Title: nat: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Diff between nat versions 1.4.10 dated 2014-04-30 and 1.5.12 dated 2014-08-21
Description: This package is a reboot of the AnalysisSuite
(https://github.com/jefferis/AnalysisSuite) bundle of R code that I have
been using for a number of years to analyse and visualise 3D biological
image data, especially traced neurons. AnalysisSuite is most easily
installed using the nat.as package presently available at
https://github.com/jefferis/nat.as. The nat package is considerably cleaner
but currently provides only a subset of the full functionality of nat.as /
AnalysisSuite. nat can read and write 3D images in NRRD and Amira formats
and read surfaces in Amira's 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. The package also has a simple representation for neurons that
have been subjected to a 3D skeletonisation but not formally traced; this
allows morphological comparison between neurons including searches and
clustering.
Author: Greg Jefferis and James Manton
Maintainer: Greg Jefferis
DESCRIPTION | 13
MD5 | 304 ++++++++--------
NAMESPACE | 32 +
NEWS | 119 ++++++
R/amiramesh-io.R | 13
R/cmtk-reformat.R | 94 +++--
R/cmtk.R | 34 +
R/cmtk_io.R | 1
R/coordinates.R | 8
R/dist3D_Segment_to_Segment.R |only
R/dotprops.R | 60 ++-
R/graph-nodes.R | 18
R/hxsurf.R | 134 ++++++-
R/im3d.R | 97 +++--
R/nat-package.R | 10
R/neuron-io-amira.R | 28 -
R/neuron-io.R | 91 +++-
R/neuron-plot.R | 144 ++++---
R/neuron.R | 173 +++++++++
R/neuronlist.R | 408 ++++++++++++++++------
R/neuronlistfh.R | 15
R/ngraph.R | 69 +++
R/pop3d.R |only
R/potential_synapses.R |only
R/seglist.R | 38 +-
R/vaa3draw-io.R |only
R/xform.R | 90 +++-
R/xformpoints.R | 30 +
R/zzz.R | 5
README.md | 135 ++++---
data/Cell07PNs.rda |binary
inst/CITATION | 21 -
man/Cell07PNs.Rd | 1
man/affmat2cmtkparams.Rd | 1
man/all.equal.dotprops.Rd | 1
man/all.equal.im3d.Rd | 1
man/all.equal.neuron.Rd | 1
man/amiralandmark-io.Rd | 1
man/amiramesh-io.Rd | 1
man/amiratype.Rd | 1
man/as.im3d.Rd | 4
man/as.mesh3d.Rd |only
man/as.neuronlist.Rd | 23 +
man/as.neuronlist.neuronlistfh.Rd | 1
man/boundingbox.Rd | 37 +
man/c.neuronlist.Rd |only
man/clampmax.Rd | 1
man/cmtk.bindir.Rd | 1
man/cmtk.call.Rd | 3
man/cmtk.dof2mat.Rd | 1
man/cmtk.mat2dof.Rd | 1
man/cmtk.reformatx.Rd | 37 -
man/cmtk.statistics.Rd |only
man/cmtk.targetvolume.Rd |only
man/cmtk.version.Rd |only
man/cmtklandmarks.Rd | 1
man/cmtkparams2affmat.Rd | 1
man/cmtkreg.Rd | 1
man/cmtkreglist.Rd | 1
man/coord2ind.Rd | 1
man/dotprops-arithmetic.Rd | 1
man/dotprops.Rd | 32 +
man/fileformats.Rd | 9
man/find.neuron.Rd | 1
man/flip.Rd | 1
man/graph.nodes.Rd | 1
man/im3d-coords.Rd | 3
man/im3d-io.Rd | 19 -
man/im3d.Rd | 4
man/image.im3d.Rd | 3
man/imexpand.grid.Rd | 4
man/imscalebar.Rd | 1
man/imslice.Rd | 4
man/ind2coord.Rd | 1
man/is.amiramesh.Rd | 1
man/is.neuronlist.Rd | 1
man/is.nrrd.Rd | 1
man/is.vaa3draw.Rd |only
man/kcs20.Rd | 1
man/materials.Rd | 11
man/mirror.Rd | 30 +
man/nat-internal.Rd | 1
man/nat-package.Rd | 9
man/ndigest.Rd | 1
man/neuron-arithmetic.Rd | 1
man/neuron.Rd | 1
man/neuronlist-arithmetic.Rd | 1
man/neuronlist-dataframe-methods.Rd | 1
man/neuronlist.Rd | 9
man/neuronlistfh.Rd | 1
man/ngraph.Rd | 1
man/nlapply.Rd | 78 +++-
man/nopen3d.Rd | 1
man/npop3d.Rd |only
man/nrrd.voxdims.Rd | 1
man/origin.Rd | 4
man/pan3d.Rd | 1
man/plot.neuron.Rd | 39 --
man/plot.neuronlist.Rd |only
man/plot3d.boundingbox.Rd |only
man/plot3d.dotprops.Rd | 16
man/plot3d.hxsurf.Rd | 16
man/plot3d.neuron.Rd | 4
man/plot3d.neuronlist.Rd | 44 ++
man/pointsinside.Rd |only
man/potential_synapses.Rd |only
man/projection.Rd | 6
man/prune.Rd | 3
man/read.cmtk.Rd | 1
man/read.cmtkreg.Rd | 1
man/read.hxsurf.Rd | 9
man/read.neuron.Rd | 1
man/read.neuron.swc.Rd | 1
man/read.neuronlistfh.Rd | 1
man/read.neurons.Rd | 3
man/read.nrrd.Rd | 1
man/read.vaa3draw.Rd |only
man/remotesync.Rd | 1
man/resample.Rd |only
man/rootpoints.Rd | 1
man/scale.dotprops.Rd | 1
man/scale.neuron.Rd | 1
man/seglengths.Rd |only
man/seglist.Rd | 18
man/seglist2swc.Rd | 1
man/segmentgraph.Rd |only
man/spine.Rd | 1
man/sub-.neuronlistfh.Rd | 1
man/sub2ind.Rd | 1
man/subset.dotprops.Rd | 5
man/subset.hxsurf.Rd |only
man/subset.neuronlist.Rd | 1
man/threshold.Rd | 4
man/unmask.Rd | 4
man/voxdims.Rd | 4
man/write.amiramesh.Rd | 1
man/write.cmtk.Rd | 1
man/write.cmtkreg.Rd | 1
man/write.hxsurf.Rd | 9
man/write.neuron.Rd | 9
man/write.neuronlistfh.Rd | 1
man/write.neurons.Rd | 18
man/write.nrrd.Rd | 1
man/xform.Rd | 18
man/xformpoints.Rd | 1
man/xyzmatrix.Rd | 12
tests/test-all.R | 7
tests/testthat/test-.neuronlistfh-remote-nocran.R | 13
tests/testthat/test-cmtk-reformat.R | 5
tests/testthat/test-cmtk.R | 47 ++
tests/testthat/test-cmtk_io.R | 2
tests/testthat/test-hxsurf.R | 53 ++
tests/testthat/test-im3d.R | 25 +
tests/testthat/test-neuron-io.R | 53 ++
tests/testthat/test-neuron.R | 65 +++
tests/testthat/test-neuronlist.R | 64 +++
tests/testthat/test-ngraph.R | 11
tests/testthat/test-pop3d.R |only
tests/testthat/test-potential_synapses.R |only
tests/testthat/test-xform.R | 17
tests/testthat/test-xformpoints.R | 6
tests/testthat/testdata/amira/JFRC2_MB_CA_L.rds |only
tests/testthat/testdata/amira/tetrahedron.surf |only
tests/testthat/testdata/nrrd/dataforstats.nrrd |only
tests/testthat/testdata/v3draw |only
165 files changed, 2478 insertions(+), 698 deletions(-)
Title: Dynamic Models in Epidemiology
Diff between EpiDynamics versions 0.1 dated 2014-06-01 and 0.2 dated 2014-08-21
Description: Mathematical models of infectious diseases in humans and animals.
Both, deterministic and stochastic models can be simulated and plotted.
Author: Oswaldo Santos Baquero [aut, cre],
Fernando Silveira Marques [aut]
Maintainer: Oswaldo Santos Baquero
EpiDynamics-0.1/EpiDynamics/R/PlotModels.R |only
EpiDynamics-0.1/EpiDynamics/man/PlotModels.Rd |only
EpiDynamics-0.2/EpiDynamics/DESCRIPTION | 20 -
EpiDynamics-0.2/EpiDynamics/MD5 | 102 +++++-----
EpiDynamics-0.2/EpiDynamics/NAMESPACE | 11 -
EpiDynamics-0.2/EpiDynamics/NEWS | 38 +++
EpiDynamics-0.2/EpiDynamics/R/EpiDynamics-package.R | 14 -
EpiDynamics-0.2/EpiDynamics/R/MultiStrainPartialImmunity.R | 9
EpiDynamics-0.2/EpiDynamics/R/PlotMods.R |only
EpiDynamics-0.2/EpiDynamics/R/SEIR.R | 10
EpiDynamics-0.2/EpiDynamics/R/SEIR4AgeClasses.R | 17 -
EpiDynamics-0.2/EpiDynamics/R/SEIRnStages.R | 19 +
EpiDynamics-0.2/EpiDynamics/R/SIR.R | 19 +
EpiDynamics-0.2/EpiDynamics/R/SIR2AgeClasses.R | 3
EpiDynamics-0.2/EpiDynamics/R/SIR2TypesImports.R |only
EpiDynamics-0.2/EpiDynamics/R/SIRAdditiveNoise.R |only
EpiDynamics-0.2/EpiDynamics/R/SIRBirthDeath.R | 15 -
EpiDynamics-0.2/EpiDynamics/R/SIRCarrierState.R | 27 +-
EpiDynamics-0.2/EpiDynamics/R/SIRDemogStoch.R |only
EpiDynamics-0.2/EpiDynamics/R/SIRInducedMortality.R | 27 +-
EpiDynamics-0.2/EpiDynamics/R/SIRInducedMortality2.R | 12 -
EpiDynamics-0.2/EpiDynamics/R/SIRPartialImmunity.R | 3
EpiDynamics-0.2/EpiDynamics/R/SIRScaledAdditiveNoise.R |only
EpiDynamics-0.2/EpiDynamics/R/SIRSinusoidalBirth.R | 6
EpiDynamics-0.2/EpiDynamics/R/SIRSinusoidalForcing.R | 8
EpiDynamics-0.2/EpiDynamics/R/SIRTauLeap.R |only
EpiDynamics-0.2/EpiDynamics/R/SIRTermTimeForcing.R | 9
EpiDynamics-0.2/EpiDynamics/R/SIRVector.R | 3
EpiDynamics-0.2/EpiDynamics/R/SIS.R | 23 +-
EpiDynamics-0.2/EpiDynamics/R/SIS2RiskGroups.R | 17 -
EpiDynamics-0.2/EpiDynamics/R/SISDemogStoch.R |only
EpiDynamics-0.2/EpiDynamics/R/SISinusoidalTransmBrith.R | 5
EpiDynamics-0.2/EpiDynamics/R/SISnRiskGroups.R | 18 -
EpiDynamics-0.2/EpiDynamics/man/EpiDynamics-package.Rd | 29 +-
EpiDynamics-0.2/EpiDynamics/man/MultiStrainPartialImmunity.Rd | 49 +---
EpiDynamics-0.2/EpiDynamics/man/PlotMods.Rd |only
EpiDynamics-0.2/EpiDynamics/man/SEIR.Rd | 48 +---
EpiDynamics-0.2/EpiDynamics/man/SEIR4AgeClasses.Rd | 62 +-----
EpiDynamics-0.2/EpiDynamics/man/SEIRnStages.Rd | 55 +----
EpiDynamics-0.2/EpiDynamics/man/SIR.Rd | 45 +---
EpiDynamics-0.2/EpiDynamics/man/SIR2TypesImports.Rd |only
EpiDynamics-0.2/EpiDynamics/man/SIRAdditiveNoise.Rd |only
EpiDynamics-0.2/EpiDynamics/man/SIRBirthDeath.Rd | 45 +---
EpiDynamics-0.2/EpiDynamics/man/SIRCarrierState.Rd | 47 +---
EpiDynamics-0.2/EpiDynamics/man/SIRDemogStoch.Rd |only
EpiDynamics-0.2/EpiDynamics/man/SIRInducedMortality.Rd | 53 +----
EpiDynamics-0.2/EpiDynamics/man/SIRInducedMortality2.Rd | 49 +---
EpiDynamics-0.2/EpiDynamics/man/SIRPartialImmunity.Rd | 49 +---
EpiDynamics-0.2/EpiDynamics/man/SIRScaledAdditiveNoise.Rd |only
EpiDynamics-0.2/EpiDynamics/man/SIRSinusoidalBirth.Rd | 61 +----
EpiDynamics-0.2/EpiDynamics/man/SIRSinusoidalForcing.Rd | 56 +----
EpiDynamics-0.2/EpiDynamics/man/SIRTauLeap.Rd |only
EpiDynamics-0.2/EpiDynamics/man/SIRTermTimeForcing.Rd | 76 ++-----
EpiDynamics-0.2/EpiDynamics/man/SIRVector.Rd | 47 +---
EpiDynamics-0.2/EpiDynamics/man/SIS.Rd | 43 +---
EpiDynamics-0.2/EpiDynamics/man/SIS2RiskGroups.Rd | 52 +----
EpiDynamics-0.2/EpiDynamics/man/SISDemogStoch.Rd |only
EpiDynamics-0.2/EpiDynamics/man/SISinusoidalTransmBrith.Rd | 53 +----
EpiDynamics-0.2/EpiDynamics/man/SISnRiskGroups.Rd | 53 +----
EpiDynamics-0.2/EpiDynamics/man/sir2AgeClasses.Rd | 59 +----
60 files changed, 547 insertions(+), 919 deletions(-)
Title: A Data Analysis Tool for Pharmacokinetics
Diff between PKfit versions 1.2.2 dated 2014-06-24 and 1.2.3 dated 2014-08-21
Description: PKfit is a nonlinear regression program
which is designed to perform model/curve fitting
and model simulations for pharmacokinetics.
Author: Chun-ying Lee, Yung-jin Lee
Maintainer: Yung-jin Lee
DESCRIPTION | 14 +-
MD5 | 34 ++++---
NEWS | 23 +++-
R/description_version.r | 2
R/err_types.R |only
R/iv.bolus.demo.R | 102 ++++++---------------
R/sbolus1.R | 169 +++++------------------------------
R/sbolus2.R | 120 ++-----------------------
R/sfirst.nolag.R | 217 +++++----------------------------------------
R/sfirst2.R | 148 +++----------------------------
R/sinfu1.R | 175 +++++-------------------------------
R/sinfu2.R | 121 ++-----------------------
R/smacro.one.R | 69 ++------------
R/smacro.three.R | 174 ++++--------------------------------
R/smacro.two.R | 119 ++-----------------------
R/szero.nolag.R | 228 ++++++------------------------------------------
R/zzz.R | 2
inst |only
man/err_types.Rd |only
19 files changed, 270 insertions(+), 1447 deletions(-)
Title: Rcpp integration for the Eigen templated linear algebra library.
Diff between RcppEigen versions 0.3.2.1.2 dated 2014-05-06 and 0.3.2.2.0 dated 2014-08-21
Description: R and Eigen integration using Rcpp.
Eigen is a C++ template library for linear algebra: matrices,
vectors, numerical solvers and related algorithms. It supports dense
and sparse matrices on integer, floating point and complex numbers,
decompositions of such matrices, and solutions of linear systems. Its
performance on many algorithms is comparable with some of the best
implementations based on Lapack and level-3 BLAS.
The RcppEigen package includes the header files from the Eigen C++
template library (currently version 3.2.2). Thus users do not need to
install Eigen itself in order to use RcppEigen.
Since version 3.1.1, Eigen is licensed under the Mozilla Public License
(version 2); earlier version were licensed under the GNU LGPL version 3 or
later. RcppEigen (the Rcpp bindings/bridge to Eigen) is licensed under the
GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Douglas Bates, Romain Francois and Dirk Eddelbuettel;
the authors of Eigen for the included version of Eigen
Maintainer: Dirk Eddelbuettel
RcppEigen-0.3.2.1.2/RcppEigen/inst/include/Eigen/src/Sparse |only
RcppEigen-0.3.2.2.0/RcppEigen/ChangeLog | 24 +
RcppEigen-0.3.2.2.0/RcppEigen/DESCRIPTION | 10
RcppEigen-0.3.2.2.0/RcppEigen/MD5 | 109 +++-----
RcppEigen-0.3.2.2.0/RcppEigen/README.md | 2
RcppEigen-0.3.2.2.0/RcppEigen/build/vignette.rds |binary
RcppEigen-0.3.2.2.0/RcppEigen/inst/NEWS.Rd | 19 +
RcppEigen-0.3.2.2.0/RcppEigen/inst/doc/RcppEigen-Introduction.pdf |binary
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/Core | 4
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/Cholesky/LDLT.h | 50 +--
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/Core/Block.h | 2
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/Core/CommaInitializer.h | 11
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/Core/DenseStorage.h | 16 -
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/Core/Functors.h | 4
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/Core/MapBase.h | 2
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/Core/Ref.h | 10
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/Core/TriangularMatrix.h | 8
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/Core/util/MKL_support.h | 19 +
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/Core/util/Macros.h | 5
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/Core/util/Memory.h | 4
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/Geometry/Quaternion.h | 14 -
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/Geometry/Transform.h | 4
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/Geometry/Umeyama.h | 10
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/Householder/BlockHouseholder.h | 2
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h | 3
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/LU/FullPivLU.h | 13
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/OrderingMethods/Ordering.h | 12
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/QR/ColPivHouseholderQR.h | 3
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/SVD/JacobiSVD.h | 105 ++++++-
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/SparseCholesky/SimplicialCholesky.h | 42 +--
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/SparseCore/CompressedStorage.h | 8
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseCwiseBinaryOp.h | 3
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseDenseProduct.h | 33 +-
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseMatrix.h | 12
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseTranspose.h | 10
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseUtil.h | 6
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/SparseQR/SparseQR.h | 136 ++++++----
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/StlSupport/StdDeque.h | 2
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/StlSupport/StdList.h | 2
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/Eigen/src/StlSupport/StdVector.h | 2
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/RcppEigenForward.h | 2
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/RcppEigenWrap.h | 71 ++++-
RcppEigen-0.3.2.2.0/RcppEigen/inst/include/unsupported/Eigen/src/IterativeSolvers/GMRES.h | 12
RcppEigen-0.3.2.2.0/RcppEigen/inst/unitTests/runit.wrap.R | 63 ++++
44 files changed, 592 insertions(+), 277 deletions(-)
Title: TableToLongForm
Diff between TableToLongForm versions 1.3.0 dated 2014-01-15 and 1.3.1 dated 2014-08-21
More information about TableToLongForm at CRAN
Description: TableToLongForm automatically converts hierarchical Tables intended for a human reader into a simple LongForm Dataframe that is machine readable.
Author: Jimmy Oh [aut, cre]
Maintainer: Jimmy Oh
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
R/TableToLongForm.R | 26 +++++++++++++++++++-------
man/TCData.Rd | 7 +++++++
man/TableToLongForm-package.Rd | 4 ++--
man/TableToLongForm.Rd | 23 ++++++++++++++++++-----
man/print.plist.Rd | 3 ++-
7 files changed, 58 insertions(+), 25 deletions(-)
Permanent link
Title: Population and Evolutionary Genetics Analysis System
Diff between pegas versions 0.5-1 dated 2014-01-10 and 0.6 dated 2014-08-21
Description: pegas provides functions for reading, writing, plotting,
analysing, and manipulating allelic and haplotypic data, and for the
analysis of population nucleotide sequences and micro-satellites including
coalescence analyses.
Author: Emmanuel Paradis [aut, cre, cph],
Klaus Schliep [aut, cph],
Alastair Potts [aut, cph],
David Winter [aut, cph]
Maintainer: Emmanuel Paradis
DESCRIPTION | 10 -
MD5 | 74 ++++++------
NAMESPACE | 16 +-
NEWS | 64 +++++++++++
R/Fst.R | 2
R/IO.R | 56 ++++++++-
R/MMD.R | 2
R/R2.test.R | 2
R/amova.R | 17 ++
R/conversion.R | 62 ++++++----
R/haplotype.R | 259 ++++++++++++++++++++++++++++++++++++++++++---
R/heterozygosity.R | 2
R/hw.test.R | 122 +++++++++------------
R/nuc.div.R | 2
R/plot.loci.R | 2
R/rr.test.R | 2
R/site.spectrum.R | 31 ++---
R/summary.loci.R | 40 ++++--
R/tajima.test.R | 10 +
R/theta.R | 2
build/vignette.rds |binary
inst/doc/ReadingFiles.R | 44 +++++--
inst/doc/ReadingFiles.Rnw | 91 +++++++++++++--
inst/doc/ReadingFiles.pdf |binary
man/LD.Rd |only
man/amova.Rd | 11 +
man/conversion.Rd | 6 -
man/haploNet.Rd | 5
man/haplotype.Rd | 31 +++++
man/haplotype.loci.Rd |only
man/pegas-package.Rd | 8 -
man/read.gtx.Rd | 2
man/read.loci.Rd | 6 -
man/read.vcf.Rd |only
man/summary.loci.Rd | 2
man/utilities.Rd | 43 +++++++
man/write.loci.Rd | 2
vignettes/ReadingFiles.Rnw | 91 +++++++++++++--
vignettes/pegas.bib | 10 +
vignettes/tyty |only
40 files changed, 855 insertions(+), 274 deletions(-)
Title: Code Analysis Tools for R
Diff between codetools versions 0.2-8 dated 2011-02-15 and 0.2-9 dated 2014-08-21
Description: Code analysis tools for R
Author: Luke Tierney
Maintainer: Luke Tierney
DESCRIPTION | 11 ++++++-----
MD5 |only
R/codetools.R | 35 ++++++++++++++++++++---------------
3 files changed, 26 insertions(+), 20 deletions(-)
Title: Generates social networks based on distance.
Diff between SocialNetworks versions 1.0 dated 2014-03-24 and 1.1 dated 2014-08-21
More information about SocialNetworks at CRAN
Description: Generates social networks using either of two
approaches: using either pairwise distances or territorial area intersections.
Author: Glenna Nightingale, Peter Nightingale
Maintainer: Glenna Nightingale
DESCRIPTION | 8 ++++----
MD5 | 15 ++++++++++-----
R/gradedareas.R |only
R/socialnetwork.R | 5 +++--
man/SocialNetworks-package.Rd | 4 ++--
man/calculate.gradedareas.Rd |only
man/calculateassociations.Rd | 7 ++++---
man/figures/redorange.jpeg |only
man/figures/smooth.jpeg |binary
man/figures/togetheratlast.jpeg |only
src/rcpp_calculate_graded_areas.cpp |only
11 files changed, 23 insertions(+), 16 deletions(-)
Permanent link
Title: Support Functions and Datasets for Venables and Ripley's MASS
Diff between MASS versions 7.3-33 dated 2014-05-05 and 7.3-34 dated 2014-08-21
Description: Functions and datasets to support Venables and Ripley,
'Modern Applied Statistics with S' (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Kurt Hornik [trl] (partial port ca 1998),
Albrecht Gebhardt [trl] (partial port ca 1998),
David Firth [ctb]
Maintainer: Brian Ripley
DESCRIPTION | 10 +++++-----
MD5 | 10 +++++-----
R/add.R | 6 +++---
inst/NEWS | 2 ++
man/OME.Rd | 14 ++++++--------
man/summary.rlm.Rd | 20 +-------------------
6 files changed, 22 insertions(+), 40 deletions(-)
Title: Graphical Analysis of Variance
Diff between granova versions 2.0 dated 2010-11-05 and 2.0.1 dated 2014-08-21
Description: This small collection of functions provides what we call
elemental graphics for display of anova results. The term
elemental derives from the fact that each function is aimed at
construction of graphical displays that afford direct
visualizations of data with respect to the fundamental
questions that drive the particular anova methods. The two main
functions are granova.1w (a graphic for one way anova) and
granova.2w (a corresponding graphic for two way anova). These
functions were written to display data for any number of
groups, regardless of their sizes (however, very large data
sets or numbers of groups can be problematic). For these two
functions a specialized approach is used to construct
data-based contrast vectors for which anova data are displayed.
The result is that the graphics use straight lines, and when
appropriate flat surfaces, to facilitate clear interpretations
while being faithful to the standard effect tests in anova. The
graphic results are complementary to standard summary tables
for these two basic kinds of analysis of variance; numerical
summary results of analyses are also provided as side effects.
Two additional functions are granova.ds (for comparing two
dependent samples), and granova.contr (which provides graphic
displays for a priori contrasts). All functions provide
relevant numerical results to supplement the graphic displays
of anova data. The graphics based on these functions should be
especially helpful for learning how the methods have been
applied to answer the question(s) posed. This means they can be
particularly helpful for students and non-statistician
analysts. But these methods should be quite generally helpful
for work-a-day applications of all kinds, as they can help to
identify outliers, clusters or patterns, as well as highlight
the role of non-linear transformations of data. In the case of
granova.1w and granova.ds especially, several arguments are
provided to facilitate flexibility in the construction of
graphics that accommodate diverse features of data, according
to their corresponding display requirements. See the help files
for individual functions.
Author: Robert M. Pruzek
Maintainer: ORPHANED
DESCRIPTION | 15 ++++++++++-----
MD5 |only
NAMESPACE | 2 +-
R/granova.1w.R | 4 ++--
R/granova.2w.R | 11 ++++-------
5 files changed, 17 insertions(+), 15 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-11 0.1.3
2013-07-25 0.1.2
2013-04-05 0.1.1
2013-03-25 0.1.0
Title: Fitting Semiparametric Symmetric Regression Models
Diff between ssym versions 1.3 dated 2014-05-07 and 1.5 dated 2014-08-21
Description: This package allows to fit a regression model suitable for data analysis in which the conditional distribution of the response is symmetric and continuous and where its location and dispersion parameters are modelled through semiparametric functions. Supported distributions for the model error include normal, Student-t, power exponential, symmetric hyperbolic, contaminated normal, slash, sinh-normal and sinh-t distributions.
Author: Luis Hernando Vanegas
Maintainer: Luis Hernando Vanegas
DESCRIPTION | 8 -
MD5 | 40 +++++----
R/itpE3.R |only
R/itpM.R | 3
R/itpM2.R | 88 +++++++++++++++-----
R/itpM3.R |only
R/rvgs.R | 2
R/ssym.l.R | 219 ++++++++++++++++++++++++++--------------------------
R/ssym.nl.R | 124 +++++++++++++++--------------
R/summary.ssym.R | 6 -
data/Biaxial.rda |binary
data/Claims.rda |binary
data/Erabbits.rda |binary
data/Snacks.rda |binary
data/gdp.rda |binary
man/Claims.Rd | 4
man/Erabbits.Rd | 3
man/Snacks.Rd | 18 ++--
man/itpE3.Rd |only
man/itpM3.Rd |only
man/ssym-package.Rd | 9 --
man/ssym.l.Rd | 166 ++++++++-------------------------------
man/ssym.nl.Rd | 181 ++++++------------------------------------
23 files changed, 353 insertions(+), 518 deletions(-)
Title: Interface to the boilerpipe Java library by Christian
Kohlschutter (http://code.google.com/p/boilerpipe/)
Diff between boilerpipeR versions 1.2 dated 2014-05-12 and 1.2.2 dated 2014-08-21
Description: Generic Extraction of main text content from HTML files; removal
of ads, sidebars and headers using the boilerpipe Java library. The
extraction heuristics from boilerpipe show a robust performance for a wide
range of web site templates.
Author: See AUTHORS file.
Maintainer: Mario Annau
DESCRIPTION | 14 +++++-------
MD5 | 32 ++++++++++++++-------------
NAMESPACE | 2 +
NEWS | 6 +++++
build/vignette.rds |binary
inst/AUTHORS |only
inst/doc/ShortIntro.pdf |binary
java |only
man/ArticleExtractor.Rd | 8 +++---
man/ArticleSentencesExtractor.Rd | 8 +++---
man/CanolaExtractor.Rd | 9 +++----
man/DefaultExtractor.Rd | 5 ++--
man/Extractor.Rd | 45 ++++++++++++++-------------------------
man/KeepEverythingExtractor.Rd | 5 ++--
man/LargestContentExtractor.Rd | 10 ++++----
man/NumWordsRulesExtractor.Rd | 9 +++----
man/boilerpipeR-package.Rd | 14 +++++-------
man/content.Rd | 6 ++---
18 files changed, 84 insertions(+), 89 deletions(-)