Title: Trust region nonlinear optimization, efficient for sparse
Hessians
Diff between trustOptim versions 0.8.0 dated 2012-12-28 and 0.8.1 dated 2013-06-12
Description: Trust region algorithm for nonlinear optimization. In
addition to being more stable and robust than optim, this
package includes methods that are scalable and efficient (in
terms of both speed and memory usage) when the Hessian is
sparse.
Author: Michael Braun
Maintainer: Michael Braun
trustOptim-0.8.0/trustOptim/inst/examples |only
trustOptim-0.8.1/trustOptim/DESCRIPTION | 13 +-
trustOptim-0.8.1/trustOptim/MD5 | 37 +++---
trustOptim-0.8.1/trustOptim/NEWS | 19 +++
trustOptim-0.8.1/trustOptim/R/demo_funcs.R |only
trustOptim-0.8.1/trustOptim/demo |only
trustOptim-0.8.1/trustOptim/inst/doc/trustOptim-vignette.R |only
trustOptim-0.8.1/trustOptim/inst/doc/trustOptim-vignette.pdf |binary
trustOptim-0.8.1/trustOptim/inst/include/CG-base.h | 62 +++++------
trustOptim-0.8.1/trustOptim/inst/include/CG-quasi.h | 2
trustOptim-0.8.1/trustOptim/inst/include/CG-sparse.h | 6 -
trustOptim-0.8.1/trustOptim/inst/include/Rfunc.cpp | 2
trustOptim-0.8.1/trustOptim/inst/include/RfuncHess.cpp | 2
trustOptim-0.8.1/trustOptim/inst/include/common_R.hpp | 2
trustOptim-0.8.1/trustOptim/inst/include/defines_optim.hpp | 2
trustOptim-0.8.1/trustOptim/inst/include/exceptions.hpp | 2
trustOptim-0.8.1/trustOptim/inst/include/include_eigen.hpp | 2
trustOptim-0.8.1/trustOptim/man/demo.funcs.Rd |only
trustOptim-0.8.1/trustOptim/man/trustOptim-package.Rd | 4
trustOptim-0.8.1/trustOptim/src/Rinterface.cpp | 5
20 files changed, 93 insertions(+), 67 deletions(-)
Title: Functions and Examples for "Software for Data Analysis"
Diff between SoDA versions 1.0-5 dated 2012-12-16 and 1.0-6 dated 2013-06-12
Description: Functions, examples and other software related to the book
"Software for Data Analysis: Programming with R". See
package?SoDA for an overview.
Author: John M Chambers
Maintainer: John M Chambers
DESCRIPTION | 11 ++++++-----
MD5 | 4 ++--
src/geodistv.f | 2 +-
3 files changed, 9 insertions(+), 8 deletions(-)
Title: Transforms input data from a PMML perspective
Diff between pmmlTransformations versions 1.0 dated 2013-01-23 and 1.1 dated 2013-06-12
More information about pmmlTransformations at CRAN
Description: Allows for data to be transformed before using it to
construct models. Builds structures to allow functions in the
PMML package to output transformation details in addition to
the model in the resulting PMML file.
Author: Tridivesh Jena
Maintainer: Tridivesh Jena
DESCRIPTION | 11 ++++---
MD5 | 32 ++++++++++++----------
R/DiscretizeXform.R |only
R/Initialize.R | 45 +++++++++++++++++++++++--------
R/MapXform.R | 35 +++++++++++++++++++-----
R/MinMaxXform.R | 34 ++++++++++++++---------
R/NormDiscreteXform.R | 36 +++++++++++++++++++++----
R/RenameVar.R |only
R/WrapData.R | 22 +++++++++++++++
R/ZScoreXform.R | 53 +++++++++++++++++++++++++++----------
man/DiscretizeXform.Rd |only
man/Initialize.Rd | 3 ++
man/MapXform.Rd | 7 +++-
man/MinMaxXform.Rd | 10 +++++-
man/NormDiscreteXform.Rd | 10 +++++-
man/RenameVar.Rd |only
man/WrapData.Rd | 5 ++-
man/ZScoreXform.Rd | 10 +++++-
man/pmmlTransformations-package.Rd | 26 ++++++++++++------
19 files changed, 253 insertions(+), 86 deletions(-)
Permanent link
Title: Independent Components Analysis (ICA) based artifact correction.
Diff between icaOcularCorrection versions 1.3 dated 2011-11-03 and 2.1 dated 2013-06-12
More information about icaOcularCorrection at CRAN
Description: Removes eye-movement and other types of known (i.e.,
recorded) or unknown (i.e., not recorded) artifacts using the
fastICA package. The correction method proposed in this package
is largely based on the method described in on Flexer, Bauer,
Pripfl, and Dorffner (2005). The process of correcting electro-
and magneto-encephalographic data (EEG/MEG) begins by running
function ``icac'', which first performs independent components
analysis (ICA) to decompose the data frame into independent
components (ICs) using function ``fastICA'' from the package of
the same name. It then calculates for each trial the
correlation between each IC and each one of the noise signals
-- there can be one or more, e.g., vertical and horizontal
electro-oculograms (VEOG and HEOG), electro-myograms (EMG),
electro-cardiograms (ECG), galvanic skin responses (GSR), and
other noise signals. Subsequently, portions of an IC
corresponding to trials at which the correlation between it and
a noise signal was at or above threshold (set to 0.4 by
default; Flexer et al., 2005, p. 1001) are either zeroed-out in
the source matrix, ``S'', or subtracted from the data that was
passed to function ``icac''. The user can then identify which
ICs correlate with the noise signals the most by looking at the
summary of the ``icac'' object (using function
``summary.icac''), the scalp topography of the ICs (using
function ``topo.ic''), the time courses of the ICs (using
functions (``plot.tric'') and ``plot.nic'', and other
diagnostic plots. Once these ICs have been identified, they can
be completely zeroed-out or subtracted using function
``update.icac'' and the resulting correction checked using
functions ``plot.avgba'' and ``plot.trba''. Some worked-out
examples with R code are provided in the following sections.
Please contact the package maintainer to obtain the data to run
the examples.
Author: Antoine Tremblay, NeuroCognitive Imaging Lab, Dalhousie
University
Maintainer: Antoine Tremblay
icaOcularCorrection-1.3/icaOcularCorrection/R/batch.icaDEN.fnc.R |only
icaOcularCorrection-1.3/icaOcularCorrection/R/batch.plotICs.fnc.R |only
icaOcularCorrection-1.3/icaOcularCorrection/R/defineElectrodeSet.fnc.R |only
icaOcularCorrection-1.3/icaOcularCorrection/R/icaDEN.fnc.R |only
icaOcularCorrection-1.3/icaOcularCorrection/R/mc.batch.icaDEN.fnc.R |only
icaOcularCorrection-1.3/icaOcularCorrection/R/plotICs.fnc.R |only
icaOcularCorrection-1.3/icaOcularCorrection/data |only
icaOcularCorrection-1.3/icaOcularCorrection/man/batch.icaDEN.fnc.Rd |only
icaOcularCorrection-1.3/icaOcularCorrection/man/batch.plotICs.fnc.Rd |only
icaOcularCorrection-1.3/icaOcularCorrection/man/defineElectrodeSet.fnc.Rd |only
icaOcularCorrection-1.3/icaOcularCorrection/man/den.Rd |only
icaOcularCorrection-1.3/icaOcularCorrection/man/eeg.Rd |only
icaOcularCorrection-1.3/icaOcularCorrection/man/icaDEN.fnc.Rd |only
icaOcularCorrection-1.3/icaOcularCorrection/man/mc.batch.icaDEN.fnc.Rd |only
icaOcularCorrection-1.3/icaOcularCorrection/man/plotICs.fnc.Rd |only
icaOcularCorrection-2.1/icaOcularCorrection/DESCRIPTION | 53 +++++-
icaOcularCorrection-2.1/icaOcularCorrection/MD5 | 73 ++++++---
icaOcularCorrection-2.1/icaOcularCorrection/NAMESPACE | 1
icaOcularCorrection-2.1/icaOcularCorrection/NEWS | 76 +++++++++
icaOcularCorrection-2.1/icaOcularCorrection/R/get.peaks.R |only
icaOcularCorrection-2.1/icaOcularCorrection/R/icac.R |only
icaOcularCorrection-2.1/icaOcularCorrection/R/mwd.thrsh.R |only
icaOcularCorrection-2.1/icaOcularCorrection/R/plot.avgba.R |only
icaOcularCorrection-2.1/icaOcularCorrection/R/plot.nic.R |only
icaOcularCorrection-2.1/icaOcularCorrection/R/plot.trba.R |only
icaOcularCorrection-2.1/icaOcularCorrection/R/plot.tric.R |only
icaOcularCorrection-2.1/icaOcularCorrection/R/summary.icac.R |only
icaOcularCorrection-2.1/icaOcularCorrection/R/topo.ic.R |only
icaOcularCorrection-2.1/icaOcularCorrection/R/update.icac.R |only
icaOcularCorrection-2.1/icaOcularCorrection/inst |only
icaOcularCorrection-2.1/icaOcularCorrection/man/get.peaks.Rd |only
icaOcularCorrection-2.1/icaOcularCorrection/man/icaOcularCorrection-package.Rd | 81 ++++------
icaOcularCorrection-2.1/icaOcularCorrection/man/icac.Rd |only
icaOcularCorrection-2.1/icaOcularCorrection/man/mwd.thrsh.Rd |only
icaOcularCorrection-2.1/icaOcularCorrection/man/plot.avgba.Rd |only
icaOcularCorrection-2.1/icaOcularCorrection/man/plot.nic.Rd |only
icaOcularCorrection-2.1/icaOcularCorrection/man/plot.trba.Rd |only
icaOcularCorrection-2.1/icaOcularCorrection/man/plot.tric.Rd |only
icaOcularCorrection-2.1/icaOcularCorrection/man/summary.icac.Rd |only
icaOcularCorrection-2.1/icaOcularCorrection/man/topo.ic.Rd |only
icaOcularCorrection-2.1/icaOcularCorrection/man/update.icac.Rd |only
icaOcularCorrection-2.1/icaOcularCorrection/vignettes |only
42 files changed, 207 insertions(+), 77 deletions(-)
Permanent link
Title: Species distribution modelling using latent Gaussian random
fields
Diff between GRaF versions 0.1-1 dated 2013-05-15 and 0.1-11 dated 2013-06-12
Description: Functions to fit, visualise and compare Gaussian random
field species distribution models.
Author: Nick Golding
Maintainer: Nick Golding
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/graf.R | 2 +-
man/GRaF-package.Rd | 4 ++--
4 files changed, 10 insertions(+), 10 deletions(-)
Title: Models for Data from Unmarked Animals
Diff between unmarked versions 0.10-0 dated 2013-04-16 and 0.10-1 dated 2013-06-12
Description: Unmarked fits hierarchical models of animal abundance and
occurrence to data collected using survey methods such as point
counts, site occupancy sampling, distance sampling, removal
sampling, and double observer sampling. Parameters governing
the state and observation processes can be modeled as functions
of covariates.
Author: Ian Fiske, Richard Chandler, David Miller, Andy Royle, Marc
Kery
Maintainer: Richard Chandler
unmarked-0.10-0/unmarked/inst/doc/cap-recap.R |only
unmarked-0.10-0/unmarked/inst/doc/colext.R |only
unmarked-0.10-0/unmarked/inst/doc/distsamp.R |only
unmarked-0.10-0/unmarked/inst/doc/spp-dist.R |only
unmarked-0.10-0/unmarked/inst/doc/unmarked.R |only
unmarked-0.10-0/unmarked/inst/unitTests/simout3.pdf |only
unmarked-0.10-0/unmarked/inst/unitTests/simout4.pdf |only
unmarked-0.10-1/unmarked/DESCRIPTION | 7 +--
unmarked-0.10-1/unmarked/MD5 | 37 ++++++++------------
unmarked-0.10-1/unmarked/inst/doc/cap-recap.pdf |binary
unmarked-0.10-1/unmarked/inst/doc/colext.pdf |binary
unmarked-0.10-1/unmarked/inst/doc/distsamp.pdf |binary
unmarked-0.10-1/unmarked/inst/doc/spp-dist.pdf |binary
unmarked-0.10-1/unmarked/inst/doc/unmarked.pdf |binary
unmarked-0.10-1/unmarked/inst/unitTests/simout1.pdf |binary
unmarked-0.10-1/unmarked/inst/unitTests/simout2.pdf |binary
unmarked-0.10-1/unmarked/man/Switzerland.Rd | 6 ++-
unmarked-0.10-1/unmarked/man/mallard.Rd | 2 -
unmarked-0.10-1/unmarked/man/occuFP.Rd | 6 ++-
unmarked-0.10-1/unmarked/man/occuRN.Rd | 2 -
unmarked-0.10-1/unmarked/man/pcount.Rd | 6 +--
unmarked-0.10-1/unmarked/man/unmarked-package.Rd | 4 +-
unmarked-0.10-1/unmarked/src/Makevars | 2 -
23 files changed, 34 insertions(+), 38 deletions(-)
Title: analysis of complex survey samples
Diff between survey versions 3.29-4 dated 2013-03-11 and 3.29-5 dated 2013-06-12
Description: Summary statistics, two-sample tests, generalised linear
models, cumulative link models, Cox models, loglinear models,
and general maximum pseudolikelihood estimation for multistage
stratified, cluster-sampled, unequally weighted survey samples.
Variances by Taylor series linearisation or replicate weights.
Post-stratification, calibration, and raking. Two-phase
subsampling designs. Graphics. Predictive margins by direct
standardization. PPS sampling without replacement. Principal
components, factor analysis.
Author: Thomas Lumley
Maintainer: Thomas Lumley
DESCRIPTION | 8 +++----
MD5 | 55 ++++++++++++++++++++++++++++------------------------
R/mrb.R | 2 -
R/olr.R | 4 +--
R/survey.R | 2 -
R/surveyby.R | 4 +--
R/surveygraph.R | 3 +-
R/surveyrep.R | 8 +++----
R/svykm.R | 2 -
R/svymi.R | 8 +++----
R/sysdata.rda |binary
data/api.rda |binary
data/crowd.rda |binary
data/election.rda |binary
data/fpc.rda |binary
data/hospital.rda |binary
data/mu284.rda |binary
data/nhanes.rda |binary
data/scd.rda |binary
inst/NEWS | 9 ++++++++
inst/doc/domain.R |only
inst/doc/domain.pdf |binary
inst/doc/epi.R |only
inst/doc/epi.pdf |binary
inst/doc/phase1.R |only
inst/doc/phase1.pdf |binary
inst/doc/pps.R |only
inst/doc/pps.pdf |binary
inst/doc/survey.R |only
inst/doc/survey.pdf |binary
man/svyplot.Rd | 7 ++++++
31 files changed, 67 insertions(+), 45 deletions(-)
Title: Bayesian variable selection and model choice for generalized
additive mixed models
Diff between spikeSlabGAM versions 1.1-5 dated 2013-03-13 and 1.1-6 dated 2013-06-12
Description: Bayesian variable selection, model choice, and regularized
estimation for (spatial) generalized additive mixed regression
models via SSVS with spike-and-slab priors.
Author: Fabian Scheipl
Maintainer: Fabian Scheipl
DESCRIPTION | 10
MD5 | 10
R/spikeAndSlab.R | 1575 ++++++++++++++++++++---------------------
R/spikeSlabGAM.R | 289 +++----
inst/doc/UsingSpikeSlabGAM.pdf |binary
man/spikeSlabGAM.Rd | 3
6 files changed, 947 insertions(+), 940 deletions(-)
Title: R package for simulating biological sequence evolution
Diff between phylosim versions 2.0.1 dated 2013-03-20 and 2.0.2 dated 2013-06-12
Description: PhyloSim is an extensible object-oriented framework for
the Monte Carlo simulation of sequence evolution written in 100
percent R. It is built on the top of the R.oo and ape packages
and uses Gillespie's direct method to simulate substitutions,
insertions and deletions.
Author: Botond Sipos
Maintainer: Botond Sipos
DESCRIPTION | 10
MD5 | 1014 +++++++++++++-------------
R/AminoAcidSubst.R | 4
R/BrownianInsertor.R | 18
R/Event.R | 8
R/GeneralInDel.R | 62 +
R/GeneralSubstitution.R | 16
R/PhyloSim.R | 18
R/PhyloSimSource.R |only
R/Sequence.R | 43 -
inst/doc/PhyloSim.R |only
inst/doc/PhyloSim.Rnw | 8
inst/doc/PhyloSim.pdf |binary
man/000==.Alphabet.Rd | 10
man/000==.Process.Rd | 10
man/Alphabet.Rd | 8
man/AminoAcidAlphabet.Rd | 8
man/AminoAcidSequence.Rd | 8
man/AminoAcidSubst.Rd | 8
man/AnyAlphabet.Rd | 8
man/BinaryAlphabet.Rd | 8
man/BinarySequence.Rd | 8
man/BinarySubst.Rd | 8
man/BrownianInsertor.Rd | 16
man/BrownianPath.BrownianInsertor.Rd | 10
man/CodonAlphabet.Rd | 8
man/CodonSequence.Rd | 11
man/CodonUNREST.Rd | 8
man/ContinuousDeletor.Rd | 8
man/ContinuousInsertor.Rd | 8
man/Debug.PhyloSim.Rd | 10
man/DiscreteDeletor.Rd | 8
man/DiscreteInsertor.Rd | 8
man/Event.Rd | 8
man/F81.Rd | 8
man/F84.Rd | 8
man/FastFieldDeletor.Rd | 11
man/GTR.Rd | 11
man/GY94.Rd | 11
man/GeneralDeletor.Rd | 11
man/GeneralInDel.Rd | 14
man/GeneralInsertor.Rd | 33
man/GeneralSubstitution.Rd | 8
man/HKY.Rd | 11
man/JC69.Rd | 8
man/JTT.Rd | 8
man/JTT.dcmut.Rd | 8
man/K80.Rd | 8
man/K81.Rd | 8
man/LG.Rd | 8
man/Log.PhyloSim.Rd | 10
man/MtZoa.Rd | 8
man/NucleotideAlphabet.Rd | 8
man/NucleotideSequence.Rd | 8
man/PAM.Rd | 8
man/PAM.dcmut.Rd | 8
man/PSRoot.Rd | 8
man/PSRootSummary.Rd | 8
man/Perform.Event.Rd | 14
man/PhyloSim.Rd | 11
man/Process.Rd | 8
man/QMatrix.Rd | 8
man/Scale.QMatrix.Rd | 10
man/Sequence.Rd | 8
man/Simulate.PhyloSim.Rd | 10
man/Site.Rd | 8
man/T92.Rd | 8
man/TN93.Rd | 11
man/Translate.CodonSequence.Rd | 10
man/UNREST.Rd | 8
man/Undocumented.PhyloSim.Rd | 10
man/WAG.Rd | 8
man/areSynonymous.CodonAlphabet.Rd | 10
man/as.character.Alphabet.Rd | 10
man/as.character.Event.Rd | 10
man/as.character.GeneralSubstitution.Rd | 10
man/as.character.PhyloSim.Rd | 10
man/as.character.Process.Rd | 10
man/as.character.QMatrix.Rd | 10
man/as.character.Sequence.Rd | 10
man/as.character.Site.Rd | 10
man/attachHookToNode.PhyloSim.Rd | 10
man/attachProcess.Sequence.Rd | 10
man/attachProcess.Site.Rd | 10
man/attachSeqToNode.PhyloSim.Rd | 10
man/buildFromPAML.AminoAcidSubst.Rd | 10
man/checkConsistency.Alphabet.Rd | 10
man/checkConsistency.AminoAcidSubst.Rd | 10
man/checkConsistency.BinarySubst.Rd | 10
man/checkConsistency.BrownianInsertor.Rd | 10
man/checkConsistency.CodonAlphabet.Rd | 10
man/checkConsistency.CodonSequence.Rd | 10
man/checkConsistency.CodonUNREST.Rd | 10
man/checkConsistency.ContinuousDeletor.Rd | 10
man/checkConsistency.ContinuousInsertor.Rd | 10
man/checkConsistency.DiscreteDeletor.Rd | 10
man/checkConsistency.DiscreteInsertor.Rd | 10
man/checkConsistency.Event.Rd | 10
man/checkConsistency.F81.Rd | 10
man/checkConsistency.F84.Rd | 10
man/checkConsistency.FastFieldDeletor.Rd | 10
man/checkConsistency.GTR.Rd | 10
man/checkConsistency.GY94.Rd | 10
man/checkConsistency.GeneralDeletor.Rd | 10
man/checkConsistency.GeneralInDel.Rd | 10
man/checkConsistency.GeneralInsertor.Rd | 10
man/checkConsistency.GeneralSubstitution.Rd | 10
man/checkConsistency.HKY.Rd | 10
man/checkConsistency.JC69.Rd | 10
man/checkConsistency.K80.Rd | 10
man/checkConsistency.K81.Rd | 10
man/checkConsistency.PSRoot.Rd | 10
man/checkConsistency.PSRootSummary.Rd | 10
man/checkConsistency.PhyloSim.Rd | 10
man/checkConsistency.Process.Rd | 10
man/checkConsistency.QMatrix.Rd | 10
man/checkConsistency.Sequence.Rd | 10
man/checkConsistency.Site.Rd | 10
man/checkConsistency.T92.Rd | 10
man/checkConsistency.TN93.Rd | 10
man/checkConsistency.UNREST.Rd | 10
man/clearStates.Sequence.Rd | 10
man/clone.GeneralSubstitution.Rd | 16
man/clone.Process.Rd | 10
man/clone.Sequence.Rd | 10
man/copySubSequence.Sequence.Rd | 10
man/cpREV.Rd | 8
man/deleteSubSequence.Sequence.Rd | 10
man/detachHookFromNode.PhyloSim.Rd | 10
man/detachProcess.Sequence.Rd | 10
man/detachProcess.Site.Rd | 10
man/detachSeqFromNode.PhyloSim.Rd | 10
man/enableVirtual.PSRoot.Rd | 10
man/exportStatTree.PhyloSim.Rd | 15
man/flagTotalRate.Site.Rd | 10
man/generateInsert.GeneralInsertor.Rd | 10
man/getAcceptBy.GeneralInDel.Rd | 16
man/getAcceptWin.GeneralInsertor.Rd | 10
man/getAlignment.PhyloSim.Rd | 10
man/getAlignmentLength.PhyloSim.Rd | 13
man/getAlphabet.GeneralSubstitution.Rd | 10
man/getAlphabet.Process.Rd | 10
man/getAlphabet.QMatrix.Rd | 10
man/getAlphabet.Site.Rd | 10
man/getAlphabets.Sequence.Rd | 10
man/getAncestral.Sequence.Rd | 10
man/getAncestral.Site.Rd | 10
man/getBaseFreqs.F81.Rd | 10
man/getBaseFreqs.F84.Rd | 10
man/getBaseFreqs.GTR.Rd | 10
man/getBaseFreqs.HKY.Rd | 10
man/getBaseFreqs.K80.Rd | 10
man/getBaseFreqs.K81.Rd | 10
man/getBaseFreqs.TN93.Rd | 10
man/getBigRate.Sequence.Rd | 10
man/getBranchEvents.PhyloSim.Rd | 14
man/getCodonFreqs.GY94.Rd | 10
man/getComments.PSRoot.Rd | 10
man/getCumulativeRates.Sequence.Rd | 10
man/getCumulativeRatesFromRange.Sequence.Rd | 16
man/getDeletionTolerance.Sequence.Rd | 10
man/getDist.ContinuousDeletor.Rd | 10
man/getDist.ContinuousInsertor.Rd | 10
man/getEdge.PhyloSim.Rd | 10
man/getEdges.PhyloSim.Rd | 10
man/getEquDist.GeneralSubstitution.Rd | 15
man/getEventRate.GeneralSubstitution.Rd | 10
man/getEventRate.QMatrix.Rd | 10
man/getEventRateAtSite.GeneralSubstitution.Rd | 10
man/getEvents.Sequence.Rd | 16
man/getEvents.Site.Rd | 10
man/getEventsAtSite.FastFieldDeletor.Rd | 10
man/getEventsAtSite.GY94.Rd | 10
man/getEventsAtSite.GeneralDeletor.Rd | 10
man/getEventsAtSite.GeneralInsertor.Rd | 10
man/getEventsAtSite.GeneralSubstitution.Rd | 10
man/getEventsAtSite.Process.Rd | 10
man/getGenerateBy.GeneralInsertor.Rd | 20
man/getHandler.Event.Rd | 14
man/getId.PhyloSim.Rd | 10
man/getId.Process.Rd | 10
man/getId.QMatrix.Rd | 10
man/getId.Sequence.Rd | 10
man/getInsertHook.GeneralInsertor.Rd | 10
man/getInsertionTolerance.Sequence.Rd | 10
man/getKappa.F84.Rd | 10
man/getKappa.GY94.Rd | 10
man/getLength.Sequence.Rd | 10
man/getLengthParam1.FastFieldDeletor.Rd | 10
man/getLengthParam2.FastFieldDeletor.Rd | 10
man/getLogFile.PhyloSim.Rd | 10
man/getLogLevel.PhyloSim.Rd | 10
man/getMatrix.QMatrix.Rd | 10
man/getMaxLength.ContinuousDeletor.Rd | 10
man/getMaxLength.ContinuousInsertor.Rd | 10
man/getMethodsList.PSRoot.Rd | 10
man/getName.Event.Rd | 10
man/getName.PhyloSim.Rd | 10
man/getName.Process.Rd | 10
man/getName.QMatrix.Rd | 10
man/getName.Sequence.Rd | 10
man/getNedges.PhyloSim.Rd | 10
man/getNodes.PhyloSim.Rd | 10
man/getNtips.PhyloSim.Rd | 10
man/getOmegaScalingFactor.GY94.Rd | 10
man/getOmegas.CodonSequence.Rd | 10
man/getParameterAtSite.Process.Rd | 10
man/getParameterAtSites.Sequence.Rd | 13
man/getPhylo.PhyloSim.Rd | 10
man/getPosition.Event.Rd | 10
man/getProbs.DiscreteDeletor.Rd | 10
man/getProbs.DiscreteInsertor.Rd | 10
man/getProcess.Event.Rd | 10
man/getProcess.QMatrix.Rd | 10
man/getProcesses.Sequence.Rd | 16
man/getProcesses.Site.Rd | 10
man/getProposeBy.GeneralInDel.Rd | 10
man/getQMatrix.GeneralSubstitution.Rd | 10
man/getRate.Event.Rd | 10
man/getRate.GeneralInDel.Rd | 10
man/getRate.GeneralSubstitution.Rd | 10
man/getRate.QMatrix.Rd | 8
man/getRateList.GeneralSubstitution.Rd | 10
man/getRateList.QMatrix.Rd | 10
man/getRateMultipliers.Sequence.Rd | 10
man/getRateParam.F81.Rd | 10
man/getRateParam.F84.Rd | 10
man/getRateParam.GTR.Rd | 10
man/getRateParam.HKY.Rd | 10
man/getRateParam.K80.Rd | 10
man/getRateParam.K81.Rd | 10
man/getRateParam.T92.Rd | 10
man/getRateParam.TN93.Rd | 10
man/getRateParamList.F81.Rd | 10
man/getRateParamList.F84.Rd | 10
man/getRateParamList.GTR.Rd | 10
man/getRateParamList.HKY.Rd | 10
man/getRateParamList.K80.Rd | 10
man/getRateParamList.K81.Rd | 10
man/getRateParamList.T92.Rd | 10
man/getRateParamList.TN93.Rd | 10
man/getRootNode.PhyloSim.Rd | 10
man/getRootSeq.PhyloSim.Rd | 10
man/getScale.BrownianInsertor.Rd | 10
man/getScaledMatrix.QMatrix.Rd | 10
man/getSeqFromNode.PhyloSim.Rd | 10
man/getSequence.Site.Rd | 10
man/getSequences.PhyloSim.Rd | 10
man/getSite.Event.Rd | 10
man/getSiteSpecificParamIds.Process.Rd | 10
man/getSiteSpecificParamList.Process.Rd | 10
man/getSites.Sequence.Rd | 10
man/getSize.Alphabet.Rd | 10
man/getSizes.DiscreteDeletor.Rd | 10
man/getSizes.DiscreteInsertor.Rd | 10
man/getState.Site.Rd | 10
man/getStates.Sequence.Rd | 10
man/getString.Sequence.Rd | 10
man/getSymbolFreqs.Sequence.Rd | 10
man/getSymbolLength.Alphabet.Rd | 10
man/getSymbols.Alphabet.Rd | 10
man/getTableId.CodonAlphabet.Rd | 10
man/getTemplateSeq.GeneralInsertor.Rd | 10
man/getTheta.T92.Rd | 10
man/getTipLabels.PhyloSim.Rd | 10
man/getTips.PhyloSim.Rd | 10
man/getToleranceMargin.FastFieldDeletor.Rd | 10
man/getTotalRate.Site.Rd | 10
man/getTotalRates.Sequence.Rd | 10
man/getTotalRatesFromRange.Sequence.Rd | 16
man/getTransTable.CodonAlphabet.Rd | 10
man/getTreeLength.PhyloSim.Rd | 10
man/getType.Alphabet.Rd | 10
man/getType.BrownianInsertor.Rd | 10
man/getType.FastFieldDeletor.Rd | 10
man/getUniqueAlphabets.Sequence.Rd | 17
man/getUniqueProcesses.Sequence.Rd | 16
man/getWriteProtected.Alphabet.Rd | 10
man/getWriteProtected.Event.Rd | 10
man/getWriteProtected.Process.Rd | 10
man/getWriteProtected.QMatrix.Rd | 10
man/getWriteProtected.Sequence.Rd | 10
man/globalConsistencyCheck.PSRoot.Rd | 10
man/hasSiteSpecificParameter.Process.Rd | 10
man/hasSymbols.Alphabet.Rd | 10
man/hasUndefinedRate.GeneralInDel.Rd | 10
man/hasUndefinedRate.GeneralSubstitution.Rd | 10
man/hasUndefinedRate.Process.Rd | 10
man/insertSequence.Sequence.Rd | 10
man/intersect.list.PSRoot.Rd | 10
man/is.Alphabet.Rd | 8
man/is.CodonAlphabet.Rd | 8
man/is.CodonUNREST.Rd | 8
man/is.Event.Rd | 8
man/is.GY94.Rd | 8
man/is.GeneralDeletor.Rd | 8
man/is.GeneralInDel.Rd | 8
man/is.GeneralInsertor.Rd | 8
man/is.GeneralSubstitution.Rd | 8
man/is.PSRoot.Rd | 8
man/is.Process.Rd | 8
man/is.QMatrix.Rd | 8
man/is.Sequence.Rd | 8
man/is.Site.Rd | 8
man/is.na.PSRoot.Rd | 10
man/is.phylo.Rd | 8
man/is.tip.PhyloSim.Rd | 10
man/isAttached.Site.Rd | 10
man/isEmpty.Alphabet.Rd | 10
man/isStartCodon.CodonAlphabet.Rd | 10
man/isStopCodon.CodonAlphabet.Rd | 10
man/ll.PSRoot.Rd | 10
man/mtArt.Rd | 8
man/mtMam.Rd | 8
man/mtREV24.Rd | 8
man/my.all.equal.PSRoot.Rd | 10
man/newAAMatrix.AminoAcidSubst.Rd | 10
man/omegaHist.CodonSequence.Rd | 10
man/omegaVarM0.CodonSequence.Rd | 10
man/omegaVarM1.CodonSequence.Rd | 10
man/omegaVarM2.CodonSequence.Rd | 10
man/omegaVarM3.CodonSequence.Rd | 10
man/omegaVarM4.CodonSequence.Rd | 10
man/plot.ContinuousDeletor.Rd | 10
man/plot.ContinuousInsertor.Rd | 10
man/plot.DiscreteDeletor.Rd | 10
man/plot.DiscreteInsertor.Rd | 10
man/plot.GeneralSubstitution.Rd | 10
man/plot.PhyloSim.Rd | 18
man/plot.Sequence.Rd | 10
man/plotParametersAtSites.Sequence.Rd | 10
man/plusGamma.Sequence.Rd | 10
man/plusInvGamma.Sequence.Rd | 10
man/print.PSRootSummary.Rd | 10
man/print.QMatrix.Rd | 10
man/proposeLength.GeneralInDel.Rd | 10
man/readAlignment.PhyloSim.Rd | 10
man/readTree.PhyloSim.Rd | 10
man/rescaleQMatrix.GeneralSubstitution.Rd | 10
man/revComp.NucleotideSequence.Rd | 10
man/sampleState.GeneralSubstitution.Rd | 10
man/sampleStates.Sequence.Rd | 10
man/saveAlignment.PhyloSim.Rd | 10
man/scaleTree.PhyloSim.Rd | 10
man/setAcceptBy.GeneralInDel.Rd | 16
man/setAcceptWin.GeneralInsertor.Rd | 10
man/setAlignment.PhyloSim.Rd | 10
man/setAlphabet.GeneralSubstitution.Rd | 10
man/setAlphabet.Process.Rd | 10
man/setAlphabet.QMatrix.Rd | 10
man/setAlphabet.Site.Rd | 10
man/setAlphabets.Sequence.Rd | 10
man/setAncestral.Sequence.Rd | 10
man/setAncestral.Site.Rd | 10
man/setBaseFreqs.F81.Rd | 10
man/setBaseFreqs.F84.Rd | 10
man/setBaseFreqs.GTR.Rd | 10
man/setBaseFreqs.HKY.Rd | 10
man/setBaseFreqs.K80.Rd | 10
man/setBaseFreqs.K81.Rd | 10
man/setBaseFreqs.TN93.Rd | 10
man/setBigRate.Sequence.Rd | 10
man/setBranchEvents.PhyloSim.Rd | 10
man/setCodonFreqs.GY94.Rd | 10
man/setComments.PSRoot.Rd | 10
man/setCumulativeRates.Sequence.Rd | 10
man/setDeletionTolerance.Sequence.Rd | 10
man/setDist.ContinuousDeletor.Rd | 10
man/setDist.ContinuousInsertor.Rd | 10
man/setEdges.PhyloSim.Rd | 10
man/setEquDist.GeneralSubstitution.Rd | 15
man/setEvents.Site.Rd | 10
man/setGenerateBy.GeneralInsertor.Rd | 19
man/setHandler.Event.Rd | 10
man/setId.PhyloSim.Rd | 10
man/setId.Process.Rd | 10
man/setId.QMatrix.Rd | 10
man/setId.Sequence.Rd | 10
man/setInsertHook.GeneralInsertor.Rd | 10
man/setInsertionTolerance.Sequence.Rd | 10
man/setKappa.F84.Rd | 10
man/setKappa.GY94.Rd | 10
man/setLength.Sequence.Rd | 10
man/setLengthParam1.FastFieldDeletor.Rd | 10
man/setLengthParam2.FastFieldDeletor.Rd | 10
man/setLogFile.PhyloSim.Rd | 10
man/setLogLevel.PhyloSim.Rd | 10
man/setMatrix.QMatrix.Rd | 10
man/setMaxLength.ContinuousDeletor.Rd | 10
man/setMaxLength.ContinuousInsertor.Rd | 10
man/setMethodsList.PSRoot.Rd | 10
man/setName.Event.Rd | 10
man/setName.PhyloSim.Rd | 10
man/setName.Process.Rd | 10
man/setName.QMatrix.Rd | 10
man/setName.Sequence.Rd | 10
man/setNedges.PhyloSim.Rd | 10
man/setNodes.PhyloSim.Rd | 10
man/setNtips.PhyloSim.Rd | 10
man/setOmegas.CodonSequence.Rd | 10
man/setParameterAtSite.Process.Rd | 10
man/setParameterAtSites.Sequence.Rd | 13
man/setPhylo.PhyloSim.Rd | 10
man/setPosition.Event.Rd | 10
man/setProbs.DiscreteDeletor.Rd | 10
man/setProbs.DiscreteInsertor.Rd | 10
man/setProcess.Event.Rd | 10
man/setProcess.QMatrix.Rd | 10
man/setProcesses.Sequence.Rd | 10
man/setProcesses.Site.Rd | 10
man/setProposeBy.GeneralInDel.Rd | 10
man/setQMatrix.GeneralSubstitution.Rd | 10
man/setRate.Event.Rd | 10
man/setRate.GY94.Rd | 10
man/setRate.GeneralInDel.Rd | 10
man/setRate.GeneralSubstitution.Rd | 10
man/setRate.QMatrix.Rd | 10
man/setRateList.GeneralSubstitution.Rd | 10
man/setRateList.QMatrix.Rd | 10
man/setRateMultipliers.Sequence.Rd | 10
man/setRateParam.F81.Rd | 10
man/setRateParam.F84.Rd | 10
man/setRateParam.GTR.Rd | 10
man/setRateParam.HKY.Rd | 10
man/setRateParam.K80.Rd | 10
man/setRateParam.K81.Rd | 10
man/setRateParam.T92.Rd | 10
man/setRateParam.TN93.Rd | 10
man/setRateParamList.F81.Rd | 10
man/setRateParamList.F84.Rd | 10
man/setRateParamList.GTR.Rd | 10
man/setRateParamList.HKY.Rd | 10
man/setRateParamList.K80.Rd | 10
man/setRateParamList.K81.Rd | 10
man/setRateParamList.T92.Rd | 10
man/setRateParamList.TN93.Rd | 10
man/setRootNode.PhyloSim.Rd | 10
man/setRootSeq.PhyloSim.Rd | 10
man/setScale.BrownianInsertor.Rd | 10
man/setScaledMatrix.QMatrix.Rd | 10
man/setSequence.Site.Rd | 10
man/setSequences.PhyloSim.Rd | 10
man/setSite.Event.Rd | 10
man/setSiteSpecificParamIds.Process.Rd | 10
man/setSiteSpecificParamList.Process.Rd | 10
man/setSize.Alphabet.Rd | 10
man/setSizes.DiscreteDeletor.Rd | 10
man/setSizes.DiscreteInsertor.Rd | 10
man/setState.Site.Rd | 10
man/setStates.Sequence.Rd | 10
man/setString.Sequence.Rd | 10
man/setSymbolLength.Alphabet.Rd | 10
man/setSymbols.Alphabet.Rd | 10
man/setTableId.CodonAlphabet.Rd | 10
man/setTemplateSeq.GeneralInsertor.Rd | 10
man/setTheta.T92.Rd | 10
man/setTipLabels.PhyloSim.Rd | 10
man/setTips.PhyloSim.Rd | 10
man/setToleranceMargin.FastFieldDeletor.Rd | 10
man/setTotalRate.Site.Rd | 10
man/setTotalRates.Sequence.Rd | 10
man/setTransTable.CodonAlphabet.Rd | 10
man/setTreeLength.PhyloSim.Rd | 10
man/setType.Alphabet.Rd | 10
man/setType.BrownianInsertor.Rd | 10
man/setType.FastFieldDeletor.Rd | 10
man/setUniqueAlphabets.Sequence.Rd | 10
man/setUniqueProcesses.Sequence.Rd | 10
man/setWriteProtected.Alphabet.Rd | 10
man/setWriteProtected.Event.Rd | 10
man/setWriteProtected.Process.Rd | 10
man/setWriteProtected.QMatrix.Rd | 10
man/setWriteProtected.Sequence.Rd | 10
man/stringLength.Rd | 8
man/stringLengthVector.Rd | 8
man/summary.Alphabet.Rd | 10
man/summary.AminoAcidSubst.Rd | 10
man/summary.BinarySubst.Rd | 10
man/summary.BrownianInsertor.Rd | 18
man/summary.CodonAlphabet.Rd | 10
man/summary.ContinuousDeletor.Rd | 10
man/summary.ContinuousInsertor.Rd | 10
man/summary.DiscreteDeletor.Rd | 10
man/summary.DiscreteInsertor.Rd | 10
man/summary.Event.Rd | 10
man/summary.F81.Rd | 10
man/summary.F84.Rd | 10
man/summary.FastFieldDeletor.Rd | 10
man/summary.GTR.Rd | 10
man/summary.GY94.Rd | 10
man/summary.GeneralDeletor.Rd | 10
man/summary.GeneralInDel.Rd | 10
man/summary.GeneralInsertor.Rd | 10
man/summary.GeneralSubstitution.Rd | 10
man/summary.HKY.Rd | 10
man/summary.JC69.Rd | 10
man/summary.K80.Rd | 10
man/summary.K81.Rd | 10
man/summary.PSRoot.Rd | 10
man/summary.PhyloSim.Rd | 10
man/summary.Process.Rd | 10
man/summary.QMatrix.Rd | 10
man/summary.Sequence.Rd | 10
man/summary.Site.Rd | 10
man/summary.T92.Rd | 10
man/summary.TN93.Rd | 10
man/summary.UNREST.Rd | 10
man/translateCodon.CodonAlphabet.Rd | 10
man/virtualAssignmentForbidden.PSRoot.Rd | 10
509 files changed, 3285 insertions(+), 2923 deletions(-)
Title: Generate PMML for various models
Diff between pmml versions 1.2.34 dated 2013-01-26 and 1.2.35 dated 2013-06-12
Description: The Predictive Modelling Markup Language (PMML) is a
language for representing models, in an application independent
way. Such models can then be loaded into other applications
supporting PMML, including ADAPA from Zementis, Teradata
Warehouse Miner and IBM's DB2. The package provides a generic
pmml function to generate pmml for an object. Using a S3
generic function the appropriate method for the class of the
supplied object is dispatched. The package currently supports
the export of PMML for linear regression, generalized linear
regression, multinomial logistic regression, SVMs, rpart
classification trees, randomSurvivalForest, randomForest, naive
bayes models and kmeans clusters. This package is part of the
Rattle toolkit.
Author: Graham Williams, Michael Hahsler (arules), Zementis Inc, Hemant
Ishwaran, Udaya B. Kogalur, Rajarshi Guha
Maintainer: Tridivesh Jena
pmml-1.2.34/pmml/R/pmml.rsf.R |only
pmml-1.2.34/pmml/man/pmml.rsf.Rd |only
pmml-1.2.35/pmml/DESCRIPTION | 18 -
pmml-1.2.35/pmml/MD5 | 22 +-
pmml-1.2.35/pmml/R/pmml.R | 309 +++++++++++++++++++++++++----
pmml-1.2.35/pmml/R/pmml.coxph.R | 16 +
pmml-1.2.35/pmml/R/pmml.cv.glmnet.R |only
pmml-1.2.35/pmml/R/pmml.multinom.R | 17 -
pmml-1.2.35/pmml/R/pmml.naiveBayes.R |only
pmml-1.2.35/pmml/R/pmml.randomForest.R | 332 ++++++++++++++++++--------------
pmml-1.2.35/pmml/R/pmml.rfsrc.R |only
pmml-1.2.35/pmml/R/pmml.rules.R | 2
pmml-1.2.35/pmml/man/pmml.Rd | 4
pmml-1.2.35/pmml/man/pmml.cv.glmnet.Rd |only
pmml-1.2.35/pmml/man/pmml.naiveBayes.Rd |only
pmml-1.2.35/pmml/man/pmml.rfsrc.Rd |only
16 files changed, 506 insertions(+), 214 deletions(-)
Title: Estimating network indices, including trophic structure of
foodwebs in R
Diff between NetIndices versions 1.4 dated 2011-08-11 and 1.4.2 dated 2013-06-12
Description: Given a network (e.g. a food web), estimates several
network indices. These include: Ascendency network indices,
Direct and indirect dependencies, Effective measures, Environ
network indices, General network indices, Pathway analysis,
Network uncertainty indices and constraint efficiencies and the
trophic level and omnivory indices of food webs.
Author: Karline Soetaert
Maintainer: Karline Soetaert
DESCRIPTION | 15 ++++++++-------
MD5 | 30 +++++++++++++++---------------
R/TrophInd.R | 4 +++-
data/Conesprings.rda |binary
data/Takapoto.rda |binary
inst/doc/NetIndices.pdf |binary
man/AscInd.Rd | 2 +-
man/Conesprings.Rd | 2 +-
man/Dependency.Rd | 2 +-
man/EffInd.Rd | 2 +-
man/EnvInd.Rd | 2 +-
man/GenInd.Rd | 2 +-
man/PathInd.Rd | 2 +-
man/Takapoto.Rd | 2 +-
man/TrophInd.Rd | 10 ++++++++--
man/UncInd.Rd | 2 +-
16 files changed, 43 insertions(+), 34 deletions(-)
Title: Linear Group Fixed Effects
Diff between lfe versions 1.4-963 dated 2013-05-07 and 1.5-1026 dated 2013-06-12
Description: Transforms away factors with many levels prior to doing an
OLS. Useful for estimating linear models with multiple group
fixed effects, and for estimating linear models which uses
factors as pure control variables.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure
lfe-1.4-963/lfe/inst/doc/CHANGELOG |only
lfe-1.5-1026/lfe/DESCRIPTION | 8
lfe-1.5-1026/lfe/MD5 | 65 ++--
lfe-1.5-1026/lfe/R/kaczmarz.R | 27 +
lfe-1.5-1026/lfe/R/lfe.R | 35 +-
lfe-1.5-1026/lfe/R/utils.R | 12
lfe-1.5-1026/lfe/inst/doc/identification.R | 195 +++++++++++---
lfe-1.5-1026/lfe/inst/doc/identification.Rnw | 361 ++++++++++++++++++++------
lfe-1.5-1026/lfe/inst/doc/identification.pdf |binary
lfe-1.5-1026/lfe/inst/doc/lfehow.Rnw | 30 +-
lfe-1.5-1026/lfe/inst/doc/lfehow.pdf |binary
lfe-1.5-1026/lfe/inst/doc/speed.R |only
lfe-1.5-1026/lfe/inst/doc/speed.Rnw |only
lfe-1.5-1026/lfe/inst/doc/speed.pdf |only
lfe-1.5-1026/lfe/man/btrap.Rd | 6
lfe-1.5-1026/lfe/man/compfactor.Rd | 16 +
lfe-1.5-1026/lfe/man/efactory.Rd | 8
lfe-1.5-1026/lfe/man/felm.Rd | 27 +
lfe-1.5-1026/lfe/man/getfe.Rd | 6
lfe-1.5-1026/lfe/man/is.estimable.Rd | 6
lfe-1.5-1026/lfe/man/kaczmarz.Rd | 5
lfe-1.5-1026/lfe/man/lfe-package.Rd | 15 -
lfe-1.5-1026/lfe/src/lfe.c | 279 +++++++++++++++++---
lfe-1.5-1026/lfe/tests/comparelm.Rout.save | 4
lfe-1.5-1026/lfe/tests/degenerate.Rout.save | 58 ++--
lfe-1.5-1026/lfe/tests/efcheck.R | 2
lfe-1.5-1026/lfe/tests/efcheck.Rout.save | 186 ++++++-------
lfe-1.5-1026/lfe/tests/fourfac.Rout.save | 24 -
lfe-1.5-1026/lfe/tests/ivtest.Rout.save | 4
lfe-1.5-1026/lfe/tests/lfetest.Rout.save | 4
lfe-1.5-1026/lfe/tests/nonest.Rout.save | 18 -
lfe-1.5-1026/lfe/tests/onefac.Rout.save | 4
lfe-1.5-1026/lfe/tests/verify.Rout.save | 10
lfe-1.5-1026/lfe/vignettes/identification.Rnw | 361 ++++++++++++++++++++------
lfe-1.5-1026/lfe/vignettes/lfehow.Rnw | 30 +-
lfe-1.5-1026/lfe/vignettes/speed.Rnw |only
36 files changed, 1318 insertions(+), 488 deletions(-)
Title: Inline C, C++, Fortran function calls from R
Diff between inline versions 0.3.11 dated 2013-02-27 and 0.3.12 dated 2013-06-12
Description: Functionality to dynamically define R functions and S4
methods with in-lined C, C++ or Fortran code supporting .C and
.Call calling conventions.
Author: Oleg Sklyar, Duncan Murdoch, Mike Smith, Dirk Eddelbuettel,
Romain Francois
Maintainer: Dirk Eddelbuettel
inline-0.3.11/inline/LICENSE |only
inline-0.3.12/inline/DESCRIPTION | 8 ++++----
inline-0.3.12/inline/MD5 | 9 ++++-----
inline-0.3.12/inline/R/package.skeleton.R | 8 ++++----
inline-0.3.12/inline/inst/NEWS.Rd | 18 ++++++++++++++----
inline-0.3.12/inline/man/cfunction.Rd | 3 ++-
6 files changed, 28 insertions(+), 18 deletions(-)
Title: Analysis of fMRI experiments
Diff between fmri versions 1.4-8 dated 2012-06-11 and 1.5-0 dated 2013-06-12
Description: The package contains R-functions to perform an fmri
analysis as described in K. Tabelow, J. Polzehl, H.U. Voss, and
V. Spokoiny, Analysing fMRI experiments with structure adaptive
smoothing procedures, NeuroImage, 33:55-62 (2006), J. Polzehl,
H.U. Voss, K. Tabelow, Structural adaptive segmentation for
statistical parametric mapping, NeuroImage, 52:515-523 (2010)
and K. Tabelow, J. Polzehl, Statistical Parametric Maps for
Functional MRI Experiments in {R}: The Package {fmri}}, Journal
of Statistical Software, 44(11):1--21 (2011).
Author: Karsten Tabelow
Maintainer: Karsten Tabelow
DESCRIPTION | 21 +++---
HISTORY | 12 +++
MD5 | 34 +++++-----
NAMESPACE | 2
R/fmri.R | 8 +-
R/io.R | 2
R/lm.R | 1
R/plot.r | 119 ++++++++++++++++++++++++++++++++----
R/segm.r | 92 +++++++++------------------
R/segmkrv.r | 89 +++++++++++++--------------
R/view23D.r | 168 +++++++++++++++++++++++++++++++++++++++++++++++++++
man/cutroi.Rd | 3
man/fmri.smooth.Rd | 8 +-
man/plot.fmridata.Rd | 12 +++
src/misc.f | 49 ++++++++++++++
src/segm3D.f | 77 ++++++++++++++++-------
src/segm3Dkrv.f | 17 ++---
src/vaws3D.f | 10 +--
18 files changed, 531 insertions(+), 193 deletions(-)
Title: Stable Distribution Functions
Diff between stabledist versions 0.6-5 dated 2012-10-01 and 0.6-6 dated 2013-06-12
Description: Density, Probability and Quantile functions, and random
number generation for (skew) stable distributions, using the
parametrizations of Nolan.
Author: Diethelm Wuertz, Martin Maechler and Rmetrics core team
members.
Maintainer: Martin Maechler
DESCRIPTION | 9 +++++----
MD5 | 8 ++++----
R/dpqr-stable.R | 6 +++---
TODO | 2 +-
tests/dstab-ex.R | 9 +++++++++
5 files changed, 22 insertions(+), 12 deletions(-)
Title: Graphical user interface for package sdcMicro
Diff between sdcMicroGUI versions 1.0.1 dated 2013-04-23 and 1.0.2 dated 2013-06-12
Description: A point and click graphical user interface based on top of
the sdcMicro package to create anonymized data set. The
graphical user interface provides full reproducibility of any
result via the script menu in the GUI.
Author: Alexander Kowarik, Matthias Templ, Bernhard Meindl, Francois
Fonteneau
Maintainer: Matthias Templ
DESCRIPTION | 10 ++++----
MD5 | 6 ++---
R/aux_functions.R | 16 +++----------
R/sdcGUI.r | 62 ++++++++++++++++++++++++++----------------------------
4 files changed, 42 insertions(+), 52 deletions(-)
Title: Reactive transport modelling in 1D, 2D and 3D
Diff between ReacTran versions 1.3.2 dated 2011-08-11 and 1.4.1 dated 2013-06-12
Description: Routines for developing models that describe reaction and
advective-diffusive transport in one, two or three dimensions.
Includes transport routines in porous media, in estuaries, and
in bodies with variable shape.
Author: Karline Soetaert
Maintainer: Karline Soetaert
ReacTran-1.3.2/ReacTran/inst/doc/bibs.bib |only
ReacTran-1.3.2/ReacTran/inst/doc/diffusion.jpeg |only
ReacTran-1.3.2/ReacTran/inst/doc/jss.bst |only
ReacTran-1.3.2/ReacTran/inst/doc/jss.cls |only
ReacTran-1.3.2/ReacTran/inst/doc/perspwave.jpeg |only
ReacTran-1.3.2/ReacTran/inst/doc/reactran-fig1.pdf |only
ReacTran-1.3.2/ReacTran/inst/doc/reactran-phase.pdf |only
ReacTran-1.4.1/ReacTran/.Rinstignore |only
ReacTran-1.4.1/ReacTran/DESCRIPTION | 15
ReacTran-1.4.1/ReacTran/MD5 | 76 +-
ReacTran-1.4.1/ReacTran/NAMESPACE | 6
ReacTran-1.4.1/ReacTran/NEWS | 7
ReacTran-1.4.1/ReacTran/R/advection.R | 31
ReacTran-1.4.1/ReacTran/R/tran.2D.R | 16
ReacTran-1.4.1/ReacTran/R/tran.3D.R | 184 ++---
ReacTran-1.4.1/ReacTran/R/tran.cylspher.R | 18
ReacTran-1.4.1/ReacTran/R/tran.volume.1D.R | 9
ReacTran-1.4.1/ReacTran/R/tran.volume.2D.R |only
ReacTran-1.4.1/ReacTran/R/tran.volume.3D.R |only
ReacTran-1.4.1/ReacTran/inst/CITATION |only
ReacTran-1.4.1/ReacTran/inst/doc/PDE.R |only
ReacTran-1.4.1/ReacTran/inst/doc/PDE.Rnw | 20
ReacTran-1.4.1/ReacTran/inst/doc/PDE.pdf |binary
ReacTran-1.4.1/ReacTran/inst/doc/ReacTran.R |only
ReacTran-1.4.1/ReacTran/inst/doc/ReacTran.pdf |binary
ReacTran-1.4.1/ReacTran/inst/doc/ReacTran.rnw | 19
ReacTran-1.4.1/ReacTran/inst/doc/fortran/tran.volume.1D.f |only
ReacTran-1.4.1/ReacTran/inst/doc/fortran/tran.volume.2D.f |only
ReacTran-1.4.1/ReacTran/inst/doc/fortran/tran.volume.3D.f |only
ReacTran-1.4.1/ReacTran/man/advection.Rd | 14
ReacTran-1.4.1/ReacTran/man/fiadeiro.Rd | 5
ReacTran-1.4.1/ReacTran/man/geometries.Rd | 4
ReacTran-1.4.1/ReacTran/man/properties.Rd | 4
ReacTran-1.4.1/ReacTran/man/setup.compaction.1D.Rd | 4
ReacTran-1.4.1/ReacTran/man/setup.grid.1D.Rd | 4
ReacTran-1.4.1/ReacTran/man/setup.grid.2D.Rd | 4
ReacTran-1.4.1/ReacTran/man/setup.prop.1D.Rd | 4
ReacTran-1.4.1/ReacTran/man/setup.prop.2D.Rd | 4
ReacTran-1.4.1/ReacTran/man/tran.1D.Rd | 4
ReacTran-1.4.1/ReacTran/man/tran.2D.Rd | 6
ReacTran-1.4.1/ReacTran/man/tran.3D.Rd | 9
ReacTran-1.4.1/ReacTran/man/tran.volume.1D.Rd | 155 ++++
ReacTran-1.4.1/ReacTran/src/advection.f | 481 ++++++++++----
ReacTran-1.4.1/ReacTran/src/tran3D.f | 7
ReacTran-1.4.1/ReacTran/vignettes |only
45 files changed, 773 insertions(+), 337 deletions(-)
Title: Constrained B-splines -- outdated 1999 version
Diff between cobs99 versions 0.9-11 dated 2012-12-10 and 0.9-12 dated 2013-06-12
Description: Qualitatively Constrained (Regression) Smoothing via
Linear Programming. OUTDATED version based on He & Ng (1999),
the modified "non-simplex" algorithm of Bartels and Conn
(1980). Use 'cobs' instead, unless for historical comparisons.
Author: Pin T. Ng
Maintainer: Martin Maechler
DESCRIPTION | 9 +-
MD5 | 8 +-
R/drqssbc.R | 10 +-
data/globtemp.rda |binary
src/drqssbc.f | 216 +++++++++++++++++++++++++++++-------------------------
5 files changed, 131 insertions(+), 112 deletions(-)
Title: Statistical Disclosure Control methods for the production of
public- and scientific-use files.
Diff between sdcMicro versions 4.0.2 dated 2013-04-22 and 4.0.3 dated 2013-06-12
Description: Data from statistical agencies and other institutions are
mostly confidential. This package can be used for the
generation of anonymized (micro)data, i.e. for the creation of
public- and scientific-use files. The package sdcMicroGUI
includes a graphical user interface for the methods in this
package.
Author: Matthias Templ, Alexander Kowarik, Bernhard Meindl
Maintainer: Matthias Templ
sdcMicro-4.0.2/sdcMicro/vignettes/guidelines.R |only
sdcMicro-4.0.3/sdcMicro/DESCRIPTION | 10
sdcMicro-4.0.3/sdcMicro/MD5 | 133 ++--
sdcMicro-4.0.3/sdcMicro/NAMESPACE | 7
sdcMicro-4.0.3/sdcMicro/R/0classes.r | 2
sdcMicro-4.0.3/sdcMicro/R/LLmodGlobalRisk.R | 72 +-
sdcMicro-4.0.3/sdcMicro/R/aux_functions.r | 46 +
sdcMicro-4.0.3/sdcMicro/R/dRisk.R | 4
sdcMicro-4.0.3/sdcMicro/R/dUtility.R | 8
sdcMicro-4.0.3/sdcMicro/R/indivRisk.R | 4
sdcMicro-4.0.3/sdcMicro/R/localSuppression.R | 14
sdcMicro-4.0.3/sdcMicro/R/mafast.R |only
sdcMicro-4.0.3/sdcMicro/R/mdav.R | 8
sdcMicro-4.0.3/sdcMicro/R/measure_risk.R | 8
sdcMicro-4.0.3/sdcMicro/R/methods.r | 4
sdcMicro-4.0.3/sdcMicro/R/microaggregation.R | 37 -
sdcMicro-4.0.3/sdcMicro/R/pram.r | 10
sdcMicro-4.0.3/sdcMicro/R/pram_strata.R | 35 -
sdcMicro-4.0.3/sdcMicro/R/rankSwap.R | 34 -
sdcMicro-4.0.3/sdcMicro/R/report.R | 468 ++++++++--------
sdcMicro-4.0.3/sdcMicro/R/shuffle.R | 19
sdcMicro-4.0.3/sdcMicro/R/timeEstimation.R | 2
sdcMicro-4.0.3/sdcMicro/R/topBotCoding.R | 41 -
sdcMicro-4.0.3/sdcMicro/R/valTable.R | 2
sdcMicro-4.0.3/sdcMicro/data/CASCrefmicrodata.rda |binary
sdcMicro-4.0.3/sdcMicro/data/EIA.rda |binary
sdcMicro-4.0.3/sdcMicro/data/Tarragona.rda |binary
sdcMicro-4.0.3/sdcMicro/data/casc1.rda |binary
sdcMicro-4.0.3/sdcMicro/data/francdat.rda |binary
sdcMicro-4.0.3/sdcMicro/data/free1.rda |binary
sdcMicro-4.0.3/sdcMicro/data/microData.rda |binary
sdcMicro-4.0.3/sdcMicro/data/testdata.RData |binary
sdcMicro-4.0.3/sdcMicro/data/testdata2.RData |binary
sdcMicro-4.0.3/sdcMicro/inst/doc/guidelines.R |only
sdcMicro-4.0.3/sdcMicro/inst/doc/guidelines.pdf |binary
sdcMicro-4.0.3/sdcMicro/inst/doc/sdcMicroPaper.R |only
sdcMicro-4.0.3/sdcMicro/inst/doc/sdcMicroPaper.pdf |binary
sdcMicro-4.0.3/sdcMicro/man/LLmodGlobalRisk.Rd | 26
sdcMicro-4.0.3/sdcMicro/man/LocalRecProg.Rd | 25
sdcMicro-4.0.3/sdcMicro/man/addNoise.Rd | 11
sdcMicro-4.0.3/sdcMicro/man/calcRisks.Rd | 5
sdcMicro-4.0.3/sdcMicro/man/dRisk.Rd | 5
sdcMicro-4.0.3/sdcMicro/man/dRiskRMD.Rd | 5
sdcMicro-4.0.3/sdcMicro/man/dUtility.Rd | 5
sdcMicro-4.0.3/sdcMicro/man/dataGen.Rd | 5
sdcMicro-4.0.3/sdcMicro/man/extractManipData-methods.Rd |only
sdcMicro-4.0.3/sdcMicro/man/globalRecode.Rd | 5
sdcMicro-4.0.3/sdcMicro/man/groupVars-methods.Rd | 5
sdcMicro-4.0.3/sdcMicro/man/localSupp.Rd | 8
sdcMicro-4.0.3/sdcMicro/man/localSupp2.Rd | 3
sdcMicro-4.0.3/sdcMicro/man/localSupp2Wrapper.Rd | 3
sdcMicro-4.0.3/sdcMicro/man/localSuppression.Rd | 11
sdcMicro-4.0.3/sdcMicro/man/mafast.Rd |only
sdcMicro-4.0.3/sdcMicro/man/measure_risk.Rd | 67 +-
sdcMicro-4.0.3/sdcMicro/man/microaggregation.Rd | 17
sdcMicro-4.0.3/sdcMicro/man/pram.Rd | 14
sdcMicro-4.0.3/sdcMicro/man/pram_strata.Rd | 43 -
sdcMicro-4.0.3/sdcMicro/man/print.sdcMicroObj.Rd | 20
sdcMicro-4.0.3/sdcMicro/man/rankSwap.Rd | 10
sdcMicro-4.0.3/sdcMicro/man/renameVars-methods.Rd | 5
sdcMicro-4.0.3/sdcMicro/man/report.Rd | 13
sdcMicro-4.0.3/sdcMicro/man/sdcMicro-deprecated.Rd | 6
sdcMicro-4.0.3/sdcMicro/man/sdcMicro-package.Rd | 29
sdcMicro-4.0.3/sdcMicro/man/sdcMicroObj-class.Rd | 8
sdcMicro-4.0.3/sdcMicro/man/shuffle.Rd | 9
sdcMicro-4.0.3/sdcMicro/man/suda2.Rd | 5
sdcMicro-4.0.3/sdcMicro/man/topBotCoding.Rd | 7
sdcMicro-4.0.3/sdcMicro/man/valTable.Rd | 17
sdcMicro-4.0.3/sdcMicro/man/varToFactor-methods.Rd | 5
sdcMicro-4.0.3/sdcMicro/src/Measure_Risk.h | 15
sdcMicro-4.0.3/sdcMicro/vignettes/guidelines.tex |only
71 files changed, 772 insertions(+), 608 deletions(-)
Title: BEFdata R package
Diff between rbefdata versions 0.3 dated 2013-06-09 and 0.3.1 dated 2013-06-12
Description: Basic R package to access the data structures offered by
the BEFdata portal.
Author: Claas-Thido Pfaff
Maintainer: Claas-Thido Pfaff
DESCRIPTION | 15 ++++++++-------
MD5 | 6 +++---
NEWS | 5 +++++
R/zzz.R | 2 +-
4 files changed, 17 insertions(+), 11 deletions(-)
Title: Survival Regression with Smoothed Error Distribution
Diff between smoothSurv versions 1.2.1 dated 2013-03-29 and 1.3-2 dated 2013-06-12
Description: This package contains primarily a function to fit a
regression model with possibly right, left or interval censored
observations and with the error distribution expressed as a
mixture of G-splines. Core part of the computation is done in
compiled C++ written using the Scythe Statistical Library
Version 0.3.
Author: Arnošt Komárek
Maintainer: Arnošt Komárek
DESCRIPTION | 12 ++++++------
MD5 | 20 ++++++++++----------
R/minPenalty.R | 12 +++---------
R/smoothSurvReg.fit.R | 8 ++------
man/smoothSurvReg.Rd | 6 +++---
man/smoothSurvReg.control.Rd | 6 ++++--
src/AKmatrix.cpp | 6 +++---
src/Scythe_Error.h | 23 +++++++++++++++++++----
src/convertCAD.h | 6 +++---
src/penalLogLik.h | 6 +++---
src/smoothSurvReg84.h | 6 +++---
11 files changed, 59 insertions(+), 52 deletions(-)
Title: Spatially explicit capture-recapture
Diff between secr versions 2.5.0 dated 2013-01-23 and 2.6.0 dated 2013-06-12
Description: Functions to estimate the density and size of a spatially
distributed animal population sampled with an array of passive
detectors, such as traps, or by searching polygons or
transects. Models incorporating distance-dependent detection
are fitted by maximizing the likelihood. Tools are included for
data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford
secr-2.5.0/secr/LICENSE |only
secr-2.6.0/secr/DESCRIPTION | 14
secr-2.6.0/secr/MD5 | 165 +--
secr-2.6.0/secr/NEWS | 959 ++-------------------
secr-2.6.0/secr/ONEWS | 854 ++++++++++++++++++
secr-2.6.0/secr/R/ClosedN.R | 6
secr-2.6.0/secr/R/D.designdata.R | 3
secr-2.6.0/secr/R/autoini.R | 3
secr-2.6.0/secr/R/circular.R | 97 +-
secr-2.6.0/secr/R/confint.secr.R | 2
secr-2.6.0/secr/R/esa.R | 13
secr-2.6.0/secr/R/fxi.R | 1
secr-2.6.0/secr/R/mask.check.R | 3
secr-2.6.0/secr/R/methods.R | 195 ++--
secr-2.6.0/secr/R/model.average.R | 100 +-
secr-2.6.0/secr/R/onAttach.R | 6
secr-2.6.0/secr/R/pdot.R | 6
secr-2.6.0/secr/R/plot.secr.R | 26
secr-2.6.0/secr/R/regionN.R | 11
secr-2.6.0/secr/R/score.test.R | 16
secr-2.6.0/secr/R/secr.design.MS.R | 236 +++--
secr-2.6.0/secr/R/secr.fit.R | 194 ++--
secr-2.6.0/secr/R/secr.make.newdata.R | 5
secr-2.6.0/secr/R/secrloglik.R | 69 -
secr-2.6.0/secr/R/sim.capthist.R | 83 +
secr-2.6.0/secr/R/sim.secr.R | 4
secr-2.6.0/secr/R/suggest.buffer.R | 19
secr-2.6.0/secr/R/telemetry.R | 16
secr-2.6.0/secr/R/trap.builder.R | 104 +-
secr-2.6.0/secr/R/utility.R | 373 +++++---
secr-2.6.0/secr/R/verify.R | 68 +
secr-2.6.0/secr/data/deermouse.RData |binary
secr-2.6.0/secr/data/hornedlizard.RData |binary
secr-2.6.0/secr/data/housemouse.RData |binary
secr-2.6.0/secr/data/ovenbird.RData |binary
secr-2.6.0/secr/data/ovensong.RData |binary
secr-2.6.0/secr/data/possum.RData |binary
secr-2.6.0/secr/data/secrdemo.RData |binary
secr-2.6.0/secr/data/skink.RData |binary
secr-2.6.0/secr/data/stoatDNA.RData |binary
secr-2.6.0/secr/inst/doc/secr-datainput.pdf |binary
secr-2.6.0/secr/inst/doc/secr-finitemixtures.pdf |binary
secr-2.6.0/secr/inst/doc/secr-manual.pdf |binary
secr-2.6.0/secr/inst/doc/secr-overview.pdf |binary
secr-2.6.0/secr/inst/doc/secr-polygondetectors.pdf |binary
secr-2.6.0/secr/inst/doc/secr-varyingeffort.pdf |binary
secr-2.6.0/secr/man/AIC.secr.Rd | 35
secr-2.6.0/secr/man/FAQ.Rd | 50 -
secr-2.6.0/secr/man/circular.Rd | 54 +
secr-2.6.0/secr/man/details.Rd |only
secr-2.6.0/secr/man/detectfn.Rd | 187 ++--
secr-2.6.0/secr/man/distancetotrap.Rd | 5
secr-2.6.0/secr/man/esaplot.Rd | 2
secr-2.6.0/secr/man/esaplotsecr.Rd | 2
secr-2.6.0/secr/man/ip.secr.Rd | 2
secr-2.6.0/secr/man/make.mask.Rd | 2
secr-2.6.0/secr/man/make.systematic.Rd | 2
secr-2.6.0/secr/man/model.average.Rd | 49 -
secr-2.6.0/secr/man/ovensong.Rd | 2
secr-2.6.0/secr/man/pdot.Rd | 2
secr-2.6.0/secr/man/plot.capthist.Rd | 4
secr-2.6.0/secr/man/plot.secr.Rd | 2
secr-2.6.0/secr/man/predict.secr.Rd | 30
secr-2.6.0/secr/man/rbind.capthist.Rd | 4
secr-2.6.0/secr/man/read.mask.Rd | 9
secr-2.6.0/secr/man/region.N.Rd | 5
secr-2.6.0/secr/man/score.test.Rd | 9
secr-2.6.0/secr/man/secr-package.Rd | 14
secr-2.6.0/secr/man/secr.design.MS.Rd | 57 +
secr-2.6.0/secr/man/secr.fit.Rd | 93 --
secr-2.6.0/secr/man/sim.capthist.Rd | 16
secr-2.6.0/secr/man/speed.Rd |only
secr-2.6.0/secr/man/stoatDNA.Rd | 2
secr-2.6.0/secr/man/subset.capthist.Rd | 15
secr-2.6.0/secr/man/suggest.buffer.Rd | 10
secr-2.6.0/secr/man/trap.builder.Rd | 31
secr-2.6.0/secr/man/troubleshooting.Rd | 18
secr-2.6.0/secr/man/usage.Rd | 8
secr-2.6.0/secr/man/usagePlot.Rd | 2
secr-2.6.0/secr/man/verify.Rd | 3
secr-2.6.0/secr/man/writeGPS.Rd | 2
secr-2.6.0/secr/src/detectfn.c | 142 ++-
secr-2.6.0/secr/src/secr.c | 388 ++++++--
secr-2.6.0/secr/src/secr.h | 30
secr-2.6.0/secr/src/trapping.c | 30
85 files changed, 3052 insertions(+), 1917 deletions(-)
Title: Gini methodology-based correlation and clustering analysis of
microarray and RNA-Seq gene expression data
Diff between rsgcc versions 1.0.4 dated 2012-09-22 and 1.0.5 dated 2013-06-12
Description: This package provides functions for calculating
associations between two genes with five correlation
methods(e.g., the Gini correlation coefficient [GCC], the
Pearson's product moment correlation coefficient [PCC], the
Kendall tau rank correlation coefficient [KCC], the Spearman's
rank correlation coefficient [SCC] and the Tukey's biweight
correlation coefficient [BiWt], and three non-correlation
methods (e.g., mutual information [MI] and the maximal
information-based nonparametric exploration [MINE], and the
euclidean distance [ED]). It can also been implemented to
perform the correlation and clustering analysis of
transcriptomic data profiled by microarray and RNA-Seq
technologies. Additionally, this package can be further applied
to construct gene co-expression networks (GCNs).
Author: Chuang Ma, Xiangfeng Wang
Maintainer: Chuang Ma
DESCRIPTION | 40 +++++-----
MD5 | 40 +++++-----
R/getdist.R | 7 +
R/gethclust.R | 11 +-
R/rsgcc.R | 193 ++++++++++++++++++++++++++++++++++++-------------
R/rsgccgui.R | 14 +--
R/tsgene.R | 97 +++++++++++++++---------
R/tsheatmap.R | 19 ++--
data/rsgcc.rda |binary
man/adjacencymatrix.Rd | 48 +++++++++---
man/gcc.corfinal.Rd | 3
man/gcc.dist.Rd | 7 -
man/gcc.hclust.Rd | 9 +-
man/gcc.heatmap.Rd | 8 +-
man/gcc.tsheatmap.Rd | 12 +--
man/getsgene.Rd | 15 ++-
man/rsgcc-package.Rd | 13 ++-
man/uniqueTissues.Rd | 4 +
src/bridge.c | 83 ++++++++++++++++++---
src/mi.c | 108 +++++++--------------------
src/mi.h | 2
21 files changed, 464 insertions(+), 269 deletions(-)
Title: publication-quality graphics.
Diff between prettyGraphs versions 1.0 dated 2012-06-19 and 2.0.3 dated 2013-06-12
Description: prettyGraphs contains simple, crisp graphics. Graphics
produced by prettyGraphs are publication-quality.
Author: Derek Beaton
Maintainer: Derek Beaton
prettyGraphs-1.0/prettyGraphs/R/colorPoints.R |only
prettyGraphs-1.0/prettyGraphs/R/createOriginalPointList.R |only
prettyGraphs-1.0/prettyGraphs/R/createOriginalPointsAndColors.R |only
prettyGraphs-1.0/prettyGraphs/R/createSingleColorVector.R |only
prettyGraphs-1.0/prettyGraphs/R/makeNewPlotWindow.R |only
prettyGraphs-1.0/prettyGraphs/R/prettyGraphs-internal.R |only
prettyGraphs-2.0.3/prettyGraphs/DESCRIPTION | 11 -
prettyGraphs-2.0.3/prettyGraphs/MD5 | 51 ++---
prettyGraphs-2.0.3/prettyGraphs/NAMESPACE | 2
prettyGraphs-2.0.3/prettyGraphs/R/colorVectorIsNull.R | 4
prettyGraphs-2.0.3/prettyGraphs/R/contributionBars.R | 80 ++++----
prettyGraphs-2.0.3/prettyGraphs/R/correlationPlotter.R | 44 ++--
prettyGraphs-2.0.3/prettyGraphs/R/createColorVectorsByDesign.R | 19 +
prettyGraphs-2.0.3/prettyGraphs/R/makeAxes.R |only
prettyGraphs-2.0.3/prettyGraphs/R/minmaxHelper.R | 50 +++--
prettyGraphs-2.0.3/prettyGraphs/R/plotCircle.R | 11 -
prettyGraphs-2.0.3/prettyGraphs/R/plotPoints.R | 77 ++++----
prettyGraphs-2.0.3/prettyGraphs/R/plotText.R | 22 +-
prettyGraphs-2.0.3/prettyGraphs/R/prettyBars.R |only
prettyGraphs-2.0.3/prettyGraphs/R/prettyGraphsColorSelection.R |only
prettyGraphs-2.0.3/prettyGraphs/R/prettyGraphsColors.R | 1
prettyGraphs-2.0.3/prettyGraphs/R/prettyGraphsHSVColorSelection.R |only
prettyGraphs-2.0.3/prettyGraphs/R/prettyPlot.R | 96 +++++++---
prettyGraphs-2.0.3/prettyGraphs/man/contributionBars.Rd | 13 -
prettyGraphs-2.0.3/prettyGraphs/man/correlationPlotter.Rd | 13 +
prettyGraphs-2.0.3/prettyGraphs/man/createColorVectorsByDesign.Rd | 8
prettyGraphs-2.0.3/prettyGraphs/man/minmaxHelper.Rd | 5
prettyGraphs-2.0.3/prettyGraphs/man/peeledHull.Rd | 3
prettyGraphs-2.0.3/prettyGraphs/man/prettyBars.Rd |only
prettyGraphs-2.0.3/prettyGraphs/man/prettyGraphs-package.Rd | 4
prettyGraphs-2.0.3/prettyGraphs/man/prettyGraphsColorSelection.Rd |only
prettyGraphs-2.0.3/prettyGraphs/man/prettyGraphsHSVColorSelection.Rd |only
prettyGraphs-2.0.3/prettyGraphs/man/prettyPlot.Rd | 76 +++++--
33 files changed, 356 insertions(+), 234 deletions(-)
More information about migration.indices at CRAN
Permanent link
Title: Visualizing Generalized Canonical Discriminant and Canonical
Correlation Analysis
Diff between candisc versions 0.6-3 dated 2013-03-15 and 0.6-5 dated 2013-06-12
Description: This package includes functions for computing and
visualizing generalized canonical discriminant analyses and
canonical correlation analysis for a multivariate linear model.
Traditional canonical discriminant analysis is restricted to a
one-way MANOVA design and is equivalent to canonical
correlation analysis between a set of quantitative response
variables and a set of dummy variables coded from the factor
variable. The candisc package generalizes this to multi-way
MANOVA designs for all factors in a multivariate linear model,
computing canonical scores and vectors for each term. The
graphic functions provide low-rank (1D, 2D, 3D) visualizations
of terms in an mlm via the plot.candisc and heplot.candisc
methods. Related plots are now provided for canonical
correlation analysis when all predictors are quantitative.
Author: Michael Friendly and John Fox
Maintainer: Michael Friendly
DESCRIPTION | 12 ++++++------
MD5 | 20 ++++++++++----------
NEWS | 9 +++++++++
R/cancor.R | 9 +++++----
R/candisc.R | 5 +++++
R/plot.candisc.R | 22 ++++++++++++----------
data/Grass.rda |binary
data/HSB.rda |binary
data/Wolves.rda |binary
man/cancor.Rd | 5 +++--
man/candisc-package.Rd | 4 ++--
11 files changed, 52 insertions(+), 34 deletions(-)