Title: Toy Example of S4 Package
Description: Illustration of the book "Petit Manuel de Programmation Orientee Objet sous R". The english version "A (Not so) Short Introduction to S4" is on CRAN, 'Contributed documentation'.
Author: Christophe Genolini
Maintainer: Christophe Genolini <genolini@u-paris10.fr>
Diff between packS4 versions 0.9.1 dated 2012-06-29 and 0.9.3 dated 2015-05-27
packS4-0.9.1/packS4/main.R |only packS4-0.9.3/packS4/DESCRIPTION | 18 +++++++++--------- packS4-0.9.3/packS4/MD5 | 14 ++++++++------ packS4-0.9.3/packS4/NAMESPACE | 6 ++++-- packS4-0.9.3/packS4/R/codeVerif.R |only packS4-0.9.3/packS4/R/global.R | 4 ++++ packS4-0.9.3/packS4/man/classCreator.Rd | 4 ++-- packS4-0.9.3/packS4/man/detectGlobal.Rd |only packS4-0.9.3/packS4/man/plot-methods.Rd | 2 +- packS4-0.9.3/packS4/man/tryBug.Rd |only 10 files changed, 28 insertions(+), 20 deletions(-)
Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Description: NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D
biological image data, especially traced neurons. Reads and writes 3D images
in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf
format. Traced neurons can be imported from and written to SWC and 'Amira'
LineSet and SkeletonGraph formats. These data can then be visualised in 3D
via 'rgl', manipulated including applying calculated registrations, e.g.
using the 'CMTK' registration suite, and analysed. There is also a simple
representation for neurons that have been subjected to 3D skeletonisation
but not formally traced; this allows morphological comparison between
neurons including searches and clustering (via the 'nat.nblast' extension
package).
Author: Greg Jefferis and James Manton
Maintainer: Greg Jefferis <jefferis@gmail.com>
Diff between nat versions 1.6.4 dated 2015-02-09 and 1.6.6 dated 2015-05-27
DESCRIPTION | 31 MD5 | 334 ++++----- NAMESPACE | 10 NEWS | 42 + R/cmtk-reformat.R | 40 - R/cmtk.R | 2 R/cmtk_geometry.R | 27 R/dotprops.R | 31 R/hxsurf.R | 75 +- R/im3d.R | 7 R/nat-data.R | 47 + R/neuron-io-neuroml.R | 2 R/neuron-io.R | 48 + R/neuron-plot.R | 103 ++ R/neuron.R | 6 R/neuronlist.R | 350 +++------- R/neuronlist_interactive_3d.R |only R/neuronlistfh.R | 2 R/xform.R | 97 ++ R/xformimage.R | 2 R/xformpoints.R | 13 README.md | 15 data/MBL.surf.rda |only man/Cell07PNs.Rd | 29 man/MBL.surf.Rd |only man/affmat2cmtkparams.Rd | 19 man/all.equal.dotprops.Rd | 24 man/all.equal.im3d.Rd | 27 man/all.equal.neuron.Rd | 39 - man/amiramesh-io.Rd | 42 - man/amiratype.Rd | 27 man/as.data.frame.neuronlist.Rd |only man/as.im3d.Rd | 51 - man/as.mesh3d.Rd | 26 man/as.neuronlist.Rd | 26 man/as.neuronlist.neuronlistfh.Rd | 7 man/boundingbox.Rd | 115 +-- man/c.neuronlist.Rd | 10 man/clampmax.Rd | 23 man/cmtk.bindir.Rd | 70 -- man/cmtk.call.Rd | 53 - man/cmtk.dof2mat.Rd | 23 man/cmtk.extract_affine.Rd | 17 man/cmtk.mat2dof.Rd | 28 man/cmtk.reformatx.Rd | 76 -- man/cmtk.statistics.Rd | 41 - man/cmtk.targetvolume.Rd | 25 man/cmtk.version.Rd | 17 man/cmtkparams2affmat.Rd | 33 man/cmtkreg.Rd | 42 - man/cmtkreglist.Rd | 29 man/coord2ind.Rd | 20 man/dotprops-arithmetic.Rd | 7 man/dotprops.Rd | 75 -- man/fileformats.Rd | 115 +-- man/find.neuron.Rd | 30 man/find.soma.Rd | 33 man/flip.Rd | 21 man/graph.nodes.Rd | 19 man/im3d-coords.Rd | 46 - man/im3d-io.Rd | 75 +- man/im3d.Rd | 83 +- man/image.im3d.Rd | 115 +-- man/imexpand.grid.Rd | 32 man/imscalebar.Rd | 32 man/imslice.Rd | 50 - man/ind2coord.Rd | 15 man/intersect.Rd | 14 man/is.amiramesh.Rd | 22 man/is.fijitraces.Rd | 18 man/is.neuroml.Rd | 14 man/is.neuronlist.Rd | 20 man/is.nrrd.Rd | 25 man/is.swc.Rd | 17 man/is.vaa3draw.Rd | 19 man/kcs20.Rd | 39 - man/materials.Rd | 32 man/mirror.Rd | 64 - man/nat-internal.Rd | 7 man/nat-package.Rd | 84 +- man/ndigest.Rd | 67 - man/neuron-arithmetic.Rd | 13 man/neuron.Rd | 116 +-- man/neuronlist-arithmetic.Rd | 13 man/neuronlist-dataframe-methods.Rd | 46 - man/neuronlist.Rd | 42 - man/neuronlistfh.Rd | 256 +++---- man/ngraph.Rd | 114 +-- man/nlapply.Rd | 107 +-- man/nlscan.Rd | 66 - man/nopen3d.Rd | 17 man/normalise_swc.Rd | 29 man/npop3d.Rd | 14 man/nrrd.voxdims.Rd | 18 man/origin.Rd | 43 - man/pan3d.Rd | 14 man/plot.neuron.Rd | 82 +- man/plot.neuronlist.Rd | 88 +- man/plot3d.Rd |only man/plot3d.boundingbox.Rd | 11 man/plot3d.dotprops.Rd | 57 - man/plot3d.hxsurf.Rd | 47 - man/plot3d.neuron.Rd | 53 - man/plot3d.neuronlist.Rd | 171 ++-- man/pointsinside.Rd | 26 man/potential_synapses.Rd | 25 man/projection.Rd | 69 - man/prune.Rd | 26 man/read.cmtk.Rd | 28 man/read.cmtkreg.Rd | 15 man/read.hxsurf.Rd | 80 +- man/read.landmarks.Rd | 74 -- man/read.morphml.Rd | 60 - man/read.neuron.Rd | 80 +- man/read.neuron.fiji.Rd | 21 man/read.neuron.neuroml.Rd | 16 man/read.neuron.swc.Rd | 18 man/read.neuronlistfh.Rd | 118 +-- man/read.neurons.Rd | 121 +-- man/read.nrrd.Rd | 33 man/read.vaa3draw.Rd | 14 man/remotesync.Rd | 35 - man/resample.Rd | 17 man/rootpoints.Rd | 19 man/scale.dotprops.Rd | 16 man/scale.neuron.Rd | 13 man/seglengths.Rd | 29 man/seglist.Rd | 62 - man/seglist2swc.Rd | 40 - man/segmentgraph.Rd | 32 man/setdiff.Rd | 23 man/spine.Rd | 34 man/sub-.neuronlistfh.Rd | 16 man/sub2ind.Rd | 7 man/subset.Rd |only man/subset.dotprops.Rd | 28 man/subset.hxsurf.Rd | 43 - man/subset.neuronlist.Rd | 42 - man/threshold.Rd | 56 - man/union.Rd | 16 man/unmask.Rd | 67 - man/voxdims.Rd | 48 - man/write.amiramesh.Rd | 27 man/write.cmtk.Rd | 28 man/write.cmtkreg.Rd | 28 man/write.hxsurf.Rd | 30 man/write.neuron.Rd | 50 - man/write.neuronlistfh.Rd | 59 - man/write.neurons.Rd | 57 - man/write.nrrd.Rd | 19 man/xform.Rd | 113 +-- man/xformimage.Rd | 81 +- man/xformpoints.Rd | 84 +- man/xyzmatrix.Rd | 64 + tests/testthat/test-cmtk-reformat.R | 11 tests/testthat/test-cmtk.R | 17 tests/testthat/test-cmtkreg.R | 6 tests/testthat/test-hxsurf.R | 19 tests/testthat/test-im3d.R | 5 tests/testthat/test-landmarks-io.R | 14 tests/testthat/test-neuroml-io.R | 10 tests/testthat/test-neuron-io.R | 23 tests/testthat/test-neuron.R | 29 tests/testthat/test-neuronlist.R | 59 + tests/testthat/test-neuronlistfh.R | 2 tests/testthat/test-potential_synapses.R | 1 tests/testthat/test-seglist.R | 7 tests/testthat/test-xform.R | 52 + tests/testthat/test-xformimage.R | 40 + tests/testthat/testdata/amira/tetrahedron_badtrianglenum.surf |only tests/testthat/testdata/amira/tetrahedron_nocol.surf |only tests/testthat/testdata/amira/tetrahedron_notriangles.surf |only tests/testthat/testdata/selfun_cell07.rds |only 173 files changed, 3680 insertions(+), 3552 deletions(-)
Title: Flexible Regression Models for Survival Data
Description: Programs for Martinussen and Scheike (2006), `Dynamic Regression
Models for Survival Data', Springer Verlag. Plus more recent developments.
Additive survival model, semiparametric proportional odds model, fast cumulative
residuals, excess risk models and more. Flexible competing risks regression
including GOF-tests. Two-stage frailty modelling.
PLS for the additive risk model. Lasso in the 'ahaz' package.
Author: Thomas Scheike with contributions from Torben Martinussen, Jeremy Silver
and Klaus Holst
Maintainer: Thomas Scheike <ts@biostat.ku.dk>
Diff between timereg versions 1.8.7 dated 2015-03-05 and 1.8.8 dated 2015-05-27
DESCRIPTION | 18 MD5 | 53 +- NAMESPACE | 38 + R/Cpred.r | 3 R/base.r | 20 R/comprisk.ipw.r | 34 + R/comprisk.r | 332 ++++++++++--- R/cox.ipw.r | 23 R/glm-comprisk.r |only R/ipcw-residualmean.r |only R/predict-timereg.r | 88 ++- R/prop-odds-subdist.r | 80 ++- R/restricted.residual.mean.r | 38 + R/two-stage-reg.r | 10 man/Gprop.odds.Rd | 3 man/comp.risk.Rd | 51 +- man/dynreg.Rd | 2 man/internal-addreg.Rd | 15 man/plot.dynreg.Rd | 3 man/prep.comp.risk.Rd |only man/prop.odds.subdist.Rd | 4 man/res.mean.Rd |only man/restricted.residual.mean.Rd | 9 man/wald.test.Rd | 7 src/comprisk.c | 1020 +++++++++++++++++++++------------------- src/cox-aalen-lwy-resamp.c |only src/cox-aalen-stratum.c |only src/ipcw-residualmean.c |only src/matrix.h | 16 src/pred.c | 71 +- src/prop-odds-subdist2.c | 3 31 files changed, 1281 insertions(+), 660 deletions(-)
Title: Framework for the Analysis of Genomic Prediction Data using R
Description: A collection of functions required for genomic prediction which were developed within the Synbreed project for synergistic plant and animal breeding (www.synbreed.tum.de). This covers data processing, data visualization, and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats in plant and animal breeding. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Hans-Juergen Auinger, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Maintainer: Valentin Wimmer <Valentin.Wimmer@kws.com>
Diff between synbreed versions 0.11-2 dated 2015-05-26 and 0.11-4 dated 2015-05-27
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- R/codeGeno.r | 13 +++++++++++-- R/create.gpData.r | 2 +- man/read.vcf2list.Rd | 2 +- 5 files changed, 23 insertions(+), 14 deletions(-)
Title: Uses an Archive to Amend Previous Stages of a Pipe using Current
Output
Description: Remedies a common problem in piping: not having access to
intermediate outputs of the pipe. Within a "loop", a piping intermediate
is stored in a stack archive, data is processed, and then both the
stored intermediate and the current output are reintegrated using an
"ending" function. Two special ending functions are provided: amend and
insert. However, any ending function can be specified, including merge
functions, join functions, setNames(), etc. This framework allows the
following work-flow: focus on a particular aspect or section of a
data set, conduct specific operations, and then reintegrate changes into
the whole.
Author: Brandon Taylor
Maintainer: Brandon Taylor <Brandon.Taylor221@gmail.com>
Diff between loopr versions 1.0.0 dated 2015-05-07 and 1.0.1 dated 2015-05-27
loopr-1.0.0/loopr/man/loop.Rd |only loopr-1.0.0/loopr/man/loopr-package.Rd |only loopr-1.0.0/loopr/man/stack.Rd |only loopr-1.0.1/loopr/DESCRIPTION | 12 loopr-1.0.1/loopr/MD5 | 29 - loopr-1.0.1/loopr/NAMESPACE | 6 loopr-1.0.1/loopr/R/loopr.R | 36 +- loopr-1.0.1/loopr/build/vignette.rds |binary loopr-1.0.1/loopr/inst/doc/Looping.R | 88 ++++- loopr-1.0.1/loopr/inst/doc/Looping.Rmd | 118 ++++++- loopr-1.0.1/loopr/inst/doc/Looping.html | 482 +++++++++++++++++++++++++++----- loopr-1.0.1/loopr/man/amend.Rd | 2 loopr-1.0.1/loopr/man/amendColumns.Rd | 2 loopr-1.0.1/loopr/man/fillColumns.Rd | 2 loopr-1.0.1/loopr/man/insert.Rd | 2 loopr-1.0.1/loopr/man/loopClass.Rd |only loopr-1.0.1/loopr/man/stackClass.Rd |only loopr-1.0.1/loopr/vignettes/Looping.Rmd | 118 ++++++- 18 files changed, 705 insertions(+), 192 deletions(-)
Title: Tests for Right and Interval-Censored Survival Data Based on the
Fleming-Harrington Class
Description: Functions to compare two or more survival curves with:
a) The Fleming-Harrington test for right-censored data based on permutations and on counting processes.
b) An extension of the Fleming-Harrington test for interval-censored data based on a permutation distribution and on a score vector distribution.
Author: Ramon Oller, Klaus Langohr
Maintainer: Ramon Oller <ramon.oller@uvic.cat>
Diff between FHtest versions 1.1 dated 2013-12-02 and 1.2 dated 2015-05-27
DESCRIPTION | 19 +++--- MD5 | 18 +++--- NAMESPACE | 8 ++ R/FHtesticp.default.R | 148 +++++++++++++++++++++++++------------------------- R/FHtestics.default.R | 6 +- man/FHtest-package.Rd | 10 +-- man/FHtesticp.Rd | 24 ++++---- man/FHtestics.Rd | 16 ++--- man/FHtestrcc.Rd | 10 +-- man/FHtestrcp.Rd | 16 ++--- 10 files changed, 144 insertions(+), 131 deletions(-)
Title: Discrete Time Survival Analysis
Description: Provides data transformations, estimation utilities,
predictive evaluation measures and simulation functions for discrete time
survival analysis.
Author: Thomas Welchowski and Matthias Schmid
Maintainer: Thomas Welchowski <welchow@imbie.meb.uni-bonn.de>
Diff between discSurv versions 1.0.0 dated 2015-04-22 and 1.1.0 dated 2015-05-27
DESCRIPTION | 8 ++--- MD5 | 9 +++-- R/DiscSurvEvaluation.R | 59 ++++++++++++++++++++++++++++++++++++- man/adjDevResidShort.Rd |only man/devResidShort.Rd |only man/gumbel.Rd | 6 --- tests/UnitTestsDiscSurvEvalShort.R |only 7 files changed, 69 insertions(+), 13 deletions(-)
Title: Aligned Rank Transform
Description: The Aligned Rank Transform for nonparametric
factorial ANOVAs as described by Wobbrock et al.
Author: Matthew Kay [aut, cre],
Jacob O. Wobbrock [aut]
Maintainer: Matthew Kay <mjskay@uw.edu>
Diff between ARTool versions 0.9.3 dated 2014-12-02 and 0.9.4 dated 2015-05-27
DESCRIPTION | 16 ++++++++-------- MD5 | 12 ++++++------ tests/testthat.R | 2 -- tests/testthat/test.art.R | 1 + tests/testthat/test.artlm.R | 17 ++++++++--------- tests/testthat/test.parse.art.formula.R | 1 + tests/testthat/test.summary.art.R | 1 + 7 files changed, 25 insertions(+), 25 deletions(-)
Title: Plot a Model's Response and Residuals
Description: Plot a model's response when varying one or two predictors
while holding the other predictors constant. A poor man's
partial dependence plot. Also plot model residuals.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between plotmo versions 3.1.0 dated 2015-05-07 and 3.1.1 dated 2015-05-27
DESCRIPTION | 6 MD5 | 47 - NEWS | 13 R/check.index.R | 12 R/elegend.R |only R/gbm.R | 2 R/lib.R | 8 R/meta.R | 2 R/plot.gbmx.R | 13 R/plot.glmnetx.R | 2 R/plotmo.R | 4 R/plotres.R | 2 R/plotresids.R | 4 R/residuals.R | 2 R/xy.R | 4 inst/doc/plotmo-notes.pdf |binary inst/doc/plotres-notes.pdf |binary inst/slowtests/test.emma.Rout.save | 164 +++--- inst/slowtests/test.non.earth.R | 3 inst/slowtests/test.non.earth.Rout.save | 71 +- inst/slowtests/test.plotmo.Rout.save | 761 ++++++++++++++---------------- inst/slowtests/test.plotmo.args.Rout.save | 2 inst/slowtests/test.plotmo3.Rout.save | 36 - inst/slowtests/test.plotres.Rout.save | 5 man/plotmo.misc.Rd | 25 25 files changed, 598 insertions(+), 590 deletions(-)
Title: Extreme Value Mixture Modelling, Threshold Estimation and
Boundary Corrected Kernel Density Estimation
Description: The usual distribution functions, maximum likelihood inference and
model diagnostics for univariate stationary extreme value mixture models
are provided. Kernel density estimation including various boundary
corrected kernel density estimation methods and a wide choice of kernels,
with cross-validation likelihood based bandwidth estimator.
Reasonable consistency with the base functions in the 'evd' package is
provided, so that users can safely interchange most code.
Author: Carl Scarrott and Yang Hu, University of Canterbury
Maintainer: Carl Scarrott <carl.scarrott@canterbury.ac.nz>
Diff between evmix versions 2.5 dated 2015-04-29 and 2.6 dated 2015-05-27
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/evmix-package.r | 4 ++-- R/pickandsplot.r | 10 +++++----- inst/CITATION | 2 +- inst/doc/Rd2.pdf |binary man/evmix-package.Rd | 4 ++-- man/pickandsplot.Rd | 12 ++++++------ 8 files changed, 28 insertions(+), 28 deletions(-)
Title: Bayesian Canonical Correlation Analysis and Group Factor
Analysis
Description: Variational Bayesian algorithms for learning canonical correlation analysis (CCA), inter-battery factor analysis (IBFA), and group factor analysis (GFA). Inference with several random initializations can be run with the functions CCAexperiment() and GFAexperiment().
Author: Seppo Virtanen [aut, cre],
Eemeli Leppaaho [aut],
Arto Klami [aut]
Maintainer: Seppo Virtanen <s.virtanen@warwick.ac.uk>
Diff between CCAGFA versions 1.0.4 dated 2014-11-18 and 1.0.5 dated 2015-05-27
DESCRIPTION | 24 ++++++++++++++++-------- MD5 | 10 +++++----- NEWS | 4 ++++ R/CCAGFA.R | 20 +++++++++++--------- R/CCAGFAtools.R | 14 +++++++------- man/CCAGFA-package.Rd | 4 ++-- 6 files changed, 45 insertions(+), 31 deletions(-)
Title: Static and Dynamic 3D Plots for the 'vegan' Package
Description: Static and dynamic 3D plots to be used with ordination
results and in diversity analysis, especially with the vegan package.
Author: Jari Oksanen [aut, cre],
Roeland Kindt [aut],
Gavin L. Simpson [aut]
Maintainer: Jari Oksanen <jari.oksanen@oulu.fi>
Diff between vegan3d versions 0.65-0 dated 2014-10-07 and 0.65-1 dated 2015-05-27
DESCRIPTION | 16 ++++++++-------- MD5 | 6 +++--- NAMESPACE | 4 ++-- R/ordiplot3d.R | 2 +- 4 files changed, 14 insertions(+), 14 deletions(-)
Title: Model-Based Clustering and Classification with the Multivariate
t Distribution
Description: Fits mixtures of multivariate t-distributions (with eigen-decomposed covariance structure) via the multi-cycle ECM algorithm under a clustering or classification paradigm.
Author: Jeffrey L. Andrews, Paul D. McNicholas
Maintainer: Jeffrey L. Andrews <jeffrey.andrews@macewan.ca>
Diff between teigen versions 2.0.8 dated 2015-01-29 and 2.0.81 dated 2015-05-27
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/teigen.R | 3 ++- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Polygon Clipping
Description: R port of the Clipper library. Performs polygon clipping operations (intersection, union, set minus, set difference) for polygonal regions of arbitrary complexity, including holes. Also computes offset polygons (spatial buffer zones, morphological dilations, Minkowski dilations) for polygonal regions and polygonal lines.
Author: Angus Johnson. Ported to R by Adrian Baddeley and Brian Ripley.
Maintainer: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>
Diff between polyclip versions 1.3-0 dated 2014-05-05 and 1.3-2 dated 2015-05-27
DESCRIPTION | 8 +-- MD5 | 12 ++--- configure | 114 +++++++++++++++++++++++++++--------------------------- configure.ac | 87 +++++++++++++++++++++++++---------------- src/Makevars.in | 1 src/clipper.cpp | 25 +++++++---- src/interface.cpp | 1 7 files changed, 137 insertions(+), 111 deletions(-)
Title: Simulation-Based False Discovery Rate in RNA-Seq
Description: Auxiliary functions for the DESeq2 package to simulate read counts according to the null hypothesis (i.e., with empirical sample size factors, per-gene total counts and dispersions, but without effects of predictor variables) and to compute the empirical false discovery rate.
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz <matz@utexas.edu>
Diff between empiricalFDR.DESeq2 versions 1.0.1 dated 2015-03-29 and 1.0.3 dated 2015-05-27
empiricalFDR.DESeq2-1.0.1/empiricalFDR.DESeq2/R/fdrBiCurve_work.R |only empiricalFDR.DESeq2-1.0.1/empiricalFDR.DESeq2/R/fdrTable_work.R |only empiricalFDR.DESeq2-1.0.3/empiricalFDR.DESeq2/DESCRIPTION | 8 +++--- empiricalFDR.DESeq2-1.0.3/empiricalFDR.DESeq2/MD5 | 12 ++++------ empiricalFDR.DESeq2-1.0.3/empiricalFDR.DESeq2/R/empiricalFDR.R | 4 +-- empiricalFDR.DESeq2-1.0.3/empiricalFDR.DESeq2/R/fdrBiCurve.R | 2 - empiricalFDR.DESeq2-1.0.3/empiricalFDR.DESeq2/R/fdrTable.R | 5 ++-- empiricalFDR.DESeq2-1.0.3/empiricalFDR.DESeq2/man/empiricalFDR.DESeq2-package.Rd | 4 +-- 8 files changed, 17 insertions(+), 18 deletions(-)
More information about empiricalFDR.DESeq2 at CRAN
Permanent link
Title: Coenocline Simulation
Description: Simulate species occurrence and abundances (counts) along
gradients.
Author: Gavin L. Simpson [aut, cre],
Jari Oksanen [ctb],
Francisco Rodriguez-Sanchez [ctb]
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between coenocliner versions 0.1-0 dated 2014-07-31 and 0.2-0 dated 2015-05-27
coenocliner-0.1-0/coenocliner/inst/tests |only coenocliner-0.2-0/coenocliner/DESCRIPTION | 16 coenocliner-0.2-0/coenocliner/MD5 | 60 +- coenocliner-0.2-0/coenocliner/NAMESPACE | 17 coenocliner-0.2-0/coenocliner/R/coenocline.R | 85 ++- coenocliner-0.2-0/coenocliner/R/coenocliner.R | 2 coenocliner-0.2-0/coenocliner/R/distributions.R | 55 +- coenocliner-0.2-0/coenocliner/R/extractor-functions.R |only coenocliner-0.2-0/coenocliner/R/persp.coenocline.R |only coenocliner-0.2-0/coenocliner/R/plot.coenocline.R |only coenocliner-0.2-0/coenocliner/R/response-functions.R | 2 coenocliner-0.2-0/coenocliner/R/utils.R | 139 ++++++ coenocliner-0.2-0/coenocliner/README.md | 11 coenocliner-0.2-0/coenocliner/build/vignette.rds |binary coenocliner-0.2-0/coenocliner/inst/ChangeLog | 13 coenocliner-0.2-0/coenocliner/inst/NEWS | 41 + coenocliner-0.2-0/coenocliner/inst/doc/coenocliner.R | 32 - coenocliner-0.2-0/coenocliner/inst/doc/coenocliner.Rnw | 60 +- coenocliner-0.2-0/coenocliner/inst/doc/coenocliner.pdf |binary coenocliner-0.2-0/coenocliner/man/coenocline.Rd | 61 +- coenocliner-0.2-0/coenocliner/man/coenocliner-internal.Rd |only coenocliner-0.2-0/coenocliner/man/coenocliner.Rd | 5 coenocliner-0.2-0/coenocliner/man/distributions.Rd | 21 coenocliner-0.2-0/coenocliner/man/expand.Rd | 3 coenocliner-0.2-0/coenocliner/man/locations.Rd |only coenocliner-0.2-0/coenocliner/man/persp.coenocline.Rd |only coenocliner-0.2-0/coenocliner/man/plot.coenocline.Rd |only coenocliner-0.2-0/coenocliner/man/showParams.Rd | 3 coenocliner-0.2-0/coenocliner/man/simJamil.Rd | 3 coenocliner-0.2-0/coenocliner/man/species-response.Rd | 3 coenocliner-0.2-0/coenocliner/man/stack.coenocline.Rd |only coenocliner-0.2-0/coenocliner/tests/Examples/coenocliner-Ex.Rout.save | 229 +++++++++- coenocliner-0.2-0/coenocliner/tests/test-all.R | 3 coenocliner-0.2-0/coenocliner/tests/testthat |only coenocliner-0.2-0/coenocliner/vignettes/coenocliner.Rnw | 60 +- 35 files changed, 702 insertions(+), 222 deletions(-)
Title: Bubble Chart to Compare Biological Annotations by using DAVID
Description: R-based graphical tool to concisely visualise and compare biological annotations queried from the DAVID web service. It provides R functions to perform enrichment analysis (via DAVID - http://david.abcc.ncifcrf.gov) on several gene lists at once, and then visualizing all the results in one generated figure that allows R users to compare the annotations found for each list.
Author: Vittorio Fortino and Dario Greco
Maintainer: Vittorio Fortino <vittorio.fortino@ttl.fi>
Diff between BACA versions 0.99.0 dated 2015-01-10 and 1.3 dated 2015-05-27
BACA-0.99.0/BACA/inst/doc/BACA.R |only BACA-0.99.0/BACA/inst/doc/BACA.Rmd |only BACA-0.99.0/BACA/vignettes |only BACA-1.3/BACA/DESCRIPTION | 12 ++++++------ BACA-1.3/BACA/MD5 | 19 ++++++++++--------- BACA-1.3/BACA/R/bbplots.R | 10 ++++++++-- BACA-1.3/BACA/build/vignette.rds |binary BACA-1.3/BACA/inst/CITATION |only BACA-1.3/BACA/inst/doc/BACA.html | 32 +++++++++++++------------------- BACA-1.3/BACA/inst/doc/BACA.md | 33 ++++++++++++--------------------- BACA-1.3/BACA/inst/doc/BACA.pdf |only BACA-1.3/BACA/inst/doc/figure |only BACA-1.3/BACA/man/BBplot.Rd | 14 ++++++++++---- 13 files changed, 59 insertions(+), 61 deletions(-)
Title: Analysis of Large Affymetrix Microarray Data Sets
Description: A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.
Author: Henrik Bengtsson [aut, cre, cph],
James Bullard [ctb],
Kasper Hansen [ctb],
Pierre Neuvial [ctb],
Elizabeth Purdom [ctb],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.affymetrix versions 2.13.0 dated 2015-01-20 and 2.13.2 dated 2015-05-27
DESCRIPTION | 38 MD5 | 185 - NAMESPACE | 1176 ++++++++++ NEWS | 18 R/021.dynamic_imports.R | 569 ++-- R/999.package.R | 16 R/AffinePlm.R | 5 R/AffymetrixCdfFile.MONOCELL.R | 22 R/AffymetrixCelSet.R | 2 R/AffymetrixCelSet.convertToUnique.R | 4 R/ChipEffectSet.calculateBaseline.R | 4 R/CnagCfhSet.R | 2 R/CopyNumberChromosomalModel.applyCCF.R | 4 R/GcContentNormalization2.plotCovariateEffects.R | 2 R/SnpChipEffectSet.exportTotalAndFracB.R | 2 R/doCRMAv1.R | 2 R/doCRMAv2.R | 6 R/doGCRMA.R | 4 R/doRMA.R | 4 R/setupExampleData.R | 83 inst/testScripts/replication/chipTypes/HG-U133_Plus_2/11.doRMA_vs_oligo.R | 3 inst/vignettes/replication-CRLMM/R/01a.downloadAnnotData.R | 38 inst/vignettes/replication-CRLMM/R/01b.downloadRawData.R | 74 inst/vignettes/replication-GCRMA/R/01a.downloadAnnotData.R | 38 inst/vignettes/replication-GCRMA/R/01b.downloadRawData.R | 74 inst/vignettes/replication-MAT/R/01a.downloadAnnotationData.R | 66 inst/vignettes/replication-MAT/R/01b.downloadRawData.R | 148 - inst/vignettes/replication-RMA/R/01a.downloadAnnotationData.R | 32 inst/vignettes/replication-RMA/R/01b.downloadRawData.R | 82 man/AbstractProbeSequenceNormalization.Rd | 2 man/AdditiveCovariatesNormalization.Rd | 2 man/AffinePlm.Rd | 5 man/AffymetrixCdfFile.Rd | 16 man/AffymetrixCelFile.Rd | 20 man/AffymetrixCelSet.Rd | 26 man/AffymetrixCelSetReporter.Rd | 2 man/AffymetrixCnChpSet.Rd | 4 man/AffymetrixFileSet.Rd | 6 man/AffymetrixPgfFile.Rd | 2 man/AlleleSummation.Rd | 2 man/AllelicCrosstalkCalibration.Rd | 2 man/AromaChipTypeAnnotationFile.Rd | 4 man/ArrayExplorer.Rd | 6 man/BackgroundCorrection.Rd | 2 man/ChipEffectFile.Rd | 2 man/ChipEffectGroupMerge.Rd | 2 man/ChipEffectSet.Rd | 6 man/CnChipEffectSet.Rd | 2 man/CnagCfhFile.Rd | 4 man/CnagCfhSet.Rd | 10 man/CrlmmParametersSet.Rd | 2 man/DChipDcpSet.Rd | 4 man/DChipGenomeInformation.Rd | 2 man/DChipQuantileNormalization.Rd | 2 man/DChipSnpInformation.Rd | 2 man/ExonChipEffectSet.Rd | 2 man/FirmaModel.Rd | 4 man/FirmaSet.Rd | 2 man/FragmentEquivalentClassNormalization.Rd | 2 man/FragmentLengthNormalization.Rd | 2 man/GcContentNormalization.Rd | 2 man/GcRmaBackgroundCorrection.Rd | 2 man/GenericReporter.Rd | 6 man/GenomeInformation.Rd | 10 man/LimmaBackgroundCorrection.Rd | 2 man/MatNormalization.Rd | 2 man/MatSmoothing.Rd | 2 man/Model.Rd | 14 man/OpticalBackgroundCorrection.Rd | 2 man/ParameterCelSet.Rd | 6 man/ProbeLevelModel.Rd | 6 man/QualityAssessmentModel.Rd | 4 man/QualityAssessmentSet.Rd | 2 man/QuantileNormalization.Rd | 2 man/ReseqCrosstalkCalibration.Rd | 2 man/ResidualSet.Rd | 2 man/RmaBackgroundCorrection.Rd | 2 man/ScaleNormalization.Rd | 2 man/ScaleNormalization3.Rd | 2 man/SingleArrayUnitModel.Rd | 2 man/SnpChipEffectSet.Rd | 2 man/SnpInformation.Rd | 6 man/SpatialReporter.Rd | 2 man/TransformReport.Rd | 12 man/UgpGenomeInformation.Rd | 2 man/UnitModel.Rd | 2 man/UnitTypeScaleNormalization.Rd | 2 man/WeightsSet.Rd | 2 man/aroma.affymetrix-package.Rd | 15 man/createExonByTranscriptCdf.AffymetrixCdfFile.Rd | 178 - man/createMonocellCdf.AffymetrixCdfFile.Rd | 2 man/setupExampleData.AromaAffymetrix.Rd | 10 man/writeCdf.AffyGenePDInfo.Rd | 96 tests/AffymetrixCdfFile.R |only 94 files changed, 2251 insertions(+), 1008 deletions(-)
More information about aroma.affymetrix at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-05-26 1.1