +-----
man/rhoCOP.Rd | 66 +++----
man/sectionCOP.Rd | 121 +++++++-------
man/simCOP.Rd | 48 ++---
man/simCOPmicro.Rd | 30 +--
man/simcomposite3COP.Rd | 86 ++++------
man/simcompositeCOP.Rd | 56 +++---
man/surCOP.Rd | 65 +++----
man/surfuncCOP.Rd |only
man/taildepCOP.Rd | 92 +++++-----
man/tauCOP.Rd | 130 ++++++---------
man/wolfCOP.Rd | 74 ++++++--
119 files changed, 2429 insertions(+), 2450 deletions(-)
Title: SNPs enrichment analysis
Diff between snpEnrichment versions 1.4-1 dated 2014-09-11 and 1.5-0 dated 2014-09-26
Description: Implements classes and methods for large scale SNP enrichment analysis (e.g. SNPs associated with genes expression in a GWAS signal)
Author: Mickael Canouil [aut, cre],
Loic Yengo [ctb]
Maintainer: Mickael Canouil
ChangeLog | 18 ++++++++++++++++
DESCRIPTION | 10 ++++-----
MD5 | 22 +++++++++++---------
R/Global.R | 6 +++--
R/enrichment.R | 3 ++
README.md |only
inst/example.R |only
man/Enrichment-class.Rd | 4 +--
man/compareEnrichment.Rd | 13 +++++++-----
man/excludeSNP-methods.Rd | 7 ++++--
man/readEnrichment.Rd | 3 --
man/snpEnrichment-package.Rd | 46 ++++++++++++++++++++++++-------------------
man/writeLD.Rd | 2 -
13 files changed, 84 insertions(+), 50 deletions(-)
Title: Training datasets for iC10 package.
Diff between iC10TrainingData versions 1.0.0 dated 2014-06-18 and 1.0.1 dated 2014-09-26
More information about iC10TrainingData at CRAN
Description: Training datasets for iC10; which implements the classifier described in the paper 'Genome-driven integrated classification of breast cancer validated in over 7,500 samples' (Ali HR et al., Genome Biology 2014). It uses copy number and/or expression form breast cancer data, trains a pamr classifier (Tibshirani et al.) with the features available and predicts the iC10 group. Genomic annotation for the training dataset has been obtained from Mark Dunning's lluminaHumanv3.db package.
Author: Oscar M Rueda
Maintainer: Oscar M. Rueda
DESCRIPTION | 10 +++++-----
MD5 | 2 +-
2 files changed, 6 insertions(+), 6 deletions(-)
Permanent link
Title: A copy number and expression-based classifier for breast
tumours.
Diff between iC10 versions 1.0.2 dated 2014-06-19 and 1.1.1 dated 2014-09-26
Description: iC10 implements the classifier described in the paper 'Genome-driven integrated classification of breast cancer validated in over 7,500 samples' (Ali HR et al., Genome Biology 2014). It uses copy number and/or expression form breast cancer data, trains a pamr classifier (Tibshirani et al.) with the features available and predicts the iC10 group.
Author: Oscar M Rueda
Maintainer: Oscar M. Rueda
DESCRIPTION | 12 +++++-----
MD5 | 30 +++++++++++++--------------
NAMESPACE | 2 -
NEWS | 5 ++++
R/getCNfeatures.R | 4 +--
R/goodnessOfFit.R | 2 -
R/normalizeFeatures.R | 52 ++++++++++++++++++++++++++++-------------------
man/compare.Rd | 6 +++--
man/goodnessOfFit.Rd | 8 ++++---
man/iC10-package.Rd | 4 ++-
man/iC10.Rd | 6 +++--
man/matchFeatures.Rd | 13 ++++++++---
man/normalizeFeatures.Rd | 23 +++++---------------
man/plot.iC10.Rd | 18 +++++++++-------
man/print.iC10.Rd | 4 ++-
man/summary.iC10.Rd | 8 ++++---
16 files changed, 111 insertions(+), 86 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-05-06 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-10-02 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-12-11 1.7.2
2013-07-01 1.7.0
2013-04-04 1.6.4
2013-01-31 1.6.3
2012-12-21 1.6.2
2012-10-26 1.6.1
2012-10-23 1.6.0
2012-02-15 1.05
2012-02-10 1.0
Title: Multidimensional Adaptive Testing
Diff between MAT versions 0.1-3 dated 2011-01-26 and 2.0 dated 2014-09-26
Description: Simulate Multidimensional Adaptive Testing
Author: Seung W. Choi and David R. King
Maintainer: Seung W. Choi
MAT-0.1-3/MAT/R/calcFI.R |only
MAT-0.1-3/MAT/R/calcHessian.R |only
MAT-0.1-3/MAT/R/dLL.R |only
MAT-0.1-3/MAT/R/makeFI.R |only
MAT-0.1-3/MAT/R/makeHessian.R |only
MAT-0.1-3/MAT/R/score.R |only
MAT-0.1-3/MAT/R/score_1.R |only
MAT-2.0/MAT/DESCRIPTION | 19 +--
MAT-2.0/MAT/MD5 |only
MAT-2.0/MAT/NAMESPACE | 5
MAT-2.0/MAT/R/MAT.R | 246 ++++++++++++++++++++--------------------
MAT-2.0/MAT/R/RcppExports.R |only
MAT-2.0/MAT/man/MAT-internal.Rd |only
MAT-2.0/MAT/man/MAT-package.Rd | 4
MAT-2.0/MAT/man/MAT.Rd | 3
MAT-2.0/MAT/man/sample.ipar.Rd | 2
MAT-2.0/MAT/man/simM3PL.Rd | 2
MAT-2.0/MAT/src |only
18 files changed, 147 insertions(+), 134 deletions(-)