Title: Target Inhibition Interaction using Maximization and
Minimization Averaging
Diff between timma versions 1.2.0 dated 2015-01-11 and 1.2.1 dated 2015-02-28
Description: Prediction and ranking of drug combinations based on their drug-target interaction profiles and single-drug sensitivities in a given cancer cell line or patient-derived sample.
Author: Liye He, Krister Wennerberg, Tero Aittokallio and Jing Tang
Maintainer: Jing Tang
DESCRIPTION | 17 +++-----
MD5 | 70 +++++++++++++++++-----------------
NAMESPACE | 1
R/binarizeDrugTargets.R | 8 +--
R/drawGraph.R | 70 ++++++++++++++++++----------------
R/drugRank.R | 27 ++++++-------
R/normalizeSensitivity.R | 2
R/sffsBinary.R | 2
R/sffsCategory.R | 2
R/sffsCategory1.R | 2
R/sffsCategoryWeighted.R | 2
R/sffsCategoryWeighted1.R | 2
R/targetRank.R |only
R/timma.R | 44 +++++++++------------
build/vignette.rds |binary
data/ci.rda |binary
data/davis.rda |binary
data/kiba.rda |binary
data/miller_drug_response.rda |binary
data/miller_drugs.rda |binary
data/miller_interaction_binary.rda |binary
data/miller_sensitivity.rda |binary
data/tyner_interaction_binary.rda |binary
data/tyner_interaction_multiclass.rda |binary
data/tyner_sensitivity.rda |binary
inst/doc/timma.pdf |binary
man/binarizeDrugTargets.Rd | 2
man/drawGraph.Rd | 6 +-
man/drugRank.Rd | 2
man/normalizeSensitivity.Rd | 2
man/sffsBinary.Rd | 2
man/sffsCategory.Rd | 2
man/sffsCategory1.Rd | 2
man/sffsCategoryWeighted.Rd | 2
man/sffsCategoryWeighted1.Rd | 2
man/targetRank.Rd |only
man/timma.Rd | 12 -----
37 files changed, 139 insertions(+), 144 deletions(-)
Title: Spatially-Explicit Power Analysis for Conservation and Ecology
Diff between rSPACE versions 1.0.4 dated 2015-01-06 and 1.1.0 dated 2015-02-28
Description: Conducts a spatially-explicit, simulation-based power analysis for detecting trends in population abundance through occupancy-based modeling. Applicable for evaluating monitoring designs in conservation and ecological settings.
Author: Martha Ellis, Jake Ivan, Jody Tucker, Mike Schwartz
Maintainer: Martha Ellis
DESCRIPTION | 8 ++++----
MD5 | 34 +++++++++++++++++-----------------
R/ClickyBox.r | 6 ++----
R/Create_Landscapes.r | 8 ++++++--
R/Encounter_history.R | 12 +++++++-----
R/PlottingFunctions.r | 12 +++++++++---
R/Test_Samples.r | 29 +++++++----------------------
R/Test_file.r | 23 +++++++++++++++++------
R/checkParameters.R | 20 +++++++++++++++-----
R/createGrid.R | 47 ++++++++++++++++++++++++++++++++---------------
man/create.landscapes.Rd | 12 +++++++-----
man/encounter.history.Rd | 6 ++++--
man/enter.parameters.Rd | 6 ++++--
man/find.power.Rd | 8 +++++---
man/plot.results.Rd | 31 ++++++++++++++++++++++++++++++-
man/rSPACE-package.Rd | 16 ++++++++--------
man/test_file.Rd | 6 ++++--
man/test_samples.Rd | 35 ++++++++++++++++++++++++++++++-----
18 files changed, 208 insertions(+), 111 deletions(-)
Title: High-Dimensional Kernel Density Estimation and Geometry
Operations
Diff between hypervolume versions 1.1.2 dated 2015-01-16 and 1.2 dated 2015-02-28
Description: Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and negative feature detection. Uses stochastic geometry approach to high-dimensional kernel density estimation. Builds n-dimensional convex hulls (polytopes). Can measure the n-dimensional ecological hypervolume and perform species distribution modeling.
Author: Benjamin Blonder
Maintainer: Benjamin Blonder
DESCRIPTION | 10 +++----
MD5 | 10 +++----
NAMESPACE | 11 +++++++-
R/hypervolume_plot.R | 58 +++++++++++++++++++++++++++++++++++++++++++--
man/hypervolume-package.Rd | 38 -----------------------------
man/plot.Hypervolume.Rd | 43 +++++++++++++++++++++++----------
6 files changed, 107 insertions(+), 63 deletions(-)
Title: Tools for Spatial Data
Diff between fields versions 7.1 dated 2014-05-16 and 8.2-1 dated 2015-02-28
Description: Fields is for curve, surface and function
fitting with an emphasis on splines, spatial data and spatial
statistics. The major methods include cubic, and thin plate splines,
Kriging and compact covariances for large data sets. The splines and
Kriging methods are supporting by functions that can determine the
smoothing parameter (nugget and sill variance) by cross validation
and also by restricted maximum likelihood. For Kriging there is
an easy to function that also estimates the correlation scale (range).
A major feature is that
any covariance function implemented in R and following a simple fields
format can be used for spatial prediction. There are also many useful
functions for plotting and
working with spatial data as images. This package also contains an
implementation of sparse matrix methods for large spatial data sets and
currently requires the sparse matrix (spam) package.
Use help(fields) to get started and for an
overview. The fields source code is deliberately commented and
provides useful explanations of numerical details in addition to the
manual pages. The commented source code can be viewed by expanding the
source code .tar.gz file and looking in R subdirectory.
Author: Douglas Nychka [aut, cre], Reinhard Furrer [aut], Stephan Sain [aut]
Maintainer: Douglas Nychka
fields-7.1/fields/R/Krig.R |only
fields-8.2-1/fields/DESCRIPTION | 29 -
fields-8.2-1/fields/MD5 | 137 ++++----
fields-8.2-1/fields/NAMESPACE | 46 ++
fields-8.2-1/fields/R/Krig.family.R | 110 ++-----
fields-8.2-1/fields/R/MLESpatialProcess.R |only
fields-8.2-1/fields/R/MLESpatialProcess.fast.R |only
fields-8.2-1/fields/R/Tps.R | 25 -
fields-8.2-1/fields/R/as.image.R | 4
fields-8.2-1/fields/R/discretize.image.R | 13
fields-8.2-1/fields/R/fastTps.family.R | 12
fields-8.2-1/fields/R/fitted.Krig.R | 2
fields-8.2-1/fields/R/gcv.Krig.R | 217 +++++++-------
fields-8.2-1/fields/R/gcv.sreg.R |only
fields-8.2-1/fields/R/image.family.R | 102 ++++++
fields-8.2-1/fields/R/image.plot.R | 114 +++----
fields-8.2-1/fields/R/plot.Krig.R | 16 -
fields-8.2-1/fields/R/plot.spatialProcess.R |only
fields-8.2-1/fields/R/predict.interp.surface.R | 25 -
fields-8.2-1/fields/R/print.Krig.R | 7
fields-8.2-1/fields/R/print.summary.spatialProcess.R |only
fields-8.2-1/fields/R/printGCVWarnings.R |only
fields-8.2-1/fields/R/quickPrint.R |only
fields-8.2-1/fields/R/quilt.plot.R | 6
fields-8.2-1/fields/R/sim.Krig.R | 6
fields-8.2-1/fields/R/sim.Krig.approx.R | 6
fields-8.2-1/fields/R/sim.mKrig.approx.R | 6
fields-8.2-1/fields/R/spatialProcess.R |only
fields-8.2-1/fields/R/sreg.family.R | 163 ----------
fields-8.2-1/fields/R/stationary.image.cov.R | 1
fields-8.2-1/fields/R/summary.spatialProcess.R |only
fields-8.2-1/fields/R/surface.family.R | 8
fields-8.2-1/fields/man/Krig.Rd | 19 -
fields-8.2-1/fields/man/Krig.replicates.Rd |only
fields-8.2-1/fields/man/MLESpatialProcess.Rd |only
fields-8.2-1/fields/man/QTps.Rd | 4
fields-8.2-1/fields/man/Tps.Rd | 20 -
fields-8.2-1/fields/man/fields-internal.Rd | 30 -
fields-8.2-1/fields/man/fields.Rd | 83 +++--
fields-8.2-1/fields/man/gcv.Krig.Rd | 40 +-
fields-8.2-1/fields/man/image.plot.Rd | 105 +++---
fields-8.2-1/fields/man/mKrig.MLE.Rd | 3
fields-8.2-1/fields/man/plot.Krig.Rd | 23 +
fields-8.2-1/fields/man/quilt.plot.Rd | 4
fields-8.2-1/fields/man/sim.Krig.Rd | 62 +++-
fields-8.2-1/fields/man/sim.rf.Rd | 26 -
fields-8.2-1/fields/man/spatialProcess.Rd |only
fields-8.2-1/fields/man/summary.Krig.Rd | 10
fields-8.2-1/fields/tests/Krig.Z.test.Rout.save | 8
fields-8.2-1/fields/tests/Krig.se.W.Rout.save | 8
fields-8.2-1/fields/tests/Krig.se.grid.test.Rout.save | 14
fields-8.2-1/fields/tests/Krig.se.test.Rout.save | 14
fields-8.2-1/fields/tests/Krig.test.R | 68 +---
fields-8.2-1/fields/tests/Krig.test.Rout.save | 40 +-
fields-8.2-1/fields/tests/Krig.test.W.Rout.save | 20 +
fields-8.2-1/fields/tests/KrigGCVREML.test.R |only
fields-8.2-1/fields/tests/KrigGCVREML.test.Rout.save |only
fields-8.2-1/fields/tests/Likelihood.test.Rout.save | 8
fields-8.2-1/fields/tests/REMLest.test.R | 28 +
fields-8.2-1/fields/tests/REMLest.test.Rout.save | 10
fields-8.2-1/fields/tests/Tps.test.R | 2
fields-8.2-1/fields/tests/Tps.test.Rout.save | 19 -
fields-8.2-1/fields/tests/Wend.test.Rout.save | 8
fields-8.2-1/fields/tests/cov.test.Rout.save | 8
fields-8.2-1/fields/tests/derivative.test.Rout.save | 30 -
fields-8.2-1/fields/tests/diag.multiply.test.Rout.save | 8
fields-8.2-1/fields/tests/diagonal2.test.Rout.save | 8
fields-8.2-1/fields/tests/evlpoly.test.Rout.save | 8
fields-8.2-1/fields/tests/mKrig.Z.Rout.save | 8
fields-8.2-1/fields/tests/mKrig.parameters.test.Rout.save | 15
fields-8.2-1/fields/tests/mKrig.se.test.Rout.save | 8
fields-8.2-1/fields/tests/mKrig.test.Rout.save | 8
fields-8.2-1/fields/tests/misc.test.Rout.save | 8
fields-8.2-1/fields/tests/spam.test.Rout.save | 8
fields-8.2-1/fields/tests/sreg.test.R | 6
fields-8.2-1/fields/tests/sreg.test.Rout.save | 14
fields-8.2-1/fields/tests/vgram.test.Rout.save | 8
77 files changed, 961 insertions(+), 915 deletions(-)
Title: Extreme Bounds Analysis (EBA)
Diff between ExtremeBounds versions 0.1.4.2 dated 2014-11-18 and 0.1.5 dated 2015-02-28
Description: An implementation of Extreme Bounds Analysis (EBA), a global sensitivity analysis that examines the robustness of determinants in regression models. The package supports both Leamer's and Sala-i-Martin's versions of EBA, and allows users to customize all aspects of the analysis.
Author: Marek Hlavac
Maintainer: Marek Hlavac
DESCRIPTION | 8 ++--
MD5 | 32 ++++++++--------
NAMESPACE | 7 ++-
R/ExtremeBounds-internal.R | 4 +-
build/vignette.rds |binary
inst/CITATION | 6 +--
inst/ChangeLog | 4 ++
inst/doc/ExtremeBounds.Rtex | 86 +++++++++++++++++++++++--------------------
inst/doc/ExtremeBounds.pdf |binary
man/ExtremeBounds.Rd | 4 +-
man/eba.Rd | 6 +--
man/hist.eba.Rd | 4 +-
man/print.eba.Rd | 4 +-
vignettes/ExtremeBounds.Rtex | 86 +++++++++++++++++++++++--------------------
vignettes/ExtremeBounds.bib | 60 +++++++++++++++++++++++-------
vignettes/naive.pdf |binary
vignettes/sophisticated.pdf |binary
17 files changed, 184 insertions(+), 127 deletions(-)
Title: Substitution and Indel Distances to Infer Evolutionary
Relationships
Diff between sidier versions 3.0 dated 2014-11-18 and 3.0.1 dated 2015-02-27
Description: Evolutionary reconstruction based on substitutions and insertion-deletion (indels) analyses in a distance-based framework.
Author: A. Jesus Muñoz Pajares
Maintainer: A.J. Muñoz-Pajares
DESCRIPTION | 12 +++++------
MD5 | 22 ++++++++++-----------
NEWS | 10 +++++++++
R/double.plot.R | 30 +++++++++++++++++-----------
R/mutation.network.R | 10 +++++----
R/perc.thr.R | 9 ++++----
R/pie.network.R | 8 ++++---
R/spatial.plot.R | 51 +++++++++++++++++++++++++++++++------------------
data/ex_alignment1.rda |binary
man/double.plot.Rd | 38 ++++++++++++++++++++++++------------
man/sidier-package.Rd | 6 ++---
man/spatial.plot.Rd | 14 +++++++------
12 files changed, 131 insertions(+), 79 deletions(-)
Title: R Object-Oriented Programming with or without References
Diff between R.oo versions 1.18.0 dated 2014-02-25 and 1.19.0 dated 2015-02-27
Description: Methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers. The package has been developed since 2001 and is now considered very stable. This is a cross-platform package implemented in pure R that defines standard S3 classes without any tricks.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson
R.oo-1.18.0/R.oo/tests/Object.finalize,reentrant.R |only
R.oo-1.19.0/R.oo/DESCRIPTION | 14 -
R.oo-1.19.0/R.oo/MD5 | 75 +++++---
R.oo-1.19.0/R.oo/NAMESPACE | 7
R.oo-1.19.0/R.oo/NEWS | 44 ++++
R.oo-1.19.0/R.oo/R/050.Object.R | 58 +-----
R.oo-1.19.0/R.oo/R/060.Class.R | 22 +-
R.oo-1.19.0/R.oo/R/999.DEPRECATED.R | 86 +++++++++
R.oo-1.19.0/R.oo/R/ASCII.R | 8
R.oo-1.19.0/R.oo/R/Class.misc.R | 55 ++----
R.oo-1.19.0/R.oo/R/Package.R | 128 --------------
R.oo-1.19.0/R.oo/R/Rdoc.R | 46 ++++-
R.oo-1.19.0/R.oo/R/abort.R | 4
R.oo-1.19.0/R.oo/R/ll.default.R | 9
R.oo-1.19.0/R.oo/R/objectSize.default.R | 8
R.oo-1.19.0/R.oo/R/objectSize.environment.R | 40 +++-
R.oo-1.19.0/R.oo/R/zzz.R | 2
R.oo-1.19.0/R.oo/man/Class.Rd | 3
R.oo-1.19.0/R.oo/man/RccViolationException.Rd | 4
R.oo-1.19.0/R.oo/man/charToInt.Rd | 2
R.oo-1.19.0/R.oo/man/gc.Object.Rd | 16 +
R.oo-1.19.0/R.oo/man/intToChar.Rd | 2
R.oo-1.19.0/R.oo/man/ll.Rd | 5
R.oo-1.19.0/R.oo/man/registerFinalizer.Object.Rd | 8
R.oo-1.19.0/R.oo/man/update.Package.Rd | 16 -
R.oo-1.19.0/R.oo/tests/ASCII.R |only
R.oo-1.19.0/R.oo/tests/BasicObject.R |only
R.oo-1.19.0/R.oo/tests/Class.R |only
R.oo-1.19.0/R.oo/tests/Exception.R |only
R.oo-1.19.0/R.oo/tests/InternalErrorException.reportBug.R |only
R.oo-1.19.0/R.oo/tests/Object.R |only
R.oo-1.19.0/R.oo/tests/Object.finalize,noattach.R | 17 +
R.oo-1.19.0/R.oo/tests/Object.finalize,onoff.R | 34 ++-
R.oo-1.19.0/R.oo/tests/Object.finalize.R |only
R.oo-1.19.0/R.oo/tests/Package.R |only
R.oo-1.19.0/R.oo/tests/Package.unload.R |only
R.oo-1.19.0/R.oo/tests/StaticMethodsAndNamespaces.R | 3
R.oo-1.19.0/R.oo/tests/abort.R |only
R.oo-1.19.0/R.oo/tests/attachLocally.Object.R |only
R.oo-1.19.0/R.oo/tests/equals.R |only
R.oo-1.19.0/R.oo/tests/extend.default.R |only
R.oo-1.19.0/R.oo/tests/getConstructorS3.R |only
R.oo-1.19.0/R.oo/tests/isBeingCreated.Class.R |only
R.oo-1.19.0/R.oo/tests/ll.R |only
R.oo-1.19.0/R.oo/tests/local.R |only
R.oo-1.19.0/R.oo/tests/objectSize.R |only
R.oo-1.19.0/R.oo/tests/throw.R |only
R.oo-1.19.0/R.oo/tests/trim.R |only
R.oo-1.19.0/R.oo/tests/typeOfClass.R |only
R.oo-1.19.0/R.oo/tests/zzz.Object.finalize,reentrant.R |only
50 files changed, 417 insertions(+), 299 deletions(-)
Title: Basic Functions for Power Analysis
Diff between pwr versions 1.1.1 dated 2009-10-26 and 1.1-2 dated 2015-02-27
Description: Power analysis functions along the lines of Cohen (1988).
Author: Stephane Champely [aut],
Claus Ekstrom [ctb],
Peter Dalgaard [ctb],
Jeffrey Gill [ctb],
Helios De Rosario [cre]
Maintainer: Helios De Rosario
ChangeLog |only
DESCRIPTION | 32 ++++++----
MD5 |only
NAMESPACE |only
R/ES.h.R | 10 +--
R/ES.w1.R | 10 +--
R/ES.w2.R | 16 ++---
R/cohen.ES.R | 58 +++++++++---------
R/pwr.2p.test.R | 128 ++++++++++++++++++++---------------------
R/pwr.2p2n.test.R | 140 ++++++++++++++++++++++-----------------------
R/pwr.anova.test.R | 88 ++++++++++++++--------------
R/pwr.chisq.test.R | 76 ++++++++++++------------
R/pwr.f2.test.R | 86 +++++++++++++--------------
R/pwr.norm.test.R | 124 ++++++++++++++++++++--------------------
R/pwr.p.test.R | 124 ++++++++++++++++++++--------------------
R/pwr.r.test.R | 142 +++++++++++++++++++++++-----------------------
R/pwr.t.test.R | 144 +++++++++++++++++++++++-----------------------
R/pwr.t2n.test.R | 154 +++++++++++++++++++++++++-------------------------
man/ES.h.Rd | 72 +++++++++++------------
man/ES.w1.Rd | 64 ++++++++++----------
man/ES.w2.Rd | 66 ++++++++++-----------
man/cohen.ES.Rd | 60 ++++++++++---------
man/pwr-package.Rd | 121 +++++++++++++++++++--------------------
man/pwr.2p.test.Rd | 100 ++++++++++++++++----------------
man/pwr.2p2n.test.Rd | 103 ++++++++++++++++-----------------
man/pwr.anova.test.Rd | 94 +++++++++++++++---------------
man/pwr.chisq.test.Rd | 102 ++++++++++++++++-----------------
man/pwr.f2.test.Rd | 82 +++++++++++++-------------
man/pwr.norm.test.Rd | 130 +++++++++++++++++++++---------------------
man/pwr.p.test.Rd | 107 +++++++++++++++++-----------------
man/pwr.r.test.Rd | 112 ++++++++++++++++++------------------
man/pwr.t.test.Rd | 130 +++++++++++++++++++++---------------------
man/pwr.t2n.test.Rd | 94 +++++++++++++++---------------
33 files changed, 1393 insertions(+), 1376 deletions(-)
Title: Designing Multi-Arm Multi-Stage Studies
Diff between MAMS versions 0.3 dated 2014-05-07 and 0.4 dated 2015-02-27
Description: Designing multi-arm multi-stage studies with normal endpoints and known variance.
Author: Thomas Jaki
Maintainer: Thomas Jaki
DESCRIPTION | 8 ++++----
MD5 | 16 ++++++++--------
NAMESPACE | 9 +++++++++
R/mams.R | 12 ++++++++++--
inst/NEWS | 6 +++++-
man/generic.Rd | 8 ++------
man/mams.Rd | 9 ++++-----
man/new.bounds.Rd | 3 ++-
man/step_down_mams.Rd | 6 +++---
9 files changed, 47 insertions(+), 30 deletions(-)
Title: Graph Estimation Based on Birth-Death MCMC Approach
Diff between BDgraph versions 2.15 dated 2015-01-23 and 2.16 dated 2015-02-27
Description: A general framework to perform Bayesian structure learning in undirected graphical models. The main target is high-dimensional data analysis wherein either continuous or discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi
BDgraph-2.15/BDgraph/src/bdmcmc.cpp |only
BDgraph-2.16/BDgraph/DESCRIPTION | 10 -
BDgraph-2.16/BDgraph/MD5 | 58 +++---
BDgraph-2.16/BDgraph/R/bdgraph.R | 258 ++++++++-------------------
BDgraph-2.16/BDgraph/R/bdgraph.npn.R | 24 +-
BDgraph-2.16/BDgraph/R/bdgraph.sim.R | 25 +-
BDgraph-2.16/BDgraph/R/compare.R | 60 ++++--
BDgraph-2.16/BDgraph/R/plotcoda.R | 2
BDgraph-2.16/BDgraph/R/select.R | 36 ++-
BDgraph-2.16/BDgraph/man/BDgraph-internal.Rd | 2
BDgraph-2.16/BDgraph/man/BDgraph-package.Rd | 8
BDgraph-2.16/BDgraph/man/I.g.Rd | 4
BDgraph-2.16/BDgraph/man/bdgraph.Rd | 10 -
BDgraph-2.16/BDgraph/man/bdgraph.npn.Rd | 6
BDgraph-2.16/BDgraph/man/bdgraph.sim.Rd | 6
BDgraph-2.16/BDgraph/man/compare.Rd | 33 +--
BDgraph-2.16/BDgraph/man/phat.Rd | 6
BDgraph-2.16/BDgraph/man/plot.bdgraph.Rd | 6
BDgraph-2.16/BDgraph/man/plot.simulate.Rd | 6
BDgraph-2.16/BDgraph/man/plotcoda.Rd | 6
BDgraph-2.16/BDgraph/man/plotroc.Rd | 8
BDgraph-2.16/BDgraph/man/print.bdgraph.Rd | 6
BDgraph-2.16/BDgraph/man/print.simulate.Rd | 6
BDgraph-2.16/BDgraph/man/prob.Rd | 6
BDgraph-2.16/BDgraph/man/rgwish.Rd | 8
BDgraph-2.16/BDgraph/man/rwish.Rd | 6
BDgraph-2.16/BDgraph/man/select.Rd | 6
BDgraph-2.16/BDgraph/man/summary.bdgraph.Rd | 11 -
BDgraph-2.16/BDgraph/man/surveyData.Rd | 8
BDgraph-2.16/BDgraph/man/traceplot.Rd | 6
BDgraph-2.16/BDgraph/src/BDgraph.cpp |only
31 files changed, 284 insertions(+), 353 deletions(-)
Title: Apache OpenNLP Tools Interface
Diff between openNLP versions 0.2-3 dated 2014-04-19 and 0.2-4 dated 2015-02-27
Description: An interface to the Apache OpenNLP tools (version 1.5.3).
The Apache OpenNLP library is a machine learning based toolkit for the
processing of natural language text written in Java.
It supports the most common NLP tasks, such as tokenization, sentence
segmentation, part-of-speech tagging, named entity extraction, chunking,
parsing, and coreference resolution.
See
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik
DESCRIPTION | 8 +++++---
MD5 | 14 +++++++-------
R/chunk.R | 4 +++-
R/ner.R | 5 ++++-
R/pos.R | 4 +++-
R/sentdetect.R | 4 +++-
R/tokenize.R | 4 +++-
R/utils.R | 3 ---
8 files changed, 28 insertions(+), 18 deletions(-)
Title: Performing Continuous-Time Microsimulation
Diff between MicSim versions 1.0.6 dated 2014-07-02 and 1.0.7 dated 2015-02-27
Description: This entry-level toolkit allows performing generic continuous-time microsimulation for a wide range of demograhic applications.
Author: Sabine Zinn
Maintainer: Sabine Zinn
DESCRIPTION | 14 +++++++-------
MD5 | 12 ++++++------
NAMESPACE | 6 +++---
R/micSim.r | 8 ++++----
inst/NEWS.Rd | 6 ++++++
man/MicSim-package.Rd | 12 +++---------
man/micSim.Rd | 7 -------
7 files changed, 29 insertions(+), 36 deletions(-)
Title: Data Mangement for Hydrology and Beyond Using the Observations
Data Model
Diff between RObsDat versions 14.12 dated 2014-12-29 and 15.02 dated 2015-02-27
Description: Data management in hydrology and other fields is facilitated with functions to enter and modify data in a database according to the Observations Data Model (ODM) standard by CUASHI (Consortium of Universities for the Advancement of Hydrologic Science). While this data model has been developed in hydrology, it is also useful for other fields. RObsDat helps in the setup of the database within one of the free database systems MariaDB, PostgreSQL or SQLite. It imports the controlled water vocabulary from the CUASHI web service and provides a smart interface between the analyst and the database: Already existing data entries are detected and duplicates avoided. The data import function converts different data table designs to make import simple. Cleaning and modifications of data are handled with a simple version control system. Variable and location names are treated in a user friendly way, accepting and processing multiple versions. When querying data from the database, it is stored in a spacetime objects within R for subsequent processing.
Author: Dominik Reusser
Maintainer: Dominik Reusser
DESCRIPTION | 10 ++++-----
MD5 | 36 ++++++++++++++++-----------------
R/addCV.R | 2 -
R/addDataValues.R | 2 -
R/addISOMetadata.R | 2 -
R/addOffsetType.R | 2 -
R/addQualityControlLevel.R | 2 -
R/addSite.R | 2 -
R/addSource.R | 2 -
R/addSpatialReferences.R | 2 -
R/addUnits.R | 2 -
R/addVariable.R | 2 -
R/class_stfdf.R | 4 +--
R/createST.R | 6 ++---
R/getDataValues.R | 2 -
R/h.m.R | 2 -
inst/doc/RObsDat_Einstiegstutorial.pdf |binary
inst/tests/test_various.R | 23 ++++++++++++++++++++-
vignettes/RObsDat.bib | 30 +++++++++++----------------
19 files changed, 75 insertions(+), 58 deletions(-)
Title: Extended Mixed Models Using Latent Classes and Latent Processes
Diff between lcmm versions 1.7.1 dated 2015-02-26 and 1.7.2 dated 2015-02-27
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method.
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima
DESCRIPTION | 8 +++---
MD5 | 20 +++++++--------
NEWS | 2 -
R/Jointlcmm.R | 12 ++++++++-
R/epoce.R | 66 +++++++++++++++++++++++++++++++++++++++++++++++-----
R/plot.predictY.R | 8 +++++-
THANKS | 4 ++-
man/epoce.Rd | 3 +-
man/lcmm-package.Rd | 4 +--
src/Makevars | 13 ++++------
src/predictCont.f90 | 6 ++--
11 files changed, 109 insertions(+), 37 deletions(-)
Title: Normalisation of Psychometric Tests
Diff between NormPsy versions 1.0.2 dated 2014-11-27 and 1.0.3 dated 2015-02-27
Description: Functions for normalizing psychometric test scores. The normalization aims at correcting the metrological properties of the psychometric tests such as the ceiling and floor effects and the curvilinearity (unequal interval scaling). Functions to compute and plot predictions in the natural scale of the psychometric test from the estimates of a linear mixed model estimated on the normalized scores are also provided.
Author: Cecile Proust-Lima, Viviane Philipps
Maintainer: Cecile Proust-Lima
DESCRIPTION | 16 ++++++++--------
MD5 | 6 +++---
R/predictMMSE.R | 6 +++---
man/NormPsy-package.Rd | 4 ++--
4 files changed, 16 insertions(+), 16 deletions(-)
Title: Finding Heterogeneous Treatment Effects
Diff between FindIt versions 0.4 dated 2015-02-07 and 0.5 dated 2015-02-27
Description: The heterogeneous treatment effect estimation procedure
proposed by Imai and Ratkovic (2013).
The proposed method is applicable, for
example, when selecting a small number of most (or least)
efficacious treatments from a large number of alternative
treatments as well as when identifying subsets of the
population who benefit (or are harmed by) a treatment of
interest. The method adapts the Support Vector Machine
classifier by placing separate LASSO constraints over the
pre-treatment parameters and causal heterogeneity parameters of
interest. This allows for the qualitative distinction between
causal and other parameters, thereby making the variable
selection suitable for the exploration of causal heterogeneity.
The package also contains the function, INT, which estimates
the average marginal treatment effect, the average treatment
combination effect, and the average marginal treatment interaction
effect proposed by Egami and Imai (2015).
Author: Naoki Egami
Maintainer: Naoki Egami
FindIt-0.4/FindIt/data/GerberGreen.tab.gz |only
FindIt-0.4/FindIt/data/LaLonde.tab.gz |only
FindIt-0.4/FindIt/data/datalist |only
FindIt-0.5/FindIt/DESCRIPTION | 20
FindIt-0.5/FindIt/MD5 | 36
FindIt-0.5/FindIt/NAMESPACE | 2
FindIt-0.5/FindIt/R/INT.R |only
FindIt-0.5/FindIt/R/SVMHet.R | 1839 ----------------------------
FindIt-0.5/FindIt/R/full.FindIt.R |only
FindIt-0.5/FindIt/R/makeallway.R |only
FindIt-0.5/FindIt/R/maketwoway.R |only
FindIt-0.5/FindIt/R/plot.PredictEffect.R |only
FindIt-0.5/FindIt/R/predict.FindIt.R |only
FindIt-0.5/FindIt/R/summary.FindIt.R |only
FindIt-0.5/FindIt/data/F.conjoint.rdata |only
FindIt-0.5/FindIt/data/GerberGreen.rdata |only
FindIt-0.5/FindIt/data/Immigration.rdata |only
FindIt-0.5/FindIt/data/LaLonde.rdata |only
FindIt-0.5/FindIt/data/Unifdata.rdata |only
FindIt-0.5/FindIt/man/FindIt.Rd | 312 ++--
FindIt-0.5/FindIt/man/GerberGreen.Rd | 103 -
FindIt-0.5/FindIt/man/INT.Rd |only
FindIt-0.5/FindIt/man/Immigration.Rd |only
FindIt-0.5/FindIt/man/LaLonde.Rd | 25
FindIt-0.5/FindIt/man/MakeTwoWay.Rd | 5
FindIt-0.5/FindIt/man/Predict.FindIt.Rd | 12
FindIt-0.5/FindIt/man/full.FindIt.Rd |only
FindIt-0.5/FindIt/man/plot.PredictFindIt.Rd | 16
28 files changed, 282 insertions(+), 2088 deletions(-)
Title: Cox Models with Dynamic Ridge Penalties
Diff between CoxRidge versions 0.9.1 dated 2013-06-26 and 0.9.2 dated 2015-02-27
Description: A package for fitting Cox models with penalized ridge-type partial likelihood. The package includes functions for fitting simple Cox models with all covariates controlled by a ridge penalty. The weight of the penalty is optimised by using a REML type-algorithm. Models with time varying effects of the covariates can also be fitted. Some of the covariates may be allowed to be fixed and thus not controlled by the penalty. There are three different penalty functions, ridge, dynamic and weighted dynamic. Time varying effects can be fitted without the need of an expanded dataset.
Author: Aris Perperoglou
Maintainer: Aris Perperoglou
DESCRIPTION | 26 ++++++++------------------
MD5 | 4 ++--
NAMESPACE | 3 +++
3 files changed, 13 insertions(+), 20 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-02 1.0.6
2014-08-20 0.0.4
Title: Quantitative Analysis Made Accessible
Diff between userfriendlyscience versions 0.1-2 dated 2014-04-22 and 0.2-0 dated 2015-02-27
More information about userfriendlyscience at CRAN
Description: Contains a number of functions that serve
two goals: first, make R more accessible to people migrating from
SPSS by adding a number of functions that behave roughly like their
SPSS equivalents; and second, make a number of slightly more
advanced functions more user friendly to relatively novice users.
Author: Gjalt-Jorn Peters
Maintainer: Gjalt-Jorn Peters
userfriendlyscience-0.1-2/userfriendlyscience/R/basicSPSStranslationFunctions.R |only
userfriendlyscience-0.1-2/userfriendlyscience/R/simpleFunctions.r |only
userfriendlyscience-0.1-2/userfriendlyscience/R/sysrev.r |only
userfriendlyscience-0.1-2/userfriendlyscience/man/userfriendlyscience-sysrev.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/ChangeLog | 7
userfriendlyscience-0.2-0/userfriendlyscience/DESCRIPTION | 18
userfriendlyscience-0.2-0/userfriendlyscience/MD5 | 70 +--
userfriendlyscience-0.2-0/userfriendlyscience/NAMESPACE | 39 +
userfriendlyscience-0.2-0/userfriendlyscience/NEWS | 18
userfriendlyscience-0.2-0/userfriendlyscience/R/associationMatrix.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/basicSPSStranslationFunctions.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/confIntV.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/didacticPlot.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/dlvPlot.r | 8
userfriendlyscience-0.2-0/userfriendlyscience/R/freq.r | 22
userfriendlyscience-0.2-0/userfriendlyscience/R/meanDiff.multi.r | 3
userfriendlyscience-0.2-0/userfriendlyscience/R/normalityAssessment.r | 231 +++++++++-
userfriendlyscience-0.2-0/userfriendlyscience/R/oneway.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/posthocTGH.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/regr.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/rnwString.r | 2
userfriendlyscience-0.2-0/userfriendlyscience/R/scaleDiagnosis.r | 44 -
userfriendlyscience-0.2-0/userfriendlyscience/R/scaleDiagnosisToPDF.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/scaleInspection.r | 20
userfriendlyscience-0.2-0/userfriendlyscience/R/scaleReliability.r | 12
userfriendlyscience-0.2-0/userfriendlyscience/R/scatterMatrix.r |only
userfriendlyscience-0.2-0/userfriendlyscience/R/userfriendlyscienceBasics.r | 40 +
userfriendlyscience-0.2-0/userfriendlyscience/data/testRetestSimData.rda |binary
userfriendlyscience-0.2-0/userfriendlyscience/inst |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-associationMatrix.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-associationMatrixHelperFunctions.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-confIntV.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-didacticPlot.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-dlvPlot.Rd | 4
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-freq.Rd | 5
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-normalityAssessment.Rd | 68 ++
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-oneway.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-package.Rd | 41 +
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-posthocTGH.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-printMethods.Rd | 47 +-
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-regr.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-scaleDiagnosis.Rd | 21
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-scaleDiagnosisToPDF.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-scaleInspection.Rd | 5
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-scatterMatrix.Rd |only
userfriendlyscience-0.2-0/userfriendlyscience/man/userfriendlyscience-userfriendlyscienceBasics.Rd | 32 +
userfriendlyscience-0.2-0/userfriendlyscience/tests/reliabilityTest.r | 50 +-
userfriendlyscience-0.2-0/userfriendlyscience/tests/sysRevExampleTemplate.r |only
48 files changed, 640 insertions(+), 167 deletions(-)
Permanent link
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Diff between spatstat versions 1.40-0 dated 2014-12-31 and 1.41-1 dated 2015-02-27
Description: Comprehensive toolbox for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, and point patterns on a linear network.
Contains about 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm, kppm, slrm similar to glm. Types of models include Poisson, Gibbs, Cox and cluster point processes. Models may involve dependence on covariates, interpoint interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise, AIC). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley
Maintainer: Adrian Baddeley
spatstat-1.40-0/spatstat/man/markcorrint.Rd |only
spatstat-1.40-0/spatstat/src/dppll.f |only
spatstat-1.40-0/spatstat/src/inxypOld.f |only
spatstat-1.41-1/spatstat/DESCRIPTION | 22
spatstat-1.41-1/spatstat/MD5 | 590 ++++++------
spatstat-1.41-1/spatstat/NAMESPACE | 145 +++
spatstat-1.41-1/spatstat/NEWS | 878 +++++++++++++++++++
spatstat-1.41-1/spatstat/R/Iest.R | 4
spatstat-1.41-1/spatstat/R/Kcom.R | 12
spatstat-1.41-1/spatstat/R/Kest.R | 13
spatstat-1.41-1/spatstat/R/Kinhom.R | 10
spatstat-1.41-1/spatstat/R/Kmeasure.R | 89 +
spatstat-1.41-1/spatstat/R/Kmulti.R | 10
spatstat-1.41-1/spatstat/R/Kmulti.inhom.R | 10
spatstat-1.41-1/spatstat/R/Kscaled.R | 5
spatstat-1.41-1/spatstat/R/Math.im.R | 6
spatstat-1.41-1/spatstat/R/Math.linim.R |only
spatstat-1.41-1/spatstat/R/Tstat.R | 4
spatstat-1.41-1/spatstat/R/anova.ppm.R | 492 +++++-----
spatstat-1.41-1/spatstat/R/cdf.test.mppm.R | 5
spatstat-1.41-1/spatstat/R/clickpoly.R | 13
spatstat-1.41-1/spatstat/R/clickppp.R | 152 +--
spatstat-1.41-1/spatstat/R/closepairs.R | 86 +
spatstat-1.41-1/spatstat/R/clusterfunctions.R |only
spatstat-1.41-1/spatstat/R/clusterinfo.R |only
spatstat-1.41-1/spatstat/R/colourtools.R | 4
spatstat-1.41-1/spatstat/R/concom.R | 4
spatstat-1.41-1/spatstat/R/crossdistlpp.R | 6
spatstat-1.41-1/spatstat/R/deldir.R | 30
spatstat-1.41-1/spatstat/R/density.ppp.R | 81 +
spatstat-1.41-1/spatstat/R/diagnoseppm.R | 25
spatstat-1.41-1/spatstat/R/diagram.R | 51 -
spatstat-1.41-1/spatstat/R/distances.psp.R | 8
spatstat-1.41-1/spatstat/R/distbdry.R | 5
spatstat-1.41-1/spatstat/R/dummy.R | 2
spatstat-1.41-1/spatstat/R/envelope.R | 7
spatstat-1.41-1/spatstat/R/fgk3.R | 36
spatstat-1.41-1/spatstat/R/fv.R | 8
spatstat-1.41-1/spatstat/R/hierstrauss.R | 21
spatstat-1.41-1/spatstat/R/hyperframe.R | 104 +-
spatstat-1.41-1/spatstat/R/hypersub.R | 13
spatstat-1.41-1/spatstat/R/images.R | 27
spatstat-1.41-1/spatstat/R/intensity.R | 4
spatstat-1.41-1/spatstat/R/interactions.R | 8
spatstat-1.41-1/spatstat/R/iplot.R | 6
spatstat-1.41-1/spatstat/R/iplotlayered.R | 30
spatstat-1.41-1/spatstat/R/istat.R | 4
spatstat-1.41-1/spatstat/R/kppm.R | 436 +++++----
spatstat-1.41-1/spatstat/R/layered.R | 64 -
spatstat-1.41-1/spatstat/R/levelset.R | 10
spatstat-1.41-1/spatstat/R/leverage.R | 19
spatstat-1.41-1/spatstat/R/linalg.R | 5
spatstat-1.41-1/spatstat/R/linearK.R | 24
spatstat-1.41-1/spatstat/R/linearKmulti.R | 11
spatstat-1.41-1/spatstat/R/lineardisc.R | 4
spatstat-1.41-1/spatstat/R/linearmrkcon.R | 13
spatstat-1.41-1/spatstat/R/linearpcf.R | 28
spatstat-1.41-1/spatstat/R/linearpcfmulti.R | 8
spatstat-1.41-1/spatstat/R/linfun.R | 45
spatstat-1.41-1/spatstat/R/linim.R | 81 +
spatstat-1.41-1/spatstat/R/linnet.R | 231 ++++
spatstat-1.41-1/spatstat/R/lpp.R | 203 +++-
spatstat-1.41-1/spatstat/R/lppm.R | 49 -
spatstat-1.41-1/spatstat/R/markcorr.R | 66 +
spatstat-1.41-1/spatstat/R/measures.R | 10
spatstat-1.41-1/spatstat/R/mincontrast.R | 524 ++---------
spatstat-1.41-1/spatstat/R/mpl.R | 46
spatstat-1.41-1/spatstat/R/multihard.R | 17
spatstat-1.41-1/spatstat/R/multistrauss.R | 3
spatstat-1.41-1/spatstat/R/multistrhard.R | 43
spatstat-1.41-1/spatstat/R/nncorr.R | 4
spatstat-1.41-1/spatstat/R/nndistlpp.R | 15
spatstat-1.41-1/spatstat/R/options.R | 16
spatstat-1.41-1/spatstat/R/pairdistlpp.R | 4
spatstat-1.41-1/spatstat/R/pairwise.family.R | 4
spatstat-1.41-1/spatstat/R/pcf.R | 6
spatstat-1.41-1/spatstat/R/pcfmulti.R | 18
spatstat-1.41-1/spatstat/R/pcfmulti.inhom.R | 10
spatstat-1.41-1/spatstat/R/pixellate.R | 57 -
spatstat-1.41-1/spatstat/R/plot.anylist.R | 5
spatstat-1.41-1/spatstat/R/plot.owin.R | 4
spatstat-1.41-1/spatstat/R/plot.plotppm.R | 8
spatstat-1.41-1/spatstat/R/plot.ppm.R | 4
spatstat-1.41-1/spatstat/R/plot3d.R |only
spatstat-1.41-1/spatstat/R/pool.R |only
spatstat-1.41-1/spatstat/R/pp3.R | 58 -
spatstat-1.41-1/spatstat/R/ppp.R | 110 --
spatstat-1.41-1/spatstat/R/predict.ppm.R | 2
spatstat-1.41-1/spatstat/R/profilepl.R | 7
spatstat-1.41-1/spatstat/R/psp2pix.R | 59 -
spatstat-1.41-1/spatstat/R/pspcross.R | 74 +
spatstat-1.41-1/spatstat/R/psst.R | 2
spatstat-1.41-1/spatstat/R/psstG.R | 8
spatstat-1.41-1/spatstat/R/quadratmtest.R | 3
spatstat-1.41-1/spatstat/R/quadrattest.R | 23
spatstat-1.41-1/spatstat/R/quantess.R |only
spatstat-1.41-1/spatstat/R/rLGCP.R | 139 +--
spatstat-1.41-1/spatstat/R/random.R | 131 +-
spatstat-1.41-1/spatstat/R/randomNS.R | 198 ++--
spatstat-1.41-1/spatstat/R/randomlpp.R | 8
spatstat-1.41-1/spatstat/R/randommk.R | 57 -
spatstat-1.41-1/spatstat/R/rat.R | 4
spatstat-1.41-1/spatstat/R/reduceformula.R | 2
spatstat-1.41-1/spatstat/R/relrisk.ppm.R | 4
spatstat-1.41-1/spatstat/R/resid4plot.R | 34
spatstat-1.41-1/spatstat/R/residuals.mppm.R | 4
spatstat-1.41-1/spatstat/R/rhohat.R | 10
spatstat-1.41-1/spatstat/R/rlabel.R | 4
spatstat-1.41-1/spatstat/R/rmh.ppm.R | 13
spatstat-1.41-1/spatstat/R/rose.R | 2
spatstat-1.41-1/spatstat/R/segtest.R |only
spatstat-1.41-1/spatstat/R/simulatelppm.R | 11
spatstat-1.41-1/spatstat/R/slrm.R | 13
spatstat-1.41-1/spatstat/R/solist.R | 39
spatstat-1.41-1/spatstat/R/split.ppp.R | 16
spatstat-1.41-1/spatstat/R/subfits.R | 28
spatstat-1.41-1/spatstat/R/summary.im.R | 80 -
spatstat-1.41-1/spatstat/R/summary.mppm.R | 78 -
spatstat-1.41-1/spatstat/R/summary.ppm.R | 2
spatstat-1.41-1/spatstat/R/terse.R | 47 -
spatstat-1.41-1/spatstat/R/tess.R | 198 +++-
spatstat-1.41-1/spatstat/R/units.R | 8
spatstat-1.41-1/spatstat/R/util.R | 56 +
spatstat-1.41-1/spatstat/R/vcov.kppm.R | 180 ++-
spatstat-1.41-1/spatstat/R/weights.R | 132 +-
spatstat-1.41-1/spatstat/R/window.R | 84 +
spatstat-1.41-1/spatstat/R/wingeom.R | 4
spatstat-1.41-1/spatstat/R/xypolygon.R | 31
spatstat-1.41-1/spatstat/R/xysegment.R | 68 -
spatstat-1.41-1/spatstat/data/Kovesi.rda |binary
spatstat-1.41-1/spatstat/data/bdspots.rda |binary
spatstat-1.41-1/spatstat/data/bei.rda |binary
spatstat-1.41-1/spatstat/data/chicago.rda |binary
spatstat-1.41-1/spatstat/data/clmfires.rda |binary
spatstat-1.41-1/spatstat/data/datalist | 2
spatstat-1.41-1/spatstat/data/demohyper.rda |binary
spatstat-1.41-1/spatstat/data/dendrite.rda |only
spatstat-1.41-1/spatstat/data/flu.rda |binary
spatstat-1.41-1/spatstat/data/gorillas.rda |binary
spatstat-1.41-1/spatstat/data/heather.rda |binary
spatstat-1.41-1/spatstat/data/murchison.rda |binary
spatstat-1.41-1/spatstat/data/osteo.rda |binary
spatstat-1.41-1/spatstat/data/pyramidal.rda |binary
spatstat-1.41-1/spatstat/data/spiders.rda |only
spatstat-1.41-1/spatstat/data/waterstriders.rda |binary
spatstat-1.41-1/spatstat/demo/data.R | 9
spatstat-1.41-1/spatstat/demo/spatstat.R | 4
spatstat-1.41-1/spatstat/inst/doc/datasets.R | 164 ++-
spatstat-1.41-1/spatstat/inst/doc/datasets.Rnw | 101 ++
spatstat-1.41-1/spatstat/inst/doc/datasets.pdf |binary
spatstat-1.41-1/spatstat/inst/doc/getstart.pdf |binary
spatstat-1.41-1/spatstat/inst/doc/replicated.pdf |binary
spatstat-1.41-1/spatstat/inst/doc/shapefiles.pdf |binary
spatstat-1.41-1/spatstat/inst/doc/updates.R | 4
spatstat-1.41-1/spatstat/inst/doc/updates.Rnw | 250 +++++
spatstat-1.41-1/spatstat/inst/doc/updates.pdf |binary
spatstat-1.41-1/spatstat/inst/rawdata/osteo |only
spatstat-1.41-1/spatstat/inst/rawdata/sandholes |only
spatstat-1.41-1/spatstat/man/Emark.Rd | 10
spatstat-1.41-1/spatstat/man/K3est.Rd | 11
spatstat-1.41-1/spatstat/man/Kmark.Rd |only
spatstat-1.41-1/spatstat/man/Math.im.Rd | 4
spatstat-1.41-1/spatstat/man/Math.linim.Rd |only
spatstat-1.41-1/spatstat/man/anova.lppm.Rd | 29
spatstat-1.41-1/spatstat/man/anova.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/anova.ppm.Rd | 10
spatstat-1.41-1/spatstat/man/anylist.Rd | 4
spatstat-1.41-1/spatstat/man/as.function.im.Rd |only
spatstat-1.41-1/spatstat/man/as.linnet.linim.Rd |only
spatstat-1.41-1/spatstat/man/as.linnet.psp.Rd |only
spatstat-1.41-1/spatstat/man/as.lpp.Rd | 7
spatstat-1.41-1/spatstat/man/as.solist.Rd | 4
spatstat-1.41-1/spatstat/man/cauchy.estK.Rd | 6
spatstat-1.41-1/spatstat/man/cauchy.estpcf.Rd | 10
spatstat-1.41-1/spatstat/man/cdf.test.Rd | 4
spatstat-1.41-1/spatstat/man/clickbox.Rd | 5
spatstat-1.41-1/spatstat/man/clickdist.Rd |only
spatstat-1.41-1/spatstat/man/clickpoly.Rd | 11
spatstat-1.41-1/spatstat/man/clickppp.Rd | 15
spatstat-1.41-1/spatstat/man/closepairs.Rd | 12
spatstat-1.41-1/spatstat/man/clusterfield.Rd |only
spatstat-1.41-1/spatstat/man/clusterfit.Rd |only
spatstat-1.41-1/spatstat/man/clusterkernel.Rd |only
spatstat-1.41-1/spatstat/man/clusterradius.Rd |only
spatstat-1.41-1/spatstat/man/coef.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/colourtools.Rd | 2
spatstat-1.41-1/spatstat/man/crossdist.psp.Rd | 10
spatstat-1.41-1/spatstat/man/delaunay.Rd | 4
spatstat-1.41-1/spatstat/man/delaunay.distance.Rd | 3
spatstat-1.41-1/spatstat/man/delaunay.network.Rd |only
spatstat-1.41-1/spatstat/man/dendrite.Rd |only
spatstat-1.41-1/spatstat/man/density.ppp.Rd | 9
spatstat-1.41-1/spatstat/man/diagnose.ppm.Rd | 23
spatstat-1.41-1/spatstat/man/dirichlet.vertices.Rd | 36
spatstat-1.41-1/spatstat/man/fitted.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/identify.ppp.Rd | 6
spatstat-1.41-1/spatstat/man/identify.psp.Rd | 4
spatstat-1.41-1/spatstat/man/improve.kppm.Rd | 2
spatstat-1.41-1/spatstat/man/integral.im.Rd | 33
spatstat-1.41-1/spatstat/man/integral.linim.Rd |only
spatstat-1.41-1/spatstat/man/integral.msr.Rd | 11
spatstat-1.41-1/spatstat/man/intersect.tess.Rd | 15
spatstat-1.41-1/spatstat/man/iplot.Rd | 14
spatstat-1.41-1/spatstat/man/is.marked.ppm.Rd | 2
spatstat-1.41-1/spatstat/man/is.multitype.ppm.Rd | 2
spatstat-1.41-1/spatstat/man/is.multitype.ppp.Rd | 8
spatstat-1.41-1/spatstat/man/kppm.Rd | 37
spatstat-1.41-1/spatstat/man/lgcp.estK.Rd | 9
spatstat-1.41-1/spatstat/man/lgcp.estpcf.Rd | 10
spatstat-1.41-1/spatstat/man/linearKcross.inhom.Rd | 5
spatstat-1.41-1/spatstat/man/linearKdot.inhom.Rd | 5
spatstat-1.41-1/spatstat/man/linearKinhom.Rd | 6
spatstat-1.41-1/spatstat/man/linearpcfcross.inhom.Rd | 5
spatstat-1.41-1/spatstat/man/linearpcfdot.inhom.Rd | 5
spatstat-1.41-1/spatstat/man/linearpcfinhom.Rd | 5
spatstat-1.41-1/spatstat/man/linfun.Rd | 30
spatstat-1.41-1/spatstat/man/linim.Rd | 3
spatstat-1.41-1/spatstat/man/linnet.Rd | 25
spatstat-1.41-1/spatstat/man/logLik.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/lpp.Rd | 5
spatstat-1.41-1/spatstat/man/markcorr.Rd | 6
spatstat-1.41-1/spatstat/man/marks.tess.Rd |only
spatstat-1.41-1/spatstat/man/matclust.estK.Rd | 11
spatstat-1.41-1/spatstat/man/matclust.estpcf.Rd | 9
spatstat-1.41-1/spatstat/man/methods.linfun.Rd | 5
spatstat-1.41-1/spatstat/man/methods.linnet.Rd | 50 -
spatstat-1.41-1/spatstat/man/methods.lppm.Rd | 4
spatstat-1.41-1/spatstat/man/mppm.Rd | 1
spatstat-1.41-1/spatstat/man/nestsplit.Rd |only
spatstat-1.41-1/spatstat/man/nndist.psp.Rd | 9
spatstat-1.41-1/spatstat/man/osteo.Rd | 2
spatstat-1.41-1/spatstat/man/pairdist.psp.Rd | 9
spatstat-1.41-1/spatstat/man/panel.contour.Rd | 2
spatstat-1.41-1/spatstat/man/paracou.Rd | 3
spatstat-1.41-1/spatstat/man/pixellate.Rd | 1
spatstat-1.41-1/spatstat/man/pixellate.psp.Rd | 18
spatstat-1.41-1/spatstat/man/plot.anylist.Rd | 12
spatstat-1.41-1/spatstat/man/plot.cdftest.Rd | 4
spatstat-1.41-1/spatstat/man/plot.fv.Rd | 4
spatstat-1.41-1/spatstat/man/plot.hyperframe.Rd | 11
spatstat-1.41-1/spatstat/man/plot.im.Rd | 11
spatstat-1.41-1/spatstat/man/plot.kppm.Rd | 39
spatstat-1.41-1/spatstat/man/plot.linim.Rd | 10
spatstat-1.41-1/spatstat/man/plot.linnet.Rd | 9
spatstat-1.41-1/spatstat/man/plot.listof.Rd | 12
spatstat-1.41-1/spatstat/man/plot.lpp.Rd | 11
spatstat-1.41-1/spatstat/man/plot.pp3.Rd | 68 -
spatstat-1.41-1/spatstat/man/plot.yardstick.Rd | 32
spatstat-1.41-1/spatstat/man/pool.Rd | 3
spatstat-1.41-1/spatstat/man/pool.anylist.Rd |only
spatstat-1.41-1/spatstat/man/pool.fv.Rd |only
spatstat-1.41-1/spatstat/man/pool.rat.Rd | 1
spatstat-1.41-1/spatstat/man/predict.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/print.owin.Rd | 3
spatstat-1.41-1/spatstat/man/quadrat.test.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/quantess.Rd |only
spatstat-1.41-1/spatstat/man/rCauchy.Rd | 68 +
spatstat-1.41-1/spatstat/man/rGaussPoisson.Rd | 8
spatstat-1.41-1/spatstat/man/rMatClust.Rd | 55 -
spatstat-1.41-1/spatstat/man/rMaternI.Rd | 8
spatstat-1.41-1/spatstat/man/rMaternII.Rd | 8
spatstat-1.41-1/spatstat/man/rNeymanScott.Rd | 33
spatstat-1.41-1/spatstat/man/rPoissonCluster.Rd | 41
spatstat-1.41-1/spatstat/man/rSSI.Rd | 8
spatstat-1.41-1/spatstat/man/rThomas.Rd | 47 -
spatstat-1.41-1/spatstat/man/rVarGamma.Rd | 69 -
spatstat-1.41-1/spatstat/man/rcell.Rd | 8
spatstat-1.41-1/spatstat/man/residuals.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/rjitter.Rd | 7
spatstat-1.41-1/spatstat/man/rmpoint.Rd | 24
spatstat-1.41-1/spatstat/man/rmpoispp.Rd | 22
spatstat-1.41-1/spatstat/man/rpoint.Rd | 7
spatstat-1.41-1/spatstat/man/rpoislpp.Rd | 5
spatstat-1.41-1/spatstat/man/rpoispp.Rd | 39
spatstat-1.41-1/spatstat/man/rpoisppOnLines.Rd | 2
spatstat-1.41-1/spatstat/man/rstrat.Rd | 7
spatstat-1.41-1/spatstat/man/rsyst.Rd | 8
spatstat-1.41-1/spatstat/man/rthin.Rd | 7
spatstat-1.41-1/spatstat/man/runifdisc.Rd | 7
spatstat-1.41-1/spatstat/man/runifpoint.Rd | 8
spatstat-1.41-1/spatstat/man/segregation.test.Rd |only
spatstat-1.41-1/spatstat/man/selfcut.psp.Rd |only
spatstat-1.41-1/spatstat/man/simulate.kppm.Rd | 8
spatstat-1.41-1/spatstat/man/simulate.lppm.Rd | 10
spatstat-1.41-1/spatstat/man/simulate.ppm.Rd | 10
spatstat-1.41-1/spatstat/man/simulate.slrm.Rd | 7
spatstat-1.41-1/spatstat/man/solapply.Rd |only
spatstat-1.41-1/spatstat/man/solist.Rd | 27
spatstat-1.41-1/spatstat/man/solutionset.Rd | 27
spatstat-1.41-1/spatstat/man/spatstat-internal.Rd | 99 +-
spatstat-1.41-1/spatstat/man/spatstat-package.Rd | 22
spatstat-1.41-1/spatstat/man/spatstat.options.Rd | 12
spatstat-1.41-1/spatstat/man/spiders.Rd |only
spatstat-1.41-1/spatstat/man/split.ppp.Rd | 13
spatstat-1.41-1/spatstat/man/spokes.Rd | 12
spatstat-1.41-1/spatstat/man/subfits.Rd | 1
spatstat-1.41-1/spatstat/man/subset.hyperframe.Rd |only
spatstat-1.41-1/spatstat/man/tess.Rd | 28
spatstat-1.41-1/spatstat/man/thomas.estK.Rd | 27
spatstat-1.41-1/spatstat/man/thomas.estpcf.Rd | 29
spatstat-1.41-1/spatstat/man/vargamma.estK.Rd | 19
spatstat-1.41-1/spatstat/man/vargamma.estpcf.Rd | 19
spatstat-1.41-1/spatstat/man/vcov.kppm.Rd | 7
spatstat-1.41-1/spatstat/man/vcov.mppm.Rd | 1
spatstat-1.41-1/spatstat/man/vertices.Rd | 13
spatstat-1.41-1/spatstat/man/waka.Rd | 2
spatstat-1.41-1/spatstat/src/close3pair.c | 8
spatstat-1.41-1/spatstat/src/closefuns.h | 162 ++-
spatstat-1.41-1/spatstat/src/closepair.c | 19
spatstat-1.41-1/spatstat/src/seg2pix.c | 151 ---
spatstat-1.41-1/spatstat/src/seg2pix.h |only
spatstat-1.41-1/spatstat/tests/alltests.R | 59 -
spatstat-1.41-1/spatstat/vignettes/datasets.Rnw | 101 ++
spatstat-1.41-1/spatstat/vignettes/packagesizes.txt | 2
spatstat-1.41-1/spatstat/vignettes/updates.Rnw | 250 +++++
315 files changed, 6877 insertions(+), 3297 deletions(-)
Title: Rcpp Integration for the Eigen Templated Linear Algebra Library
Diff between RcppEigen versions 0.3.2.3.0 dated 2014-12-23 and 0.3.2.4.0 dated 2015-02-27
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 3.2.3). 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-0.3.2.3.0/RcppEigen/inst/include/Eigen/src/Core/Product.h |only
RcppEigen-0.3.2.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/CoreIterators.h |only
RcppEigen-0.3.2.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseAssign.h |only
RcppEigen-0.3.2.4.0/RcppEigen/ChangeLog | 24 +++
RcppEigen-0.3.2.4.0/RcppEigen/DESCRIPTION | 12 -
RcppEigen-0.3.2.4.0/RcppEigen/MD5 | 36 ++---
RcppEigen-0.3.2.4.0/RcppEigen/R/RcppEigen.package.skeleton.R | 45 ++++--
RcppEigen-0.3.2.4.0/RcppEigen/README.md | 25 +--
RcppEigen-0.3.2.4.0/RcppEigen/inst/NEWS.Rd | 11 +
RcppEigen-0.3.2.4.0/RcppEigen/inst/doc/RcppEigen-Introduction.pdf |binary
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/CholmodSupport/CholmodSupport.h | 70 ----------
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/Core/MapBase.h | 11 -
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/Complex.h | 2
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/PacketMath.h | 4
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/Core/util/Macros.h | 4
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/Core/util/Memory.h | 5
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/RealQZ.h | 2
RcppEigen-0.3.2.4.0/RcppEigen/inst/include/Eigen/src/Geometry/Rotation2D.h | 2
RcppEigen-0.3.2.4.0/RcppEigen/inst/skeleton/Makevars | 4
RcppEigen-0.3.2.4.0/RcppEigen/inst/skeleton/Makevars.win | 4
RcppEigen-0.3.2.4.0/RcppEigen/inst/skeleton/rcppeigen_hello_world.Rd |only
21 files changed, 118 insertions(+), 143 deletions(-)
Title: Multi-Analysis Distance Sampling
Diff between mads versions 0.1.1 dated 2014-12-23 and 0.1.2 dated 2015-02-27
Description: Performs distance sampling analyses on a number of species
accounting for unidentified sightings, model uncertainty and covariate
uncertainty.
Author: Laura Marshall
Maintainer: Laura Marshall
DESCRIPTION | 8 ++++----
MD5 | 18 +++++++++---------
NEWS | 11 +++++++++++
R/calculate.dht.R | 5 +++--
R/check.bootstrap.options.r | 6 +++---
R/check.ddf.models.R | 1 -
R/execute.multi.analysis.R | 9 +++++----
R/fit.ddf.models.R | 19 ++++++++++---------
R/mae.warning.R | 6 +++---
R/process.warnings.R | 5 ++++-
10 files changed, 52 insertions(+), 36 deletions(-)
Title: Geostatistical Modelling with Likelihood and Bayes
Diff between geostatsp versions 1.1.9 dated 2015-01-23 and 1.2.1 dated 2015-02-27
Description: Geostatistical modelling facilities using Raster and SpatialPoints objects are provided. Non-Gaussian models are fit using INLA, and Gaussian geostatistical models use Maximum Likelihood Estimation..
Author: Patrick Brown
Maintainer: Patrick Brown
geostatsp-1.1.9/geostatsp/src/maternLogLgr.c |only
geostatsp-1.2.1/geostatsp/DESCRIPTION | 12
geostatsp-1.2.1/geostatsp/MD5 | 100 ++-
geostatsp-1.2.1/geostatsp/NAMESPACE | 9
geostatsp-1.2.1/geostatsp/R/RFsimulate.R | 45 -
geostatsp-1.2.1/geostatsp/R/excProb.R | 2
geostatsp-1.2.1/geostatsp/R/informationLgm.R | 72 +-
geostatsp-1.2.1/geostatsp/R/krige.R | 150 +++-
geostatsp-1.2.1/geostatsp/R/lgm.R | 55 -
geostatsp-1.2.1/geostatsp/R/lgm.Raster.R | 2
geostatsp-1.2.1/geostatsp/R/loglikGmrf.R | 321 ++++++++--
geostatsp-1.2.1/geostatsp/R/loglikLgm.R | 675 ++++++++++++----------
geostatsp-1.2.1/geostatsp/R/matern.R | 17
geostatsp-1.2.1/geostatsp/R/maternGmrfPrec.R | 17
geostatsp-1.2.1/geostatsp/R/param.R | 11
geostatsp-1.2.1/geostatsp/R/profLlgm.R | 150 ++--
geostatsp-1.2.1/geostatsp/R/spdfToBrick.R |only
geostatsp-1.2.1/geostatsp/R/variog.R | 8
geostatsp-1.2.1/geostatsp/data/datalist | 4
geostatsp-1.2.1/geostatsp/data/murder.RData |binary
geostatsp-1.2.1/geostatsp/data/torontoPop.RData |binary
geostatsp-1.2.1/geostatsp/inst/extdata |only
geostatsp-1.2.1/geostatsp/man/krige.Rd | 22
geostatsp-1.2.1/geostatsp/man/likfitLgm.Rd | 37 -
geostatsp-1.2.1/geostatsp/man/maternGmrfPrec.Rd | 10
geostatsp-1.2.1/geostatsp/man/murder.Rd | 199 ++++++
geostatsp-1.2.1/geostatsp/man/profLlgm.Rd | 2
geostatsp-1.2.1/geostatsp/man/stackRasterList.Rd | 19
geostatsp-1.2.1/geostatsp/man/variog.Rd | 12
geostatsp-1.2.1/geostatsp/src/geostatsp.h | 16
geostatsp-1.2.1/geostatsp/src/matern.c | 20
geostatsp-1.2.1/geostatsp/src/maternLogL.c | 203 +++---
geostatsp-1.2.1/geostatsp/src/maternLogLopt.c |only
geostatsp-1.2.1/geostatsp/src/sparseLogL.c |only
geostatsp-1.2.1/geostatsp/tests/RFsimulate.R | 39 -
geostatsp-1.2.1/geostatsp/tests/krige.R | 11
geostatsp-1.2.1/geostatsp/tests/lgm.R | 14
geostatsp-1.2.1/geostatsp/tests/lgmRaster.R | 76 --
geostatsp-1.2.1/geostatsp/tests/likfitLgm.R | 80 ++
geostatsp-1.2.1/geostatsp/tests/maternGmrfPrec.R | 4
geostatsp-1.2.1/geostatsp/tests/profLlgm.R | 111 ++-
geostatsp-1.2.1/geostatsp/tests/stackRasterList.R |only
42 files changed, 1635 insertions(+), 890 deletions(-)
Title: Distance Sampling Simulations
Diff between DSsim versions 1.0.2 dated 2014-12-23 and 1.0.3 dated 2015-02-27
Description: Performs distance sampling simulations. It repeatedly
generates instances of a user defined population within a given survey
region, generates realisations of a survey design (currently these must
be pre-generated using Distance software) and simulates the detection
process. The data are then analysed so that the results can be compared for
accuracy and precision across all replications. This will allow users to
select survey designs which will give them the best accuracy and precision
given their expectations about population distribution. Any uncertainty in
population distribution or population parameters can be included by running
the different survey designs for a number of different population
descriptions. An example simulation can be found in the help file
for make.simulation.
Author: Laura Marshall
Maintainer: Laura Marshall
DESCRIPTION | 8 +-
MD5 | 37 ++++-----
NEWS | 71 +++++++++++-------
R/Class.Constructors.R | 20 +++--
R/DDF.Analysis.R | 14 +--
R/Density.R | 156 +++++++++++++++++++++++++++++------------
R/LT.Design.R | 10 +-
R/Population.Description.R | 4 -
R/Region.R | 29 ++++---
R/Simulation.R | 2
R/add.dist.error.R | 2
R/check.intersection.R | 4 -
R/get.sampler.info.R | 4 -
R/is.gap.R | 2
R/single.simulation.loop.R | 10 --
inst/tests/test_Constructors.R |only
man/Density-class.Rd | 16 ++--
man/Region-class.Rd | 11 +-
man/make.density.Rd | 10 ++
man/make.simulation.Rd | 2
20 files changed, 256 insertions(+), 156 deletions(-)
Title: Biological Structure Analysis
Diff between bio3d versions 2.1-3 dated 2014-10-27 and 2.2-1 dated 2015-02-27
Description: Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
Author: Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide
Maintainer: Barry Grant
bio3d-2.1-3/bio3d/R/cmap.filter.R |only
bio3d-2.1-3/bio3d/R/combine.sel.R |only
bio3d-2.1-3/bio3d/R/dssp.trj.R |only
bio3d-2.1-3/bio3d/R/ide.filter.R |only
bio3d-2.1-3/bio3d/R/pdbs.filter.R |only
bio3d-2.1-3/bio3d/R/plot.bio3d.R |only
bio3d-2.1-3/bio3d/R/plot.dccm2.R |only
bio3d-2.1-3/bio3d/R/rmsd.filter.R |only
bio3d-2.1-3/bio3d/data/aa.mass.rda |only
bio3d-2.1-3/bio3d/man/aa.mass.Rd |only
bio3d-2.1-3/bio3d/man/cmap.filter.Rd |only
bio3d-2.1-3/bio3d/man/combine.sel.Rd |only
bio3d-2.1-3/bio3d/man/dssp.pdbs.Rd |only
bio3d-2.1-3/bio3d/man/dssp.trj.Rd |only
bio3d-2.1-3/bio3d/man/ide.filter.Rd |only
bio3d-2.1-3/bio3d/man/mktrj.enma.Rd |only
bio3d-2.1-3/bio3d/man/mktrj.nma.Rd |only
bio3d-2.1-3/bio3d/man/mktrj.pca.Rd |only
bio3d-2.1-3/bio3d/man/pdbs.filter.Rd |only
bio3d-2.1-3/bio3d/man/plot.blast.Rd |only
bio3d-2.1-3/bio3d/man/rmsd.filter.Rd |only
bio3d-2.1-3/bio3d/tests/test-all.R |only
bio3d-2.2-1/bio3d/DESCRIPTION | 6
bio3d-2.2-1/bio3d/MD5 | 453 ++++++++++----------
bio3d-2.2-1/bio3d/NAMESPACE | 100 ++++
bio3d-2.2-1/bio3d/NEWS | 78 ++-
bio3d-2.2-1/bio3d/R/aa2mass.R | 44 +
bio3d-2.2-1/bio3d/R/aa321.R | 43 +
bio3d-2.2-1/bio3d/R/amsm.xyz.R | 2
bio3d-2.2-1/bio3d/R/as.fasta.R |only
bio3d-2.2-1/bio3d/R/as.pdb.R |only
bio3d-2.2-1/bio3d/R/as.pdb.mol2.R |only
bio3d-2.2-1/bio3d/R/as.pdb.prmtop.R |only
bio3d-2.2-1/bio3d/R/as.select.R |only
bio3d-2.2-1/bio3d/R/as.xyz.R | 2
bio3d-2.2-1/bio3d/R/atom.select.R | 287 ------------
bio3d-2.2-1/bio3d/R/atom.select.pdb.R |only
bio3d-2.2-1/bio3d/R/atom.select.prmtop.R |only
bio3d-2.2-1/bio3d/R/basename.pdb.R |only
bio3d-2.2-1/bio3d/R/binding.site.R | 164 ++++---
bio3d-2.2-1/bio3d/R/biounit.R |only
bio3d-2.2-1/bio3d/R/bounds.sse.R |only
bio3d-2.2-1/bio3d/R/cat.pdb.R |only
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270 files changed, 3382 insertions(+), 2420 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-10-17 1.2-6
Title: Tests for Normality
Diff between nortest versions 1.0-2 dated 2012-05-30 and 1.0-3 dated 2015-02-26
Description: Five omnibus tests for testing the composite hypothesis of
normality.
Author: Juergen Gross [aut],
Uwe Ligges [aut, cre]
Maintainer: Uwe Ligges
ChangeLog |only
DESCRIPTION | 21 ++++++++++++---------
MD5 | 7 ++++---
R/ad.test.R | 12 ++++++++----
man/cvm.test.Rd | 4 ++--
5 files changed, 26 insertions(+), 18 deletions(-)
Title: Generalized Turnbull's Estimator
Diff between gte versions 1.2-1 dated 2014-01-06 and 1.2-2 dated 2015-02-26
Description: Generalized Turnbull's estimator proposed by Dehghan and Duchesne
(2011).
Author: Mohammad Hossein Dehghan, Thierry Duchesne and Sophie Baillargeon
Maintainer: Thierry Duchesne
DESCRIPTION | 10 +-
MD5 | 16 +--
NAMESPACE | 3
NEWS | 5 +
R/gte-package.R | 4
R/gte.R | 54 ++++++-----
man/gte-package.Rd | 33 +++----
man/gte.Rd | 240 +++++++++++++++++++++--------------------------------
man/simul.Rd | 20 ++--
9 files changed, 175 insertions(+), 210 deletions(-)
Title: Additive and Multiplicative Effects Models for Networks and
Relational Data
Diff between amen versions 0.999 dated 2014-03-01 and 1.0 dated 2015-02-26
Description: Analysis of network and relational data using additive and
multiplicative effects (AME) models. The basic model includes
regression terms, the covariance structure of the social relations model
(Warner, Kenny and Stoto (1979), Wong (1982)), and multiplicative factor
models (Hoff(2009)). Four different link functions accommodate different
relational data structures, including binary/network data (bin), normal
relational data (nrm), ordinal relational data (ord) and data from
fixed-rank nomination schemes (frn). Several of these link functions are
discussed in Hoff, Fosdick, Volfovsky and Stovel (2013). Development of this
software was supported in part by NICHD grant R01HD067509.
Author: Peter Hoff, Bailey Fosdick, Alex Volfovsky, Yanjun He
Maintainer: Peter Hoff
DESCRIPTION | 44 ++++++------
MD5 | 164 ++++++++++++++++++++++++++++--------------------
NAMESPACE | 33 +++++++++
R/Xbeta.R | 24 +++++++
R/ame.R | 81 +++++++++++++++++++++++
R/ame_rep.R |only
R/amen-package.R |only
R/design_array.R | 19 +++++
R/gofstats.R | 18 +++++
R/mhalf.R | 19 +++++
R/plot.ame.R | 48 ++++++++++++++
R/rUV_fc.R | 63 ++++++++++++++++++
R/rUV_rep_fc.R |only
R/rZ_bin_fc.R | 42 ++++++++++++
R/rZ_cbin_fc.R | 70 ++++++++++++++++++++
R/rZ_frn_fc.R | 80 +++++++++++++++++++++++
R/rZ_nrm_fc.R | 27 +++++++
R/rZ_ord_fc.R | 50 ++++++++++++++
R/rZ_rrl.R | 67 +++++++++++++++++++
R/raSab_bin_fc.R | 43 ++++++++++++
R/raSab_cbin_fc.R | 53 +++++++++++++++
R/raSab_frn_fc.R | 46 +++++++++++++
R/rbeta_ab_fc.R | 106 +++++++++++++++++++++++++++++++
R/rbeta_ab_rep_fc.R |only
R/rmvnorm.R | 23 ++++++
R/rrho_mh.R | 34 +++++++++
R/rrho_mh_rep.R |only
R/rs2_fc.R | 21 ++++++
R/rs2_rep.R |only
R/rwish.R | 25 +++++++
R/simY_bin.R | 26 +++++++
R/simY_frn.R | 46 +++++++++++++
R/simY_nrm.R | 26 +++++++
R/simY_ord.R | 33 +++++++++
R/simY_rrl.R | 40 +++++++++++
R/simZ.R | 24 +++++++
R/summary.ame.R | 32 +++++++++
R/zscores.R | 19 +++++
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data/addhealthc9.RData |only
data/coldwar.RData |only
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data/conflict90s.RData |only
data/datalist |only
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data/lazegalaw.RData |only
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man/YX_cbin.Rd | 32 ++++-----
man/YX_frn.Rd | 29 +++-----
man/YX_nrm.Rd | 29 +++-----
man/YX_ord.Rd | 28 +++-----
man/YX_rrl.Rd | 29 +++-----
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man/addhealthc9.Rd |only
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man/conflict90s.Rd |only
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man/plot.ame.Rd | 27 +++----
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man/rUV_rep_fc.Rd |only
man/rZ_bin_fc.Rd | 43 +++++-------
man/rZ_cbin_fc.Rd | 80 +++++++++--------------
man/rZ_frn_fc.Rd | 80 +++++++++--------------
man/rZ_nrm_fc.Rd | 42 ++++--------
man/rZ_ord_fc.Rd | 42 ++++--------
man/rZ_rrl_fc.Rd | 52 ++++++---------
man/raSab_bin_fc.Rd | 62 +++++++-----------
man/raSab_cbin_fc.Rd | 70 ++++++++------------
man/raSab_frn_fc.Rd | 73 ++++++++-------------
man/rbeta_ab_fc.Rd | 77 ++++++++++------------
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man/rmvnorm.Rd | 28 ++++----
man/rrho_mh.Rd | 40 +++++------
man/rrho_mh_rep.Rd |only
man/rs2_fc.Rd | 26 +++----
man/rs2_rep_fc.Rd |only
man/rwish.Rd | 33 +++++----
man/sampsonmonks.Rd |only
man/simY_bin.Rd | 27 +++----
man/simY_frn.Rd | 63 ++++++++----------
man/simY_nrm.Rd | 33 ++++-----
man/simY_ord.Rd | 34 ++++-----
man/simY_rrl.Rd | 41 +++++-------
man/simZ.Rd | 32 ++++-----
man/summary.ame.Rd | 45 ++++++-------
man/zscores.Rd | 27 +++----
98 files changed, 2087 insertions(+), 964 deletions(-)
Title: Rcpp Integration for the Armadillo Templated Linear Algebra
Library
Diff between RcppArmadillo versions 0.4.600.4.0 dated 2015-01-25 and 0.4.650.1.1 dated 2015-02-26
Description: R and Armadillo integration using Rcpp
Armadillo is a templated C++ linear algebra library (by Conrad Sanderson)
that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The RcppArmadillo package includes the header files from the templated
Armadillo library. Thus users do not need to install Armadillo itself in
order to use RcppArmadillo. Armadillo is licensed under the MPL 2.0, while
RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel
ChangeLog | 13
DESCRIPTION | 8
MD5 | 83
README.md | 6
inst/NEWS.Rd | 16
inst/doc/RcppArmadillo-intro.pdf |binary
inst/doc/RcppArmadillo-unitTests.pdf |binary
inst/include/armadillo | 12
inst/include/armadillo_bits/Col_bones.hpp | 4
inst/include/armadillo_bits/Col_meat.hpp | 81
inst/include/armadillo_bits/Mat_bones.hpp | 20
inst/include/armadillo_bits/Mat_meat.hpp | 201 ++
inst/include/armadillo_bits/Row_bones.hpp | 4
inst/include/armadillo_bits/Row_meat.hpp | 81
inst/include/armadillo_bits/SpMat_bones.hpp | 57
inst/include/armadillo_bits/SpMat_iterators_meat.hpp | 2
inst/include/armadillo_bits/SpMat_meat.hpp | 1308 +++++++--------
inst/include/armadillo_bits/SpSubview_iterators_meat.hpp | 4
inst/include/armadillo_bits/SpSubview_meat.hpp | 107 -
inst/include/armadillo_bits/arma_rng.hpp | 33
inst/include/armadillo_bits/arma_rng_cxx11.hpp | 30
inst/include/armadillo_bits/arma_version.hpp | 6
inst/include/armadillo_bits/arrayops_meat.hpp | 145 -
inst/include/armadillo_bits/compiler_setup.hpp | 17
inst/include/armadillo_bits/config.hpp | 14
inst/include/armadillo_bits/diskio_meat.hpp | 30
inst/include/armadillo_bits/eglue_core_bones.hpp | 6
inst/include/armadillo_bits/eglue_core_meat.hpp | 8
inst/include/armadillo_bits/eop_core_bones.hpp | 6
inst/include/armadillo_bits/eop_core_meat.hpp | 8
inst/include/armadillo_bits/fn_accu.hpp | 8
inst/include/armadillo_bits/fn_conv_to.hpp | 224 +-
inst/include/armadillo_bits/fn_misc.hpp | 47
inst/include/armadillo_bits/fn_randg.hpp |only
inst/include/armadillo_bits/op_pinv_meat.hpp | 14
inst/include/armadillo_bits/running_stat_vec_meat.hpp | 4
inst/include/armadillo_bits/sp_auxlib_bones.hpp | 2
inst/include/armadillo_bits/sp_auxlib_meat.hpp | 17
inst/include/armadillo_bits/subview_bones.hpp | 7
inst/include/armadillo_bits/subview_cube_bones.hpp | 6
inst/include/armadillo_bits/subview_cube_meat.hpp | 25
inst/include/armadillo_bits/subview_meat.hpp | 26
inst/include/armadillo_bits/unwrap.hpp | 24
43 files changed, 1641 insertions(+), 1073 deletions(-)
Title: PDQ Functions via Gram Charlier, Edgeworth, and Cornish Fisher
Approximations
Diff between PDQutils versions 0.1.0 dated 2015-02-12 and 0.1.1 dated 2015-02-26
Description: A collection of tools for approximating the 'PDQ' functions (respectively, the
cumulative distribution, density, and quantile) of probability distributions via classical
expansions involving moments and cumulants.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav
PDQutils-0.1.0/PDQutils/R/appx.r |only
PDQutils-0.1.1/PDQutils/DESCRIPTION | 15 +-
PDQutils-0.1.1/PDQutils/MD5 | 37 +++---
PDQutils-0.1.1/PDQutils/NAMESPACE | 2
PDQutils-0.1.1/PDQutils/R/PDQutils.r | 10 +
PDQutils-0.1.1/PDQutils/R/cornish_fisher.r |only
PDQutils-0.1.1/PDQutils/R/edgeworth.r |only
PDQutils-0.1.1/PDQutils/R/gram_charlier.r |only
PDQutils-0.1.1/PDQutils/README.md | 151 ++++++++++++++++++++++---
PDQutils-0.1.1/PDQutils/inst/CITATION | 5
PDQutils-0.1.1/PDQutils/inst/doc/PDQutils.R | 73 +++++++++++-
PDQutils-0.1.1/PDQutils/inst/doc/PDQutils.Rnw | 119 +++++++++++++++++++
PDQutils-0.1.1/PDQutils/inst/doc/PDQutils.pdf |binary
PDQutils-0.1.1/PDQutils/man/AS269.Rd | 2
PDQutils-0.1.1/PDQutils/man/NEWS.Rd | 7 +
PDQutils-0.1.1/PDQutils/man/PDQutils.Rd | 4
PDQutils-0.1.1/PDQutils/man/dapx_edgeworth.Rd |only
PDQutils-0.1.1/PDQutils/man/dapx_gca.Rd | 12 +
PDQutils-0.1.1/PDQutils/man/qapx_cf.Rd | 12 +
PDQutils-0.1.1/PDQutils/man/rapx_cf.Rd | 7 -
PDQutils-0.1.1/PDQutils/vignettes/PDQutils.Rnw | 119 +++++++++++++++++++
PDQutils-0.1.1/PDQutils/vignettes/PDQutils.bib | 32 +++++
22 files changed, 540 insertions(+), 67 deletions(-)
Title: Association Analysis of CNV Data and Imputed SNPs
Diff between CNVassoc versions 2.0.1 dated 2013-09-19 and 2.1 dated 2015-02-26
Description: The CNVassoc package carries out analysis of common
Copy Number Variants (CNVs) and imputed Single Nucleotide
Polymorphisms (SNPs) in population-based studies.
It includes tools for estimating association under a series
of study designs (case-control, cohort, etc), using several
dependent variables (class status, censored data, counts)
as response, adjusting for covariates and considering
various inheritance models. Moreover, it is possible to
perform epistasis studies with pairs of CNVs or imputed SNPs.
It has been optimized in order to make feasible the analyses
of Genome Wide Association studies (GWAs) with hundreds of
thousands of genetic variants (CNVs / imputed SNPs). Also,
it incorporates functions for inferring copy number (CNV
genotype calling). Various classes and methods for generic
functions (print, summary, plot, anova, ...) have been
created to facilitate the analysis.
Author: Juan R González, Isaac Subirana
Maintainer: Isaac Subirana
DESCRIPTION | 38 ++++++++++++++++++++++----------------
MD5 | 31 ++++++++++++++++++++++---------
NAMESPACE | 10 +++++++++-
R/fastCNVassoc.R | 12 +++++++++---
R/fastCNVinter.R |only
R/getProbs.cghCall.R | 22 ++++++++++++----------
R/plapply.R | 2 +-
build |only
inst/doc/changelog.txt | 5 +++++
man/fastCNVassoc.Rd | 4 +++-
man/fastCNVinter.Rd |only
man/simCNVdataWeibull.Rd | 2 +-
src/CNVassoc.h | 10 ++++++++++
src/NRinterlogistic.c |only
src/NRinterlogisticcov.c |only
src/NRinterweibull.c |only
src/NRinterweibullcov.c |only
src/loglikinterlogistic.c |only
src/loglikinterlogisticcov.c |only
src/loglikinterweibull.c |only
src/loglikinterweibullcov.c |only
src/outerC.c |only
src/simcensrespC.c |only
23 files changed, 94 insertions(+), 42 deletions(-)
Title: Rcmdr Receiver Operator Characteristic Plug-In PACKAGE
Diff between RcmdrPlugin.ROC versions 1.0-17 dated 2014-12-20 and 1.0-18 dated 2015-02-26
More information about RcmdrPlugin.ROC at CRAN
Description: Rcmdr GUI extension plug-in for Receiver Operator Characteristic tools from pROC and ROCR packages. Also it ads a Rcmdr GUI extension for Hosmer and Lemeshow GOF test from the package ResourceSelection.
Author: Daniel-Corneliu Leucuta [aut, cre],
Mihaela Hedesiu [ctb],
Andrei Achimas [ctb],
Oana Almasan [ctb]
Maintainer: Daniel-Corneliu Leucuta
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
NAMESPACE | 6 +++---
inst/CHANGES | 2 ++
4 files changed, 13 insertions(+), 11 deletions(-)
Permanent link
Title: An R Interface to the Oniguruma Regular Expression Library
Diff between ore versions 1.0.6 dated 2015-01-01 and 1.1.0 dated 2015-02-26
Description: Provides an alternative to R's built-in functionality for handling
regular expressions, based on the Oniguruma library. It offers first-class
compiled regex objects, partial matching and function-based substitutions,
amongst other features.
Author: Jon Clayden, based on Onigmo by K. Kosako and K. Takata
Maintainer: Jon Clayden
ore-1.0.6/ore/src/main.c |only
ore-1.0.6/ore/src/main.h |only
ore-1.0.6/ore/src/onig/enc/big5.c |only
ore-1.0.6/ore/src/onig/enc/cp1251.c |only
ore-1.0.6/ore/src/onig/enc/cp932.c |only
ore-1.0.6/ore/src/onig/enc/euc_jp.c |only
ore-1.0.6/ore/src/onig/enc/euc_kr.c |only
ore-1.0.6/ore/src/onig/enc/euc_tw.c |only
ore-1.0.6/ore/src/onig/enc/gb18030.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_10.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_11.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_13.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_14.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_15.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_16.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_2.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_3.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_4.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_5.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_6.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_7.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_8.c |only
ore-1.0.6/ore/src/onig/enc/iso8859_9.c |only
ore-1.0.6/ore/src/onig/enc/jis |only
ore-1.0.6/ore/src/onig/enc/koi8.c |only
ore-1.0.6/ore/src/onig/enc/koi8_r.c |only
ore-1.0.6/ore/src/onig/enc/sjis.c |only
ore-1.0.6/ore/src/onig/enc/utf16_be.c |only
ore-1.0.6/ore/src/onig/enc/utf16_le.c |only
ore-1.0.6/ore/src/onig/enc/utf32_be.c |only
ore-1.0.6/ore/src/onig/enc/utf32_le.c |only
ore-1.1.0/ore/DESCRIPTION | 9 +-
ore-1.1.0/ore/MD5 | 81 +++++++-----------
ore-1.1.0/ore/NAMESPACE | 5 -
ore-1.1.0/ore/NEWS | 25 +++++
ore-1.1.0/ore/R/dict.R |only
ore-1.1.0/ore/R/es.R |only
ore-1.1.0/ore/R/match.R | 92 ++++++++++++--------
ore-1.1.0/ore/R/ore.R | 23 +++--
ore-1.1.0/ore/R/workspace.R |only
ore-1.1.0/ore/README.md | 66 +++++++++++++-
ore-1.1.0/ore/man/es.Rd |only
ore-1.1.0/ore/man/matches.Rd | 6 +
ore-1.1.0/ore/man/ore.Rd | 23 +++--
ore-1.1.0/ore/man/ore.dict.Rd |only
ore-1.1.0/ore/man/ore.ismatch.Rd | 3
ore-1.1.0/ore/man/ore.lastmatch.Rd | 3
ore-1.1.0/ore/man/ore.search.Rd | 26 ++++-
ore-1.1.0/ore/man/ore.split.Rd | 3
ore-1.1.0/ore/man/ore.subst.Rd | 12 ++
ore-1.1.0/ore/src/Makevars | 4
ore-1.1.0/ore/src/compile.c |only
ore-1.1.0/ore/src/compile.h |only
ore-1.1.0/ore/src/match.c |only
ore-1.1.0/ore/src/match.h |only
ore-1.1.0/ore/src/onig/oniguruma.h | 125 +++++++++++++++-------------
ore-1.1.0/ore/src/print.c |only
ore-1.1.0/ore/src/print.h |only
ore-1.1.0/ore/src/split.c |only
ore-1.1.0/ore/src/split.h |only
ore-1.1.0/ore/src/subst.c |only
ore-1.1.0/ore/src/subst.h |only
ore-1.1.0/ore/src/zzz.c |only
ore-1.1.0/ore/src/zzz.h |only
ore-1.1.0/ore/tests/testthat/test-20-dict.R |only
ore-1.1.0/ore/tests/testthat/test-25-es.R |only
66 files changed, 324 insertions(+), 182 deletions(-)
Title: Tools for Nonlinear Regression Analysis
Diff between nlstools versions 1.0-0 dated 2014-06-25 and 1.0-1 dated 2015-02-26
Description: Several tools for assessing the quality of fit of a
gaussian nonlinear model are provided.
Author: Florent Baty
Maintainer: Florent Baty
ChangeLog | 7 ++++++-
DESCRIPTION | 10 +++++-----
MD5 | 14 +++++++++-----
NAMESPACE | 4 ++++
R/confint2.R |only
data/L.minor.rda |only
inst/CITATION | 8 ++++----
inst/NEWS | 10 +++++++++-
man/L.minor.Rd |only
man/confint2.Rd |only
10 files changed, 37 insertions(+), 16 deletions(-)
Title: Graphical Tests for Hardy-Weinberg Equilibrium
Diff between HardyWeinberg versions 1.5.4 dated 2014-08-11 and 1.5.5 dated 2015-02-26
Description: Contains tools for exploring Hardy-Weinberg equilibrium for
diallelic genetic marker data. All classical tests (chi-square, exact,
likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium
are included in the package, as well as functions for power computation and
for the simulation of marker data under equilibrium and disequilibrium.
Functions for testing equilibrium in the presence of missing data by
using multiple imputation are also provided. Implements several graphics
for exploring the equilibrium status of a large set of diallelic markers:
ternary plots with acceptance regions, log-ratio plots and Q-Q plots.
Author: Jan Graffelman
Maintainer: Jan Graffelman
HardyWeinberg-1.5.4/HardyWeinberg/R/combineC.R |only
HardyWeinberg-1.5.5/HardyWeinberg/DESCRIPTION | 25 +
HardyWeinberg-1.5.5/HardyWeinberg/MD5 | 62 +++-
HardyWeinberg-1.5.5/HardyWeinberg/NAMESPACE | 2
HardyWeinberg-1.5.5/HardyWeinberg/R/CombineChisquare.R |only
HardyWeinberg-1.5.5/HardyWeinberg/R/CombineExact.R |only
HardyWeinberg-1.5.5/HardyWeinberg/R/HWAlltests.R | 12
HardyWeinberg-1.5.5/HardyWeinberg/R/HWChisq.R | 6
HardyWeinberg-1.5.5/HardyWeinberg/R/HWMissing.R | 137 +++++-----
HardyWeinberg-1.5.5/HardyWeinberg/R/HWPerm.R | 4
HardyWeinberg-1.5.5/HardyWeinberg/R/HWTernaryPlot.R | 6
HardyWeinberg-1.5.5/HardyWeinberg/R/MakeFactor.R |only
HardyWeinberg-1.5.5/HardyWeinberg/R/mipvalue.R |only
HardyWeinberg-1.5.5/HardyWeinberg/R/missingentirerow.R |only
HardyWeinberg-1.5.5/HardyWeinberg/build |only
HardyWeinberg-1.5.5/HardyWeinberg/inst |only
HardyWeinberg-1.5.5/HardyWeinberg/man/HWAlltests.Rd | 7
HardyWeinberg-1.5.5/HardyWeinberg/man/HWChisq.Rd | 7
HardyWeinberg-1.5.5/HardyWeinberg/man/HWIlrPlot.Rd | 4
HardyWeinberg-1.5.5/HardyWeinberg/man/HWMissing.Rd | 32 +-
HardyWeinberg-1.5.5/HardyWeinberg/man/HWPerm.Rd | 6
HardyWeinberg-1.5.5/HardyWeinberg/man/HWPower.Rd | 9
HardyWeinberg-1.5.5/HardyWeinberg/man/HWQqplot.Rd | 2
HardyWeinberg-1.5.5/HardyWeinberg/man/HWTernaryPlot.Rd | 6
HardyWeinberg-1.5.5/HardyWeinberg/man/HardyWeinberg-package.Rd | 28 +-
HardyWeinberg-1.5.5/HardyWeinberg/man/MakeFactor.Rd |only
HardyWeinberg-1.5.5/HardyWeinberg/man/Markers.Rd | 7
HardyWeinberg-1.5.5/HardyWeinberg/vignettes |only
28 files changed, 233 insertions(+), 129 deletions(-)
Title: Tools to Deal with Fuzzy Numbers
Diff between FuzzyNumbers versions 0.3-5 dated 2014-10-01 and 0.4-1 dated 2015-02-26
Description: S4 classes and methods
to deal with fuzzy numbers. With them you can compute any arithmetic
operations (e.g. by using the Zadeh extension principle),
perform approximation of arbitrary FNs by trapezoidal and piecewise
linear FNs, prepare plots of FNs for publications, calculate
possibility and necessity values for comparisons, etc.
Author: Marek Gagolewski [aut, cre],
Jan Caha [ctb]
Maintainer: Marek Gagolewski
DESCRIPTION | 19 +-
MD5 | 117 +++++++-----
NAMESPACE | 13 +
NEWS | 16 +
R/methods-Arithmetic.R | 6
R/methods-compare.R |only
R/methods-min_max.R |only
R/methods-special_functions.R |only
build/vignette.rds |binary
inst/CITATION | 6
inst/doc/FuzzyNumbersTutorial.R | 72 +++++++
inst/doc/FuzzyNumbersTutorial.Rnw | 175 ++++++++++++++++++-
inst/doc/FuzzyNumbersTutorial.pdf |binary
man/Arithmetic-methods.Rd | 31 +++
man/DiscontinuousFuzzyNumber-class.Rd | 3
man/DiscontinuousFuzzyNumber.Rd | 3
man/Extract-methods.Rd | 3
man/FuzzyNumber-class.Rd | 3
man/FuzzyNumber.Rd | 3
man/FuzzyNumbers-package.Rd | 3
man/PiecewiseLinearFuzzyNumber-class.Rd | 28 ++-
man/PiecewiseLinearFuzzyNumber.Rd | 28 ++-
man/PowerFuzzyNumber-class.Rd | 3
man/PowerFuzzyNumber.Rd | 3
man/TrapezoidalFuzzyNumber-class.Rd | 3
man/TrapezoidalFuzzyNumber.Rd | 3
man/TriangularFuzzyNumber.Rd | 3
man/alphaInterval-methods.Rd | 28 ++-
man/alphacut-methods.Rd | 3
man/ambiguity-methods.Rd | 3
man/approxInvert.Rd | 3
man/arctan2.Rd |only
man/as.FuzzyNumber.Rd | 3
man/as.PiecewiseLinearFuzzyNumber.Rd | 28 ++-
man/as.PowerFuzzyNumber.Rd | 28 ++-
man/as.TrapezoidalFuzzyNumber.Rd | 28 ++-
man/as.character-methods.Rd | 28 ++-
man/convertAlpha.Rd | 3
man/convertSide.Rd | 3
man/core-methods.Rd | 3
man/distance-methods.Rd | 3
man/evaluate-methods.Rd | 3
man/expectedInterval-methods.Rd | 28 ++-
man/expectedValue-methods.Rd | 3
man/fapply-methods.Rd | 31 +++
man/integrateAlpha-methods.Rd | 3
man/integrate_discont_val.Rd | 3
man/maximum.Rd |only
man/minimum.Rd |only
man/necessityExceedance.Rd |only
man/necessityStrictExceedance.Rd |only
man/necessityStrictUndervaluation.Rd |only
man/necessityUndervaluation.Rd |only
man/piecewiseLinearApproximation-methods.Rd | 3
man/plot-methods.Rd | 28 ++-
man/possibilityExceedance.Rd |only
man/possibilityStrictExceedance.Rd |only
man/possibilityStrictUndervaluation.Rd |only
man/possibilityUndervaluation.Rd |only
man/pow-PiecewiseLinearFuzzyNumber-numeric-method.Rd |only
man/show-methods.Rd | 3
man/supp-methods.Rd | 3
man/trapezoidalApproximation-methods.Rd | 3
man/value-methods.Rd | 3
man/weightedExpectedValue-methods.Rd | 3
man/width-methods.Rd | 3
vignettes/FuzzyNumbersTutorial.Rnw | 175 ++++++++++++++++++-
67 files changed, 866 insertions(+), 137 deletions(-)
Title: Forecasting Functions for Time Series and Linear Models
Diff between forecast versions 5.8 dated 2015-01-06 and 5.9 dated 2015-02-26
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob J Hyndman
Maintainer: Rob J Hyndman
ChangeLog | 8 +++
DESCRIPTION | 10 ++--
MD5 | 22 ++++-----
NAMESPACE | 3 -
R/arfima.R | 6 +-
R/arima.R | 135 ++++++++++++++++++++++++++++----------------------------
R/errors.R | 3 +
R/fpp.R | 31 ++++++++++--
R/getResponse.R | 4 -
R/newarima2.R | 21 ++++----
R/tbats.R | 4 -
man/accuracy.Rd | 24 ++++++++-
12 files changed, 162 insertions(+), 109 deletions(-)
Title: Exact Conditional Tests and Confidence Intervals for 2x2 tables
Diff between exact2x2 versions 1.4.0 dated 2014-08-25 and 1.4.1 dated 2015-02-26
Description: Calculates Fisher's exact test, Blaker's exact test, or the exact McNemar's test with appropriate matching confidence intervals. Provides power and sample size calculations. Also gives melded confidence intervals for the binomial case.
Author: Michael P. Fay
Maintainer: Michael P. Fay
ChangeLog | 6 ++++++
DESCRIPTION | 8 ++++----
MD5 | 20 ++++++++++----------
R/ss2x2.R | 29 +++++++++++++++++++++++++----
build/vignette.rds |binary
inst/doc/exact2x2.pdf |binary
inst/doc/exactMcNemar.R | 6 +++---
inst/doc/exactMcNemar.Rnw | 21 ++++++++++++++++-----
inst/doc/exactMcNemar.pdf |binary
man/exact2x2-package.Rd | 4 ++--
vignettes/exactMcNemar.Rnw | 21 ++++++++++++++++-----
11 files changed, 82 insertions(+), 33 deletions(-)
Title: ODBC Database Access
Diff between RODBC versions 1.3-10 dated 2013-11-25 and 1.3-11 dated 2015-02-26
Description: An ODBC database interface.
Author: Brian Ripley [aut, cre],
Michael Lapsley [aut] (1999 to Oct 2002)
Maintainer: Brian Ripley
ChangeLog | 11 +++++
DESCRIPTION | 14 +++----
MD5 | 22 +++++------
R/RODBC.R | 4 +-
R/sql.R | 1
build/vignette.rds |binary
cleanup | 2 -
inst/doc/RODBC.Rnw | 98 ++++++++++++++++++++++++++--------------------------
inst/doc/RODBC.pdf |binary
man/sqlColumns.Rd | 4 +-
man/sqlTypeInfo.Rd | 2 -
vignettes/RODBC.Rnw | 98 ++++++++++++++++++++++++++--------------------------
12 files changed, 135 insertions(+), 121 deletions(-)
Title: Extended Mixed Models Using Latent Classes and Latent Processes
Diff between lcmm versions 1.6.6 dated 2014-09-11 and 1.7.1 dated 2015-02-26
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method.
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima
lcmm-1.6.6/lcmm/R/VarCov.lcmm..R |only
lcmm-1.6.6/lcmm/R/link.confint.lcmm.R |only
lcmm-1.6.6/lcmm/R/link.confint.multlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.Jointlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.baselinerisk.Jointlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.hlme.R |only
lcmm-1.6.6/lcmm/R/plot.lcmm.R |only
lcmm-1.6.6/lcmm/R/plot.linkfunction.lcmm.R |only
lcmm-1.6.6/lcmm/R/plot.linkfunction.multlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.multlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.postprob.Jointlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.postprob.hlme.R |only
lcmm-1.6.6/lcmm/R/plot.postprob.lcmm.R |only
lcmm-1.6.6/lcmm/R/plot.postprob.multlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.predict.Jointlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.predict.hlme.R |only
lcmm-1.6.6/lcmm/R/plot.predict.lcmm.R |only
lcmm-1.6.6/lcmm/R/plot.predict.multlcmm.R |only
lcmm-1.6.6/lcmm/R/plot.survival.Jointlcmm.R |only
lcmm-1.6.6/lcmm/man/link.confint.Rd |only
lcmm-1.6.6/lcmm/man/multlcmm.rd |only
lcmm-1.6.6/lcmm/man/plot.baselinerisk.Rd |only
lcmm-1.6.6/lcmm/man/plot.linkfunction.Rd |only
lcmm-1.6.6/lcmm/man/plot.postprob.Rd |only
lcmm-1.6.6/lcmm/man/plot.survival.Rd |only
lcmm-1.6.6/lcmm/src/predictDyn.f90 |only
lcmm-1.7.1/lcmm/DESCRIPTION | 17
lcmm-1.7.1/lcmm/MD5 | 187
lcmm-1.7.1/lcmm/NAMESPACE | 42
lcmm-1.7.1/lcmm/NEWS | 42
lcmm-1.7.1/lcmm/R/Contlcmm.R | 25
lcmm-1.7.1/lcmm/R/Jointlcmm.R | 2976 ++++++------
lcmm-1.7.1/lcmm/R/Ordlcmm.R | 18
lcmm-1.7.1/lcmm/R/VarCov.Jointlcmm.R | 53
lcmm-1.7.1/lcmm/R/VarCov.lcmm.R |only
lcmm-1.7.1/lcmm/R/VarCovRE.Jointlcmm.R | 314 -
lcmm-1.7.1/lcmm/R/VarCovRE.hlme.R | 39
lcmm-1.7.1/lcmm/R/VarCovRE.lcmm.R | 36
lcmm-1.7.1/lcmm/R/VarCovRE.multlcmm.R | 32
lcmm-1.7.1/lcmm/R/VarExpl.Jointlcmm.R | 251 -
lcmm-1.7.1/lcmm/R/VarExpl.hlme.R | 235
lcmm-1.7.1/lcmm/R/VarExpl.lcmm.R | 246 -
lcmm-1.7.1/lcmm/R/VarExpl.multlcmm.R | 261 -
lcmm-1.7.1/lcmm/R/WaldMult.R | 46
lcmm-1.7.1/lcmm/R/cuminc.R |only
lcmm-1.7.1/lcmm/R/dynpred.R | 1936 +++++--
lcmm-1.7.1/lcmm/R/epoce.R | 893 +--
lcmm-1.7.1/lcmm/R/estimates.Jointlcmm.R | 66
lcmm-1.7.1/lcmm/R/fitY.Jointlcmm.R |only
lcmm-1.7.1/lcmm/R/fitY.lcmm.R |only
lcmm-1.7.1/lcmm/R/fitY.multlcmm.R |only
lcmm-1.7.1/lcmm/R/hlme.R | 21
lcmm-1.7.1/lcmm/R/lcmm.R | 42
lcmm-1.7.1/lcmm/R/multlcmm.R | 100
lcmm-1.7.1/lcmm/R/plot.Diffepoce.R | 71
lcmm-1.7.1/lcmm/R/plot.R |only
lcmm-1.7.1/lcmm/R/plot.cuminc.R |only
lcmm-1.7.1/lcmm/R/plot.dynpred.R | 632 +-
lcmm-1.7.1/lcmm/R/plot.epoce.R | 22
lcmm-1.7.1/lcmm/R/plot.predictL.R |only
lcmm-1.7.1/lcmm/R/plot.predictY.R |only
lcmm-1.7.1/lcmm/R/plot.predictlink.R |only
lcmm-1.7.1/lcmm/R/plotbaselinerisk.R |only
lcmm-1.7.1/lcmm/R/plotfit.R |only
lcmm-1.7.1/lcmm/R/plotlinkfunction.R |only
lcmm-1.7.1/lcmm/R/plotlinkfunctionmult.R |only
lcmm-1.7.1/lcmm/R/plotpostprob.R |only
lcmm-1.7.1/lcmm/R/plotresid.R |only
lcmm-1.7.1/lcmm/R/plotsurvival.R |only
lcmm-1.7.1/lcmm/R/postprob.Jointlcmm.R | 45
lcmm-1.7.1/lcmm/R/predictL.Jointlcmm.R |only
lcmm-1.7.1/lcmm/R/predictL.lcmm.R | 236
lcmm-1.7.1/lcmm/R/predictL.multlcmm.R | 173
lcmm-1.7.1/lcmm/R/predictY.Jointlcmm.R | 1238 +++--
lcmm-1.7.1/lcmm/R/predictY.hlme.R | 189
lcmm-1.7.1/lcmm/R/predictY.lcmm.R | 85
lcmm-1.7.1/lcmm/R/predictY.multlcmm.R | 59
lcmm-1.7.1/lcmm/R/predictlink.Jointlcmm.R |only
lcmm-1.7.1/lcmm/R/predictlink.lcmm.R |only
lcmm-1.7.1/lcmm/R/predictlink.multlcmm.R |only
lcmm-1.7.1/lcmm/R/print.Diffepoce.R | 2
lcmm-1.7.1/lcmm/R/print.Jointlcmm.R | 187
lcmm-1.7.1/lcmm/R/risq_spl.R |only
lcmm-1.7.1/lcmm/R/risqcum_spl.R |only
lcmm-1.7.1/lcmm/R/summary.Jointlcmm.R | 565 +-
lcmm-1.7.1/lcmm/R/summarytable.R |only
lcmm-1.7.1/lcmm/man/Diffepoce.Rd | 6
lcmm-1.7.1/lcmm/man/ForInternalUse.Rd | 11
lcmm-1.7.1/lcmm/man/Jointlcmm.Rd | 119
lcmm-1.7.1/lcmm/man/VarExpl.Rd | 3
lcmm-1.7.1/lcmm/man/cuminc.Rd |only
lcmm-1.7.1/lcmm/man/data_hlme.Rd | 2
lcmm-1.7.1/lcmm/man/dynpred.Rd | 32
lcmm-1.7.1/lcmm/man/epoce.Rd | 6
lcmm-1.7.1/lcmm/man/fitY.Rd |only
lcmm-1.7.1/lcmm/man/hlme.Rd | 12
lcmm-1.7.1/lcmm/man/lcmm-package.Rd | 12
lcmm-1.7.1/lcmm/man/lcmm.Rd | 40
lcmm-1.7.1/lcmm/man/multlcmm.Rd |only
lcmm-1.7.1/lcmm/man/plot.cuminc.Rd |only
lcmm-1.7.1/lcmm/man/plot.dynpred.Rd | 19
lcmm-1.7.1/lcmm/man/plot.lcmm.Rd | 162
lcmm-1.7.1/lcmm/man/plot.pred.accuracy.Rd | 3
lcmm-1.7.1/lcmm/man/plot.predict.Rd | 81
lcmm-1.7.1/lcmm/man/postprob.Rd | 4
lcmm-1.7.1/lcmm/man/predictL.Rd | 41
lcmm-1.7.1/lcmm/man/predictY.Rd | 43
lcmm-1.7.1/lcmm/man/predictlink.Rd |only
lcmm-1.7.1/lcmm/man/print.lcmm.Rd | 2
lcmm-1.7.1/lcmm/man/summary.lcmm.Rd | 3
lcmm-1.7.1/lcmm/man/summarytable.Rd |only
lcmm-1.7.1/lcmm/src/AOptim.f90 | 26
lcmm-1.7.1/lcmm/src/Jointhet.f90 | 5841 +++++++++++++-----------
lcmm-1.7.1/lcmm/src/Makevars | 14
lcmm-1.7.1/lcmm/src/calculusTransfo.f90 | 6
lcmm-1.7.1/lcmm/src/cvpl.f90 | 3208 +++++++------
lcmm-1.7.1/lcmm/src/hetmixCont.f90 | 54
lcmm-1.7.1/lcmm/src/hetmixContMult.f90 | 71
lcmm-1.7.1/lcmm/src/hetmixOrd.f90 | 20
lcmm-1.7.1/lcmm/src/hetmixlin.f90 | 25
lcmm-1.7.1/lcmm/src/postprob2.f90 |only
lcmm-1.7.1/lcmm/src/predictCont.f90 | 7
lcmm-1.7.1/lcmm/src/predictMult.f90 | 4
123 files changed, 12217 insertions(+), 9042 deletions(-)
Title: Convert R Graphics to Flash Animations
Diff between R2SWF versions 0.8-2 dated 2014-12-19 and 0.9 dated 2015-02-26
Description: Using the Ming library
(http://www.libming.org/) to create Flash animations.
Users can either use the SWF device swf() to generate SWF file
directly through plotting functions like plot() and lines(),
or convert images of other formats (SVG, PNG, JPEG) into SWF.
Author: Yixuan Qiu, Yihui Xie, Cameron Bracken and authors of included
software. See file AUTHORS for details.
Maintainer: Yixuan Qiu
DESCRIPTION | 12 +-
MD5 | 8 -
NEWS | 44 +++++---
R/svg2swf.R | 299 ++++++++++++++++++++++++++++----------------------------
src/image2swf.c | 2
5 files changed, 189 insertions(+), 176 deletions(-)
Title: Cubature over Polygonal Domains
Diff between polyCub versions 0.5-1 dated 2014-10-24 and 0.5-2 dated 2015-02-26
Description: The following methods for cubature (numerical integration)
over polygonal domains are currently implemented:
the two-dimensional midpoint rule as a simple wrapper around
as.im.function() from package spatstat (Baddeley and Turner, 2005),
the product Gauss cubature by Sommariva and Vianello (2007),
an adaptive cubature for isotropic functions via line integrate()
along the boundary (Meyer and Held, 2014),
and quasi-exact methods specific to the integration of the
bivariate Gaussian density over polygonal and circular domains
(based on formulae from the Abramowitz and Stegun (1972) handbook).
For cubature over simple hypercubes, the packages "cubature" and
"R2Cuba" are more appropriate.
Author: Sebastian Meyer [aut, cre, trl],
Leonhard Held [ths],
Michael Hoehle [ths]
Maintainer: Sebastian Meyer
DESCRIPTION | 19 +++++----
MD5 | 64 ++++++++++++++++----------------
NAMESPACE | 8 +++-
R/coerce-gpc-methods.R | 22 ++++++++---
R/coerce-sp-methods.R | 63 ++++++++++++++++++++++----------
R/polyCub.exact.Gauss.R | 88 +++++++++++++++++++++++++++------------------
R/polyCub.iso.R | 41 +++++++++++++-------
R/polyCub.midpoint.R | 21 +++++-----
R/tools.R | 5 +-
R/xylist.R | 12 ++----
inst/CITATION | 10 -----
inst/NEWS.Rd | 24 ++++++++++++
man/checkintrfr.Rd | 3 +
man/circleCub.Gauss.Rd | 3 +
man/coerce-gpc-methods.Rd | 15 +++++--
man/coerce-sp-methods.Rd | 38 +++++++++++++++----
man/dotprod.Rd | 3 +
man/gpclibPermit.Rd | 3 +
man/isClosed.Rd | 3 +
man/isScalar.Rd | 3 +
man/makegrid.Rd | 3 +
man/plot_polyregion.Rd | 3 +
man/plotpolyf.Rd | 3 +
man/polyCub-package.Rd | 3 +
man/polyCub.Rd | 3 +
man/polyCub.SV.Rd | 3 +
man/polyCub.exact.Gauss.Rd | 9 ++--
man/polyCub.iso.Rd | 3 +
man/polyCub.midpoint.Rd | 10 ++++-
man/polygauss.Rd | 3 +
man/vecnorm.Rd | 3 +
man/xylist.Rd | 11 +++--
tests/test-all.R | 3 -
33 files changed, 324 insertions(+), 184 deletions(-)
Title: Permutations of Multisets in Cool-Lex Order
Diff between multicool versions 0.1-2 dated 2013-07-10 and 0.1-5 dated 2015-02-26
Description: A set of tools to permute multisets without loops or hash tables and to generate integer partitions. The permutation functions are based on C code from Aaron Williams. Cool-lex order is similar to colexicographical order. The algorithm is described in Williams, A. Loopless Generation of Multiset Permutations by Prefix Shifts. SODA 2009, Symposium on Discrete Algorithms, New York, United States. The permutation code is distributed without restrictions. The code for stable and efficient computation of multinomial coefficients comes from Dave Barber. The code can be download from http://home.comcast.net/~tamivox/dave/multinomial/index.html and is distributed without conditions. The package also generates the integer partitions of a positive, non-zero integer n. The C++ code for this is based on Python code from Jerome Kelleher which can be found here http://jeromekelleher.net/partitions.php. The C++ code and Python code are distributed without conditions.
Author: James Curran, Aaron Williams, Jerome Kelleher, Dave Barber
Maintainer: James Curran
DESCRIPTION | 21 +-
MD5 | 25 ++
NAMESPACE | 20 +-
R/RcppExports.R |only
R/Stirling2.R |only
R/allPerm.R | 28 +--
R/genComp.R |only
R/initMC.r | 91 +++++-----
R/multinom.R | 11 -
R/nextPerm.R | 28 +--
README.md |only
man/Bell.Rd |only
man/Stirling2.Rd |only
man/genComp.Rd |only
src/RcppExports.cpp |only
src/compositions.cpp |only
src/multicool.cpp | 430 ++++++++++++++++++++++++++++-----------------------
src/multinomial.h | 2
18 files changed, 354 insertions(+), 302 deletions(-)
Title: Precision-Recall and ROC Curves for Weighted and Unweighted Data
Diff between PRROC versions 1.0 dated 2014-12-16 and 1.1 dated 2015-02-25
Description: Computes the areas under the precision-recall (PR) and ROC curve for weighted (e.g., soft-labeled) and unweighted data. In contrast to other implementations, the interpolation between points of the PR curve is done by a non-linear piecewise function. In addition to the areas under the curves, the curves themselves can also be computed and plotted by a specific S3-method.
Author: Jan Grau and Jens Keilwagen
Maintainer: Jan Grau
DESCRIPTION | 9 ++-
MD5 | 21 +++++---
R/PRROC.R | 15 +-----
inst/doc/PRROC.R | 121 +++++++++++++++++++++++++++++++++++++--------------
inst/doc/PRROC.Rnw | 94 ++++++++++++++++++++++++++++++++++++++-
inst/doc/PRROC.pdf |binary
inst/tests |only
man/PRROC-package.Rd | 4 -
man/pr.curve.Rd | 7 +-
man/roc.curve.Rd | 6 --
tests |only
vignettes/PRROC.Rnw | 94 ++++++++++++++++++++++++++++++++++++++-
12 files changed, 300 insertions(+), 71 deletions(-)
Title: Hierarchical Exponential-Family Random Graph Models
Diff between hergm versions 2.1-1 dated 2015-01-11 and 2.2-0 dated 2015-02-25
Description: Estimate and simulate hierarchical exponential-family random graph models with local dependence.
Author: Michael Schweinberger
Maintainer: Michael Schweinberger
DESCRIPTION | 11 +++++------
MD5 | 14 +++++++-------
R/hergm.gof.R | 2 +-
R/hergm.postprocess.R | 24 ++++++++++++++----------
R/hergm.preprocess.R | 9 +++------
R/zzz.R | 1 +
man/hergm.gof.Rd | 14 +++++++++++++-
src/h_ergm.c | 19 +++++++++----------
8 files changed, 53 insertions(+), 41 deletions(-)
Title: General Frailty Models: Shared, Joint and Nested Frailty Models
with Prediction
Diff between frailtypack versions 2.7.2 dated 2014-10-16 and 2.7.4 dated 2015-02-25
Description: Frailtypack fits several classes of frailty models using a penalized likelihood
estimation on the hazard function but also a parametric estimation.
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox
proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated
random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of
clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of joint modelling for recurrent events
with terminal event for clustered data or not.
Prediction values are available. Left-truncated (not for Joint model),
right-censored data, interval-censored data (only for Cox proportional hazard
and shared frailty model) and strata are allowed. In each model,
the random effects have a gamma distribution, but you can switch to a log-normal
in shared and joint models. Now, you can also consider time-varying covariates
effects in Cox, shared and joint models. The package includes concordance measures
for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Agnieszka Krol-Listwon, Amadou Diakite and Alexandre Laurent
Maintainer: Virginie Rondeau
DESCRIPTION | 8
MD5 | 39 -
NEWS | 10
R/epoce.R | 37 +
R/frailtyPenal.R | 4
R/multivPenal.R | 6
R/plot.predFrailty.R | 8
R/prediction.R | 1291 ++++++++++++++++++++++-------------------
R/print.jointPenal.R | 2
R/print.predFrailty.R | 2
man/SurvIC.Rd | 2
man/prediction.Rd | 15
src/Aparameters.f90 | 3
src/Makevars | 3
src/aaOptim.f90 | 5
src/distance.f90 | 43 -
src/epoce_log.f90 |only
src/frailtypack.f90 | 46 -
src/funcpassplines_intcens.f90 | 10
src/joint.f90 | 1
src/prediction_log.f90 |only
src/prediction_sha_logn.f90 |only
22 files changed, 881 insertions(+), 654 deletions(-)
Title: Modelling Spatial Variation in Disease Risk for Areal Data
Diff between diseasemapping versions 1.1.5 dated 2015-01-15 and 1.1.7 dated 2015-02-25
More information about diseasemapping at CRAN
Description: Formatting of population and case data, calculation of Standardized Incidence Ratios, and fitting the BYM model using INLA.
Author: Patrick Brown
Maintainer: Patrick Brown
diseasemapping-1.1.5/diseasemapping/R/formatPopulation.SpatialPolygonsDataFrame.R |only
diseasemapping-1.1.5/diseasemapping/R/formatPopulation.data.frame.R |only
diseasemapping-1.1.5/diseasemapping/R/formatPopulation.list.R |only
diseasemapping-1.1.5/diseasemapping/R/getSMR.SpatialPolygonsDataFrame.R |only
diseasemapping-1.1.5/diseasemapping/R/getSMR.data.frame.R |only
diseasemapping-1.1.5/diseasemapping/R/getSMR.list.r |only
diseasemapping-1.1.7/diseasemapping/DESCRIPTION | 14 -
diseasemapping-1.1.7/diseasemapping/MD5 | 27 +--
diseasemapping-1.1.7/diseasemapping/NAMESPACE | 19 --
diseasemapping-1.1.7/diseasemapping/R/formatPopulation.R |only
diseasemapping-1.1.7/diseasemapping/R/getBreaks.R | 2
diseasemapping-1.1.7/diseasemapping/R/getSMR.R |only
diseasemapping-1.1.7/diseasemapping/R/mergeBugsData.R | 23 +-
diseasemapping-1.1.7/diseasemapping/man/cancerRates.Rd | 2
diseasemapping-1.1.7/diseasemapping/man/formatPopulation.Rd | 41 ++--
diseasemapping-1.1.7/diseasemapping/man/getSMR.Rd | 87 +++++++---
diseasemapping-1.1.7/diseasemapping/man/kentucky.Rd | 17 +
diseasemapping-1.1.7/diseasemapping/man/mergeBugsData.Rd | 20 +-
diseasemapping-1.1.7/diseasemapping/tests/getSMR.R |only
19 files changed, 156 insertions(+), 96 deletions(-)
Permanent link
Title: Visualization of Regression Models
Diff between visreg versions 2.1-0 dated 2014-11-27 and 2.1-1 dated 2015-02-25
Description: Provides a convenient interface for constructing plots to visualize the fit of regression models arising from a wide variety of models in R (lm, glm, coxph, rlm, gam, locfit, etc.)
Author: Patrick Breheny, Woodrow Burchett
Maintainer: Patrick Breheny
DESCRIPTION | 14 +++++++-------
MD5 | 21 +++++++++++----------
NEWS | 6 ++++++
R/Terms.R | 11 +++++++++--
R/plot.visreg.R | 3 ++-
R/setupX.R | 6 ++++++
R/visreg2d.R | 3 +--
R/visregLatticePlot.R | 1 +
README.md |only
inst/tests/formulas.R | 2 +-
inst/tests/mixed-models.R | 14 ++++++++++++++
tests/visreg-coxph.R | 1 +
12 files changed, 59 insertions(+), 23 deletions(-)
Title: Miscellaneous Functions for Survival Data
Diff between survMisc versions 0.4.4 dated 2015-01-06 and 0.4.5 dated 2015-02-25
Description: A collection of functions for analysis of survival data. These
extend the methods available in the survival package.
Author: Chris Dardis
Maintainer: Chris Dardis
DESCRIPTION | 6 +++---
MD5 | 10 +++++-----
NAMESPACE | 1 +
R/survMisc_package.R | 3 ++-
man/gof.Rd | 4 ++--
man/survMisc-package.Rd | 2 +-
6 files changed, 14 insertions(+), 12 deletions(-)
Title: Multitaper Spectral Analysis Tools
Diff between multitaper versions 1.0-10 dated 2015-02-18 and 1.0-11 dated 2015-02-25
Description: Implements multitaper spectral analysis using discrete prolate spheroidal sequences (Slepians) and sine tapers. It includes an adaptive weighted multitaper spectral estimate, a coherence estimate, Thomson's Harmonic F-test, and complex demodulation. The Slepians sequences are generated efficiently using a tridiagonal matrix solution, and jackknifed confidence intervals are available for most estimates.
Author: Karim Rahim
Maintainer: Karim Rahim
multitaper-1.0-10/multitaper/man/multitaper-package.Rd |only
multitaper-1.0-11/multitaper/DESCRIPTION | 10 ++++----
multitaper-1.0-11/multitaper/MD5 | 11 ++++-----
multitaper-1.0-11/multitaper/R/demod.R | 1
multitaper-1.0-11/multitaper/R/multitaper.R | 9 +++----
multitaper-1.0-11/multitaper/R/plots.R | 20 ++++++++---------
multitaper-1.0-11/multitaper/R/plotsHelper.R | 6 ++---
7 files changed, 27 insertions(+), 30 deletions(-)
Title: Multi-Model Inference
Diff between MuMIn versions 1.12.1 dated 2014-12-17 and 1.13.4 dated 2015-02-25
Description: Model selection and model averaging based on information criteria
(AICc and alike).
Author: Kamil Bartoń
Maintainer: Kamil Bartoń
MuMIn-1.12.1/MuMIn/R/QAIC.R |only
MuMIn-1.12.1/MuMIn/R/oldR.R |only
MuMIn-1.13.4/MuMIn/DESCRIPTION | 12
MuMIn-1.13.4/MuMIn/MD5 | 107 +++----
MuMIn-1.13.4/MuMIn/NAMESPACE | 20 -
MuMIn-1.13.4/MuMIn/NEWS | 46 +++
MuMIn-1.13.4/MuMIn/R/AICc.R | 102 ++++---
MuMIn-1.13.4/MuMIn/R/Cp.R | 2
MuMIn-1.13.4/MuMIn/R/DIC.R | 2
MuMIn-1.13.4/MuMIn/R/Weights.R | 2
MuMIn-1.13.4/MuMIn/R/coefTable.R | 9
MuMIn-1.13.4/MuMIn/R/dredge.R | 308 ++++++++++++-----------
MuMIn-1.13.4/MuMIn/R/ext-gamm.R | 2
MuMIn-1.13.4/MuMIn/R/ext.R | 60 +++-
MuMIn-1.13.4/MuMIn/R/formulas.R | 32 ++
MuMIn-1.13.4/MuMIn/R/get.models.R | 30 +-
MuMIn-1.13.4/MuMIn/R/getAllTerms.R | 192 +++++++-------
MuMIn-1.13.4/MuMIn/R/makeArgs.R | 37 +-
MuMIn-1.13.4/MuMIn/R/methods-logLik.R | 8
MuMIn-1.13.4/MuMIn/R/model.avg.R | 194 +++++++-------
MuMIn-1.13.4/MuMIn/R/model.sel.R | 93 +++---
MuMIn-1.13.4/MuMIn/R/model.selection.R | 66 ++--
MuMIn-1.13.4/MuMIn/R/pdredge.R | 272 +++++++++++---------
MuMIn-1.13.4/MuMIn/R/predict.R |only
MuMIn-1.13.4/MuMIn/R/quasiLik.R | 4
MuMIn-1.13.4/MuMIn/R/r.squaredGLMM.R | 31 --
MuMIn-1.13.4/MuMIn/R/r.squaredLR.R | 4
MuMIn-1.13.4/MuMIn/R/stdize.R | 115 ++++++--
MuMIn-1.13.4/MuMIn/R/substitution.R | 84 ++----
MuMIn-1.13.4/MuMIn/R/termdeps.R | 2
MuMIn-1.13.4/MuMIn/R/updateable.R | 20 -
MuMIn-1.13.4/MuMIn/R/utils-misc.R | 36 +-
MuMIn-1.13.4/MuMIn/R/utils-models.R | 102 ++++++-
MuMIn-1.13.4/MuMIn/man/AICc.Rd | 31 +-
MuMIn-1.13.4/MuMIn/man/ICs.Rd | 4
MuMIn-1.13.4/MuMIn/man/MuMIn-package.Rd | 5
MuMIn-1.13.4/MuMIn/man/QAIC.Rd | 12
MuMIn-1.13.4/MuMIn/man/QIC.Rd | 7
MuMIn-1.13.4/MuMIn/man/dredge.Rd | 42 +--
MuMIn-1.13.4/MuMIn/man/get.models.Rd | 9
MuMIn-1.13.4/MuMIn/man/importance.Rd | 8
MuMIn-1.13.4/MuMIn/man/mod.sel.Rd | 33 +-
MuMIn-1.13.4/MuMIn/man/model-utils.Rd | 19 -
MuMIn-1.13.4/MuMIn/man/model.avg.Rd | 83 +++---
MuMIn-1.13.4/MuMIn/man/nested.Rd | 4
MuMIn-1.13.4/MuMIn/man/pdredge.Rd | 4
MuMIn-1.13.4/MuMIn/man/predict.averaging.Rd | 29 +-
MuMIn-1.13.4/MuMIn/man/r.squaredGLMM.Rd | 5
MuMIn-1.13.4/MuMIn/man/stdize.Rd | 152 +++++++----
MuMIn-1.13.4/MuMIn/man/subset.model.selection.Rd | 10
MuMIn-1.13.4/MuMIn/man/updateable.Rd | 33 +-
MuMIn-1.13.4/MuMIn/man/weights.Rd | 10
MuMIn-1.13.4/MuMIn/tests/_gam.R | 3
MuMIn-1.13.4/MuMIn/tests/classes.R | 12
MuMIn-1.13.4/MuMIn/tests/coxme.R | 11
MuMIn-1.13.4/MuMIn/tests/unmarked.R | 36 +-
56 files changed, 1515 insertions(+), 1041 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-30 2.11.2.1
2014-06-25 2.11.1.1
2013-07-16 1.0.4
2013-06-25 1.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-14 0.9.5
Title: Construction, Simulation and Analysis of Boolean Networks
Diff between BoolNet versions 2.1.0 dated 2015-02-23 and 2.1.1 dated 2015-02-25
Description: Provides methods to reconstruct and generate synchronous,
asynchronous, probabilistic and temporal Boolean networks, and to
analyze and visualize attractors in Boolean networks.
Author: Christoph Müssel [aut],
Martin Hopfensitz [aut],
Dao Zhou [aut],
Hans A. Kestler [aut, cre],
Armin Biere [ctb] (contributed PicoSAT code),
Troy D. Hanson [ctb] (contributed uthash macros)
Maintainer: Hans A. Kestler
DESCRIPTION | 10
MD5 | 13
inst/NEWS.Rd | 6
inst/doc/BoolNet_package_vignette.pdf | 1555 +++++++++++++++++-----------------
man/BoolNet-package.Rd | 4
src/Makevars.win |only
src/picosat.c | 15
src/symbolic_simulator.c | 2
8 files changed, 809 insertions(+), 796 deletions(-)
Title: Serial Dependence Diagrams
Diff between SDD versions 1.1 dated 2014-02-27 and 1.2 dated 2015-02-25
Description: Allows for computing (and by default plotting) different types of serial dependence diagrams.
Author: Luca Bagnato, Lucio De Capitani, Angelo Mazza and Antonio Punzo
Maintainer: Angelo Mazza
DESCRIPTION | 10 +++++-----
MD5 | 9 +++++----
inst |only
man/ADF.Rd | 6 ++++--
man/SDD-package.Rd | 12 +++++++-----
man/SMI.Rd | 2 ++
6 files changed, 23 insertions(+), 16 deletions(-)
Title: Log-Gaussian Cox Process
Diff between lgcp versions 1.3-8 dated 2015-02-04 and 1.3-9 dated 2015-02-25
Description: Spatial and spatio-temporal modelling of point patterns using the
log-Gaussian Cox process. Bayesian inference for spatial, spatiotemporal,
multivariate and aggregated point processes using Markov chain Monte Carlo.
Author: B. M. Taylor, T. M. Davies, B. S. Rowlingson, P. J. Diggle. Additional
code contributions from E. Pebesma.
Maintainer: Benjamin M. Taylor
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
inst/doc/lgcp.pdf |binary
3 files changed, 6 insertions(+), 6 deletions(-)
Title: Feature Grouping and Selection Over an Undirected Graph
Diff between FGSG versions 1.0 dated 2014-04-13 and 1.0.2 dated 2015-02-25
Description: Implement algorithms for feature grouping and selection over an undirected graph, solves problems like graph fused lasso, graph OSCAR and so on.
Author: Xiaotong Shen, Yiwen Sun, Julie Langou
Maintainer: Yiwen Sun
DESCRIPTION | 10 +++++-----
MD5 | 20 ++++++++++----------
NAMESPACE | 8 +++++++-
man/gflasso.Rd | 28 +++++++++++++++-------------
man/goscar.Rd | 27 ++++++++++++++-------------
man/ncFGS.Rd | 27 ++++++++++++++-------------
man/ncTF.Rd | 27 ++++++++++++++-------------
man/ncTFGS.Rd | 28 +++++++++++++++-------------
man/ncTL.Rd | 29 +++++++++++++++--------------
man/ncTLF.Rd | 29 +++++++++++++++--------------
src/lafunc.h | 22 +++++++++++-----------
11 files changed, 135 insertions(+), 120 deletions(-)
Title: Soil Database Interface
Diff between soilDB versions 1.5 dated 2015-02-20 and 1.5-2 dated 2015-02-25
Description: A collection of functions for reading data from USDA-NCSS soil databases.
Author: D.E. Beaudette and J.M. Skovlin
Maintainer: D.E. Beaudette
DESCRIPTION | 15 -
MD5 | 44 ++--
NEWS | 3
R/SDA_query.R | 2
R/SSURGO_spatial_query.R | 2
R/fetchNASIS.R | 4
R/fetchPedonPC.R | 4
R/get_colors_from_NASIS_db.R | 4
R/get_extended_data_from_NASIS_db.R | 4
R/get_hz_data_from_NASIS_db.R | 4
R/get_lablayer_data_from_NASIS_db.R | 6
R/get_labpedon_data_from_NASIS_db.R | 4
R/get_site_data_from_NASIS_db.R | 4
R/get_text_notes_from_NASIS_db.R | 4
R/mapunit_geom_by_ll_bbox.R | 2
R/nasis_component_data.R | 338 ++++++++++++++++++------------------
R/seriesExtent.R | 4
data/andic.subset.rda |binary
data/cisne.rda |binary
data/gSSURGO.chunk.rda |binary
data/gopheridge.rda |binary
data/loafercreek.rda |binary
man/SDA_query.Rd | 2
23 files changed, 224 insertions(+), 226 deletions(-)
Title: Skewed Generalized T Distribution
Diff between sgt versions 1.0 dated 2015-02-16 and 1.1 dated 2015-02-25
Description: Density, distribution function, quantile function and random generation for the skewed generalized t distribution. This package also provides a function that can fit data to the skewed generalized t distribution using maximum likelihood estimation.
Author: Carter Davis
Maintainer: Carter Davis
sgt-1.0/sgt/src |only
sgt-1.1/sgt/DESCRIPTION | 12 ++---
sgt-1.1/sgt/MD5 | 16 ++----
sgt-1.1/sgt/NAMESPACE | 2
sgt-1.1/sgt/R/SGT.R | 114 ++++++++++++++++++++++++------------------------
sgt-1.1/sgt/R/SGTMLE.R | 2
sgt-1.1/sgt/man/sgt.Rd | 24 ++--------
7 files changed, 77 insertions(+), 93 deletions(-)
Title: Read and Write MAT Files and Call MATLAB from Within R
Diff between R.matlab versions 3.1.1 dated 2014-10-10 and 3.2.0 dated 2015-02-25
Description: Methods readMat() and writeMat() for reading and writing MAT files. For user with MATLAB v6 or newer installed (either locally or on a remote host), the package also provides methods for controlling MATLAB (trademark) via R and sending and retrieving data between R and MATLAB.
Author: Henrik Bengtsson [aut, cre, cph], Andy Jacobson [ctb] (Internal MAT v4 reader), Jason Riedy [ctb] (Support for reading compressed files (via 'Rcompression'), sparse matrices and UTF-encoded strings.)
Maintainer: Henrik Bengtsson
DESCRIPTION | 17 +--
MD5 | 25 ++--
NEWS | 25 ++++
R/999.package.R | 2
R/Matlab.R | 25 +++-
R/readMat.R | 142 +++++++++++++++++---------
R/zzz.R | 2
inst/externals/MatlabServer.m | 9 +
inst/mat-files/SparseMatrix,all_zeros.mat |only
man/1._The_MATLAB_server_running_in_MATLAB.Rd | 9 +
man/Matlab.Rd | 43 +++++++
man/R.matlab-package.Rd | 9 -
man/readMat.Rd | 16 ++
tests/readMat.R | 84 +++++++++++----
14 files changed, 291 insertions(+), 117 deletions(-)
Title: Nonparametric Comparison of Multivariate Samples
Diff between npmv versions 2.1 dated 2013-12-04 and 2.2 dated 2015-02-25
Description: Performs analysis of one-way multivariate data, for small samples using Nonparametric techniques. Using approximations for ANOVA Type, Wilks' Lambda, Lawley Hotelling, and Bartlett Nanda Pillai Test statics, the package compares the multivariate distributions for a single explanatory variable. The comparison is also performed using a permutation test for each of the four test statistics. The package also performs an all-subsets algorithm regarding variables and regarding factor levels.
Author: Woodrow Burchett and Amanda Ellis
Maintainer: Amanda Ellis
DESCRIPTION | 10 +++---
MD5 | 14 ++++-----
NAMESPACE | 1
R/basenonpartest.R | 17 ++++++++++-
R/nonpartest.R | 56 ++++++++++++++++++++++++++++++--------
R/ssnonpartest.R | 76 +++++++++++++++++++++++++++++++++++++++++-----------
man/nonpartest.Rd | 7 +++-
man/npmv-package.Rd | 4 +-
8 files changed, 141 insertions(+), 44 deletions(-)
Title: Variable Importance Analysis with Population Intervention Models
Diff between multiPIM versions 1.4-1 dated 2014-04-14 and 1.4-3 dated 2015-02-25
Description: Performs variable importance analysis using a causal inference approach. This is done by fitting Population Intervention Models. The default is to use a Targeted Maximum Likelihood Estimator (TMLE). The other available estimators are Inverse Probability of Censoring Weighted (IPCW), Double-Robust IPCW (DR-IPCW), and Graphical Computation (G-COMP) estimators. Inference can be obtained from the influence curve (plug-in) or by bootstrapping.
Author: Stephan Ritter
Maintainer: Stephan Ritter
multiPIM-1.4-1/multiPIM/R/zzz.R |only
multiPIM-1.4-3/multiPIM/ChangeLog | 4 ++++
multiPIM-1.4-3/multiPIM/DESCRIPTION | 8 ++++----
multiPIM-1.4-3/multiPIM/MD5 | 7 +++----
multiPIM-1.4-3/multiPIM/R/multiPIMboot.R | 15 +++++++--------
5 files changed, 18 insertions(+), 16 deletions(-)
Title: Less Code, More Results
Diff between lessR versions 3.1.1 dated 2014-09-23 and 3.2 dated 2015-02-25
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate descriptive statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function and color themes. The function Help provides a help system that suggests specific analyses and functions. Variable labels are available. A confirmatory factor analysis of multiple indicator measurement models is also available as is a pedagogical routines for data simulation such as for the Central Limit Theorem.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing
lessR-3.1.1/lessR/R/den.zmain.R |only
lessR-3.2/lessR/DESCRIPTION | 8
lessR-3.2/lessR/MD5 | 87 +++----
lessR-3.2/lessR/NEWS | 33 ++
lessR-3.2/lessR/R/ANOVA.R | 17 +
lessR-3.2/lessR/R/ANOVAz1.R | 46 ++-
lessR-3.2/lessR/R/ANOVAz2.R | 36 ++
lessR-3.2/lessR/R/BarChart.R | 6
lessR-3.2/lessR/R/BoxPlot.R | 4
lessR-3.2/lessR/R/Density.R | 4
lessR-3.2/lessR/R/Help.R | 272 +++++++++-------------
lessR-3.2/lessR/R/Histogram.R | 6
lessR-3.2/lessR/R/LineChart.R | 4
lessR-3.2/lessR/R/Logit.R | 2
lessR-3.2/lessR/R/Regression.R | 21 +
lessR-3.2/lessR/R/ScatterPlot.R | 27 +-
lessR-3.2/lessR/R/bc.data.frame.R | 4
lessR-3.2/lessR/R/bc.zmain.R | 6
lessR-3.2/lessR/R/bx.zmain.R | 8
lessR-3.2/lessR/R/corScree.R | 33 ++
lessR-3.2/lessR/R/dn.zmain.R | 6
lessR-3.2/lessR/R/dp.zmain.R | 4
lessR-3.2/lessR/R/hst.zmain.R | 6
lessR-3.2/lessR/R/lc.zmain.R | 6
lessR-3.2/lessR/R/logit.z4Pred.R | 7
lessR-3.2/lessR/R/pc.zmain.R | 31 ++
lessR-3.2/lessR/R/plt.zmain.R | 10
lessR-3.2/lessR/R/reg.z3Residual.R | 297 ++++++++++++------------
lessR-3.2/lessR/R/reg.z5Plot.R | 56 +++-
lessR-3.2/lessR/R/simCLT.R | 2
lessR-3.2/lessR/R/tt.z1graph.R | 2
lessR-3.2/lessR/R/tt.z1group.R | 86 ++++--
lessR-3.2/lessR/R/tt.z2graph.R | 2
lessR-3.2/lessR/R/tt.z2group.R | 75 +++---
lessR-3.2/lessR/R/ttest.R | 456 ++++++++++++++++++++++++++++++++-----
lessR-3.2/lessR/R/ttp2zgraph.R | 2
lessR-3.2/lessR/R/zzz.R | 67 +++--
lessR-3.2/lessR/man/BarChart.Rd | 5
lessR-3.2/lessR/man/BoxPlot.Rd | 7
lessR-3.2/lessR/man/Density.Rd | 9
lessR-3.2/lessR/man/Histogram.Rd | 14 -
lessR-3.2/lessR/man/LineChart.Rd | 21 +
lessR-3.2/lessR/man/PieChart.Rd | 4
lessR-3.2/lessR/man/ScatterPlot.Rd | 9
lessR-3.2/lessR/man/ttest.Rd | 2
45 files changed, 1179 insertions(+), 631 deletions(-)
Title: Interactive Q-Learning
Diff between iqLearn versions 1.2 dated 2014-03-04 and 1.3 dated 2015-02-25
Description: Estimate an optimal dynamic treatment regime using Interactive Q-learning.
Author: Kristin A. Linn, Eric B. Laber, Leonard A. Stefanski
Maintainer: Kristin A. Linn
DESCRIPTION | 10 +++---
MD5 | 68 ++++++++++++++++++++++----------------------
NAMESPACE | 36 +++++++++++++++++++++++
README.md |only
build/vignette.rds |binary
inst/CITATION |only
inst/doc/iqLearn.Rnw | 2 -
inst/doc/iqLearn.pdf |binary
man/IQ1.Rd | 5 +--
man/IQ2.Rd | 5 +--
man/iqLearn-package.Rd | 5 +--
man/learnIQ1.Rd | 5 +--
man/learnIQ1cm.Rd | 5 +--
man/learnIQ1main.Rd | 5 +--
man/learnIQ1var.Rd | 5 +--
man/learnIQ2.Rd | 5 +--
man/plot.iqResids.Rd | 5 +--
man/plot.learnIQ1cm.Rd | 5 +--
man/plot.learnIQ1main.Rd | 5 +--
man/plot.learnIQ1var.Rd | 5 +--
man/plot.learnIQ2.Rd | 5 +--
man/plot.qLearnS1.Rd | 5 +--
man/plot.qLearnS2.Rd | 5 +--
man/qLearnQ1.Rd | 5 +--
man/qLearnQ2.Rd | 5 +--
man/qLearnS1.Rd | 5 +--
man/qLearnS2.Rd | 5 +--
man/summary.learnIQ1cm.Rd | 5 +--
man/summary.learnIQ1main.Rd | 5 +--
man/summary.learnIQ1var.Rd | 5 +--
man/summary.learnIQ2.Rd | 5 +--
man/summary.qLearnS1.Rd | 5 +--
man/summary.qLearnS2.Rd | 5 +--
man/summary.value.Rd | 5 +--
man/value.Rd | 5 +--
vignettes/iqLearn.Rnw | 2 -
36 files changed, 159 insertions(+), 94 deletions(-)
Title: Dunn's Test of Multiple Comparisons Using Rank Sums
Diff between dunn.test versions 1.2.2 dated 2015-01-03 and 1.2.3 dated 2015-02-25
Description: Computes Dunn's test (1964) for stochastic dominance and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. dunn.test makes k(k-1)/2 multiple pairwise comparisons based on Dunn's z-test-statistic approximations to the actual rank statistics. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Dunn's test may be understood as a test for median difference. dunn.test accounts for tied ranks.
Author: Alexis Dinno
Maintainer: Alexis Dinno
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
R/dunn.test.R | 18 ++++++++++++++----
man/dunn.test.Rd | 3 ++-
4 files changed, 24 insertions(+), 13 deletions(-)
More information about BayesSummaryStatLM at CRAN
Permanent link
Title: Pull Data from 'trakt.tv'
Diff between tRakt versions 0.7.4 dated 2015-02-23 and 0.9.0 dated 2015-02-24
Description: A wrapper for the trakt.tv APIv2 which uses httr and jsonlite to send non-OAuth2 requests and receive tidied data.
Author: Lukas Burk [aut, cre]
Maintainer: Lukas Burk
DESCRIPTION | 13 -
MD5 | 98 ++++----
NAMESPACE | 4
R/api.R | 25 +-
R/trakt.getEpisodeData.R | 63 ++---
R/trakt.getFullShowData.R | 32 +-
R/trakt.getSeasons.R | 11
R/trakt.search.R | 21 -
R/trakt.search.byid.R | 15 -
R/trakt.show.people.R | 20 +
R/trakt.show.related.R | 18 +
R/trakt.show.season.R | 41 ++-
R/trakt.show.stats.R | 13 -
R/trakt.show.summary.R | 19 -
R/trakt.shows.popular.R | 21 +
R/trakt.shows.trending.R | 25 +-
R/trakt.user.collection.R | 5
R/trakt.user.followers.R |only
R/trakt.user.following.R |only
R/trakt.user.friends.R |only
R/trakt.user.ratings.R |only
R/trakt.user.stats.R | 10
R/trakt.user.watched.R | 18 -
R/trakt.user.watchlist.R | 4
README.md | 39 ---
inst/doc/tRakt-Usage.R | 10
inst/doc/tRakt-Usage.Rmd | 10
inst/doc/tRakt-Usage.html | 180 +++++++--------
man/get_trakt_credentials.Rd | 7
man/trakt.api.call.Rd | 5
man/trakt.getEpisodeData.Rd | 19 +
man/trakt.getFullShowData.Rd | 11
man/trakt.getSeasons.Rd | 11
man/trakt.search.Rd | 9
man/trakt.search.byid.Rd | 7
man/trakt.show.people.Rd | 15 +
man/trakt.show.related.Rd | 15 +
man/trakt.show.season.Rd | 14 +
man/trakt.show.stats.Rd | 11
man/trakt.show.summary.Rd | 11
man/trakt.shows.popular.Rd | 16 +
man/trakt.shows.trending.Rd | 16 +
man/trakt.user.collection.Rd | 9
man/trakt.user.followers.Rd |only
man/trakt.user.following.Rd |only
man/trakt.user.friends.Rd |only
man/trakt.user.ratings.Rd |only
man/trakt.user.stats.Rd | 16 +
man/trakt.user.watched.Rd | 9
man/trakt.user.watchlist.Rd | 9
vignettes/tRakt-Usage.Rmd | 10
vignettes/tRakt-Usage_files/figure-html/Graphing_1-1.png |binary
vignettes/tRakt-Usage_files/figure-html/Graphing_1-2.png |binary
vignettes/tRakt-Usage_files/figure-html/Graphing_1-3.png |binary
54 files changed, 575 insertions(+), 360 deletions(-)
Title: A Probe-Level Data File Format Used by 'aroma.affymetrix'
[deprecated]
Diff between aroma.apd versions 0.5.0 dated 2014-02-27 and 0.6.0 dated 2015-02-24
Description: DEPRECATED. Do not start building new projects based on this package. (The (in-house) APD file format was initially developed to store Affymetrix probe-level data, e.g. normalized CEL intensities. Chip types can be added to APD file and similar to methods in the affxparser package, this package provides methods to read APDs organized by units (probesets). In addition, the probe elements can be arranged optimally such that the elements are guaranteed to be read in order when, for instance, data is read unit by unit. This speeds up the read substantially. This package is supporting the Aroma framework and should not be used elsewhere.)
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson
DESCRIPTION | 27 +++++++++++++++------------
MD5 | 30 ++++++++++++++++++------------
NEWS | 7 +++++++
R/cdfToApdMap.R | 8 ++++----
R/celToApd.R | 10 +++++-----
R/gtypeCelToPQ.R | 17 +++++++++--------
R/readApdRectangle.R | 6 +++---
R/readApdUnits.R | 24 ++++++++++--------------
R/updateApdUnits.R | 18 ++++++++++--------
R/zzz.R | 14 ++++++++------
man/aroma.apd-package.Rd | 2 +-
man/gtypeCelToPQ.Rd | 4 ++--
man/readApdUnits.Rd | 6 ------
tests |only
14 files changed, 92 insertions(+), 81 deletions(-)
Title: Tools for Nuclear Magnetic Resonance Spectrum Alignment and
Quantitative Analysis
Diff between speaq versions 1.2.0 dated 2015-01-14 and 1.2.1 dated 2015-02-24
Description: We introduce a novel suite of informatics tools for the quantitative analysis of NMR metabolomic profile data. The core of the processing cascade is a novel peak alignment algorithm, called hierarchical Cluster-based Peak Alignment (CluPA). The algorithm aligns a target spectrum to the reference spectrum in a top-down fashion by building a hierarchical cluster tree from peak lists of reference and target spectra and then dividing the spectra into smaller segments based on the most distant clusters of the tree. To reduce the computational time to estimate the spectral misalignment, the method makes use of Fast Fourier Transformation (FFT) cross-correlation. Since the method returns a high-quality alignment, we can propose a simple methodology to study the variability of the NMR spectra. For each aligned NMR data point the ratio of the between-group and within-group sum of squares (BW-ratio) is calculated to quantify the difference in variability between and within predefined groups of NMR spectra. This differential analysis is related to the calculation of the F-statistic or a one-way ANOVA, but without distributional assumptions. Statistical inference based on the BW-ratio is achieved by bootstrapping the null distribution from the experimental data. Related publication is available at http://www.biomedcentral.com/1471-2105/12/405/.
Author: Trung Nghia Vu, Kris Laukens and Dirk Valkenborg
Maintainer: Trung Nghia Vu
DESCRIPTION | 14 +++++++-------
MD5 | 6 +++---
NEWS | 6 ++++++
man/speaq-package.Rd | 6 +++---
4 files changed, 19 insertions(+), 13 deletions(-)
Title: Random Forests Model Selection and Performance Evaluation
Diff between rfUtilities versions 1.0 dated 2014-11-21 and 1.0-1 dated 2015-02-24
Description: Utilities for Random Forest model selection, class balance
correction, significance test, cross validation and partial dependency
plots.
Author: Jeffrey S. Evans [cre, aut],
Melanie A. Murphy [ctb]
Maintainer: Jeffrey S. Evans
rfUtilities-1.0-1/rfUtilities/DESCRIPTION | 26 +++++-----
rfUtilities-1.0-1/rfUtilities/MD5 | 34 ++++++++------
rfUtilities-1.0-1/rfUtilities/NAMESPACE | 3 -
rfUtilities-1.0-1/rfUtilities/R/multi.collinear.R |only
rfUtilities-1.0-1/rfUtilities/R/rf.class.sensitivity.R |only
rfUtilities-1.0-1/rfUtilities/R/rf.classBalance.R |only
rfUtilities-1.0-1/rfUtilities/R/rf.crossValidation.R | 6 +-
rfUtilities-1.0-1/rfUtilities/R/rf.modelSel.R | 8 +--
rfUtilities-1.0-1/rfUtilities/R/rf.partial.ci.R |only
rfUtilities-1.0-1/rfUtilities/R/rf.partial.prob.R |only
rfUtilities-1.0-1/rfUtilities/R/rf.significance.R | 12 ++--
rfUtilities-1.0-1/rfUtilities/inst |only
rfUtilities-1.0-1/rfUtilities/man/multi.collinear.Rd |only
rfUtilities-1.0-1/rfUtilities/man/rf.class.sensitivity.Rd |only
rfUtilities-1.0-1/rfUtilities/man/rf.classBalance.Rd |only
rfUtilities-1.0-1/rfUtilities/man/rf.crossValidation.Rd | 7 +-
rfUtilities-1.0-1/rfUtilities/man/rf.modelSel.Rd | 9 ++-
rfUtilities-1.0-1/rfUtilities/man/rf.partial.ci.Rd |only
rfUtilities-1.0-1/rfUtilities/man/rf.partial.prob.Rd |only
rfUtilities-1.0-1/rfUtilities/man/rf.significance.Rd | 13 ++---
rfUtilities-1.0/rfUtilities/R/MultiColinear.R |only
rfUtilities-1.0/rfUtilities/R/probPartialPlot.R |only
rfUtilities-1.0/rfUtilities/R/rf.ClassBalance.R |only
rfUtilities-1.0/rfUtilities/man/MultiColinear.Rd |only
rfUtilities-1.0/rfUtilities/man/probPartialPlot.Rd |only
rfUtilities-1.0/rfUtilities/man/rf.ClassBalance.Rd |only
26 files changed, 64 insertions(+), 54 deletions(-)
Title: R interface to Global Biotic Interactions
Diff between rglobi versions 0.2.4 dated 2015-01-28 and 0.2.5 dated 2015-02-24
Description: A programmatic interface to the web service methods
provided by Global Biotic Interactions (GloBI). GloBI provides
access to spatial-temporal species interaction records from
source all over the world. rglobi provides methods to search
species interactions by location, interaction type, and
taxonomic name. In addition, it supports Cypher, a graph query
language, to allow for executing custom queries on the GloBI
aggregate species interaction dataset.
Author: Jorrit Poelen [aut, cre],
Stephen Gosnell [aut],
Sergey Slyusarev [aut]
Maintainer: Jorrit Poelen
rglobi-0.2.4/rglobi/rglobi_0.2.4.tar.gz |only
rglobi-0.2.5/rglobi/DESCRIPTION | 8 ++--
rglobi-0.2.5/rglobi/MD5 | 7 +---
rglobi-0.2.5/rglobi/README.md | 41 +++++++++++++++---------
rglobi-0.2.5/rglobi/tests/testthat/test-globi.R | 2 -
5 files changed, 35 insertions(+), 23 deletions(-)
Title: Visualization Methods for Raster Data
Diff between rasterVis versions 0.32 dated 2014-10-25 and 0.35 dated 2015-02-24
Description: Methods for enhanced visualization and interaction with raster data. It implements visualization methods for quantitative data and categorical data, both for univariate and multivariate rasters. It also provides methods to display spatiotemporal rasters, and vector fields. See the website for examples.
Author: Oscar Perpinan Lamigueiro [cre, aut],
Robert Hijmans [aut]
Maintainer: Oscar Perpinan Lamigueiro
ChangeLog | 18 ++---
DESCRIPTION | 16 ++--
MD5 | 18 ++---
NAMESPACE | 2
R/grid.R | 26 +++++++
R/streamplot.R | 53 +++++++---------
R/vectorplot.R | 153 ++++++++++++++++++++++++++++++++---------------
README.md | 2
man/hovmoller-methods.Rd | 51 ++++++++++-----
man/vectorplot.Rd | 49 ++++++++++-----
10 files changed, 249 insertions(+), 139 deletions(-)
Title: Nonparametric Stability Analysis
Diff between phenability versions 1.0 dated 2014-04-23 and 2.0 dated 2015-02-24
Description: An alternative to carrying out phenotypic adaptability and stability analyses, taking into account nonparametric statistics. Can be used as a robust approach, less sensitive to departures from common genotypic, environmental, and GxE effects data assumptions (e.g., normal distribution of errors).
Author: Leonardo Castelo Branco
Maintainer: Leonardo C. Branco
DESCRIPTION | 10 +-
MD5 | 21 ++--
R/fox.R | 62 ++++++++-----
R/kang.R | 54 ++++++++---
R/nahu.R | 212 +++++++++++++++++++++++---------------------
R/phenability-internal.R |only
R/thsu.R | 213 ++++++++++++++++++++++++---------------------
man/fox.Rd | 11 +-
man/kang.Rd | 9 +
man/nahu.Rd | 9 +
man/phenability-package.Rd | 15 ++-
man/thsu.Rd | 9 +
12 files changed, 357 insertions(+), 268 deletions(-)
Title: Methods for Maximum Likelihood Estimation
Diff between likelihood versions 1.6 dated 2014-06-27 and 1.7 dated 2015-02-24
Description: Tools for maximum likelihood estimation of parameters
of scientific models.
Author: Lora Murphy
Maintainer: Lora Murphy
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
R/anneal.R | 7 +++++--
man/anneal.Rd | 4 ++--
man/simulated_annealing_algorithm.Rd | 4 ++--
5 files changed, 18 insertions(+), 15 deletions(-)
Title: Freedom from Disease
Diff between FFD versions 1.0-2 dated 2013-04-22 and 1.0-6 dated 2015-02-24
Description: Functions, S4 classes/methods and a graphical user interface (GUI) to design surveys to substantiate freedom from disease using a modified hypergeometric function (see Cameron and Baldock, 1997). Herd sensitivities are computed according to sampling strategies "individual sampling" or "limited sampling" (see M. Ziller, T. Selhorst, J. Teuffert, M. Kramer and H. Schlueter, 2002). Methods to compute the a-posteriori alpha-error are implemented. Risk-based targeted sampling is supported.
Author: Ian Kopacka
Maintainer: Ian Kopacka
DESCRIPTION | 25 +++++------------
MD5 | 24 ++++++++--------
NAMESPACE | 1
R/FFD_GUI-internal.R | 6 ++--
R/FFD_GUI.R | 3 +-
R/computeAlphaLimitedSampling.R | 2 -
R/computeAposterioriError.R | 14 ++++-----
build |only
inst/doc/FFD-intro.R |only
inst/doc/FFD-intro.Rnw | 58 ++++++++++++++++++++--------------------
inst/doc/FFD-intro.pdf |binary
man/lls.Rd | 6 ++--
vignettes/FFD-intro.Rnw | 58 ++++++++++++++++++++--------------------
vignettes/FFD.bib | 9 ++++++
14 files changed, 106 insertions(+), 100 deletions(-)
Title: Clinical Trial Design and Data Analysis Functions
Diff between clinfun versions 1.0.6 dated 2014-07-22 and 1.0.9 dated 2015-02-24
Description: Utilities to make your clinical collaborations easier if not fun.
Author: Venkatraman E. Seshan
Maintainer: Venkatraman E. Seshan
CHANGES | 13 +++++++++
DESCRIPTION | 6 ++--
INDEX | 3 ++
MD5 | 18 ++++++-------
NAMESPACE | 2 -
R/calogrank.R | 3 +-
R/coxphQuantile.R | 32 +++++++++++------------
R/fedesign.R | 74 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
R/permlogrank.R | 9 +++---
man/fedesign.Rd | 16 +++++++++--
10 files changed, 139 insertions(+), 37 deletions(-)
Title: Applied Econometrics with R
Diff between AER versions 1.2-2 dated 2014-01-28 and 1.2-3 dated 2015-02-24
Description: Functions, data sets, examples, demos, and vignettes for the book
Christian Kleiber and Achim Zeileis (2008),
Applied Econometrics with R, Springer-Verlag, New York.
ISBN 978-0-387-77316-2. (See the vignette for a package overview.)
Author: Christian Kleiber [aut],
Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis
DESCRIPTION | 13 -
MD5 | 282 +++++++++++++++++------------------
NAMESPACE | 4
NEWS | 9 +
R/dispersiontest.R | 9 -
R/tobit.R | 6
build/vignette.rds |binary
data/Affairs.rda |binary
data/ArgentinaCPI.rda |binary
data/BankWages.rda |binary
data/BenderlyZwick.rda |binary
data/BondYield.rda |binary
data/CASchools.rda |binary
data/CPS1985.rda |binary
data/CPS1988.rda |binary
data/CPSSW04.rda |binary
data/CPSSW3.rda |binary
data/CPSSW8.rda |binary
data/CPSSW9204.rda |binary
data/CPSSW9298.rda |binary
data/CPSSWEducation.rda |binary
data/CartelStability.rda |binary
data/ChinaIncome.rda |binary
data/CigarettesB.rda |binary
data/CigarettesSW.rda |binary
data/CollegeDistance.rda |binary
data/ConsumerGood.rda |binary
data/CreditCard.rda |binary
data/DJFranses.rda |binary
data/DoctorVisits.rda |binary
data/DutchAdvert.rda |binary
data/DutchSales.rda |binary
data/Electricity1955.rda |binary
data/Electricity1970.rda |binary
data/EquationCitations.rda |binary
data/Equipment.rda |binary
data/EuroEnergy.rda |binary
data/Fatalities.rda |binary
data/Fertility.rda |binary
data/Fertility2.rda |binary
data/FrozenJuice.rda |binary
data/GSOEP9402.rda |binary
data/GSS7402.rda |binary
data/GermanUnemployment.rda |binary
data/GrowthDJ.rda |binary
data/GrowthSW.rda |binary
data/Grunfeld.rda |binary
data/Guns.rda |binary
data/HMDA.rda |binary
data/HealthInsurance.rda |binary
data/HousePrices.rda |binary
data/Journals.rda |binary
data/KleinI.rda |binary
data/Longley.rda |binary
data/MASchools.rda |binary
data/ManufactCosts.rda |binary
data/MarkDollar.rda |binary
data/MarkPound.rda |binary
data/Medicaid1986.rda |binary
data/Mortgage.rda |binary
data/MotorCycles.rda |binary
data/Municipalities.rda |binary
data/MurderRates.rda |binary
data/NMES1988.rda |binary
data/NYSESW.rda |binary
data/NaturalGas.rda |binary
data/OECDGas.rda |binary
data/OECDGrowth.rda |binary
data/OlympicTV.rda |binary
data/OrangeCounty.rda |binary
data/PSID1976.rda |binary
data/PSID1982.rda |binary
data/PSID7682.rda |binary
data/Parade2005.rda |binary
data/PepperPrice.rda |binary
data/PhDPublications.rda |binary
data/ProgramEffectiveness.rda |binary
data/RecreationDemand.rda |binary
data/ResumeNames.rda |binary
data/SIC33.rda |binary
data/STAR.rda |binary
data/ShipAccidents.rda |binary
data/SmokeBan.rda |binary
data/SportsCards.rda |binary
data/StrikeDuration.rda |binary
data/SwissLabor.rda |binary
data/TeachingRatings.rda |binary
data/TechChange.rda |binary
data/TradeCredit.rda |binary
data/TravelMode.rda |binary
data/UKInflation.rda |binary
data/UKNonDurables.rda |binary
data/USAirlines.rda |binary
data/USConsump1950.rda |binary
data/USConsump1979.rda |binary
data/USConsump1993.rda |binary
data/USCrudes.rda |binary
data/USGasB.rda |binary
data/USGasG.rda |binary
data/USInvest.rda |binary
data/USMacroB.rda |binary
data/USMacroG.rda |binary
data/USMacroSW.rda |binary
data/USMacroSWM.rda |binary
data/USMacroSWQ.rda |binary
data/USMoney.rda |binary
data/USProdIndex.rda |binary
data/USSeatBelts.rda |binary
data/USStocksSW.rda |binary
data/WeakInstrument.rda |binary
inst/doc/AER.pdf |binary
inst/doc/Sweave-journals.pdf |binary
man/Baltagi2002.Rd | 1
man/BenderlyZwick.Rd | 4
man/CigarettesB.Rd | 4
man/DoctorVisits.Rd | 2
man/Equipment.Rd | 2
man/EuroEnergy.Rd | 4
man/GSOEP9402.Rd | 2
man/GSS7402.Rd | 2
man/GrowthDJ.Rd | 2
man/HousePrices.Rd | 2
man/MarkDollar.Rd | 2
man/MarkPound.Rd | 2
man/Mortgage.Rd | 4
man/Municipalities.Rd | 2
man/NMES1988.Rd | 2
man/NaturalGas.Rd | 4
man/OECDGas.Rd | 4
man/OrangeCounty.Rd | 4
man/PSID1982.Rd | 4
man/RecreationDemand.Rd | 2
man/TradeCredit.Rd | 4
man/USConsump1993.Rd | 4
man/USCrudes.Rd | 4
man/USGasB.Rd | 4
man/USMacroB.Rd | 4
man/tobit.Rd | 2
tests/Ch-Intro.Rout.save | 20 +-
tests/Ch-LinearRegression.R | 1
tests/Ch-LinearRegression.Rout.save | 11 -
tests/Ch-Microeconometrics.Rout.save | 12 -
142 files changed, 214 insertions(+), 230 deletions(-)
Title: Nomograms for Right-Censored Outcomes from Survey Designs
Diff between SvyNom versions 1.0 dated 2012-12-07 and 1.1 dated 2015-02-24
Description: Builds, evaluates and validates a nomogram with survey data and right-censored outcomes.
Author: Mithat Gonen, Marinela Capanu
Maintainer: Mithat Gonen
DESCRIPTION | 15 +++++++--------
MD5 | 17 ++++++++++-------
NAMESPACE | 7 +++++++
R/SvyNom.R |only
data/noNA.txt |only
inst |only
man/SvyNom-package.Rd | 17 +++++++++--------
man/noNA.Rd | 2 +-
man/svycox.calibrate.Rd | 10 +++++++---
man/svycox.nomogram.Rd | 17 ++++++++++-------
man/svycox.validate.Rd | 24 ++++++++++++++----------
11 files changed, 65 insertions(+), 44 deletions(-)
Title: Histogram-Valued Data Analysis
Diff between HistDAWass versions 0.1 dated 2015-02-18 and 0.1.1 dated 2015-02-24
Description: In the framework of Symbolic Data Analysis, a relatively new approach
to the statistical analysis of multi-valued data, we consider histogram-valued data, i.e.,
data described by univariate histograms. The methods and the basic statistics for
histogram-valued data are mainly based
on the L2 Wasserstein metric between distributions, i.e., a Euclidean metric
between quantile functions. The package contains unsupervised classification techniques,
least square regression and tools for histogram-valued data and for histogram time series.
Author: Antonio Irpino [aut, cre]
Maintainer: Antonio Irpino
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/HistDAWass-package.R | 2 +-
R/unsuperv_classification.R | 2 +-
man/HistDAWass-package.Rd | 2 +-
man/WH_hclust.Rd | 2 +-
6 files changed, 13 insertions(+), 13 deletions(-)
Title: Construction Methods of some Series of PBIB Designs
Diff between CombinS versions 1.0 dated 2013-12-12 and 1.1 dated 2015-02-24
Description: The Combinatory Method (s) to Construct a series of PBIB designs and we give their associated U-type design.
Author: Mohamed Laib, Imane Rezgui, Zebida Gheribi-Aoulmi and Herve Monod
Maintainer: Mohamed Laib
CombinS-1.0/CombinS/R/PBIB4.R |only
CombinS-1.0/CombinS/R/PBIB5.R |only
CombinS-1.0/CombinS/R/PBIB7.R |only
CombinS-1.0/CombinS/man/PBIB4.Rd |only
CombinS-1.0/CombinS/man/PBIB5.Rd |only
CombinS-1.0/CombinS/man/PBIB7.Rd |only
CombinS-1.1/CombinS/DESCRIPTION | 17 ++----
CombinS-1.1/CombinS/MD5 | 26 +++++----
CombinS-1.1/CombinS/R/CombS.R | 79 +++++++++++++++++++----------
CombinS-1.1/CombinS/R/GPBIB4A.R |only
CombinS-1.1/CombinS/R/GPBIB4B.R |only
CombinS-1.1/CombinS/R/GPBIB5.R |only
CombinS-1.1/CombinS/R/GPBIB7A.R |only
CombinS-1.1/CombinS/R/GPBIB7B.R |only
CombinS-1.1/CombinS/R/UType.R |only
CombinS-1.1/CombinS/man/CombS.Rd | 51 ++++++++++--------
CombinS-1.1/CombinS/man/CombinS-package.Rd | 52 +++++++++++++------
CombinS-1.1/CombinS/man/GPBIB4A.Rd |only
CombinS-1.1/CombinS/man/GPBIB4B.Rd |only
CombinS-1.1/CombinS/man/GPBIB5.Rd |only
CombinS-1.1/CombinS/man/GPBIB7A.Rd |only
CombinS-1.1/CombinS/man/GPBIB7B.Rd |only
CombinS-1.1/CombinS/man/UType.Rd |only
23 files changed, 143 insertions(+), 82 deletions(-)
Title: Partial Least Squares Regression with Backward Selection of
Predictors
Diff between autopls versions 1.2-7 dated 2013-08-13 and 1.3 dated 2015-02-24
Description: Some convenience functions for pls regression, including backward
variable selection and validation procedures, image based predictions
and plotting.
Author: Sebastian Schmidtlein, with contributions from C. Oldenburg and H. Feilhauer
and with a code snipped borrowed from Bjorn-Helge Mevik
Maintainer: Sebastian Schmidtlein
DESCRIPTION | 20 ++++++++++++--------
MD5 | 22 +++++++++++-----------
NAMESPACE | 1 +
R/autopls.R | 21 +++++----------------
R/autoplsVAL.R | 2 +-
R/postprocessing.R | 2 +-
R/predict.autopls.R | 14 +++++++-------
R/predict.slim.R | 14 +++++++-------
R/prepro.R | 2 +-
man/autopls.Rd | 36 ++++++++++++++++++++----------------
man/autoplsVAL.Rd | 12 +++++++++---
man/murnau.X.Rd | 2 +-
12 files changed, 76 insertions(+), 72 deletions(-)
Title: Diff, Patch and Merge for Data.frames
Diff between daff versions 0.1.1 dated 2015-02-23 and 0.1.2 dated 2015-02-24
Description: Diff, patch and merge for data frames. Document changes in data sets and use them to apply patches.
Changes to data can be made visible by using render_diff. Daff uses the V8 package to
wrap the 'daff.js' javascript library which is included in the package.
Daff exposes a subset of 'daff.js' functionality, tailored for usage within R.
Author: Paul Fitzpatrick [aut] (javascript original,
http://paulfitz.github.io/daff/),
Edwin de Jonge [aut, cre] (R wrapper)
Maintainer: Edwin de Jonge
DESCRIPTION | 9 ++++-----
MD5 | 11 ++++++-----
NEWS |only
R/TableView.R | 6 ++++--
README.md | 13 ++++++++++---
inst/js/util.js | 7 +++++--
tests/testthat/testdiff-data.R | 6 ++++++
7 files changed, 35 insertions(+), 17 deletions(-)
Title: Constrained Dual Scaling for Detecting Response Styles
Diff between cds versions 1.0 dated 2015-02-16 and 1.0.1 dated 2015-02-24
Description: This is an implementation of constrained dual scaling for detecting response
styles in categorical data, including utility functions. The procedure involves adding
additional columns to the data matrix representing the boundaries between the rating categories.
The resulting matrix is then doubled and analyzed by dual scaling. One-dimensional solutions are
sought which provide optimal scores for the rating categories. These optimal scores are
constrained to follow monotone quadratic splines. Clusters are introduced within which the
response styles can vary. The type of response style present in a cluster can be diagnosed
from the optimal scores for said cluster, and this can be used to construct an
imputed version of the data set which adjusts for response styles.
Author: Pieter Schoonees [aut, cre]
Maintainer: Pieter Schoonees
DESCRIPTION | 8 ++---
MD5 | 10 +++----
R/cds.sim.R | 4 +-
R/sensory.R | 79 +++------------------------------------------------------
man/cds.sim.Rd | 4 +-
man/sensory.Rd | 79 +++------------------------------------------------------
6 files changed, 23 insertions(+), 161 deletions(-)
Title: Test Analysis Modules
Diff between TAM versions 1.4-1 dated 2015-01-16 and 1.5-2 dated 2015-02-24
Description:
Includes marginal and joint maximum likelihood
estimation of uni- and multidimensional item response models
(Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models,
Cognitive Diagnostic Models). Latent regression models and
plausible value imputation are also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch
DESCRIPTION | 18 -
MD5 | 153 ++++++-----
NAMESPACE | 44 +++
R/IRT.WrightMap.R | 37 ++
R/IRT.data.tam.R |only
R/IRT.expectedCounts.tam.R |only
R/IRT.irfprob.tam.R | 6
R/IRT.likelihood.TAM.R | 6
R/IRT.linearCFA.R |only
R/IRT.modelfit.tam.R |only
R/IRT.threshold.R |only
R/calc_exp_TK.R | 2
R/calc_prob.v5.R | 9
R/doparse.R | 6
R/extend.label.group.R | 5
R/lavaanify.IRT.R | 5
R/msq.itemfit.R |only
R/mstep.regression.R | 4
R/plot.ctt.R | 50 +++
R/plot.tam.R | 2
R/plotDevianceTAM.R | 8
R/predict.tam.R |only
R/summary.msq.itemfit.R |only
R/tam.mml.2pl.R | 38 ++
R/tam.mml.3pl.R | 21 +
R/tam.mml.R | 18 +
R/tam.mml.mfr.R | 10
R/tam.modelfit.R | 321 ++++++++++++-------------
R/tam.modelfit.func.R |only
R/tam.parameterfix.defaults.R |only
R/tam.pv.R | 10
R/tamaan.3pl.trait.R | 1
R/tamaan.R | 6
R/tamaanify.R | 7
R/tamaanify.define.method.R | 12
R/tamaanify.modelconstraint.loadings.R | 28 ++
R/tamaanify.proc.lavaanmodel.R | 2
R/tamaanify.tam.mml.3pl.designMatrices.TRAIT.R | 4
data/data.cqc01.rda |binary
data/data.cqc02.rda |binary
data/data.cqc03.rda |binary
data/data.cqc04.rda |binary
data/data.cqc05.rda |binary
data/data.ctest1.rda |binary
data/data.ctest2.rda |binary
data/data.ex08.rda |binary
data/data.ex10.rda |binary
data/data.ex11.rda |binary
data/data.ex12.rda |binary
data/data.ex14.rda |binary
data/data.ex15.rda |binary
data/data.exJ03.rda |binary
data/data.fims.Aus.Jpn.raw.rda |binary
data/data.fims.Aus.Jpn.scored.rda |binary
data/data.geiser.rda |binary
data/data.gpcm.rda |binary
data/data.janssen.rda |binary
data/data.janssen2.rda |binary
data/data.mc.rda |binary
data/data.numeracy.rda |binary
data/data.timssAusTwn.rda |binary
data/data.timssAusTwn.scored.rda |binary
data/sim.facets.rda |binary
data/sim.mfr.rda |binary
data/sim.rasch.missing.rda |binary
data/sim.rasch.pweights.rda |binary
data/sim.rasch.rda |binary
inst/NEWS | 56 +++-
man/IRT.WrightMap.Rd | 5
man/IRT.data.tam.Rd |only
man/IRT.expectedCounts.tam.Rd |only
man/IRT.likelihood.tam.Rd | 8
man/IRT.linearCFA.Rd |only
man/IRT.threshold.Rd |only
man/TAM-package.Rd | 4
man/data.cqc.Rd | 2
man/msq.itemfit.Rd |only
man/plot.tam.Rd | 18 -
man/predict.Rd |only
man/tam.ctt.Rd | 13 -
man/tam.fit.Rd | 2
man/tam.jml.Rd | 2
man/tam.latreg.Rd | 8
man/tam.mml.Rd | 60 ++++
man/tam.modelfit.Rd | 72 ++++-
src/msq_itemfit.cpp |only
86 files changed, 724 insertions(+), 359 deletions(-)
Title: Survival Analysis
Diff between survival versions 2.37-7 dated 2014-01-22 and 2.38-1 dated 2015-02-24
Description: Contains the core survival analysis routines, including
definition of Surv objects,
Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models,
and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre],
Thomas Lumley [ctb, trl] (original S->R port and maintainer until 2009)
Maintainer: Terry M Therneau
survival-2.37-7/survival/R/basehaz.S |only
survival-2.37-7/survival/inst/doc/sourcecode.pdf |only
survival-2.37-7/survival/src/msurv.c |only
survival-2.37-7/survival/vignettes/raheart.rda |only
survival-2.38-1/survival/.Rinstignore |only
survival-2.38-1/survival/DESCRIPTION | 21
survival-2.38-1/survival/MD5 | 306 ++++---
survival-2.38-1/survival/NAMESPACE | 20
survival-2.38-1/survival/R/agreg.fit.R | 37
survival-2.38-1/survival/R/agsurv.R | 1
survival-2.38-1/survival/R/anova.coxph.S | 52 -
survival-2.38-1/survival/R/anova.coxphlist.S | 5
survival-2.38-1/survival/R/basehaz.R |only
survival-2.38-1/survival/R/cch.R | 4
survival-2.38-1/survival/R/clogit.R | 21
survival-2.38-1/survival/R/coxexact.fit.R | 3
survival-2.38-1/survival/R/coxpenal.fit.R | 82 +
survival-2.38-1/survival/R/coxph.R | 58 -
survival-2.38-1/survival/R/coxph.detail.S | 1
survival-2.38-1/survival/R/frailty.controlaic.S | 2
survival-2.38-1/survival/R/frailty.controlgauss.S | 1
survival-2.38-1/survival/R/frailty.gamma.S | 11
survival-2.38-1/survival/R/frailty.gammacon.S | 1
survival-2.38-1/survival/R/frailty.gaussian.S | 11
survival-2.38-1/survival/R/frailty.t.S | 4
survival-2.38-1/survival/R/logLik.coxph.R | 13
survival-2.38-1/survival/R/model.matrix.coxph.R | 4
survival-2.38-1/survival/R/neardate.R |only
survival-2.38-1/survival/R/plot.survfit.R | 64 -
survival-2.38-1/survival/R/predict.coxph.penal.S | 9
survival-2.38-1/survival/R/predict.survreg.S | 5
survival-2.38-1/survival/R/print.coxph.S | 3
survival-2.38-1/survival/R/print.coxph.penal.S | 3
survival-2.38-1/survival/R/print.summary.coxph.S | 4
survival-2.38-1/survival/R/print.summary.coxph.penal.S | 4
survival-2.38-1/survival/R/print.summary.survexp.R | 13
survival-2.38-1/survival/R/print.summary.survfit.S | 11
survival-2.38-1/survival/R/print.summary.survfitms.S | 11
survival-2.38-1/survival/R/print.summary.survreg.S | 1
survival-2.38-1/survival/R/print.survexp.S | 12
survival-2.38-1/survival/R/print.survreg.penal.S | 3
survival-2.38-1/survival/R/pspline.S | 7
survival-2.38-1/survival/R/pyears.R | 20
survival-2.38-1/survival/R/strata.S | 24
survival-2.38-1/survival/R/summary.survreg.S | 2
survival-2.38-1/survival/R/survSplit.R | 4
survival-2.38-1/survival/R/survexp.R | 2
survival-2.38-1/survival/R/survfit.R | 2
survival-2.38-1/survival/R/survfitCI.R | 1
survival-2.38-1/survival/R/survfitTurnbull.S | 6
survival-2.38-1/survival/R/survfitms.R | 16
survival-2.38-1/survival/R/survreg.S | 5
survival-2.38-1/survival/R/survreg.distributions.S | 26
survival-2.38-1/survival/R/survreg.fit.S | 3
survival-2.38-1/survival/R/tmerge.R |only
survival-2.38-1/survival/R/xtras.R | 35
survival-2.38-1/survival/build/vignette.rds |binary
survival-2.38-1/survival/cleanup |only
survival-2.38-1/survival/cleanup.win |only
survival-2.38-1/survival/data/cgd.rda |binary
survival-2.38-1/survival/data/datalist | 6
survival-2.38-1/survival/data/kidney.rda |binary
survival-2.38-1/survival/data/mgus.rda |binary
survival-2.38-1/survival/data/mgus2.rda |only
survival-2.38-1/survival/data/ovarian.rda |binary
survival-2.38-1/survival/data/rats.rda |binary
survival-2.38-1/survival/data/transplant.rda |only
survival-2.38-1/survival/inst/CITATION | 12
survival-2.38-1/survival/inst/NEWS.Rd | 81 +
survival-2.38-1/survival/inst/NEWS.Rd.orig |only
survival-2.38-1/survival/inst/doc/adjcurve.R | 170 ++-
survival-2.38-1/survival/inst/doc/adjcurve.Rnw | 497 ++++++-----
survival-2.38-1/survival/inst/doc/adjcurve.pdf |binary
survival-2.38-1/survival/inst/doc/compete.R |only
survival-2.38-1/survival/inst/doc/compete.Rnw |only
survival-2.38-1/survival/inst/doc/compete.pdf |only
survival-2.38-1/survival/inst/doc/splines.R |only
survival-2.38-1/survival/inst/doc/splines.Rnw |only
survival-2.38-1/survival/inst/doc/splines.pdf |only
survival-2.38-1/survival/inst/doc/tests.R | 25
survival-2.38-1/survival/inst/doc/tests.Rnw | 213 ++--
survival-2.38-1/survival/inst/doc/tests.pdf |binary
survival-2.38-1/survival/inst/doc/timedep.R | 130 ++-
survival-2.38-1/survival/inst/doc/timedep.Rnw | 735 ++++++++++++-----
survival-2.38-1/survival/inst/doc/timedep.pdf |binary
survival-2.38-1/survival/man/basehaz.Rd | 45 -
survival-2.38-1/survival/man/bladder.Rd | 8
survival-2.38-1/survival/man/cgd.Rd | 52 -
survival-2.38-1/survival/man/cgd0.Rd |only
survival-2.38-1/survival/man/cluster.Rd | 6
survival-2.38-1/survival/man/dsurvreg.Rd | 4
survival-2.38-1/survival/man/frailty.Rd | 6
survival-2.38-1/survival/man/mgus.Rd | 48 -
survival-2.38-1/survival/man/mgus2.Rd |only
survival-2.38-1/survival/man/neardate.Rd |only
survival-2.38-1/survival/man/ovarian.Rd | 3
survival-2.38-1/survival/man/pbcseq.Rd | 11
survival-2.38-1/survival/man/plot.survfit.Rd | 21
survival-2.38-1/survival/man/predict.coxph.Rd | 26
survival-2.38-1/survival/man/print.survfit.Rd | 4
survival-2.38-1/survival/man/rats.Rd | 7
survival-2.38-1/survival/man/strata.Rd | 11
survival-2.38-1/survival/man/summary.survfit.Rd | 3
survival-2.38-1/survival/man/survexp.Rd | 9
survival-2.38-1/survival/man/survfit.Rd | 3
survival-2.38-1/survival/man/survfit.coxph.Rd | 15
survival-2.38-1/survival/man/survfit.formula.Rd | 13
survival-2.38-1/survival/man/survreg.Rd | 2
survival-2.38-1/survival/man/survreg.object.Rd | 105 +-
survival-2.38-1/survival/man/tmerge.Rd |only
survival-2.38-1/survival/man/transplant.Rd |only
survival-2.38-1/survival/noweb |only
survival-2.38-1/survival/src/agexact.c | 1
survival-2.38-1/survival/src/agfit4.c | 4
survival-2.38-1/survival/src/agfit5.c | 151 ---
survival-2.38-1/survival/src/agmart.c | 6
survival-2.38-1/survival/src/agmart2.c | 2
survival-2.38-1/survival/src/agmart3.c |only
survival-2.38-1/survival/src/coxfit6.c | 37
survival-2.38-1/survival/src/init.c | 7
survival-2.38-1/survival/src/pyears2.c | 1
survival-2.38-1/survival/src/pyears3b.c | 1
survival-2.38-1/survival/src/survfitci.c | 2
survival-2.38-1/survival/src/survproto.h | 10
survival-2.38-1/survival/src/tmerge.c |only
survival-2.38-1/survival/tests/book1.R | 2
survival-2.38-1/survival/tests/book1.Rout.save | 12
survival-2.38-1/survival/tests/book2.R | 9
survival-2.38-1/survival/tests/book2.Rout.save | 20
survival-2.38-1/survival/tests/book3.R | 2
survival-2.38-1/survival/tests/book3.Rout.save | 13
survival-2.38-1/survival/tests/fr_rat1.R | 6
survival-2.38-1/survival/tests/fr_rat1.Rout.save | 24
survival-2.38-1/survival/tests/fr_resid.R | 10
survival-2.38-1/survival/tests/fr_resid.Rout.save | 23
survival-2.38-1/survival/tests/fr_simple.R | 2
survival-2.38-1/survival/tests/fr_simple.Rout.save | 11
survival-2.38-1/survival/tests/gray1.rda |binary
survival-2.38-1/survival/tests/model.matrix.R | 4
survival-2.38-1/survival/tests/model.matrix.Rout.save | 11
survival-2.38-1/survival/tests/plot.R |only
survival-2.38-1/survival/tests/plot1.pdf.save |only
survival-2.38-1/survival/tests/pspline.R | 21
survival-2.38-1/survival/tests/pspline.Rout.save | 36
survival-2.38-1/survival/tests/quantile.R | 6
survival-2.38-1/survival/tests/quantile.Rout.save | 14
survival-2.38-1/survival/tests/survreg2.R | 4
survival-2.38-1/survival/tests/survreg2.Rout.save | 13
survival-2.38-1/survival/tests/testci.R | 43
survival-2.38-1/survival/tests/testci.Rout.save | 51 -
survival-2.38-1/survival/tests/tt.R | 10
survival-2.38-1/survival/tests/tt.Rout.save | 18
survival-2.38-1/survival/vignettes/.install_extras |only
survival-2.38-1/survival/vignettes/adjcurve.Rnw | 497 ++++++-----
survival-2.38-1/survival/vignettes/compete.Rnw |only
survival-2.38-1/survival/vignettes/figures |only
survival-2.38-1/survival/vignettes/splines.Rnw |only
survival-2.38-1/survival/vignettes/tests.Rnw | 213 ++--
survival-2.38-1/survival/vignettes/timedep.Rnw | 735 ++++++++++++-----
159 files changed, 3225 insertions(+), 2032 deletions(-)
Title: Causal Inference in Spatiotemporal Event Data
Diff between mwa versions 0.4 dated 2014-12-17 and 0.4.1 dated 2015-02-24
Description: Matched Wake Analysis (mwa) grants insights into causal relationships in spatiotemporal event data.
Author: Sebastian Schutte and Karsten Donnay
Maintainer: Sebastian Schutte
DESCRIPTION | 12 ++---
MD5 | 20 ++++----
R/mwa.R | 107 +++++++++++++++++++++++++++++++++++++--------
man/matchedwake.Rd | 8 +--
man/mwa-package.Rd | 6 +-
man/mwa_data.Rd | 6 +-
man/plot.matchedwake.Rd | 2
man/print.matchedwake.Rd | 2
man/slideWakeMatch.Rd | 2
man/slidingWake.Rd | 2
man/summary.matchedwake.Rd | 4 -
11 files changed, 122 insertions(+), 49 deletions(-)
Title: Digital PCR Analysis
Diff between dpcR versions 0.1.3.2 dated 2014-12-24 and 0.1.3.3 dated 2015-02-24
Description: Analysis, visualisation and simulation of digital PCR experiments.
Author: Michal Burdukiewicz [cre, aut],
Stefan Roediger [aut]
Maintainer: Michal Burdukiewicz
CHANGELOG | 3 +
DESCRIPTION | 8 ++--
MD5 | 80 +++++++++++++++++++++++------------------------
NAMESPACE | 2 -
R/count_test-class.R | 1
R/qpcrpp.R | 2 -
man/adpcr-class.Rd | 3 +
man/adpcr2ppp.Rd | 3 +
man/binarize.Rd | 3 +
man/bind_dpcr-methods.Rd | 3 +
man/bioamp.Rd | 3 +
man/compare_dens.Rd | 3 +
man/count_test-class.Rd | 7 ++--
man/create_dpcr.Rd | 3 +
man/ddpcr-class.Rd | 3 +
man/dpcR-package.Rd | 3 +
man/dpcr_density.Rd | 3 +
man/dpcr_density_gui.Rd | 3 +
man/extract_dpcr.Rd | 3 +
man/limit_cq.Rd | 3 +
man/many_peaks.Rd | 3 +
man/moments-methods.Rd | 3 +
man/num2int.Rd | 3 +
man/pds.Rd | 3 +
man/pds_raw.Rd | 3 +
man/plot.qpcrpp.Rd | 4 +-
man/plot_panel.Rd | 3 +
man/plot_vic_fam.Rd | 3 +
man/qpcr2pp.Rd | 3 +
man/qpcr_analyser.Rd | 3 +
man/qpcrpp-class.Rd | 3 +
man/rtadpcr-class.Rd | 3 +
man/show-methods.Rd | 3 +
man/sim_adpcr.Rd | 3 +
man/sim_ddpcr.Rd | 3 +
man/summary-methods.Rd | 3 +
man/test_counts.Rd | 3 +
man/test_counts_gui.Rd | 3 +
man/test_panel.Rd | 3 +
man/test_peaks.Rd | 3 +
man/test_ratio.Rd | 3 +
41 files changed, 124 insertions(+), 82 deletions(-)
Title: Spatial Analysis and Modeling
Diff between spatialEco versions 0.1-0 dated 2015-02-02 and 0.1-1 dated 2015-02-24
Description: Utilities to support spatial data manipulation, query, sampling and modeling.
Functions include models for species population density, download utilities for
climate and global deforestation spatial products, spatial smoothing,
multivariate separability, point process model for creating pseudo-absences
and subsampling, polygon and point-distance landscape metrics, auto-logistic
model, sampling models, cluster optimization and statistical exploratory tools.
Author: Jeffrey S. Evans [aut, cre],
Karthik Ram [ctb]
Maintainer: Jeffrey S. Evans
DESCRIPTION | 8 +-
MD5 | 81 +++++++++++++----------
NAMESPACE | 3
R/breeding.density.R | 6 -
R/correlogram.R | 4 -
R/csi.R |only
R/download.daymet.R | 6 -
R/download.prism.R | 4 -
R/idw.smoothing.R | 6 -
R/land.metrics.R | 2
R/local.min.max.R |only
R/logistic.regression.R | 58 ++++++++++-------
R/moments.R | 6 -
R/nni.R | 14 ++--
R/o.ring.R | 6 -
R/optimal.k.R | 2
R/outliers.R |only
R/parea.sample.R | 2
R/point.in.poly.R | 13 +--
R/pp.subsample.R | 2
R/pseudo.absence.R | 6 -
R/separability.R | 8 +-
R/stratified.random.R | 4 -
R/trend.line.R | 2
inst/NEWS |only
man/breeding.density.Rd | 130 +++++++++++++++++++-------------------
man/correlogram.Rd | 4 -
man/csi.Rd |only
man/download.daymet.Rd | 6 -
man/download.prism.Rd | 4 -
man/idw.smoothing.Rd | 90 +++++++++++++-------------
man/land.metrics.Rd | 118 +++++++++++++++++-----------------
man/local.min.max.Rd |only
man/logistic.regression.Rd | 36 ++++++----
man/moments.Rd | 6 -
man/nni.Rd | 88 +++++++++++++-------------
man/o.ring.Rd | 78 +++++++++++------------
man/optimal.k.Rd | 100 ++++++++++++++---------------
man/outliers.Rd |only
man/parea.sample.Rd | 108 +++++++++++++++----------------
man/pp.subsample.Rd | 2
man/pseudo.absence.Rd | 6 -
man/separability.Rd | 152 ++++++++++++++++++++++-----------------------
man/stratified.random.Rd | 150 ++++++++++++++++++++++----------------------
man/trend.line.Rd | 86 ++++++++++++-------------
45 files changed, 717 insertions(+), 690 deletions(-)
Title: Database Interface and MySQL Driver for R
Diff between RMySQL versions 0.10.1 dated 2015-01-15 and 0.10.2 dated 2015-02-24
Description: Implements DBI-compliant Interface to MySQL and MariaDB Databases.
Author: Jeroen Ooms [aut, cre],
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
configure | 10 ++++++++++
src/Makevars.win | 4 ++--
tools/winlibs.R | 4 ++--
5 files changed, 21 insertions(+), 11 deletions(-)
Title: Tools for Working with JavaScript in R
Diff between js versions 0.1 dated 2015-02-15 and 0.2 dated 2015-02-24
Description: A set of utility functions for working with JavaScript in R.
Currently includes functions to compile, validate, reformat, optimize
and analyze JavaScript code.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
DESCRIPTION | 12 ++--
MD5 | 17 ++++--
NAMESPACE | 1
NEWS |only
R/coffee.R |only
inst/doc/intro.R | 13 +++++
inst/doc/intro.Rmd | 35 +++++++++++--
inst/doc/intro.html | 126 ++++++++++++++++++++++++++++++++++++++++++++++----
inst/example |only
inst/js/coffee.min.js |only
man/coffee_compile.Rd |only
vignettes/intro.Rmd | 35 +++++++++++--
12 files changed, 208 insertions(+), 31 deletions(-)
Title: Integrative Bayesian Analysis of Transcriptomic and CGH Data
Diff between iBATCGH versions 1.1 dated 2014-09-13 and 1.2 dated 2015-02-24
Description: Bayesian integrative models of gene expression and comparative genomic hybridization data. The package provides inference on copy number variations and their association with gene expression.
Author: Alberto Cassese
Maintainer: Alberto Cassese
DESCRIPTION | 18 +++++++++---------
MD5 | 8 ++++----
src/Makevars | 2 +-
src/Makevars.win | 3 +--
src/ProbitMain.cpp | 8 +++++---
5 files changed, 20 insertions(+), 19 deletions(-)
Title: Chi-Square Tests for Non-Parametric Functional Dependencies
Diff between FunChisq versions 2.0.0 dated 2015-02-16 and 2.0.1 dated 2015-02-24
Description: Statistical hypothesis testing methods for non-parametric functional dependencies based on chi-square statistics. These tests were designed to reveal causality based on evidence from non-parametric functional dependencies. They include an asymptotic non-constant functional chi-square test, an exact functional test, and a comparative functional chi-square test. The normalized functional chi-square test was used by the Best Performer NMSUSongLab in DREAM8 Breast Cancer Network Inference Challenges. These tests offer an advantage over regression analysis when a parametric functional form cannot be assumed.
Author: Yang Zhang, Hua Zhong, and Joe Song
Maintainer: Joe Song
FunChisq-2.0.0/FunChisq/src/Makevars |only
FunChisq-2.0.0/FunChisq/src/Makevars.win |only
FunChisq-2.0.0/FunChisq/src/TransitionTableIO.cpp |only
FunChisq-2.0.0/FunChisq/tests/testthat/test_EFT.R |only
FunChisq-2.0.1/FunChisq/DESCRIPTION | 10 -
FunChisq-2.0.1/FunChisq/MD5 | 39 +++----
FunChisq-2.0.1/FunChisq/NAMESPACE | 3
FunChisq-2.0.1/FunChisq/NEWS | 58 +++++------
FunChisq-2.0.1/FunChisq/man/FunChisq-package.Rd | 10 -
FunChisq-2.0.1/FunChisq/man/cp.fun.chisq.test.Rd | 16 +--
FunChisq-2.0.1/FunChisq/man/fun.chisq.test.Rd | 48 ++++-----
FunChisq-2.0.1/FunChisq/src/AdjustPvalue.cpp | 88 ++++++++---------
FunChisq-2.0.1/FunChisq/src/ChisqDirTest.cpp | 2
FunChisq-2.0.1/FunChisq/src/ChisqTests.cpp | 66 ++++++------
FunChisq-2.0.1/FunChisq/src/ChisqTests.h | 2
FunChisq-2.0.1/FunChisq/src/ExactFunctionalTest.cpp | 29 +----
FunChisq-2.0.1/FunChisq/src/ExactFunctionalTest.h | 4
FunChisq-2.0.1/FunChisq/src/ExactMultiTableTest.cpp | 20 +--
FunChisq-2.0.1/FunChisq/src/ExactMultiTableTest.h | 10 +
FunChisq-2.0.1/FunChisq/src/StatDistributions.cpp | 4
FunChisq-2.0.1/FunChisq/src/TransitionTable.cpp | 26 ++---
FunChisq-2.0.1/FunChisq/src/TransitionTable.h | 6 -
FunChisq-2.0.1/FunChisq/tests/testthat/test_FunChisq.R |only
23 files changed, 214 insertions(+), 227 deletions(-)
Title: Cairo-based Graphics Device Driver
Diff between cairoDevice versions 2.21 dated 2015-01-20 and 2.22 dated 2015-02-24
Description: This device uses Cairo and GTK to draw to the screen,
file (png, svg, pdf, and ps) or memory (arbitrary GdkDrawable
or Cairo context). The screen device may be embedded into RGtk2
interfaces and supports all interactive features of other graphics
devices, including getGraphicsEvent().
Author: Michael Lawrence
Maintainer: Michael Lawrence
DESCRIPTION | 12 ++++++------
MD5 | 4 ++--
src/cairoDevice.c | 3 ---
3 files changed, 8 insertions(+), 11 deletions(-)
Title: Copy-Number Analysis of Large Microarray Data Sets
Diff between aroma.cn versions 1.5.0 dated 2013-10-17 and 1.6.0 dated 2015-02-24
Description: Methods for analyzing DNA copy-number data. Specifically,
this package implements the multi-source copy-number normalization (MSCN)
method for normalizing copy-number data obtained on various platforms and
technologies. It also implements the TumorBoost method for normalizing
paired tumor-normal SNP data.
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut]
Maintainer: Henrik Bengtsson
aroma.cn-1.5.0/aroma.cn/R/PSCBS.flips.R |only
aroma.cn-1.5.0/aroma.cn/R/PairedPSCBS.calibrateC1C2.R |only
aroma.cn-1.5.0/aroma.cn/R/PairedPSCBS.deShearC1C2.R |only
aroma.cn-1.5.0/aroma.cn/inst/NEWS |only
aroma.cn-1.5.0/aroma.cn/inst/testScripts/system/chipTypes/GenomeWideSNP_6/01a.downloadAnnotationData.R |only
aroma.cn-1.5.0/aroma.cn/inst/testScripts/system/chipTypes/GenomeWideSNP_6/01b.downloadRawData.R |only
aroma.cn-1.5.0/aroma.cn/inst/testScripts/system/ortho |only
aroma.cn-1.5.0/aroma.cn/man/calibrateC1C2.PairedPSCBS.Rd |only
aroma.cn-1.5.0/aroma.cn/man/deShearC1C2_20120922.PairedPSCBS.Rd |only
aroma.cn-1.6.0/aroma.cn/DESCRIPTION | 27
aroma.cn-1.6.0/aroma.cn/MD5 | 90
aroma.cn-1.6.0/aroma.cn/NAMESPACE | 47
aroma.cn-1.6.0/aroma.cn/NEWS |only
aroma.cn-1.6.0/aroma.cn/R/009.setup.R | 6
aroma.cn-1.6.0/aroma.cn/R/021.dynamic_imports.R |only
aroma.cn-1.6.0/aroma.cn/R/AbstractCurveNormalization.R | 11
aroma.cn-1.6.0/aroma.cn/R/AromaUnitPscnBinarySet.doSegmentByPairedPSCBS.R |only
aroma.cn-1.6.0/aroma.cn/R/C1C2.R | 72
aroma.cn-1.6.0/aroma.cn/R/MultiSourceCopyNumberNormalization.R | 14
aroma.cn-1.6.0/aroma.cn/R/PairedPSCBS.CALL2.R | 2
aroma.cn-1.6.0/aroma.cn/R/PairedPSCBS.NORM.R | 4
aroma.cn-1.6.0/aroma.cn/R/PairedPSCBS.PLOT3.R | 5
aroma.cn-1.6.0/aroma.cn/R/PairedPSCBS.backgroundCorrect.R |only
aroma.cn-1.6.0/aroma.cn/R/PairedPSCBS.fitC1C2Peaks.R |only
aroma.cn-1.6.0/aroma.cn/R/PairedPscbsModel.R | 10
aroma.cn-1.6.0/aroma.cn/R/PrincipalCurve.XTRAS.R | 2
aroma.cn-1.6.0/aroma.cn/R/PrincipalCurveNormalization.R | 6
aroma.cn-1.6.0/aroma.cn/R/TotalFracBSnpData.R | 2
aroma.cn-1.6.0/aroma.cn/R/TumorBoostNormalization.R | 3
aroma.cn-1.6.0/aroma.cn/R/XYCurveNormalization.R | 4
aroma.cn-1.6.0/aroma.cn/R/callXXorXY.numeric.R | 6
aroma.cn-1.6.0/aroma.cn/R/normalizeMirroredBAFsByRegions.R | 7
aroma.cn-1.6.0/aroma.cn/R/normalizePrincipalCurve.matrix.R | 5
aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/CondSegmentation/test20091014,TBN,plot.Rex | 1020 +++++-----
aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/TumorBoost/test20090620a,NGC.Rex | 414 ++--
aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/pairedPSCN/R/00.setup.R | 54
aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/pairedPSCN/R/getTumorNormalPairs.R | 34
aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/pairedPSCN/R/loadAllDataSets.R | 204 +-
aroma.cn-1.6.0/aroma.cn/inst/testScripts/system/pairedPSCN/R/zzz.R | 62
aroma.cn-1.6.0/aroma.cn/man/AbstractCurveNormalization.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/MultiSourceCopyNumberNormalization.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/Non-documented_objects.Rd | 36
aroma.cn-1.6.0/aroma.cn/man/PairedPscbsModel.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/PrincipalCurveNormalization.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/TotalCnBinnedSmoothing.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/TotalCnKernelSmoothing.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/TotalCnSmoothing.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/TumorBoostNormalization.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/XYCurveNormalization.Rd | 2
aroma.cn-1.6.0/aroma.cn/man/findAtomicAberrations.CopyNumberRegions.Rd | 75
aroma.cn-1.6.0/aroma.cn/man/normalizeBAFsByRegions.PairedPSCBS.Rd | 61
aroma.cn-1.6.0/aroma.cn/tests |only
52 files changed, 1100 insertions(+), 1201 deletions(-)
Title: Stepwise Covariate Selection for the Fine & Gray Competing Risks
Regression Model
Diff between crrstep versions 2014-07.16 dated 2014-07-17 and 2015-2.1 dated 2015-02-23
Description: Performs forward and backwards stepwise regression for the Proportional subdistribution hazards model in competing risks (Fine & Gray 1999). Procedure uses AIC, BIC and BICcr as selection criteria. BICcr has a penalty of k = log(n*), where n* is the number of primary events.
Author: Ravi Varadhan & Deborah Kuk
Maintainer: Ravi Varadhan
DESCRIPTION | 14 ++++-----
MD5 | 8 ++---
R/crrstep.r | 88 ++++++++++++++++++++++++++++++++++-----------------------
inst/NEWS.Rd | 9 +++++
man/crrstep.Rd | 2 -
5 files changed, 74 insertions(+), 47 deletions(-)
Title: Improved Allele-Specific Copy Number of SNP Microarrays for
Downstream Segmentation
Diff between calmate versions 0.11.0 dated 2013-10-17 and 0.12.0 dated 2015-02-23
Description: A multi-array post-processing method of allele-specific copy-number estimates (ASCNs).
Author: Maria Ortiz [aut, ctb],
Ander Aramburu [ctb],
Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut, ctb],
Angel Rubio [aut, ctb]
Maintainer: Henrik Bengtsson
calmate-0.11.0/calmate/inst/NEWS |only
calmate-0.11.0/calmate/inst/testScripts/publications/CalMaTe/R |only
calmate-0.11.0/calmate/inst/testScripts/publications/CalMaTe/dataSets |only
calmate-0.12.0/calmate/DESCRIPTION | 30 ++++-----
calmate-0.12.0/calmate/MD5 | 33 +++-------
calmate-0.12.0/calmate/NAMESPACE | 4 -
calmate-0.12.0/calmate/NEWS |only
calmate-0.12.0/calmate/R/000.R | 2
calmate-0.12.0/calmate/R/zzz.R | 11 +--
calmate-0.12.0/calmate/man/CalMaTeCalibration.Rd | 4 -
calmate-0.12.0/calmate/man/calmate-package.Rd | 4 -
calmate-0.12.0/calmate/man/calmateByThetaAB.array.Rd | 2
calmate-0.12.0/calmate/man/calmateByTotalAndFracB.array.Rd | 2
calmate-0.12.0/calmate/man/fitCalMaTe.matrix.Rd | 2
calmate-0.12.0/calmate/man/fitCalMaTeInternal.Rd | 2
calmate-0.12.0/calmate/tests/calmateByTotalAndFracB.R |only
calmate-0.12.0/calmate/tests/thetaAB2TotalAndFracB.R |only
17 files changed, 46 insertions(+), 50 deletions(-)
Title: Affymetrix SNP Probe-Summarization using Non-Negative Matrix
Factorization
Diff between ACNE versions 0.7.0 dated 2013-10-18 and 0.8.0 dated 2015-02-23
Description: A summarization method to estimate allele-specific copy number signals for Affymetrix SNP microarrays using non-negative matrix factorization (NMF).
Author: Maria Ortiz [aut],
Henrik Bengtsson [aut, cre, cph],
Angel Rubio [aut]
Maintainer: Henrik Bengtsson
ACNE-0.7.0/ACNE/inst/NEWS |only
ACNE-0.8.0/ACNE/DESCRIPTION | 28 +++++++++--------
ACNE-0.8.0/ACNE/MD5 | 23 +++++++-------
ACNE-0.8.0/ACNE/NAMESPACE | 7 ++++
ACNE-0.8.0/ACNE/NEWS |only
ACNE-0.8.0/ACNE/R/000.R | 1
ACNE-0.8.0/ACNE/R/SnpNmfFit.plot.R | 2 -
ACNE-0.8.0/ACNE/R/pseudoinverse.R | 8 ++---
ACNE-0.8.0/ACNE/R/robustWInit.R | 53 +++++++++++++++++++++++++---------
ACNE-0.8.0/ACNE/R/zzz.R | 11 +++----
ACNE-0.8.0/ACNE/man/NmfPlm.Rd | 4 +-
ACNE-0.8.0/ACNE/man/NmfSnpPlm.Rd | 4 +-
ACNE-0.8.0/ACNE/man/fitSnpNmfArray.Rd | 18 +++++++----
ACNE-0.8.0/ACNE/tests |only
14 files changed, 102 insertions(+), 57 deletions(-)
Title: Some Additional Multiple Imputation Functions, Especially for
'mice'
Diff between miceadds versions 1.0 dated 2014-11-07 and 1.1-1 dated 2015-02-23
Description:
Contains some auxiliary functions for multiple imputation which
complements existing functionality in R.
In addition to some utility functions, main features include
plausible value imputation, multilevel imputation functions,
imputation using partial least squares (PLS) for high dimensional
predictors and two-way imputation.
Author: Alexander Robitzsch [aut, cre]
Maintainer: Alexander Robitzsch
DESCRIPTION | 28 +++++----
MD5 | 92 +++++++++++++++---------------
NAMESPACE | 3 -
R/datalist2mids.R | 56 +++++++++++++++---
R/load.data.R | 10 ++-
R/mice.impute.2l.plausible.values.R | 61 +++++++++++++-------
R/micombine.cor.R | 6 +-
R/mids2datlist.R | 4 +
R/save.data.R | 30 ++++++++--
R/write.mice.imputation.R | 15 -----
data/data.allison.gssexp.rda |binary
data/data.allison.hip.rda |binary
data/data.allison.usnews.rda |binary
data/data.enders.depression.rda |binary
data/data.enders.eatingattitudes.rda |binary
data/data.enders.employee.rda |binary
data/data.internet.rda |binary
data/data.largescale.rda |binary
data/data.ma01.rda |binary
data/data.ma02.rda |binary
data/data.ma03.rda |binary
data/data.ma04.rda |binary
data/data.ma05.rda |binary
data/data.smallscale.rda |binary
inst/NEWS | 19 +++++-
man/Reval.Rd | 4 -
man/Rhat.mice.Rd | 8 +-
man/Rsessinfo.Rd | 4 -
man/data.allison.Rd | 30 +++++-----
man/datalist2mids.Rd | 50 ++++++++--------
man/grep.vec.Rd | 16 ++---
man/index.dataframe.Rd | 20 +++---
man/ma.scale2.Rd | 12 ++--
man/mice.1chain.Rd | 71 +++++++++++------------
man/mice.impute.2l.plausible.values.Rd | 99 +++++++++++++++++++++++++++++++--
man/miceadds-package.Rd | 18 +++---
man/micombine.F.Rd | 8 +-
man/micombine.cor.Rd | 16 ++---
man/output.format1.Rd | 4 -
man/pca.covridge.Rd | 20 +++---
man/round2.Rd | 40 ++++++-------
man/save.data.Rd | 6 +-
man/scan.vector.Rd | 6 +-
man/str_C.expand.grid.Rd | 8 +-
man/sumpreserving.rounding.Rd | 24 ++++----
man/systime.Rd | 6 +-
man/tw.imputation.Rd | 20 +++---
47 files changed, 496 insertions(+), 318 deletions(-)
Title: Correlation and Regression Analyses for Randomized Response Data
Diff between RRreg versions 0.2.0 dated 2014-11-18 and 0.3.0 dated 2015-02-23
Description: Univariate and multivariate methods to analyze
randomized response (RR) survey designs (e.g., Warner, S. L. (1965).
Randomized response: A survey technique for eliminating evasive answer
bias. Journal of the American Statistical Association, 60, 63–69).
Besides univariate estimates of true proportions, RR variables can be used
for correlations, as dependent variable in a logistic regression and as
predictors in a linear regression. For simulation and bootstrap purposes,
RR data can be generated according to several models.
Author: Daniel W. Heck [aut, cre], Morten Moshagen [aut]
Maintainer: Daniel W. Heck
DESCRIPTION | 10 -
MD5 | 70 ++++++-------
NAMESPACE | 4
NEWS | 9 +
R/RRcor.R | 4
R/RRgen.R | 4
R/RRlin.R | 49 ++++-----
R/RRlin.ll.R | 4
R/RRlog.CDM.R | 9 -
R/RRlog.FR.R | 4
R/RRlog.Kuk.R | 5
R/RRlog.Mangat.R | 4
R/RRlog.R | 246 +++++++++++++++++++++++++++++-----------------
R/RRlog.SLD.R | 4
R/RRlog.UQTknown.R | 6 -
R/RRlog.UQTunknown.R | 4
R/RRlog.Warner.R | 4
R/RRreg-package.R | 6 -
R/RRsimu.R | 267 +++++++++++++++++++++++++-------------------------
R/RRuni.R | 40 +++++--
R/RRuni.models.R | 2
R/powerplot.R | 15 +-
build/vignette.rds |binary
inst/doc/RRreg.R | 6 -
inst/doc/RRreg.Rmd | 6 -
inst/doc/RRreg.html | 144 +++++++++++++-------------
man/RRcor.Rd | 5
man/RRgen.Rd | 7 -
man/RRlin.Rd | 19 ++-
man/RRlog.Rd | 25 ++--
man/RRreg-package.Rd | 9 -
man/RRsimu.Rd | 21 ++-
man/RRuni.Rd | 36 +++++-
man/plot.powerplot.Rd |only
man/powerplot.Rd | 5
man/predict.RRlog.Rd |only
vignettes/RRreg.Rmd | 6 -
37 files changed, 601 insertions(+), 458 deletions(-)
Title: R Interface to SDMX Web Services
Diff between RJSDMX versions 1.2 dated 2014-11-07 and 1.3 dated 2015-02-23
Description: Provides functions to retrieve data and metadata from providers
that disseminate data by means of SDMX web services.
SDMX (Statistical Data and Metadata eXchange) is a standard that
has been developed with the aim of simplifying the exchange of
statistical information.
More about the SDMX standard and the SDMX Web Services
can be found at: http://sdmx.org .
Author: Attilio Mattiocco, Diana Nicoletti, Gianpaolo Lopez, Banca d'Italia
Maintainer: Attilio Mattiocco
DESCRIPTION | 15 ++++---
MD5 | 17 ++++----
NAMESPACE | 1
R/SdmxClient.R | 32 ++++++++++-----
R/TSConverter.R | 88 +++++++++++++++++++++++++++++-------------
R/onLoad.R | 2
inst/configuration.properties | 3 -
inst/java/SDMX.jar |binary
man/addProvider.Rd | 6 ++
man/sdmxdf.Rd |only
10 files changed, 112 insertions(+), 52 deletions(-)
Title: Power/Sample Size Calculation for Mediation Analysis
Diff between powerMediation versions 0.1.7 dated 2013-11-09 and 0.2.3 dated 2015-02-23
More information about powerMediation at CRAN
Description: Functions to
calculate power and sample size for testing
(1) mediation effects;
(2) the slope in a simple linear regression;
(3) odds ratio in a simple logistic regression;
(4) mean change for longitudinal study with 2 time points;
and (5) interaction effect in 2-way ANOVA.
Author: Weiliang Qiu
Maintainer: Weiliang Qiu
DESCRIPTION | 28 +++++++++++++---------------
INDEX | 6 ++++++
MD5 | 20 ++++++++++++--------
NAMESPACE | 4 ++++
NEWS | 23 +++++++++++++++++++++++
R/powerLogisticsReg.R | 2 +-
R/powerLongitudinal.R | 41 +++++++++++++++++++++++++++++++++++++++--
R/power_interaction.R |only
man/SSizeLogisticCon.Rd | 1 +
man/powerInteract.Rd |only
man/powerLogisticCon.Rd | 4 ++--
man/powerLong.multiTime.Rd |only
man/ssLong.multiTime.Rd |only
13 files changed, 101 insertions(+), 28 deletions(-)
Permanent link
Title: Help to Fit of a Parametric Distribution to Non-Censored or
Censored Data
Diff between fitdistrplus versions 1.0-3 dated 2014-12-12 and 1.0-4 dated 2015-02-23
Description: Extends the fitdistr function (of the MASS package) with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left censored, right censored and interval censored values, with several lower and upper bounds. In addition to maximum likelihood estimation method the package provides moment matching, quantile matching and maximum goodness-of-fit estimation methods (available only for non-censored data).
Author: Marie Laure Delignette-Muller [aut, cre],
Christophe Dutang [aut],
Regis Pouillot [ctb],
Jean-Baptiste Denis [ctb]
Maintainer: Marie Laure Delignette-Muller
DESCRIPTION | 12
MD5 | 44 +-
R/plotdistcens.R | 2
inst/CITATION | 35 -
inst/NEWS | 4
inst/doc/paper2JSS.Rnw | 2
inst/doc/paper2JSS.pdf |binary
man/bootdist.Rd | 6
man/bootdistcens.Rd | 6
man/cdfcompcens.Rd | 207 ++++-----
man/descdist.Rd | 268 ++++++------
man/fitdist.Rd | 1031 ++++++++++++++++++++++++------------------------
man/fitdistcens.Rd | 501 +++++++++++------------
man/gofstat.Rd | 373 ++++++++---------
man/graphcomp.Rd | 403 +++++++++---------
man/mgedist.Rd | 315 +++++++-------
man/mledist.Rd | 375 ++++++++---------
man/mmedist.Rd | 306 +++++++-------
man/plotdist.Rd | 245 +++++------
man/plotdistcens.Rd | 222 +++++-----
man/qmedist.Rd | 270 ++++++------
man/quantiles.Rd | 310 +++++++-------
vignettes/paper2JSS.Rnw | 2
23 files changed, 2516 insertions(+), 2423 deletions(-)
Title: Cognitive Diagnosis Modeling
Diff between CDM versions 4.1 dated 2014-12-17 and 4.2-12 dated 2015-02-23
Description: Functions for cognitive diagnosis modeling
and multidimensional item response modeling for dichotomous
and polytomous data. This package enables the estimation of the
DINA and DINO model, the multiple group (polytomous) GDINA model,
the multiple choice DINA model, the general diagnostic model (GDM),
the multidimensional linear compensatory item response model and
the structured latent class model (SLCA).
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut],
Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch
DESCRIPTION | 13 -
MD5 | 125 ++++++++------
NAMESPACE | 57 ++++++
R/IRT.compareModels.R | 40 ++++
R/IRT.data.R |only
R/IRT.derivedParameters.R |only
R/IRT.expectedCounts.R |only
R/IRT.irfprob.R | 7
R/IRT.irfprobPlot.R |only
R/IRT.jackknife.R |only
R/IRT.jackknife.gdina.R |only
R/IRT.likelihood.R | 5
R/IRT.predict.R |only
R/IRT.repDesign.R |only
R/cdi.kli.R | 6
R/din.R | 23 +-
R/equivalent.skillclasses.R | 74 --------
R/gdina.R | 289 ++++++++++++++++++++++------------
R/gdina.partable.R |only
R/gdm.R | 53 +-----
R/gdm_algorithm.R | 10 -
R/jkestimates.R |only
R/logLik_CDM.R | 8
R/mcdina.R | 8
R/modelfit.cor.R | 10 -
R/modelfit.cor2.R | 21 +-
R/predict.CDM.R |only
R/print.summary.din.R | 6
R/skill.cor.R | 73 +++++++-
R/slca.R | 4
R/summary.din.R | 3
R/summary.gdina.R | 23 +-
data/data.Students.rda |binary
data/data.cdm01.rda |binary
data/data.cdm02.rda |binary
data/data.dcm.rda |binary
data/data.dtmr.rda |binary
data/data.ecpe.rda |binary
data/data.fraction1.rda |binary
data/data.fraction2.rda |binary
data/data.hr.rda |binary
data/data.jang.rda |binary
data/data.melab.rda |binary
data/data.mg.rda |binary
data/data.pgdina.rda |binary
data/data.sda6.rda |binary
data/data.timss03.G8.su.rda |binary
data/data.timss07.G4.lee.rda |binary
data/data.timss11.G4.AUT.part.rda |only
data/data.timss11.G4.AUT.rda |only
data/fraction.subtraction.data.rda |binary
data/fraction.subtraction.qmatrix.rda |binary
data/sim.dina.rda |binary
data/sim.dino.rda |binary
data/sim.qmatrix.rda |binary
inst/NEWS | 37 ++++
man/CDM-package.Rd | 131 ++++++++-------
man/IRT.compareModels.Rd | 10 +
man/IRT.data.Rd |only
man/IRT.expectedCounts.Rd |only
man/IRT.irfprob.Rd | 5
man/IRT.irfprobPlot.Rd |only
man/IRT.jackknife.Rd |only
man/IRT.modelfit.Rd | 3
man/IRT.repDesign.Rd |only
man/data.dcm.Rd | 2
man/data.timss11.G4.AUT.Rd |only
man/din.deterministic.Rd | 2
man/din.equivalent.class.Rd | 4
man/gdina.Rd | 53 ++++--
man/personfit.appropriateness.Rd | 2
man/predict.Rd |only
man/skill.cor.Rd | 24 +-
src/irt_predict_c.cpp |only
74 files changed, 702 insertions(+), 429 deletions(-)
Title: Construction, Simulation and Analysis of Boolean Networks
Diff between BoolNet versions 2.0.2 dated 2014-12-11 and 2.1.0 dated 2015-02-23
Description: Provides methods to reconstruct and generate synchronous,
asynchronous, and probabilistic Boolean networks, and to
analyze and visualize attractors in Boolean networks.
Author: Christoph Müssel [aut],
Martin Hopfensitz [aut],
Dao Zhou [aut],
Hans A. Kestler [aut, cre],
Armin Biere [ctb] (contributed PicoSAT code),
Troy D. Hanson [ctb] (contributed uthash macros)
Maintainer: Hans A. Kestler
BoolNet-2.0.2/BoolNet/src/boolean_network.c |only
BoolNet-2.1.0/BoolNet/DESCRIPTION | 28
BoolNet-2.1.0/BoolNet/MD5 | 91
BoolNet-2.1.0/BoolNet/R/attractorsToLaTeX.R | 38
BoolNet-2.1.0/BoolNet/R/fixGenes.R | 2
BoolNet-2.1.0/BoolNet/R/getAttractors.R | 66
BoolNet-2.1.0/BoolNet/R/helpers.R | 2
BoolNet-2.1.0/BoolNet/R/loadBioTapestry.R | 2
BoolNet-2.1.0/BoolNet/R/loadNetwork.R | 2
BoolNet-2.1.0/BoolNet/R/loadSBML.R | 2
BoolNet-2.1.0/BoolNet/R/parseBooleanFunction.R | 3
BoolNet-2.1.0/BoolNet/R/plotAttractors.R | 32
BoolNet-2.1.0/BoolNet/R/plotSequence.R | 12
BoolNet-2.1.0/BoolNet/R/sequenceToLaTeX.R | 10
BoolNet-2.1.0/BoolNet/R/simulateSymbolicModel.R | 90
BoolNet-2.1.0/BoolNet/R/stateTransition.R | 2
BoolNet-2.1.0/BoolNet/R/symbolicToTruthTable.R | 2
BoolNet-2.1.0/BoolNet/R/truthTableToSymbolic.R | 2
BoolNet-2.1.0/BoolNet/build/vignette.rds |binary
BoolNet-2.1.0/BoolNet/inst/NEWS.Rd | 13
BoolNet-2.1.0/BoolNet/inst/doc/BoolNet_package_vignette.R | 186
BoolNet-2.1.0/BoolNet/inst/doc/BoolNet_package_vignette.Snw | 106
BoolNet-2.1.0/BoolNet/inst/doc/BoolNet_package_vignette.pdf |binary
BoolNet-2.1.0/BoolNet/man/BoolNet-package.Rd | 15
BoolNet-2.1.0/BoolNet/man/attractorsToLaTeX.Rd | 8
BoolNet-2.1.0/BoolNet/man/getAttractors.Rd | 40
BoolNet-2.1.0/BoolNet/man/markovSimulation.Rd | 2
BoolNet-2.1.0/BoolNet/man/plotAttractors.Rd | 8
BoolNet-2.1.0/BoolNet/man/plotNetworkWiring.Rd | 2
BoolNet-2.1.0/BoolNet/man/plotPBNTransitions.Rd | 2
BoolNet-2.1.0/BoolNet/man/plotSequence.Rd | 11
BoolNet-2.1.0/BoolNet/man/reconstructNetwork.Rd | 2
BoolNet-2.1.0/BoolNet/man/sequenceToLaTeX.Rd | 12
BoolNet-2.1.0/BoolNet/man/simulateSymbolicModel.Rd | 66
BoolNet-2.1.0/BoolNet/man/testNetworkProperties.Rd | 48
BoolNet-2.1.0/BoolNet/src/attractor_info.c |only
BoolNet-2.1.0/BoolNet/src/attractor_info.h |only
BoolNet-2.1.0/BoolNet/src/attractor_search_interface.c |only
BoolNet-2.1.0/BoolNet/src/boolean_network.h |only
BoolNet-2.1.0/BoolNet/src/common.c | 2
BoolNet-2.1.0/BoolNet/src/common.h | 50
BoolNet-2.1.0/BoolNet/src/picosat.c |only
BoolNet-2.1.0/BoolNet/src/picosat.h |only
BoolNet-2.1.0/BoolNet/src/probabilistic_boolean_network.c | 42
BoolNet-2.1.0/BoolNet/src/sat_search.c |only
BoolNet-2.1.0/BoolNet/src/sat_search.h |only
BoolNet-2.1.0/BoolNet/src/statespace_search.c |only
BoolNet-2.1.0/BoolNet/src/statespace_search.h |only
BoolNet-2.1.0/BoolNet/src/symbolic_network.c |only
BoolNet-2.1.0/BoolNet/src/symbolic_network.h |only
BoolNet-2.1.0/BoolNet/src/symbolic_simulator.c | 2628 +++++------
BoolNet-2.1.0/BoolNet/vignettes/BoolNet_package_vignette.Snw | 106
BoolNet-2.1.0/BoolNet/vignettes/BoolNet_package_vignette.bib | 18
53 files changed, 2004 insertions(+), 1749 deletions(-)
Title: SYMPHONY in R
Diff between Rsymphony versions 0.1-18 dated 2015-01-10 and 0.1-19 dated 2015-02-23
Description: An R interface to the SYMPHONY solver for mixed-integer linear programs.
Author: Reinhard Harter [aut],
Kurt Hornik [aut, cre],
Stefan Theussl [aut],
Cyrille Szymanski [ctb]
Maintainer: Kurt Hornik
DESCRIPTION | 6 +++---
MD5 | 4 ++--
R/symphony.R | 27 ++++++++++++++++-----------
3 files changed, 21 insertions(+), 16 deletions(-)
Title: R Commander Plug-In for University Level Applied Statistics
Diff between RcmdrPlugin.NMBU versions 1.8.0 dated 2015-01-22 and 1.8.0.1 dated 2015-02-23
More information about RcmdrPlugin.NMBU at CRAN
Description: An R Commander "plug-in" extending functionality of linear models and providing an interface to Partial Least Squares Regression and Linear and Quadratic Discriminant analysis. Several statistical summaries are extended, predictions are offered for additional types of analyses, and extra plots, tests and mixed models are available.
Author: Kristian Hovde Liland [aut, cre],
Solve Sæbø [aut]
Maintainer: Kristian Hovde Liland
DESCRIPTION | 17 -
MD5 | 14
NAMESPACE | 4
R/NMBU.GUI.Models.R | 2
R/NMBU.GUI.Statistics.R | 600 ++++++++++++++++++++--------------------
R/NMBU.Utilities.R | 1
inst/etc/menus.txt | 10
man/RcmdrPlugin.NMBU-package.Rd | 1
8 files changed, 333 insertions(+), 316 deletions(-)
Permanent link
Title: Biostatistics Utilities for Nephrology
Diff between nephro versions 1.0 dated 2013-01-30 and 1.1 dated 2015-02-23
Description: Set of functions to estimate the Glomerular Filtration Rate (GFR) using different biomarkers and other phenotypes of interest for nephrology.
Author: Cristian Pattaro
Maintainer: Cristian Pattaro
nephro-1.0/nephro/R/nephro.r |only
nephro-1.1/nephro/ChangeLog |only
nephro-1.1/nephro/DESCRIPTION | 15 +++-----
nephro-1.1/nephro/MD5 | 28 ++++++++-------
nephro-1.1/nephro/NAMESPACE | 2 -
nephro-1.1/nephro/R/nephro.R |only
nephro-1.1/nephro/man/CG.Rd |only
nephro-1.1/nephro/man/CKDEpi.creat.Rd | 17 +++------
nephro-1.1/nephro/man/CKDEpi.creat.cys.Rd | 13 ++----
nephro-1.1/nephro/man/CKDEpi.cys.Rd | 14 +++----
nephro-1.1/nephro/man/MDRD4.Rd | 22 ++++-------
nephro-1.1/nephro/man/MDRD6.Rd | 20 ++++------
nephro-1.1/nephro/man/Stevens.creat.cys.Rd | 16 +++-----
nephro-1.1/nephro/man/Stevens.cys1.Rd | 26 ++++---------
nephro-1.1/nephro/man/Stevens.cys2.Rd | 22 +++--------
nephro-1.1/nephro/man/Virga.Rd | 37 ++++++++++++-------
nephro-1.1/nephro/man/nephro-package.Rd | 54 +++++++++++++++++++----------
17 files changed, 137 insertions(+), 149 deletions(-)
Title: Provides Access to Git Repositories
Diff between git2r versions 0.6 dated 2015-02-18 and 0.7 dated 2015-02-23
Description: Interface to the libgit2 library, which is a pure C
implementation of the Git core methods. Provides access to Git
repositories to extract data and running some basic git commands.
Author: See AUTHORS file.
Maintainer: Stefan Widgren
filter.h | 38
tmp/cranberry50814e554202/git2r-0.7/git2r/DESCRIPTION | 8
tmp/cranberry50814e554202/git2r-0.7/git2r/MD5 | 42 -
tmp/cranberry50814e554202/git2r-0.7/git2r/NEWS | 10
tmp/cranberry50814e554202/git2r-0.7/git2r/configure | 17
tmp/cranberry50814e554202/git2r-0.7/git2r/src/Makevars.in | 7
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/attr.c | 5
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/blob.c | 14
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/buffer.c | 14
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/buffer.h | 6
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/checkout.c | 136 ++-
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/crlf.c | 2
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/diff.c | 2
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/diff_driver.c | 9
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/diff_file.c | 2
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/filter.c | 416 +++++++---
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/filter.h | 13
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/include/git2/types.h | 9
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/integer.h | 2
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/pack.c | 11
tmp/cranberry50814e554202/git2r-0.7/git2r/src/libgit2/repository.c | 2
21 files changed, 565 insertions(+), 200 deletions(-)
Title: An R Plug-in for the Distributed Hydrological Model GEOtop
Diff between geotopbricks versions 1.3.5.4 dated 2014-05-22 and 1.3.6 dated 2015-02-23
Description: It analyzes raster maps and other information as input/output
files from the Hydrological Distributed Model GEOtop. It contains functions
and methods to import maps and other keywords from geotop.inpts file. Some
examples with simulation cases of GEOtop 2.0 are presented in the package.
Any information about the GEOtop Distributed Hydrological Model source code
is available on http://code.google.com/p/geotop/ or
https://github.com/se27xx/GEOtop. Technical details about the model are
available in Endrizzi et al, 2014
(http://www.geosci-model-dev.net/7/2831/2014/gmd-7-2831-2014.html).
Author: Emanuele Cordano, Daniele Andreis, Fabio Zottele
Maintainer: Emanuele Cordano
geotopbricks-1.3.5.4/geotopbricks/R/geotopbricks-package.R |only
geotopbricks-1.3.5.4/geotopbricks/man/geotopbricks-package.Rd |only
geotopbricks-1.3.6/geotopbricks/DESCRIPTION | 34 +++---
geotopbricks-1.3.6/geotopbricks/MD5 | 41 +++----
geotopbricks-1.3.6/geotopbricks/NAMESPACE | 1
geotopbricks-1.3.6/geotopbricks/R/aggregate.brick.at.depth.R | 2
geotopbricks-1.3.6/geotopbricks/R/bar.color.raster.R | 55 +++++++++-
geotopbricks-1.3.6/geotopbricks/R/brickFromOutput3DTensor.R | 7 -
geotopbricks-1.3.6/geotopbricks/R/declared.geotop.inpts.keywords.R | 18 ++-
geotopbricks-1.3.6/geotopbricks/R/geotopbrick_S3.R | 10 -
geotopbricks-1.3.6/geotopbricks/R/get.keyword.value.R | 45 +++++++-
geotopbricks-1.3.6/geotopbricks/R/listFromOutput3DTensor.R | 4
geotopbricks-1.3.6/geotopbricks/R/writeRasterxgeotop.R | 40 +++++++
geotopbricks-1.3.6/geotopbricks/data/bondone.rda |binary
geotopbricks-1.3.6/geotopbricks/inst/doc/examples/example.brickFromOutput3DTensor.R | 2
geotopbricks-1.3.6/geotopbricks/inst/doc/examples/example.time.aggragation.R |only
geotopbricks-1.3.6/geotopbricks/inst/rendena100 |only
geotopbricks-1.3.6/geotopbricks/man/bondone.Rd | 2
geotopbricks-1.3.6/geotopbricks/man/brickFromOutputSoil3DTensor.Rd | 12 +-
geotopbricks-1.3.6/geotopbricks/man/color.bar.raster.Rd | 26 ++++
geotopbricks-1.3.6/geotopbricks/man/declared.geotop.inpts.keywords.Rd | 7 +
geotopbricks-1.3.6/geotopbricks/man/listFromOutputSoil3DTensor.Rd | 10 -
geotopbricks-1.3.6/geotopbricks/man/writeRasterxGEOtop.Rd | 15 ++
23 files changed, 254 insertions(+), 77 deletions(-)
Title: Estimate Permutation p-Values for Random Forest Importance
Metrics
Diff between rfPermute versions 1.6.1 dated 2014-08-12 and 1.6.2 dated 2015-02-23
Description: Estimate significance of importance metrics
for a Random Forest model by permuting the response
variable. Produces null distribution of importance
metrics for each predictor variable and p-value of
observed.
Author: Eric Archer
Maintainer: Eric Archer
DESCRIPTION | 16 ++++++++--------
MD5 | 32 ++++++++++++++++----------------
NAMESPACE | 13 +++++++------
R/plot.rfPermute.R | 4 ++--
R/plot.rp.importance.r | 17 ++++++++---------
R/rfPermute.R | 2 +-
R/rfPermute.default.R | 2 ++
R/rfPermute.formula.R | 3 +++
R/rp.importance.R | 7 +++++--
man/calc.imp.pval.Rd | 3 ++-
man/clean.rf.data.Rd | 3 ++-
man/plot.rfPermute.Rd | 5 +++--
man/plot.rp.importance.Rd | 5 +++--
man/proximity.plot.Rd | 3 ++-
man/rfPermute.Rd | 9 +++++----
man/rp.combine.Rd | 3 ++-
man/rp.importance.Rd | 9 ++++++---
17 files changed, 77 insertions(+), 59 deletions(-)
Title: Easy Handling of and Access to Files Organized in Structured
Directories
Diff between R.filesets versions 2.6.0 dated 2014-08-27 and 2.7.0 dated 2015-02-23
Description: A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson
DESCRIPTION | 20 +--
MD5 | 64 +++++-----
NAMESPACE | 12 +
NEWS | 22 +++
R/ChecksumFile.R | 11 +
R/GenericDataFileSet.PARALLEL.R | 9 -
R/GenericDataFileSet.R | 33 +++--
R/RDataFile.R |only
R/RDataFileSet.R |only
R/RdsFile.R | 1
inst/exData/dataSetA,original/1.2(a).txt | 26 ++--
inst/exData/dataSetA,original/11.2(a).txt | 26 ++--
inst/exData/dataSetA,original/fileF.txt | 26 ++--
inst/exData/dataSetA,original/fileFF.txt | 26 ++--
inst/exData/dataSetB/fileG,EOL.txt | 22 +--
inst/exData/dataSetB/fileG,noEOL.txt | 20 +--
man/FullNameInterface.Rd | 2
man/GenericDataFile.Rd | 2
man/GenericDataFileSet.Rd | 36 ++---
man/GenericTabularFile.Rd | 12 -
man/RDataFile.Rd |only
man/RDataFileSet.Rd |only
man/RdsFile.Rd | 1
man/TabularTextFile.Rd | 10 -
man/TabularTextFileSet.Rd | 2
man/getFile.GenericDataFileSet.Rd | 5
man/loadToEnv.Rd |only
tests/GenericDataFile.R | 17 ++
tests/GenericDataFileSet,dsApply.R | 18 +-
tests/GenericDataFileSet,sortBy.R | 42 +++---
tests/GenericDataFileSet.R | 8 -
tests/RdsFileSet.R | 2
tests/TabularTextFile,huge.R |only
tests/TabularTextFile.R | 184 +++++++++++++++---------------
tests/TabularTextFileSet.R | 146 ++++++++++++-----------
tests/VectorAndListAPI.R | 14 +-
36 files changed, 458 insertions(+), 361 deletions(-)
Title: Mixed Model ANOVA and Statistics for Education
Diff between mixlm versions 1.0.8.1 dated 2015-01-31 and 1.0.8.3 dated 2015-02-23
Description: The main functions perform mixed models analysis by least squares or REML by adding the function r() to formulas of lm and glm. A collection of text-book statistics for higher education is also included, e.g. modifications of the functions lm, glm and associated summaries from the package stats.
Author: Kristian Hovde Liland [aut, cre],
Solve Sæbø [ctb],
R-Core [ctb]
Maintainer: Kristian Hovde Liland
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/statistics.R | 25 ++++++++++++++++++++++---
3 files changed, 28 insertions(+), 9 deletions(-)
Title: Summaries and Population Structure Analyses of Haplotypic and
Genotypic Data
Diff between strataG versions 0.9.2 dated 2014-12-31 and 0.9.4 dated 2015-02-22
Description: A toolkit for analyzing stratified population genetic data.
Author: Eric Archer
Maintainer: Eric Archer
DESCRIPTION | 8 -
MD5 | 234 +++++++++++++++++-----------------
NAMESPACE | 2
R/gtypes.R | 20 +-
R/gtypes.default.R | 249 ++++++++++++++++++-------------------
R/is.gtypes.R | 2
R/jmodeltest.run.R | 39 +++--
R/merge.gtypes.R | 6
R/nucleotide.diversity.R | 13 +
R/pop.diff.test.R | 18 ++
man/align.clustal.Rd | 3
man/align.folder.Rd | 3
man/align.mafft.Rd | 3
man/allele.freq.format.Rd | 3
man/allele.freqs.Rd | 3
man/allele.split.Rd | 3
man/allelic.richness.Rd | 3
man/as.data.frame.gtypes.Rd | 3
man/as.dna.seq.Rd | 3
man/as.matrix.gtypes.Rd | 3
man/base.freqs.Rd | 3
man/bowhead.snp.position.Rd | 3
man/bowhead.snps.Rd | 3
man/check.genotypes.Rd | 3
man/check.seqs.Rd | 3
man/clumpp.run.Rd | 3
man/create.consensus.Rd | 3
man/decode.Rd | 3
man/diversity.Rd | 3
man/dolph.haps.Rd | 3
man/dolph.msats.Rd | 3
man/dolph.seqs.Rd | 3
man/dolph.strata.Rd | 3
man/dup.genotypes.Rd | 3
man/exptd.het.Rd | 3
man/fastsimcoal.run.Rd | 3
man/fisher.method.p.Rd | 3
man/fixed.differences.Rd | 3
man/fixed.sites.Rd | 3
man/fst.to.nm.Rd | 3
man/gelato.plot.Rd | 3
man/gelato.run.Rd | 3
man/gen.data.from.freq.Rd | 3
man/genepop.run.Rd | 3
man/gtype.struct.func.Rd | 3
man/gtypes.Rd | 21 +--
man/h.stats.Rd | 3
man/hap.freqs.Rd | 3
man/haplotype.likelihoods.Rd | 3
man/haplotypic.diversity.Rd | 3
man/hwe.genepop.Rd | 3
man/is.diploid.Rd | 3
man/is.gtype.struct.func.Rd | 3
man/iupac.code.Rd | 3
man/jack.hwe.Rd | 3
man/jmodeltest.run.Rd | 10 +
man/label.haplotypes.Rd | 3
man/linkage.genepop.Rd | 3
man/locus.names.Rd | 3
man/low.freq.subs.Rd | 3
man/merge.gtypes.Rd | 10 +
man/most.distant.sequences.Rd | 3
man/na.omit.gtypes.Rd | 3
man/nei.Da.Rd | 3
man/nucleotide.divergence.Rd | 3
man/nucleotide.diversity.Rd | 7 -
man/num.alleles.Rd | 3
man/num.alleles.shared.Rd | 3
man/num.gens.eq.Rd | 3
man/num.missing.Rd | 3
man/obsvd.het.Rd | 3
man/p.val.Rd | 3
man/pairwise.shared.loci.Rd | 3
man/pct.unique.haplotypes.Rd | 3
man/phase.run.Rd | 3
man/pop.diff.test.Rd | 19 ++
man/print.gtypeSummary.Rd | 3
man/read.arlequin.Rd | 3
man/read.fasta.Rd | 3
man/read.gen.data.Rd | 3
man/read.mega.Rd | 3
man/relabel.sequences.Rd | 3
man/restratify.Rd | 3
man/sequence.summary.Rd | 3
man/shared.haps.Rd | 3
man/sim.gamma.haps.Rd | 3
man/smry.by.locus.Rd | 3
man/smry.by.sample.Rd | 3
man/stat.chi2.Rd | 3
man/stat.d.jost.Rd | 3
man/stat.fst.Rd | 3
man/stat.fst.prime.Rd | 3
man/stat.gst.Rd | 3
man/stat.gst.dbl.prime.Rd | 3
man/stat.gst.prime.hedrick.Rd | 3
man/stat.gst.prime.nei.Rd | 3
man/stat.phist.Rd | 3
man/stopifnot.gtype.struct.func.Rd | 3
man/strata.pairs.Rd | 3
man/strata.split.Rd | 3
man/strataG-package.Rd | 3
man/structure.evanno.Rd | 3
man/structure.parse.q.mat.Rd | 3
man/structure.plot.Rd | 3
man/structure.run.Rd | 3
man/subset.gtypes.Rd | 3
man/summarize.loci.Rd | 3
man/summarize.sequences.Rd | 3
man/summary.gtypes.Rd | 3
man/tajimas.d.Rd | 3
man/theta.Rd | 3
man/ti.tv.ratio.Rd | 3
man/trim.ns.Rd | 3
man/valid.iupac.codes.Rd | 3
man/variable.sites.Rd | 3
man/wright.fst.Rd | 3
man/write.gtypes.Rd | 3
man/write.snapp.nexus.Rd | 3
118 files changed, 563 insertions(+), 404 deletions(-)
Title: Mixed Models, Particularly Spatial GLMMs
Diff between spaMM versions 1.4.1 dated 2014-11-08 and 1.5.1 dated 2015-02-22
Description: Implements a collection of functions for inference in mixed models. It was developed in particular for GLMMs with spatial correlations, but also fits models with non-Gaussian random effects (e.g., Beta Binomial, or negative-binomial mixed models). Heteroskedasticity can further be fitted by a linear model. The algorithms are currently various Laplace approximations methods for ML or REML, in particular h-likelihood and penalized-likelihood methods.
Author: François Rousset [aut, cre, cph],
Jean-Baptiste Ferdy [aut, cph]
Maintainer: François Rousset
spaMM-1.4.1/spaMM/R/blockDiag.R |only
spaMM-1.4.1/spaMM/R/ordinaryKrigingCoefs.R |only
spaMM-1.4.1/spaMM/man/spaMM-internal-blockDiag.Rd |only
spaMM-1.5.1/spaMM/DESCRIPTION | 8
spaMM-1.5.1/spaMM/MD5 | 126 +--
spaMM-1.5.1/spaMM/NAMESPACE | 17
spaMM-1.5.1/spaMM/R/HLCor.R | 31
spaMM-1.5.1/spaMM/R/HLFactorList.R | 65 -
spaMM-1.5.1/spaMM/R/HLfit.R | 789 ++++++++++++-------
spaMM-1.5.1/spaMM/R/HLframes.R | 63 +
spaMM-1.5.1/spaMM/R/LR.R | 12
spaMM-1.5.1/spaMM/R/MakeCovEst.R |only
spaMM-1.5.1/spaMM/R/RcppExports.R | 8
spaMM-1.5.1/spaMM/R/auglinmodfit.R | 156 ++-
spaMM-1.5.1/spaMM/R/calc.p_v.R | 20
spaMM-1.5.1/spaMM/R/confint.R | 6
spaMM-1.5.1/spaMM/R/corrHLfit.R | 66 -
spaMM-1.5.1/spaMM/R/corrMM.LRT.R | 16
spaMM-1.5.1/spaMM/R/correlationFns.R | 77 +
spaMM-1.5.1/spaMM/R/extractors.R | 42 -
spaMM-1.5.1/spaMM/R/is.diagonal.R | 15
spaMM-1.5.1/spaMM/R/locoptim.R | 2
spaMM-1.5.1/spaMM/R/locoptimthroughsmooth.R | 12
spaMM-1.5.1/spaMM/R/mapMM.R | 377 +++++----
spaMM-1.5.1/spaMM/R/migraineLike.R | 51 -
spaMM-1.5.1/spaMM/R/plot.HLfit.R | 15
spaMM-1.5.1/spaMM/R/predict.R | 223 +++--
spaMM-1.5.1/spaMM/R/preprocess.R | 11
spaMM-1.5.1/spaMM/R/profile.R | 2
spaMM-1.5.1/spaMM/R/simulate.HL.R | 31
spaMM-1.5.1/spaMM/R/spaMM.data.R | 15
spaMM-1.5.1/spaMM/R/summary.HL.R | 16
spaMM-1.5.1/spaMM/R/utils.R | 10
spaMM-1.5.1/spaMM/inst/CITATION | 8
spaMM-1.5.1/spaMM/inst/NEWS.Rd |only
spaMM-1.5.1/spaMM/man/HLCor.Rd | 21
spaMM-1.5.1/spaMM/man/HLfit.Rd | 2
spaMM-1.5.1/spaMM/man/Matern.corr.Rd | 4
spaMM-1.5.1/spaMM/man/Predictor.Rd | 2
spaMM-1.5.1/spaMM/man/arabidopsis.Rd | 2
spaMM-1.5.1/spaMM/man/confint.Rd | 8
spaMM-1.5.1/spaMM/man/corMatern.Rd | 14
spaMM-1.5.1/spaMM/man/corrHLfit.Rd | 37
spaMM-1.5.1/spaMM/man/extractors.Rd | 17
spaMM-1.5.1/spaMM/man/fixed.LRT.Rd | 16
spaMM-1.5.1/spaMM/man/make.scaled.dist.Rd | 25
spaMM-1.5.1/spaMM/man/mapMM.Rd | 96 +-
spaMM-1.5.1/spaMM/man/options.Rd | 13
spaMM-1.5.1/spaMM/man/predict.Rd | 52 -
spaMM-1.5.1/spaMM/man/salamander.Rd | 6
spaMM-1.5.1/spaMM/man/scotlip.Rd | 2
spaMM-1.5.1/spaMM/man/seaMask.Rd | 6
spaMM-1.5.1/spaMM/man/seeds.Rd | 2
spaMM-1.5.1/spaMM/man/simulate.HLCor.Rd | 6
spaMM-1.5.1/spaMM/man/spaMM-internal-Rcpp.Rd | 3
spaMM-1.5.1/spaMM/man/spaMM-internal-migraine.Rd | 1
spaMM-1.5.1/spaMM/man/spaMM-internal.Rd | 21
spaMM-1.5.1/spaMM/man/spaMM.Rd | 29
spaMM-1.5.1/spaMM/man/spaMM.filled.contour.Rd | 27
spaMM-1.5.1/spaMM/man/spaMMcolors.Rd | 4
spaMM-1.5.1/spaMM/src/RcppExports.cpp | 31
spaMM-1.5.1/spaMM/src/spaMM_linear.cpp | 99 +-
spaMM-1.5.1/spaMM/tests/test-all.R |only
spaMM-1.5.1/spaMM/tests/testthat/test-HLfit.R | 2
spaMM-1.5.1/spaMM/tests/testthat/test-filled.mapMM.R | 11
spaMM-1.5.1/spaMM/tests/testthat/test-sp-nsp.R | 2
spaMM-1.5.1/spaMM/tests/testthat/test-spaMM.R | 4
67 files changed, 1797 insertions(+), 1058 deletions(-)
Title: A Framework for Comparing the Performance of MCMC Samplers
Diff between SamplerCompare versions 1.2.5 dated 2013-12-22 and 1.2.6 dated 2015-02-22
More information about SamplerCompare at CRAN
Description: A framework for running sets of MCMC samplers on sets of
distributions with a variety of tuning parameters, along with plotting
functions to visualize the results of those simulations. See sc-intro.pdf
for an introduction.
Author: Madeleine Thompson, except dchud.f and dchdd.f, which were written by
G. W. Stewart.
Maintainer: Madeleine Thompson
DESCRIPTION | 21 ++++++++++-----------
MD5 | 42 +++++++++++++++++++++---------------------
NAMESPACE | 3 ++-
R/00dist-util.R | 10 +++++-----
R/act.R | 2 +-
R/compare-samplers.R | 2 +-
R/distributions.R | 4 +++-
build/vignette.rds |binary
inst/doc/glue.Rnw | 6 +++---
inst/doc/glue.pdf |binary
inst/doc/sc-intro.Rnw | 2 +-
inst/doc/sc-intro.pdf |binary
man/SamplerCompare-package.Rd | 16 ++++++++--------
man/compare.samplers.Rd | 4 ++--
man/dist-class.Rd | 4 ++--
man/make.c.dist.Rd | 2 +-
man/make.cone.dist.Rd | 2 +-
man/make.dist.Rd | 2 +-
man/make.multimodal.dist.Rd | 2 +-
man/make.mv.gamma.dist.Rd | 2 +-
vignettes/glue.Rnw | 6 +++---
vignettes/sc-intro.Rnw | 2 +-
22 files changed, 68 insertions(+), 66 deletions(-)
Permanent link
Title: Analysis of Parent-Specific DNA Copy Numbers
Diff between PSCBS versions 0.43.0 dated 2014-06-09 and 0.44.0 dated 2015-02-22
Description: Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut],
Venkatraman E. Seshan [aut],
Adam B. Olshen [aut],
Paul T. Spellman [aut],
Richard A. Olshen [aut]
Maintainer: Henrik Bengtsson
PSCBS-0.43.0/PSCBS/R/PairedPSCBS.BOOT,DEPRECATED.R |only
PSCBS-0.44.0/PSCBS/DESCRIPTION | 20 +++++------
PSCBS-0.44.0/PSCBS/MD5 | 34 ++++++++++----------
PSCBS-0.44.0/PSCBS/NAMESPACE | 6 ++-
PSCBS-0.44.0/PSCBS/NEWS | 12 ++++++-
PSCBS-0.44.0/PSCBS/R/AbstractCBS.PRUNE.R | 2 -
PSCBS-0.44.0/PSCBS/R/PairedPSCBS.BOOT,DEFUNCT.R |only
PSCBS-0.44.0/PSCBS/R/PairedPSCBS.estimateDeltaLOH.R | 2 -
PSCBS-0.44.0/PSCBS/R/PairedPSCBS.estimateKappa.R | 2 -
PSCBS-0.44.0/PSCBS/R/prememoize.R | 2 -
PSCBS-0.44.0/PSCBS/build/vignette.rds |binary
PSCBS-0.44.0/PSCBS/inst/doc/CBS.R | 5 +-
PSCBS-0.44.0/PSCBS/inst/doc/CBS.pdf |binary
PSCBS-0.44.0/PSCBS/inst/doc/CBS.tex.rsp | 14 ++++----
PSCBS-0.44.0/PSCBS/inst/doc/PairedPSCBS.R | 5 +-
PSCBS-0.44.0/PSCBS/inst/doc/PairedPSCBS.pdf |binary
PSCBS-0.44.0/PSCBS/inst/doc/PairedPSCBS.tex.rsp | 17 +++++-----
PSCBS-0.44.0/PSCBS/vignettes/CBS.tex.rsp | 14 ++++----
PSCBS-0.44.0/PSCBS/vignettes/PairedPSCBS.tex.rsp | 17 +++++-----
19 files changed, 89 insertions(+), 63 deletions(-)
Title: Mazama Science Spatial Data Download and Utility Functions
Diff between MazamaSpatialUtils versions 0.1.2 dated 2015-02-11 and 0.2.1 dated 2015-02-22
More information about MazamaSpatialUtils at CRAN
Description: A suite of conversion scripts to create internally standardized
spatial polygons dataframes. Utility scripts use these datasets to return
values such as country, state, timezone, watershed, etc. associated with a
set of longitude/latitude pairs. (They also make cool maps.)
Author: Jonathan Callahan [aut, cre],
Will Leahy [aut],
Henry Nguyen [aut]
Maintainer: Jonathan Callahan
MazamaSpatialUtils-0.1.2/MazamaSpatialUtils/man/CountryTable.Rd |only
MazamaSpatialUtils-0.1.2/MazamaSpatialUtils/man/StateTable.Rd |only
MazamaSpatialUtils-0.1.2/MazamaSpatialUtils/man/TimezoneTable.Rd |only
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/DESCRIPTION | 15
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/MD5 | 116 ++++---
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/NAMESPACE | 7
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/MazamaSpatialUtils.R | 151 +++-------
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/convertGADM.R |only
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/convertLayer.R | 9
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/convertNaturalEarthAdm1.R | 85 +++--
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/convertTMWorldBorders.R | 45 +-
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/convertTMWorldBordersSimple.R | 51 +--
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/convertUSCensusCounties.R | 43 +-
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/convertUSGSHUC8.R |only
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/convertWikipediaTimezoneTable.R | 20 -
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/convertWorldTimezones.R | 29 -
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/getCountry.R | 16 -
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/getCountryCode.R | 18 -
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/getCountryName.R | 18 -
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/getSpatialData.R | 7
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/getState.R | 13
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/getStateCode.R | 17 -
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/getStateName.R | 13
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/getTimezone.R | 10
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/getUSCounty.R | 11
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/getVariable.R |only
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/installSpatialData.R | 14
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/loadSpatialData.R | 5
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/R/organizePolygons.R |only
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/data/SimpleCountries.RData |binary
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/data/SimpleTimezones.RData |binary
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/inst/doc/introduction.html | 19 -
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/MazamaSpatialUtils.Rd | 1
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/SpatialDataDir.Rd | 6
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/codeToCode.Rd |only
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/codeToCountry.Rd | 6
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/codeToState.Rd | 4
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/convertGADM.Rd |only
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/convertLayer.Rd | 9
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/convertNaturalEarthAdm1.Rd | 15
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/convertTMWorldBorders.Rd | 11
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/convertTMWorldBordersSimple.Rd | 11
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/convertUSCensusCounties.Rd | 11
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/convertUSGSHUC8.Rd |only
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/convertWikipediaTimezoneTable.Rd | 7
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/convertWorldTimezones.Rd | 11
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/countryToCode.Rd | 4
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/getCountry.Rd | 15
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/getCountryCode.Rd | 15
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/getCountryName.Rd | 17 -
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/getSpatialData.Rd | 6
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/getSpatialDataDir.Rd | 6
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/getState.Rd | 12
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/getStateCode.Rd | 14
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/getStateName.Rd | 12
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/getTimezone.Rd | 10
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/getUSCounty.Rd | 8
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/getVariable.Rd |only
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/initializeSpatialData.Rd | 17 -
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/installSpatialData.Rd | 6
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/loadSpatialData.Rd | 2
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/organizePolygons.Rd |only
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/setSpatialDataDir.Rd | 6
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/man/stateToCode.Rd | 8
MazamaSpatialUtils-0.2.1/MazamaSpatialUtils/tests/testthat/test1.R | 4
65 files changed, 499 insertions(+), 487 deletions(-)
Permanent link
Title: Statistical Estimation of Game-Theoretic Models
Diff between games versions 1.1-1 dated 2014-01-17 and 1.1.2 dated 2015-02-22
Description: Provides estimation and analysis functions for
strategic statistical models.
Author: Curtis S. Signorino [aut],
Brenton Kenkel [aut, cre]
Maintainer: Brenton Kenkel
games-1.1-1/games/NEWS |only
games-1.1-1/games/R/helpers.r |only
games-1.1.2/games/DESCRIPTION | 14 +--
games-1.1.2/games/MD5 | 101 ++++++++++++++---------
games-1.1.2/games/NAMESPACE | 2
games-1.1.2/games/R/checkFormulas.r |only
games-1.1.2/games/R/checkLocalID.r |only
games-1.1.2/games/R/convergenceCriterion.r |only
games-1.1.2/games/R/doc.r | 17 ---
games-1.1.2/games/R/egame12.r | 48 -----------
games-1.1.2/games/R/egame122.r | 33 -------
games-1.1.2/games/R/egame123.r | 21 ----
games-1.1.2/games/R/finiteProbs.r |only
games-1.1.2/games/R/gameBoot.r |only
games-1.1.2/games/R/games.r | 26 +-----
games-1.1.2/games/R/getGameVcov.r |only
games-1.1.2/games/R/intersectAll.r |only
games-1.1.2/games/R/latexTable.r | 16 ---
games-1.1.2/games/R/makeFormulas.r | 86 -------------------
games-1.1.2/games/R/makeUtils.r |only
games-1.1.2/games/R/makeVarNames.r |only
games-1.1.2/games/R/nonnest.r | 38 --------
games-1.1.2/games/R/predProbs.r | 98 ++--------------------
games-1.1.2/games/R/profile.r | 25 -----
games-1.1.2/games/R/svalsFromProfile.r |only
games-1.1.2/games/R/ultimatum.r | 43 +++------
games-1.1.2/games/inst/examples |only
games-1.1.2/games/man/LW.Rd | 4
games-1.1.2/games/man/Mode.Rd | 14 +--
games-1.1.2/games/man/data_122.Rd | 2
games-1.1.2/games/man/data_123.Rd | 2
games-1.1.2/games/man/data_ult.Rd | 2
games-1.1.2/games/man/egame12.Rd | 121 ++++++++++++----------------
games-1.1.2/games/man/egame122.Rd | 118 +++++++++++----------------
games-1.1.2/games/man/egame123.Rd | 108 +++++++++++-------------
games-1.1.2/games/man/games-package.Rd | 6 -
games-1.1.2/games/man/latexTable.Rd | 47 +++++-----
games-1.1.2/games/man/leblang2003.Rd | 28 ++++--
games-1.1.2/games/man/makeFormulas.Rd | 31 +++----
games-1.1.2/games/man/plot.predProbs.Rd | 55 ++++++------
games-1.1.2/games/man/plot.profile.game.Rd | 13 +--
games-1.1.2/games/man/predProbs.Rd | 59 ++++++-------
games-1.1.2/games/man/predict.game.Rd | 24 ++---
games-1.1.2/games/man/print.game.Rd | 6 -
games-1.1.2/games/man/print.summary.game.Rd | 9 +-
games-1.1.2/games/man/profile.game.Rd | 55 ++++++------
games-1.1.2/games/man/student_offers.Rd | 2
games-1.1.2/games/man/summary.game.Rd | 10 +-
games-1.1.2/games/man/ultimatum.Rd | 84 ++++++++-----------
games-1.1.2/games/man/vuong.Rd | 50 +++++------
games-1.1.2/games/man/war1800.Rd | 2
games-1.1.2/games/tests |only
52 files changed, 539 insertions(+), 881 deletions(-)
Title: Toolkit of Helper Functions to Pre-Process Amplification Data
Diff between chipPCR versions 0.0.8-3 dated 2014-09-29 and 0.0.8-6 dated 2015-02-22
Description: A collection of functions to pre-process amplification curve data from polymerase chain reaction (PCR) or isothermal amplification reactions. The package contains functions to normalize and baseline amplification curves, to detect both the start and end of an amplification reaction, several smoothers (e.g., LOWESS, moving average, cubic splines, Savitzky-Golay), a function to detect false positive amplification reactions and a function to determine the amplification efficiency. Quantification point (Cq) methods include the first (FDM) and second approximate derivative maximum (SDM) methods (calculated by a 5-point-stencil) and the cycle threshold method. Data sets of experimental nucleic acid amplification systems (VideoScan HCU, capillary convective PCR (ccPCR)) and commercial systems are included. Amplification curves were generated by helicase dependent amplification (HDA), ccPCR or PCR. As detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were used.
Author: Stefan Roediger [cre, aut],
Michal Burdukiewicz [aut],
Konstantin A. Blagodatskikh [ctb]
Maintainer: Stefan Roediger
chipPCR-0.0.8-3/chipPCR/man/chipPCR.sp.Rd |only
chipPCR-0.0.8-6/chipPCR/CHANGELOG | 18
chipPCR-0.0.8-6/chipPCR/DESCRIPTION | 40
chipPCR-0.0.8-6/chipPCR/MD5 | 179
chipPCR-0.0.8-6/chipPCR/R/CPP.R | 8
chipPCR-0.0.8-6/chipPCR/R/MFIaggr.R | 5
chipPCR-0.0.8-6/chipPCR/R/classes.R | 217
chipPCR-0.0.8-6/chipPCR/R/effcalc.R | 28
chipPCR-0.0.8-6/chipPCR/R/linreg.R |only
chipPCR-0.0.8-6/chipPCR/R/smoother.R | 4
chipPCR-0.0.8-6/chipPCR/R/th.cyc.R | 66
chipPCR-0.0.8-6/chipPCR/README.md | 4
chipPCR-0.0.8-6/chipPCR/build/vignette.rds |binary
chipPCR-0.0.8-6/chipPCR/data/C126EG595.rda |binary
chipPCR-0.0.8-6/chipPCR/data/C126EG685.rda |binary
chipPCR-0.0.8-6/chipPCR/data/C127EGHP.rda |binary
chipPCR-0.0.8-6/chipPCR/data/C17.rda |binary
chipPCR-0.0.8-6/chipPCR/data/C54.rda |binary
chipPCR-0.0.8-6/chipPCR/data/C60.amp.rda |binary
chipPCR-0.0.8-6/chipPCR/data/C60.melt.rda |binary
chipPCR-0.0.8-6/chipPCR/data/C67.rda |binary
chipPCR-0.0.8-6/chipPCR/data/C81.rda |binary
chipPCR-0.0.8-6/chipPCR/data/C85.rda |binary
chipPCR-0.0.8-6/chipPCR/data/CD74.rda |binary
chipPCR-0.0.8-6/chipPCR/data/CD75.rda |binary
chipPCR-0.0.8-6/chipPCR/data/Eff1000.rda |binary
chipPCR-0.0.8-6/chipPCR/data/Eff625.rda |binary
chipPCR-0.0.8-6/chipPCR/data/Eff750.rda |binary
chipPCR-0.0.8-6/chipPCR/data/Eff875.rda |binary
chipPCR-0.0.8-6/chipPCR/data/VIMCFX96_60.rda |binary
chipPCR-0.0.8-6/chipPCR/data/VIMCFX96_69.rda |binary
chipPCR-0.0.8-6/chipPCR/data/VIMCFX96_meltcurve.rda |binary
chipPCR-0.0.8-6/chipPCR/data/VIMiQ5_595.rda |binary
chipPCR-0.0.8-6/chipPCR/data/VIMiQ5_685.rda |binary
chipPCR-0.0.8-6/chipPCR/data/VIMiQ5_melt.rda |binary
chipPCR-0.0.8-6/chipPCR/data/capillaryPCR.rda |binary
chipPCR-0.0.8-6/chipPCR/inst/CITATION |only
chipPCR-0.0.8-6/chipPCR/inst/doc/chipPCR.R | 411 -
chipPCR-0.0.8-6/chipPCR/inst/doc/chipPCR.Rnw | 4813 +++++-------
chipPCR-0.0.8-6/chipPCR/inst/doc/chipPCR.pdf |binary
chipPCR-0.0.8-6/chipPCR/man/AmpSim.Rd | 20
chipPCR-0.0.8-6/chipPCR/man/AmpSim.gui.Rd | 14
chipPCR-0.0.8-6/chipPCR/man/C126EG595.Rd | 22
chipPCR-0.0.8-6/chipPCR/man/C126EG685.Rd | 24
chipPCR-0.0.8-6/chipPCR/man/C127EGHP.Rd | 87
chipPCR-0.0.8-6/chipPCR/man/C17.Rd | 22
chipPCR-0.0.8-6/chipPCR/man/C54.Rd | 2
chipPCR-0.0.8-6/chipPCR/man/C60.amp.Rd | 10
chipPCR-0.0.8-6/chipPCR/man/C60.melt.Rd | 10
chipPCR-0.0.8-6/chipPCR/man/C67.Rd | 10
chipPCR-0.0.8-6/chipPCR/man/C81.Rd | 12
chipPCR-0.0.8-6/chipPCR/man/C85.Rd | 175
chipPCR-0.0.8-6/chipPCR/man/CD74.Rd | 50
chipPCR-0.0.8-6/chipPCR/man/CD75.Rd | 8
chipPCR-0.0.8-6/chipPCR/man/CPP.Rd | 62
chipPCR-0.0.8-6/chipPCR/man/Eff1000.Rd | 2
chipPCR-0.0.8-6/chipPCR/man/Eff625.Rd | 2
chipPCR-0.0.8-6/chipPCR/man/Eff750.Rd | 2
chipPCR-0.0.8-6/chipPCR/man/Eff875.Rd | 2
chipPCR-0.0.8-6/chipPCR/man/MFIaggr.Rd | 4
chipPCR-0.0.8-6/chipPCR/man/MFIaggr.gui.Rd | 13
chipPCR-0.0.8-6/chipPCR/man/VIMCFX96_60.Rd | 14
chipPCR-0.0.8-6/chipPCR/man/VIMCFX96_69.Rd | 14
chipPCR-0.0.8-6/chipPCR/man/VIMCFX96_meltcurve.Rd | 8
chipPCR-0.0.8-6/chipPCR/man/VIMiQ5_595.Rd | 14
chipPCR-0.0.8-6/chipPCR/man/VIMiQ5_685.Rd | 14
chipPCR-0.0.8-6/chipPCR/man/VIMiQ5_melt.Rd | 8
chipPCR-0.0.8-6/chipPCR/man/amptest-class.Rd | 1
chipPCR-0.0.8-6/chipPCR/man/amptester.Rd | 9
chipPCR-0.0.8-6/chipPCR/man/amptester.gui.Rd | 11
chipPCR-0.0.8-6/chipPCR/man/bg.max.Rd | 103
chipPCR-0.0.8-6/chipPCR/man/chipPCR-package.Rd | 13
chipPCR-0.0.8-6/chipPCR/man/chipPCR.datasets.Rd | 49
chipPCR-0.0.8-6/chipPCR/man/effcalc.Rd | 11
chipPCR-0.0.8-6/chipPCR/man/fixNA.Rd | 12
chipPCR-0.0.8-6/chipPCR/man/humanrater.Rd | 9
chipPCR-0.0.8-6/chipPCR/man/inder.Rd | 13
chipPCR-0.0.8-6/chipPCR/man/lm.coefs.Rd | 4
chipPCR-0.0.8-6/chipPCR/man/normalizer.Rd | 14
chipPCR-0.0.8-6/chipPCR/man/plot-bg.Rd | 3
chipPCR-0.0.8-6/chipPCR/man/plot-der.Rd | 6
chipPCR-0.0.8-6/chipPCR/man/plot-eff.Rd | 11
chipPCR-0.0.8-6/chipPCR/man/plot-refMFI.Rd | 17
chipPCR-0.0.8-6/chipPCR/man/plotCurves.Rd | 6
chipPCR-0.0.8-6/chipPCR/man/refMFI-class.Rd | 14
chipPCR-0.0.8-6/chipPCR/man/rounder.Rd | 4
chipPCR-0.0.8-6/chipPCR/man/smoother.Rd | 18
chipPCR-0.0.8-6/chipPCR/man/th.cyc.Rd | 8
chipPCR-0.0.8-6/chipPCR/vignettes/chipPCR.Rnw | 4813 +++++-------
chipPCR-0.0.8-6/chipPCR/vignettes/datdf.RData |binary
chipPCR-0.0.8-6/chipPCR/vignettes/natbib.bst |only
chipPCR-0.0.8-6/chipPCR/vignettes/natbib.sty |only
chipPCR-0.0.8-6/chipPCR/vignettes/roediger-burdukiewicz.bib | 4270 ++++------
93 files changed, 7421 insertions(+), 8416 deletions(-)
Title: R Commander
Diff between Rcmdr versions 2.1-6 dated 2015-02-03 and 2.1-7 dated 2015-02-22
Description:
A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre],
Milan Bouchet-Valat [aut],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ctb],
Kosar Karimi Pour [ctb],
G. Jay Kerns [ctb],
Renaud Lancelot [ctb],
Matthieu Lesnoff [ctb],
Uwe Ligges [ctb],
Samir Messad [ctb],
Martin Maechler [ctb],
Robert Muenchen [ctb],
Duncan Murdoch [ctb],
Erich Neuwirth [ctb],
Dan Putler [ctb],
Brian Ripley [ctb],
Miroslav Ristic [ctb],
Peter Wolf [ctb],
Kevin Wright [ctb]
Maintainer: John Fox
DESCRIPTION | 8 ++--
MD5 | 12 +++---
NEWS | 6 +++
inst/po/ca/LC_MESSAGES/R-Rcmdr.mo |binary
inst/po/zh_CN |only
man/Rcmdr-package.Rd | 5 +-
po/R-ca.po | 69 ++++++++++++++++++--------------------
po/R-zh_CN.po |only
8 files changed, 53 insertions(+), 47 deletions(-)
Title: Lattice Graphics
Diff between lattice versions 0.20-29 dated 2014-04-04 and 0.20-30 dated 2015-02-22
Description: Lattice is a powerful and elegant high-level data
visualization system, with an emphasis on multivariate data, that is
sufficient for typical graphics needs, and is also flexible enough
to handle most nonstandard requirements. See ?Lattice for an
introduction.
Author: Deepayan Sarkar
Maintainer: Deepayan Sarkar
DESCRIPTION | 8
MD5 | 72 ++--
R/bwplot.R | 16 -
R/cloud.R | 6
R/densityplot.R | 5
R/histogram.R | 3
R/interaction.R | 2
R/layout.R | 2
R/legend.R | 2
R/levelplot.R | 3
R/miscellaneous.R | 17 -
R/panels.R | 35 --
R/parallel.R | 4
R/print.trellis.R | 51 ---
R/qq.R | 4
R/qqmath.R | 4
R/scales.R | 2
R/settings.R | 496 +++++++++++++++----------------
R/splom.R | 4
R/xyplot.R | 3
data/barley.rda |binary
data/environmental.rda |binary
data/ethanol.rda |binary
data/melanoma.rda |binary
data/singer.rda |binary
inst/po/de/LC_MESSAGES/R-lattice.mo |binary
inst/po/en@quot/LC_MESSAGES/R-lattice.mo |binary
inst/po/fr/LC_MESSAGES/R-lattice.mo |binary
inst/po/ko/LC_MESSAGES/R-lattice.mo |binary
inst/po/pl/LC_MESSAGES/R-lattice.mo |binary
man/xyplot.Rd | 5
po/R-de.po | 11
po/R-en@quot.po | 11
po/R-fr.po | 11
po/R-ko.po | 274 ++++++++---------
po/R-lattice.pot | 9
po/R-pl.po | 15
37 files changed, 513 insertions(+), 562 deletions(-)
Title: Methods for Accessing Huge Amounts of Data [deprecated]
Diff between R.huge versions 0.8.0 dated 2014-02-26 and 0.9.0 dated 2015-02-22
Description: DEPRECATED. Do not start building new projects based on this package. Cross-platform alternatives are the following packages: bigmemory (CRAN), ff (CRAN), BufferedMatrix (Bioconductor). The main usage of it was inside the aroma.affymetrix package. (The package currently provides a class representing a matrix where the actual data is stored in a binary format on the local file system. This way the size limit of the data is set by the file system and not the memory.)
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson
.Rinstignore |only
DESCRIPTION | 18 +++++++------
MD5 | 20 +++++++-------
NAMESPACE | 4 ++
NEWS | 4 ++
man/AbstractFileArray.Rd | 2 -
man/FileMatrix.Rd | 2 -
man/FileVector.Rd | 2 -
man/R.huge-package.Rd | 2 -
tests/FileByteVector.R | 5 ++-
tests/FileMatrix,bug20070719.R | 41 ++++++++++++++++--------------
tests/FileMatrix,bug20070821.R | 55 +++++++++++++++++++++--------------------
12 files changed, 87 insertions(+), 68 deletions(-)
Title: Data Analysis Toolbox for Dota2
Diff between RDota versions 1.1 dated 2015-01-26 and 1.2 dated 2015-02-22
Description: Data analysis functions for Dota2. Dota2 is a popular online game (see, e.g.
Author: Xiao Lei
Maintainer: Xiao Lei
DESCRIPTION | 10 +++++-----
MD5 | 14 ++++++++------
NAMESPACE | 1 +
R/globalonline.R |only
R/quickpick.R | 6 +++---
data/antitable.rda |binary
data/matchtable.rda |binary
data/winrate.rda |binary
man/globalonline.Rd |only
9 files changed, 17 insertions(+), 14 deletions(-)
Title: Circular Visualization in R
Diff between circlize versions 0.2.2 dated 2015-01-30 and 0.2.3 dated 2015-02-22
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here the circlize package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of this package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
circlize gives users more convenience and freedom to design figures for
better understanding complex patterns behind multi-dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu
DESCRIPTION | 21 +-
MD5 | 154 +++++++++++----------
NAMESPACE | 107 +++++++--------
NEWS | 11 +
R/chordDiagram.R | 28 +++
R/genomic.R | 133 ++++++------------
R/genomic_utils.R | 175 ++++++++++++++++++++++--
R/plot.R | 98 +++++++++++++
R/utils.R | 48 ++++++
inst/doc/circlize.R | 38 +++++
inst/doc/circlize.Rnw | 33 ++++
inst/doc/circlize.pdf |binary
inst/doc/circular_phylogenetic_tree.pdf |binary
inst/doc/circular_visualization_of_matrix.R | 47 ++++--
inst/doc/circular_visualization_of_matrix.Rnw | 56 ++++++-
inst/doc/circular_visualization_of_matrix.pdf |binary
inst/doc/draw_ideogram.R | 4
inst/doc/draw_ideogram.Rnw | 2
inst/doc/draw_ideogram.pdf |binary
inst/doc/genomic_plot.R | 28 +--
inst/doc/genomic_plot.Rnw | 45 +++---
inst/doc/genomic_plot.pdf |binary
inst/doc/interesting_graphics.pdf |binary
inst/extdata/chromInfo.txt |only
man/adjacencyList2Matrix.rd |only
man/chordDiagram.rd | 118 ++++++++--------
man/circlize-package.rd | 176 +++++++++++++------------
man/circlize.rd | 67 ++++-----
man/circos.axis.rd | 109 +++++++--------
man/circos.clear.rd | 50 +++----
man/circos.genomicDensity.rd | 89 ++++++------
man/circos.genomicInitialize.rd | 85 ++++++------
man/circos.genomicLines.rd | 107 +++++++--------
man/circos.genomicLink.rd | 87 ++++++------
man/circos.genomicPoints.rd | 85 ++++++------
man/circos.genomicPosTransformLines.rd | 85 ++++++------
man/circos.genomicRainfall.rd | 81 +++++------
man/circos.genomicRect.rd | 95 ++++++-------
man/circos.genomicText.rd | 103 +++++++-------
man/circos.genomicTrackPlotRegion.rd | 95 ++++++-------
man/circos.info.rd | 69 ++++-----
man/circos.initialize.rd | 83 +++++------
man/circos.initializeWithIdeogram.rd | 93 ++++++-------
man/circos.lines.rd | 103 +++++++-------
man/circos.link.rd | 107 +++++++--------
man/circos.par.rd | 92 ++++++-------
man/circos.points.rd | 83 +++++------
man/circos.polygon.rd | 79 +++++------
man/circos.rect.rd | 83 +++++------
man/circos.text.rd | 93 ++++++-------
man/circos.trackHist.rd | 101 +++++++-------
man/circos.trackLines.rd | 95 ++++++-------
man/circos.trackPlotRegion.rd | 121 ++++++++---------
man/circos.trackPoints.rd | 77 +++++-----
man/circos.trackText.rd | 87 ++++++------
man/circos.updatePlotRegion.rd | 73 +++++-----
man/colorRamp2.rd | 75 +++++-----
man/cytoband.col.rd | 61 ++++----
man/draw.sector.rd | 83 +++++------
man/generateRandomBed.rd | 69 ++++-----
man/genomicDensity.rd | 75 +++++-----
man/get.all.sector.index.rd | 52 +++----
man/get.all.track.index.rd | 46 +++---
man/get.cell.meta.data.rd | 114 ++++++++--------
man/get.current.chromosome.rd | 52 +++----
man/getI.rd | 63 ++++----
man/highlight.chromosome.rd | 71 ++++------
man/highlight.sector.rd |only
man/posTransform.default.rd | 67 ++++-----
man/posTransform.text.rd | 75 +++++-----
man/rainfallTransform.rd | 63 ++++----
man/rand_color.rd | 51 +++----
man/read.chromInfo.rd |only
man/read.cytoband.rd | 93 ++++++-------
man/reverse.circlize.rd | 73 +++++-----
man/show.index.rd | 46 +++---
vignettes/circlize.Rnw | 33 ++++
vignettes/circular_visualization_of_matrix.Rnw | 56 ++++++-
vignettes/draw_ideogram.Rnw | 2
vignettes/genomic_plot.Rnw | 45 +++---
80 files changed, 2894 insertions(+), 2370 deletions(-)
Title: Tools for Survey Statistics in Educational Assessment
Diff between BIFIEsurvey versions 1.1 dated 2014-11-22 and 1.2-6 dated 2015-02-22
Description:
Contains tools for survey statistics (especially in educational
assessment) for datasets with replication designs (jackknife,
bootstrap, replicate weights). Descriptive statistics, linear
and logistic regression, path models for manifest variables
with measurement error correction and two-level hierarchical
regressions for weighted samples are included. Statistical
inference can be conducted for multiply-imputed datasets.
This package is developed by BIFIE (Federal Institute for
Educational Research, Innovation and Development of the Austrian
School System; Salzburg, Austria).
Author: BIFIE [aut], Alexander Robitzsch [ctb,cre],
Konrad Oberwimmer [ctb]
Maintainer: Alexander Robitzsch
DESCRIPTION | 32
MD5 | 45 -
NAMESPACE | 24
R/BIFIE.correl.R | 2
R/BIFIE.data.R | 71 -
R/BIFIE.data.jack.R | 29
R/BIFIE.derivedParameters.R | 3
R/BIFIE.linreg.R | 2
R/BIFIE.pathmodel.R |only
R/BIFIE.twolevelreg.R |only
R/coef.BIFIEsurvey.R | 14
R/extract.replicated.pars.R | 14
R/summary.BIFIE.data.R |only
R/vcov.BIFIE.survey.R | 16
data/data.bifie01.rda |only
data/datalist | 1
inst/NEWS | 51 -
man/BIFIE.BIFIEdata2BIFIEcdata.Rd | 2
man/BIFIE.data.Rd | 52 +
man/BIFIE.data.jack.Rd | 5
man/BIFIE.pathmodel.Rd |only
man/BIFIE.twolevelreg.Rd |only
man/BIFIEsurvey-package.Rd | 43 -
man/data.bifie.Rd |only
man/data.timss1.Rd | 58 +
src/univar.cpp | 719 ++++++++++++++++++
src/univar_helpers.h | 1496 +++++++++++++++++++++++++++++++++++++-
27 files changed, 2490 insertions(+), 189 deletions(-)
Title: Unified Handling of Graphics Devices
Diff between R.devices versions 2.12.0 dated 2014-10-17 and 2.13.0 dated 2015-02-22
Description: Functions for creating plots and image files in a unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). Default device options as well as scales and aspect ratios are controlled in a uniform way across all device types. Switching output format requires minimal changes in code. This package is ideal for large-scale batch processing, because it will never leave open graphics devices or incomplete image files behind, even on errors or user interrupts.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson
DESCRIPTION | 16 +++---
MD5 | 49 +++++++++----------
NAMESPACE | 1
NEWS | 22 ++++++++
R/devEval.R | 60 +++++++++++++++--------
R/devNew.R | 35 +++++++++++++
R/devOptions.R | 8 +--
R/deviceUtils.R | 5 -
R/eps.R | 6 +-
R/toNNN.R | 2
R/zzz.R | 2
build/vignette.rds |binary
inst/doc/R.devices-overview.R | 20 +++----
inst/doc/R.devices-overview.pdf |binary
inst/doc/R.devices-overview.tex.rsp | 42 ++++++++--------
man/R.devices-package.Rd | 7 +-
man/devEval.Rd | 4 -
man/eps.Rd | 4 +
man/toNNN.Rd | 6 +-
tests/DevEvalFileProduct.R | 7 ++
tests/devDump.R | 2
tests/devEval,error.R |only
tests/devEval.R | 90 ++++++++++++++++++++++++++++++++++-
tests/devList.R | 26 ++++++++--
tests/devTypeName.R | 37 ++++++++++++--
vignettes/R.devices-overview.tex.rsp | 42 ++++++++--------
26 files changed, 363 insertions(+), 130 deletions(-)
Title: Easy Interface to Advanced PostgreSQL Features
Diff between rpg versions 1.2 dated 2014-09-02 and 1.4 dated 2015-02-22
Description: Allows ad hoc queries and reading and
writing data frames to and from a database.
Author: Timothy H. Keitt
Maintainer: Timothy H. Keitt
DESCRIPTION | 14 ++---
MD5 | 49 ++++++++++----------
NAMESPACE | 9 ++-
R/RcppExports.R | 80 ---------------------------------
R/rpg.R | 116 ++++++++++++++++++++++++++++++++++++++----------
R/utils.R | 71 +++++++++++++++++++++++------
man/async.Rd | 3 -
man/connection-utils.Rd | 3 -
man/connection.Rd | 3 -
man/copy.Rd | 3 -
man/cursor.Rd | 3 -
man/format_for_send.Rd |only
man/misc.Rd | 3 -
man/prepare.Rd | 53 +++++++--------------
man/psql.Rd | 3 -
man/query.Rd | 3 -
man/rpg-package.Rd | 9 ++-
man/stack.Rd | 3 -
man/stow.Rd | 3 -
man/table-info.Rd | 3 -
man/table-io.Rd | 3 -
man/tracing.Rd | 3 -
man/transactions.Rd | 3 -
src/RcppExports.cpp | 8 +--
src/rpg.cpp | 78 --------------------------------
src/rpg.h | 22 +++++++--
26 files changed, 264 insertions(+), 287 deletions(-)
Title: Hierarchical Clustering with Prototypes
Diff between protoclust versions 1.4 dated 2015-01-28 and 1.5 dated 2015-02-21
Description: Performs minimax linkage hierarchical clustering. Every cluster
has an associated prototype element that represents that cluster as
described in Bien, J., and Tibshirani, R. (2011), "Hierarchical Clustering
with Prototypes via Minimax Linkage," accepted for publication in The
Journal of the American Statistical Association, DOI:
10.1198/jasa.2011.tm10183.
Author: Jacob Bien and Rob Tibshirani
Maintainer: Jacob Bien
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
src/hier.c | 18 ++++++++++++------
3 files changed, 18 insertions(+), 12 deletions(-)
Title: Utilities for Producing Maps
Diff between mapmisc versions 1.1.1 dated 2015-01-05 and 1.1.3 dated 2015-02-21
Description: A minimal, light-weight set of tools for producing nice looking maps in R.
Author: Patrick Brown
Maintainer: Patrick Brown
DESCRIPTION | 14 ++++----
MD5 | 23 ++++++-------
R/colourScale.R | 11 +++++-
R/legendBreaks.R | 85 ++++++++++++++++++++++++++++++++++++++++++++++++-
R/openmap.R | 14 ++++----
R/utils.R | 76 +++++++++++++++++++++++++++++++++----------
inst/doc/mapLayers.pdf |binary
inst/doc/mapmisc.pdf |binary
man/colourScale.Rd | 16 ++-------
man/legendBreaks.Rd |only
man/netherlands.Rd | 2 -
man/openmap.Rd | 6 ++-
man/scaleBar.Rd | 2 -
13 files changed, 190 insertions(+), 59 deletions(-)
Title: Simultaneous Critical Values for t-Tests in Very High Dimensions
Diff between highTtest versions 1.0 dated 2014-10-17 and 1.1 dated 2015-02-21
Description: Implements the method developed by Cao and Kosorok (2011) for the significance analysis of thousands of features in high-dimensional biological studies. It is an asymptotically valid data-driven procedure to find critical values for rejection regions controlling the k-familywise error rate, false discovery rate, and the tail probability of false discovery proportion.
Author: Hongyuan Cao [aut],
Michael Kosorok [aut],
Shannon Holloway [aut, cre]
Maintainer: Shannon Holloway
DESCRIPTION | 11 ++++++-----
MD5 | 8 ++++----
NAMESPACE | 1 -
R/methods-venn.R | 9 +++++++--
man/highTtest.Rd | 6 ++++--
5 files changed, 21 insertions(+), 14 deletions(-)
Title: A Toolkit for Recursive Partytioning
Diff between partykit versions 0.8-4 dated 2015-01-07 and 1.0-0 dated 2015-02-21
Description: A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources (rpart, RWeka, PMML) yielding objects that share
functionality for print/plot/predict methods. Furthermore, new and improved
reimplementations of conditional inference trees (ctree) and model-based
recursive partitioning (mob) from the party package are provided based
on the new infrastructure.
Author: Torsten Hothorn [aut, cre],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn
DESCRIPTION | 8 ++++----
MD5 | 22 +++++++++++-----------
NAMESPACE | 12 ++++++++++++
R/cforest.R | 4 ++--
inst/CITATION | 15 +++++----------
inst/NEWS.Rd | 10 ++++++++++
inst/doc/constparty.pdf |binary
inst/doc/ctree.pdf |binary
inst/doc/mob.pdf |binary
inst/doc/partykit.pdf |binary
man/cforest.Rd | 2 +-
vignettes/ctree.Rout.save | 18 +++++++++---------
12 files changed, 54 insertions(+), 37 deletions(-)
Title: Easy Handling Discrete Time Markov Chains
Diff between markovchain versions 0.1.0 dated 2015-01-04 and 0.1.1 dated 2015-02-21
Description: Functions and S4 methods to create and manage discrete time Markov chains (DTMC) more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of DTMC proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato
Maintainer: Giorgio Alfredo Spedicato
ChangeLog | 4 +
DESCRIPTION | 12 ++---
MD5 | 28 ++++++------
NEWS | 8 +--
R/1_functions4Fitting.R | 44 ++++++++++++++-----
data/blanden.rda |binary
data/craigsendi.rda |binary
data/holson.rda |binary
data/preproglucacon.rda |binary
data/rain.rda |binary
inst/doc/an_introduction_to_markovchain_package.R | 3 -
inst/doc/an_introduction_to_markovchain_package.Rnw | 3 -
inst/doc/an_introduction_to_markovchain_package.pdf |binary
man/markovchain-package.Rd | 4 -
vignettes/an_introduction_to_markovchain_package.Rnw | 3 -
15 files changed, 69 insertions(+), 40 deletions(-)
Title: Improved Predictors
Diff between ipred versions 0.9-3 dated 2013-12-20 and 0.9-4 dated 2015-02-21
Description: Improved predictive models by indirect classification and
bagging for classification, regression and survival problems
as well as resampling based estimators of prediction error.
Author: Andrea Peters [aut],
Torsten Hothorn [aut, cre],
Brian D. Ripley [ctb],
Terry Therneau [ctb],
Beth Atkinson [ctb]
Maintainer: Torsten Hothorn
DESCRIPTION | 8 ++++----
MD5 | 20 ++++++++++----------
NAMESPACE | 2 +-
build/vignette.rds |binary
inst/NEWS | 4 ++++
inst/doc/ipred-examples.pdf |binary
man/bagging.Rd | 2 +-
tests/Examples/ipred-Ex.Rout.save | 12 +++++-------
tests/ipred-bugs.Rout.save | 8 +++-----
tests/ipred-segfault.Rout.save | 8 +++-----
tests/ipred-smalltest.Rout.save | 8 +++-----
11 files changed, 34 insertions(+), 38 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-19 2.0
2014-09-11 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-07-05 1.2
2013-03-19 1.1
2012-11-06 1.0
Title: Generating Synthetic Versions of Sensitive Microdata for
Statistical Disclosure Control
Diff between synthpop versions 1.0-0 dated 2014-08-18 and 1.1-0 dated 2015-02-20
Description: A tool for producing synthetic versions of microdata containing confidential information so that they are safe to be released to users for exploratory analysis. The key objective of generating synthetic data is to replace sensitive original values with synthetic ones causing minimal distortion of the statistical information contained in the data set. Variables, which can be categorical or continuous, are synthesised one-by-one using sequential modelling. Replacements are generated by drawing from conditional distributions fitted to the original data using parametric or classification and regression trees models. Data are synthesised via the function syn() which can be largely automated, if default settings are used, or with methods defined by the user. Optional parameters can be used to influence the disclosure risk and the analytical quality of the synthesised data.
Author: Beata Nowok, Gillian M Raab and Chris Dibben
Maintainer: Beata Nowok
synthpop-1.0-0/synthpop/vignettes/Zcompare.pdf |only
synthpop-1.0-0/synthpop/vignettes/income.pdf |only
synthpop-1.0-0/synthpop/vignettes/incomeNA.pdf |only
synthpop-1.0-0/synthpop/vignettes/ls.pdf |only
synthpop-1.1-0/synthpop/DESCRIPTION | 18
synthpop-1.1-0/synthpop/MD5 | 72 +--
synthpop-1.1-0/synthpop/NAMESPACE | 20
synthpop-1.1-0/synthpop/NEWS |only
synthpop-1.1-0/synthpop/R/IO.r |only
synthpop-1.1-0/synthpop/R/compare.syn.r | 438 +++++++++-----------
synthpop-1.1-0/synthpop/R/functions.syn.r | 25 -
synthpop-1.1-0/synthpop/R/methods.syn.r | 78 ++-
synthpop-1.1-0/synthpop/R/padMis.syn.r | 47 +-
synthpop-1.1-0/synthpop/R/padModel.syn.r | 60 +-
synthpop-1.1-0/synthpop/R/sampler.syn.r | 30 -
synthpop-1.1-0/synthpop/R/syn.r | 296 +++++++------
synthpop-1.1-0/synthpop/build/vignette.rds |binary
synthpop-1.1-0/synthpop/inst/doc/synthpop.R | 157 +++----
synthpop-1.1-0/synthpop/inst/doc/synthpop.Rnw | 238 +++++-----
synthpop-1.1-0/synthpop/inst/doc/synthpop.pdf |binary
synthpop-1.1-0/synthpop/man/compare.fit.synds.Rd | 71 ++-
synthpop-1.1-0/synthpop/man/compare.synds.Rd | 34 +
synthpop-1.1-0/synthpop/man/glm.synds.Rd | 28 -
synthpop-1.1-0/synthpop/man/read.obs.Rd |only
synthpop-1.1-0/synthpop/man/replicated.uniques.Rd |only
synthpop-1.1-0/synthpop/man/sdc.Rd |only
synthpop-1.1-0/synthpop/man/summary.fit.synds.Rd | 62 +-
synthpop-1.1-0/synthpop/man/summary.synds.Rd | 4
synthpop-1.1-0/synthpop/man/syn.Rd | 183 ++++----
synthpop-1.1-0/synthpop/man/syn.cart.Rd | 1
synthpop-1.1-0/synthpop/man/syn.lognorm.Rd |only
synthpop-1.1-0/synthpop/man/syn.norm.Rd | 6
synthpop-1.1-0/synthpop/man/syn.normrank.Rd | 4
synthpop-1.1-0/synthpop/man/syn.pmm.Rd | 2
synthpop-1.1-0/synthpop/man/syn.polr.Rd | 4
synthpop-1.1-0/synthpop/man/syn.sample.Rd | 2
synthpop-1.1-0/synthpop/man/syn.surv.ctree.Rd | 2
synthpop-1.1-0/synthpop/man/synthpop-package.Rd | 20
synthpop-1.1-0/synthpop/man/write.syn.Rd |only
synthpop-1.1-0/synthpop/vignettes/Figure1ls.pdf |only
synthpop-1.1-0/synthpop/vignettes/Figure2income.pdf |only
synthpop-1.1-0/synthpop/vignettes/Figure3Z.pdf |only
synthpop-1.1-0/synthpop/vignettes/synthpop.Rnw | 238 +++++-----
synthpop-1.1-0/synthpop/vignettes/synthpop.bib | 435 +++++++++++++------
44 files changed, 1425 insertions(+), 1150 deletions(-)
Title: Soil Database Interface
Diff between soilDB versions 1.3-2 dated 2014-04-30 and 1.5 dated 2015-02-20
Description: A collection of functions for reading data from USDA-NCSS soil databases.
Author: D.E. Beaudette and J.M. Skovlin
Maintainer: D.E. Beaudette
DESCRIPTION | 19 ++---
MD5 | 95 ++++++++++++++--------------
NAMESPACE | 28 ++++++--
NEWS | 28 +++++++-
R/MUKEYS_by_ll_bbox.R | 9 +-
R/SDA_query.R | 14 ++--
R/SSURGO_spatial_query.R |only
R/fetchHenry.R |only
R/fetchKSSL.R | 4 -
R/fetchNASIS.R | 85 +++++++++++++++++++------
R/fetchNASISLabData.R | 7 +-
R/fetchOSD.R | 3
R/fetchPedonPC.R | 11 +++
R/fetchRaCA.R | 14 ++--
R/fetchSCAN.R | 3
R/get_colors_from_NASIS_db.R | 44 ++++++++-----
R/get_colors_from_pedon_db.R | 10 ++-
R/get_extended_data_from_NASIS_db.R | 86 ++++++++++++++------------
R/get_extended_data_from_pedon_db.R | 20 +++---
R/get_hz_data_from_NASIS_db.R | 12 ++-
R/get_hz_data_from_pedon_db.R | 12 ++-
R/get_lablayer_data_from_NASIS_db.R | 11 ++-
R/get_labpedon_data_from_NASIS_db.R | 11 ++-
R/get_site_data_from_NASIS_db.R | 12 ++-
R/get_site_data_from_pedon_db.R | 11 ++-
R/get_text_notes_from_NASIS_db.R | 19 +++--
R/get_veg_from_AK_Site.R | 10 ++-
R/get_veg_from_MT_veg_db.R | 9 +-
R/get_veg_from_NPS_PLOTS_db.R | 11 ++-
R/get_veg_other_from_MT_veg_db.R | 10 ++-
R/get_veg_species_from_MT_veg_db.R | 11 ++-
R/mapunit_geom_by_ll_bbox.R | 11 +--
R/mix_and_clean_colors.R | 54 +++++++++-------
R/nasis_component_data.R | 37 +++++++----
R/seriesExtent.R | 61 +++++++++---------
R/utils.R | 109 ++++++++++++++++++++++++++++++++-
data/andic.subset.rda |binary
data/cisne.rda |binary
data/gSSURGO.chunk.rda |binary
data/gopheridge.rda |binary
data/loafercreek.rda |binary
man/MUKEYS_by_ll_bbox.Rd | 6 -
man/SSURGO_spatial_query.Rd |only
man/fetchNASIS.Rd | 4 -
man/fetchOSD.Rd | 2
man/fetchRaCA.Rd | 7 +-
man/fetchSCAN.Rd | 1
man/gSSURGO.chunk.Rd | 2
man/get_extended_data_from_pedon_db.Rd | 2
man/seriesExtent.Rd | 6 -
50 files changed, 615 insertions(+), 306 deletions(-)
Title: Package Management Tool
Diff between pacman versions 0.2.0 dated 2015-02-15 and 0.3.0 dated 2015-02-20
Description: Tools to more conveniently perform tasks
associated with add-on packages. pacman conveniently wraps library and
package related functions and names them in an intuitive and consistent
fashion. It seeks to combine functionality from lower level functions which
can speed up workflow.
Author: Tyler Rinker [aut, cre, ctb], Dason Kurkiewicz [aut, ctb]
Maintainer: Tyler Rinker
DESCRIPTION | 10 +++++-----
MD5 | 10 +++++-----
NEWS | 12 ++++++++++++
README.md | 2 +-
inst/CITATION | 4 ++--
inst/doc/Introduction_to_pacman.html | 16 ++++++++--------
6 files changed, 33 insertions(+), 21 deletions(-)
Title: Compute the Personalized Activity Index Based on a Flexible
Bayesian Negative Binomial Model
Diff between lmeNBBayes versions 1.3 dated 2015-01-20 and 1.3.1 dated 2015-02-20
Description: The functions in this package implement the safety monitoring procedures proposed in the paper titled "A flexible mixed effect negative binomial regression model for detecting unusual increases in MRI lesion counts in individual multiple sclerosis patients" by Kondo, Y., Zhao, Y. and Petkau, A.J. The procedure first models longitudinally collected count variables with a negative binomial mixed-effect regression model. To account for the correlation among repeated measures from the same patient, the model has subject-specific random intercept, which is modelled with the infinite mixture of Beta distributions, very flexible distribution that theoretically allows any form. The package also has the option of a single beta distribution for random effects. These mixed-effect models could be useful beyond the application of the safety monitoring. The inference is based on MCMC samples and this package contains a Gibbs sampler to sample from the posterior distribution of the negative binomial mixed-effect regression model. Based on the fitted model, the personalized activity index is computed for each patient. Lastly, this package is companion to R package lmeNB, which contains the functions to compute the Personalized Activity Index in the frequentist framework.
Author: Yumi Kondo
Maintainer: Yumi Kondo
DESCRIPTION | 12 ++++++------
MD5 | 16 ++++++++--------
NAMESPACE | 7 +++++++
R/nbinDPmix_C.R | 2 +-
man/dqmix.Rd | 3 +--
man/getDIC.Rd | 5 ++---
man/getS.StatInMed.Rd | 3 +--
man/index_batch_Bayes.Rd | 3 +--
man/lmeNBBayes.Rd | 3 +--
9 files changed, 28 insertions(+), 26 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrologic and Water
Quality Data
Diff between dataRetrieval versions 2.1.1 dated 2015-01-30 and 2.1.2 dated 2015-02-20
Description: Collection of functions to help retrieve U.S. Geological Survey
(USGS) and U.S. Environmental Protection Agency (EPA) water quality and
hydrology data from web services. USGS web services are discovered from the
National Water Information System (NWIS) tools. Both EPA and USGS water
quality data are obtained from the Water Quality Portal.
Author: Robert Hirsch [aut],
Laura DeCicco [aut, cre],
David Lorenz [aut]
Maintainer: Laura DeCicco
dataRetrieval-2.1.1/dataRetrieval/inst/tests |only
dataRetrieval-2.1.2/dataRetrieval/DESCRIPTION | 13
dataRetrieval-2.1.2/dataRetrieval/MD5 | 75 +-
dataRetrieval-2.1.2/dataRetrieval/NAMESPACE | 2
dataRetrieval-2.1.2/dataRetrieval/NEWS | 1
dataRetrieval-2.1.2/dataRetrieval/R/getWebServiceData.R | 2
dataRetrieval-2.1.2/dataRetrieval/R/importWQP.R | 22
dataRetrieval-2.1.2/dataRetrieval/R/importWaterML1.r | 3
dataRetrieval-2.1.2/dataRetrieval/R/readNWISdata.r | 45 +
dataRetrieval-2.1.2/dataRetrieval/R/readNWISdv.r | 5
dataRetrieval-2.1.2/dataRetrieval/R/readNWISpCode.r | 4
dataRetrieval-2.1.2/dataRetrieval/R/readNWISqw.r | 103 ++-
dataRetrieval-2.1.2/dataRetrieval/R/readNWISunit.r | 10
dataRetrieval-2.1.2/dataRetrieval/R/readWQPdata.R | 3
dataRetrieval-2.1.2/dataRetrieval/R/renameColumns.R | 2
dataRetrieval-2.1.2/dataRetrieval/R/tabbedDataRetrievals.R | 58 ++
dataRetrieval-2.1.2/dataRetrieval/R/whatNWISsites.R | 5
dataRetrieval-2.1.2/dataRetrieval/inst/doc/dataRetrieval.R | 274 ++++------
dataRetrieval-2.1.2/dataRetrieval/inst/doc/dataRetrieval.Rnw | 110 +---
dataRetrieval-2.1.2/dataRetrieval/inst/doc/dataRetrieval.pdf |binary
dataRetrieval-2.1.2/dataRetrieval/inst/extdata/temperatureAndFlow.RData |only
dataRetrieval-2.1.2/dataRetrieval/man/dataRetrieval-package.Rd | 2
dataRetrieval-2.1.2/dataRetrieval/man/pCodeToName.Rd |only
dataRetrieval-2.1.2/dataRetrieval/man/parameterCdFile.Rd |only
dataRetrieval-2.1.2/dataRetrieval/man/readNWISdata.Rd | 10
dataRetrieval-2.1.2/dataRetrieval/man/readNWISdv.Rd | 5
dataRetrieval-2.1.2/dataRetrieval/man/readNWISgwl.Rd | 2
dataRetrieval-2.1.2/dataRetrieval/man/readNWISmeas.Rd | 2
dataRetrieval-2.1.2/dataRetrieval/man/readNWISpCode.Rd | 4
dataRetrieval-2.1.2/dataRetrieval/man/readNWISpeak.Rd | 2
dataRetrieval-2.1.2/dataRetrieval/man/readNWISqw.Rd | 36 +
dataRetrieval-2.1.2/dataRetrieval/man/readNWISrating.Rd | 2
dataRetrieval-2.1.2/dataRetrieval/man/readNWISuv.Rd | 2
dataRetrieval-2.1.2/dataRetrieval/man/renameNWISColumns.Rd | 2
dataRetrieval-2.1.2/dataRetrieval/tests |only
dataRetrieval-2.1.2/dataRetrieval/vignettes/dataRetrieval-concordance.tex | 13
dataRetrieval-2.1.2/dataRetrieval/vignettes/dataRetrieval.Rnw | 110 +---
dataRetrieval-2.1.2/dataRetrieval/vignettes/figure/getNWIStemperaturePlot-1.pdf |binary
38 files changed, 526 insertions(+), 403 deletions(-)
Title: Analysis of Spatially Distributed Data
Diff between RSurvey versions 0.8-2 dated 2014-09-24 and 0.8-3 dated 2015-02-20
Description: A processing program for spatially distributed data.
It features graphing tools, query building, and polygon clipping.
A graphical user interface is provided.
Author: Jason C. Fisher
Maintainer: Jason C. Fisher
DESCRIPTION | 14 +++---
MD5 | 82 ++++++++++++++++++-------------------
NEWS | 7 +++
R/BuildPackage.R | 3 -
R/Data.R | 2
R/LoadPackages.R | 104 ++++++++++++++++++++++++++++++++---------------
R/ManageVariables.R | 5 +-
R/SetSortOrder.R | 4 -
README.md | 18 ++++----
data/ex.project.RData |binary
man/Autocrop.Rd | 2
man/AutocropRegion.Rd | 2
man/BuildHistogram.Rd | 2
man/ChooseColor.Rd | 2
man/ChoosePch.Rd | 2
man/EditData.Rd | 2
man/EditFunction.Rd | 2
man/EditText.Rd | 2
man/ExportData.Rd | 2
man/Format.Rd | 2
man/FormatDateTime.Rd | 2
man/GetBitmapImage.Rd | 2
man/GetFile.Rd | 2
man/ImportPackage.Rd | 2
man/ImportSpreadsheet.Rd | 2
man/ImportText.Rd | 2
man/LoadPackages.Rd | 2
man/ManagePolygons.Rd | 2
man/ManageVariables.Rd | 2
man/OpenRSurvey.Rd | 2
man/Plot3d.Rd | 2
man/ProgressBar.Rd | 2
man/RSurvey-package.Rd | 2
man/Rename.Rd | 2
man/Search.Rd | 2
man/SetAxesLimits.Rd | 2
man/SetConfiguration.Rd | 2
man/SetInterpolation.Rd | 2
man/SetPolygonLimits.Rd | 2
man/SetSortOrder.Rd | 2
man/ex.data.Rd | 2
man/ex.project.Rd | 2
42 files changed, 175 insertions(+), 128 deletions(-)
Title: Analysis of Heavy Tailed Distributions
Diff between poweRlaw versions 0.20.5 dated 2014-06-12 and 0.30.0 dated 2015-02-20
Description: An implementation of maximum likelihood estimators for a variety
of heavy tailed distributions, including both the discrete and continuous
power law distributions. Additionally, a goodness-of-fit based approach is
used to estimate the lower cut-off for the scaling region.
Author: Colin Gillespie [aut, cre]
Maintainer: Colin Gillespie
poweRlaw-0.20.5/poweRlaw/tests |only
poweRlaw-0.20.5/poweRlaw/vignettes/plpva.r |only
poweRlaw-0.30.0/poweRlaw/DESCRIPTION | 20 -
poweRlaw-0.30.0/poweRlaw/MD5 | 134 +++++------
poweRlaw-0.30.0/poweRlaw/NAMESPACE | 5
poweRlaw-0.30.0/poweRlaw/NEWS | 22 +
poweRlaw-0.30.0/poweRlaw/R/AllGenerics.R | 30 +-
poweRlaw-0.30.0/poweRlaw/R/bootstrap.R | 34 +-
poweRlaw-0.30.0/poweRlaw/R/bootstrap_p.R | 38 +--
poweRlaw-0.30.0/poweRlaw/R/checks.R | 6
poweRlaw-0.30.0/poweRlaw/R/data_help_files.R | 26 +-
poweRlaw-0.30.0/poweRlaw/R/def_conexp.R | 48 +++
poweRlaw-0.30.0/poweRlaw/R/def_conlorm.R | 49 +++-
poweRlaw-0.30.0/poweRlaw/R/def_conpl.R | 32 +-
poweRlaw-0.30.0/poweRlaw/R/def_disexp.R | 24 +
poweRlaw-0.30.0/poweRlaw/R/def_dislnorm.R | 32 +-
poweRlaw-0.30.0/poweRlaw/R/def_displ.R | 42 ++-
poweRlaw-0.30.0/poweRlaw/R/def_dispois.R | 29 +-
poweRlaw-0.30.0/poweRlaw/R/dist_data_cdf_methods.R | 65 ++---
poweRlaw-0.30.0/poweRlaw/R/estimate_xmin.R | 118 ++++++---
poweRlaw-0.30.0/poweRlaw/R/lines_methods.R | 2
poweRlaw-0.30.0/poweRlaw/build/vignette.rds |binary
poweRlaw-0.30.0/poweRlaw/data/bootstrap_moby.RData |binary
poweRlaw-0.30.0/poweRlaw/data/bootstrap_p_moby.RData |binary
poweRlaw-0.30.0/poweRlaw/demo/moby.R | 4
poweRlaw-0.30.0/poweRlaw/inst/CITATION | 29 +-
poweRlaw-0.30.0/poweRlaw/inst/doc/compare_distributions.Rnw | 2
poweRlaw-0.30.0/poweRlaw/inst/doc/compare_distributions.pdf |binary
poweRlaw-0.30.0/poweRlaw/inst/doc/examples.R | 92 ++++---
poweRlaw-0.30.0/poweRlaw/inst/doc/examples.Rnw | 123 +++++-----
poweRlaw-0.30.0/poweRlaw/inst/doc/examples.pdf |binary
poweRlaw-0.30.0/poweRlaw/inst/doc/poweRlaw.R | 36 +-
poweRlaw-0.30.0/poweRlaw/inst/doc/poweRlaw.Rnw | 48 +--
poweRlaw-0.30.0/poweRlaw/inst/doc/poweRlaw.pdf |binary
poweRlaw-0.30.0/poweRlaw/inst/doc/v61i10.Rnw |only
poweRlaw-0.30.0/poweRlaw/inst/doc/v61i10.pdf |only
poweRlaw-0.30.0/poweRlaw/man/bootstrap_moby.Rd | 26 +-
poweRlaw-0.30.0/poweRlaw/man/compare_distributions.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/displ.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/dist_cdf-methods.Rd | 53 ++--
poweRlaw-0.30.0/poweRlaw/man/dist_data_cdf-methods.Rd | 30 +-
poweRlaw-0.30.0/poweRlaw/man/dist_ll-methods.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/dist_pdf-methods.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/dist_rand-methods.Rd | 9
poweRlaw-0.30.0/poweRlaw/man/dplcon.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/dpldis.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/estimate_pars.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/estimate_xmin.Rd | 54 ++--
poweRlaw-0.30.0/poweRlaw/man/moby.Rd | 6
poweRlaw-0.30.0/poweRlaw/man/native_american.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/plot-distribution-ANY-method.Rd | 17 -
poweRlaw-0.30.0/poweRlaw/man/plot.bs_xmin.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/population.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/poweRlaw-package.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/show-distribution-method.Rd | 3
poweRlaw-0.30.0/poweRlaw/man/swiss_prot.Rd | 3
poweRlaw-0.30.0/poweRlaw/vignettes/compare_distributions.Rnw | 2
poweRlaw-0.30.0/poweRlaw/vignettes/examples.Rnw | 123 +++++-----
poweRlaw-0.30.0/poweRlaw/vignettes/examples1.rds |only
poweRlaw-0.30.0/poweRlaw/vignettes/figure1.pdf |only
poweRlaw-0.30.0/poweRlaw/vignettes/figure2.pdf |only
poweRlaw-0.30.0/poweRlaw/vignettes/figure3.pdf |only
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poweRlaw-0.30.0/poweRlaw/vignettes/plfit_res.rds |only
poweRlaw-0.30.0/poweRlaw/vignettes/poweRlaw.Rnw | 48 +--
poweRlaw-0.30.0/poweRlaw/vignettes/poweRlaw.bib | 46 +--
poweRlaw-0.30.0/poweRlaw/vignettes/v61i10.Rnw |only
poweRlaw-0.30.0/poweRlaw/vignettes/v61i10.bib |only
70 files changed, 917 insertions(+), 626 deletions(-)
Title: Bayesian Reconstruction of Disease Outbreaks by Combining
Epidemiologic and Genomic Data
Diff between outbreaker versions 1.1-4 dated 2014-12-05 and 1.1-5 dated 2015-02-20
Description: Bayesian reconstruction of disease outbreaks using epidemiological and genetic information.
Author: Thibaut Jombart
Maintainer: Thibaut Jombart
ChangeLog | 14 ++++++++++++--
DESCRIPTION | 14 +++++++-------
MD5 | 14 +++++++-------
NAMESPACE | 15 +++++++++++----
data/fakeOutbreak.RData |binary
src/likelihood.c | 19 ++++++++++++++++---
src/likelihood.h | 3 +++
src/outbreaker.c | 12 ++++++------
8 files changed, 62 insertions(+), 29 deletions(-)
Title: Maximally Selected Rank Statistics
Diff between maxstat versions 0.7-21 dated 2015-01-19 and 0.7-22 dated 2015-02-20
Description: Maximally selected rank statistics with
several p-value approximations.
Author: Torsten Hothorn
Maintainer: Torsten Hothorn
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
NAMESPACE | 2 ++
inst/NEWS | 4 ++++
inst/doc/maxstat.pdf |binary
5 files changed, 14 insertions(+), 8 deletions(-)
Title: Convert Spatial Grids to Polygons
Diff between Grid2Polygons versions 0.1-4 dated 2013-08-31 and 0.1-5 dated 2015-02-20
Description: Converts a spatial object from class SpatialGridDataFrame to
SpatialPolygonsDataFrame.
Author: Jason C. Fisher
Maintainer: Jason C. Fisher
Grid2Polygons-0.1-4/Grid2Polygons/README.md |only
Grid2Polygons-0.1-5/Grid2Polygons/DESCRIPTION | 12 ++++++------
Grid2Polygons-0.1-5/Grid2Polygons/MD5 | 9 ++++-----
Grid2Polygons-0.1-5/Grid2Polygons/NAMESPACE | 7 +++++++
Grid2Polygons-0.1-5/Grid2Polygons/NEWS | 4 ++++
Grid2Polygons-0.1-5/Grid2Polygons/R/Grid2Polygons.R | 2 +-
6 files changed, 22 insertions(+), 12 deletions(-)
Title: Regression Analysis of Fractional Responses Under Unobserved
Heterogeneity
Diff between frmhet versions 1.0 dated 2014-11-20 and 1.1.2 dated 2015-02-20
Description: Estimation and specification analysis of fractional regression models with neglected heterogeneity and/or endogenous covariates.
Author: Joaquim J.S. Ramalho
Maintainer: Joaquim J.S. Ramalho
DESCRIPTION | 8 +--
MD5 | 12 ++---
R/frmhet.R | 119 +++++++++++++++++++++++++++++++-------------------
man/frmhet-package.Rd | 4 -
man/frmhet.Rd | 27 ++++++++++-
man/frmhet.pe.Rd | 22 ++++++++-
man/frmhet.reset.Rd | 19 +++++++
7 files changed, 149 insertions(+), 62 deletions(-)
Title: Regression Analysis of Fractional Responses
Diff between frm versions 1.2 dated 2014-05-27 and 1.2.2 dated 2015-02-20
Description: Estimation and specification analysis of one- and two-part fractional regression models and calculation of partial effects.
Author: Joaquim J.S. Ramalho
Maintainer: Joaquim J.S. Ramalho
DESCRIPTION | 16 ++++++++--------
MD5 | 16 ++++++++--------
R/frm.R | 16 ++++++++++------
man/frm-package.Rd | 8 ++++----
man/frm.Rd | 35 ++++++++++++++++++++++++++++++++---
man/frm.ggoff.Rd | 25 +++++++++++++++++++++++--
man/frm.pe.Rd | 38 ++++++++++++++++++++++++++++++++------
man/frm.ptest.Rd | 22 ++++++++++++++++++++++
man/frm.reset.Rd | 24 +++++++++++++++++++++++-
9 files changed, 162 insertions(+), 38 deletions(-)
Title: Exact Distributions for Rank and Permutation Tests
Diff between exactRankTests versions 0.8-27 dated 2013-09-24 and 0.8-28 dated 2015-02-20
More information about exactRankTests at CRAN
Description: Computes exact conditional p-values and quantiles using an
implementation of the Shift-Algorithm by Streitberg & Roehmel.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut]
Maintainer: Torsten Hothorn
DESCRIPTION | 10 +++++-----
MD5 | 26 +++++++++++++-------------
NAMESPACE | 9 +++++++++
data/ASAT.rda |binary
data/bloodp.rda |binary
data/ears.rda |binary
data/glioma.rda |binary
data/globulin.rda |binary
data/lungcancer.rda |binary
data/neuropathy.rda |binary
data/ocarcinoma.rda |binary
data/rotarod.rda |binary
data/sal.rda |binary
inst/NEWS | 4 ++++
14 files changed, 31 insertions(+), 18 deletions(-)
Permanent link
Title: Conditional Density Estimation Network Construction and
Evaluation
Diff between CaDENCE versions 1.2.1 dated 2013-06-28 and 1.2.2 dated 2015-02-20
Description: Parameters of a user-specified probability distribution are modelled by a multi-layer perceptron artificial neural network. This framework can be used to implement probabilistic nonlinear models including mixture density networks, heteroscedastic regression models, zero-inflated models, and the like.
Author: Alex J. Cannon
Maintainer: Alex J. Cannon
DESCRIPTION | 11 +++++------
MD5 | 10 +++++-----
NAMESPACE | 4 +---
R/cadence.fit.R | 27 ++++++++++-----------------
man/CaDENCE-package.Rd | 8 ++++----
man/cadence.fit.Rd | 10 +++++++---
6 files changed, 32 insertions(+), 38 deletions(-)
Title: Algorithms for Quantitative Pedology
Diff between aqp versions 1.7-7 dated 2014-11-13 and 1.8 dated 2015-02-20
Description: A collection of algorithms related to modeling of soil resources, soil classification, soil profile aggregation, and visualization.
Author: Dylan Beaudette
Maintainer: Dylan Beaudette
DESCRIPTION | 13 +-
MD5 | 50 +++++-----
NEWS | 13 ++
R/SoilProfileCollection-methods.R | 43 ++++++++-
R/SoilProfileCollection-spatial.R | 4
R/evalGenHz.R | 106 +++++++++++-----------
R/get.ml.hz.R | 2
R/panel.depth_function.R | 17 +--
R/profile_plot.R | 38 ++++----
R/setters.R | 48 +++++++++-
R/texture-low-rv-high.R | 168 +++++++++++++++++++-----------------
data/amarillo.rda |binary
data/ca630.rda |binary
data/munsell.rda |binary
data/rruff.sample.rda |binary
data/sp1.rda |binary
data/sp2.rda |binary
data/sp3.rda |binary
data/sp4.rda |binary
data/sp5.rda |binary
man/SPC-plotting.Rd | 1
man/SoilProfileCollection-class.Rd | 13 ++
man/addBracket.Rd | 7 +
man/hzDistinctnessCodeToOffset.Rd | 2
man/random_profile.Rd | 2
man/texture.triangle.low.rv.high.Rd | 31 ++++--
26 files changed, 341 insertions(+), 217 deletions(-)
Title: Time Series Analysis and Computational Finance
Diff between tseries versions 0.10-33 dated 2015-02-10 and 0.10-34 dated 2015-02-20
Description: Time series analysis and computational finance.
Author: Adrian Trapletti [aut],
Kurt Hornik [aut, cre],
Blake LeBaron [ctb] (BDS test code)
Maintainer: Kurt Hornik
ChangeLog | 7 +++++++
DESCRIPTION | 6 +++---
MD5 | 6 +++---
R/finance.R | 11 +++++++----
4 files changed, 20 insertions(+), 10 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-16 1.0.0
2013-06-11 0.0.1
Title: STK++ Integration to R Using Rcpp
Diff between rtkpp versions 0.8.4 dated 2014-11-18 and 0.8.5 dated 2015-02-20
Description: STK++ (http://www.stkpp.org) is a collection of
C++ classes for statistics, clustering, linear algebra, arrays (with an
Eigen-like API), regression, dimension reduction, etc. The integration of
the library to R is using Rcpp. Some functionalities of the Clustering
project provided by the library are available in the R environment as R
functions.
The rtkpp package includes the header files from the STK++
library (currently version 0.8.5). Thus users do not need to
install STK++ itself in order to use it.
STK++ is licensed under the GNU LGPL version 2 or later. rtkpp
(the stkpp integration into R) is licensed under the
GNU GPL version 2 or later.
Author: Serge Iovleff [aut, cre],
Vincent Kubicki [ctb],
Quentin Grimonprez [ctb],
Parmeet Bhatia [ctb]
Maintainer: Serge Iovleff
rtkpp-0.8.4/rtkpp/inst/AUTHORS |only
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rtkpp-0.8.4/rtkpp/inst/projects/Analysis/include/STK_Funct_util.h |only
rtkpp-0.8.4/rtkpp/inst/projects/Arrays/include/STK_ITContainer2D.h |only
rtkpp-0.8.4/rtkpp/inst/projects/Arrays/include/STK_Wrappers.h |only
rtkpp-0.8.4/rtkpp/inst/projects/Arrays/include/operators/STK_SliceOperators.h |only
rtkpp-0.8.4/rtkpp/inst/projects/Arrays/include/products/STK_GeneralByGeneralProduct.h |only
rtkpp-0.8.4/rtkpp/inst/projects/Arrays/include/products/STK_GeneralByVectorProduct.h |only
rtkpp-0.8.4/rtkpp/inst/projects/Clustering/include/STK_MixtureComponent.h |only
rtkpp-0.8.4/rtkpp/inst/projects/Clustering/src/STK_IDataManager.cpp |only
rtkpp-0.8.4/rtkpp/inst/projects/Regress/src/STK_BSplineCoefficients.cpp |only
rtkpp-0.8.4/rtkpp/inst/projects/Rtkpp/include/STK_RcppMatrix.h |only
rtkpp-0.8.4/rtkpp/inst/projects/Rtkpp/include/STK_RcppVector.h |only
rtkpp-0.8.5/rtkpp/DESCRIPTION | 19
rtkpp-0.8.5/rtkpp/MD5 | 533 ++--
rtkpp-0.8.5/rtkpp/NAMESPACE | 17
rtkpp-0.8.5/rtkpp/R/ClusterCategorical.R | 14
rtkpp-0.8.5/rtkpp/R/ClusterGamma.R | 7
rtkpp-0.8.5/rtkpp/R/ClusterInit.R | 90
rtkpp-0.8.5/rtkpp/R/ClusterModelNames.R | 86
rtkpp-0.8.5/rtkpp/R/ClusterPlot.R | 4
rtkpp-0.8.5/rtkpp/R/ClusterPoisson.R |only
rtkpp-0.8.5/rtkpp/R/ClusterStrategy.R | 8
rtkpp-0.8.5/rtkpp/R/rtkpp.R | 37
rtkpp-0.8.5/rtkpp/R/rtkppFlags.R | 14
rtkpp-0.8.5/rtkpp/build |only
rtkpp-0.8.5/rtkpp/cleanup | 2
rtkpp-0.8.5/rtkpp/data/DebTrivedi.rda |only
rtkpp-0.8.5/rtkpp/data/HeartDisease.cat.rda |binary
rtkpp-0.8.5/rtkpp/data/HeartDisease.cont.rda |binary
rtkpp-0.8.5/rtkpp/data/HeartDisease.target.rda |binary
rtkpp-0.8.5/rtkpp/data/birds.rda |binary
rtkpp-0.8.5/rtkpp/data/car.rda |binary
rtkpp-0.8.5/rtkpp/data/geyser.rda |binary
rtkpp-0.8.5/rtkpp/data/titanic.rda |binary
rtkpp-0.8.5/rtkpp/inst/NEWS.Rd | 8
rtkpp-0.8.5/rtkpp/inst/doc |only
rtkpp-0.8.5/rtkpp/inst/include/Algebra.h | 8
rtkpp-0.8.5/rtkpp/inst/include/Analysis.h | 2
rtkpp-0.8.5/rtkpp/inst/include/Arrays.h | 8
rtkpp-0.8.5/rtkpp/inst/include/Clustering.h | 3
rtkpp-0.8.5/rtkpp/inst/include/RTKpp.h | 7
rtkpp-0.8.5/rtkpp/inst/include/RTKppForward.h | 43
rtkpp-0.8.5/rtkpp/inst/include/STKpp.h | 130 -
rtkpp-0.8.5/rtkpp/inst/include/STatistiK.h | 1
rtkpp-0.8.5/rtkpp/inst/include/StatModels.h | 4
rtkpp-0.8.5/rtkpp/inst/projects/AAModels/include/STK_GaussianAAModel.h | 18
rtkpp-0.8.5/rtkpp/inst/projects/AAModels/include/STK_IAAModel.h | 42
rtkpp-0.8.5/rtkpp/inst/projects/AAModels/include/STK_LinearAAModel.h | 12
rtkpp-0.8.5/rtkpp/inst/projects/AAModels/src/STK_GaussianAAModel.cpp | 16
rtkpp-0.8.5/rtkpp/inst/projects/AAModels/src/STK_IAAModel.cpp | 16
rtkpp-0.8.5/rtkpp/inst/projects/AAModels/src/STK_LinearAAModel.cpp | 20
rtkpp-0.8.5/rtkpp/inst/projects/AAModels/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/projects/AAModels/src/makevars.local |only
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/include/STK_Givens.h | 10
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/include/STK_Householder.h | 16
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/include/STK_IQr.h | 27
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/include/STK_ISymEigen.h | 18
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/include/STK_Qr.h | 4
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/include/STK_Svd.h | 42
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/include/STK_SymEigen.h | 8
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/include/STK_lapack_Qr.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/include/STK_lapack_SymEigen.h | 4
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/src/STK_Qr.cpp | 3
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/src/STK_Svd.cpp | 14
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/src/STK_SymEigen.cpp | 6
rtkpp-0.8.5/rtkpp/inst/projects/Algebra/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/include/STK_Funct_Util.h |only
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/include/STK_Funct_raw.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/include/STK_IFunction.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/src/STK_Funct_betaRatio.cpp | 6
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/src/STK_Funct_dev0.cpp | 2
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/src/STK_Funct_expm1.cpp | 2
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/src/STK_Funct_g0.cpp | 2
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/src/STK_Funct_gamma.cpp | 10
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/src/STK_Funct_gammaRatio.cpp | 4
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/src/STK_Funct_log1p.cpp | 2
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/src/STK_Funct_poisson_raw.cpp | 2
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/src/STK_Funct_psi_raw.cpp | 2
rtkpp-0.8.5/rtkpp/inst/projects/Analysis/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_AllocatorBase.h | 11
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_Array1D.h | 6
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_Array2D.h | 62
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_Array2DDiagonal.h | 28
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_Array2DLowerTriangular.h | 29
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_Array2DPoint.h | 31
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_Array2DSquare.h | 32
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_Array2DUpperTriangular.h | 34
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_Array2DVector.h | 27
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_Array2D_Functors.h | 65
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ArrayBase.h | 143 -
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ArrayBaseApplier.h | 86
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ArrayBaseAssign.h | 68
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ArrayBaseInitializer.h | 25
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_Arrays_Util.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_CAllocator.h | 1153 ++++++----
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_CArray.h | 120 -
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_CArrayNumber.h | 49
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_CArrayPoint.h | 68
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_CArraySquare.h | 78
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_CArrayVector.h | 56
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_Const_Arrays.h | 107
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ExprBase.h | 174 +
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ExprBaseFunctors.h | 213 +
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ExprBaseProduct.h | 22
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ExprBaseVisitor.h | 246 +-
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_IArray2D.h | 561 +++-
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_IArray2DBase.h | 408 ++-
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ICAllocator.h |only
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ICArray.h | 101
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/STK_ITContainer.h |only
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/operators/STK_BinaryOperators.h | 88
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/operators/STK_DiagOperator.h | 37
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/operators/STK_DotOperators.h | 10
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/operators/STK_SlicingOperators.h |only
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/operators/STK_TransposeOperator.h | 10
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/operators/STK_UnaryOperators.h | 11
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/products/STK_ArrayByArrayProduct.h |only
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/products/STK_ArrayByVectorProduct.h |only
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/products/STK_ProductImpl.h | 127 -
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/products/STK_ProductOperators.h | 245 +-
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/visitors/STK_SlicingVisitors.h |only
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/visitors/STK_VisitorSelector.h | 246 --
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/visitors/STK_Visitors.h | 210 +
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/include/visitors/STK_VisitorsImpl.h | 469 ++--
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/src/STK_Arrays_Util.cpp | 8
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/projects/Arrays/src/makevars.local | 2
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/CategoricalMixtureModels/STK_CategoricalBase.h | 32
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/CategoricalMixtureModels/STK_CategoricalParameters.h | 102
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/CategoricalMixtureModels/STK_Categorical_pjk.h | 26
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/CategoricalMixtureModels/STK_Categorical_pk.h | 19
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/ExponentialMixtureModels/STK_ExponentialBase.h | 36
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/ExponentialMixtureModels/STK_ExponentialParameters.h | 66
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/ExponentialMixtureModels/STK_Exponential_bjk.h | 18
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/ExponentialMixtureModels/STK_Exponential_bk.h | 17
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_GammaBase.h | 59
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_GammaParameters.h | 595 +++--
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_a_bjk.h | 38
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_a_bk.h | 42
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_aj_bjk.h | 37
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_aj_bk.h | 37
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ajk_b.h | 35
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ajk_bj.h | 39
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ajk_bjk.h | 13
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ajk_bk.h | 11
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ak_b.h | 37
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ak_bj.h | 39
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ak_bjk.h | 11
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GammaMixtureModels/STK_Gamma_ak_bk.h | 18
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GaussianMixtureModels/STK_DiagGaussianBase.h | 78
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GaussianMixtureModels/STK_DiagGaussianParameters.h | 153 -
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GaussianMixtureModels/STK_Gaussian_s.h | 36
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GaussianMixtureModels/STK_Gaussian_sj.h | 34
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GaussianMixtureModels/STK_Gaussian_sjk.h | 22
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/GaussianMixtureModels/STK_Gaussian_sk.h | 16
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/MixturesBridges/STK_IMixtureBridge.h | 33
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/MixturesBridges/STK_MixtureBridge.h | 91
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/PoissonMixtureModels |only
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/STK_Clust_Util.h | 13
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/STK_IMixture.h | 95
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/STK_IMixtureComposer.h | 61
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/STK_IMixtureManager.h | 5
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/STK_IMixtureModel.h | 113
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/STK_IMixtureModelBase.h | 37
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/STK_MixtureComposer.h | 32
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/STK_MixtureManager.h | 170 +
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/include/STK_MixtureParamStat.h |only
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/STK_Clust_Util.cpp | 34
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/STK_IMixture.cpp | 28
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/STK_IMixtureComposer.cpp | 111
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/STK_IMixtureData.cpp |only
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/STK_IMixtureModelBase.cpp | 34
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/STK_MixtureAlgo.cpp | 105
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/STK_MixtureComposer.cpp | 28
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/STK_MixtureFacade.cpp | 8
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/STK_MixtureInit.cpp | 60
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/STK_MixtureStrategy.cpp | 62
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/projects/Clustering/src/makevars.local | 1
rtkpp-0.8.5/rtkpp/inst/projects/DManager/include/STK_CsvToArray.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/DManager/include/STK_DataFrame.h | 16
rtkpp-0.8.5/rtkpp/inst/projects/DManager/include/STK_ExportToCsv.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/DManager/include/STK_IVariable.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/DManager/include/STK_Variable.h | 44
rtkpp-0.8.5/rtkpp/inst/projects/DManager/src/STK_DataFrame.cpp | 28
rtkpp-0.8.5/rtkpp/inst/projects/DManager/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/projects/Reduct/include/STK_ILinearReduct.h | 12
rtkpp-0.8.5/rtkpp/inst/projects/Reduct/include/STK_IReduct.h | 14
rtkpp-0.8.5/rtkpp/inst/projects/Reduct/include/STK_LocalVariance.h | 20
rtkpp-0.8.5/rtkpp/inst/projects/Reduct/include/STK_ProjectedVariance.h | 8
rtkpp-0.8.5/rtkpp/inst/projects/Reduct/src/STK_ILinearReduct.cpp | 6
rtkpp-0.8.5/rtkpp/inst/projects/Reduct/src/STK_IReduct.cpp | 4
rtkpp-0.8.5/rtkpp/inst/projects/Reduct/src/STK_LocalVariance.cpp | 21
rtkpp-0.8.5/rtkpp/inst/projects/Reduct/src/STK_ProjectedVariance.cpp | 4
rtkpp-0.8.5/rtkpp/inst/projects/Reduct/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/projects/Regress/include/STK_AdditiveBSplineCoefficients.h | 12
rtkpp-0.8.5/rtkpp/inst/projects/Regress/include/STK_AdditiveBSplineRegression.h | 22
rtkpp-0.8.5/rtkpp/inst/projects/Regress/include/STK_BSplineCoefficients.h | 364 +++
rtkpp-0.8.5/rtkpp/inst/projects/Regress/include/STK_BSplineRegression.h | 34
rtkpp-0.8.5/rtkpp/inst/projects/Regress/include/STK_IRegression.h | 81
rtkpp-0.8.5/rtkpp/inst/projects/Regress/include/STK_MultidimRegression.h | 14
rtkpp-0.8.5/rtkpp/inst/projects/Regress/src/STK_AdditiveBSplineRegression.cpp | 27
rtkpp-0.8.5/rtkpp/inst/projects/Regress/src/STK_BSplineRegression.cpp | 22
rtkpp-0.8.5/rtkpp/inst/projects/Regress/src/STK_MultidimRegression.cpp | 27
rtkpp-0.8.5/rtkpp/inst/projects/Regress/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/projects/Rtkpp/include/Rcpp_as.h | 6
rtkpp-0.8.5/rtkpp/inst/projects/Rtkpp/include/Rcpp_wrap.h | 54
rtkpp-0.8.5/rtkpp/inst/projects/Rtkpp/include/STK_ClusterLauncher.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/Rtkpp/include/STK_RDataHandler.h | 19
rtkpp-0.8.5/rtkpp/inst/projects/Rtkpp/include/STK_RMatrix.h |only
rtkpp-0.8.5/rtkpp/inst/projects/Rtkpp/include/STK_RVector.h |only
rtkpp-0.8.5/rtkpp/inst/projects/Rtkpp/include/STK_wrap.h |only
rtkpp-0.8.5/rtkpp/inst/projects/STKernel/include/STK_Arithmetic.h | 25
rtkpp-0.8.5/rtkpp/inst/projects/STKernel/include/STK_Constants.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/STKernel/include/STK_Functors.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/STKernel/include/STK_Range.h | 8
rtkpp-0.8.5/rtkpp/inst/projects/STKernel/src/STK_Real.cpp | 2
rtkpp-0.8.5/rtkpp/inst/projects/STKernel/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/MersenneTwister.h | 23
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Law_Bernoulli.h | 1
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Law_Beta.h | 12
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Law_Categorical.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Law_Cauchy.h | 1
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Law_Gamma.h | 22
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Law_IUnivLaw.h | 13
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Law_MultiNormal.h | 18
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Law_Normal.h | 1
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Law_Poisson.h |only
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_RandBase.h | 120 -
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Stat_Functors.h | 400 +--
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Stat_MultivariateReal.h | 35
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/include/STK_Stat_UnivariateReal.h | 18
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/src/STK_Law_Beta.cpp | 26
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/src/STK_Law_Categorical.cpp | 13
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/src/STK_Law_Cauchy.cpp | 12
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/src/STK_Law_Exponential.cpp | 12
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/src/STK_Law_Gamma.cpp | 28
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/src/STK_Law_Normal.cpp | 98
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/src/STK_Law_Poisson.cpp |only
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/src/STK_Law_Uniform.cpp | 15
rtkpp-0.8.5/rtkpp/inst/projects/STatistiK/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/projects/Sdk/include/STK_MetaTemplate.h | 67
rtkpp-0.8.5/rtkpp/inst/projects/Sdk/include/STK_StaticAssert.h | 7
rtkpp-0.8.5/rtkpp/inst/projects/Sdk/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/include/STK_Gaussian2BlocksModel.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/include/STK_GaussianModel.h | 14
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/include/STK_IGaussianModel.h | 2
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/include/STK_IMultiParameters.h | 5
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/include/STK_IMultiStatModel.h | 4
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/include/STK_IStatModelBase.h | 7
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/include/STK_JointBernoulliModel.h | 9
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/include/STK_JointGammaParameters.h | 19
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/include/STK_JointGaussianModel.h | 11
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/src/STK_Gaussian2BlocksModel.cpp | 16
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/src/STK_GaussianModel.cpp | 10
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/src/STK_IGaussianModel.cpp | 2
rtkpp-0.8.5/rtkpp/inst/projects/StatModels/src/makefile | 2
rtkpp-0.8.5/rtkpp/inst/unitTests/runit.wrap.R | 6
rtkpp-0.8.5/rtkpp/man/ClusterInit-class.Rd | 4
rtkpp-0.8.5/rtkpp/man/ClusterPoisson-class.Rd |only
rtkpp-0.8.5/rtkpp/man/DebTrivedi.Rd |only
rtkpp-0.8.5/rtkpp/man/IClusterComponent-class.Rd | 11
rtkpp-0.8.5/rtkpp/man/clusterDiagGaussianNames.Rd | 7
rtkpp-0.8.5/rtkpp/man/clusterGamma.Rd | 2
rtkpp-0.8.5/rtkpp/man/clusterInit.Rd | 10
rtkpp-0.8.5/rtkpp/man/clusterPoisson.Rd |only
rtkpp-0.8.5/rtkpp/man/clusterPoissonNames.Rd |only
rtkpp-0.8.5/rtkpp/man/clusterStrategy.Rd | 4
rtkpp-0.8.5/rtkpp/man/extract-methods.Rd | 3
rtkpp-0.8.5/rtkpp/man/initialize-methods.Rd | 18
rtkpp-0.8.5/rtkpp/man/missingValues-methods.Rd | 6
rtkpp-0.8.5/rtkpp/man/plot-ClusterGamma-method.Rd | 3
rtkpp-0.8.5/rtkpp/man/plot-ClusterPoisson-method.Rd |only
rtkpp-0.8.5/rtkpp/man/print-methods.Rd | 6
rtkpp-0.8.5/rtkpp/man/rtkppFlags.Rd | 5
rtkpp-0.8.5/rtkpp/man/show-methods.Rd | 8
rtkpp-0.8.5/rtkpp/man/summary-methods.Rd | 3
rtkpp-0.8.5/rtkpp/src/Makevars | 12
rtkpp-0.8.5/rtkpp/src/STK_ClusterFacade.cpp | 4
rtkpp-0.8.5/rtkpp/src/STK_ClusterLauncher.cpp | 50
rtkpp-0.8.5/rtkpp/src/STK_RDataHandler.cpp | 4
rtkpp-0.8.5/rtkpp/tests/clusterGammaLikelihood.R | 4
rtkpp-0.8.5/rtkpp/vignettes |only
284 files changed, 6964 insertions(+), 4795 deletions(-)
Title: Forecastable Component Analysis
Diff between ForeCA versions 0.1 dated 2014-03-02 and 0.2.0 dated 2015-02-20
Description: Forecastable Component Analysis (ForeCA) is a novel dimension
reduction (DR) technique for temporally dependent signals. Contrary to
other popular DR methods, such as PCA or ICA, ForeCA takes time dependency
explicitly into account and searches for the most ''forecastable'' signal.
The measure of forecastability is based on the Shannon entropy of the
spectral density of the transformed signal. This R package provides the
main algorithms and auxiliary function (summary, plotting, etc.) to apply
ForeCA to multivariate time series data.
Author: Georg M. Goerg
Maintainer: Georg M. Goerg
ForeCA-0.1/ForeCA/R/foreca.EM.R |only
ForeCA-0.1/ForeCA/man/foreca.EM.Rd |only
ForeCA-0.2.0/ForeCA/DESCRIPTION | 28
ForeCA-0.2.0/ForeCA/MD5 | 94 +-
ForeCA-0.2.0/ForeCA/NAMESPACE | 27
ForeCA-0.2.0/ForeCA/NEWS | 82 ++
ForeCA-0.2.0/ForeCA/R/ForeCA-package.R | 66 +
ForeCA-0.2.0/ForeCA/R/Omega.R | 196 ++---
ForeCA-0.2.0/ForeCA/R/SDF2mvspectrum.R | 75 +-
ForeCA-0.2.0/ForeCA/R/common-arguments.R |only
ForeCA-0.2.0/ForeCA/R/complete_controls.R |only
ForeCA-0.2.0/ForeCA/R/continuous_entropy.R | 146 ++--
ForeCA-0.2.0/ForeCA/R/discrete_entropy.R | 158 ++--
ForeCA-0.2.0/ForeCA/R/foreca-utils.R | 240 +++----
ForeCA-0.2.0/ForeCA/R/foreca.EM-aux.R | 399 ++++++-----
ForeCA-0.2.0/ForeCA/R/foreca.EM.one_weightvector.R |only
ForeCA-0.2.0/ForeCA/R/foreca.R | 503 ++++++++++++++-
ForeCA-0.2.0/ForeCA/R/foreca.one_weightvector-utils.R |only
ForeCA-0.2.0/ForeCA/R/initialize_weightvector.R | 163 ++--
ForeCA-0.2.0/ForeCA/R/mvspec2mvspectrum.R | 56 -
ForeCA-0.2.0/ForeCA/R/mvspectrum.R | 383 ++++++++---
ForeCA-0.2.0/ForeCA/R/mvspectrum2wcov.R | 240 ++++---
ForeCA-0.2.0/ForeCA/R/quadratic_form.R | 86 +-
ForeCA-0.2.0/ForeCA/R/sfa.R |only
ForeCA-0.2.0/ForeCA/R/spectral_entropy.R | 254 +++----
ForeCA-0.2.0/ForeCA/R/univariate_spectrum-functions.R |only
ForeCA-0.2.0/ForeCA/R/whiten.R | 274 ++++++--
ForeCA-0.2.0/ForeCA/R/zzz.R |only
ForeCA-0.2.0/ForeCA/man/ForeCA-package.Rd | 43 -
ForeCA-0.2.0/ForeCA/man/Omega.Rd | 125 +--
ForeCA-0.2.0/ForeCA/man/common-arguments.Rd |only
ForeCA-0.2.0/ForeCA/man/complete-controls.Rd |only
ForeCA-0.2.0/ForeCA/man/continuous_entropy.Rd | 60 -
ForeCA-0.2.0/ForeCA/man/discrete_entropy.Rd | 95 +-
ForeCA-0.2.0/ForeCA/man/foreca-utils.Rd | 66 -
ForeCA-0.2.0/ForeCA/man/foreca.EM-aux.Rd | 160 ++--
ForeCA-0.2.0/ForeCA/man/foreca.EM.one_weightvector.Rd |only
ForeCA-0.2.0/ForeCA/man/foreca.Rd | 175 ++++-
ForeCA-0.2.0/ForeCA/man/foreca.one_weightvector-utils.Rd |only
ForeCA-0.2.0/ForeCA/man/initialize_weightvector.Rd | 116 +--
ForeCA-0.2.0/ForeCA/man/mvspectrum.Rd | 257 +++++--
ForeCA-0.2.0/ForeCA/man/mvspectrum2wcov.Rd | 98 ++
ForeCA-0.2.0/ForeCA/man/quadratic_form.Rd | 26
ForeCA-0.2.0/ForeCA/man/sfa.Rd |only
ForeCA-0.2.0/ForeCA/man/spectral_entropy.Rd | 118 +--
ForeCA-0.2.0/ForeCA/man/whiten.Rd | 99 ++
ForeCA-0.2.0/ForeCA/tests |only
47 files changed, 3116 insertions(+), 1792 deletions(-)
Title: High-Speed Processing of VCF, FASTA and Alignment Data
Diff between WhopGenome versions 0.9.1 dated 2015-02-19 and 0.9.2 dated 2015-02-20
Description: Provides very fast access to whole genome, population scale variation data
from VCF files and sequence data from FASTA-formatted files.
It also reads in alignments from FASTA, Phylip, MAF and other file formats.
Provides easy-to-use interfaces to genome annotation from UCSC and Bioconductor and gene ontology data
from AmiGO and is capable to read, modify and write PLINK .PED-format pedigree files.
Author: Ulrich Wittelsbuerger [aut, cre], Heng Li [ctb], Bob Handsaker [ctb]
Maintainer: Ulrich Wittelsbuerger
DESCRIPTION | 7 +
MD5 | 7 +
inst/CITATION |only
src/Makevars | 16 ----
src/Makevars.win | 212 +++++++++++++++++++++++++++----------------------------
5 files changed, 116 insertions(+), 126 deletions(-)
Title: S3 Methods Simplified
Diff between R.methodsS3 versions 1.6.1 dated 2014-01-05 and 1.7.0 dated 2015-02-20
Description: Methods that simplify the setup of S3 generic functions and S3 methods. Major effort has been made in making definition of methods as simple as possible with a minimum of maintenance for package developers. For example, generic functions are created automatically, if missing, and naming conflict are automatically solved, if possible. The method setMethodS3() is a good start for those who in the future may want to migrate to S4. This is a cross-platform package implemented in pure R that generates standard S3 methods.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson
R.methodsS3-1.6.1/R.methodsS3/inst/NEWS |only
R.methodsS3-1.7.0/R.methodsS3/DESCRIPTION | 10 ++---
R.methodsS3-1.7.0/R.methodsS3/MD5 | 27 ++++++++++------
R.methodsS3-1.7.0/R.methodsS3/NEWS |only
R.methodsS3-1.7.0/R.methodsS3/R/000.R | 10 +++++
R.methodsS3-1.7.0/R.methodsS3/R/010.setGenericS3.R | 12 +++----
R.methodsS3-1.7.0/R.methodsS3/R/030.setMethodS3.R | 7 ++--
R.methodsS3-1.7.0/R.methodsS3/R/findDispatchMethodsS3.R | 27 ++++++++++++++++
R.methodsS3-1.7.0/R.methodsS3/R/isGenericS3.R | 15 +++++++-
R.methodsS3-1.7.0/R.methodsS3/R/pkgStartupMessage.R | 1
R.methodsS3-1.7.0/R.methodsS3/R/zzz.R | 22 +++++--------
R.methodsS3-1.7.0/R.methodsS3/tests |only
12 files changed, 91 insertions(+), 40 deletions(-)
Title: Multi-Class Sparse Discriminant Analysis
Diff between msda versions 1.0.1 dated 2014-10-02 and 1.0.2 dated 2015-02-20
Description: Efficient procedures for computing a new Multi-Class Sparse Discriminant Analysis method that estimates all discriminant directions simultaneously.
Author: Qing Mai
Maintainer: Yi Yang
ChangeLog | 5 +
DESCRIPTION | 10 +--
MD5 | 28 +++++-----
NAMESPACE | 1
R/cv.msda.R | 19 +++---
R/msda.R | 6 +-
R/plot.msda.R |only
R/predict.msda.R | 11 ++--
R/utilities.R | 11 ++--
data/GDS1615.rda |binary
man/GDS1615.Rd | 56 ++++++++++----------
man/cv.msda.Rd | 142 ++++++++++++++++++++++++++--------------------------
man/msda.Rd | 16 +++--
man/plot.msda.Rd |only
man/predict.msda.Rd | 84 +++++++++++++++---------------
src/msda_new.f90 | 11 ++--
16 files changed, 216 insertions(+), 184 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Diff between MASS versions 7.3-37 dated 2015-01-10 and 7.3-39 dated 2015-02-20
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 | 12 ++++++------
MD5 | 32 ++++++++++++++++----------------
NAMESPACE | 5 +++--
R/lda.R | 3 ++-
R/loglm.R | 2 +-
R/lqs.R | 2 +-
R/mvrnorm.R | 6 +++---
R/neg.bin.R | 2 +-
R/negbin.R | 2 +-
inst/NEWS | 3 ++-
man/OME.Rd | 2 +-
man/corresp.Rd | 2 +-
man/denumerate.Rd | 2 +-
man/geyser.Rd | 3 +++
man/mvrnorm.Rd | 9 ++++-----
man/npr1.Rd | 2 +-
man/summary.rlm.Rd | 2 +-
17 files changed, 48 insertions(+), 43 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-17 0.3
2015-01-29 0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-11 1.0
Title: R/KEA Interface
Diff between RKEA versions 0.0-4 dated 2014-06-12 and 0.0-5 dated 2015-02-20
Description: An R interface to KEA (Version 5.0).
KEA (for Keyphrase Extraction Algorithm) allows for extracting
keyphrases from text documents. It can be either used for free
indexing or for indexing with a controlled vocabulary. For more
information see
Author: Ingo Feinerer [aut],
Kurt Hornik [aut, cre],
Eibe Frank [ctb, cph] (KEA Java library),
Olena Medelyan [ctb, cph] (KEA Java library),
The Apache Software Foundation [ctb, cph] (Apache Commons Logging and
Apache Jena Java libraries),
International Business Machines Corporation and others [ctb, cph]
(International Components for Unicode for Java (ICU4J)),
Martin Porter [ctb, cph] (Snowball base),
Richard Boulton [ctb, cph] (Snowball Java library),
University of Waikato [ctb, cph] (Weka Java library)
Maintainer: Kurt Hornik
DESCRIPTION | 33 ++++++++++++++++++++++++++-------
MD5 | 11 ++++++-----
R/kea.R | 28 ++++++++++++++++++++++++++++
build/vignette.rds |binary
inst/doc/kea.pdf |binary
java |only
man/createModel.Rd | 23 +++++++++++++++++------
7 files changed, 77 insertions(+), 18 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Diff between nlme versions 3.1-119 dated 2015-01-10 and 3.1-120 dated 2015-02-20
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version),
Douglas Bates [aut] (up to 2007),
Saikat DebRoy [ctb] (up to 2002),
Deepayan Sarkar [ctb] (up to 2005),
EISPACK authors [ctb] (src/rs.f),
R-core [aut, cre]
Maintainer: R-core
ChangeLog | 22 ++++++++-
DESCRIPTION | 10 ++--
MD5 | 80 +++++++++++++++++-----------------
NAMESPACE | 3 -
R/VarCorr.R | 4 -
R/corStruct.R | 1
R/groupedData.R | 6 --
R/lmList.R | 4 -
R/lme.R | 5 --
R/modelStruct.R | 5 --
R/newFunc.R | 5 --
R/newGenerics.R | 5 --
R/newMethods.R | 4 -
R/nlsList.R | 4 -
R/pdMat.R | 6 --
R/reStruct.R | 15 ------
inst/po/de/LC_MESSAGES/R-nlme.mo |binary
inst/po/de/LC_MESSAGES/nlme.mo |binary
inst/po/en@quot/LC_MESSAGES/R-nlme.mo |binary
inst/po/en@quot/LC_MESSAGES/nlme.mo |binary
inst/po/fr/LC_MESSAGES/nlme.mo |binary
inst/po/ko/LC_MESSAGES/nlme.mo |binary
inst/po/pl/LC_MESSAGES/nlme.mo |binary
inst/scripts/ch01.R | 2
inst/scripts/ch02.R | 2
inst/scripts/ch03.R | 2
inst/scripts/ch04.R | 2
inst/scripts/ch05.R | 2
inst/scripts/ch06.R | 2
inst/scripts/ch08.R | 2
man/bdf.Rd | 2
po/R-de.po | 27 ++++++++---
po/R-nlme.pot | 4 -
po/de.po | 22 ++++-----
po/fr.po | 22 ++++-----
po/ko.po | 22 ++++-----
po/nlme.pot | 24 +++++-----
po/pl.po | 22 ++++-----
tests/nlme.R | 1
tests/nlme.Rout.save | 2
tests/nlme2.R | 2
41 files changed, 157 insertions(+), 186 deletions(-)
Title: Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, Weka,
dBase, ...
Diff between foreign versions 0.8-62 dated 2015-01-07 and 0.8-63 dated 2015-02-20
Description: Functions for reading and writing data stored by some versions of
Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka
and for reading and writing some dBase files.
Author: R Core Team [aut, cph, cre],
Roger Bivand [ctb, cph],
Vincent J. Carey [ctb, cph],
Saikat DebRoy [ctb, cph],
Stephen Eglen [ctb, cph],
Rajarshi Guha [ctb, cph],
Nicholas Lewin-Koh [ctb, cph],
Mark Myatt [ctb, cph],
Ben Pfaff [ctb],
Brian Quistorff [ctb],
Frank Warmerdam [ctb, cph],
Stephen Weigand [ctb, cph],
Free Software Foundation, Inc. [cph]
Maintainer: R Core Team
ChangeLog | 15 +++++++++++++++
DESCRIPTION | 8 ++++----
MD5 | 22 +++++++++++-----------
R/spss.R | 9 +++++----
R/writeForeignSAS.R | 5 +++--
man/lookup.xport.Rd | 2 +-
man/read.arff.Rd | 2 +-
man/read.dta.Rd | 2 ++
man/read.spss.Rd | 38 ++++++++++++++++++++------------------
man/read.xport.Rd | 2 +-
man/write.arff.Rd | 2 +-
src/stataread.c | 9 +++++----
12 files changed, 69 insertions(+), 47 deletions(-)
Title: Tools for Partial Least Squares Path Modeling (PLS-PM)
Description: plspm contains a set of functions for performing Partial Least
Squares Path Modeling (PLS-PM) analysis for both metric and non-metric
data, as well as REBUS analysis.
Author: Gaston Sanchez [aut, cre],
Laura Trinchera [aut],
Giorgio Russolillo [aut]
Maintainer: ORPHANED
Diff between plspm versions 0.4.1 dated 2013-12-08 and 0.4.2 dated 2015-02-20
DESCRIPTION | 11 +++++++---- MD5 | 6 +++--- NAMESPACE | 1 + build/vignette.rds |binary 4 files changed, 11 insertions(+), 7 deletions(-)
More information about faisalconjoint at CRAN
Permanent link
Title: A Soil Survey Toolkit
Diff between sharpshootR versions 0.6-3 dated 2014-05-06 and 0.7-2 dated 2015-02-19
Description: Miscellaneous soil data management, summary, visualization, and conversion utilities to support soil survey.
Author: USDA-NRCS Soil Survey Staff
Maintainer: Dylan Beaudette
DESCRIPTION | 24 +++++----
MD5 | 41 +++++++++--------
NAMESPACE | 25 ++++++++--
R/SoilTaxonomyDendrogram.R | 6 +-
R/aspect.plot.R | 19 ++++---
R/component.adj.matrix.R | 26 ++++++----
R/diagnosticPropertyPlot.R | 16 +++++-
R/dueling.dendrograms.R | 12 ++++
R/hillslope.probability.R | 2
R/plotAvailWater.R |only
R/plotSoilRelationGraph.R | 101 +++++++++++++++++++++++++++++++++++-------
R/polygonAdjacency.R |only
R/transect-functions.R |only
data/CDEC.snow.courses.rda |binary
data/amador.rda |binary
man/CDECquery.Rd | 74 ++++++++++++++++++++++++++++--
man/SoilTaxonomyDendrogram.Rd | 6 ++
man/aspect.plot.Rd | 5 +-
man/component.adj.matrix.Rd | 3 -
man/diagnosticPropertyPlot.Rd | 2
man/dist.along.grad.Rd |only
man/plotAvailWater.Rd |only
man/plotSoilRelationGraph.Rd | 28 +++++++++++
man/plotTransect.Rd |only
man/polygonAdjacency.Rd |only
25 files changed, 307 insertions(+), 83 deletions(-)
Title: Analysis of Evolutionary Rates in an OU Framework
Diff between OUwie versions 1.43 dated 2014-07-26 and 1.44 dated 2015-02-19
Description: Calculates and compares rate differences of continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck-based Hansen models that allow the strength of selection and stochastic motion to vary across selective regimes.
Author: Jeremy M. Beaulieu
Maintainer: Jeremy Beaulieu
DESCRIPTION | 10 +-
MD5 | 23 +++---
R/OUwie.R | 153 ++++++++++++++++++++++++++++++++++--------
R/OUwie.boot.R | 4 -
R/OUwie.fixed.R | 1
R/OUwie.joint.R | 190 ++++++++++++++++++++++++++++-------------------------
R/OUwie.sim.R | 8 +-
R/OUwie.slice.R | 17 ++--
R/expect.trendy.R |only
man/OUwie.Rd | 8 --
man/OUwie.boot.Rd | 4 -
man/OUwie.joint.Rd | 7 -
man/OUwie.slice.Rd | 6 -
13 files changed, 267 insertions(+), 164 deletions(-)
Title: Earth Mover's Distance for Differential Analysis of Genomics
Data
Diff between EMDomics versions 0.99.0 dated 2014-11-15 and 0.99.1 dated 2015-02-19
Description: The EMDomics algorithm is used to perform a supervised two-class
analysis to measure the magnitude and statistical significance of observed
continuous genomics data between two groups. Usually the data will be gene
expression values from array-based or sequence-based experiments, but data
from other types of experiments can also be analyzed (e.g. copy number
variation). Traditional methods like Significance Analysis of Microarrays
(SAM) and Linear Models for Microarray Data (LIMMA) use significance tests
based on summary statistics (mean and standard deviation) of the two
distributions. This approach lacks power to identify expression differences
between groups that show high levels of intra-group heterogeneity. The Earth
Mover's Distance (EMD) algorithm instead computes the "work" needed to
transform one distribution into the other, thus providing a metric of the
overall difference in shape between two distributions. Permutation of sample
labels is used to generate q-values for the observed EMD scores.
Author: Daniel Schmolze [aut, cre],
Andrew Beck [aut],
Sheida Nabavi [aut]
Maintainer: Daniel Schmolze
DESCRIPTION | 8 -
MD5 | 28 +--
NAMESPACE | 2
NEWS | 6
R/main.R | 4
build/vignette.rds |binary
inst/doc/EMDomics.R | 128 ++++++++---------
inst/doc/EMDomics.html | 346 +++++++++++++++++++++++-----------------------
man/EMDomics.Rd | 3
man/calculate_emd.Rd | 3
man/calculate_emd_gene.Rd | 3
man/emdomics-package.Rd | 3
man/plot_density.Rd | 3
man/plot_emdnull.Rd | 3
man/plot_perms.Rd | 3
15 files changed, 278 insertions(+), 265 deletions(-)
Title: Error Grid Analysis
Diff between ega versions 1.0.0 dated 2014-11-13 and 1.0.1 dated 2015-02-19
Description: Functions for assigning Clarke or Parkes (Consensus) error grid
zones to blood glucose values, and for plotting both types of error grids.
Author: Daniel Schmolze [aut, cre]
Maintainer: Daniel Schmolze
DESCRIPTION | 6 +++---
MD5 | 23 ++++++++++++-----------
NAMESPACE | 2 +-
NEWS |only
R/ega.R | 18 +++++++++++-------
R/plots.R | 11 ++++++-----
inst/doc/ega.html | 14 +++++++-------
man/ega-package.Rd | 3 ++-
man/getClarkeZones.Rd | 3 ++-
man/getParkesZones.Rd | 3 ++-
man/glucose_data.Rd | 3 ++-
man/plotClarkeGrid.Rd | 3 ++-
man/plotParkesGrid.Rd | 3 ++-
13 files changed, 52 insertions(+), 40 deletions(-)
More information about disparityfilter at CRAN
Permanent link
Title: Geographic Display of Survey Data Statistics
Diff between mapStats versions 1.17 dated 2014-04-14 and 2.3 dated 2015-02-19
Description: Automated calculation and visualization of survey data statistics on a color-coded map.
Author: Samuel Ackerman
Maintainer: Samuel Ackerman
DESCRIPTION | 15 -
INDEX | 4
MD5 | 22 +-
NAMESPACE | 3
R/calcQuantiles.R | 113 --------------
R/calcStats.R | 219 +++++++++++++++++----------
R/mapStats.R | 78 +++------
R/plotStats.R | 374 +++++++++++++++++++++++++++++++++--------------
demo/map_examples.R | 184 +++++++++++++----------
man/mapStats-internal.Rd | 30 ++-
man/mapStats-package.Rd | 15 -
man/mapStats.Rd | 139 +++++++----------
12 files changed, 646 insertions(+), 550 deletions(-)
Title: FeatuRE Selection Algorithms for Computer Aided Diagnosis
Diff between FRESA.CAD versions 1.0 dated 2014-09-11 and 2.0 dated 2015-02-19
Description: Contains a set of utilities for building and testing formula-based models (linear, logistic or COX) for Computer Aided Diagnosis/Prognosis applications. Utilities include data adjustment, univariate analysis, model building, model-validation, longitudinal analysis, reporting and visualization.
Author: Jose Gerardo Tamez-Pena, Antonio Martinez-Torteya and Israel Alanis
Maintainer: Jose Gerardo Tamez-Pena
FRESA.CAD-1.0/FRESA.CAD/R/BootVarNeRIElimination.r |only
FRESA.CAD-1.0/FRESA.CAD/R/boostrapVarElimination.r |only
FRESA.CAD-1.0/FRESA.CAD/data/CancerVarNames.rda |only
FRESA.CAD-1.0/FRESA.CAD/man/bootVarNeRIElimination.Rd |only
FRESA.CAD-2.0/FRESA.CAD/DESCRIPTION | 21
FRESA.CAD-2.0/FRESA.CAD/MD5 | 154 -
FRESA.CAD-2.0/FRESA.CAD/NAMESPACE | 11
FRESA.CAD-2.0/FRESA.CAD/NEWS |only
FRESA.CAD-2.0/FRESA.CAD/R/FRESA.Model.R | 494 ++--
FRESA.CAD-2.0/FRESA.CAD/R/NeRIBasedFRESA.Model.R | 377 +--
FRESA.CAD-2.0/FRESA.CAD/R/ReclassificationFRESA.Model.R | 617 +----
FRESA.CAD-2.0/FRESA.CAD/R/backVarElimination.r | 250 +-
FRESA.CAD-2.0/FRESA.CAD/R/backVarNeRIElimination.r | 32
FRESA.CAD-2.0/FRESA.CAD/R/bootstrapValidation.R | 545 +----
FRESA.CAD-2.0/FRESA.CAD/R/bootstrapValidationNeRI.R | 255 --
FRESA.CAD-2.0/FRESA.CAD/R/bootstrapVarElimination.r | 284 +-
FRESA.CAD-2.0/FRESA.CAD/R/bootstrapVarNeRIElimination.r |only
FRESA.CAD-2.0/FRESA.CAD/R/crossValidationFeatureSelection.R | 1032 ++++------
FRESA.CAD-2.0/FRESA.CAD/R/crossValidationNeRIFeatureSelection.R | 210 +-
FRESA.CAD-2.0/FRESA.CAD/R/featureAdjustment.R | 61
FRESA.CAD-2.0/FRESA.CAD/R/getKNNpredictionFromFormula.r | 22
FRESA.CAD-2.0/FRESA.CAD/R/getVarNeRI.R | 35
FRESA.CAD-2.0/FRESA.CAD/R/getVarReclassification.R | 39
FRESA.CAD-2.0/FRESA.CAD/R/heatMaps.R | 86
FRESA.CAD-2.0/FRESA.CAD/R/improvedResiduals.R | 8
FRESA.CAD-2.0/FRESA.CAD/R/listTopCorrelatedVariables.R | 8
FRESA.CAD-2.0/FRESA.CAD/R/medianPredict.r | 44
FRESA.CAD-2.0/FRESA.CAD/R/modelFitting.R | 96
FRESA.CAD-2.0/FRESA.CAD/R/plot.bootstrapValidation.R | 31
FRESA.CAD-2.0/FRESA.CAD/R/plot.bootstrapValidationNeRI.R |only
FRESA.CAD-2.0/FRESA.CAD/R/plotModels.ROC.R | 31
FRESA.CAD-2.0/FRESA.CAD/R/predictForFresa.R | 26
FRESA.CAD-2.0/FRESA.CAD/R/rankInverseNormalDataFrame.R | 91
FRESA.CAD-2.0/FRESA.CAD/R/reportEquivalentVariables.R | 12
FRESA.CAD-2.0/FRESA.CAD/R/residualtForNeRIs.R | 33
FRESA.CAD-2.0/FRESA.CAD/R/summary.bootstrapValidation.R | 26
FRESA.CAD-2.0/FRESA.CAD/R/summaryReport.r | 2
FRESA.CAD-2.0/FRESA.CAD/R/timeSerieAnalysis.R | 34
FRESA.CAD-2.0/FRESA.CAD/R/uniRankVar.r |only
FRESA.CAD-2.0/FRESA.CAD/R/univariateRankVariables.R | 731 -------
FRESA.CAD-2.0/FRESA.CAD/R/update.uniRankVar.r |only
FRESA.CAD-2.0/FRESA.CAD/R/updateModel.R | 512 ++--
FRESA.CAD-2.0/FRESA.CAD/R/updateNeRImodel.R | 128 -
FRESA.CAD-2.0/FRESA.CAD/data/cancerVarNames.rda |only
FRESA.CAD-2.0/FRESA.CAD/man/CancerVarNames.Rd | 44
FRESA.CAD-2.0/FRESA.CAD/man/FRESA.CAD-package.Rd | 264 +-
FRESA.CAD-2.0/FRESA.CAD/man/FRESA.Model.Rd | 396 +--
FRESA.CAD-2.0/FRESA.CAD/man/NeRIBasedFRESA.Model.Rd | 272 +-
FRESA.CAD-2.0/FRESA.CAD/man/ReclassificationFRESA.Model.Rd | 237 +-
FRESA.CAD-2.0/FRESA.CAD/man/backVarElimination.Rd | 181 +
FRESA.CAD-2.0/FRESA.CAD/man/backVarNeRIElimination.Rd | 187 +
FRESA.CAD-2.0/FRESA.CAD/man/bootstrapValidation.Rd | 292 +-
FRESA.CAD-2.0/FRESA.CAD/man/bootstrapValidationNeRI.Rd | 237 +-
FRESA.CAD-2.0/FRESA.CAD/man/bootstrapVarElimination.Rd | 226 +-
FRESA.CAD-2.0/FRESA.CAD/man/bootstrapVarNeRIElimination.Rd |only
FRESA.CAD-2.0/FRESA.CAD/man/crossValidationFeatureSelection.Rd | 447 ++--
FRESA.CAD-2.0/FRESA.CAD/man/crossValidationNeRIFeatureSelection.Rd | 433 ++--
FRESA.CAD-2.0/FRESA.CAD/man/featureAdjustment.Rd | 146 -
FRESA.CAD-2.0/FRESA.CAD/man/getKNNpredictionFromFormula.Rd | 145 -
FRESA.CAD-2.0/FRESA.CAD/man/getVarNeRI.Rd | 184 +
FRESA.CAD-2.0/FRESA.CAD/man/getVarReclassification.Rd | 176 -
FRESA.CAD-2.0/FRESA.CAD/man/heatMaps.Rd | 189 +
FRESA.CAD-2.0/FRESA.CAD/man/improvedResiduals.Rd | 177 +
FRESA.CAD-2.0/FRESA.CAD/man/listTopCorrelatedVariables.Rd | 128 -
FRESA.CAD-2.0/FRESA.CAD/man/medianPredict.Rd | 186 +
FRESA.CAD-2.0/FRESA.CAD/man/modelFitting.Rd | 120 -
FRESA.CAD-2.0/FRESA.CAD/man/plot.bootstrapValidation.Rd | 121 -
FRESA.CAD-2.0/FRESA.CAD/man/plot.bootstrapValidationNeRI.Rd |only
FRESA.CAD-2.0/FRESA.CAD/man/plotModels.ROC.Rd | 165 -
FRESA.CAD-2.0/FRESA.CAD/man/predictForFresa.Rd | 118 -
FRESA.CAD-2.0/FRESA.CAD/man/rankInverseNormalDataFrame.Rd | 111 -
FRESA.CAD-2.0/FRESA.CAD/man/reportEquivalentVariables.Rd | 159 -
FRESA.CAD-2.0/FRESA.CAD/man/residualForNeRIs.Rd | 123 -
FRESA.CAD-2.0/FRESA.CAD/man/summary.bootstrapValidation.Rd | 129 -
FRESA.CAD-2.0/FRESA.CAD/man/summaryReport.Rd | 162 -
FRESA.CAD-2.0/FRESA.CAD/man/timeSeriesAnalysis.Rd | 173 -
FRESA.CAD-2.0/FRESA.CAD/man/uniRankVar.Rd |only
FRESA.CAD-2.0/FRESA.CAD/man/univariateRankVariables.Rd | 461 ++--
FRESA.CAD-2.0/FRESA.CAD/man/update.uniRankVar.Rd |only
FRESA.CAD-2.0/FRESA.CAD/man/updateModel.Rd | 214 +-
FRESA.CAD-2.0/FRESA.CAD/man/updateNeRImodel.Rd | 236 +-
FRESA.CAD-2.0/FRESA.CAD/src |only
82 files changed, 6463 insertions(+), 6714 deletions(-)
Title: Analysis of Phenotypic, Genotypic and Environmental Data
Diff between EcoGenetics versions 1.0 dated 2015-01-30 and 1.1.0 dated 2015-02-19
Description: Analysis of phenotypic, genotypic and environmental data
with an object of class "ecogen", designed to make easy the
integration of the available information from multiple sources.
Also including geostatistical tools and extra functions.
Author: Leandro Roser, Juan Vilardi, Beatriz Saidman and Laura Ferreyra
Maintainer: Leandro Roser
EcoGenetics-1.0/EcoGenetics/R/auxiliar.R |only
EcoGenetics-1.0/EcoGenetics/R/coordinates.R |only
EcoGenetics-1.0/EcoGenetics/R/eco.R |only
EcoGenetics-1.0/EcoGenetics/R/eco.sortalleles.R |only
EcoGenetics-1.0/EcoGenetics/R/environment.R |only
EcoGenetics-1.0/EcoGenetics/R/genotype.R |only
EcoGenetics-1.0/EcoGenetics/R/phenotype.R |only
EcoGenetics-1.0/EcoGenetics/R/structure.R |only
EcoGenetics-1.0/EcoGenetics/R/tab.R |only
EcoGenetics-1.0/EcoGenetics/man/auxiliar.Rd |only
EcoGenetics-1.0/EcoGenetics/man/eco.lmtree-summary.Rd |only
EcoGenetics-1.0/EcoGenetics/man/eco.sortalleles.Rd |only
EcoGenetics-1.1.0/EcoGenetics/DESCRIPTION | 46
EcoGenetics-1.1.0/EcoGenetics/MD5 | 158 +-
EcoGenetics-1.1.0/EcoGenetics/NAMESPACE | 23
EcoGenetics-1.1.0/EcoGenetics/NEWS |only
EcoGenetics-1.1.0/EcoGenetics/R/ZZZ.R | 2
EcoGenetics-1.1.0/EcoGenetics/R/eco.2columns.R | 109 -
EcoGenetics-1.1.0/EcoGenetics/R/eco.2geneland.R | 99 -
EcoGenetics-1.1.0/EcoGenetics/R/eco.2genepop.R | 186 +-
EcoGenetics-1.1.0/EcoGenetics/R/eco.2gstudio.R | 55
EcoGenetics-1.1.0/EcoGenetics/R/eco.2hierfstat.R | 89 -
EcoGenetics-1.1.0/EcoGenetics/R/eco.NDVI.R | 362 ++---
EcoGenetics-1.1.0/EcoGenetics/R/eco.NDVI.post.R | 300 +---
EcoGenetics-1.1.0/EcoGenetics/R/eco.alfreq.R | 104 -
EcoGenetics-1.1.0/EcoGenetics/R/eco.append.R | 24
EcoGenetics-1.1.0/EcoGenetics/R/eco.association.R | 326 ++--
EcoGenetics-1.1.0/EcoGenetics/R/eco.autocor.R | 629 ++++----
EcoGenetics-1.1.0/EcoGenetics/R/eco.boothet.R | 721 ++++------
EcoGenetics-1.1.0/EcoGenetics/R/eco.cbind.R | 232 +--
EcoGenetics-1.1.0/EcoGenetics/R/eco.char2num.R | 175 --
EcoGenetics-1.1.0/EcoGenetics/R/eco.clear.R | 32
EcoGenetics-1.1.0/EcoGenetics/R/eco.cormantel.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.forestplot.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.geary.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.getisord.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.joincount.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.laglistw.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.lmtree.R | 235 +--
EcoGenetics-1.1.0/EcoGenetics/R/eco.localmoran.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.mantel.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.merge.R | 254 +--
EcoGenetics-1.1.0/EcoGenetics/R/eco.moran.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.order.R | 191 +-
EcoGenetics-1.1.0/EcoGenetics/R/eco.pairtest.R | 30
EcoGenetics-1.1.0/EcoGenetics/R/eco.post.geneland.R | 113 -
EcoGenetics-1.1.0/EcoGenetics/R/eco.rankplot.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.rarefact.R | 315 ++--
EcoGenetics-1.1.0/EcoGenetics/R/eco.rbind.R | 93 -
EcoGenetics-1.1.0/EcoGenetics/R/eco.remove.R | 42
EcoGenetics-1.1.0/EcoGenetics/R/eco.rescale.R | 21
EcoGenetics-1.1.0/EcoGenetics/R/eco.sort.R |only
EcoGenetics-1.1.0/EcoGenetics/R/eco.subset.R | 24
EcoGenetics-1.1.0/EcoGenetics/R/eco.theilsen.R | 203 +-
EcoGenetics-1.1.0/EcoGenetics/R/eco.variogram.R | 119 -
EcoGenetics-1.1.0/EcoGenetics/R/ecogen.definition.R | 667 +++------
EcoGenetics-1.1.0/EcoGenetics/R/latlon2distm.R |only
EcoGenetics-1.1.0/EcoGenetics/R/other.classes.R | 577 ++++----
EcoGenetics-1.1.0/EcoGenetics/man/EcoGenetics-package.Rd | 152 +-
EcoGenetics-1.1.0/EcoGenetics/man/RelDist-methods.Rd | 51
EcoGenetics-1.1.0/EcoGenetics/man/eco.2columns.Rd | 8
EcoGenetics-1.1.0/EcoGenetics/man/eco.2geneland.Rd | 6
EcoGenetics-1.1.0/EcoGenetics/man/eco.2genepop.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.2gstudio.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.2hierfstat.Rd | 2
EcoGenetics-1.1.0/EcoGenetics/man/eco.NDVI.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.NDVI.post.Rd | 2
EcoGenetics-1.1.0/EcoGenetics/man/eco.alfreq.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.append.Rd | 6
EcoGenetics-1.1.0/EcoGenetics/man/eco.association.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.autocor.Rd | 110 -
EcoGenetics-1.1.0/EcoGenetics/man/eco.boothet.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.cbind.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.char2num.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.clear.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.cormantel.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.geary.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.getisord.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.joincount.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.laglistw.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.lmtree.Rd | 2
EcoGenetics-1.1.0/EcoGenetics/man/eco.lmtree.mctree-summary.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.localmoran.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.mantel.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.merge.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.moran.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.order.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.pairtest.Rd | 6
EcoGenetics-1.1.0/EcoGenetics/man/eco.rarefact.Rd | 2
EcoGenetics-1.1.0/EcoGenetics/man/eco.rbind.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.remove.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.rescale.Rd | 2
EcoGenetics-1.1.0/EcoGenetics/man/eco.sort.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/eco.subset.Rd | 4
EcoGenetics-1.1.0/EcoGenetics/man/eco.theilsen.Rd | 2
EcoGenetics-1.1.0/EcoGenetics/man/eco.variogram.Rd | 35
EcoGenetics-1.1.0/EcoGenetics/man/forestplot-methods.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/latlon2distm.Rd |only
EcoGenetics-1.1.0/EcoGenetics/man/rankplot-methods.Rd |only
99 files changed, 3261 insertions(+), 3737 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-02-25 2.55
2009-11-13 2.5
2009-09-23 2.4
2009-07-18 2.3
2009-06-26 2.1
2009-05-17 1.0
Title: Interact with Simile Models
Diff between Simile versions 1.3.2 dated 2015-02-14 and 1.3.3 dated 2015-02-19
Description: Allows a Simile model saved as a compiled binary to be
loaded, parameterized, executed and interrogated. This version works
with Simile v5.97 on.
Author: Simulistics Ltd
Maintainer: Jasper Taylor
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
exec/client5d.tcl | 20 +++++++++++++++-----
man/Simile-package.Rd | 7 +++++--
4 files changed, 27 insertions(+), 14 deletions(-)
Title: Data Augmentation and Multiple Imputation for Interval Censored
Data
Diff between MIICD versions 1.1 dated 2014-04-24 and 2.0 dated 2015-02-19
Description: Implements data augmentation schemes with multiple imputation steps for proportional hazards regression with interval censored data or proportional subdistribution hazards regression for interval censored competing risks data. The main functions allow to estimate survival function, cumulative incidence function, Cox and Fine & Gray regression coefficients and associated variance-covariance matrix. MIICD functions call Surv, survfit and coxph from survival package, FGR from riskRegression package, and mvrnorm from the MASS package.
Author: Marc Delord [aut, cre]
Maintainer: Marc Delord
MIICD-1.1/MIICD/R/get.est.cr.cox.R |only
MIICD-1.1/MIICD/data/bcos.rda |only
MIICD-1.1/MIICD/man/ANDA.coxph.Rd |only
MIICD-1.1/MIICD/man/ANDA.crreg.Rd |only
MIICD-1.1/MIICD/man/PMDA.coxph.Rd |only
MIICD-1.1/MIICD/man/PMDA.crreg.Rd |only
MIICD-1.1/MIICD/man/get.est.FG.Rd |only
MIICD-1.1/MIICD/man/get.est.Rd |only
MIICD-1.1/MIICD/man/get.est.cr.cox.Rd |only
MIICD-1.1/MIICD/man/get.set.Rd |only
MIICD-1.1/MIICD/man/preproc.coxph.Rd |only
MIICD-1.1/MIICD/man/preproc.crreg.Rd |only
MIICD-2.0/MIICD/DESCRIPTION | 21 ++-
MIICD-2.0/MIICD/MD5 | 70 +++++++-----
MIICD-2.0/MIICD/NAMESPACE | 24 +++-
MIICD-2.0/MIICD/R/ANDA.coxph.R | 182 ++++++++++++++++----------------
MIICD-2.0/MIICD/R/ANDA.crreg.R | 164 ++++++++++++++--------------
MIICD-2.0/MIICD/R/DA.ci.R |only
MIICD-2.0/MIICD/R/DA.surv.R |only
MIICD-2.0/MIICD/R/ICCRD.R |only
MIICD-2.0/MIICD/R/MI.ci.R |only
MIICD-2.0/MIICD/R/MI.surv.R |only
MIICD-2.0/MIICD/R/MIICD.coxph.R | 138 ++++++++++++++++++++----
MIICD-2.0/MIICD/R/MIICD.crreg.R | 154 +++++++++++++++++++++------
MIICD-2.0/MIICD/R/PMDA.coxph.R | 143 ++++++++++++++-----------
MIICD-2.0/MIICD/R/PMDA.crreg.R | 145 ++++++++++++++-----------
MIICD-2.0/MIICD/R/bcos.R |only
MIICD-2.0/MIICD/R/get.est.FG.R | 26 +---
MIICD-2.0/MIICD/R/get.est.R | 12 --
MIICD-2.0/MIICD/R/get.set.R | 11 +
MIICD-2.0/MIICD/R/get_est_mi.R |only
MIICD-2.0/MIICD/R/get_est_mi_surv.R |only
MIICD-2.0/MIICD/R/get_values_at_time.R |only
MIICD-2.0/MIICD/R/get_z.R |only
MIICD-2.0/MIICD/R/post_point_est_CI.R |only
MIICD-2.0/MIICD/R/preproc.coxph.R | 10 -
MIICD-2.0/MIICD/R/preproc.crreg.R | 12 --
MIICD-2.0/MIICD/data/BCOS.rda |only
MIICD-2.0/MIICD/data/ICCRD.rda |only
MIICD-2.0/MIICD/man/DA.ci.Rd |only
MIICD-2.0/MIICD/man/DA.surv.Rd |only
MIICD-2.0/MIICD/man/ICCRD.Rd |only
MIICD-2.0/MIICD/man/MI.ci.Rd |only
MIICD-2.0/MIICD/man/MI.surv.Rd |only
MIICD-2.0/MIICD/man/MIICD-package.Rd | 52 +++++----
MIICD-2.0/MIICD/man/MIICD.coxph.Rd | 104 ++++++++++--------
MIICD-2.0/MIICD/man/MIICD.crreg.Rd | 127 ++++++++++++++--------
MIICD-2.0/MIICD/man/bcos.Rd | 39 +++---
MIICD-2.0/MIICD/man/plot.DA_ci.Rd |only
MIICD-2.0/MIICD/man/plot.DA_surv.Rd |only
MIICD-2.0/MIICD/man/plot.MIICD_coxph.Rd |only
MIICD-2.0/MIICD/man/plot.MIICD_crreg.Rd |only
MIICD-2.0/MIICD/man/plot.MI_ci.Rd |only
MIICD-2.0/MIICD/man/plot.MI_surv.Rd |only
54 files changed, 867 insertions(+), 567 deletions(-)
Title: Dynamic Generation of Scientific Reports
Diff between R.rsp versions 0.19.0 dated 2014-06-08 and 0.20.0 dated 2015-02-19
Description: The RSP markup language makes any text-based document come alive. RSP provides a powerful markup for controlling the content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr documents (and more), e.g. 'Today's date is <%=Sys.Date()%>'. Contrary to many other literate programming languages, with RSP it is straightforward to loop over mixtures of code and text sections, e.g. in month-by-month summaries. RSP has also several preprocessing directives for incorporating static and dynamic contents of external files (local or online) among other things. Functions rstring() and rcat() make it easy to process RSP strings, rsource() sources an RSP file as it was an R script, while rfile() compiles it (even online) into its final output format, e.g. rfile('report.tex.rsp') generates 'report.pdf' and rfile('report.md.rsp') generates 'report.html'. RSP is ideal for self-contained scientific reports and R package vignettes. It's easy to use - if you know how to write an R script, you'll be up and running within minutes.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson
R.rsp-0.19.0/R.rsp/R/captureViaRaw.R |only
R.rsp-0.19.0/R.rsp/inst/doc/RSP-intro.html |only
R.rsp-0.19.0/R.rsp/inst/doc/RSP-intro.md.rsp |only
R.rsp-0.19.0/R.rsp/inst/doc/RSP-refcard.pdf |only
R.rsp-0.19.0/R.rsp/inst/doc/RSP-refcard.tex.rsp |only
R.rsp-0.19.0/R.rsp/man/getAttributes.RspObject.Rd |only
R.rsp-0.19.0/R.rsp/man/getMetadata.RspDocument.Rd |only
R.rsp-0.19.0/R.rsp/man/getMetadata.RspProduct.Rd |only
R.rsp-0.19.0/R.rsp/man/getMetadata.RspString.Rd |only
R.rsp-0.19.0/R.rsp/vignettes/RSP-intro.md.rsp |only
R.rsp-0.19.0/R.rsp/vignettes/RSP-refcard.tex.rsp |only
R.rsp-0.20.0/R.rsp/DESCRIPTION | 19
R.rsp-0.20.0/R.rsp/MD5 | 257 ++++---
R.rsp-0.20.0/R.rsp/NAMESPACE | 241 ++++++
R.rsp-0.20.0/R.rsp/NEWS | 85 ++
R.rsp-0.20.0/R.rsp/R/006.fixVarArgs.R | 7
R.rsp-0.20.0/R.rsp/R/999.NonDocumentedObjects.R | 1
R.rsp-0.20.0/R.rsp/R/999.RRspPackage.R | 6
R.rsp-0.20.0/R.rsp/R/999.package.R | 1
R.rsp-0.20.0/R.rsp/R/FileRspResponse.R | 4
R.rsp-0.20.0/R.rsp/R/HttpDaemon.R | 4
R.rsp-0.20.0/R.rsp/R/HttpDaemonRspResponse.R | 4
R.rsp-0.20.0/R.rsp/R/RspDirective,COPY-PASTE.R |only
R.rsp-0.20.0/R.rsp/R/RspDirective,IF-THEN-ELSE.R | 25
R.rsp-0.20.0/R.rsp/R/RspDirective.R | 106 ++-
R.rsp-0.20.0/R.rsp/R/RspDocument.R | 346 ++++++----
R.rsp-0.20.0/R.rsp/R/RspException.R | 4
R.rsp-0.20.0/R.rsp/R/RspFileProduct.R | 40 +
R.rsp-0.20.0/R.rsp/R/RspObject.R | 95 --
R.rsp-0.20.0/R.rsp/R/RspParser.R | 13
R.rsp-0.20.0/R.rsp/R/RspProduct.R | 61 -
R.rsp-0.20.0/R.rsp/R/RspRSourceCode.R | 2
R.rsp-0.20.0/R.rsp/R/RspRSourceCodeFactory.R | 8
R.rsp-0.20.0/R.rsp/R/RspResponse.R | 2
R.rsp-0.20.0/R.rsp/R/RspString.R | 58 -
R.rsp-0.20.0/R.rsp/R/RspVoid.R |only
R.rsp-0.20.0/R.rsp/R/attributes.R |only
R.rsp-0.20.0/R.rsp/R/buildNonSweaveVignette.R | 2
R.rsp-0.20.0/R.rsp/R/compileAsciiDocNoweb.R | 2
R.rsp-0.20.0/R.rsp/R/compileKnitr.R | 2
R.rsp-0.20.0/R.rsp/R/compileLaTeX.R | 20
R.rsp-0.20.0/R.rsp/R/compileMarkdown.R | 37 -
R.rsp-0.20.0/R.rsp/R/epsDev.DEPRECATED.R | 36 -
R.rsp-0.20.0/R.rsp/R/indexOfNonQuoted.R | 12
R.rsp-0.20.0/R.rsp/R/parseInternetMediaType.R | 2
R.rsp-0.20.0/R.rsp/R/parseRVignetteMetadata.R | 53 -
R.rsp-0.20.0/R.rsp/R/rcat.R | 33
R.rsp-0.20.0/R.rsp/R/rfile.R | 10
R.rsp-0.20.0/R.rsp/R/rsptex.R | 2
R.rsp-0.20.0/R.rsp/R/translateRsp.R | 5
R.rsp-0.20.0/R.rsp/R/translateRspV1.R | 6
R.rsp-0.20.0/R.rsp/R/xweavetangle.R | 193 ++---
R.rsp-0.20.0/R.rsp/R/zzz.CmdArgsFunctions.R |only
R.rsp-0.20.0/R.rsp/R/zzz.R | 23
R.rsp-0.20.0/R.rsp/build/vignette.rds |binary
R.rsp-0.20.0/R.rsp/exec |only
R.rsp-0.20.0/R.rsp/inst/doc/Dynamic_document_creation_using_RSP.pdf |binary
R.rsp-0.20.0/R.rsp/inst/doc/Dynamic_document_creation_using_RSP.tex.rsp | 153 ++--
R.rsp-0.20.0/R.rsp/inst/doc/RSP_intro.html |only
R.rsp-0.20.0/R.rsp/inst/doc/RSP_intro.md.rsp |only
R.rsp-0.20.0/R.rsp/inst/doc/RSP_refcard.pdf |only
R.rsp-0.20.0/R.rsp/inst/doc/RSP_refcard.tex.rsp |only
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-LaTeX_vignettes.ltx |only
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-LaTeX_vignettes.pdf |only
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-RSP_vignettes.html | 35 -
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-RSP_vignettes.md.rsp | 19
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-Static_PDF_and_HTML_vignettes.pdf |binary
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-Static_PDF_and_HTML_vignettes.pdf.asis | 4
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-Vignettes_prior_to_R300.pdf |binary
R.rsp-0.20.0/R.rsp/inst/doc/R_packages-Vignettes_prior_to_R300.tex.rsp | 9
R.rsp-0.20.0/R.rsp/inst/doc/templates/,install_extras | 2
R.rsp-0.20.0/R.rsp/inst/doc/templates/Makefile | 7
R.rsp-0.20.0/R.rsp/inst/doc/templates/enginesMap.R | 2
R.rsp-0.20.0/R.rsp/inst/rsp/src/simpleFooter.html.rsp | 2
R.rsp-0.20.0/R.rsp/inst/rsp_LoremIpsum/LoremIpsum.asciidoc.Rnw | 1
R.rsp-0.20.0/R.rsp/inst/rsp_LoremIpsum/LoremIpsum.knitr.Rnw.rsp | 2
R.rsp-0.20.0/R.rsp/inst/rsp_encodings |only
R.rsp-0.20.0/R.rsp/inst/rsp_examples/LoremIpsum.tex.rsp | 5
R.rsp-0.20.0/R.rsp/inst/rsp_examples/R_packages-Static_PDF_and_HTML_vignettes.pdf.asis.rsp | 3
R.rsp-0.20.0/R.rsp/inst/rsp_examples/R_packages-Static_PDF_and_HTML_vignettes.tex.rsp | 7
R.rsp-0.20.0/R.rsp/inst/rsp_tests/R-vignette.tex.rsp | 5
R.rsp-0.20.0/R.rsp/inst/rsp_tests/cutnpaste.txt.rsp |only
R.rsp-0.20.0/R.rsp/inst/rsp_tests/ifdef.R | 3
R.rsp-0.20.0/R.rsp/inst/rsp_tests/ifdef.R.rsp | 5
R.rsp-0.20.0/R.rsp/inst/rsp_tests/numerics.txt |only
R.rsp-0.20.0/R.rsp/inst/rsp_tests/numerics.txt.rsp |only
R.rsp-0.20.0/R.rsp/inst/rsp_tests/strings.txt | 54 +
R.rsp-0.20.0/R.rsp/inst/rsp_tests/strings.txt.rsp | 54 +
R.rsp-0.20.0/R.rsp/inst/rsp_tests/trimming-4.txt.rsp |only
R.rsp-0.20.0/R.rsp/inst/tcl/r-httpd.tcl | 4
R.rsp-0.20.0/R.rsp/man/Non-documented_objects.Rd | 1
R.rsp-0.20.0/R.rsp/man/R.rsp-package.Rd | 7
R.rsp-0.20.0/R.rsp/man/RRspPackage.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspCode.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspCodeChunk.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspComment.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspConstruct.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspCutDirective.Rd |only
R.rsp-0.20.0/R.rsp/man/RspDirective.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspDocument.Rd | 5
R.rsp-0.20.0/R.rsp/man/RspErrorDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspEvalDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspException.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspExpression.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspFileProduct.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspIfDirective.Rd | 48 -
R.rsp-0.20.0/R.rsp/man/RspIncludeDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspMetaDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspObject.Rd | 7
R.rsp-0.20.0/R.rsp/man/RspPageDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspProduct.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspRSourceCode.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspShSourceCode.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspSourceCode.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspString.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspStringProduct.Rd | 4
R.rsp-0.20.0/R.rsp/man/RspText.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspUnknownDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspUnparsedDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspUnparsedExpression.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspVariableDirective.Rd | 2
R.rsp-0.20.0/R.rsp/man/RspVoid.Rd |only
R.rsp-0.20.0/R.rsp/man/buildNonSweaveTexToPdf.Rd | 2
R.rsp-0.20.0/R.rsp/man/compileLaTeX.Rd | 11
R.rsp-0.20.0/R.rsp/man/compileMarkdown.Rd | 5
R.rsp-0.20.0/R.rsp/man/getAttributes.default.Rd |only
R.rsp-0.20.0/R.rsp/man/preprocess.RspDocument.Rd | 11
R.rsp-0.20.0/R.rsp/man/rargs.Rd | 2
R.rsp-0.20.0/R.rsp/man/rfile.Rd | 6
R.rsp-0.20.0/R.rsp/tests/000.session_information.R |only
R.rsp-0.20.0/R.rsp/tests/RspConstruct.R |only
R.rsp-0.20.0/R.rsp/tests/RspProduct.R |only
R.rsp-0.20.0/R.rsp/tests/RspString.R |only
R.rsp-0.20.0/R.rsp/tests/capabilities.R | 6
R.rsp-0.20.0/R.rsp/tests/deparse.R | 7
R.rsp-0.20.0/R.rsp/tests/rclean.R |only
R.rsp-0.20.0/R.rsp/tests/rcompile.R | 2
R.rsp-0.20.0/R.rsp/tests/rscript.R | 34
R.rsp-0.20.0/R.rsp/tests/wstring.R |only
R.rsp-0.20.0/R.rsp/vignettes/Dynamic_document_creation_using_RSP.tex.rsp | 153 ++--
R.rsp-0.20.0/R.rsp/vignettes/RSP_intro.md.rsp |only
R.rsp-0.20.0/R.rsp/vignettes/RSP_refcard.tex.rsp |only
R.rsp-0.20.0/R.rsp/vignettes/R_packages-LaTeX_vignettes.ltx |only
R.rsp-0.20.0/R.rsp/vignettes/R_packages-RSP_vignettes.md.rsp | 19
R.rsp-0.20.0/R.rsp/vignettes/R_packages-Static_PDF_and_HTML_vignettes.pdf.asis | 4
R.rsp-0.20.0/R.rsp/vignettes/R_packages-Vignettes_prior_to_R300.tex.rsp | 9
146 files changed, 1629 insertions(+), 983 deletions(-)
Title: Statistical Methods for the Randomized Response Technique
Diff between rr versions 1.0 dated 2015-02-07 and 1.1 dated 2015-02-19
Description: Enables researchers to conduct multivariate statistical analyses of survey data with randomized response technique items from several designs, including mirrored question, forced question, and unrelated question. This includes regression with the randomized response as the outcome and logistic regression with the randomized response item as a predictor. In addition, tools for conducting power analysis for designing randomized response items are included. The package implements methods described in Blair, Imai, and Zhou (2015) ''Design and Analysis of the Randomized Response Technique,'' Working paper available at
Author: Graeme Blair
Maintainer: Graeme Blair
ChangeLog | 1
DESCRIPTION | 8
MD5 | 15
NAMESPACE | 2
R/power.R | 851 +++++++++++++++++++++++++++------------------------
inst/CITATION | 16
man/power.rr.plot.Rd |only
man/power.rr.test.Rd | 228 ++++++-------
man/rr-package.Rd | 6
9 files changed, 605 insertions(+), 522 deletions(-)
Title: Floating Grid Permutation Technique
Diff between fgpt versions 2.2 dated 2015-02-18 and 2.3 dated 2015-02-19
Description: A permutation technique to explore and control for spatial autocorrelation. This package contains low level functions for performing permutations and calculating statistics as well as higher level functions. Higher level functions are an easy to use function for performing spatially restricted permutation tests and summarize and plot results.
Author: Reinder Radersma & Ben Sheldon
Maintainer: Reinder Radersma
DESCRIPTION | 12
MD5 | 22 -
inst/doc/intro-fgpt.R | 3
inst/doc/intro-fgpt.Rnw | 1006 +++++++++++++++++++++++------------------------
inst/doc/intro-fgpt.pdf |binary
man/Gpulex.Rd | 2
man/Pmajor.Rd | 2
man/fgeasy.Rd | 2
man/fgperm.Rd | 2
man/fgpt-package.Rd | 2
man/fgstat.Rd | 2
vignettes/intro-fgpt.Rnw | 1006 +++++++++++++++++++++++------------------------
12 files changed, 1030 insertions(+), 1031 deletions(-)
Title: Functions for the Book "An Introduction to the Bootstrap"
Diff between bootstrap versions 2014.4 dated 2014-04-27 and 2015.2 dated 2015-02-19
Description: Software (bootstrap, cross-validation, jackknife) and data
for the book "An Introduction to the Bootstrap" by B. Efron and
R. Tibshirani, 1993, Chapman and Hall.
_____________________________________________________________
This package is primarily provided for projects already based
on it, and for support of the book. New projects should
preferentially use the recommended package "boot".
Author: S original, from StatLib, by Rob Tibshirani. R port by
Friedrich Leisch.
Maintainer: Scott Kostyshak
DESCRIPTION | 8 ++++----
MD5 | 11 ++++++-----
NEWS | 22 ++++++++++++++++++----
R/bcanon.R | 11 +++++++++--
man/bcanon.Rd | 2 +-
man/scor.Rd | 2 +-
tests |only
7 files changed, 39 insertions(+), 17 deletions(-)
Title: Bayesian Inference for Beta Regression and Zero/One Inflated
Beta Regression
Diff between zoib versions 1.1 dated 2015-02-01 and 1.2 dated 2015-02-18
Description: Fits beta regression and zero/one inflated beta regression and obtains Bayesian Inference of the model via the Markov Chain Monte Carlo approach implemented in JAGS.
Author: Fang Liu
Maintainer: Fang Liu
DESCRIPTION | 15 +++----
MD5 | 90 +++++++++++++++++++++---------------------
NAMESPACE | 2
R/check.psrf.R | 37 ++++-------------
R/joint.1z.R | 6 +-
R/joint.1z0.R | 6 +-
R/joint.1z01.R | 6 +-
R/joint.1z1.R | 6 +-
R/joint.2z.R | 8 +--
R/joint.2z0.R | 8 +--
R/joint.2z01.R | 8 +--
R/joint.2z1.R | 8 +--
R/paraplot.R |only
R/sep.1z.R | 6 +-
R/sep.1z0.R | 6 +-
R/sep.1z01.R | 7 +--
R/sep.1z1.R | 6 +-
R/sep.2z.R | 10 ++--
R/sep.2z0.R | 8 +--
R/sep.2z01.R | 8 +--
R/sep.2z1.R | 9 +---
R/zoib.R | 32 ++-------------
data/AlcoholUse.rda |binary
data/BiRepeated.rda |binary
data/GasolineYield.rda |binary
inst/bugs/sep_2z.bug | 1
man/AlcoholUse.Rd | 52 ++++++++++++------------
man/BiRepeated.Rd | 53 ++++++++++--------------
man/GasolineYield.Rd | 45 +++++++++------------
man/check.psrf.Rd | 24 +++--------
man/joint.1z0.Rd | 2
man/joint.1z1.Rd | 6 +-
man/joint.2z01.Rd | 2
man/joint.2z1.Rd | 4 -
man/paraplot.Rd |only
man/sep.1z.Rd | 4 -
man/sep.1z0.Rd | 4 -
man/sep.1z01.Rd | 4 -
man/sep.1z1.Rd | 4 -
man/sep.2z.Rd | 4 -
man/sep.2z0.Rd | 4 -
man/sep.2z01.Rd | 4 -
man/sep.2z1.Rd | 4 -
man/zoib-package.Rd | 19 +++++---
man/zoib.Rd | 104 ++++++++++++++++++-------------------------------
tests/test1.R | 4 -
tests/test2.R | 14 +++---
47 files changed, 288 insertions(+), 366 deletions(-)
Title: Blinder-Oaxaca Decomposition
Diff between oaxaca versions 0.1 dated 2014-11-20 and 0.1.2 dated 2015-02-18
Description: An implementation of the Blinder-Oaxaca decomposition for linear regression models.
Author: Marek Hlavac
Maintainer: Marek Hlavac
DESCRIPTION | 10 +++++-----
MD5 | 32 ++++++++++++++++----------------
NAMESPACE | 6 ++++--
R/oaxaca-internal.R | 4 ++--
build/vignette.rds |binary
inst/CITATION | 6 +++---
inst/ChangeLog | 6 +++++-
inst/doc/oaxaca.Rtex | 43 +++++++++++++++++++------------------------
inst/doc/oaxaca.pdf |binary
man/oaxaca.Rd | 4 ++--
man/plot.oaxaca.Rd | 4 ++--
vignettes/figure1.pdf |binary
vignettes/figure2.pdf |binary
vignettes/figure3.pdf |binary
vignettes/figure4.pdf |binary
vignettes/oaxaca.Rtex | 43 +++++++++++++++++++------------------------
vignettes/oaxaca.bib | 10 +++++-----
17 files changed, 82 insertions(+), 86 deletions(-)
Title: Random Cluster Generation (with Specified Degree of Separation)
Diff between clusterGeneration versions 1.3.1 dated 2013-01-08 and 1.3.4 dated 2015-02-18
More information about clusterGeneration at CRAN
Description: We developed the clusterGeneration package to provide functions
for generating random clusters, generating random
covariance/correlation matrices,
calculating a separation index (data and population version)
for pairs of clusters or cluster distributions, and 1-D and 2-D
projection plots to visualize clusters. The package also
contains a function to generate random clusters based on
factorial designs with factors such as degree of separation,
number of clusters, number of variables, number of noisy
variables.
Author: Weiliang Qiu
Maintainer: Weiliang Qiu
DESCRIPTION | 16 +++++++++-------
MD5 | 6 +++---
NEWS | 7 +++++++
R/separation.R | 4 ++--
4 files changed, 21 insertions(+), 12 deletions(-)
Permanent link
Title: Clustering Method Based on Local Shrinking
Diff between clues versions 0.5-4 dated 2014-05-21 and 0.5.6 dated 2015-02-18
Description: We developed the clues R package to provide functions
for automatically estimating the number of clusters and
getting the final cluster partition without any input
parameter except the stopping rule for convergence.
The package also provides functions to
evaluate and compare the performances of partitions of a data
set both numerically and graphically.
Author: Fang Chang
Maintainer: Weiliang Qiu
DESCRIPTION | 17 +++++++++--------
MD5 | 11 ++++++-----
NEWS |only
R/clues.R | 17 ++++++++++++-----
R/clues_CH.R | 31 +++++++++++++++++++++++--------
R/clues_sil.R | 30 ++++++++++++++++++++++--------
man/clues.Rd | 2 +-
7 files changed, 73 insertions(+), 35 deletions(-)
Title: Convert Statistical Analysis Objects into Tidy Data Frames
Diff between broom versions 0.3.5 dated 2015-01-05 and 0.3.6 dated 2015-02-18
Description: Convert statistical analysis objects from R into tidy data frames,
so that they can more easily be combined, reshaped and otherwise processed
with tools like dplyr, tidyr and ggplot2. The package provides three S3
generics: tidy, which summarizes a model's statistical findings such as
coefficients of a regression; augment, which adds columns to the original
data such as predictions, residuals and cluster assignments; and glance,
which provides a one-row summary of model-level statistics.
Author: David Robinson [aut, cre],
Matthieu Gomez [ctb],
Boris Demeshev [ctb],
Hadley Wickham [ctb]
Maintainer: David Robinson
DESCRIPTION | 24 ++++++++++++------------
MD5 | 24 +++++++++++++-----------
NAMESPACE | 3 +++
R/anova_tidiers.R | 40 +++++++++++++++++++++++++++++++++++++---
R/globals.R | 2 +-
R/lm_tidiers.R | 4 +++-
R/matrix_tidiers.R |only
R/stats_tidiers.R | 14 +++++++++-----
inst/doc/bootstrapping.html | 2 +-
inst/doc/broom_and_dplyr.html | 2 +-
inst/doc/kmeans.html | 6 +++---
man/anova_tidiers.Rd | 15 ++++++++++++++-
man/matrix_tidiers.Rd |only
man/tidy.pairwise.htest.Rd | 7 +++++--
14 files changed, 102 insertions(+), 41 deletions(-)
Title: Probabilistic Suffix Trees and Variable Length Markov Chains
Diff between PST versions 0.84.1 dated 2013-12-20 and 0.86 dated 2015-02-18
Description: Provides a framework for analysing state sequences with probabilistic suffix trees (PST), the construction that stores variable length Markov chains (VLMC). Besides functions for learning and optimizing VLMC models, the PST library includes many additional tools to analyse sequence data with these models: visualization tools, functions for sequence prediction and artificial sequences generation, as well as for context and pattern mining. The package is specifically adapted to the field of social sciences by allowing to learn VLMC models from sets of individual sequences possibly containing missing values, and by accounting for case weights. The library also allows to compute probabilistic divergence between two models, and to fit segmented VLMC, where sub-models fitted to distinct strata of the learning sample are stored in a single PST. This software results from research work executed within the framework of the Swiss National Centre of Competence in Research LIVES, which is financed by the Swiss National Science Foundation. The authors are grateful to the Swiss National Science Foundation for its financial support.
Author: Alexis Gabadinho [aut, cre, cph]
Maintainer: Alexis Gabadinho
DESCRIPTION | 22 ++++++++++++----------
MD5 | 38 +++++++++++++++++++-------------------
NAMESPACE | 2 +-
NEWS | 12 ++++++++++++
R/PSTf-functions.R | 11 +++++++++++
R/cprob.R | 12 +++++++-----
R/generate.R | 34 ++++++++++++++++++++++------------
R/plotNode.R | 28 +++++-----------------------
R/prune.R | 12 +++---------
R/pstree.R | 13 ++++---------
data/SRH.RData |binary
data/s1.rda |binary
man/PSTf-class.Rd | 2 +-
man/PSTr-class.Rd | 4 ++--
man/SRH-data.Rd | 2 +-
man/cprob.Rd | 2 +-
man/generate.Rd | 7 +++++--
man/nobs.Rd | 2 +-
man/prune.Rd | 3 ++-
man/pstree.Rd | 13 +++++++------
20 files changed, 116 insertions(+), 103 deletions(-)
Title: Simultaneous Inference in General Parametric Models
Diff between multcomp versions 1.3-8 dated 2014-12-01 and 1.3-9 dated 2015-02-18
Description: Simultaneous tests and confidence intervals
for general linear hypotheses in parametric models, including
linear, generalized linear, linear mixed effects, and survival models.
The package includes demos reproducing analyzes presented
in the book "Multiple Comparisons Using R" (Bretz, Hothorn,
Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre],
Frank Bretz [aut],
Peter Westfall [aut],
Richard M. Heiberger [ctb],
Andre Schuetzenmeister [ctb]
Maintainer: Torsten Hothorn
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
R/expressions.R | 2 +-
R/helpers.R | 9 ++++++---
inst/NEWS | 5 +++++
inst/doc/chfls1.pdf |binary
inst/doc/generalsiminf.pdf |binary
inst/doc/multcomp-examples.pdf |binary
8 files changed, 23 insertions(+), 15 deletions(-)
Title: A Laboratory for Recursive Partytioning
Diff between party versions 1.0-19 dated 2014-12-18 and 1.0-20 dated 2015-02-18
Description: A computational toolbox for recursive partitioning.
The core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems, including
nominal, ordinal, numeric, censored as well as multivariate response
variables and arbitrary measurement scales of the covariates.
Based on conditional inference trees, cforest() provides an
implementation of Breiman's random forests. The function mob()
implements an algorithm for recursive partitioning based on
parametric models (e.g. linear models, GLMs or survival
regression) employing parameter instability tests for split
selection. Extensible functionality for visualizing tree-structured
regression models is available.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut],
Carolin Strobl [aut],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn
DESCRIPTION | 11 ++++++-----
MD5 | 10 +++++-----
NAMESPACE | 2 +-
inst/NEWS | 5 +++++
inst/doc/MOB.pdf |binary
inst/doc/party.pdf |binary
6 files changed, 17 insertions(+), 11 deletions(-)
Title: Regression Models with Breakpoints/Changepoints Estimation
Diff between segmented versions 0.5-1.0 dated 2014-12-12 and 0.5-1.1 dated 2015-02-18
Description: Given a regression model, segmented `updates' the model by adding one or more segmented (i.e., piecewise-linear) relationships. Several variables with multiple breakpoints are allowed.
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo
segmented |only
1 file changed
Title: Medical Image Registration Using the NiftyReg Library
Diff between RNiftyReg versions 1.1.2 dated 2013-11-07 and 1.1.3 dated 2015-02-18
Description: Provides an R interface to the NiftyReg image registration tools
Author: Jon Clayden, based on original code by Marc Modat and Pankaj Daga
Maintainer: Jon Clayden
DESCRIPTION | 17 +++++++++--------
MD5 | 14 +++++++-------
NEWS | 7 +++++++
R/transform.R | 6 ++----
src/_reg_localTransformation_be.cpp | 4 ++++
src/_reg_localTransformation_jac.cpp | 4 ++++
src/_reg_tools.cpp | 12 ++++++++++++
src/niftyreg.cpp | 12 ++++++++----
8 files changed, 53 insertions(+), 23 deletions(-)
Title: Multitaper Spectral Analysis Tools
Diff between multitaper versions 1.0-9 dated 2014-12-13 and 1.0-10 dated 2015-02-18
Description: Implements multitaper spectral analysis using discrete prolate spheroidal sequences (Slepians) and sine tapers. It includes an adaptive weighted multitaper spectral estimate, a coherence estimate, Thomson's Harmonic F-test, and complex demodulation. The Slepians sequences are generated efficiently using a tridiagonal matrix solution, and jackknifed confidence intervals are available for most estimates.
Author: Karim Rahim
Maintainer: Karim Rahim
DESCRIPTION | 8 ++++----
MD5 | 24 ++++++++++++------------
NAMESPACE | 1 +
R/demod.R | 3 ++-
R/multitaper.R | 33 +++++++++++++++------------------
R/plots.R | 22 ++++++++++++----------
R/plotsHelper.R | 18 +++++++++++-------
man/mtm.coh.Rd | 3 ++-
man/plot.mtm.coh.Rd | 5 +++++
src/Makevars | 12 ++++++------
src/djt.f | 14 ++++++--------
src/dpss.f90 | 14 +++++++-------
src/sine.f | 19 ++++++++-----------
13 files changed, 91 insertions(+), 85 deletions(-)
More information about MortalitySmooth at CRAN
Permanent link
Title: Probabilistic Forecasting using Ensembles and Bayesian Model
Averaging
Diff between ensembleBMA versions 5.0.8 dated 2014-04-14 and 5.1 dated 2015-02-18
Description: Bayesian Model Averaging to create probabilistic forecasts
from ensemble forecasts and weather observations.
Author: Chris Fraley, Adrian E. Raftery, J. McLean Sloughter, Tilmann
Gneiting, University of Washington.
Maintainer: Chris Fraley
CHANGELOG | 5 +++
DESCRIPTION | 8 +++---
MD5 | 26 ++++++++++----------
NAMESPACE | 62 ++++++++++++++++++++++++++++++++++++++++++++++++
R/controlBMAgamma.R | 5 ++-
R/controlBMAgamma0.R | 5 ++-
R/controlBMAnormal.R | 2 -
R/dataNA.ensembleData.R | 2 -
R/ensembleBMAnormal.R | 3 +-
R/fitBMAgamma.R | 12 ++++++---
R/fitBMAgamma0.R | 8 +++++-
R/plotProbcast.R | 16 ++++++------
man/controlBMAgamma.Rd | 14 ++++++++--
man/controlBMAgamma0.Rd | 10 ++++++-
14 files changed, 137 insertions(+), 41 deletions(-)
Title: Finnish Open Government Data Toolkit
Diff between sorvi versions 0.6.23 dated 2014-06-03 and 0.7.20 dated 2015-02-17
Description: Algorithms for Finnish open government data.
Author: Leo Lahti, Juuso Parkkinen, Joona Lehtomaki, Juuso Haapanen, Jussi
Paananen, Einari Happonen
Maintainer: Leo Lahti
sorvi-0.6.23/sorvi/man/get_municipality_info_statfi.Rd |only
sorvi-0.7.20/sorvi/DESCRIPTION | 21
sorvi-0.7.20/sorvi/MD5 | 67 -
sorvi-0.7.20/sorvi/NAMESPACE | 5
sorvi-0.7.20/sorvi/R/firstlib.R | 15
sorvi-0.7.20/sorvi/R/provinceinfo.R | 76 -
sorvi-0.7.20/sorvi/R/visualization.R | 3
sorvi-0.7.20/sorvi/README.md | 5
sorvi-0.7.20/sorvi/build/vignette.rds |binary
sorvi-0.7.20/sorvi/inst/doc/sorvi.Rnw |only
sorvi-0.7.20/sorvi/inst/doc/sorvi.pdf |only
sorvi-0.7.20/sorvi/inst/doc/sorvi_tutorial.R | 107 +-
sorvi-0.7.20/sorvi/inst/doc/sorvi_tutorial.Rmd | 85 +-
sorvi-0.7.20/sorvi/inst/doc/sorvi_tutorial.html | 592 ++++++---------
sorvi-0.7.20/sorvi/man/convert_municipality_codes.Rd | 3
sorvi-0.7.20/sorvi/man/convert_municipality_names.Rd | 3
sorvi-0.7.20/sorvi/man/fi.en.maakunnat.Rd | 3
sorvi-0.7.20/sorvi/man/get_municipality_info_mml.Rd | 13
sorvi-0.7.20/sorvi/man/get_postal_code_info.Rd | 3
sorvi-0.7.20/sorvi/man/get_province_info_wikipedia.Rd | 3
sorvi-0.7.20/sorvi/man/hetu.Rd | 3
sorvi-0.7.20/sorvi/man/is_url.Rd | 3
sorvi-0.7.20/sorvi/man/korvaa_skandit.Rd | 3
sorvi-0.7.20/sorvi/man/load_sorvi_data.Rd | 3
sorvi-0.7.20/sorvi/man/municipality_to_province.Rd | 5
sorvi-0.7.20/sorvi/man/regression_plot.Rd | 5
sorvi-0.7.20/sorvi/man/ropengov_storage_path.Rd | 3
sorvi-0.7.20/sorvi/man/sorvi-package.Rd | 3
sorvi-0.7.20/sorvi/man/strip.Rd | 3
sorvi-0.7.20/sorvi/man/strstrip.Rd | 3
sorvi-0.7.20/sorvi/man/strstrip_single.Rd | 3
sorvi-0.7.20/sorvi/man/valid_hetu.Rd | 3
sorvi-0.7.20/sorvi/vignettes/TODO.Rmd |only
sorvi-0.7.20/sorvi/vignettes/figure/regressionline-1.png |only
sorvi-0.7.20/sorvi/vignettes/figure/regressionline.png |binary
sorvi-0.7.20/sorvi/vignettes/sorvi.Rnw |only
sorvi-0.7.20/sorvi/vignettes/sorvi_tutorial.Rmd | 85 +-
sorvi-0.7.20/sorvi/vignettes/sorvi_tutorial.md |only
38 files changed, 489 insertions(+), 640 deletions(-)
Title: Data Exchange Between R and LabKey Server
Diff between Rlabkey versions 2.1.126 dated 2014-12-17 and 2.1.127 dated 2015-02-17
Description: Allow a user to discover, query and modify data from a LabKey Server.
Author: Peter Hussey
Maintainer: Cory Nathe
DESCRIPTION | 12 ++++++------
MD5 | 24 ++++++++++++------------
NEWS | 7 +++++++
R/labkey.executeSql.R | 14 +++++++++-----
R/labkey.getFolders.R | 15 ++++++++-------
R/labkey.selectRows.R | 6 ++++--
R/labkey.setCurlOptions.R | 4 ++--
inst/doc/RlabkeyExample.pdf |binary
inst/doc/usersguide.pdf |binary
man/Rlabkey-package.Rd | 4 ++--
man/labkey.executeSql.Rd | 8 ++++++--
man/labkey.getFolders.Rd | 4 +++-
man/labkey.selectRows.Rd | 8 ++++----
13 files changed, 63 insertions(+), 43 deletions(-)
Title: Latent Variable Models
Diff between lava versions 1.3 dated 2014-11-18 and 1.4.0 dated 2015-02-17
Description: Estimation and simulation of latent variable models.
Author: Klaus K. Holst
Maintainer: Klaus K. Holst
DESCRIPTION | 16 -
INDEX | 13 -
MD5 | 433 +++++++++++++++++++++++------------------------
NAMESPACE | 14 -
NEWS | 15 +
R/By.R | 4
R/Expand.R | 22 +-
R/Missing.R | 22 +-
R/Objective.R | 64 +++---
R/addattr.R | 12 -
R/addhook.R | 20 +-
R/addvar.R | 19 --
R/assoc.R | 4
R/baptize.R | 16 -
R/bootstrap.R | 28 +--
R/cancel.R | 2
R/categorical.R | 12 -
R/cluster.hook.R | 12 -
R/coef.R | 144 +++++++--------
R/compare.R | 48 ++---
R/confint.R | 17 -
R/constrain.R | 76 ++++----
R/copy.R | 4
R/correlation.R | 6
R/covariance.R | 91 ++++-----
R/curereg.R | 61 +++---
R/deriv.R | 75 ++++----
R/describecoef.R | 15 -
R/diagtest.R |only
R/distribution.R | 123 +++++++++----
R/dsort.R | 17 +
R/effects.R | 61 +++---
R/endogenous.R | 2
R/equivalence.R | 44 ++--
R/estimate.default.R | 191 +++++++++++---------
R/estimate.lvm.R | 173 +++++++++---------
R/estimate.multigroup.R | 158 ++++++++---------
R/eventTime.R | 108 +++++------
R/exogenous.R | 12 -
R/finalize.R | 74 +++-----
R/fix.R | 128 +++++++------
R/fixsome.R | 28 +--
R/formula.R | 3
R/functional.R | 13 -
R/glmest.R | 69 +++----
R/gof.R | 84 ++++-----
R/graph.R | 15 -
R/graph2lvm.R | 5
R/heavytail.R | 8
R/iid.R | 16 -
R/index.sem.R | 49 ++---
R/information.R | 30 +--
R/iv.R | 85 ++++-----
R/kill.R | 12 -
R/labels.R | 111 +++++-------
R/latent.R | 11 -
R/lava-package.R | 32 +--
R/lisrel.R | 14 -
R/lmers.R | 2
R/logLik.R | 82 ++++----
R/logo.R | 10 -
R/lvm.R | 27 +-
R/makemissing.R | 5
R/manifest.R | 5
R/matrices.R | 110 +++++------
R/measurement.R | 9
R/merge.R | 22 +-
R/missingMLE.R | 52 ++---
R/model.R | 14 -
R/modelPar.R | 30 +--
R/modelsearch.R | 49 ++---
R/moments.R | 10 -
R/multigroup.R | 62 +++---
R/multinomial.R | 53 ++---
R/multipletesting.R | 12 -
R/nested.R | 3
R/nodecolor.R | 2
R/normal.R | 40 +++-
R/onload.R | 10 -
R/optims.R | 60 +++---
R/ordinal.R | 14 -
R/ordreg.R | 13 -
R/parameter.R | 2
R/parpos.R | 12 -
R/pars.R | 9
R/partialcor.R | 12 -
R/path.R | 47 ++---
R/pcor.R | 29 +--
R/plot.R | 66 +++----
R/predict.R | 40 ++--
R/print.R | 26 +-
R/profile.R | 4
R/randomslope.R | 11 -
R/regression.R | 118 ++++++------
R/reorder.R | 2
R/residuals.R | 12 -
R/scheffe.R | 3
R/score.R | 38 ++--
R/sim.R | 157 ++++++++---------
R/spaghetti.R |only
R/stack.R |only
R/startvalues.R | 64 +++---
R/subgraph.R | 3
R/subset.R | 14 -
R/summary.R | 18 -
R/survival.R | 3
R/transform.R | 22 +-
R/utils.R | 119 ++++++++----
R/variances.R | 5
R/vars.R | 28 +--
R/vcov.R | 1
R/zCol.R | 22 +-
R/zblockdiag.R | 1
R/zclick.R | 8
R/zcolorbar.R | 10 -
R/zcombine.R | 13 -
R/zcommutation.R | 10 -
R/zconfband.R | 45 ++--
R/zdevcoords.R | 9
R/zgetmplus.R | 56 +++---
R/zgetsas.R | 18 -
R/zimages.R | 14 -
R/zksmooth.R | 20 +-
R/zmypal.R | 1
R/zoperators.R | 23 +-
R/zorg.R | 23 +-
R/zpdfconvert.R | 8
R/zplotConf.R | 359 +++++++++++++++++++++++++++++++++++---
R/zrevdiag.R | 2
R/ztoformula.R | 18 -
R/ztr.R | 13 -
R/ztrim.R | 2
inst/doc/reference.pdf |binary
inst/gof1.png |only
inst/lava1.png |only
man/By.Rd | 2
man/Col.Rd | 2
man/Combine.Rd | 2
man/Expand.Rd | 6
man/Graph.Rd | 2
man/Missing.Rd | 4
man/Model.Rd | 2
man/PD.Rd | 2
man/Range.lvm.Rd | 2
man/addvar.Rd | 2
man/baptize.Rd | 2
man/blockdiag.Rd | 2
man/bmd.Rd | 2
man/bmidata.Rd | 2
man/bootstrap.Rd | 2
man/bootstrap.lvm.Rd | 2
man/brisa.Rd | 2
man/calcium.Rd | 2
man/cancel.Rd | 2
man/children.Rd | 2
man/click.Rd | 4
man/closed.testing.Rd | 2
man/colorbar.Rd | 2
man/compare.Rd | 3
man/confband.Rd | 9
man/confint.lvmfit.Rd | 2
man/constrain-set.Rd | 2
man/correlation.Rd | 2
man/covariance.Rd | 2
man/curereg.Rd | 2
man/devcoords.Rd | 2
man/diagtest.Rd |only
man/dsort.Rd | 8
man/equivalence.Rd | 2
man/estimate.default.Rd | 23 +-
man/estimate.lvm.Rd | 2
man/eventTime.Rd | 2
man/getMplus.Rd | 2
man/getSAS.Rd | 2
man/gof.Rd | 2
man/hubble.Rd | 2
man/hubble2.Rd | 2
man/iid.Rd | 2
man/images.Rd | 2
man/indoorenv.Rd | 2
man/intercept.Rd | 2
man/internal.Rd | 3
man/kill.Rd | 2
man/ksmooth2.Rd | 5
man/labels-set.Rd | 2
man/lava-package.Rd | 2
man/lava.options.Rd | 2
man/lvm.Rd | 2
man/makemissing.Rd | 4
man/measurement.error.Rd |only
man/missingdata.Rd | 2
man/modelsearch.Rd | 2
man/multinomial.Rd | 2
man/nldata.Rd | 2
man/nsem.Rd | 2
man/op_concat.Rd | 10 -
man/op_match.Rd | 2
man/ordreg.Rd | 2
man/org.Rd | 2
man/parpos.Rd | 2
man/partialcor.Rd | 2
man/path.Rd | 2
man/pdfconvert.Rd | 2
man/plot.lvm.Rd | 4
man/plotConf.Rd | 8
man/predict.lvm.Rd | 2
man/regression-set.Rd | 8
man/revdiag.Rd | 2
man/scheffe.Rd | 2
man/semdata.Rd | 2
man/serotonin.Rd | 2
man/serotonin2.Rd | 2
man/sim.Rd | 26 +-
man/spaghetti.Rd |only
man/stack.estimate.Rd |only
man/subset.lvm.Rd | 2
man/timedep.Rd | 2
man/toformula.Rd | 2
man/tr.Rd | 2
man/trim.Rd | 2
man/twindata.Rd | 2
man/vars.Rd | 2
222 files changed, 2939 insertions(+), 2499 deletions(-)
Title: Fast Hierarchical Clustering Routines for R and Python
Diff between fastcluster versions 1.1.15 dated 2015-01-05 and 1.1.16 dated 2015-02-17
Description: This is a two-in-one package which provides interfaces to
both R and Python. It implements fast hierarchical, agglomerative
clustering routines. Part of the functionality is designed as drop-in
replacement for existing routines: "linkage" in the SciPy package
"scipy.cluster.hierarchy", "hclust" in R's "stats" package, and the
"flashClust" package. It provides the same functionality with the
benefit of a much faster implementation. Moreover, there are
memory-saving routines for clustering of vector data, which go beyond
what the existing packages provide. For information on how to install
the Python files, see the file INSTALL in the source distribution.
Author: Daniel Müllner [aut, cph, cre]
Maintainer: Daniel Müllner
DESCRIPTION | 18 +++++++++---------
MD5 | 22 +++++++++++-----------
NEWS | 7 ++++++-
inst/doc/fastcluster.Rtex | 4 ++--
inst/doc/fastcluster.pdf |binary
src/fastcluster.cpp | 5 ++++-
src/fastcluster_R.cpp | 37 +++++++++++++------------------------
src/python/fastcluster.py | 2 +-
src/python/test/nantest.py | 2 +-
src/python/test/test.py | 2 +-
src/python/test/vectortest.py | 2 +-
vignettes/fastcluster.Rtex | 4 ++--
12 files changed, 51 insertions(+), 54 deletions(-)
Title: High Performance Cluster Models Based on Kiefer-Wolfowitz
Recursion
Diff between hpcwld versions 0.4 dated 2014-07-16 and 0.5 dated 2015-02-17
Description: Probabilistic models describing the behavior
of workload and queue on a High Performance Cluster and computing GRID
under FIFO service discipline basing on modified Kiefer-Wolfowitz
recursion. Also sample data for inter-arrival times, service times,
number of cores per task and waiting times of HPC of Karelian
Research Centre are included, measurements took place from 06/03/2009 to 02/30/2011.
Functions provided to import/export workload traces in Standard Workload Format (swf).
Stability condition of the model may be verified either exactly, or approximately.
Author: Alexander Rumyantsev [aut, cre]
Maintainer: Alexander Rumyantsev
DESCRIPTION | 19 ++++++++++++-------
MD5 | 16 ++++++++++------
NAMESPACE | 4 +++-
R/ApproxC.R |only
R/StabC.R |only
data/HPC_KRC.rda |binary
data/HPC_KRC2.rda |binary
data/X.rda |binary
man/ApproxC.Rd |only
man/StabC.Rd |only
man/hpcwld-package.Rd | 13 +++++++++++--
11 files changed, 36 insertions(+), 16 deletions(-)
Title: Implementation of gWidgets2 for the RGtk2 Package
Diff between gWidgets2RGtk2 versions 1.0-2 dated 2013-10-29 and 1.0-3 dated 2015-02-17
More information about gWidgets2RGtk2 at CRAN
Description: Implements the gWidgets2 API for RGtk2.
Author: John Verzani
Maintainer: John Verzani
DESCRIPTION | 28 -
MD5 | 62 +--
NAMESPACE | 3
NEWS | 8
R/GComponent.R | 52 ++
R/dialogs.R | 6
R/gbutton.R | 8
R/gcheckbox.R | 33 -
R/gcheckboxgroup.R | 4
R/gcombobox.R | 22 -
R/gdf.R | 50 ++
R/gedit.R | 16
R/gfile.R | 6
R/gformlayout.R | 16
R/ggraphics.R | 21 -
R/gimage.R | 56 +--
R/glabel.R | 47 +-
R/glayout.R | 9
R/gnotebook.R | 18
R/gprogressbar.R | 1
R/gtable.R | 57 +--
R/gtext.R | 44 +-
R/gtk-misc.R | 2
R/gtree.R | 33 +
R/gwindow.R | 3
man/add_editable_cell_renderer.Rd | 17
man/ensure_type.Rd | 12
man/gWidgets2RGtk2-package.Rd | 217 +++++++----
man/gWidgets2RGtk2-undocumented.Rd | 665 +++++++++++++++---------------------
man/guiWidgetsToolkitRGtk2-class.Rd | 4
man/isFirstMouseClick.Rd | 9
man/isRightMouseClick.Rd | 9
32 files changed, 862 insertions(+), 676 deletions(-)
Permanent link
Title: Exploration and Graphics for RivEr Trends (EGRET)
Diff between EGRET versions 2.1.0 dated 2014-12-18 and 2.1.1 dated 2015-02-17
Description: Statistics and graphics for streamflow history,
water quality trends, and the statistical modeling algorithm: Weighted
Regressions on Time, Discharge, and Season (WRTDS).
Author: Robert Hirsch [aut],
Laura DeCicco [aut, cre]
Maintainer: Laura DeCicco
EGRET-2.1.0/EGRET/man/readNWISInfo.Rd |only
EGRET-2.1.0/EGRET/man/readUserInfo.Rd |only
EGRET-2.1.0/EGRET/man/readWQPInfo.Rd |only
EGRET-2.1.0/EGRET/vignettes/cache |only
EGRET-2.1.1/EGRET/DESCRIPTION | 10
EGRET-2.1.1/EGRET/MD5 | 184 ++++------
EGRET-2.1.1/EGRET/NAMESPACE | 3
EGRET-2.1.1/EGRET/NEWS | 8
EGRET-2.1.1/EGRET/R/EGRET.R | 26 +
EGRET-2.1.1/EGRET/R/fluxBiasEight.R | 3
EGRET-2.1.1/EGRET/R/generalAxis.R | 10
EGRET-2.1.1/EGRET/R/logPretty3.R | 2
EGRET-2.1.1/EGRET/R/mergeReport.r | 11
EGRET-2.1.1/EGRET/R/objectDefinitions.R | 19 -
EGRET-2.1.1/EGRET/R/plotConcQ.R | 3
EGRET-2.1.1/EGRET/R/plotConcQSmooth.R | 3
EGRET-2.1.1/EGRET/R/plotConcTime.R | 5
EGRET-2.1.1/EGRET/R/plotConcTimeDaily.R | 5
EGRET-2.1.1/EGRET/R/plotConcTimeSmooth.R | 3
EGRET-2.1.1/EGRET/R/plotFluxTimeDaily.R | 6
EGRET-2.1.1/EGRET/R/plotQTimeDaily.R | 6
EGRET-2.1.1/EGRET/R/populateParameterINFO.r | 3
EGRET-2.1.1/EGRET/R/printFluxUnitCheatSheet.R | 1
EGRET-2.1.1/EGRET/R/readMetaData.r | 144 ++++---
EGRET-2.1.1/EGRET/R/readNWISDaily.r | 4
EGRET-2.1.1/EGRET/R/sysdata.rda |binary
EGRET-2.1.1/EGRET/README.md | 6
EGRET-2.1.1/EGRET/demo/checkData.R | 7
EGRET-2.1.1/EGRET/inst/doc/EGRET.R | 11
EGRET-2.1.1/EGRET/inst/doc/EGRET.Rnw | 16
EGRET-2.1.1/EGRET/inst/doc/EGRET.pdf |binary
EGRET-2.1.1/EGRET/man/Constants.Rd |only
EGRET-2.1.1/EGRET/man/EGRET-package.Rd | 4
EGRET-2.1.1/EGRET/man/INFOdataframe.Rd |only
EGRET-2.1.1/EGRET/man/fluxBiasMulti.Rd | 3
EGRET-2.1.1/EGRET/man/generalAxis.Rd | 5
EGRET-2.1.1/EGRET/man/getDaily.Rd | 2
EGRET-2.1.1/EGRET/man/getInfo.Rd | 2
EGRET-2.1.1/EGRET/man/getSample.Rd | 2
EGRET-2.1.1/EGRET/man/getSurfaces.Rd | 2
EGRET-2.1.1/EGRET/man/plotConcQ.Rd | 3
EGRET-2.1.1/EGRET/man/plotConcQSmooth.Rd | 3
EGRET-2.1.1/EGRET/man/plotConcTime.Rd | 5
EGRET-2.1.1/EGRET/man/plotConcTimeDaily.Rd | 5
EGRET-2.1.1/EGRET/man/plotConcTimeSmooth.Rd | 3
EGRET-2.1.1/EGRET/man/plotFluxTimeDaily.Rd | 4
EGRET-2.1.1/EGRET/man/plotQTimeDaily.Rd | 5
EGRET-2.1.1/EGRET/man/populateParameterINFO.Rd | 3
EGRET-2.1.1/EGRET/man/printFluxUnitCheatSheet.Rd | 1
EGRET-2.1.1/EGRET/man/readNWISDaily.Rd | 3
EGRET-2.1.1/EGRET/tests |only
EGRET-2.1.1/EGRET/vignettes/EGRET-concordance.tex | 8
EGRET-2.1.1/EGRET/vignettes/EGRET.Rnw | 16
EGRET-2.1.1/EGRET/vignettes/figure/Mercedplot-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/Mercedplot-2.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/MississippiPlot-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/adjustSize-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/adjustSize-2.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/boxConcThree-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/boxResidMonth-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/boxResidMonth-2.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/customPanel-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/easyFontChange-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/fluxBiasMulti-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/modifiedContour1-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/modifiedDiffContour-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/multiPlotDataOverview-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotBoxes-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotBoxes-2.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotConcQComparison-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotConcQComparison-2.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotConcQSmooth-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotConcQSmooth-2.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotConcTime-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotConcTime-2.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotConcTimeDaily-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotConcTimeDaily-2.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotConcTimeSmooth-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotConcTimeSmooth-2.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotContours-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotDiffContours-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotFluxHist-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotFluxHist-2.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotFluxPred-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotFluxPred-2.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotFluxQ-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotFour-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotFourStats-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotResidQ-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotResidQ-2.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotSingleandSD-1.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/plotSingleandSD-2.pdf |binary
EGRET-2.1.1/EGRET/vignettes/figure/tinyPlot1-1.pdf |binary
93 files changed, 343 insertions(+), 235 deletions(-)
Title: Toolkit for Electroencephalography Data
Diff between eegkit versions 1.0-1 dated 2014-10-13 and 1.0-2 dated 2015-02-17
Description: Analysis and visualization tools for electroencephalography (EEG) data. Includes functions for plotting (a) EEG caps, (b) single- and multi-channel EEG time courses, and (c) EEG spatial maps. Also includes smoothing and Independent Component Analysis functions for EEG data analysis, and a function for simulating event-related potential EEG data.
Author: Nathaniel E. Helwig
Maintainer: Nathaniel E. Helwig
ChangeLog | 42 +++++++++++++++++
DESCRIPTION | 8 +--
MD5 | 58 +++++++++++------------
R/colorbar3d.R | 20 ++++----
R/eegcap.R | 68 +++++++++++++++------------
R/eegcapdense.R | 76 +++++++++++++++++-------------
R/eegica.R | 20 ++++----
R/eegsim.R | 77 ++++++++++++++++---------------
R/eegsmooth.R | 40 ++++++++--------
R/eegspace.R | 123 +++++++++++++++++++++++++++-----------------------
R/eegtime.R | 64 +++++++++++++++-----------
R/eegtimemc.R | 70 +++++++++++++++++++---------
R/voltcol.R | 10 ++--
data/eegcoord.rda |binary
data/eegdense.rda |binary
data/eeghead.rda |binary
data/eegmesh.rda |binary
man/eegcap.Rd | 43 ++++++++---------
man/eegcapdense.Rd | 26 ++++++----
man/eegcoord.Rd | 6 +-
man/eegdense.Rd | 2
man/eeghead.Rd | 8 +--
man/eegica.Rd | 57 +++++++++++------------
man/eegkit-package.Rd | 6 +-
man/eegmesh.Rd | 8 +--
man/eegsim.Rd | 79 +++++++++++++++-----------------
man/eegsmooth.Rd | 83 +++++++++++++++++----------------
man/eegspace.Rd | 37 +++++++--------
man/eegtime.Rd | 31 ++++++------
man/eegtimemc.Rd | 34 ++++++++-----
30 files changed, 610 insertions(+), 486 deletions(-)
Title: Model Layer for Automatic Data Analysis via CSV File
Interpretation
Diff between analyz versions 1.3.21 dated 2015-02-07 and 1.4 dated 2015-02-17
Description: Class with methods to read and execute R commands described as steps in a CSV file.
Author: Rodrigo Buhler
Maintainer: Rodrigo Buhler
DESCRIPTION | 13 +++++++------
MD5 | 30 +++++++++++++++---------------
NAMESPACE | 2 +-
R/ClassAnalyz.R | 12 +++---------
man/Analyz-class.Rd | 4 ++--
man/Analyz.coerceType-methods.Rd | 10 +++++-----
man/Analyz.getNrColumns-methods.Rd | 8 ++++----
man/Analyz.getNrRows-methods.Rd | 8 ++++----
man/Analyz.getResult-methods.Rd | 10 +++++-----
man/Analyz.getStepCommand-methods.Rd | 8 ++++----
man/Analyz.getStepParameters-methods.Rd | 8 ++++----
man/Analyz.getStepTitle-methods.Rd | 8 ++++----
man/Analyz.loadSteps-methods.Rd | 10 +++++-----
man/Analyz.runAnalysis-methods.Rd | 12 ++++++------
man/Analyz.setResult-methods.Rd | 10 +++++-----
man/Analyz.setStepItems-methods.Rd | 10 +++++-----
16 files changed, 79 insertions(+), 84 deletions(-)
Title: Efficient Discrete Stochastic Simulation
Diff between StochKit2R versions 0.2 dated 2015-01-29 and 0.3 dated 2015-02-17
Description: Efficient discrete stochastic simulation using the Gillespie algorithm (aka the Stochastic Simulation Algorithm or SSA) and adaptive tau-leaping. It provides an R interface to simulation algorithms and it provides functions for visualizing (plotting) simulation output.
Author: Kevin R. Sanft
Maintainer: Kevin R. Sanft
DESCRIPTION | 8 -
MD5 | 12 +-
inst/doc/StochKit2R-UserGuide.R | 18 +--
inst/doc/StochKit2R-UserGuide.Rmd | 12 --
inst/doc/StochKit2R-UserGuide.html | 211 +++++++++++++++++++------------------
vignettes/StochKit2R-UserGuide.Rmd | 12 --
vignettes/ex_out |only
7 files changed, 139 insertions(+), 134 deletions(-)
Title: Data Sets from Ramsey and Schafer's "Statistical Sleuth (3rd
Ed)"
Diff between Sleuth3 versions 0.1-6 dated 2013-03-10 and 0.1-8 dated 2015-02-17
Description: Data sets from Ramsey, F.L. and Schafer, D.W. (2013), "The
Statistical Sleuth: A Course in Methods of Data Analysis (3rd
ed)", Cengage Learning.
Author: Original by F.L. Ramsey and D.W. Schafer,
modifications by Daniel W. Schafer, Jeannie Sifneos and Berwin A. Turlach
Maintainer: Berwin A Turlach
Sleuth3-0.1-6/Sleuth3/LICENSE.GPL-2 |only
Sleuth3-0.1-6/Sleuth3/LICENSE.GPL-3 |only
Sleuth3-0.1-8/Sleuth3/DESCRIPTION | 26 -
Sleuth3-0.1-8/Sleuth3/GPL-2 |only
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189 files changed, 211 insertions(+), 210 deletions(-)
Title: Significance Tests for Palaeoenvironmental Reconstructions
Diff between palaeoSig versions 1.1-2 dated 2013-04-18 and 1.1-3 dated 2015-02-17
Description: Tests if quantitative palaeoenvironmental reconstructions are statistically significant.
Author: Richard Telford, Mathias Trachsel
Maintainer: Richard Telford
palaeoSig-1.1-2/palaeoSig/R/rotate.R |only
palaeoSig-1.1-2/palaeoSig/R/simulateSpatial.R |only
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palaeoSig-1.1-3/palaeoSig/DESCRIPTION | 19 ++++---
palaeoSig-1.1-3/palaeoSig/MD5 | 51 +++++++++++++--------
palaeoSig-1.1-3/palaeoSig/NAMESPACE | 32 +++++++++++--
palaeoSig-1.1-3/palaeoSig/R/Code1.r |only
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palaeoSig-1.1-3/palaeoSig/R/make.dist.R | 6 +-
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palaeoSig-1.1-3/palaeoSig/R/randomTF.R | 1
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palaeoSig-1.1-3/palaeoSig/inst/CITATION | 24 ++++-----
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palaeoSig-1.1-3/palaeoSig/man/mat.h.Rd | 41 ++++++----------
palaeoSig-1.1-3/palaeoSig/man/multi.mat.Rd | 24 +--------
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palaeoSig-1.1-3/palaeoSig/man/randomTF.Rd | 5 +-
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37 files changed, 164 insertions(+), 109 deletions(-)
Title: Multivariate Sensitivity Analysis
Diff between multisensi versions 1.0-7 dated 2013-07-19 and 1.0-8 dated 2015-02-17
Description: Functions to perform sensitivity analysis on a model with multivariate output.
Author: Matieyendou LAMBONI
Maintainer: Herve MONOD
DESCRIPTION | 11 +++++------
MD5 | 22 +++++++++++-----------
NAMESPACE | 7 +++++++
NEWS | 9 +++++++++
R/anoasg.r | 28 ++++++++++++++++------------
R/graph.pc.r | 4 ++--
R/plot.gsi.r | 6 ++++--
R/summary.gsi.r | 2 +-
inst/CITATION | 8 +++-----
inst/doc/multisensi-manual.pdf |binary
man/graph.pc.Rd | 3 ++-
man/plot.gsi.Rd | 5 +++--
12 files changed, 63 insertions(+), 42 deletions(-)
Title: Functions for the Analysis of IBD Haplo Output
Diff between IBDhaploRtools versions 1.7 dated 2014-07-23 and 1.8 dated 2015-02-16
More information about IBDhaploRtools at CRAN
Description: Functions to analyze, plot, and store the output of running IBD_Haplo software package. More information regarding IBD_Haplo can be found at http://www.stat.washington.edu/thompson/Genepi/pangaea.shtml.
Author: Marshall Brown, Fiona Grimson
Maintainer: Fiona Grimson
DESCRIPTION | 16 +++++++--------
MD5 | 30 ++++++++++++++---------------
R/ibdhap.make.calls.R | 4 +--
R/ibdhap.make.true.R | 25 ++++++++++++++++++++----
build/vignette.rds |binary
data/ids_phased.RData |binary
data/ids_unphased.RData |binary
data/posvec.RData |binary
data/qibd_phased.RData |binary
data/qibd_unphased.RData |binary
data/trueibd_phased.RData |binary
inst/doc/IBDhaploRtools_tutorial.R | 2 -
inst/doc/IBDhaploRtools_tutorial.Rnw | 35 +++++++++++++++++++---------------
inst/doc/IBDhaploRtools_tutorial.pdf |binary
man/IBDhaploRtools-package.Rd | 4 +--
vignettes/IBDhaploRtools_tutorial.Rnw | 35 +++++++++++++++++++---------------
16 files changed, 89 insertions(+), 62 deletions(-)
Permanent link
Title: Random Uniform Forests for Classification, Regression and
Unsupervised Learning
Diff between randomUniformForest versions 1.1.2 dated 2015-01-06 and 1.1.5 dated 2015-02-16
More information about randomUniformForest at CRAN
Description: Ensemble model, for classification, regression
and unsupervised learning, based on a forest of unpruned
and randomized binary decision trees. Each tree is grown
by sampling, with replacement, a set of variables at each node.
Each cut-point is generated randomly, according to the continuous
Uniform distribution. For each tree, data are either bootstrapped
or subsampled. The unsupervised mode introduces clustering, dimension reduction
and variable importance, using a three-layer engine. Random Uniform Forests are mainly
aimed to lower correlation between trees (or trees residuals), to provide a deep analysis
of variable importance and to allow native distributed and incremental learning.
Author: Saip Ciss
Maintainer: Saip Ciss
randomUniformForest-1.1.2/randomUniformForest/man/combine.unsupervised.Rd |only
randomUniformForest-1.1.5/randomUniformForest/DESCRIPTION | 8
randomUniformForest-1.1.5/randomUniformForest/MD5 | 50
randomUniformForest-1.1.5/randomUniformForest/NAMESPACE | 6
randomUniformForest-1.1.5/randomUniformForest/NEWS | 57
randomUniformForest-1.1.5/randomUniformForest/R/DecisionTreesCPP.R | 23
randomUniformForest-1.1.5/randomUniformForest/R/OnliningRandomUniformForests.R | 44
randomUniformForest-1.1.5/randomUniformForest/R/RandomUniformForestsCPP.R | 1142 +++++++---
randomUniformForest-1.1.5/randomUniformForest/R/genericFunctions.R | 68
randomUniformForest-1.1.5/randomUniformForest/inst/doc/VariableImportanceInRandomUniformForests.pdf |binary
randomUniformForest-1.1.5/randomUniformForest/inst/doc/randomUniformForestsOverview.pdf |binary
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randomUniformForest-1.1.5/randomUniformForest/man/fillNA2.randomUniformForest.Rd | 97
randomUniformForest-1.1.5/randomUniformForest/man/generic.cv.Rd | 4
randomUniformForest-1.1.5/randomUniformForest/man/importance.randomUniformForest.Rd | 147 -
randomUniformForest-1.1.5/randomUniformForest/man/internalFunctions.Rd | 3
randomUniformForest-1.1.5/randomUniformForest/man/modifyClusters.Rd | 2
randomUniformForest-1.1.5/randomUniformForest/man/partialDependenceBetweenPredictors.Rd | 66
randomUniformForest-1.1.5/randomUniformForest/man/predict.randomUniformForest.Rd | 8
randomUniformForest-1.1.5/randomUniformForest/man/rUniformForest.big.Rd | 2
randomUniformForest-1.1.5/randomUniformForest/man/randomUniformForest-package.Rd | 153 +
randomUniformForest-1.1.5/randomUniformForest/man/randomUniformForest.Rd | 268 +-
randomUniformForest-1.1.5/randomUniformForest/man/reSMOTE.Rd | 147 -
randomUniformForest-1.1.5/randomUniformForest/man/splitClusters.Rd |only
randomUniformForest-1.1.5/randomUniformForest/man/unsupervised.randomUniformForest.Rd | 335 +-
randomUniformForest-1.1.5/randomUniformForest/man/update.unsupervised.Rd | 25
28 files changed, 1932 insertions(+), 762 deletions(-)
Permanent link
Title: Wild Binary Segmentation for Multiple Change-Point Detection
Diff between wbs versions 1.2 dated 2014-08-08 and 1.3 dated 2015-02-16
Description: Provides efficient implementation of the Wild Binary Segmentation and Binary
Segmentation algorithms for estimation of the number and locations of
multiple change-points in the piecewise constant function plus Gaussian
noise model.
Author: Rafal Baranowski and Piotr Fryzlewicz
Maintainer: Rafal Baranowski
wbs-1.2/wbs/R/mean.from.cpt.R |only
wbs-1.2/wbs/man/mean.from.cpt.Rd |only
wbs-1.3/wbs/DESCRIPTION | 12 -
wbs-1.3/wbs/MD5 | 45 ++---
wbs-1.3/wbs/NAMESPACE | 4
wbs-1.3/wbs/R/changepoints.R | 2
wbs-1.3/wbs/R/means.between.cpt.R |only
wbs-1.3/wbs/R/plot.R | 4
wbs-1.3/wbs/R/sbs.R | 7
wbs-1.3/wbs/R/wbs.R | 25 ++-
wbs-1.3/wbs/man/bic.penalty.Rd | 2
wbs-1.3/wbs/man/changepoints.Rd | 8 -
wbs-1.3/wbs/man/fixed.intervals.Rd | 2
wbs-1.3/wbs/man/mbic.penalty.Rd | 2
wbs-1.3/wbs/man/means.between.cpt.Rd |only
wbs-1.3/wbs/man/plot.sbs.Rd | 2
wbs-1.3/wbs/man/plot.wbs.Rd | 2
wbs-1.3/wbs/man/print.sbs.Rd | 2
wbs-1.3/wbs/man/print.wbs.Rd | 2
wbs-1.3/wbs/man/random.intervals.Rd | 2
wbs-1.3/wbs/man/sbs.Rd | 2
wbs-1.3/wbs/man/ssic.penalty.Rd | 2
wbs-1.3/wbs/man/wbs-package.Rd | 2
wbs-1.3/wbs/man/wbs.Rd | 6
wbs-1.3/wbs/src/wbs.c | 276 +++++++++++++++--------------------
wbs-1.3/wbs/src/wbs.h |only
26 files changed, 196 insertions(+), 215 deletions(-)
Title: An R Convenience Layer for CouchDB
Diff between R4CouchDB versions 0.6 dated 2014-08-12 and 0.7.1 dated 2015-02-16
Description: Provides a collection of functions for basic
database and document management operations such as add, get, list or
delete. Every cdbFunction() gets and returns a list() containing the
connection setup.
Such a list (in the documentation mostly called cdb) can be generated by
cdb <- cdbIni(). Then, the list cdb provides some functions respectively
functionality e.g cdb$baseUrl() or cdb$getDocRev().
Author: Thomas Bock
Maintainer: Thomas Bock
DESCRIPTION | 17 ++--
MD5 | 58 ++++++++--------
NAMESPACE | 3
R/cdbAddDocS.R |only
R/cdbDeleteDoc.R | 2
R/cdbGetConfig.R | 4 -
R/cdbGetDoc.R | 2
R/cdbGetList.R | 3
R/cdbGetUuid.R | 3
R/cdbGetUuidS.R | 4 -
R/cdbGetView.R | 4 -
R/cdbIni.R | 167 ++++++++++++++++++++++++++----------------------
R/cdbListDB.R | 6 -
R/cdbMakeDB.R | 1
R/cdbRemoveDB.R | 1
R/cdbUpdateDoc.R | 8 --
man/cdbAddAttachment.Rd | 3
man/cdbAddDoc.Rd | 3
man/cdbAddDocS.Rd |only
man/cdbDeleteDoc.Rd | 6 -
man/cdbGetConfig.Rd | 7 --
man/cdbGetDoc.Rd | 6 -
man/cdbGetList.Rd | 8 --
man/cdbGetUuid.Rd | 7 --
man/cdbGetUuidS.Rd | 7 --
man/cdbGetView.Rd | 8 --
man/cdbIni.Rd | 5 -
man/cdbListDB.Rd | 10 --
man/cdbMakeDB.Rd | 6 -
man/cdbRemoveDB.Rd | 6 -
man/cdbUpdateDoc.Rd | 7 --
31 files changed, 167 insertions(+), 205 deletions(-)
Title: Subnetwork Integration for Multi-Modal Signatures
Diff between SIMMS versions 0.0.1 dated 2013-06-11 and 1.0.0 dated 2015-02-16
Description: Algorithms to create prognostic biomarkers using biological networks.
Author: Syed Haider, Michal Grzadkowski, Paul C. Boutros
Maintainer: Syed Haider
mRNA_abundance.txt | 6
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/DESCRIPTION | 15
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/MD5 | 116 ++-
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/NAMESPACE | 26
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/calculate.meta.survival.R | 93 +--
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/calculate.network.coefficients.R | 301 ++++++---
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/create.KM.plot.R | 12
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/create.classifier.multivariate.R |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/create.classifier.univariate.R |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/create.sensitivity.plot.R | 9
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/create.survivalplots.R | 225 +++----
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/create.survobj.R | 7
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/derive.network.features.R | 307 +++++-----
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/dichotomize.meta.dataset.R | 11
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/fit.coxmodel.R | 135 +++-
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/fit.interaction.model.R | 124 ++--
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/fit.survivalmodel.R | 34 -
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/get.adjacency.matrix.R | 2
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/get.program.defaults.R | 2
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/load.cancer.datasets.R | 7
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/pred.survivalmodel.R | 80 --
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/R/prepare.training.validation.datasets.R | 241 +++++--
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/build |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/doc |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/MEMo |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/MEMo.BRCA |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/MEMo.COADREAD |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/MEMo.GBM |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/MEMo.KIRC |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/MEMo.OV |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/Mammaprint |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/Oncotypedx |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/PI3K |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/test/pathway_based_networks_flattened.txt | 18
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/test/pathway_based_sub_networks.txt | 19
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/networkdb/test/pathway_based_sub_networks_all.txt | 19
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/inst/programdata/testdata/Breastdata1/mRNA_abundance.txt | 6
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/SIMMS.Rd | 14
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/calculate.meta.survival.Rd | 4
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/calculate.network.coefficients.Rd | 5
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/create.KM.plot.Rd | 4
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/create.classifier.multivariate.Rd |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/create.classifier.univariate.Rd |only
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/create.survivalplots.Rd | 14
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/create.survobj.Rd | 6
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/derive.network.features.Rd | 9
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/dichotomize.meta.dataset.Rd | 4
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/fit.coxmodel.Rd | 6
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/fit.interaction.model.Rd | 78 +-
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/fit.survivalmodel.Rd | 5
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/get.program.defaults.Rd | 2
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/load.cancer.datasets.Rd | 7
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/pred.survivalmodel.Rd | 10
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/man/prepare.training.validation.datasets.Rd | 10
tmp/cranberry712862096ace/SIMMS-1.0.0/SIMMS/vignettes |only
55 files changed, 1200 insertions(+), 793 deletions(-)
Title: Supervised Component Generalized Linear Regression
Diff between SCGLR versions 2.0.1 dated 2014-10-14 and 2.0.2 dated 2015-02-16
Description: The Fisher Scoring Algorithm is extended so as to combine Partial Least Squares
regression with Generalized Linear Model estimation in the multivariate context.
Author: Guillaume Cornu [cre, aut],
Frederic Mortier [aut],
Catherine Trottier [aut],
Xavier Bry [aut]
Maintainer: Guillaume Cornu
DESCRIPTION | 30 ++++++++-------
MD5 | 84 +++++++++++++++++++++---------------------
NAMESPACE | 4 +-
NEWS | 3 +
R/critConvergence.r | 2 -
R/customize.r | 2 -
R/data.r | 2 -
R/infoCriterion.r | 28 +++++++-------
R/ingUtils.r | 26 ++++++-------
R/methods.r | 2 -
R/metric.r | 2 -
R/multivariateFormula.r | 2 -
R/multivariateGlm.r | 8 ++--
R/multivariatePredictGlm.r | 4 +-
R/oneComponent.r | 10 +++--
R/package.r | 8 ++--
R/plot.r | 4 +-
R/print.r | 2 -
R/scglrCrossVal.r | 16 +++-----
R/summary.r | 6 +--
build/vignette.rds |binary
demo/scglrPrediction.r | 4 +-
inst/doc/scglrVignettes.R | 6 +--
inst/doc/scglrVignettes.pdf |binary
inst/doc/scglrVignettes.rnw | 8 ++--
inst/examples/exPrediction.r | 4 +-
man/barplot.SCGLR.Rd | 3 +
man/critConvergence.Rd | 3 +
man/customize.Rd | 3 +
man/genus.Rd | 5 +-
man/infoCriterion.Rd | 3 +
man/method.Rd | 3 +
man/multivariateFormula.Rd | 3 +
man/multivariateGlm.Rd | 5 +-
man/multivariatePredictGlm.Rd | 5 +-
man/pairs.SCGLR.Rd | 3 +
man/plot.SCGLR.Rd | 3 +
man/print.SCGLR.Rd | 3 +
man/scglr-package.Rd | 7 ++-
man/scglr.Rd | 3 +
man/scglrCrossVal.Rd | 3 +
man/summary.SCGLR.Rd | 3 +
vignettes/scglrVignettes.rnw | 8 ++--
43 files changed, 178 insertions(+), 155 deletions(-)
Title: Data Analysis Tool for Pharmacokinetics
Diff between PKfit versions 1.2.4 dated 2014-10-21 and 1.2.5 dated 2015-02-16
Description: 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
PKfit-1.2.4/PKfit/inst/CITATION |only
PKfit-1.2.4/PKfit/inst/UserDefinedModels/mymodel.R |only
PKfit-1.2.5/PKfit/DESCRIPTION | 18 ++++++++---------
PKfit-1.2.5/PKfit/MD5 | 21 +++++++++-----------
PKfit-1.2.5/PKfit/NEWS | 16 ++++++++++++++-
PKfit-1.2.5/PKfit/R/description_version.r | 7 +++++-
PKfit-1.2.5/PKfit/R/finfu2.R | 3 +-
PKfit-1.2.5/PKfit/R/fzero.nolag.R | 2 -
PKfit-1.2.5/PKfit/R/mmpk.demo.R | 2 -
PKfit-1.2.5/PKfit/R/sinfu1.R | 20 ++++---------------
PKfit-1.2.5/PKfit/R/sinfu2.R | 14 +++----------
PKfit-1.2.5/PKfit/R/zzz.R | 2 -
PKfit-1.2.5/PKfit/inst/UserDefinedModels/fitmodel.R |only
13 files changed, 54 insertions(+), 51 deletions(-)
Title: Partial Correlation Coefficient with Information Theory
Diff between PCIT versions 1.04-5 dated 2014-01-29 and 1.5-3 dated 2015-02-16
Description: Apply Partial Correlation coefficient with Information
Theory (PCIT) to a correlation matrix.
The PCIT algorithm identifies meaningful correlations to define
edges in a weighted network. The algorithm can be applied to
any correlation-based network including but not limited to gene
co-expression networks.
To reduce compute time by making use of multiple compute cores,
simply run PCIT on a computer with has multiple cores and also
has the Rmpi package installed. PCIT will then auto-detect the
multicore environment and run in parallel mode without the need
to rewrite your scripts. This makes scripts, using PCIT, portable
across single core (or no Rmpi package installed) computers
which will run in serial mode and multicore (with Rmpi package
installed) computers which will run in parallel mode.
Author: Nathan S. Watson-Haigh
Maintainer: Nathan S. Watson-Haigh
ChangeLog | 39 +++++++++++++++++++++++++++++++++++++++
DESCRIPTION | 24 +++++++++++++++---------
MD5 | 12 ++++++------
R/PCIT.R | 36 ++++++++++++++++++------------------
R/internal.R | 28 ++++++++++++++--------------
README.md | 20 ++++++++++++++++++++
inst/CITATION | 3 +--
7 files changed, 113 insertions(+), 49 deletions(-)
Title: Chi-Square Tests for Non-Parametric Functional Dependencies
Diff between FunChisq versions 1.0 dated 2014-03-07 and 2.0.0 dated 2015-02-16
Description: Statistical hypothesis testing methods for non-parametric functional dependencies based on chi-square statistics. These tests were designed to reveal causality based on evidence from non-parametric functional dependencies. It implements an asymptotic non-constant functional chi-square test, an exact functional test, and a comparative functional chi-square test. The normalized functional chi-square test was used by the Best Performer NMSUSongLab in DREAM8 Breast Cancer Network Inference Challenges. These tests offer an advantage over regression analysis when a parametric functional form cannot be assumed.
Author: Yang Zhang, Hua Zhong, and Joe Song
Maintainer: Joe Song
FunChisq-1.0/FunChisq/INDEX |only
FunChisq-2.0.0/FunChisq/DESCRIPTION | 22 +-
FunChisq-2.0.0/FunChisq/MD5 | 32 +++
FunChisq-2.0.0/FunChisq/NAMESPACE | 6
FunChisq-2.0.0/FunChisq/NEWS |only
FunChisq-2.0.0/FunChisq/R/FunChisq.R | 145 ++++++++++++++---
FunChisq-2.0.0/FunChisq/inst |only
FunChisq-2.0.0/FunChisq/man/FunChisq-package.Rd | 76 ++++-----
FunChisq-2.0.0/FunChisq/man/cp.fun.chisq.test.Rd |only
FunChisq-2.0.0/FunChisq/man/fun.chisq.test.Rd | 188 ++++++++++++++++-------
FunChisq-2.0.0/FunChisq/src |only
FunChisq-2.0.0/FunChisq/tests |only
12 files changed, 333 insertions(+), 136 deletions(-)
Title: Boosting Functional Regression Models
Diff between FDboost versions 0.0-5 dated 2014-04-22 and 0.0-8 dated 2015-02-16
Description: Regression models for functional data, i.e. scalar-on-function,
function-on-scalar and function-on-function regression models are fitted
using a component-wise gradient boosting algorithm.
Author: Sarah Brockhaus
Maintainer: Sarah Brockhaus
FDboost-0.0-5/FDboost/R/bkroneckerTrafo.R |only
FDboost-0.0-5/FDboost/data/datalist |only
FDboost-0.0-5/FDboost/data/fuel.RData |only
FDboost-0.0-5/FDboost/inst/fuelAllModels |only
FDboost-0.0-5/FDboost/man/fuel.Rd |only
FDboost-0.0-5/FDboost/vignettes/mboostDevel-inference.R |only
FDboost-0.0-8/FDboost/DESCRIPTION | 20
FDboost-0.0-8/FDboost/MD5 | 103 -
FDboost-0.0-8/FDboost/NAMESPACE | 5
FDboost-0.0-8/FDboost/R/FDboost.R | 189 +
FDboost-0.0-8/FDboost/R/baselearners.R | 1645 +++++++++-------
FDboost-0.0-8/FDboost/R/crossvalidation.R | 48
FDboost-0.0-8/FDboost/R/internalsMboost.R |only
FDboost-0.0-8/FDboost/R/methods.R | 180 +
FDboost-0.0-8/FDboost/R/utilityFunctions.R | 155 +
FDboost-0.0-8/FDboost/build/vignette.rds |binary
FDboost-0.0-8/FDboost/data/fuelSubset.RData |only
FDboost-0.0-8/FDboost/inst/CITATION |only
FDboost-0.0-8/FDboost/inst/doc/FLAM_canada.R | 2
FDboost-0.0-8/FDboost/inst/doc/FLAM_canada.Rnw | 2
FDboost-0.0-8/FDboost/inst/doc/FLAM_canada.pdf |binary
FDboost-0.0-8/FDboost/inst/doc/FLAM_fuel.R | 3
FDboost-0.0-8/FDboost/inst/doc/FLAM_fuel.Rnw | 3
FDboost-0.0-8/FDboost/inst/doc/FLAM_fuel.pdf |binary
FDboost-0.0-8/FDboost/inst/doc/FLAM_viscosity.R | 6
FDboost-0.0-8/FDboost/inst/doc/FLAM_viscosity.Rnw | 6
FDboost-0.0-8/FDboost/inst/doc/FLAM_viscosity.pdf |binary
FDboost-0.0-8/FDboost/inst/sim/analyze_results.R | 105 -
FDboost-0.0-8/FDboost/inst/sim/run_FDboost.R | 182 +
FDboost-0.0-8/FDboost/inst/sim/run_PlotModels.R | 150 -
FDboost-0.0-8/FDboost/inst/sim/run_pffr.R | 185 +
FDboost-0.0-8/FDboost/inst/sim/run_time.R |only
FDboost-0.0-8/FDboost/inst/sim/simfuns.R | 102
FDboost-0.0-8/FDboost/man/FDboost.Rd | 234 +-
FDboost-0.0-8/FDboost/man/bbsc.Rd | 168 -
FDboost-0.0-8/FDboost/man/bsignal.Rd | 242 +-
FDboost-0.0-8/FDboost/man/coef.FDboost.Rd | 81
FDboost-0.0-8/FDboost/man/extract.blg.Rd | 46
FDboost-0.0-8/FDboost/man/fitted.FDboost.Rd | 16
FDboost-0.0-8/FDboost/man/fuelSubset.Rd |only
FDboost-0.0-8/FDboost/man/funMRD.Rd | 52
FDboost-0.0-8/FDboost/man/funMSE.Rd | 70
FDboost-0.0-8/FDboost/man/funRsquared.Rd | 79
FDboost-0.0-8/FDboost/man/funplot.Rd | 29
FDboost-0.0-8/FDboost/man/integrationWeights.Rd | 72
FDboost-0.0-8/FDboost/man/o_control.Rd | 25
FDboost-0.0-8/FDboost/man/plot.FDboost.Rd | 111 -
FDboost-0.0-8/FDboost/man/plot.validateFDboost.Rd | 86
FDboost-0.0-8/FDboost/man/predict.FDboost.Rd | 56
FDboost-0.0-8/FDboost/man/print.FDboost.Rd | 15
FDboost-0.0-8/FDboost/man/residuals.FDboost.Rd | 18
FDboost-0.0-8/FDboost/man/summary.FDboost.Rd | 15
FDboost-0.0-8/FDboost/man/truncateTime.Rd | 25
FDboost-0.0-8/FDboost/man/validateFDboost.Rd | 222 --
FDboost-0.0-8/FDboost/man/viscosity.Rd | 28
FDboost-0.0-8/FDboost/vignettes/FLAM_canada.Rnw | 2
FDboost-0.0-8/FDboost/vignettes/FLAM_fuel.Rnw | 3
FDboost-0.0-8/FDboost/vignettes/FLAM_viscosity.Rnw | 6
58 files changed, 2749 insertions(+), 2043 deletions(-)
Title: Bayesian Network Feature Finder
Diff between BANFF versions 0.2 dated 2015-01-08 and 0.3 dated 2015-02-16
Description: Provides a full package of posterior inference, model comparison, and graphical illustration of model fitting. A parallel computing algorithm for the Markov chain Monte Carlo (MCMC) based posterior inference and an Expectation-Maximization (EM) based algorithm for posterior approximation are are developed, both of which greatly reduce the computational time for model inference.
Author: Zhou Lan, Yize Zhao, Jian Kang, Tianwei Yu
Maintainer: Zhou Lan
DESCRIPTION | 10 ++--
MD5 | 16 ++++---
NAMESPACE | 13 ++++++
R/All_functions.R | 10 ----
R/main.R | 89 +++++++++++++++++++++++++++++++++++++++----
man/Networks.Fast.Rd | 5 +-
man/Networks.STD.Rd | 7 +--
man/plot.Networks.Fast.Rd |only
man/plot.Networks.STD.Rd |only
man/summary.Networks.Fast.Rd |only
man/summary.Networks.STD.Rd |only
11 files changed, 117 insertions(+), 33 deletions(-)
Title: Simulation Tools for Small Area Estimation
Diff between saeSim versions 0.6.0 dated 2014-10-22 and 0.7.0 dated 2015-02-16
Description: Tools for the simulation of data in the context of small area
estimation. Combine all steps of your simulation - from data generation
over drawing samples to model fitting - in one object. This enables easy
modification and combination of different scenarios. You can store your
results in a folder or start the simulation in parallel.
Author: Sebastian Warnholz [aut, cre],
Timo Schmid [aut]
Maintainer: Sebastian Warnholz
saeSim-0.6.0/saeSim/R/01-s_dplyr.R |only
saeSim-0.6.0/saeSim/R/02-mclapply.R |only
saeSim-0.6.0/saeSim/inst/doc/addingComputations.R |only
saeSim-0.6.0/saeSim/inst/doc/addingComputations.Rmd |only
saeSim-0.6.0/saeSim/inst/doc/addingComputations.html |only
saeSim-0.6.0/saeSim/inst/doc/drawingSamples.R |only
saeSim-0.6.0/saeSim/inst/doc/drawingSamples.Rmd |only
saeSim-0.6.0/saeSim/inst/doc/drawingSamples.html |only
saeSim-0.6.0/saeSim/inst/doc/generalOverview.R |only
saeSim-0.6.0/saeSim/inst/doc/generalOverview.Rmd |only
saeSim-0.6.0/saeSim/inst/doc/generalOverview.html |only
saeSim-0.6.0/saeSim/inst/doc/generatingData.R |only
saeSim-0.6.0/saeSim/inst/doc/generatingData.Rmd |only
saeSim-0.6.0/saeSim/inst/doc/generatingData.html |only
saeSim-0.6.0/saeSim/man/show-sim_setup-method.Rd |only
saeSim-0.6.0/saeSim/man/summary.sim_setup.Rd |only
saeSim-0.6.0/saeSim/vignettes/addingComputations.Rmd |only
saeSim-0.6.0/saeSim/vignettes/drawingSamples.Rmd |only
saeSim-0.6.0/saeSim/vignettes/generalOverview.Rmd |only
saeSim-0.6.0/saeSim/vignettes/generatingData.Rmd |only
saeSim-0.7.0/saeSim/DESCRIPTION | 19 -
saeSim-0.7.0/saeSim/MD5 | 131 ++++------
saeSim-0.7.0/saeSim/NAMESPACE | 13
saeSim-0.7.0/saeSim/NEWS | 27 ++
saeSim-0.7.0/saeSim/R/00-sim-lib.R | 17 -
saeSim-0.7.0/saeSim/R/01-as.data.frame.R | 2
saeSim-0.7.0/saeSim/R/01-helper-lib.R | 48 +++
saeSim-0.7.0/saeSim/R/01-plot.R | 1
saeSim-0.7.0/saeSim/R/01-show.R | 7
saeSim-0.7.0/saeSim/R/01-sim.R | 115 +++++---
saeSim-0.7.0/saeSim/R/01-summary.R | 64 ++--
saeSim-0.7.0/saeSim/R/03-agg.R | 12
saeSim-0.7.0/saeSim/R/03-base-lib.R | 2
saeSim-0.7.0/saeSim/R/03-comp_var.R | 24 -
saeSim-0.7.0/saeSim/R/03-generator.R | 19 -
saeSim-0.7.0/saeSim/R/03-sample.R | 44 +++
saeSim-0.7.0/saeSim/R/03-sim_agg.R | 2
saeSim-0.7.0/saeSim/R/03-sim_base.R | 4
saeSim-0.7.0/saeSim/R/03-sim_comp.R | 6
saeSim-0.7.0/saeSim/R/03-sim_comp_preconf.R | 8
saeSim-0.7.0/saeSim/R/03-sim_gen.R | 13
saeSim-0.7.0/saeSim/R/03-sim_gen_cont.R | 7
saeSim-0.7.0/saeSim/R/03-sim_resp.R | 4
saeSim-0.7.0/saeSim/R/03-sim_sample.R | 2
saeSim-0.7.0/saeSim/R/NAMESPACE.R |only
saeSim-0.7.0/saeSim/build/vignette.rds |binary
saeSim-0.7.0/saeSim/inst/doc/Introduction.R |only
saeSim-0.7.0/saeSim/inst/doc/Introduction.Rmd |only
saeSim-0.7.0/saeSim/inst/doc/Introduction.html |only
saeSim-0.7.0/saeSim/man/agg_all.Rd | 3
saeSim-0.7.0/saeSim/man/as.data.frame.sim_setup.Rd | 3
saeSim-0.7.0/saeSim/man/autoplot.Rd | 3
saeSim-0.7.0/saeSim/man/base_add_id.Rd | 3
saeSim-0.7.0/saeSim/man/base_id.Rd | 3
saeSim-0.7.0/saeSim/man/comp_var.Rd | 3
saeSim-0.7.0/saeSim/man/generators.Rd | 7
saeSim-0.7.0/saeSim/man/pipe.Rd | 3
saeSim-0.7.0/saeSim/man/plot.sim_setup.Rd | 3
saeSim-0.7.0/saeSim/man/sampling.Rd | 21 +
saeSim-0.7.0/saeSim/man/showMethods.Rd |only
saeSim-0.7.0/saeSim/man/sim.Rd | 48 ++-
saeSim-0.7.0/saeSim/man/sim_agg.Rd | 3
saeSim-0.7.0/saeSim/man/sim_base.Rd | 3
saeSim-0.7.0/saeSim/man/sim_comp.Rd | 3
saeSim-0.7.0/saeSim/man/sim_comp_preconf.Rd | 3
saeSim-0.7.0/saeSim/man/sim_gen.Rd | 13
saeSim-0.7.0/saeSim/man/sim_gen_cont.Rd | 3
saeSim-0.7.0/saeSim/man/sim_gen_preconf.Rd | 3
saeSim-0.7.0/saeSim/man/sim_read_data.Rd | 3
saeSim-0.7.0/saeSim/man/sim_resp.Rd | 3
saeSim-0.7.0/saeSim/man/sim_sample.Rd | 3
saeSim-0.7.0/saeSim/man/sim_setup_preconfigured.Rd | 3
saeSim-0.7.0/saeSim/man/sim_simName.Rd | 3
saeSim-0.7.0/saeSim/man/summary-sim_setup-method.Rd |only
saeSim-0.7.0/saeSim/tests/testthat/helper.R |only
saeSim-0.7.0/saeSim/tests/testthat/test-preserve_attributes.R |only
saeSim-0.7.0/saeSim/tests/testthat/test-sim.R | 2
saeSim-0.7.0/saeSim/tests/testthat/test-sim_comp.R | 7
saeSim-0.7.0/saeSim/tests/testthat/test-sim_generate.R | 12
saeSim-0.7.0/saeSim/tests/testthat/test-sim_sample.R | 26 +
saeSim-0.7.0/saeSim/vignettes/Introduction.Rmd |only
81 files changed, 505 insertions(+), 279 deletions(-)
Title: Ensemble Empirical Mode Decomposition (EEMD) and Its Complete
Variant (CEEMDAN)
Diff between Rlibeemd versions 1.3.1 dated 2015-02-09 and 1.3.2 dated 2015-02-16
Description: An R interface for C library libeemd for performing the ensemble
empirical mode decomposition (EEMD), its complete variant (CEEMDAN) or the
regular empirical mode decomposition (EMD).
Author: Jouni Helske [aut, cre] (R interface),
Perttu Luukko [aut] (Original libeemd C library)
Maintainer: Jouni Helske
DESCRIPTION | 8
MD5 | 18
R/RcppExports.R | 4
R/Rlibeemd-package.R | 2
R/init.R |only
configure | 1529 ++++++++++++++++++++++-----------------------
configure.ac | 8
inst/CITATION | 5
man/Rlibeemd.Rd | 2
src/RcppExports.cpp | 11
src/gslErrorHandlerOff.cpp |only
11 files changed, 805 insertions(+), 782 deletions(-)
Title: Retinal Reconstruction Program
Diff between retistruct versions 0.5.9 dated 2014-12-02 and 0.5.10 dated 2015-02-16
Description: Reconstructs retinae by morphing a flat surface with
cuts (a dissected flat-mount retina) onto a curvilinear surface (the a
standard retinal shape). It can estimate the position of a point on the
intact adult retina to within 8 degrees of arc (3.6% of nasotemporal axis).
The coordinates in reconstructed retinae can be transformed to visuotopic
coordinates.
Author: David C. Sterratt [aut, cre, cph],
Daniel Lyngholm [aut, cph]
Maintainer: David C. Sterratt
DESCRIPTION | 18 +++++++++++-------
MD5 | 15 ++++++++-------
NAMESPACE | 2 ++
NEWS |only
R/ReconstructedDataset.R | 2 +-
R/geometry.R | 2 ++
R/revision.R | 2 +-
inst/CITATION | 8 ++++++--
man/retistruct.global.revision.Rd | 2 +-
9 files changed, 32 insertions(+), 19 deletions(-)
Title: Least-Squares Bilinear Clustering for Three-Way Data
Diff between lsbclust versions 1.0 dated 2015-02-10 and 1.0.1 dated 2015-02-16
Description: Functions for performing least-squares bilinear clustering of three-way data. The
method uses the bilinear decomposition (or biadditive model) to model two-way matrix slices
while clustering over the third way. Up to four different types of clusters are included, one
for each term of the bilinear decomposition. In this way, matrices are clustered simultaneously
on (a subset of) their overall means, row margins, column margins and row-column interactions.
The orthogonality of the bilinear model results in separability of the joint clustering problem
into four separate ones. Three of these subproblems are specific k-means problems, while a
special algorithm is implemented for the interactions. Plotting methods are provided, including
biplots for the low-rank approximations of the interactions.
Author: Pieter Schoonees [aut, cre], Patrick Groenen [ctb]
Maintainer: Pieter Schoonees
DESCRIPTION | 18 +++-
MD5 | 12 +-
R/plot.int.lsbclust.R | 5 -
R/supermarkets.R | 2
man/supermarkets.Rd | 2
tests/testthat/test_interactions.R | 159 +++++++++++++++++++++++++++++--------
tests/testthat/test_orc.R | 33 ++++++-
7 files changed, 178 insertions(+), 53 deletions(-)
Title: High-Dimensional Penalized Regression
Diff between HDPenReg versions 0.90 dated 2014-11-03 and 0.91 dated 2015-02-16
Description: Algorithms for lasso and fused-lasso
problems: implementation of the lars algorithm [1], for the
lasso and fusion penalization and EM-based algorithms for (logistic) lasso
and fused-lasso.
Author: Quentin Grimonprez [aut, cre],
Serge Iovleff [ctb]
Maintainer: Quentin Grimonprez
HDPenReg-0.90/HDPenReg/inst/doc/vignette.R |only
HDPenReg-0.90/HDPenReg/inst/doc/vignette.Rnw |only
HDPenReg-0.90/HDPenReg/inst/doc/vignette.pdf |only
HDPenReg-0.90/HDPenReg/man/predict.Rd |only
HDPenReg-0.90/HDPenReg/src/stkpp |only
HDPenReg-0.90/HDPenReg/vignettes/vignette.Rnw |only
HDPenReg-0.90/HDPenReg/vignettes/vignette.bib |only
HDPenReg-0.91/HDPenReg/DESCRIPTION | 28
HDPenReg-0.91/HDPenReg/MD5 | 434 +---------
HDPenReg-0.91/HDPenReg/NAMESPACE | 6
HDPenReg-0.91/HDPenReg/NEWS | 7
HDPenReg-0.91/HDPenReg/R/HDPenReg-package.R | 6
HDPenReg-0.91/HDPenReg/R/predict.R | 4
HDPenReg-0.91/HDPenReg/build/vignette.rds |binary
HDPenReg-0.91/HDPenReg/inst/doc/HDPenReg.R |only
HDPenReg-0.91/HDPenReg/inst/doc/HDPenReg.Rnw |only
HDPenReg-0.91/HDPenReg/inst/doc/HDPenReg.pdf |only
HDPenReg-0.91/HDPenReg/man/EMcvfusedlasso.Rd | 3
HDPenReg-0.91/HDPenReg/man/EMcvlasso.Rd | 3
HDPenReg-0.91/HDPenReg/man/EMfusedlasso.Rd | 3
HDPenReg-0.91/HDPenReg/man/EMlasso.Rd | 3
HDPenReg-0.91/HDPenReg/man/HDPenReg-package.Rd | 7
HDPenReg-0.91/HDPenReg/man/HDcvlars.Rd | 3
HDPenReg-0.91/HDPenReg/man/HDfusion.Rd | 3
HDPenReg-0.91/HDPenReg/man/HDlars.Rd | 3
HDPenReg-0.91/HDPenReg/man/LarsPath-class.Rd | 3
HDPenReg-0.91/HDPenReg/man/coef.LarsPath.Rd | 3
HDPenReg-0.91/HDPenReg/man/coeff.Rd | 3
HDPenReg-0.91/HDPenReg/man/computeCoefficients.Rd | 3
HDPenReg-0.91/HDPenReg/man/plot-methods.Rd | 3
HDPenReg-0.91/HDPenReg/man/plot.HDcvlars.Rd | 3
HDPenReg-0.91/HDPenReg/man/plotCoefficient.Rd | 3
HDPenReg-0.91/HDPenReg/man/predict.LarsPath.Rd |only
HDPenReg-0.91/HDPenReg/man/simul.Rd | 3
HDPenReg-0.91/HDPenReg/src/HDPenReg/lars.mk | 6
HDPenReg-0.91/HDPenReg/src/HDPenReg/lars/Cvlars.cpp | 1
HDPenReg-0.91/HDPenReg/src/HDPenReg/lars/Lars.cpp | 7
HDPenReg-0.91/HDPenReg/src/HDPenReg/lars/Lars.h | 2
HDPenReg-0.91/HDPenReg/src/HDPenReg/lars/PathState.h | 2
HDPenReg-0.91/HDPenReg/src/HDPenReg/lars/makefile | 34
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels.mk | 17
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/CV.cpp | 1
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/EM.cpp |only
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/FusedLasso.cpp |only
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/IMeasure.h | 2
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/IPenalizedSolver.h | 2
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/IPenalty.h | 2
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/Lasso.cpp |only
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/LogisticFusedLasso.cpp |only
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/LogisticLasso.cpp |only
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/LogisticLassoPenalty.cpp | 1
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/PenalizedModels.h | 44 -
HDPenReg-0.91/HDPenReg/src/HDPenReg/lassoModels/makefile | 2
HDPenReg-0.91/HDPenReg/src/Makevars | 45 -
HDPenReg-0.91/HDPenReg/src/emR.cpp | 3
HDPenReg-0.91/HDPenReg/src/emR.h | 5
HDPenReg-0.91/HDPenReg/src/larsR.cpp | 1
HDPenReg-0.91/HDPenReg/src/larsR.h | 5
HDPenReg-0.91/HDPenReg/vignettes/HDPenReg.Rnw |only
HDPenReg-0.91/HDPenReg/vignettes/HDPenReg.bib |only
60 files changed, 182 insertions(+), 537 deletions(-)
More information about fdrDiscreteNull at CRAN
Permanent link
Title: Bounded Density Estimation
Diff between bde versions 1.0 dated 2014-11-13 and 1.0.1 dated 2015-02-16
Description: A collection of S4 classes which implements different methods to estimate and deal with densities in bounded domains. That is, densities defined within the interval [lower.limit, upper.limit], where lower.limit and upper.limit are values that can be set by the user.
Author: Guzman Santafe, Borja Calvo, Aritz Perez and Jose A. Lozano
Maintainer: Guzman Santafe
DESCRIPTION | 12 ++++++------
MD5 | 5 +++--
NEWS |only
inst/App/server.R | 10 +++++-----
4 files changed, 14 insertions(+), 13 deletions(-)
Title: Using Gene Expression Data to Improve Flux Balance Analysis
Predictions
Diff between sybilEFBA versions 1.0.1 dated 2013-10-24 and 1.0.2 dated 2015-02-16
Description: Three different approaches to use gene expression data (or protein measurements) for improving FBA predictions.
Author: Abdelmoneim Amer Desouki [aut, cre]
Maintainer: Abdelmoneim Amer Desouki
DESCRIPTION | 16 +-
MD5 | 28 ++--
NEWS | 10 +
R/FECorr.R | 27 +++-
R/eFBA_gene.R | 329 +++++++++++++++++++++++++++++++++++------------------
R/eFBA_rxn.R | 105 +++++++---------
R/findMDCFlux.R | 7 -
R/gene2Rule.R | 8 -
data/iAF1260.RData |binary
data/iMM904.RData |binary
data/iND750.RData |binary
man/eFBA_gene.Rd | 6
man/eFBA_rxn.Rd | 6
man/findMDCFlux.Rd | 7 -
man/gen2Rule.Rd | 2
15 files changed, 344 insertions(+), 207 deletions(-)
Title: Regression Modeling Strategies
Diff between rms versions 4.2-1 dated 2014-09-18 and 4.3-0 dated 2015-02-16
Description: Regression modeling, testing, estimation, validation,
graphics, prediction, and typesetting by storing enhanced model design
attributes in the fit. rms is a collection of functions that
assist with and streamline modeling. It also contains functions for
binary and ordinal logistic regression models, ordinal models for
continuous Y with a variety of distribution families, and the Buckley-James
multiple regression model for right-censored responses, and implements
penalized maximum likelihood estimation for logistic and ordinary
linear models. rms works with almost any regression model, but it
was especially written to work with binary or ordinal regression
models, Cox regression, accelerated failure time models,
ordinary linear models, the Buckley-James model, generalized least
squares for serially or spatially correlated observations, generalized
linear models, and quantile regression.
Author: Frank E Harrell Jr
Maintainer: Frank E Harrell Jr
DESCRIPTION | 11
INDEX | 2
MD5 | 113 ++++----
NAMESPACE | 12
NEWS | 30 ++
R/Function.rms.s | 10
R/Glm.s | 5
R/Predict.s | 433 ++++++++++++++++-----------------
R/Rq.s | 3
R/anova.rms.s | 14 -
R/bj.s | 7
R/bootcov.s | 11
R/calibrate.s | 190 +++++++-------
R/contrast.s | 110 +++++---
R/cph.s | 7
R/datadist.s | 295 ++++++++++------------
R/ggplot.Predict.s |only
R/latex.rms.s | 33 +-
R/lrm.s | 3
R/ols.s | 7
R/orm.s | 3
R/plot.Predict.s | 146 +++++++----
R/pphsm.s | 2
R/predictrms.s | 67 ++---
R/print.psm.s | 17 -
R/residuals.lrm.s | 30 +-
R/rmsMisc.s | 52 +++
R/robcov.s | 35 +-
R/summary.rms.s | 8
R/survplot.npsurv.s | 6
R/survplot.rms.s | 3
R/validate.cph.s | 25 -
man/Gls.Rd | 7
man/Predict.Rd | 10
man/anova.rms.Rd | 3
man/bootcov.Rd | 7
man/calibrate.Rd | 6
man/contrast.Rd | 52 ++-
man/cph.Rd | 8
man/datadist.Rd | 7
man/ggplot.Predict.Rd |only
man/lrm.Rd | 4
man/nomogram.Rd | 4
man/npsurv.Rd | 8
man/plot.Predict.Rd | 5
man/predictrms.Rd | 15 -
man/psm.Rd | 4
man/residuals.lrm.Rd | 20 +
man/rms-internal.Rd | 2
man/rms.Rd | 8
man/robcov.Rd | 6
man/sensuc.Rd | 3
man/survplot.Rd | 2
man/zzzrmsOverview.Rd | 9
tests/cph3.r |only
tests/ggplot2-without-ggplot.Predict.r |only
tests/ggplot2.r |only
tests/orm-bootcov.r |only
tests/orm-residuals.r |only
tests/robcov.r |only
tests/summary.r |only
tests/validate.cph.s | 2
62 files changed, 1068 insertions(+), 814 deletions(-)
Title: Bayesian Geostatistical Modeling with RAMPS
Diff between ramps versions 0.6-12 dated 2013-11-12 and 0.6-13 dated 2015-02-16
Description: Bayesian geostatistical modeling of Gaussian processes using a reparameterized and marginalized posterior sampling (RAMPS) algorithm designed to lower autocorrelation in MCMC samples. Package performance is tuned for large spatial datasets.
Author: Brian J Smith [aut, cre],
Jun Yan [aut],
Mary Kathryn Cowles [aut]
Maintainer: Brian J Smith
ramps-0.6-12/ramps/man/corClasses.Rd |only
ramps-0.6-13/ramps/DESCRIPTION | 8 +-
ramps-0.6-13/ramps/MD5 | 34 ++++----
ramps-0.6-13/ramps/NAMESPACE | 30 +++----
ramps-0.6-13/ramps/R/corStruct.R | 88 +++++++++++------------
ramps-0.6-13/ramps/man/corRCauchy.Rd | 126 ++++++++++++++++-----------------
ramps-0.6-13/ramps/man/corRClasses.Rd |only
ramps-0.6-13/ramps/man/corRExp.Rd | 126 ++++++++++++++++-----------------
ramps-0.6-13/ramps/man/corRExp2.Rd | 6 -
ramps-0.6-13/ramps/man/corRExpwr.Rd | 6 -
ramps-0.6-13/ramps/man/corRExpwr2.Rd | 6 -
ramps-0.6-13/ramps/man/corRExpwr2Dt.Rd | 6 -
ramps-0.6-13/ramps/man/corRGaus.Rd | 126 ++++++++++++++++-----------------
ramps-0.6-13/ramps/man/corRGneit.Rd | 126 ++++++++++++++++-----------------
ramps-0.6-13/ramps/man/corRLin.Rd | 126 ++++++++++++++++-----------------
ramps-0.6-13/ramps/man/corRMatern.Rd | 6 -
ramps-0.6-13/ramps/man/corRSpher.Rd | 126 ++++++++++++++++-----------------
ramps-0.6-13/ramps/man/corRWave.Rd | 126 ++++++++++++++++-----------------
ramps-0.6-13/ramps/man/georamps.Rd | 6 -
19 files changed, 527 insertions(+), 551 deletions(-)
Title: Post-Hoc Interaction Analysis
Diff between phia versions 0.1-5 dated 2013-10-12 and 0.2-0 dated 2015-02-16
Description: Analysis of terms in linear, generalized and mixed linear models,
on the basis of multiple comparisons of factor contrasts. Specially suited
for the analysis of interaction terms.
Author: Helios De Rosario-Martinez [aut, cre],
John Fox [ctb],
R Core Team [ctb]
Maintainer: Helios De Rosario-Martinez
ChangeLog | 19 ++++
DESCRIPTION | 10 +-
MD5 | 34 ++++----
NAMESPACE | 4 -
R/contrastCoefficients.R | 2
R/getElements.R | 5 -
R/interactionMeans.R | 91 ++++++++++++++++++++--
R/testFactors.R | 187 +++++++++++++++++++----------------------------
build/vignette.rds |binary
data/Boik.rda |binary
data/Keselman.rda |binary
data/Rosnow.rda |binary
inst/doc/phia.Rnw | 97 ++++++++++++++----------
inst/doc/phia.pdf |binary
man/interactionMeans.Rd | 11 ++
man/phia-package.Rd | 6 -
man/testFactors.Rd | 5 -
vignettes/phia.Rnw | 97 ++++++++++++++----------
18 files changed, 334 insertions(+), 234 deletions(-)
Title: Analysis of Multivariate Event Times
Diff between mets versions 1.0 dated 2014-11-18 and 1.1.0 dated 2015-02-16
Description: Implementation of various statistical models for multivariate
event history data. Including multivariate cumulative incidence models, and
bivariate random effects probit models (Liability models). Also contains
two-stage binomial modelling that can do pairwise odds-ratio dependence
modelling based marginal logistic regression models. This is an alternative
to the alternating logistic regression approach (ALR).
Author: Klaus K. Holst and Thomas Scheike
Maintainer: Klaus K. Holst
mets-1.0/mets/R/newbptwin.R |only
mets-1.1.0/mets/DESCRIPTION | 10 -
mets-1.1.0/mets/MD5 | 159 +++++++++++++-------------
mets-1.1.0/mets/NAMESPACE | 14 --
mets-1.1.0/mets/NEWS | 8 +
mets-1.1.0/mets/R/aalenfrailty.R | 8 -
mets-1.1.0/mets/R/bicomprisk.R | 2
mets-1.1.0/mets/R/biprobit.R | 20 +--
mets-1.1.0/mets/R/bptwin.R | 4
mets-1.1.0/mets/R/bptwin2.R | 2
mets-1.1.0/mets/R/cor.R | 14 --
mets-1.1.0/mets/R/divide.conquer.R | 6
mets-1.1.0/mets/R/event.R | 10 -
mets-1.1.0/mets/R/fastapprox.R | 33 +++--
mets-1.1.0/mets/R/fastreshape.R | 29 +++-
mets-1.1.0/mets/R/ipw.R | 1
mets-1.1.0/mets/R/lifetable.R | 120 ++++++++++++++++++-
mets-1.1.0/mets/R/mets-package.R | 2
mets-1.1.0/mets/R/normal0.R | 20 ++-
mets-1.1.0/mets/R/onload.R | 4
mets-1.1.0/mets/R/phreg.par.R | 6
mets-1.1.0/mets/R/tetrachor.R | 16 ++
mets-1.1.0/mets/R/twinlm.R | 6
mets-1.1.0/mets/R/twostage.R | 2
mets-1.1.0/mets/inst/mets1.png |only
mets-1.1.0/mets/man/ClaytonOakes.Rd | 3
mets-1.1.0/mets/man/Dbvn.Rd | 3
mets-1.1.0/mets/man/Event.Rd | 3
mets-1.1.0/mets/man/Grandom.cif.Rd | 19 +--
mets-1.1.0/mets/man/aalenfrailty.Rd | 11 +
mets-1.1.0/mets/man/back2timereg.Rd | 3
mets-1.1.0/mets/man/bicomprisk.Rd | 3
mets-1.1.0/mets/man/binomial.twostage.Rd | 3
mets-1.1.0/mets/man/biprobit.Rd | 23 +--
mets-1.1.0/mets/man/blocksample.Rd | 7 -
mets-1.1.0/mets/man/bptwin.Rd | 13 --
mets-1.1.0/mets/man/casewise.Rd | 3
mets-1.1.0/mets/man/casewise.test.Rd | 3
mets-1.1.0/mets/man/concordance.Rd | 3
mets-1.1.0/mets/man/cor.cif.Rd | 5
mets-1.1.0/mets/man/dermalridges.Rd | 3
mets-1.1.0/mets/man/dermalridgesMZ.Rd | 3
mets-1.1.0/mets/man/divide.conquer.Rd | 5
mets-1.1.0/mets/man/divide.conquer.timereg.Rd | 7 -
mets-1.1.0/mets/man/easy.binomial.twostage.Rd | 7 -
mets-1.1.0/mets/man/easy.twostage.Rd | 3
mets-1.1.0/mets/man/fast.approx.Rd | 13 +-
mets-1.1.0/mets/man/fast.pattern.Rd | 3
mets-1.1.0/mets/man/fast.reshape.Rd | 12 +
mets-1.1.0/mets/man/internal.Rd | 4
mets-1.1.0/mets/man/ipw.Rd | 3
mets-1.1.0/mets/man/lifetable.matrix.Rd | 11 -
mets-1.1.0/mets/man/mena.Rd | 3
mets-1.1.0/mets/man/mets-package.Rd | 3
mets-1.1.0/mets/man/migr.Rd | 3
mets-1.1.0/mets/man/multcif.Rd | 3
mets-1.1.0/mets/man/np.Rd | 3
mets-1.1.0/mets/man/phreg.Rd | 3
mets-1.1.0/mets/man/plack.cif.Rd | 3
mets-1.1.0/mets/man/printcasewisetest.Rd | 3
mets-1.1.0/mets/man/prt.Rd | 3
mets-1.1.0/mets/man/random.cif.Rd | 3
mets-1.1.0/mets/man/simAalenFrailty.Rd | 3
mets-1.1.0/mets/man/simClaytonOakes.Rd | 3
mets-1.1.0/mets/man/simClaytonOakesWei.Rd | 3
mets-1.1.0/mets/man/summary.cor.Rd | 3
mets-1.1.0/mets/man/survpois.Rd |only
mets-1.1.0/mets/man/test.conc.Rd | 3
mets-1.1.0/mets/man/tetrachoric.Rd |only
mets-1.1.0/mets/man/twin.clustertrunc.Rd | 3
mets-1.1.0/mets/man/twinbmi.Rd | 3
mets-1.1.0/mets/man/twinlm.Rd | 7 -
mets-1.1.0/mets/man/twinsim.Rd | 3
mets-1.1.0/mets/man/twinstut.Rd | 3
mets-1.1.0/mets/man/twostage.Rd | 3
mets-1.1.0/mets/src/fastcox.cpp | 2
mets-1.1.0/mets/src/mvn.cpp | 48 ++++++-
mets-1.1.0/mets/src/mvn.h | 5
mets-1.1.0/mets/src/mvt.f | 14 +-
mets-1.1.0/mets/src/tools.cpp | 35 +++--
mets-1.1.0/mets/src/tools.h | 2
mets-1.1.0/mets/src/tvpack.f | 8 -
mets-1.1.0/mets/tests/testthat/test_approx.R |only
83 files changed, 551 insertions(+), 305 deletions(-)
Title: Linear Predictor Score, for Binary Inference from Multiple
Continuous Variables
Diff between LPS versions 1.0.4 dated 2013-12-20 and 1.0.10 dated 2015-02-16
Description: An implementation of the Linear Predictor Score approach, as initiated by Radmacher et al. (J Comput Biol 2001) and enhanced by Wright et al. (PNAS 2003) for gene expression signatures. Several tools for unsupervised clustering of gene expression data are also provided.
Author: Sylvain Mareschal
Maintainer: Sylvain Mareschal
DESCRIPTION | 17 +++++-----
MD5 | 31 +++++++++---------
R/LPS.coeff.r | 13 ++-----
R/LPS.r | 2 +
R/clusterize.r | 44 +++++++++++++++++++-------
R/heat.map.r | 89 ++++++++++++++++++++++++++++++++---------------------
R/heat.r | 2 -
R/heat.scale.r | 22 ++++++++++---
R/plot.LPS.r | 75 ++++++++++++++++++++++++++++++++++++++------
R/predict.LPS.r | 68 +++++++++++++++++++++++++---------------
README.md |only
inst/NEWS.Rd | 45 ++++++++++++++++++++++++++
man/clusterize.Rd | 22 ++++++++-----
man/heat.map.Rd | 24 ++++++++------
man/heat.scale.Rd | 9 ++++-
man/plot.LPS.Rd | 20 ++++++++++-
man/predict.LPS.Rd | 22 ++++++++-----
17 files changed, 359 insertions(+), 146 deletions(-)
Title: Harrell Miscellaneous
Diff between Hmisc versions 3.14-6 dated 2014-11-21 and 3.15-0 dated 2015-02-16
Description: Contains many functions useful for data
analysis, high-level graphics, utility operations, functions for
computing sample size and power, importing and annotating datasets,
imputing missing values, advanced table making, variable clustering,
character string manipulation, conversion of R objects to LaTeX code,
and recoding variables.
Author: Frank E Harrell Jr
Maintainer: Frank E Harrell Jr
DESCRIPTION | 17 ++--
INDEX | 2
MD5 | 59 ++++++++-------
NAMESPACE | 190 ++++++++++++++++++++++++++++++++++++++++++++++++++
NEWS | 18 ++++
R/Misc.s | 16 +---
R/aregImpute.s | 47 ++++++------
R/histSpikeg.s |only
R/labcurve.s | 13 +--
R/latex.s | 58 +++++++++++----
R/rcspline.plot.s | 9 --
R/rcspline.restate.s | 12 +--
R/sas.get.s | 3
R/scat1d.s | 53 ++++++-------
R/stat-plsmo.r |only
R/summary.formula.s | 1
R/summaryM.s | 23 +++---
R/summaryP.s | 81 +++++++++++++++++++++
R/transace.s | 2
R/transcan.s | 54 +++++++++++++-
man/Hmisc-internal.Rd | 3
man/describe.Rd | 3
man/format.df.Rd | 9 +-
man/getHdata.Rd | 13 ---
man/labcurve.Rd | 12 +--
man/plsmo.Rd | 10 ++
man/scat1d.Rd | 86 +++++++++++++++++++---
man/stat_plsmo.Rd |only
man/summaryM.Rd | 10 +-
man/summaryP.Rd | 25 +++++-
man/transcan.Rd | 30 +++++--
tests/histSpike.r |only
tests/histSpikeg.r |only
33 files changed, 659 insertions(+), 200 deletions(-)
Title: Statistical Analysis and Data Display: Heiberger and Holland
Diff between HH versions 3.1-14 dated 2015-01-09 and 3.1-15 dated 2015-02-16
Description: Support software for Statistical Analysis and Data Display (First Edition, Springer, ISBN 0-387-40270-5, 2004) and (Second Edition, Springer, ISBN 978-1-4939-2121-8, anticipated 2015) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
Author: Richard M. Heiberger
Maintainer: Richard M. Heiberger
HH-3.1-14/HH/R/t.trellis.R |only
HH-3.1-14/HH/man/t.trellis.Rd |only
HH-3.1-15/HH/DESCRIPTION | 8
HH-3.1-15/HH/MD5 | 76 ++--
HH-3.1-15/HH/NAMESPACE | 7
HH-3.1-15/HH/NEWS | 47 ++-
HH-3.1-15/HH/R/ARIMA-trellis.R | 65 ----
HH-3.1-15/HH/R/extra.r | 5
HH-3.1-15/HH/R/interaction2wt.R | 2
HH-3.1-15/HH/R/intxplot.s | 24 -
HH-3.1-15/HH/R/matrix.trellis.r | 8
HH-3.1-15/HH/R/mmcplot.R | 22 +
HH-3.1-15/HH/R/normal.and.t.R | 27 -
HH-3.1-15/HH/R/normal.and.t.power.R | 30 +
HH-3.1-15/HH/R/normal.and.t.shiny.R | 80 ++---
HH-3.1-15/HH/R/normal.and.t.support.R | 2
HH-3.1-15/HH/R/panel.interaction2wt.R | 23 +
HH-3.1-15/HH/R/rbind.trellis.R | 111 +++++--
HH-3.1-15/HH/R/transpose.trellis.R | 20 -
HH-3.1-15/HH/inst/CITATION | 2
HH-3.1-15/HH/inst/scripts/hh2/conc.R | 196 ++++++++----
HH-3.1-15/HH/inst/scripts/hh2/grap.R | 48 +--
HH-3.1-15/HH/inst/scripts/hh2/iinf.R | 451 +++++++++++++++++++++++++++++
HH-3.1-15/HH/inst/scripts/hh2/logi.R | 30 -
HH-3.1-15/HH/inst/shiny/PopulationPyramid |only
HH-3.1-15/HH/man/NormalAndT.Rd | 8
HH-3.1-15/HH/man/NormalAndTplot.Rd | 10
HH-3.1-15/HH/man/ae.dotplot.Rd | 60 +--
HH-3.1-15/HH/man/as.vector.trellis.Rd | 37 +-
HH-3.1-15/HH/man/datasets.Rd | 3
HH-3.1-15/HH/man/extra.Rd | 3
HH-3.1-15/HH/man/intxplot.Rd | 5
HH-3.1-15/HH/man/mmc.Rd | 248 ++++++---------
HH-3.1-15/HH/man/normal.and.t.and.power.Rd | 4
HH-3.1-15/HH/man/normalApproxBinomial.Rd | 7
HH-3.1-15/HH/man/panel.confintMMC.Rd | 4
HH-3.1-15/HH/man/panel.interaction2wt.Rd | 2
HH-3.1-15/HH/man/rbind.trellis.Rd | 24 -
HH-3.1-15/HH/man/seqplot.Rd | 2
39 files changed, 1138 insertions(+), 563 deletions(-)
Title: High Dimensional Supervised Classification and Clustering
Diff between HDclassif versions 1.2.2 dated 2013-01-08 and 1.2.3 dated 2015-02-16
Description: Discriminant analysis and data clustering methods for high dimensional data, based on the assumption that high-dimensional data live in different subspaces with low dimensionality proposing a new parametrization of the Gaussian mixture model which combines the ideas of dimension reduction and constraints on the model.
Author: Laurent Berge, Charles Bouveyron and Stephane Girard
Maintainer: Laurent Berge
HDclassif-1.2.2/HDclassif/HDclassif-Ex.R |only
HDclassif-1.2.2/HDclassif/R/demo_hddc.R |only
HDclassif-1.2.2/HDclassif/R/demo_hddc_acp.R |only
HDclassif-1.2.2/HDclassif/R/demo_hddc_crabs.R |only
HDclassif-1.2.2/HDclassif/R/hdda.R |only
HDclassif-1.2.2/HDclassif/R/hddc.R |only
HDclassif-1.2.2/HDclassif/R/pck_hdclassif_dim_choice.R |only
HDclassif-1.2.2/HDclassif/R/pck_hdda_bic.R |only
HDclassif-1.2.2/HDclassif/R/pck_hdda_prms.R |only
HDclassif-1.2.2/HDclassif/R/pck_hdda_prms_bis.R |only
HDclassif-1.2.2/HDclassif/R/pck_hdda_tclass.R |only
HDclassif-1.2.2/HDclassif/R/pck_hddc.R |only
HDclassif-1.2.2/HDclassif/R/pck_hddc_e_step.R |only
HDclassif-1.2.2/HDclassif/R/pck_hddc_m_step.R |only
HDclassif-1.2.2/HDclassif/R/plot.hdc.R |only
HDclassif-1.2.2/HDclassif/R/predict.hdc.R |only
HDclassif-1.2.2/HDclassif/R/print.hd.R |only
HDclassif-1.2.2/HDclassif/R/print.hdc.R |only
HDclassif-1.2.2/HDclassif/R/simuldata.R |only
HDclassif-1.2.3/HDclassif/ChangeLog | 4
HDclassif-1.2.3/HDclassif/DESCRIPTION | 20 +-
HDclassif-1.2.3/HDclassif/MD5 | 40 +----
HDclassif-1.2.3/HDclassif/R/hdclassif.R |only
HDclassif-1.2.3/HDclassif/man/Crabs.Rd | 2
HDclassif-1.2.3/HDclassif/man/HDclassif-package.Rd | 12 -
HDclassif-1.2.3/HDclassif/man/demo_hddc.Rd | 4
HDclassif-1.2.3/HDclassif/man/hdda.Rd | 130 ++++++++---------
HDclassif-1.2.3/HDclassif/man/hddc.Rd | 118 +++++++++++----
HDclassif-1.2.3/HDclassif/man/plot.hdc.Rd | 8 -
HDclassif-1.2.3/HDclassif/man/predict.hdc.Rd | 14 -
HDclassif-1.2.3/HDclassif/man/simuldata.Rd | 2
31 files changed, 196 insertions(+), 158 deletions(-)
Title: Data Visualization for Statistics in Social Science
Diff between sjPlot versions 1.6.8 dated 2015-02-02 and 1.6.9 dated 2015-02-15
Description: Collection of several plotting and table output functions for
visualizing data, and utility functions.
Author: Daniel Lüdecke
Maintainer: Daniel Lüdecke
DESCRIPTION | 8
MD5 | 199 ++---
NAMESPACE | 188 ++--
NEWS | 902 +++++++++++------------
R/helpfunctions.R | 978 ++++++++++++------------
R/sjImportSPSS.R | 859 +++++++++++----------
R/sjPlotAnova.R | 9
R/sjPlotDist.R |only
R/sjPlotFrequencies.R | 1684 ++++++++++++++++++++++---------------------
R/sjPlotGLME.R | 4
R/sjPlotInteractions.R | 19
R/sjPlotLinreg.R | 47 -
R/sjPlotScatter.R | 28
R/sjPlotSetTheme.R | 42 -
R/sjRecode.R | 8
R/sjStatistics.R | 29
R/sjTabCorr.R | 1036 +++++++++++++-------------
R/sjTabDataFrame.R | 14
R/sjTabFrequencies.R | 1324 +++++++++++++++++----------------
R/sjTabGrpmean.R | 340 ++++----
R/sjTabItemAnalysis.R | 842 ++++++++++-----------
R/sjTabLinReg.R | 1604 ++++++++++++++++++++--------------------
R/sjTabOdds.R | 1432 ++++++++++++++++++------------------
R/sjTabPCA.R | 14
R/sjTabPropTable.R | 1658 +++++++++++++++++++++---------------------
R/sjTabSPSS.R | 14
R/sjTabStackFrq.R | 28
README.md | 35
man/efc.Rd | 92 +-
man/sj.setGeomColors.Rd | 52 -
man/sjPlot-package.Rd | 4
man/sjc.cluster.Rd | 180 ++--
man/sjc.dend.Rd | 104 +-
man/sjc.elbow.Rd | 76 -
man/sjc.grpdisc.Rd | 110 +-
man/sjc.kgap.Rd | 134 +--
man/sjc.qclus.Rd | 386 ++++-----
man/sjd.chisq.Rd |only
man/sjd.f.Rd |only
man/sjd.norm.Rd |only
man/sjd.t.Rd |only
man/sji.SPSS.Rd | 107 +-
man/sji.convertToLabel.Rd | 80 +-
man/sji.convertToValue.Rd | 78 -
man/sji.getValueLabels.Rd | 94 +-
man/sji.getVariableLabels.Rd | 92 +-
man/sji.setValueLabels.Rd | 98 +-
man/sji.setVariableLabels.Rd | 124 +--
man/sji.viewSPSS.Rd | 252 +++---
man/sjp.aov1.Rd | 311 ++++---
man/sjp.chi2.Rd | 122 +--
man/sjp.corr.Rd | 248 +++---
man/sjp.emm.int.Rd | 268 +++---
man/sjp.frq.Rd | 589 +++++++--------
man/sjp.glm.Rd | 394 +++++-----
man/sjp.glmer.Rd | 420 +++++-----
man/sjp.glmm.Rd | 324 ++++----
man/sjp.grpfrq.Rd | 562 +++++++-------
man/sjp.int.Rd | 450 +++++------
man/sjp.likert.Rd | 442 +++++------
man/sjp.lm.Rd | 486 ++++++------
man/sjp.lmer.Rd | 384 ++++-----
man/sjp.lmm.Rd | 310 +++----
man/sjp.pca.Rd | 288 +++----
man/sjp.scatter.Rd | 314 ++++----
man/sjp.setTheme.Rd | 22
man/sjp.stackfrq.Rd | 360 ++++-----
man/sjp.xtab.Rd | 470 ++++++------
man/sjs.aov1.levene.Rd | 56 -
man/sjs.chi2.gof.Rd | 78 -
man/sjs.cramer.Rd | 54 -
man/sjs.cronbach.Rd | 60 -
man/sjs.etasq.Rd | 100 +-
man/sjs.mic.Rd | 98 +-
man/sjs.mwu.Rd | 114 +-
man/sjs.phi.Rd | 54 -
man/sjs.reliability.Rd | 178 ++--
man/sjs.se.Rd | 42 -
man/sjs.stdb.Rd | 94 +-
man/sjs.table.values.Rd | 80 +-
man/sjt.corr.Rd | 363 ++++-----
man/sjt.df.Rd | 295 +++----
man/sjt.frq.Rd | 450 +++++------
man/sjt.glm.Rd | 512 ++++++-------
man/sjt.grpmean.Rd | 162 ++--
man/sjt.itemanalysis.Rd | 397 +++++-----
man/sjt.lm.Rd | 557 +++++++-------
man/sjt.pca.Rd | 358 ++++-----
man/sjt.stackfrq.Rd | 397 +++++-----
man/sjt.xtab.Rd | 453 +++++------
man/sju.adjustPlotRange.y.Rd | 90 +-
man/sju.dicho.Rd | 78 -
man/sju.groupString.Rd | 98 +-
man/sju.groupVar.Rd | 132 +--
man/sju.groupVarLabels.Rd | 150 +--
man/sju.mean.n.Rd | 80 +-
man/sju.recode.Rd | 48 -
man/sju.recodeTo.Rd | 96 +-
man/sju.setNA.Rd | 62 -
man/sju.strpos.Rd | 138 +--
man/sju.weight.Rd | 78 -
man/sju.weight2.Rd | 90 +-
man/sju.wordwrap.Rd | 56 -
103 files changed, 14423 insertions(+), 13897 deletions(-)
Title: Zebra-Striped Tables in LaTeX and HTML Formats
Diff between ztable versions 0.1.4 dated 2015-02-06 and 0.1.5 dated 2015-02-15
Description: Makes zebra-striped tables (tables with alternating row colors)
in LaTeX and HTML formats easily from a data.frame, matrix, lm, aov, anova,
glm, coxph, nls, fitdistr, mytable and cbind.mytable objects.
Author: Keon-Woong Moon [aut, cre]
Maintainer: Keon-Woong Moon
DESCRIPTION | 8
MD5 | 139
NAMESPACE | 2
NEWS | 11
R/print.ztable.html.R | 104
R/ztable.R | 5
R/ztable1.R | 44
R/zzz.R | 2
README.md | 9581 ++++++++++++++++++++++----------------------
inst/doc/ztable.R | 29
inst/doc/ztable.Rmd | 41
inst/doc/ztable.html | 3992 +++++++++++++-----
man/addCellColor.Rd | 3
man/addColColor.Rd | 3
man/addRowColor.Rd | 3
man/addSubColNames.Rd | 3
man/addcgroup.Rd | 3
man/addrgroup.Rd | 3
man/align2html.Rd | 3
man/align2lines.Rd | 3
man/align2nd.Rd | 3
man/alignCheck.Rd | 3
man/alignCount.Rd | 3
man/cGroupSpan.Rd | 3
man/caption2minipage.Rd | 3
man/colGroupCount.Rd | 3
man/data2table.Rd | 3
man/define_colors.Rd | 3
man/extractAlign.Rd | 3
man/getNewAlign.Rd | 3
man/getNewSpanCol.Rd | 3
man/getNewSpanRow.Rd | 3
man/getspanRowData.Rd | 3
man/getspanRowLength.Rd | 3
man/hlines.Rd |only
man/isGroupCol.Rd | 3
man/isspanCol.Rd | 3
man/isspanRow.Rd | 3
man/make.cell.color.Rd | 3
man/myhtmlStyle.Rd | 3
man/name2rgb.Rd | 3
man/parallelTables.Rd | 3
man/parallelTablesHTML.Rd | 3
man/parallelTablesLatex.Rd | 3
man/print.ztable.Rd | 3
man/printHTMLHead.Rd | 3
man/printLatexHead.Rd | 3
man/printRowGroup.Rd | 3
man/print_ztable.Rd | 3
man/repColor.Rd | 3
man/spanCol.Rd | 3
man/spanColWidth.Rd | 3
man/spanRow.Rd | 3
man/tableLength.Rd | 3
man/totalCol.Rd | 3
man/tr.Rd | 3
man/tr2.Rd | 3
man/update_ztable.Rd | 3
man/validColor.Rd | 3
man/validColor2.Rd | 3
man/vline2align.Rd | 3
man/vlines.Rd | 5
man/zcolors.Rd | 3
man/ztable.Rd | 13
man/ztable.cbind.mytable.Rd | 3
man/ztable.mytable.Rd | 3
man/ztable2html.Rd | 3
man/ztable2latex.Rd | 3
man/ztable2viewer.Rd | 3
man/ztable_sub.Rd | 3
vignettes/ztable.Rmd | 41
71 files changed, 8304 insertions(+), 5878 deletions(-)
Title: Sparse Biclustering of Transposable Data
Diff between sparseBC versions 1.0 dated 2013-10-02 and 1.1 dated 2015-02-15
Description: Implements the sparse biclustering proposal of Tan and Witten (2014), Sparse biclustering of transposable data. Journal of Computational and Graphical Statistics 23(4):985-1008.
Author: Kean Ming Tan
Maintainer: Kean Ming Tan
DESCRIPTION | 13 +++++++------
MD5 | 30 +++++++++++++++++++-----------
NAMESPACE | 12 +++++++++++-
R/image.matrixBC.R |only
R/image.sparseBC.R |only
R/matrixBC.R | 16 +++++++++++++++-
R/print.matrixBC.R |only
R/print.sparseBC.R |only
R/sparseBC.R | 29 ++++++++++++++++++++++++++---
R/summary.matrixBC.R |only
R/summary.sparseBC.R |only
man/image.sparseBC.Rd |only
man/lung.Rd | 2 +-
man/matrixBC.BIC.Rd | 8 ++++----
man/matrixBC.Rd | 31 ++++++++++++++++++++++---------
man/sparseBC-package.Rd | 42 +++++++++++++++++++++++-------------------
man/sparseBC.BIC.Rd | 6 +++---
man/sparseBC.Rd | 29 +++++++++++++++++++++--------
man/sparseBC.choosekr.Rd | 34 +++++++++++++++++-----------------
man/summary.sparseBC.Rd |only
20 files changed, 169 insertions(+), 83 deletions(-)
Title: Spectral Analysis for Physical Applications
Diff between sapa versions 2.0-0 dated 2013-12-30 and 2.0-1 dated 2015-02-15
Description: Software for the book Spectral Analysis for Physical
Applications, Donald B. Percival and Andrew T. Walden,
Cambridge University Press, 1993.
Author: William Constantine and Donald Percival (Applied Physics
Laboratory, University of Washington)
Maintainer: Don Percival
DESCRIPTION | 10
MD5 | 10
NAMESPACE | 3
man/ACVS.Rd | 82 ++++----
man/SDF.Rd | 596 +++++++++++++++++++++++++++++------------------------------
man/taper.Rd | 587 +++++++++++++++++++++++++++++-----------------------------
6 files changed, 646 insertions(+), 642 deletions(-)
Title: Bayesian Optimal Interval Design for Phase I Clinical Trials
Diff between BOIN versions 1.0 dated 2014-09-19 and 1.1 dated 2015-02-15
Description: The Bayesian optimal interval (BOIN) design is a novel phase I clinical trial design for finding the maximum tolerated dose (MTD). The BOIN design is motivated by the top priority and concern of clinicians when testing a new drug, which is to effectively treat patients and minimize the chance of exposing them to subtherapeutic or overly toxic doses. The prominent advantage of the BOIN design is that it achieves simplicity and superior performance at the same time. The BOIN design is algorithm-based and can be implemented in a simple way similar to the traditional 3+3 design. The BOIN design yields average performance comparable to the continual reassessment method (CRM, one of the best model-based design) in terms of selecting the MTD, but has a substantially lower risk of assigning patients to subtherapeutic or overly toxic doses.
Author: Ying Yuan and Suyu Liu
Maintainer: Ying Yuan
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
R/get.boundary.R | 32 ++++++++++++++++++--------------
R/get.oc.R | 43 ++++++++++++++++++++++++-------------------
man/BOIN-package.Rd | 6 +++---
man/get.boundary.Rd | 18 +++++++++++++-----
man/get.oc.Rd | 19 ++++++++++++++-----
man/select.mtd.Rd | 2 +-
8 files changed, 84 insertions(+), 58 deletions(-)
Title: A Tool Set for Analyzing Political Behavior Data
Diff between SciencesPo versions 0.11.21 dated 2014-11-21 and 1.02.12 dated 2015-02-14
Description: A data analysis tool for the political science crowd
for ease analyzing random and nonrandom data.
Author: Daniel Marcelino
Maintainer: Daniel Marcelino
SciencesPo-0.11.21/SciencesPo/R/KFpredict.R |only
SciencesPo-0.11.21/SciencesPo/R/KFupdate.R |only
SciencesPo-0.11.21/SciencesPo/R/accent.R |only
SciencesPo-0.11.21/SciencesPo/R/add.alpha.R |only
SciencesPo-0.11.21/SciencesPo/R/add.footnote.R |only
SciencesPo-0.11.21/SciencesPo/R/anonymize.R |only
SciencesPo-0.11.21/SciencesPo/R/as.beta.R |only
SciencesPo-0.11.21/SciencesPo/R/beta.parms.R |only
SciencesPo-0.11.21/SciencesPo/R/cv.R |only
SciencesPo-0.11.21/SciencesPo/R/data.clean.R |only
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SciencesPo-1.02.12/SciencesPo/MD5 | 292 ++++++++------
SciencesPo-1.02.12/SciencesPo/NAMESPACE | 271 +++++++-----
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261 files changed, 974 insertions(+), 921 deletions(-)
Title: Tools for Reading SDMX Data and Metadata
Diff between rsdmx versions 0.4-4 dated 2015-01-16 and 0.4-5 dated 2015-02-14
Description: Set of classes and methods to read data and metadata documents
exchanged through the Statistical Data and Metadata Exchange (SDMX) framework,
currently focusing on the SDMX XML standard format (SDMX-ML).
Author: Emmanuel Blondel [aut, cre],
Matthieu Stigler [ctb]
Maintainer: Emmanuel Blondel
DESCRIPTION | 16 ++++++------
MD5 | 10 +++----
R/SDMXGenericData-methods.R | 56 +++++++++++++++++++++++++++++---------------
README.md | 8 +++---
man/readSDMX.Rd | 22 +++++++++++++++--
man/rsdmx-package.Rd | 4 +--
6 files changed, 77 insertions(+), 39 deletions(-)
Title: Multidimensional Latent Class Item Response Theory Models
Diff between MultiLCIRT versions 2.7 dated 2014-06-22 and 2.9 dated 2015-02-14
Description: Framework for the Item Response Theory analysis of dichotomous and ordinal polytomous outcomes under the assumption of multidimensionality and discreteness of the latent traits. The fitting algorithms allow for missing responses and for different item parameterizations and are based on the Expectation-Maximization paradigm. Individual covariates affecting the class weights may be included in the new version (since 2.1).
Author: Francesco Bartolucci, Silvia Bacci, Michela Gnaldi - University of Perugia (IT)
Maintainer: Francesco Bartolucci
DESCRIPTION | 12 +++---
MD5 | 22 +++++------
NAMESPACE | 10 +++++
R/est_multi_glob.R | 49 +++++++++----------------
R/est_multi_poly.R | 38 +++++++++++--------
R/est_multi_poly_clust.R | 89 +++++++++++++++++++++-------------------------
R/inv_glob.R | 9 ++--
R/lk_obs_score_clust.R | 22 ++++++++---
R/prob_multi_glob.R | 4 --
man/MultiLCIRT-package.Rd | 6 +--
man/est_multi_glob.Rd | 6 ++-
man/est_multi_poly.Rd | 8 ++--
12 files changed, 143 insertions(+), 132 deletions(-)
Title: Functions and Datasets for the Book by Keon-Woong Moon
Diff between moonBook versions 0.1.1 dated 2014-12-04 and 0.1.3 dated 2015-02-14
Description: Several analysis-related functions for the book entitled "R
statistics and graph for medical articles" (written in Korean), version 1,
by Keon-Woong Moon with Korean demographic data with several plot
functions.
Author: Keon-Woong Moon [aut, cre]
Maintainer: Keon-Woong Moon
moonBook-0.1.1/moonBook/man/myhtml.cbind.mytable.Rd |only
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moonBook-0.1.3/moonBook/DESCRIPTION | 15
moonBook-0.1.3/moonBook/MD5 | 115 -
moonBook-0.1.3/moonBook/NAMESPACE | 15
moonBook-0.1.3/moonBook/NEWS | 18
moonBook-0.1.3/moonBook/R/ORplot.R | 69
moonBook-0.1.3/moonBook/R/myhtml.R | 57
moonBook-0.1.3/moonBook/R/mylatex.R | 109 -
moonBook-0.1.3/moonBook/R/mytable.R | 15
moonBook-0.1.3/moonBook/README.md | 472 +++---
moonBook-0.1.3/moonBook/build/vignette.rds |binary
moonBook-0.1.3/moonBook/inst/doc/moonBook.R | 61
moonBook-0.1.3/moonBook/inst/doc/moonBook.Rmd | 88 -
moonBook-0.1.3/moonBook/inst/doc/moonBook.html | 1492 ++++++++++++-------
moonBook-0.1.3/moonBook/man/HRplot.Rd | 3
moonBook-0.1.3/moonBook/man/ORplot.Rd | 3
moonBook-0.1.3/moonBook/man/ORplot.sub.Rd | 3
moonBook-0.1.3/moonBook/man/acs.Rd | 3
moonBook-0.1.3/moonBook/man/cbind.mytable.Rd | 3
moonBook-0.1.3/moonBook/man/centerprint.Rd | 3
moonBook-0.1.3/moonBook/man/densityplot.Rd | 3
moonBook-0.1.3/moonBook/man/extractHR.Rd | 3
moonBook-0.1.3/moonBook/man/extractOR.Rd | 3
moonBook-0.1.3/moonBook/man/my.chisq.test.Rd | 3
moonBook-0.1.3/moonBook/man/my.t.test.Rd | 3
moonBook-0.1.3/moonBook/man/mycph.Rd | 3
moonBook-0.1.3/moonBook/man/mycsv.Rd | 3
moonBook-0.1.3/moonBook/man/mycsv.cbind.mytable.Rd | 3
moonBook-0.1.3/moonBook/man/mycsv.mytable.Rd | 3
moonBook-0.1.3/moonBook/man/myhtml.Rd | 34
moonBook-0.1.3/moonBook/man/myhtmlHead.Rd | 3
moonBook-0.1.3/moonBook/man/mylatex.Rd | 48
moonBook-0.1.3/moonBook/man/mytable.Rd | 3
moonBook-0.1.3/moonBook/man/mytable.sub.Rd | 3
moonBook-0.1.3/moonBook/man/mytable2.Rd | 3
moonBook-0.1.3/moonBook/man/mytable2df.Rd | 3
moonBook-0.1.3/moonBook/man/mytable2html.Rd | 3
moonBook-0.1.3/moonBook/man/num_summary.Rd | 3
moonBook-0.1.3/moonBook/man/obj2linecount.Rd | 3
moonBook-0.1.3/moonBook/man/p2sig.Rd | 3
moonBook-0.1.3/moonBook/man/print.cbind.mytable.Rd | 3
moonBook-0.1.3/moonBook/man/print.mytable.Rd | 3
moonBook-0.1.3/moonBook/man/printmytable2.Rd | 3
moonBook-0.1.3/moonBook/man/r.Rd | 3
moonBook-0.1.3/moonBook/man/radial.Rd | 3
moonBook-0.1.3/moonBook/man/rank2group.Rd | 3
moonBook-0.1.3/moonBook/man/reprint.Rd | 3
moonBook-0.1.3/moonBook/man/space.Rd | 3
moonBook-0.1.3/moonBook/man/summary.cbind.mytable.Rd | 3
moonBook-0.1.3/moonBook/man/summary.mytable.Rd | 3
moonBook-0.1.3/moonBook/man/validColname.Rd | 3
moonBook-0.1.3/moonBook/vignettes/figure |only
moonBook-0.1.3/moonBook/vignettes/moonBook.Rmd | 88 -
56 files changed, 1748 insertions(+), 1053 deletions(-)
Title: Methods that Apply to Rows and Columns of a Matrix
Diff between matrixStats versions 0.13.1 dated 2015-01-22 and 0.14.0 dated 2015-02-13
Description: Methods operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). There are also some vector-based methods, e.g. binMeans(), madDiff() and weightedMedians(). All methods have been optimized for speed and memory usage.
Author: Henrik Bengtsson [aut, cre, cph], Hector Corrada Bravo [ctb], Robert Gentleman [ctb], Ola Hossjer [ctb], Harris Jaffee [ctb], Peter Langfelder [ctb]
Maintainer: Henrik Bengtsson
matrixStats-0.13.1/matrixStats/R/anyMissing.S4.R |only
matrixStats-0.14.0/matrixStats/DESCRIPTION | 12
matrixStats-0.14.0/matrixStats/MD5 | 92 ++--
matrixStats-0.14.0/matrixStats/NAMESPACE | 2
matrixStats-0.14.0/matrixStats/NEWS | 39 +
matrixStats-0.14.0/matrixStats/R/anyMissing.R |only
matrixStats-0.14.0/matrixStats/R/benchmark.R | 2
matrixStats-0.14.0/matrixStats/R/pkgStartupMessage.R |only
matrixStats-0.14.0/matrixStats/R/rowCounts.R | 21
matrixStats-0.14.0/matrixStats/R/rowMads.R | 38 +
matrixStats-0.14.0/matrixStats/R/rowSds.R | 3
matrixStats-0.14.0/matrixStats/R/rowVars.R | 6
matrixStats-0.14.0/matrixStats/R/varDiff.R | 18
matrixStats-0.14.0/matrixStats/R/weightedMedian.R | 225 ----------
matrixStats-0.14.0/matrixStats/R/zzz.R | 1
matrixStats-0.14.0/matrixStats/build/vignette.rds |binary
matrixStats-0.14.0/matrixStats/inst/benchmarking/colRowMads.md.rsp | 23 +
matrixStats-0.14.0/matrixStats/inst/doc/matrixStats-methods.html | 80 ++-
matrixStats-0.14.0/matrixStats/inst/doc/matrixStats-methods.md.rsp | 90 ++--
matrixStats-0.14.0/matrixStats/man/anyMissing.Rd | 3
matrixStats-0.14.0/matrixStats/man/matrixStats-package.Rd | 2
matrixStats-0.14.0/matrixStats/man/rowSds.Rd | 7
matrixStats-0.14.0/matrixStats/man/rowVars.Rd | 4
matrixStats-0.14.0/matrixStats/src/allocMatrix2.c | 2
matrixStats-0.14.0/matrixStats/src/logSumExp_internal.c | 66 +-
matrixStats-0.14.0/matrixStats/src/psortKM.c | 2
matrixStats-0.14.0/matrixStats/src/rowCumMinMaxs_TYPE-template.h | 8
matrixStats-0.14.0/matrixStats/src/rowCumprods_TYPE-template.h | 10
matrixStats-0.14.0/matrixStats/src/rowCumsums_TYPE-template.h | 8
matrixStats-0.14.0/matrixStats/src/rowMads_TYPE-template.h | 9
matrixStats-0.14.0/matrixStats/src/rowMedians_TYPE-template.h | 13
matrixStats-0.14.0/matrixStats/src/rowVars_TYPE-template.h | 5
matrixStats-0.14.0/matrixStats/src/types.h | 4
matrixStats-0.14.0/matrixStats/tests/anyMissing.R | 2
matrixStats-0.14.0/matrixStats/tests/benchmark.R |only
matrixStats-0.14.0/matrixStats/tests/indexByRow.R | 7
matrixStats-0.14.0/matrixStats/tests/logSumExp.R | 64 ++
matrixStats-0.14.0/matrixStats/tests/rowAllAnys.R | 94 +++-
matrixStats-0.14.0/matrixStats/tests/rowCounts.R | 24 +
matrixStats-0.14.0/matrixStats/tests/rowIQRs.R | 57 ++
matrixStats-0.14.0/matrixStats/tests/rowLogSumExps.R | 99 ++++
matrixStats-0.14.0/matrixStats/tests/rowMads.R | 4
matrixStats-0.14.0/matrixStats/tests/rowRanges.R | 9
matrixStats-0.14.0/matrixStats/tests/rowTabulates.R | 5
matrixStats-0.14.0/matrixStats/tests/rowWeightedVars.R |only
matrixStats-0.14.0/matrixStats/tests/sumOver.R | 43 +
matrixStats-0.14.0/matrixStats/tests/varDiff_etal.R | 25 -
matrixStats-0.14.0/matrixStats/tests/weightedMedian.R | 42 -
matrixStats-0.14.0/matrixStats/tests/zzz.package-unload.R |only
matrixStats-0.14.0/matrixStats/vignettes/matrixStats-methods.md.rsp | 90 ++--
50 files changed, 841 insertions(+), 519 deletions(-)
Title: Phylogenetic Analysis in R
Diff between phangorn versions 1.99-11 dated 2014-11-11 and 1.99-12 dated 2015-02-13
Description: Phylogenetic analysis in R: Estimation of phylogenetic
trees and networks using Maximum Likelihood, Maximum Parsimony,
distance methods and Hadamard conjugation.
Author: Klaus Schliep, Emmanuel Paradis
Maintainer: Klaus Schliep
DESCRIPTION | 21 +-
MD5 | 80 +++++----
NAMESPACE | 11 -
NEWS | 32 +++
R/RcppExports.R |only
R/fitch.R | 6
R/neighborNet.R |only
R/networx.R | 328 +++++++++++++++++++++++++++++++++-------
R/parsimony.R | 161 +++++++------------
R/phylo.R | 318 +++++++++++++-------------------------
R/treeManipulation.R | 43 ++++-
R/treedist.R | 19 --
build/vignette.rds |binary
inst/doc/Ancestral.R | 14 -
inst/doc/Ancestral.Rnw | 15 -
inst/doc/Networx.R |only
inst/doc/Networx.Rmd |only
inst/doc/Networx.html |only
inst/doc/Trees.R | 44 ++---
inst/doc/Trees.Rnw | 9 -
inst/doc/phangorn-specials.R | 18 +-
inst/doc/phangorn-specials.Rnw | 27 +--
man/SOWH.test.Rd | 2
man/ancestral.pml.Rd | 5
man/as.splits.Rd | 6
man/bootstrap.pml.Rd | 8
man/consensusNet.Rd | 4
man/densiTree.Rd | 4
man/designTree.Rd | 104 ++++++------
man/neighborNet.Rd |only
man/plot.networx.Rd | 10 -
man/read.aa.Rd | 87 +++++-----
man/splitsNetwork.Rd | 14 -
src/dist.c | 2
src/fitch.c | 34 +++-
src/init.c | 26 +--
src/ml.c | 2
src/phangorn.c | 2
src/sankoff.c | 135 +++-------------
vignettes/Ancestral.Rnw | 15 -
vignettes/Networx.Rmd |only
vignettes/Trees.Rnw | 9 -
vignettes/movie.gif |only
vignettes/phangorn-specials.Rnw | 27 +--
vignettes/phangorn.bib | 43 +++++
45 files changed, 919 insertions(+), 766 deletions(-)
Title: Variable Selection Deviation Measures and Instability Tests for
High-Dimensional Generalized Linear Models
Diff between glmvsd versions 1.1 dated 2014-11-21 and 1.2 dated 2015-02-13
Description: Variable selection deviation (VSD) measures and instability tests for high-dimensional model selection methods such as LASSO, SCAD and MCP, etc., to decide whether the sparse patterns identified by those methods are reliable.
Author: Ying Nan
Maintainer: Yi Yang
ChangeLog | 3 +++
DESCRIPTION | 12 ++++++------
MD5 | 6 +++---
R/lsARM.R | 2 +-
4 files changed, 13 insertions(+), 10 deletions(-)
Title: Bridge Regression
Diff between BayesBridge versions 0.5 dated 2014-07-21 and 0.6 dated 2015-02-13
Description: Bayesian bridge regression.
Author: Nicholas G. Polson, James G. Scott, and Jesse Windle
Maintainer: Jesse Windle
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
R/BridgeNMix.R | 2 +-
R/BridgeWrapper.R | 3 +--
4 files changed, 10 insertions(+), 11 deletions(-)
Title: Regression Estimation and Presentation
Diff between rockchalk versions 1.8.91 dated 2015-01-30 and 1.8.92 dated 2015-02-13
Description: A collection of functions for ease of
presentation and interpretation of regression analysis.
These functions are used to produce the statistics lectures
in http://pj.freefaculty.org/guides. There
are functions to explore the effect (or lack thereof) from
"mean centering," "residual centering", and standardization.
The vignette "rockchalk" offers a fairly comprehensive overview.
The vignette "Rstyle" has advice about coding in R.
See the outreg function for a convenient way to generate
regression models for reports. For nice, easy to use pictures,
see plotSlopes, plotCurves, plotPlane.
The package title "rockchalk" refers to our school motto,
"Rock Chalk Jayhawk, Go K.U.".
Author: Paul E. Johnson
Maintainer: Paul E. Johnson
DESCRIPTION | 8 ++++----
MD5 | 20 ++++++++++----------
R/genCorrelatedData.R | 7 ++-----
R/pctable.R | 8 ++++++--
R/plotCurves.R | 9 ++++++---
R/predictOMatic.R | 4 ++--
inst/ChangeLog | 5 +++++
inst/doc/Rchaeology.pdf |binary
inst/doc/Rstyle.pdf |binary
inst/doc/rockchalk.pdf |binary
man/mvrnorm.Rd | 6 +-----
11 files changed, 36 insertions(+), 31 deletions(-)
Title: Extraction of Business Financial Information from XBRL Documents
Diff between XBRL versions 0.99.14 dated 2015-01-08 and 0.99.15 dated 2015-02-13
Description:
Functions to extract business financial information from
an Extensible Business Reporting Language (XBRL) instance file and the
associated collection of files that defines its Discoverable Taxonomy
Set (DTS), usually disseminated across different remote locations.
XBRL documents employ many technologies defined by XML standards, such
as XML Schema, Namespaces, XLink, and XPath, which make the extraction
of information involved. The functions provided by this package
address this complexity, returning data frames containing the enclosed
information readily available to perform analyses.
XBRL has been successfully tested in analyzing 10-K and 10-Q
submissions from USA filing companies that are publicly available at
the EDGAR system of the Securities and Exchange Commission (SEC).
It has been reported to work with inline XBRL documents.
As published taxonomy files (such as
"http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd")
are immutable and are used by most filers, XBRL offers the option of
downloading them only the first time they are referred, keeping a
local cache copy that can be used from then on. This speeds-up the
process, specially on slow connections.
XBRL is not and does not aim to be (at least yet) a validating XBRL
processor.
XBRL is still a work in progress. As such, functions and produced data
frames may change structure in future versions until stabilization.
Author: Roberto Bertolusso and Marek Kimmel
Maintainer: Roberto Bertolusso
ChangeLog | 8 +++++
DESCRIPTION | 16 +++++-----
MD5 | 66 +++++++++++++++++++++----------------------
R/XBRL.R | 2 -
R/xbrlDoAll.R | 2 -
R/xbrlFree.R | 2 -
R/xbrlGetImportNames.R | 2 -
R/xbrlGetLinkbaseNames.R | 2 -
R/xbrlGetSchemaName.R | 2 -
R/xbrlParse.R | 2 -
R/xbrlProcessArcs.R | 2 -
R/xbrlProcessContexts.R | 2 -
R/xbrlProcessElements.R | 2 -
R/xbrlProcessFacts.R | 2 -
R/xbrlProcessFootnotes.R | 2 -
R/xbrlProcessLabels.R | 2 -
R/xbrlProcessRoles.R | 2 -
R/xbrlProcessUnits.R | 2 -
R/xbrlSECdev01.R | 2 -
man/XBRL-package.Rd | 8 ++---
src/XBRL.h | 2 -
src/xbrlFree.cpp | 2 -
src/xbrlGetImportNames.cpp | 2 -
src/xbrlGetLinkbaseNames.cpp | 2 -
src/xbrlGetSchemaName.cpp | 2 -
src/xbrlParse.cpp | 2 -
src/xbrlProcessArcs.cpp | 2 -
src/xbrlProcessContexts.cpp | 2 -
src/xbrlProcessElements.cpp | 2 -
src/xbrlProcessFacts.cpp | 7 +++-
src/xbrlProcessFootnotes.cpp | 2 -
src/xbrlProcessLabels.cpp | 2 -
src/xbrlProcessRoles.cpp | 2 -
src/xbrlProcessUnits.cpp | 2 -
34 files changed, 87 insertions(+), 76 deletions(-)
Title: Teitz and Bart's p-Median Algorithm
Diff between tbart versions 0.9.1 dated 2014-08-16 and 1.0 dated 2015-02-13
Description: Solves Teitz and Bart's p-median problem - given a set of
points attempts to find subset of size p such that summed distances of any
point in the set to the nearest point in p is minimised. Although
generally effective, this algorithm does not guarantee that a globally
optimal subset is found.
Author: Chris Brunsdon
Maintainer: Chris Brunsdon
DESCRIPTION | 13 +--
MD5 | 26 +++---
R/RcppExports.R | 8 +
R/tbart-describes.R | 7 -
R/tbmain.R | 218 ++++++++++++++++++++++++++++++++++++++++++---------
man/allocate.Rd | 12 +-
man/allocations.Rd |only
man/euc.dists.Rd | 2
man/mink.dists.Rd |only
man/star.diagram.Rd | 12 ++
man/tb.Rd | 10 +-
man/tb.raw.Rd | 2
man/tbart-package.Rd | 22 ++---
src/RcppExports.cpp | 37 ++++++++
src/tb.cpp | 54 ++++++++++++
15 files changed, 343 insertions(+), 80 deletions(-)
Title: R Interface For OAuth
Diff between ROAuth versions 0.9.5 dated 2014-12-03 and 0.9.6 dated 2015-02-13
Description: Provides an interface to the OAuth 1.0 specification
allowing users to authenticate via OAuth to the
server of their choice.
Author: Jeff Gentry
Maintainer: Pablo Barbera
DESCRIPTION | 8 ++++----
MD5 | 2 +-
2 files changed, 5 insertions(+), 5 deletions(-)
Title: Differential Expression from Multiple Indicators
Diff between demi versions 1.1.1 dated 2013-11-05 and 1.1.2 dated 2015-02-13
Description: Implementation of the DEMI method for the analysis of high-density microarray data.
Author: Sten Ilmjarv [aut, cre],
Hendrik Luuk [aut]
Maintainer: Sten Ilmjarv
demi-1.1.1/demi/inst/doc/demi.R |only
demi-1.1.2/demi/DESCRIPTION | 16
demi-1.1.2/demi/MD5 | 232 +++++-----
demi-1.1.2/demi/NAMESPACE | 97 ++--
demi-1.1.2/demi/R/AllClasses.R | 6
demi-1.1.2/demi/R/AllGenerics.R | 54 ++
demi-1.1.2/demi/R/Constructors.R | 6
demi-1.1.2/demi/R/DEMICel-methods.R | 3
demi-1.1.2/demi/R/DEMIClust-methods.R | 12
demi-1.1.2/demi/R/DEMIDiff-methods.R | 27 -
demi-1.1.2/demi/R/DEMIExperiment-methods.R | 121 +++--
demi-1.1.2/demi/R/DEMIGroup-methods.R | 8
demi-1.1.2/demi/R/DEMIResult-methods.R | 5
demi-1.1.2/demi/R/custom-methods.R | 2
demi-1.1.2/demi/R/diffexp-methods.R | 6
demi-1.1.2/demi/R/messages.R | 2
demi-1.1.2/demi/R/normalization-methods.R | 4
demi-1.1.2/demi/R/zzz.R | 2
demi-1.1.2/demi/build |only
demi-1.1.2/demi/inst/doc/demi.Rnw | 6
demi-1.1.2/demi/inst/doc/demi.pdf |binary
demi-1.1.2/demi/man/DEMICel-class.Rd | 14
demi-1.1.2/demi/man/DEMICel-methods.Rd | 29 -
demi-1.1.2/demi/man/DEMIClust-class.Rd | 44 -
demi-1.1.2/demi/man/DEMIClust-methods.Rd | 152 ++----
demi-1.1.2/demi/man/DEMIDiff-class.Rd | 26 -
demi-1.1.2/demi/man/DEMIDiff-methods.Rd | 42 -
demi-1.1.2/demi/man/DEMIExperiment-class.Rd | 158 ++----
demi-1.1.2/demi/man/DEMIExperiment-methods.Rd | 218 +++------
demi-1.1.2/demi/man/DEMIGroup-class.Rd | 26 -
demi-1.1.2/demi/man/DEMIGroup-methods.Rd | 51 --
demi-1.1.2/demi/man/DEMIMessages.Rd | 191 +++++++-
demi-1.1.2/demi/man/DEMIPathway-methods.Rd | 31 -
demi-1.1.2/demi/man/DEMIResult-class.Rd | 16
demi-1.1.2/demi/man/DEMIWrap-methods.Rd | 341 +++++----------
demi-1.1.2/demi/man/addCustomTargets-methods.Rd | 75 +--
demi-1.1.2/demi/man/addCytoband-methods.Rd | 27 -
demi-1.1.2/demi/man/adjust4maxprobes-methods.Rd | 22
demi-1.1.2/demi/man/attachResult-methods.Rd | 62 +-
demi-1.1.2/demi/man/calcHypergeoExon-methods.Rd | 16
demi-1.1.2/demi/man/calcHypergeoProb-methods.Rd | 16
demi-1.1.2/demi/man/celMatrixNormalize-methods.Rd | 24 -
demi-1.1.2/demi/man/check4probe-methods.Rd | 29 -
demi-1.1.2/demi/man/check4target-methods.Rd | 28 -
demi-1.1.2/demi/man/checkDEMIExperiment_analysis.Rd | 16
demi-1.1.2/demi/man/checkDEMIExperiment_celpath.Rd | 16
demi-1.1.2/demi/man/checkDEMIExperiment_experiment.Rd | 15
demi-1.1.2/demi/man/checkDEMIExperiment_maxprobes.Rd | 15
demi-1.1.2/demi/man/checkDEMIExperiment_maxtargets.Rd | 15
demi-1.1.2/demi/man/checkDEMIExperiment_normalization.Rd | 20
demi-1.1.2/demi/man/checkDEMIExperiment_pmsize.Rd | 18
demi-1.1.2/demi/man/cleanorganismname-methods.Rd | 15
demi-1.1.2/demi/man/cluster-methods.Rd | 26 -
demi-1.1.2/demi/man/createGroup-methods.Rd | 26 -
demi-1.1.2/demi/man/customObject-methods.Rd | 25 -
demi-1.1.2/demi/man/demi.comp.test-methods.Rd | 30 -
demi-1.1.2/demi/man/demi.t.test-methods.Rd | 26 -
demi-1.1.2/demi/man/demi.wilcox.test-methods.Rd | 26 -
demi-1.1.2/demi/man/demi.wilcox.test.fast-methods.Rd | 30 -
demi-1.1.2/demi/man/demiequal-methods.Rd | 28 -
demi-1.1.2/demi/man/demisummary-methods.Rd | 60 +-
demi-1.1.2/demi/man/diffSpliceScore-methods.Rd | 16
demi-1.1.2/demi/man/diffexp-methods.Rd | 22
demi-1.1.2/demi/man/findCytoband-methods.Rd | 21
demi-1.1.2/demi/man/getAlignment-methods.Rd | 22
demi-1.1.2/demi/man/getAnalysis-methods.Rd | 22
demi-1.1.2/demi/man/getAnnotation-methods.Rd | 22
demi-1.1.2/demi/man/getArraytype-methods.Rd | 20
demi-1.1.2/demi/man/getCelMatrix-methods.Rd | 22
demi-1.1.2/demi/man/getCelpath-methods.Rd | 24 -
demi-1.1.2/demi/man/getClustMethod-methods.Rd | 21
demi-1.1.2/demi/man/getCluster-methods.Rd | 21
demi-1.1.2/demi/man/getCutoffPvalue-methods.Rd | 23 -
demi-1.1.2/demi/man/getCytoband-methods.Rd | 29 -
demi-1.1.2/demi/man/getDEMIClust-methods.Rd | 20
demi-1.1.2/demi/man/getExperiment-methods.Rd | 39 -
demi-1.1.2/demi/man/getGroup-methods.Rd | 24 -
demi-1.1.2/demi/man/getGroupA-methods.Rd | 21
demi-1.1.2/demi/man/getGroupB-methods.Rd | 21
demi-1.1.2/demi/man/getGroupNames-methods.Rd | 24 -
demi-1.1.2/demi/man/getIndexA-methods.Rd | 21
demi-1.1.2/demi/man/getIndexB-methods.Rd | 21
demi-1.1.2/demi/man/getMaxprobes-methods.Rd | 30 -
demi-1.1.2/demi/man/getMaxtargets-methods.Rd | 29 -
demi-1.1.2/demi/man/getName-methods.Rd | 24 -
demi-1.1.2/demi/man/getNormMatrix-methods.Rd | 22
demi-1.1.2/demi/man/getOrganism-methods.Rd | 21
demi-1.1.2/demi/man/getPathway-methods.Rd | 26 -
demi-1.1.2/demi/man/getProbeLevel-methods.Rd | 39 -
demi-1.1.2/demi/man/getResult-methods.Rd | 48 +-
demi-1.1.2/demi/man/getResultTable-methods.Rd | 27 -
demi-1.1.2/demi/man/getTargetAnnotation-methods.Rd | 39 -
demi-1.1.2/demi/man/getTargetProbes-methods.Rd | 45 +
demi-1.1.2/demi/man/initialize.DEMICel.Rd | 14
demi-1.1.2/demi/man/initialize.DEMIClust.Rd | 14
demi-1.1.2/demi/man/initialize.DEMIDiff.Rd | 14
demi-1.1.2/demi/man/initialize.DEMIExperiment.Rd | 14
demi-1.1.2/demi/man/initialize.DEMIGroup.Rd | 14
demi-1.1.2/demi/man/initialize.DEMIResult.Rd | 14
demi-1.1.2/demi/man/loadAnnotation-methods.Rd | 23 -
demi-1.1.2/demi/man/loadBlat-methods.Rd | 23 -
demi-1.1.2/demi/man/loadCel-methods.Rd | 24 -
demi-1.1.2/demi/man/loadCytoband-methods.Rd | 23 -
demi-1.1.2/demi/man/loadDEMILibrary-methods.Rd | 33 -
demi-1.1.2/demi/man/loadPathway-methods.Rd | 23 -
demi-1.1.2/demi/man/makeDEMIResultsTable-methods.Rd | 21
demi-1.1.2/demi/man/makeUCSCLink-methods.Rd | 19
demi-1.1.2/demi/man/matchExonGene-methods.Rd | 23 -
demi-1.1.2/demi/man/norm.quantile-methods.Rd | 21
demi-1.1.2/demi/man/norm.rrank-methods.Rd | 22
demi-1.1.2/demi/man/probe.levels-methods.Rd | 31 -
demi-1.1.2/demi/man/probe.plot-methods.Rd | 31 -
demi-1.1.2/demi/man/totalMatches_all-methods.Rd | 17
demi-1.1.2/demi/man/totalMatches_cluster-methods.Rd | 20
demi-1.1.2/demi/man/validDEMIClust.Rd | 12
demi-1.1.2/demi/man/validDEMIExperiment.Rd | 10
demi-1.1.2/demi/man/wprob-methods.Rd | 22
demi-1.1.2/demi/vignettes/demi.Rnw | 6
118 files changed, 2107 insertions(+), 1861 deletions(-)
Title: Community Assembly by Traits: Individuals and Beyond
Diff between cati versions 0.8 dated 2014-06-24 and 0.96 dated 2015-02-13
Description: A package to detect and quantify community assembly processes
using trait values of individuals or populations, the T-statistics and
other metrics, and dedicated null models.
Author: Adrien Taudiere, Cyrille Violle with contribution of Francois Munoz
Maintainer: Adrien Taudiere
cati-0.8/cati/man/ab_to_ind.Rd |only
cati-0.8/cati/man/bar_partvar.Rd |only
cati-0.8/cati/man/com.index.Rd |only
cati-0.8/cati/man/com.index.multi.Rd |only
cati-0.8/cati/man/decomp_whithin.Rd |only
cati-0.8/cati/man/pie_partvar.Rd |only
cati-0.8/cati/man/plot_cor.Tstats.Rd |only
cati-0.8/cati/man/plot_dens.Rd |only
cati-0.8/cati/man/plot_randtest.Rd |only
cati-0.8/cati/man/plot_ses.var.Rd |only
cati-0.8/cati/man/plot_sp_pop.Rd |only
cati-0.8/cati/man/plot_sp_var.Rd |only
cati-0.8/cati/man/trait.flex.anova.Rd |only
cati-0.96/cati/DESCRIPTION | 16
cati-0.96/cati/MD5 | 61
cati-0.96/cati/NAMESPACE | 23
cati-0.96/cati/R/allfunctions_cati.r | 3140 ------------------------------
cati-0.96/cati/data/finch.ind.RData |binary
cati-0.96/cati/inst |only
cati-0.96/cati/man/AbToInd.Rd |only
cati-0.96/cati/man/Auxiliary.functions.rd |only
cati-0.96/cati/man/CVNND.Rd | 144 -
cati-0.96/cati/man/ComIndex.Rd |only
cati-0.96/cati/man/ComIndexMulti.Rd |only
cati-0.96/cati/man/Fred.Rd |only
cati-0.96/cati/man/IndexByGroups.Rd |only
cati-0.96/cati/man/MinMaxMST.Rd |only
cati-0.96/cati/man/Pval.Rd |only
cati-0.96/cati/man/RandCom.Rd |only
cati-0.96/cati/man/RaoRel.Rd | 348 +--
cati-0.96/cati/man/SumBL.Rd |only
cati-0.96/cati/man/Tstats.Rd | 490 ++--
cati-0.96/cati/man/as.listofindex.Rd | 166 -
cati-0.96/cati/man/cati-package.Rd | 60
cati-0.96/cati/man/decompCTRE.Rd |only
cati-0.96/cati/man/finch.ind.Rd | 74
cati-0.96/cati/man/partvar.Rd | 165 -
cati-0.96/cati/man/plot.listofindex.Rd | 388 +--
cati-0.96/cati/man/plotCorTstats.Rd |only
cati-0.96/cati/man/plotDistri.Rd |only
cati-0.96/cati/man/plotRandtest.Rd |only
cati-0.96/cati/man/plotSESvar.Rd |only
cati-0.96/cati/man/plotSpPop.Rd |only
cati-0.96/cati/man/plotSpVar.Rd |only
cati-0.96/cati/man/samplingSubsetData.Rd |only
cati-0.96/cati/man/ses.Rd | 124 -
cati-0.96/cati/man/ses.listofindex.Rd | 177 -
cati-0.96/cati/man/traitflex.anova.Rd |only
48 files changed, 1097 insertions(+), 4279 deletions(-)
Title: Hierarchical Modelling of Faecal Egg Counts
Diff between eggCounts versions 0.3 dated 2014-09-06 and 0.4-1 dated 2015-02-13
Description: An implementation of hierarchical models
for faecal egg count data to assess anthelmintic
efficacy. Bayesian inference is done via MCMC sampling.
Author: Michaela Paul [aut], Reinhard Furrer [cre, ctb]
Maintainer: Reinhard Furrer
eggCounts-0.3/eggCounts/tests/regtest-fecModelling.Rout.save |only
eggCounts-0.4-1/eggCounts/ChangeLog | 6
eggCounts-0.4-1/eggCounts/DESCRIPTION | 28 +-
eggCounts-0.4-1/eggCounts/MD5 | 132 +++++------
eggCounts-0.4-1/eggCounts/NAMESPACE | 2
eggCounts-0.4-1/eggCounts/R/FECR_PoGa.R | 67 ++++-
eggCounts-0.4-1/eggCounts/R/FEC_PoGa.R | 64 ++++-
eggCounts-0.4-1/eggCounts/R/MHsteps.R | 43 ++-
eggCounts-0.4-1/eggCounts/R/eggCounts-package.R | 8
eggCounts-0.4-1/eggCounts/R/printSummary.R | 21 +
eggCounts-0.4-1/eggCounts/R/profile.R | 6
eggCounts-0.4-1/eggCounts/R/updates.R | 68 ++++-
eggCounts-0.4-1/eggCounts/demo/fecm.R | 7
eggCounts-0.4-1/eggCounts/inst/NEWS | 13 +
eggCounts-0.4-1/eggCounts/man/MH_RW_unif.Rd | 16 -
eggCounts-0.4-1/eggCounts/man/MH_RW_unif01.Rd | 16 -
eggCounts-0.4-1/eggCounts/man/MHstep.Rd | 22 -
eggCounts-0.4-1/eggCounts/man/checkAR.Rd | 16 -
eggCounts-0.4-1/eggCounts/man/echinococcus.Rd | 11
eggCounts-0.4-1/eggCounts/man/eggCounts-package.Rd | 24 +-
eggCounts-0.4-1/eggCounts/man/epgs.Rd | 11
eggCounts-0.4-1/eggCounts/man/fc_approx_beta.Rd | 14 -
eggCounts-0.4-1/eggCounts/man/fc_approx_gamma.Rd | 12 -
eggCounts-0.4-1/eggCounts/man/fc_approx_invgamma.Rd | 12 -
eggCounts-0.4-1/eggCounts/man/fc_approx_logNormal.Rd | 12 -
eggCounts-0.4-1/eggCounts/man/fec_mcmc.Rd | 90 +++----
eggCounts-0.4-1/eggCounts/man/fecr_mcmc.Rd | 116 ++++-----
eggCounts-0.4-1/eggCounts/man/fecrtCI.Rd | 59 ++--
eggCounts-0.4-1/eggCounts/man/logdgammaMixture.Rd | 21 -
eggCounts-0.4-1/eggCounts/man/modeCurvature_delta.Rd | 16 -
eggCounts-0.4-1/eggCounts/man/modeCurvature_h.Rd | 15 -
eggCounts-0.4-1/eggCounts/man/modeCurvature_phi.Rd | 22 -
eggCounts-0.4-1/eggCounts/man/modeCurvature_psi.Rd | 18 -
eggCounts-0.4-1/eggCounts/man/print.fecm.Rd | 18 +
eggCounts-0.4-1/eggCounts/man/print.fecrm.Rd | 18 +
eggCounts-0.4-1/eggCounts/man/samples2mcmc.Rd | 10
eggCounts-0.4-1/eggCounts/man/setDefaults1.Rd | 41 +--
eggCounts-0.4-1/eggCounts/man/setDefaults2.Rd | 82 +++---
eggCounts-0.4-1/eggCounts/man/setInitials1.Rd | 20 +
eggCounts-0.4-1/eggCounts/man/setInitials2.Rd | 30 +-
eggCounts-0.4-1/eggCounts/man/setUpdates_PoGa2.Rd | 14 -
eggCounts-0.4-1/eggCounts/man/setUpdates_PoGa_mu.Rd | 14 -
eggCounts-0.4-1/eggCounts/man/setUpdates_PoGa_p.Rd | 22 -
eggCounts-0.4-1/eggCounts/man/setUpdates_PoGa_u.Rd | 22 -
eggCounts-0.4-1/eggCounts/man/setUpdates_ZIPoGa2.Rd | 14 -
eggCounts-0.4-1/eggCounts/man/setUpdates_ZIPoGa_mu.Rd | 14 -
eggCounts-0.4-1/eggCounts/man/setUpdates_ZIPoGa_u.Rd | 21 -
eggCounts-0.4-1/eggCounts/man/setUpdates_ZIPoGa_u_pd.Rd | 22 -
eggCounts-0.4-1/eggCounts/man/simData1s.Rd | 25 +-
eggCounts-0.4-1/eggCounts/man/simData2s.Rd | 37 +--
eggCounts-0.4-1/eggCounts/man/statusMsg.Rd | 10
eggCounts-0.4-1/eggCounts/man/tab1morgan.Rd | 56 ++--
eggCounts-0.4-1/eggCounts/man/update_Y.Rd | 16 -
eggCounts-0.4-1/eggCounts/man/update_delta_beta.Rd | 20 -
eggCounts-0.4-1/eggCounts/man/update_h_gamma.Rd | 22 -
eggCounts-0.4-1/eggCounts/man/update_h_invGamma.Rd | 20 -
eggCounts-0.4-1/eggCounts/man/update_h_kl.Rd | 25 --
eggCounts-0.4-1/eggCounts/man/update_h_logNormal.Rd | 19 -
eggCounts-0.4-1/eggCounts/man/update_phi_gamma.Rd | 24 +-
eggCounts-0.4-1/eggCounts/man/update_phi_unif.Rd | 24 +-
eggCounts-0.4-1/eggCounts/man/update_psi_beta.Rd | 29 +-
eggCounts-0.4-1/eggCounts/man/update_theta_beta.Rd | 17 -
eggCounts-0.4-1/eggCounts/man/update_theta_gamma.Rd | 14 -
eggCounts-0.4-1/eggCounts/man/update_theta_gamma1.Rd | 19 -
eggCounts-0.4-1/eggCounts/man/update_theta_gammaAdd.Rd | 18 -
eggCounts-0.4-1/eggCounts/man/update_theta_gammaMix.Rd | 31 +-
eggCounts-0.4-1/eggCounts/tests/regtest-fecModelling.Rout |only
eggCounts-0.4-1/eggCounts/tests/special-cases.R |only
eggCounts-0.4-1/eggCounts/tests/special-cases.Rout |only
69 files changed, 978 insertions(+), 798 deletions(-)
Title: TAP-Compliant Unit Testing
Diff between unittest versions 1.1-1 dated 2014-12-14 and 1.2-0 dated 2015-02-13
Description:
Concise TAP (http://testanything.org/) compliant unit testing package. Authored tests can be run using CMD check with minimal implementation overhead.
Author: Jamie Lentin [aut, cre],
Anthony Hennessey [aut]
Maintainer: Jamie Lentin
ChangeLog | 8 +
DESCRIPTION | 8 -
MD5 | 24 ++---
NEWS | 3
R/non_interactive_summary.R | 18 +---
R/ok.R | 14 +--
README.md | 4
man/ok.Rd | 14 +--
man/ok_group.Rd | 14 +--
man/unittest-package.Rd | 175 ++++++++++++++++++++-----------------------
tests/test_non_interactive.R | 36 +++++++-
tests/test_ok.R | 34 ++++----
tests/test_ok_group.R | 4
13 files changed, 188 insertions(+), 168 deletions(-)
Title: Variance Dispersion Graphs and Fraction of Design Space Plots
Diff between vdg versions 1.0 dated 2014-06-17 and 1.0.1 dated 2015-02-13
Description: Facilities for constructing variance dispersion graphs, fraction-of-design-space plots
and similar graphics for exploring the properties of experimental designs. The design region is
explored via random sampling, which allows for more flexibility than traditional variance
dispersion graphs. A formula interface is leveraged to provide access to complex model
formulae. Graphics can be constructed simultaneously for multiple experimental designs and/or
multiple model formulae. Instead of using pointwise optimization to find the minimum and
maximum scaled prediction variance curves, which can be inaccurate and time consuming, this
package uses quantile regression as an alternative.
Author: Pieter Schoonees [aut, cre, cph]
Maintainer: Pieter Schoonees
DESCRIPTION | 22 +-
MD5 | 64 +++----
NAMESPACE | 43 +++-
R/GJ54.R | 18 +-
R/LHS.R | 202 +++++++++++-----------
R/meanspv.R | 213 ++++++++++++-----------
R/plot.spv.R | 418 ++++++++++++++++++++++++-----------------------
R/plot.spvforlist.R | 282 +++++++++++++++----------------
R/plot.spvlist.R | 290 ++++++++++++++++----------------
R/plot.spvlistforlist.R | 310 +++++++++++++++++-----------------
R/print.spv.R | 46 ++---
R/print.spvforlist.R | 38 ++--
R/print.spvlist.R | 40 ++--
R/print.spvlistforlist.R | 36 ++--
R/runif_cube.R | 49 ++---
R/runif_sphere.R | 88 ++++-----
R/sampler.R | 62 +++---
R/spv.R | 72 ++++----
R/spv.data.frame.R | 156 ++++++++---------
R/spv.list.R | 140 +++++++--------
R/spv.matrix.R | 156 ++++++++---------
R/stdrange.R | 60 +++---
R/vdg-package.R | 26 +-
inst |only
man/GJ54.Rd | 33 +--
man/LHS.Rd | 119 ++++++-------
man/meanspv.Rd | 81 ++++-----
man/plot.spv.Rd | 272 +++++++++++++++---------------
man/print.spv.Rd | 61 +++---
man/runif_sphere.Rd | 85 ++++-----
man/sampler.Rd | 75 ++++----
man/spv.Rd | 133 +++++++-------
man/stdrange.Rd | 55 +++---
man/vdg-package.Rd |only
34 files changed, 1896 insertions(+), 1849 deletions(-)
Title: Functions for University of Auckland Course STATS 201/208 Data
Analysis
Diff between s20x versions 3.1-11 dated 2015-01-13 and 3.1-12 dated 2015-02-13
Description: A set of functions used in teaching STATS 201/208 Data Analysis at the University of Auckland. The functions are designed to make parts of R more accessible to a large undergraduate population who are mostly not statistics majors.
Author: Andrew Balemi, Dineika Chandra, James Curran, Brant Deppa, Mike Forster, Brendan McArdle, Chris Wild
Maintainer: James Curran
s20x-3.1-11/s20x/inst/rmarkdown/templates/STATS20x_Assignment/skeleton/styles.css |only
s20x-3.1-12/s20x/DESCRIPTION | 12
s20x-3.1-12/s20x/MD5 | 135 ++++----
s20x-3.1-12/s20x/inst/rmarkdown/templates/STATS20x_Assignment/skeleton/skeleton.Rmd | 48 +--
s20x-3.1-12/s20x/inst/rmarkdown/templates/STATS20x_Assignment/template.yaml | 7
s20x-3.1-12/s20x/man/airpass.df.Rd | 26 -
s20x-3.1-12/s20x/man/apples.df.Rd | 72 ++--
s20x-3.1-12/s20x/man/arousal.df.Rd | 36 +-
s20x-3.1-12/s20x/man/autocor.plot.Rd | 42 +-
s20x-3.1-12/s20x/man/beer.df.Rd | 26 -
s20x-3.1-12/s20x/man/body.df.Rd | 46 +-
s20x-3.1-12/s20x/man/books.df.Rd | 54 +--
s20x-3.1-12/s20x/man/boxqq.Rd | 60 +--
s20x-3.1-12/s20x/man/bursary.df.Rd | 34 +-
s20x-3.1-12/s20x/man/butterfat.df.Rd | 54 +--
s20x-3.1-12/s20x/man/camplake.df.Rd | 36 +-
s20x-3.1-12/s20x/man/chalk.df.Rd | 40 +-
s20x-3.1-12/s20x/man/ciReg.Rd | 52 +--
s20x-3.1-12/s20x/man/computer.df.Rd | 34 +-
s20x-3.1-12/s20x/man/cooks20x.Rd | 42 +-
s20x-3.1-12/s20x/man/course.df.Rd | 60 +--
s20x-3.1-12/s20x/man/course2way.df.Rd | 36 +-
s20x-3.1-12/s20x/man/crossFactors.Rd | 86 ++---
s20x-3.1-12/s20x/man/crosstabs.Rd | 54 +--
s20x-3.1-12/s20x/man/diamonds.df.Rd | 34 +-
s20x-3.1-12/s20x/man/eovcheck.Rd | 1
s20x-3.1-12/s20x/man/estimateContrasts.Rd | 74 ++--
s20x-3.1-12/s20x/man/fire.df.Rd | 34 +-
s20x-3.1-12/s20x/man/freq1way.Rd | 86 ++---
s20x-3.1-12/s20x/man/fruitfly.df.Rd | 50 +--
s20x-3.1-12/s20x/man/getVersion.Rd | 34 +-
s20x-3.1-12/s20x/man/house.df.Rd | 34 +-
s20x-3.1-12/s20x/man/incomes.df.Rd | 20 -
s20x-3.1-12/s20x/man/lakemary.df.Rd | 34 +-
s20x-3.1-12/s20x/man/larain.df.Rd | 26 -
s20x-3.1-12/s20x/man/layout20x.Rd | 46 +-
s20x-3.1-12/s20x/man/levene.test.Rd | 66 ++--
s20x-3.1-12/s20x/man/mazda.df.Rd | 34 +-
s20x-3.1-12/s20x/man/mening.df.Rd | 26 -
s20x-3.1-12/s20x/man/mergers.df.Rd | 20 -
s20x-3.1-12/s20x/man/mozart.df.Rd | 36 +-
s20x-3.1-12/s20x/man/multipleComp.Rd | 46 +-
s20x-3.1-12/s20x/man/nail.df.Rd | 38 +-
s20x-3.1-12/s20x/man/normcheck.Rd | 2
s20x-3.1-12/s20x/man/onewayPlot.Rd | 156 +++++-----
s20x-3.1-12/s20x/man/oysters.df.Rd | 34 +-
s20x-3.1-12/s20x/man/pairs20x.Rd | 56 +--
s20x-3.1-12/s20x/man/peru.df.Rd | 40 +-
s20x-3.1-12/s20x/man/predict20x.Rd | 108 +++---
s20x-3.1-12/s20x/man/propslsd.new.Rd | 32 +-
s20x-3.1-12/s20x/man/rain.df.Rd | 40 +-
s20x-3.1-12/s20x/man/residPlot.Rd | 60 +--
s20x-3.1-12/s20x/man/rowdistr.Rd | 1
s20x-3.1-12/s20x/man/rr.Rd | 14
s20x-3.1-12/s20x/man/seeds.df.Rd | 42 +-
s20x-3.1-12/s20x/man/sheep.df.Rd | 32 +-
s20x-3.1-12/s20x/man/skewness.Rd | 40 +-
s20x-3.1-12/s20x/man/skulls.df.Rd | 48 +--
s20x-3.1-12/s20x/man/soyabean.df.Rd | 38 +-
s20x-3.1-12/s20x/man/stripqq.Rd | 58 +--
s20x-3.1-12/s20x/man/summary1way.Rd | 106 +++---
s20x-3.1-12/s20x/man/summary2way.Rd | 94 +++---
s20x-3.1-12/s20x/man/summaryStats.Rd | 112 +++----
s20x-3.1-12/s20x/man/teach.df.Rd | 36 +-
s20x-3.1-12/s20x/man/technitron.df.Rd | 46 +-
s20x-3.1-12/s20x/man/thyroid.df.Rd | 36 +-
s20x-3.1-12/s20x/man/toothpaste.df.Rd | 34 +-
s20x-3.1-12/s20x/man/trendscatter.Rd | 1
s20x-3.1-12/s20x/man/zoo.df.Rd | 42 +-
69 files changed, 1566 insertions(+), 1573 deletions(-)
Title: Plot Spatial or Spatio-Temporal Data Over Google Maps
Diff between plotGoogleMaps versions 2.1 dated 2014-06-19 and 2.2 dated 2015-02-13
More information about plotGoogleMaps at CRAN
Description: Provides an interactive plot device for handling the geographic data for web browsers, designed for the automatic creation of web maps as a combination of users' data and Google Maps layers.
Author: Milan Kilibarda
Maintainer: Milan Kilibarda
plotGoogleMaps-2.1/plotGoogleMaps/build |only
plotGoogleMaps-2.1/plotGoogleMaps/inst/doc |only
plotGoogleMaps-2.1/plotGoogleMaps/vignettes |only
plotGoogleMaps-2.2/plotGoogleMaps/DESCRIPTION | 13
plotGoogleMaps-2.2/plotGoogleMaps/MD5 | 41 -
plotGoogleMaps-2.2/plotGoogleMaps/R/PolyCol.R | 195 +++---
plotGoogleMaps-2.2/plotGoogleMaps/R/bubbleGoogleMaps.R | 102 ++-
plotGoogleMaps-2.2/plotGoogleMaps/R/bubbleLegend.R | 124 ++--
plotGoogleMaps-2.2/plotGoogleMaps/R/bubbleSP.R | 147 +++--
plotGoogleMaps-2.2/plotGoogleMaps/R/createInfoWindowEvent.R | 15
plotGoogleMaps-2.2/plotGoogleMaps/R/createInfoWindowEventM.R | 9
plotGoogleMaps-2.2/plotGoogleMaps/R/ellipseGoogleMaps.R | 2
plotGoogleMaps-2.2/plotGoogleMaps/R/mcGoogleMaps.R | 10
plotGoogleMaps-2.2/plotGoogleMaps/R/pieSP.R | 308 +++++------
plotGoogleMaps-2.2/plotGoogleMaps/R/plotGoogleMaps.R | 19
plotGoogleMaps-2.2/plotGoogleMaps/R/segmentGoogleMaps.R | 2
plotGoogleMaps-2.2/plotGoogleMaps/man/bubbleGoogleMaps.Rd | 286 +++++-----
plotGoogleMaps-2.2/plotGoogleMaps/man/ellipseGoogleMaps.Rd | 268 ++++-----
plotGoogleMaps-2.2/plotGoogleMaps/man/mcGoogleMaps.Rd | 8
plotGoogleMaps-2.2/plotGoogleMaps/man/pieSP.Rd | 98 +--
plotGoogleMaps-2.2/plotGoogleMaps/man/plotGoogleMaps.Rd | 4
plotGoogleMaps-2.2/plotGoogleMaps/man/segmentGoogleMaps.Rd | 2
22 files changed, 862 insertions(+), 791 deletions(-)
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-15 1.0.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-06-26 1.5.1
2013-06-19 1.5.0
2008-08-27 1.3.3
2008-08-25 1.3.2
2008-03-21 1.2.0
2007-09-10 1.1.6.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-12-14 0.3
2005-12-13 0.2
Title: Maxwell Bolzano Bose Einstein Fermi Dirac Distribution and
Exposure Curve
Diff between mbbefd versions 0.5.0.1 dated 2015-01-16 and 0.6 dated 2015-02-13
Description: It contains the definition of Maxwell Bolzano Bose Einstein Fermi Dirac (MBBEFD) distribution (distribution, density, quantile, random generation functions) as well as MBBEFD exposure curve, used in actuarial application to price reinsurance contracts. The vignette shows code snippets to fit the distribution to empirical data.
Author: Giorgio Spedicato
Maintainer: Giorgio Spedicato
DESCRIPTION | 12 ++++++----
MD5 | 36 ++++++++++++++++++-------------
NAMESPACE | 6 ++++-
NEWS | 7 +++---
R/RcppExports.R |only
R/distributionDefinition.R | 44 +++++++++++++++++++++-----------------
R/zzz.R |only
inst/CITATION | 4 +--
inst/doc/mbbefd.R | 4 +--
inst/doc/mbbefd.Rnw | 12 +++++-----
inst/doc/mbbefd.pdf |binary
man/exposureCurve.Rd | 5 ----
man/g2a.Rd |only
man/mbbefd-package.Rd | 4 +--
src |only
vignettes/mbbefd-distrPlot.pdf |binary
vignettes/mbbefd-drateplot.pdf |binary
vignettes/mbbefd-survivalPlot.pdf |only
vignettes/mbbefd.Rnw | 12 +++++-----
vignettes/mbbefd.bib | 9 +++++++
vignettes/mbbefd.tex | 8 +++---
21 files changed, 93 insertions(+), 70 deletions(-)
Title: Plot a Correlogram
Diff between corrgram versions 1.6 dated 2014-08-28 and 1.7 dated 2015-02-13
Description: Calculates correlation of variables and displays the results graphically. Included panel functions can display points, shading, ellipses, and correlation values with confidence intervals.
Author: Kevin Wright
Maintainer: Kevin Wright
corrgram-1.6/corrgram/inst/doc/corrgram_examples.rnw |only
corrgram-1.6/corrgram/vignettes/corrgram_examples.rnw |only
corrgram-1.7/corrgram/DESCRIPTION | 12 +++----
corrgram-1.7/corrgram/MD5 | 30 +++++++++---------
corrgram-1.7/corrgram/NEWS | 6 +++
corrgram-1.7/corrgram/R/corrgram.r | 10 ++++++
corrgram-1.7/corrgram/build/vignette.rds |binary
corrgram-1.7/corrgram/data/auto.rda |binary
corrgram-1.7/corrgram/data/baseball.rda |binary
corrgram-1.7/corrgram/data/vote.rda |binary
corrgram-1.7/corrgram/inst/doc/corrgram_examples.R | 3 -
corrgram-1.7/corrgram/inst/doc/corrgram_examples.Rnw |only
corrgram-1.7/corrgram/inst/doc/corrgram_examples.pdf |binary
corrgram-1.7/corrgram/man/baseball.Rd | 2 -
corrgram-1.7/corrgram/man/corrgram.Rd | 8 +++-
corrgram-1.7/corrgram/tests/misc.r | 7 +++-
corrgram-1.7/corrgram/tests/spearman.r | 29 -----------------
corrgram-1.7/corrgram/vignettes/corrgram_examples.Rnw |only
18 files changed, 49 insertions(+), 58 deletions(-)
Title: Voxelwise Semiparametrics
Diff between vows versions 0.3.1 dated 2015-01-08 and 0.4 dated 2015-02-12
Description: Parametric and semiparametric inference for massively parallel
models, i.e., a large number of models with common design matrix, as often
occurs with brain imaging data.
Author: Philip Reiss, Yin-Hsiu Chen, Lei Huang, Lan Huo, Ruixin Tan, and Rong Jiao
Maintainer: Philip Reiss
vows-0.3.1/vows/R/vows_0.3-package.R |only
vows-0.4/vows/DESCRIPTION | 15 --
vows-0.4/vows/MD5 | 74 +++++-----
vows-0.4/vows/NAMESPACE | 9 +
vows-0.4/vows/R/R2nii.R | 62 ++++----
vows-0.4/vows/R/nii2R.R | 178 ++++++++++++------------
vows-0.4/vows/R/rlrt4d.R | 73 +++++-----
vows-0.4/vows/R/vows-internal.R | 135 +++++++++---------
vows-0.4/vows/R/vows-mgcv.R | 250 +++++++++++++++++------------------
vows-0.4/vows/R/vows_0.4-package.R |only
vows-0.4/vows/man/F.mp.Rd | 3
vows-0.4/vows/man/Fdr.rlrt.Rd | 3
vows-0.4/vows/man/R2nii.Rd | 7
vows-0.4/vows/man/extract.fd.Rd | 3
vows-0.4/vows/man/funkmeans.Rd | 3
vows-0.4/vows/man/funkmeans4d.Rd | 3
vows-0.4/vows/man/funkpanel.Rd | 3
vows-0.4/vows/man/lm.mp.Rd | 3
vows-0.4/vows/man/lm4d.Rd | 3
vows-0.4/vows/man/nii2R.Rd | 7
vows-0.4/vows/man/permF.mp.Rd | 3
vows-0.4/vows/man/plot.funkmeans.Rd | 3
vows-0.4/vows/man/plot.rlrt4d.Rd | 3
vows-0.4/vows/man/plot.semipar.mp.Rd | 3
vows-0.4/vows/man/qplsc.mp.Rd | 3
vows-0.4/vows/man/rlrt.mp.Rd | 9 -
vows-0.4/vows/man/rlrt.mp.fit.Rd | 3
vows-0.4/vows/man/rlrt4d.Rd | 5
vows-0.4/vows/man/rlrtpanel.Rd | 3
vows-0.4/vows/man/screen.vox.Rd | 3
vows-0.4/vows/man/semipar.mix.mp.Rd | 3
vows-0.4/vows/man/semipar.mp.Rd | 3
vows-0.4/vows/man/semipar4d.Rd | 3
vows-0.4/vows/man/sf.Rd | 3
vows-0.4/vows/man/summary.lm.mp.Rd | 3
vows-0.4/vows/man/test.Rd | 3
vows-0.4/vows/man/vows-internal.Rd | 10 +
vows-0.4/vows/man/vows-mgcv.Rd | 3
vows-0.4/vows/man/vows-package.Rd | 5
39 files changed, 478 insertions(+), 430 deletions(-)
Title: Stereo Camera Calibration and Reconstruction
Diff between StereoMorph versions 1.2.1 dated 2014-09-02 and 1.3 dated 2015-02-12
Description: Functions for the collection of 3D points and curves using a stereo camera setup.
Author: Aaron Olsen, Annat Haber
Maintainer: Aaron Olsen
DESCRIPTION | 13
MD5 | 42 +-
NAMESPACE | 22 +
R/digitizeImage.R | 40 +-
R/dltCalibrateCameras.R | 276 +++++++++++++---
R/dltMatchCurvePoints.R | 5
R/findCheckerboardCorners.R | 77 +++-
R/inverseGridTransform.R |only
inst/extdata/apps/digitizeImage/digitize_image.html | 2
inst/extdata/apps/digitizeImage/digitize_image_pre.html | 16
inst/extdata/apps/digitizeImage/initial_parameters.R | 45 +-
inst/extdata/apps/digitizeImage/server.R | 12
inst/extdata/apps/digitizeImage/www/digitize_image.css | 12
inst/extdata/apps/digitizeImage/www/digitize_image.js | 59 ++-
inst/extdata/apps/digitizeImage/www/help.html | 31 +
inst/extdata/apps/initial_parameters.R |only
man/StereoMorph-package.Rd | 6
man/digitizeImage.Rd | 2
man/dltCalibrateCameras.Rd | 41 +-
man/dltMatchCurvePoints.Rd | 3
man/dltReconstruct.Rd | 2
man/findCheckerboardCorners.Rd | 16
src/Makevars.win | 10
23 files changed, 552 insertions(+), 180 deletions(-)
Title: Spherical K-Function
Diff between SphericalK versions 1.0 dated 2014-11-26 and 1.1 dated 2015-02-12
Description: Spherical K-function for point-pattern analysis on the sphere.
Author: Scott Robeson, Ao Li, Chunfeng Huang
Maintainer: Ao Li
DESCRIPTION | 12 ++++++------
MD5 | 18 +++++++++---------
R/SphericalK.R | 3 ++-
man/Hex272.Rd | 2 +-
man/Hex92.Rd | 2 +-
man/SphericalK-package.Rd | 4 ++--
man/sphere_grid.Rd | 2 +-
man/sphere_khat.Rd | 4 ++--
man/sphere_montekhat.Rd | 2 +-
man/sphere_random.Rd | 4 ++--
10 files changed, 27 insertions(+), 26 deletions(-)
Title: Tools for Simplifying the Population and Querying of SQLite
Databases
Diff between poplite versions 0.99.5 dated 2014-11-05 and 0.99.16 dated 2015-02-12
Description: Provides objects and accompanying methods which facilitates populating and querying SQLite databases.
Author: Daniel Bottomly [cre, aut],
Shannon McWeeney [aut],
Beth Wilmot [aut]
Maintainer: Daniel Bottomly
DESCRIPTION | 22 +-
MD5 | 21 +-
NAMESPACE | 4
R/Database.R | 375 ++++++++++++++++++++++++++++++------------
R/external_funcs.R | 57 ++++--
R/tableSchemaList.R | 49 +++++
README.md |only
build/vignette.rds |binary
data/clinical.rda |binary
inst/doc/poplite.pdf |binary
tests/testthat.R | 92 ++++++++++
tests/testthat/test-poplite.R | 94 ++++++++++
12 files changed, 570 insertions(+), 144 deletions(-)
Title: Geometric Morphometric Analyses of 2d/3D Landmark Data
Diff between geomorph versions 2.1.2 dated 2014-11-04 and 2.1.3 dated 2015-02-12
Description: Geomorph allows users to read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams, Michael Collyer, Erik Otarola-Castillo, Emma Sherratt
Maintainer: Dean Adams
geomorph-2.1.2/geomorph/R/plotAllometry.r |only
geomorph-2.1.3/geomorph/DESCRIPTION | 16
geomorph-2.1.3/geomorph/MD5 | 188 ++--
geomorph-2.1.3/geomorph/NAMESPACE | 5
geomorph-2.1.3/geomorph/NEWS | 29
geomorph-2.1.3/geomorph/R/advanced.procD.lm.r | 12
geomorph-2.1.3/geomorph/R/bilat.symmetry.r | 50 -
geomorph-2.1.3/geomorph/R/build.template.r | 190 ++--
geomorph-2.1.3/geomorph/R/compare.evol.rates.r | 8
geomorph-2.1.3/geomorph/R/compare.modular.partitions.r | 3
geomorph-2.1.3/geomorph/R/define.links.R |only
geomorph-2.1.3/geomorph/R/define.modules.R | 86 +
geomorph-2.1.3/geomorph/R/define.sliders.3d.r | 188 ++--
geomorph-2.1.3/geomorph/R/digit.fixed.r | 250 ++---
geomorph-2.1.3/geomorph/R/digitsurface.r | 198 ++--
geomorph-2.1.3/geomorph/R/editTemplate.r | 114 +-
geomorph-2.1.3/geomorph/R/geomorph.support.code.r | 621 +++++++-------
geomorph-2.1.3/geomorph/R/pairwise.slope.test.r | 40
geomorph-2.1.3/geomorph/R/pairwiseD.test.r | 41
geomorph-2.1.3/geomorph/R/phylo.pls.R | 33
geomorph-2.1.3/geomorph/R/physignal.r | 37
geomorph-2.1.3/geomorph/R/plotAllometry.R |only
geomorph-2.1.3/geomorph/R/plotOutliers.R |only
geomorph-2.1.3/geomorph/R/plotRefToTarget.r | 17
geomorph-2.1.3/geomorph/R/plotTangentSpace.r | 253 ++---
geomorph-2.1.3/geomorph/R/procD.lm.r | 7
geomorph-2.1.3/geomorph/R/procD.pgls.r | 11
geomorph-2.1.3/geomorph/R/read.ply.r | 7
geomorph-2.1.3/geomorph/R/readland.tps.r | 72 +
geomorph-2.1.3/geomorph/R/trajectory.analysis.r | 410 +++++----
geomorph-2.1.3/geomorph/data/hummingbirds.rda |binary
geomorph-2.1.3/geomorph/data/mosquito.rda |binary
geomorph-2.1.3/geomorph/data/motionpaths.rda |binary
geomorph-2.1.3/geomorph/data/plethShapeFood.rda |binary
geomorph-2.1.3/geomorph/data/plethodon.rda |binary
geomorph-2.1.3/geomorph/data/plethspecies.rda |binary
geomorph-2.1.3/geomorph/data/pupfish.rda |binary
geomorph-2.1.3/geomorph/data/ratland.rda |binary
geomorph-2.1.3/geomorph/data/scallopPLY.rda |binary
geomorph-2.1.3/geomorph/data/scallops.rda |binary
geomorph-2.1.3/geomorph/man/advanced.procD.lm.Rd | 5
geomorph-2.1.3/geomorph/man/arrayspecs.Rd | 3
geomorph-2.1.3/geomorph/man/bilat.symmetry.Rd | 3
geomorph-2.1.3/geomorph/man/buildtemplate.Rd | 7
geomorph-2.1.3/geomorph/man/compare.evol.rates.Rd | 3
geomorph-2.1.3/geomorph/man/compare.modular.partitions.Rd | 6
geomorph-2.1.3/geomorph/man/define.links.Rd |only
geomorph-2.1.3/geomorph/man/define.modules.Rd | 23
geomorph-2.1.3/geomorph/man/define.sliders.2d.Rd | 3
geomorph-2.1.3/geomorph/man/define.sliders.3d.Rd | 15
geomorph-2.1.3/geomorph/man/digit.fixed.Rd | 7
geomorph-2.1.3/geomorph/man/digitize2d.Rd | 3
geomorph-2.1.3/geomorph/man/digitsurface.Rd | 7
geomorph-2.1.3/geomorph/man/editTemplate.Rd | 7
geomorph-2.1.3/geomorph/man/estimate.missing.Rd | 3
geomorph-2.1.3/geomorph/man/findMeanSpec.Rd | 3
geomorph-2.1.3/geomorph/man/fixed.angle.Rd | 3
geomorph-2.1.3/geomorph/man/geomorph-package.Rd | 3
geomorph-2.1.3/geomorph/man/gpagen.Rd | 3
geomorph-2.1.3/geomorph/man/hummingbirds.Rd | 3
geomorph-2.1.3/geomorph/man/morphol.disparity.Rd | 3
geomorph-2.1.3/geomorph/man/morphol.integr.Rd | 3
geomorph-2.1.3/geomorph/man/mosquito.Rd | 3
geomorph-2.1.3/geomorph/man/motionpaths.Rd | 3
geomorph-2.1.3/geomorph/man/mshape.Rd | 3
geomorph-2.1.3/geomorph/man/pairwise.slope.test.Rd | 19
geomorph-2.1.3/geomorph/man/pairwiseD.test.Rd | 15
geomorph-2.1.3/geomorph/man/phylo.pls.Rd | 5
geomorph-2.1.3/geomorph/man/physignal.Rd | 5
geomorph-2.1.3/geomorph/man/plethShapeFood.Rd | 3
geomorph-2.1.3/geomorph/man/plethodon.Rd | 3
geomorph-2.1.3/geomorph/man/plethspecies.Rd | 3
geomorph-2.1.3/geomorph/man/plotAllSpecimens.Rd | 3
geomorph-2.1.3/geomorph/man/plotAllometry.Rd | 15
geomorph-2.1.3/geomorph/man/plotGMPhyloMorphoSpace.Rd | 3
geomorph-2.1.3/geomorph/man/plotOutliers.Rd |only
geomorph-2.1.3/geomorph/man/plotRefToTarget.Rd | 15
geomorph-2.1.3/geomorph/man/plotTangentSpace.Rd | 13
geomorph-2.1.3/geomorph/man/plotspec.Rd | 3
geomorph-2.1.3/geomorph/man/procD.lm.Rd | 7
geomorph-2.1.3/geomorph/man/procD.pgls.Rd | 9
geomorph-2.1.3/geomorph/man/pupfish.Rd | 13
geomorph-2.1.3/geomorph/man/ratland.Rd | 3
geomorph-2.1.3/geomorph/man/read.morphologika.Rd | 3
geomorph-2.1.3/geomorph/man/read.ply.Rd | 10
geomorph-2.1.3/geomorph/man/readland.nts.Rd | 3
geomorph-2.1.3/geomorph/man/readland.tps.Rd | 17
geomorph-2.1.3/geomorph/man/readmulti.nts.Rd | 3
geomorph-2.1.3/geomorph/man/scallopPLY.Rd | 3
geomorph-2.1.3/geomorph/man/scallops.Rd | 3
geomorph-2.1.3/geomorph/man/trajectory.analysis.Rd | 27
geomorph-2.1.3/geomorph/man/two.b.pls.Rd | 3
geomorph-2.1.3/geomorph/man/two.d.array.Rd | 3
geomorph-2.1.3/geomorph/man/warpRefMesh.Rd | 3
geomorph-2.1.3/geomorph/man/warpRefOutline.Rd | 3
geomorph-2.1.3/geomorph/man/writeland.tps.Rd | 3
geomorph-2.1.3/geomorph/src/Makevars | 2
geomorph-2.1.3/geomorph/src/Makevars.win | 2
98 files changed, 1790 insertions(+), 1446 deletions(-)
Title: Discovering Multiple, Statistically-Equivalent Signatures
Diff between MXM versions 0.2.1 dated 2014-08-04 and 0.3 dated 2015-02-12
Description: Feature selection methods for identifying minimal, statistically-equivalent and equally-predictive feature subsets. MXM stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin.
Author: Ioannis Tsamardinos, Vincenzo Lagani, Giorgos Borboudakis, Giorgos Athineou
Maintainer: Giorgos Athineou
MXM-0.2.1/MXM/man/SES-internal.Rd |only
MXM-0.3/MXM/DESCRIPTION | 11 ++--
MXM-0.3/MXM/MD5 | 28 +++++------
MXM-0.3/MXM/NAMESPACE | 18 ++++++-
MXM-0.3/MXM/R/SES.R | 14 ++---
MXM-0.3/MXM/R/censIndLR.R | 8 +--
MXM-0.3/MXM/R/gSquare.R | 8 +--
MXM-0.3/MXM/R/testIndFisher.R | 38 +++++++++------
MXM-0.3/MXM/R/testIndLogistic.R | 32 ++++++-------
MXM-0.3/MXM/man/MXM-internal.Rd |only
MXM-0.3/MXM/man/MXM-package.Rd | 2
MXM-0.3/MXM/man/SES.Rd | 6 ++
MXM-0.3/MXM/man/SESoutput-class.Rd | 5 ++
MXM-0.3/MXM/man/censIndLR.Rd | 36 +++++++-------
MXM-0.3/MXM/man/gSquare.Rd | 25 +++++-----
MXM-0.3/MXM/man/testIndLogistic.Rd | 89 ++++++++++++++++++++-----------------
16 files changed, 182 insertions(+), 138 deletions(-)
Title: All-Purpose Toolkit for Analyzing Multivariate Time Series (MTS)
and Estimating Multivariate Volatility Models
Diff between MTS versions 0.32 dated 2014-03-01 and 0.33 dated 2015-02-12
Description: Multivariate Time Series (MTS) is a general package for analyzing multivariate linear time series and estimating multivariate volatility models. It also handles factor models, constrained factor models, asymptotic principal component analysis commonly used in finance and econometrics, and principal volatility component analysis. (a) For the multivariate linear time series analysis, the package performs model specification, estimation, model checking, and prediction for many widely used models, including vector AR models, vector MA models, vector ARMA models, seasonal vector ARMA models, VAR models with exogenous variables, multivariate regression models with time series errors, augmented VAR models, and Error-correction VAR models for co-integrated time series. For model specification, the package performs structural specification to overcome the difficulties of identifiability of VARMA models. The methods used for structural specification include Kronecker indices and Scalar Component Models. (b) For multivariate volatility modeling, the MTS package handles several commonly used models, including multivariate exponentially weighted moving-average volatility, Cholesky decomposition volatility models, dynamic conditional correlation (DCC) models, copula-based volatility models, and low-dimensional BEKK models. The package also considers multiple tests for conditional heteroscedasticity, including rank-based statistics. (c) Finally, the MTS package also performs forecasting using diffusion index, transfer function analysis, Bayesian estimation of VAR models, and multivariate time series analysis with missing values.Users can also use the package to simulate VARMA models, to compute impulse response functions of a fitted VARMA model, and to calculate theoretical cross-covariance matrices of a given VARMA model.
Author: Ruey S. Tsay
Maintainer: Ruey S. Tsay
DESCRIPTION | 12
MD5 | 21 -
R/MTS.R | 777 +++++++++++++++++++++++++++++++++++++++++++++++++----
R/VARMACpp.R | 4
R/sVARMACpp.R | 8
man/BVAR.Rd | 2
man/Btfm2.Rd |only
man/GrangerTest.Rd |only
man/MTS-package.Rd | 4
man/tfm.Rd | 2
man/tfm1.Rd | 11
man/tfm2.Rd |only
src/varma.cpp | 361 +++++++++++++++---------
13 files changed, 982 insertions(+), 220 deletions(-)
Title: Model-Based Boosting
Diff between mboost versions 2.4-1 dated 2014-12-15 and 2.4-2 dated 2015-02-12
Description: Functional gradient descent algorithm
(boosting) for optimizing general risk functions utilizing
component-wise (penalised) least squares estimates or regression
trees as base-learners for fitting generalized linear, additive
and interaction models to potentially high-dimensional data.
Author: Torsten Hothorn [aut, cre],
Peter Buehlmann [aut],
Thomas Kneib [aut],
Matthias Schmid [aut],
Benjamin Hofner [aut],
Fabian Sobotka [ctb],
Fabian Scheipl [ctb]
Maintainer: Torsten Hothorn
DESCRIPTION | 8 ++--
MD5 | 31 ++++++++---------
NAMESPACE | 4 +-
R/bl.R | 5 +-
R/bmono.R | 2 -
R/bmrf.R | 4 +-
R/brad.R | 5 --
R/btree.R | 2 -
inst/CITATION | 69 +++++++++++++++++++++++++-------------
inst/NEWS.Rd | 25 +++++++++++++
inst/doc/SurvivalEnsembles.pdf |binary
inst/doc/mboost.pdf |binary
inst/doc/mboost_illustrations.pdf |binary
inst/doc/mboost_tutorial.pdf |binary
man/blackboost.Rd | 18 +++++----
man/helper.Rd |only
man/mboost_package.Rd | 9 +++-
17 files changed, 117 insertions(+), 65 deletions(-)
Title: Genetic Algorithm (GA) for Variable Selection from
High-Dimensional Data
Diff between gaselect versions 1.0.4 dated 2015-02-10 and 1.0.5 dated 2015-02-12
Description: Provides a genetic algorithm for finding variable
subsets in high dimensional data with high prediction performance. The
genetic algorithm can use ordinary least squares (OLS) regression models or
partial least squares (PLS) regression models to evaluate the prediction
power of variable subsets. By supporting different cross-validation
schemes, the user can fine-tune the tradeoff between speed and quality of
the solution.
Author: David Kepplinger
Maintainer: David Kepplinger
ChangeLog | 4 ++++
DESCRIPTION | 6 +++---
MD5 | 10 +++++-----
src/BICEvaluator.cpp | 4 ++--
src/LMEvaluator.cpp | 2 +-
src/PLSEvaluator.cpp | 2 +-
6 files changed, 16 insertions(+), 12 deletions(-)
Title: Biodiversity Assessment Tools
Diff between BAT versions 1.1 dated 2015-01-13 and 1.2 dated 2015-02-12
Description: Includes algorithms to assess alpha and beta
diversity in all their dimensions (taxon, phylogenetic and functional
diversity), whether communities are completely sampled or not. It allows
performing a number of analyses based on either species identities or
ultrametric trees depicting species relationships.
Author: Pedro Cardoso, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso
DESCRIPTION | 8 -
MD5 | 46 +++----
NAMESPACE | 6
R/BAT.R | 294 +++++++++++++++++++++++++++++++++++++++++++++--
man/accuracy.Rd | 3
man/alpha.Rd | 3
man/alpha.accum.Rd | 3
man/alpha.estimate.Rd | 3
man/arrabida.Rd | 3
man/beta.Rd | 3
man/beta.accum.Rd | 3
man/beta.multi.Rd | 3
man/functree.Rd | 3
man/geres.Rd | 3
man/guadiana.Rd | 3
man/optim.alpha.Rd |only
man/optim.alpha.stats.Rd |only
man/optim.beta.Rd |only
man/optim.beta.stats.Rd |only
man/phylotree.Rd | 3
man/sim.plot.Rd | 3
man/sim.sad.Rd | 3
man/sim.sample.Rd | 3
man/sim.spatial.Rd | 3
man/sim.tree.Rd | 13 +-
man/slope.Rd | 3
26 files changed, 359 insertions(+), 59 deletions(-)
Title: Generalized Linear Mixed Models via Monte Carlo Likelihood
Approximation
Diff between glmm versions 1.0 dated 2015-02-11 and 1.0.1 dated 2015-02-12
Description: Approximates the likelihood of a generalized linear mixed model using Monte Carlo likelihood approximation. Then maximizes the likelihood approximation to return maximum likelihood estimates, observed Fisher information, and other model information.
Author: Christina Knudson
Maintainer: Christina Knudson
DESCRIPTION | 8 +-
MD5 | 4 -
src/objfunc.c | 187 ++++++++++++++++++++++++++++------------------------------
3 files changed, 98 insertions(+), 101 deletions(-)
Title: Calculate Generalized Eigenvalues of a Matrix Pair
Diff between geigen versions 1.4 dated 2014-08-18 and 1.5 dated 2015-02-12
Description: Compute generalized eigenvalues and eigenvectors of a pair of matrices,
using routines from Lapack (dggev and zggev). Compute the
generalized Schur decomposition of a pair of matrices using Lapack routines.
In the latter case options for ordering the generalized eigenvalues are provided.
Author: Berend Hasselman, Lapack authors
Maintainer: Berend Hasselman
DESCRIPTION | 12 ++++++------
MD5 | 14 +++++++-------
NEWS | 5 +++++
R/cmplxdiv.R | 14 +++++++-------
inst/CITATION | 8 ++++----
man/geigen-package.Rd | 10 +++++-----
man/geigen.Rd | 10 +++++-----
man/gevalues.Rd | 10 +++++-----
8 files changed, 44 insertions(+), 39 deletions(-)
Title: Estimability Tools for Linear Models
Diff between estimability versions 1.0-2 dated 2015-01-31 and 1.1 dated 2015-02-12
Description: Provides tools for determining estimability of linear functions of regression coefficients,
and 'epredict' methods that handle non-estimable cases correctly.
Author: Russell V. Lenth
Maintainer: Russell V. Lenth
DESCRIPTION | 12 +++----
MD5 | 13 ++++----
NAMESPACE | 14 ++++++---
R/epredict.lm.R | 79 ++++++++++++++++++++++++++++++++++------------------
R/estimability.R | 30 +++++++++++++++----
inst |only
man/epredict.lm.Rd | 66 ++++++++++++++++++++++++++++++++-----------
man/nonest.basis.Rd | 38 +++++++++++++++++--------
8 files changed, 174 insertions(+), 78 deletions(-)
Title: Multiple Hypothesis Testing
Diff between sgof versions 2.1.1 dated 2014-10-23 and 2.2 dated 2015-02-11
Description: seven different methods for multiple testing problems. The SGoF-type methods and the BH and BY false discovery rate controlling procedures.
Author: Irene Castro Conde and Jacobo de Una Alvarez
Maintainer: Irene Castro Conde
DESCRIPTION | 17 +++++++++--------
MD5 | 41 ++++++++++++++++++++++-------------------
NAMESPACE | 2 ++
R/BBSGoF.R | 9 +++++++--
R/BH.R | 2 +-
R/BY.R | 2 +-
R/Bayesian.SGoF.R | 2 +-
R/Binomial.SGoF.R | 2 +-
R/Discrete.SGoF.R |only
R/SGoF.R | 2 +-
R/print.Discrete.SGoF.R |only
man/BBSGoF.Rd | 9 +++++----
man/BH.Rd | 2 +-
man/BY.Rd | 4 ++--
man/Bayesian.SGoF.Rd | 2 +-
man/Binomial.SGoF.Rd | 6 +++---
man/Discrete.SGoF.Rd |only
man/SGoF.Rd | 6 +++---
man/plot.Binomial.SGoF.Rd | 2 +-
man/plot.SGoF.Rd | 3 ++-
man/sgof-package.Rd | 37 +++++++++++++++++++++++++++++--------
man/summary.Binomial.SGoF.Rd | 2 +-
man/summary.SGoF.Rd | 2 +-
23 files changed, 94 insertions(+), 60 deletions(-)
Title: Efficient Score Statistics For Genome-Wide SNP Set Analysis
Diff between RSNPset versions 0.3 dated 2014-12-16 and 0.4 dated 2015-02-11
Description: RSNPset is an implementation of the use of efficient score statistics
in genome-wide SNP set analysis with complex traits. The package provides three standard
score statistics (Cox, binomial, and Gaussian) but is easily extensible to include
others. Code implementing the inferential procedure is primarily written in C++ and
utilizes parallelization of the analysis to reduce runtime. A supporting function offers
simple computation of observed, permutation, and FWER and FDR adjusted p-values.
Author: Chanhee Yi, Alexander Sibley, and Kouros Owzar
Maintainer: Alexander Sibley
DESCRIPTION | 10 +-
MD5 | 31 +++----
NEWS |only
R/rsnpset.R | 184 ++++++++++++++++++++++++------------------
R/rsnpset.pvalue.R | 2
R/summary.RSNPset.R | 4
R/summary.RSNPset.pvalue.R | 4
inst/doc/rsnpset.R | 15 ++-
inst/doc/rsnpset.Rnw | 161 ++++++++++++++++++++++++++----------
inst/doc/rsnpset.pdf |binary
man/RSNPset-package.Rd | 16 +--
man/rsnpset.Rd | 44 +++++-----
man/rsnpset.pvalue.Rd | 30 +++---
man/summary.RSNPset.Rd | 33 +++----
man/summary.RSNPset.pvalue.Rd | 22 ++---
src/rsnpset.cpp | 60 ++++++++++---
vignettes/rsnpset.Rnw | 161 ++++++++++++++++++++++++++----------
17 files changed, 502 insertions(+), 275 deletions(-)
Title: Selection of K in K-Means Clustering
Diff between kselection versions 0.1.1 dated 2014-10-17 and 0.2.0 dated 2015-02-11
Description: Selection of k in k-means clustering based on Pham et al. paper
``Selection of k in k-means clustering''.
Author: Daniel Rodriguez
Maintainer: Daniel Rodriguez
kselection-0.1.1/kselection/inst |only
kselection-0.2.0/kselection/DESCRIPTION | 18 -
kselection-0.2.0/kselection/MD5 | 30 +--
kselection-0.2.0/kselection/NAMESPACE | 2
kselection-0.2.0/kselection/NEWS | 9
kselection-0.2.0/kselection/R/kselection.R | 6
kselection-0.2.0/kselection/R/pham.R | 173 +++++++++++-------
kselection-0.2.0/kselection/man/get_f_k.Rd | 5
kselection-0.2.0/kselection/man/get_k_threshold.Rd | 5
kselection-0.2.0/kselection/man/kselection-package.Rd | 9
kselection-0.2.0/kselection/man/kselection.Rd | 34 ++-
kselection-0.2.0/kselection/man/num_clusters.Rd | 5
kselection-0.2.0/kselection/man/num_clusters_all.Rd | 5
kselection-0.2.0/kselection/man/set_k_threshold.Rd | 5
kselection-0.2.0/kselection/tests |only
15 files changed, 190 insertions(+), 116 deletions(-)
Title: Bootstrap 2 Web Components for Use with Shiny
Diff between shinybootstrap2 versions 0.2 dated 2015-01-22 and 0.2.1 dated 2015-02-11
More information about shinybootstrap2 at CRAN
Description: Provides Bootstrap 2 web components for use with the Shiny
package. With versions of Shiny prior to 0.11, these Bootstrap 2 components
were included as part of the package. Later versions of Shiny include
Bootstrap 3, so the Bootstrap 2 components have been moved into this
package for those uses who rely on features specific to Bootstrap 2.
Author: Winston Chang [aut, cre],
RStudio [cph],
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library; authors listed at
https://github.com/twbs/bootstrap/graphs/contributors),
Twitter, Inc [cph] (Bootstrap library),
Brian Reavis [ctb, cph] (selectize.js library),
Egor Khmelev [ctb, cph] (jslider library),
SpryMedia Limited [ctb, cph] (DataTables library)
Maintainer: Winston Chang
DESCRIPTION | 8 ++++----
MD5 | 7 ++++---
NEWS |only
R/output-datatable.R | 28 +++++++++++++++-------------
README.md | 2 +-
5 files changed, 24 insertions(+), 21 deletions(-)
Permanent link
Title: Phylogenetics for the Environmental Sciences
Diff between pez versions 0.9-0 dated 2014-11-07 and 1.0-0 dated 2015-02-11
Description: Eco-phylogenetic and community phylogenetic analyses.
Keeps community ecological and phylogenetic data matched up and
comparable using 'comparative.comm' objects. Wrappers for common
community phylogenetic indices ('shape', 'evenness', 'dispersion',
and 'dissimilarity' metrics). Implementation of Cavender-Bares
(2004) correlation of phylogenetic and ecological matrices
('fingerprint.regression'). Phylogenetic Generalised Linear Mixed
Models (PGLMMs) following ('pglmm') following Ives & Helmus (2011)
and Rafferty & Ives (2013). Simulation of null assemblages,
traits, and phylogenies ('scape', 'sim.meta.comm').
Author: William D. Pearse, Marc W. Cadotte, Jeannine Cavender-Bares,
Anthony R. Ives, Caroline Tucker, Steve C. Walker, Matthew R. Helmus
Maintainer: William D. Pearse
pez-0.9-0/pez/inst/tests/vert.txt |only
pez-1.0-0/pez/DESCRIPTION | 19 +-
pez-1.0-0/pez/MD5 | 40 ++---
pez-1.0-0/pez/NAMESPACE | 29 +++-
pez-1.0-0/pez/NEWS |only
pez-1.0-0/pez/R/comparative.comm.R | 101 +++++++++++++-
pez-1.0-0/pez/R/dispersion.R | 8 -
pez-1.0-0/pez/R/dissimilarity.R | 8 -
pez-1.0-0/pez/R/evenness.R | 8 -
pez-1.0-0/pez/R/pglmm.R |only
pez-1.0-0/pez/R/phy.signal.R | 6
pez-1.0-0/pez/R/plotting.R | 8 -
pez-1.0-0/pez/R/shape.R | 23 +--
pez-1.0-0/pez/R/utility.R | 10 +
pez-1.0-0/pez/inst/doc/pez-intro.R | 61 ++++++++
pez-1.0-0/pez/inst/doc/pez-intro.Rnw | 163 +++++++++++++++++++++--
pez-1.0-0/pez/inst/doc/pez-intro.pdf |binary
pez-1.0-0/pez/inst/tests/test_comparative.comm.R | 57 +++++---
pez-1.0-0/pez/inst/tests/test_shape.R | 4
pez-1.0-0/pez/man/cc.manip.Rd | 49 ++++++
pez-1.0-0/pez/man/pglmm.Rd |only
pez-1.0-0/pez/man/plot.comparative.comm.Rd | 5
pez-1.0-0/pez/vignettes/pez-intro.Rnw | 163 +++++++++++++++++++++--
23 files changed, 629 insertions(+), 133 deletions(-)
Title: Smoothing Splines for Large Samples
Diff between bigsplines versions 1.0-4 dated 2014-10-03 and 1.0-5 dated 2015-02-11
Description: Fits smoothing spline regression models using scalable algorithms designed for large samples. Five marginal spline types are supported: cubic, different cubic, cubic periodic, cubic thin-plate, and nominal. Parametric predictors are also supported. Response can be Gaussian or non-Gaussian: Binomial, Poisson, Gamma, Inverse Gaussian, or Negative Binomial.
Author: Nathaniel E. Helwig
Maintainer: Nathaniel E. Helwig
bigsplines-1.0-4/bigsplines/R/predict.css.R |only
bigsplines-1.0-4/bigsplines/R/predict.ssa.R |only
bigsplines-1.0-4/bigsplines/R/predict.ssg.R |only
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bigsplines-1.0-5/bigsplines/ChangeLog | 32 ++++
bigsplines-1.0-5/bigsplines/DESCRIPTION | 8 -
bigsplines-1.0-5/bigsplines/MD5 | 117 ++++++++--------
bigsplines-1.0-5/bigsplines/NAMESPACE | 23 +++
bigsplines-1.0-5/bigsplines/R/bigspline.R | 4
bigsplines-1.0-5/bigsplines/R/bigssa.R | 10 -
bigsplines-1.0-5/bigsplines/R/bigssg.R | 9 -
bigsplines-1.0-5/bigsplines/R/bigssp.R | 10 -
bigsplines-1.0-5/bigsplines/R/bigtps.R | 4
bigsplines-1.0-5/bigsplines/R/gcvgss.R | 79 ++++++++--
bigsplines-1.0-5/bigsplines/R/gcvssg.R | 75 ++++++++--
bigsplines-1.0-5/bigsplines/R/imagebar.R | 1
bigsplines-1.0-5/bigsplines/R/lamcoefg.R | 77 ++++++++--
bigsplines-1.0-5/bigsplines/R/lamloopg.R | 75 ++++++++--
bigsplines-1.0-5/bigsplines/R/makeZtX.R |only
bigsplines-1.0-5/bigsplines/R/makeZtZ.R |only
bigsplines-1.0-5/bigsplines/R/makessa.R | 48 +++++-
bigsplines-1.0-5/bigsplines/R/makessg.R | 13 +
bigsplines-1.0-5/bigsplines/R/makessp.R | 49 +++++-
bigsplines-1.0-5/bigsplines/R/predict.bigspline.R |only
bigsplines-1.0-5/bigsplines/R/predict.bigssa.R |only
bigsplines-1.0-5/bigsplines/R/predict.bigssg.R |only
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bigsplines-1.0-5/bigsplines/R/remlri.R |only
bigsplines-1.0-5/bigsplines/R/remlvc.R |only
bigsplines-1.0-5/bigsplines/R/smartssg.R | 14 -
bigsplines-1.0-5/bigsplines/R/ssawork.R | 82 ++++++++++-
bigsplines-1.0-5/bigsplines/R/ssblup.R |only
bigsplines-1.0-5/bigsplines/R/ssgwork.R | 30 ++--
bigsplines-1.0-5/bigsplines/R/sspwork.R | 76 ++++++++++
bigsplines-1.0-5/bigsplines/R/summary.bigspline.R |only
bigsplines-1.0-5/bigsplines/R/summary.bigssa.R |only
bigsplines-1.0-5/bigsplines/R/summary.bigssg.R |only
bigsplines-1.0-5/bigsplines/R/summary.bigssp.R |only
bigsplines-1.0-5/bigsplines/R/summary.bigtps.R |only
bigsplines-1.0-5/bigsplines/man/bigspline.Rd | 4
bigsplines-1.0-5/bigsplines/man/bigsplines-internal.Rd | 5
bigsplines-1.0-5/bigsplines/man/bigssa.Rd | 25 +++
bigsplines-1.0-5/bigsplines/man/bigssg.Rd | 20 ++
bigsplines-1.0-5/bigsplines/man/bigssp.Rd | 25 +++
bigsplines-1.0-5/bigsplines/man/bigtps.Rd | 2
bigsplines-1.0-5/bigsplines/man/makessa.Rd | 14 +
bigsplines-1.0-5/bigsplines/man/makessg.Rd | 6
bigsplines-1.0-5/bigsplines/man/makessp.Rd | 14 +
bigsplines-1.0-5/bigsplines/man/predict.bigspline.Rd |only
bigsplines-1.0-5/bigsplines/man/predict.bigssa.Rd |only
bigsplines-1.0-5/bigsplines/man/predict.bigssg.Rd |only
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bigsplines-1.0-5/bigsplines/man/print.Rd | 62 ++++----
bigsplines-1.0-5/bigsplines/man/summary.Rd | 39 ++---
87 files changed, 806 insertions(+), 246 deletions(-)
Title: Tree-Based Varying Coefficient Regression for Generalized Linear
and Ordinal Mixed Models
Diff between vcrpart versions 0.3-1 dated 2015-01-04 and 0.3-2 dated 2015-02-11
Description: Recursive partitioning for varying coefficient generalized linear models and ordinal linear mixed models. Special features are coefficient-wise partitioning, non-varying coefficients and partitioning of time-varying variables in longitudinal regression.
Author: Reto Buergin [aut, cre, cph],
Gilbert Ritschard [ctb, ths]
Maintainer: Reto Buergin
DESCRIPTION | 9 +-
MD5 | 50 +++++++-------
NEWS | 18 +++++
R/olmm-methods.R | 129 ++++++++++++++++++++++---------------
R/olmm.R | 10 +-
R/utils.R | 20 +++--
ToDo | 4 -
inst/CITATION | 15 ++--
man/PL.Rd | 2
man/fvcm-methods.Rd | 6 -
man/fvcm.Rd | 4 -
man/olmm-gefp.Rd | 5 -
man/olmm-methods.Rd | 6 -
man/olmm-predict.Rd | 118 ++++++++++++++++++++++++----------
man/olmm.Rd | 38 +++++++---
man/otsplot.Rd | 4 -
man/poverty.Rd | 2
man/schizo.Rd | 4 -
man/tvcglm.Rd | 11 +--
man/tvcm-cv.Rd | 9 +-
man/tvcm-plot.Rd | 4 -
man/tvcm.Rd | 7 +-
man/tvcolmm.Rd | 7 +-
src/init.c | 1
src/olmm.c | 180 +++++++++++++++++++++++++++++++++++++++++++++++++++-
src/olmm.h | 3
26 files changed, 478 insertions(+), 188 deletions(-)
Title: Functions for Kriging and Point Pattern Analysis
Diff between spatial versions 7.3-8 dated 2014-03-28 and 7.3-9 dated 2015-02-11
Description: Functions for kriging and point pattern analysis.
Author: Brian Ripley [aut, cre, cph],
Roger Bivand [ctb],
William Venables [cph]
Maintainer: Brian Ripley
DESCRIPTION | 10 +++++-----
MD5 | 8 +++++---
inst/po/en@quot/LC_MESSAGES/R-spatial.mo |binary
inst/po/ko |only
po/R-ko.po |only
po/R-spatial.pot | 4 ++--
6 files changed, 12 insertions(+), 10 deletions(-)
Title: Tools for Simulating and Plotting Quantities of Interest
Estimated From Cox Proportional Hazards Models
Diff between simPH versions 1.2.6.1 dated 2015-01-31 and 1.3 dated 2015-02-11
Description: Simulates and plots quantities of interest (relative
hazards, first differences, and hazard ratios) for linear coefficients,
multiplicative interactions, polynomials, penalised splines, and
non-proportional hazards, as well as stratified survival curves from Cox
Proportional Hazard models. It also simulates and plots marginal effects
for multiplicative interactions.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud
DESCRIPTION | 13 -
MD5 | 55 ++---
NAMESPACE | 2
NEWS | 24 ++
R/MinMaxLines.R | 4
R/SmoothSim.R | 42 ++--
R/coxsimInteract.R | 17 +
R/coxsimLinear.R | 238 +++++++++++------------
R/coxsimPoly.R | 194 +++++++++----------
R/coxsimSpline.R | 36 ++-
R/coxsimtvc.R | 299 ++++++++++++++---------------
R/simGG.siminteract.R | 418 +++++++++++++++++++++--------------------
R/simGG.simlinear.R | 288 +++++++++++++---------------
R/simGG.simpoly.R | 436 +++++++++++++++++++++----------------------
R/simGG.simspline.R | 316 +++++++++++++------------------
R/simGG.simtvc.R | 402 +++++++++++++++++----------------------
R/smallUtils.R | 51 +++++
README.md | 33 ++-
man/as.data.frame.coxsim.Rd |only
man/coxsimLinear.Rd | 12 -
man/coxsimPoly.Rd | 6
man/coxsimSpline.Rd | 9
man/coxsimtvc.Rd | 2
man/simGG.siminteract.Rd | 22 +-
man/simGG.simlinear.Rd | 21 +-
man/simGG.simpoly.Rd | 21 +-
man/simGG.simspline.Rd | 64 ++----
man/simGG.simtvc.Rd | 13 -
vignettes/simPH-overview.Rnw | 146 +++++++-------
29 files changed, 1630 insertions(+), 1554 deletions(-)
Title: A Tool to Associate FASTA Sequences and Features
Diff between SeqFeatR versions 0.1.5 dated 2014-06-10 and 0.1.7 dated 2015-02-11
Description: SeqFeatR provides user friendly methods for the identification of sequence patterns that are statistically significantly associated with a property of the sequence. For instance, SeqFeatR allows to identify viral immune escape mutations for hosts of given HLA types. The underlying statistical method is Fisher's exact test, with appropriate corrections for multiple testing. Patterns may be point mutations or n-tuple of mutations. SeqFeatR offers several ways to visualize the results of the statistical analyses.
Author: Bettina Budeus
Maintainer: Bettina Budeus
SeqFeatR-0.1.5/SeqFeatR/R/assocpointtuple.R |only
SeqFeatR-0.1.5/SeqFeatR/R/founderelim.R |only
SeqFeatR-0.1.5/SeqFeatR/R/hlaTree.R |only
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SeqFeatR-0.1.7/SeqFeatR/DESCRIPTION | 16
SeqFeatR-0.1.7/SeqFeatR/INSTALL |only
SeqFeatR-0.1.7/SeqFeatR/MD5 | 104
SeqFeatR-0.1.7/SeqFeatR/NAMESPACE | 16
SeqFeatR-0.1.7/SeqFeatR/NEWS |only
SeqFeatR-0.1.7/SeqFeatR/R/SeqFeatR_GUI.R | 4713 +++++-----
SeqFeatR-0.1.7/SeqFeatR/R/assocpair.R | 12
SeqFeatR-0.1.7/SeqFeatR/R/assocpairfeat.R | 12
SeqFeatR-0.1.7/SeqFeatR/R/assocpoint.R | 413
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SeqFeatR-0.1.7/SeqFeatR/R/assoctuple.R | 43
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SeqFeatR-0.1.7/SeqFeatR/R/getfreqs.R |only
SeqFeatR-0.1.7/SeqFeatR/R/orPlot.R | 105
SeqFeatR-0.1.7/SeqFeatR/R/q-values.R | 6
SeqFeatR-0.1.7/SeqFeatR/R/rewritetuple.R | 10
SeqFeatR-0.1.7/SeqFeatR/R/tartan.R | 8
SeqFeatR-0.1.7/SeqFeatR/R/visualizepair.R |only
SeqFeatR-0.1.7/SeqFeatR/R/visualizepairfeat.R |only
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SeqFeatR-0.1.7/SeqFeatR/inst/doc |only
SeqFeatR-0.1.7/SeqFeatR/inst/extdata/Example_HLA_binding_motifs_aa.csv | 1
SeqFeatR-0.1.7/SeqFeatR/inst/extdata/Example_aa.fasta | 28
SeqFeatR-0.1.7/SeqFeatR/inst/extdata/Example_epitopes_aa.csv | 2
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SeqFeatR-0.1.7/SeqFeatR/inst/extdata/config.cfg | 13
SeqFeatR-0.1.7/SeqFeatR/man/SeqFeatR-package.Rd | 19
SeqFeatR-0.1.7/SeqFeatR/man/SeqFeatR_GUI.Rd | 6
SeqFeatR-0.1.7/SeqFeatR/man/assocpair.Rd | 68
SeqFeatR-0.1.7/SeqFeatR/man/assocpairfeat.Rd | 103
SeqFeatR-0.1.7/SeqFeatR/man/assocpoint.Rd | 209
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SeqFeatR-0.1.7/SeqFeatR/man/assoctuple.Rd | 159
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SeqFeatR-0.1.7/SeqFeatR/man/orPlot.Rd | 99
SeqFeatR-0.1.7/SeqFeatR/man/q-values.Rd | 29
SeqFeatR-0.1.7/SeqFeatR/man/rewritetuple.Rd | 53
SeqFeatR-0.1.7/SeqFeatR/man/tartan.Rd | 124
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73 files changed, 3602 insertions(+), 2769 deletions(-)
Title: Recursive Partitioning and Regression Trees
Diff between rpart versions 4.1-8 dated 2014-03-28 and 4.1-9 dated 2015-02-11
Description: Recursive partitioning for classification,
regression and survival trees. An implementation of most of the
functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.
Author: Terry Therneau [aut],
Beth Atkinson [aut],
Brian Ripley [aut, trl, cre] (author of initial R port)
Maintainer: Brian Ripley
ChangeLog | 8 +
DESCRIPTION | 10 +-
MD5 | 28 ++---
R/rpart.R | 6 -
R/xpred.rpart.R | 2
inst/doc/longintro.pdf |binary
inst/doc/usercode.pdf |binary
inst/po/en@quot/LC_MESSAGES/R-rpart.mo |binary
inst/po/en@quot/LC_MESSAGES/rpart.mo |binary
inst/po/ko/LC_MESSAGES/R-rpart.mo |binary
inst/po/ko/LC_MESSAGES/rpart.mo |binary
po/R-ko.po | 159 +++++++++++++++------------------
po/R-rpart.pot | 4
po/ko.po | 47 ++++-----
po/rpart.pot | 4
15 files changed, 130 insertions(+), 138 deletions(-)
Title: Feed-Forward Neural Networks and Multinomial Log-Linear Models
Diff between nnet versions 7.3-8 dated 2014-03-28 and 7.3-9 dated 2015-02-11
Description: Software for feed-forward neural networks with a single
hidden layer, and for multinomial log-linear models.
Author: Brian Ripley [aut, cre, cph],
William Venables [cph]
Maintainer: Brian Ripley
DESCRIPTION | 12 ++---
MD5 | 14 +++---
inst/po/en@quot/LC_MESSAGES/R-nnet.mo |binary
inst/po/ko/LC_MESSAGES/R-nnet.mo |binary
man/multinom.Rd | 15 ------
man/which.is.max.Rd | 6 +-
po/R-ko.po | 73 ++++++++++++++++------------------
po/R-nnet.pot | 4 -
8 files changed, 55 insertions(+), 69 deletions(-)
Title: Functions for Kernel Smoothing Supporting Wand & Jones (1995)
Diff between KernSmooth versions 2.23-13 dated 2014-09-14 and 2.23-14 dated 2015-02-11
Description: Functions for kernel smoothing (and density estimation)
corresponding to the book:
Wand, M.P. and Jones, M.C. (1995) "Kernel Smoothing".
Author: Matt Wand [aut],
Brian Ripley [trl, cre, ctb] (R port and updates)
Maintainer: Brian Ripley
DESCRIPTION | 14 ++++++------
MD5 | 14 ++++++------
PORTING | 7 ++++++
R/all.R | 4 +--
inst/po/en@quot/LC_MESSAGES/R-KernSmooth.mo |binary
inst/po/ko/LC_MESSAGES/R-KernSmooth.mo |binary
po/R-KernSmooth.pot | 4 +--
po/R-ko.po | 31 +++++++++++++---------------
8 files changed, 40 insertions(+), 34 deletions(-)
Title: Tools for Easily Combining and Cleaning Data Sets
Diff between DataCombine versions 0.2.8.3 dated 2015-01-31 and 0.2.9 dated 2015-02-11
Description: Tools for combining and cleaning data sets, particularly
with grouped and time series data.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
NAMESPACE | 1 +
NEWS | 4 ++++
R/slide.R | 43 ++++++++++++++++++++++++-------------------
README.md | 2 +-
man/slideMA.Rd | 8 ++++----
7 files changed, 44 insertions(+), 34 deletions(-)
Title: Functions for Classification
Diff between class versions 7.3-11 dated 2014-07-21 and 7.3-12 dated 2015-02-11
Description: Various functions for classification.
Author: Brian Ripley [aut, cre, cph],
William Venables [cph]
Maintainer: Brian Ripley
DESCRIPTION | 10 +++---
MD5 | 10 +++---
inst/po/en@quot/LC_MESSAGES/R-class.mo |binary
inst/po/ko/LC_MESSAGES/R-class.mo |binary
po/R-class.pot | 4 +-
po/R-ko.po | 51 ++++++++++++++++-----------------
6 files changed, 37 insertions(+), 38 deletions(-)
Title: Bootstrap Functions (Originally by Angelo Canty for S)
Diff between boot versions 1.3-14 dated 2015-01-10 and 1.3-15 dated 2015-02-11
Description: Functions and datasets for bootstrapping from the
book "Bootstrap Methods and Their Applications" by A. C. Davison and
D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.
Author: Angelo Canty [aut],
Brian Ripley [aut, trl, cre] (author of parallel support)
Maintainer: Brian Ripley
ChangeLog | 8 +
DESCRIPTION | 16 +--
MD5 | 14 +-
R/bootfuns.q | 5
inst/po/en@quot/LC_MESSAGES/R-boot.mo |binary
inst/po/ko/LC_MESSAGES/R-boot.mo |binary
po/R-boot.pot | 4
po/R-ko.po | 176 ++++++++++++++++------------------
8 files changed, 114 insertions(+), 109 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-09-29 1.0-18
More information about MazamaSpatialUtils at CRAN
Permanent link
Title: Grammatical Evolution for R
Diff between gramEvol versions 1.2-1 dated 2014-10-22 and 2.0-2 dated 2015-02-11
Description: Context Free Grammar and Grammatical Evolution for R.
Author: Farzad Noorian, Anthony Mihirana de Silva
Maintainer: Farzad Noorian
gramEvol-1.2-1/gramEvol/NEWS |only
gramEvol-1.2-1/gramEvol/R/ApplyGrammarRule.R |only
gramEvol-1.2-1/gramEvol/R/ChosenGrammarRule.R |only
gramEvol-1.2-1/gramEvol/R/GetFirstNonTerminalandRest.R |only
gramEvol-1.2-1/gramEvol/R/GetGrammarDepth.R |only
gramEvol-1.2-1/gramEvol/R/GetGrammarMaxRuleSize.R |only
gramEvol-1.2-1/gramEvol/R/GetGrammarMaxSequenceLen.R |only
gramEvol-1.2-1/gramEvol/R/GetGrammarNumOfExpressions.R |only
gramEvol-1.2-1/gramEvol/R/GetGrammarRuleIndex.R |only
gramEvol-1.2-1/gramEvol/R/GetPossibleRuleChoices.R |only
gramEvol-1.2-1/gramEvol/R/GrammarGenotypeToPhenotype.R |only
gramEvol-1.2-1/gramEvol/R/IsGrammarTerminal.R |only
gramEvol-1.2-1/gramEvol/R/TraverseCodon.R |only
gramEvol-1.2-1/gramEvol/man/GrammarGenotypeToPhenotype.Rd |only
gramEvol-1.2-1/gramEvol/tests/grammar.R |only
gramEvol-2.0-2/gramEvol/ChangeLog | 14
gramEvol-2.0-2/gramEvol/DESCRIPTION | 14
gramEvol-2.0-2/gramEvol/MD5 | 95 +-
gramEvol-2.0-2/gramEvol/NAMESPACE | 47 +
gramEvol-2.0-2/gramEvol/R/CreateGrammar.R | 59 +
gramEvol-2.0-2/gramEvol/R/EvalExpressions.R | 59 -
gramEvol-2.0-2/gramEvol/R/EvolutionStrategy.int.R |only
gramEvol-2.0-2/gramEvol/R/GEPhenotype.R |only
gramEvol-2.0-2/gramEvol/R/GERule.R |only
gramEvol-2.0-2/gramEvol/R/GERule_Concat.R |only
gramEvol-2.0-2/gramEvol/R/GeneticAlg.int.R | 487 ++++++-------
gramEvol-2.0-2/gramEvol/R/GeneticAlg_helpers.R |only
gramEvol-2.0-2/gramEvol/R/GrammarGetDepth.R |only
gramEvol-2.0-2/gramEvol/R/GrammarGetFirstSequence.R |only
gramEvol-2.0-2/gramEvol/R/GrammarGetNextSequence.R |only
gramEvol-2.0-2/gramEvol/R/GrammarIsRecursive.R |only
gramEvol-2.0-2/gramEvol/R/GrammarIsTerminal.R |only
gramEvol-2.0-2/gramEvol/R/GrammarMap.R |only
gramEvol-2.0-2/gramEvol/R/GrammarMaxRuleSize.R |only
gramEvol-2.0-2/gramEvol/R/GrammarMaxSequenceLen.R |only
gramEvol-2.0-2/gramEvol/R/GrammarMaxSequenceRange.R |only
gramEvol-2.0-2/gramEvol/R/GrammarNumOfExpressions.R |only
gramEvol-2.0-2/gramEvol/R/GrammarOverflow.R |only
gramEvol-2.0-2/gramEvol/R/GrammarRandomExpression.R |only
gramEvol-2.0-2/gramEvol/R/GrammarStartSymbol.R |only
gramEvol-2.0-2/gramEvol/R/GrammarVerboseMap.R |only
gramEvol-2.0-2/gramEvol/R/Grammar_escape.R |only
gramEvol-2.0-2/gramEvol/R/Grammar_helpers.R |only
gramEvol-2.0-2/gramEvol/R/GrammaticalEvolution.R | 146 ++-
gramEvol-2.0-2/gramEvol/R/GrammaticalExhaustiveSearch.R |only
gramEvol-2.0-2/gramEvol/R/GrammaticalRandomSearch.R |only
gramEvol-2.0-2/gramEvol/R/ReadBNFFile.R | 15
gramEvol-2.0-2/gramEvol/R/SymbolicRuleToListRule.R |only
gramEvol-2.0-2/gramEvol/R/print.GESearch.R |only
gramEvol-2.0-2/gramEvol/R/print.grammar.R | 29
gramEvol-2.0-2/gramEvol/R/summary.grammar.R |only
gramEvol-2.0-2/gramEvol/README.md | 6
gramEvol-2.0-2/gramEvol/build |only
gramEvol-2.0-2/gramEvol/inst |only
gramEvol-2.0-2/gramEvol/man/CreateGrammar.Rd | 110 +-
gramEvol-2.0-2/gramEvol/man/EvalExpressions.Rd | 24
gramEvol-2.0-2/gramEvol/man/EvolutionStrategy.int.Rd |only
gramEvol-2.0-2/gramEvol/man/GeneticAlg.int.Rd | 111 +-
gramEvol-2.0-2/gramEvol/man/GrammarGetNextSequence.Rd |only
gramEvol-2.0-2/gramEvol/man/GrammarIsTerminal.Rd |only
gramEvol-2.0-2/gramEvol/man/GrammarMap.Rd |only
gramEvol-2.0-2/gramEvol/man/GrammarRandomExpression.Rd |only
gramEvol-2.0-2/gramEvol/man/GrammaticalEvolution.Rd | 146 ++-
gramEvol-2.0-2/gramEvol/man/GrammaticalExhaustiveSearch.Rd |only
gramEvol-2.0-2/gramEvol/man/GrammaticalRandomSearch.Rd |only
gramEvol-2.0-2/gramEvol/man/summary.grammar.Rd |only
gramEvol-2.0-2/gramEvol/tests/bnf.R | 8
gramEvol-2.0-2/gramEvol/tests/es.R |only
gramEvol-2.0-2/gramEvol/tests/exhaustive.R |only
gramEvol-2.0-2/gramEvol/tests/ga.R | 6
gramEvol-2.0-2/gramEvol/tests/ge.R | 16
gramEvol-2.0-2/gramEvol/tests/grammar_newstyle.R |only
gramEvol-2.0-2/gramEvol/tests/grammar_oldstyle.R |only
gramEvol-2.0-2/gramEvol/tests/grammar_sequence.R |only
gramEvol-2.0-2/gramEvol/tests/randomsearch.R |only
gramEvol-2.0-2/gramEvol/vignettes |only
76 files changed, 818 insertions(+), 574 deletions(-)
Title: Tools for Simulating Direct Behavioral Observation Recording
Procedures Based on Alternating Renewal Processes
Diff between ARPobservation versions 1.0 dated 2014-05-29 and 1.1 dated 2015-02-11
More information about ARPobservation at CRAN
Description: Tools for simulating data generated by direct observation
recording. Behavior streams are simulated based on an alternating renewal
process, given specified distributions of event durations and interim
times. Different procedures for recording data can then be applied to the
simulated behavior streams. Functions are provided for the following
recording methods: continuous duration recording, event counting, momentary
time sampling, partial interval recording, and whole interval recording.
Author: James E. Pustejovsky, with contributions from Daniel M. Swan
Maintainer: James E. Pustejovsky
ARPobservation-1.0/ARPobservation/vignettes/Observation-algorithms-concordance.tex |only
ARPobservation-1.0/ARPobservation/vignettes/Observation-algorithms.tex |only
ARPobservation-1.1/ARPobservation/DESCRIPTION | 29
ARPobservation-1.1/ARPobservation/MD5 | 69 +-
ARPobservation-1.1/ARPobservation/NAMESPACE | 13
ARPobservation-1.1/ARPobservation/NEWS | 7
ARPobservation-1.1/ARPobservation/R/ARPobservation-package.r | 8
ARPobservation-1.1/ARPobservation/R/PIRapp.R |only
ARPobservation-1.1/ARPobservation/R/effect_size_estimators.R |only
ARPobservation-1.1/ARPobservation/R/simulate_behavior_stream.R | 308 ++++++++++
ARPobservation-1.1/ARPobservation/README.md | 3
ARPobservation-1.1/ARPobservation/build/vignette.rds |binary
ARPobservation-1.1/ARPobservation/data |only
ARPobservation-1.1/ARPobservation/demo/00Index | 1
ARPobservation-1.1/ARPobservation/demo/study_planning.R |only
ARPobservation-1.1/ARPobservation/inst/mc_est_test.R |only
ARPobservation-1.1/ARPobservation/man/ARPobservation.Rd | 9
ARPobservation-1.1/ARPobservation/man/Dunlap.Rd |only
ARPobservation-1.1/ARPobservation/man/F_const.Rd | 3
ARPobservation-1.1/ARPobservation/man/F_exp.Rd | 3
ARPobservation-1.1/ARPobservation/man/F_gam.Rd | 3
ARPobservation-1.1/ARPobservation/man/F_gam_mix.Rd | 3
ARPobservation-1.1/ARPobservation/man/F_unif.Rd | 3
ARPobservation-1.1/ARPobservation/man/F_weib.Rd | 3
ARPobservation-1.1/ARPobservation/man/Moes.Rd |only
ARPobservation-1.1/ARPobservation/man/PIR_MOM.Rd |only
ARPobservation-1.1/ARPobservation/man/PIR_loglik.Rd |only
ARPobservation-1.1/ARPobservation/man/augmented_recording.Rd | 3
ARPobservation-1.1/ARPobservation/man/continuous_duration_recording.Rd | 3
ARPobservation-1.1/ARPobservation/man/eq_dist.Rd | 3
ARPobservation-1.1/ARPobservation/man/event_counting.Rd | 3
ARPobservation-1.1/ARPobservation/man/incidence_bounds.Rd |only
ARPobservation-1.1/ARPobservation/man/interim_bounds.Rd |only
ARPobservation-1.1/ARPobservation/man/interval_recording.Rd | 3
ARPobservation-1.1/ARPobservation/man/logRespRatio.Rd |only
ARPobservation-1.1/ARPobservation/man/momentary_time_recording.Rd | 3
ARPobservation-1.1/ARPobservation/man/prevalence_bounds.Rd |only
ARPobservation-1.1/ARPobservation/man/r_MTS.Rd |only
ARPobservation-1.1/ARPobservation/man/r_PIR.Rd |only
ARPobservation-1.1/ARPobservation/man/r_WIR.Rd |only
ARPobservation-1.1/ARPobservation/man/r_behavior_stream.Rd | 3
ARPobservation-1.1/ARPobservation/man/r_continuous_recording.Rd |only
ARPobservation-1.1/ARPobservation/man/r_event_counting.Rd |only
ARPobservation-1.1/ARPobservation/man/reported_observations.Rd | 3
ARPobservation-1.1/ARPobservation/tests |only
45 files changed, 431 insertions(+), 58 deletions(-)
Permanent link
Title: Extensions of Exponential Random Graph Models
Diff between xergm versions 1.3 dated 2014-11-01 and 1.4.1 dated 2015-02-10
Description: Extensions of Exponential Random Graph Models (ERGM): Temporal Exponential Random Graph Models (TERGM), Generalized Exponential Random Graph Models (GERGM), and Temporal Network Autocorrelation Models (TNAM).
Author: Philip Leifeld [aut, cre],
Skyler J. Cranmer [aut],
Bruce A. Desmarais [aut]
Maintainer: Philip Leifeld
xergm-1.3/xergm/vignettes/boxplots1.pdf |only
xergm-1.3/xergm/vignettes/boxplots2.pdf |only
xergm-1.3/xergm/vignettes/coefs.pdf |only
xergm-1.3/xergm/vignettes/nw.pdf |only
xergm-1.3/xergm/vignettes/rocpr.pdf |only
xergm-1.4.1/xergm/DESCRIPTION | 30 +-
xergm-1.4.1/xergm/MD5 | 50 ++--
xergm-1.4.1/xergm/NAMESPACE | 10
xergm-1.4.1/xergm/R/RcppExports.R |only
xergm-1.4.1/xergm/R/btergm.R | 42 ++-
xergm-1.4.1/xergm/R/gof.R | 245 ++++++++++++++++++++---
xergm-1.4.1/xergm/R/preprocess.R | 51 ++++
xergm-1.4.1/xergm/R/tnam.R | 77 +++----
xergm-1.4.1/xergm/build/vignette.rds |binary
xergm-1.4.1/xergm/data/knecht.rda |binary
xergm-1.4.1/xergm/inst/CITATION | 3
xergm-1.4.1/xergm/inst/doc/btergm.R | 54 ++---
xergm-1.4.1/xergm/inst/doc/btergm.Rnw | 20 +
xergm-1.4.1/xergm/inst/doc/btergm.pdf |binary
xergm-1.4.1/xergm/man/btergm.Rd | 75 +++++--
xergm-1.4.1/xergm/man/gof.Rd | 63 ++++-
xergm-1.4.1/xergm/man/preprocess.Rd | 6
xergm-1.4.1/xergm/man/timecov.Rd |only
xergm-1.4.1/xergm/man/tnam.Rd | 6
xergm-1.4.1/xergm/man/xergm-package.Rd | 12 -
xergm-1.4.1/xergm/src |only
xergm-1.4.1/xergm/vignettes/btergm-boxplots1.pdf |only
xergm-1.4.1/xergm/vignettes/btergm-boxplots2.pdf |only
xergm-1.4.1/xergm/vignettes/btergm-coefs.pdf |only
xergm-1.4.1/xergm/vignettes/btergm-nw.pdf |only
xergm-1.4.1/xergm/vignettes/btergm-rocpr.pdf |only
xergm-1.4.1/xergm/vignettes/btergm.Rnw | 20 +
32 files changed, 551 insertions(+), 213 deletions(-)
Title: Lucid Printing of Floating Point Numbers
Diff between lucid versions 1.0 dated 2014-11-25 and 1.1 dated 2015-02-10
Description: Print vectors (and data frames) of floating point numbers using a non-scientific format optimized for human readers. Vectors of numbers are rounded using significant digits, aligned at the decimal point, and all zeros trailing the decimal point are dropped.
Author: Kevin Wright
Maintainer: Kevin Wright
lucid-1.0/lucid/inst/doc/lucid.R |only
lucid-1.0/lucid/inst/doc/lucid.Rnw |only
lucid-1.0/lucid/inst/doc/lucid.pdf |only
lucid-1.0/lucid/vignettes/figs |only
lucid-1.0/lucid/vignettes/lucid-concordance.tex |only
lucid-1.0/lucid/vignettes/lucid.Rnw |only
lucid-1.1/lucid/DESCRIPTION | 10 -
lucid-1.1/lucid/MD5 | 33 ++--
lucid-1.1/lucid/NEWS | 5
lucid-1.1/lucid/R/lucid.r | 105 +++++++++++----
lucid-1.1/lucid/R/vc.r | 29 ++--
lucid-1.1/lucid/README.md | 8 +
lucid-1.1/lucid/build/vignette.rds |binary
lucid-1.1/lucid/inst/doc/lucid_printing.R |only
lucid-1.1/lucid/inst/doc/lucid_printing.Rnw |only
lucid-1.1/lucid/inst/doc/lucid_printing.pdf |only
lucid-1.1/lucid/man/lucid.Rd | 38 +++--
lucid-1.1/lucid/man/vc.Rd | 3
lucid-1.1/lucid/vignettes/figure |only
lucid-1.1/lucid/vignettes/lucid.bib | 56 +++++++-
lucid-1.1/lucid/vignettes/lucid_printing-concordance.tex |only
lucid-1.1/lucid/vignettes/lucid_printing.Rnw |only
22 files changed, 212 insertions(+), 75 deletions(-)
Title: Multidimensional Iterative Proportional Fitting
Diff between mipfp versions 1.0 dated 2014-12-01 and 1.5 dated 2015-02-10
Description: An implementation of the iterative proportional fitting procedure for updating a N-dimensional array with respect to given target marginal distributions (which, in turn can be multi-dimensional).
Author: Johan Barthelemy [aut, cre], Thomas Suesse [aut], Mohammad Namazi-Rad [ctb]
Maintainer: Johan Barthelemy
DESCRIPTION | 11 -
MD5 | 13 +
NAMESPACE | 1
R/ipfpMultiDim.R | 380 ++++++++++++++++++++++++++++++++++++---------------
man/Ipfp.Rd | 103 +++++++++----
man/IpfpCovar.Rd |only
man/array2vector.Rd |only
man/mipfp-package.Rd | 56 ++++---
man/vector2array.Rd |only
9 files changed, 392 insertions(+), 172 deletions(-)
Title: R Based Twitter Client
Diff between twitteR versions 1.1.7 dated 2013-07-09 and 1.1.8 dated 2015-02-10
Description: Provides an interface to the Twitter web API.
Author: Jeff Gentry
Maintainer: Jeff Gentry
twitteR-1.1.7/twitteR/inst/sweave |only
twitteR-1.1.7/twitteR/inst/vignette |only
twitteR-1.1.8/twitteR/DESCRIPTION | 20 +
twitteR-1.1.8/twitteR/MD5 | 66 +++---
twitteR-1.1.8/twitteR/NAMESPACE | 16 +
twitteR-1.1.8/twitteR/NEWS | 44 ++++
twitteR-1.1.8/twitteR/R/account.R | 28 ++
twitteR-1.1.8/twitteR/R/base.R | 5
twitteR-1.1.8/twitteR/R/comm.R | 191 ++++++++----------
twitteR-1.1.8/twitteR/R/convert.R | 22 ++
twitteR-1.1.8/twitteR/R/db.R |only
twitteR-1.1.8/twitteR/R/db_connections.R |only
twitteR-1.1.8/twitteR/R/db_search.R |only
twitteR-1.1.8/twitteR/R/db_utils.R |only
twitteR-1.1.8/twitteR/R/df_columns.R |only
twitteR-1.1.8/twitteR/R/dm.R | 6
twitteR-1.1.8/twitteR/R/followers.R | 20 +
twitteR-1.1.8/twitteR/R/oauth.R |only
twitteR-1.1.8/twitteR/R/search.R | 20 +
twitteR-1.1.8/twitteR/R/statuses.R | 132 ++++++++----
twitteR-1.1.8/twitteR/R/toys.R | 2
twitteR-1.1.8/twitteR/R/trends.R | 15 +
twitteR-1.1.8/twitteR/R/users.R | 51 +++-
twitteR-1.1.8/twitteR/R/utils.R | 84 ++++++-
twitteR-1.1.8/twitteR/R/zzz.R | 5
twitteR-1.1.8/twitteR/README.md | 14 +
twitteR-1.1.8/twitteR/inst/doc |only
twitteR-1.1.8/twitteR/inst/vignettes |only
twitteR-1.1.8/twitteR/man/getCurRateLimitInfo.Rd | 12 -
twitteR-1.1.8/twitteR/man/getUser.Rd | 2
twitteR-1.1.8/twitteR/man/get_latest_tweet_id.Rd |only
twitteR-1.1.8/twitteR/man/load_tweets_db.Rd |only
twitteR-1.1.8/twitteR/man/registerTwitterOAuth.Rd | 38 ---
twitteR-1.1.8/twitteR/man/register_db_backend.Rd |only
twitteR-1.1.8/twitteR/man/retweets.Rd |only
twitteR-1.1.8/twitteR/man/search.Rd | 45 +++-
twitteR-1.1.8/twitteR/man/search_twitter_and_store.Rd |only
twitteR-1.1.8/twitteR/man/setup_twitter_oauth.Rd |only
twitteR-1.1.8/twitteR/man/showStatus.Rd | 23 +-
twitteR-1.1.8/twitteR/man/strip_retweets.Rd |only
twitteR-1.1.8/twitteR/man/timelines.Rd | 9
twitteR-1.1.8/twitteR/man/updateStatus.Rd | 8
42 files changed, 577 insertions(+), 301 deletions(-)
Title: Web Application Framework for R
Diff between shiny versions 0.11 dated 2015-01-17 and 0.11.1 dated 2015-02-10
Description: Shiny makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between inputs and
outputs and extensive pre-built widgets make it possible to build
beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut, cre],
Joe Cheng [aut],
JJ Allaire [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
RStudio [cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/www/shared/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/www/shared/jqueryui/1.10.4/AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Stefan Petre [ctb, cph] (Bootstrap-datepicker library),
Andrew Rowls [ctb, cph] (Bootstrap-datepicker library),
Dave Gandy [ctb, cph] (Font-Awesome font),
Brian Reavis [ctb, cph] (selectize.js library),
Kristopher Michael Kowal [ctb, cph] (es5-shim library),
es5-shim contributors [ctb, cph] (es5-shim library),
Denis Ineshin [ctb, cph] (ion.rangeSlider library),
SpryMedia Limited [ctb, cph] (DataTables library),
John Fraser [ctb, cph] (showdown.js library),
John Gruber [ctb, cph] (showdown.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
R Core Team [ctb, cph] (tar implementation from R)
Maintainer: Winston Chang
DESCRIPTION | 16
MD5 | 114 +++---
NEWS | 36 ++
R/app.R | 45 +-
R/bootstrap.R | 180 +++++-----
R/jqueryui.R | 4
R/middleware.R | 2
R/reactives.R | 51 +-
R/run-url.R | 33 +
R/server.R | 95 +++--
R/shiny.R | 10
R/shinyui.R | 8
R/shinywrappers.R | 35 +
R/update-input.R | 49 +-
R/utils.R | 16
inst/examples/04_mpg/server.R | 2
inst/tests/test-bootstrap.r | 4
inst/tests/test-utils.R | 12
inst/www/shared/ionrangeslider/css/ion.rangeSlider.css | 11
inst/www/shared/ionrangeslider/css/ion.rangeSlider.skinFlat.css | 4
inst/www/shared/ionrangeslider/css/ion.rangeSlider.skinHTML5.css | 4
inst/www/shared/ionrangeslider/css/ion.rangeSlider.skinModern.css | 4
inst/www/shared/ionrangeslider/css/ion.rangeSlider.skinNice.css | 4
inst/www/shared/ionrangeslider/css/ion.rangeSlider.skinSimple.css | 4
inst/www/shared/ionrangeslider/js/ion.rangeSlider.js | 157 ++++----
inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js | 130 +++----
inst/www/shared/shiny.css | 12
inst/www/shared/shiny.js | 64 ++-
inst/www/shared/shiny.min.js | 6
inst/www/shared/shiny.min.js.map | 2
man/absolutePanel.Rd | 4
man/bootstrapPage.Rd | 10
man/checkboxGroupInput.Rd | 4
man/checkboxInput.Rd | 4
man/dateInput.Rd | 4
man/dateRangeInput.Rd | 4
man/fileInput.Rd | 4
man/htmlOutput.Rd | 20 -
man/navbarPage.Rd | 2
man/numericInput.Rd | 6
man/observeEvent.Rd | 51 +-
man/parseQueryString.Rd | 2
man/passwordInput.Rd | 6
man/plotOutput.Rd | 4
man/radioButtons.Rd | 4
man/renderDataTable.Rd | 35 +
man/runApp.Rd | 46 +-
man/runExample.Rd | 15
man/runUrl.Rd | 33 +
man/selectInput.Rd | 22 -
man/shinyApp.Rd | 45 +-
man/shinyServer.Rd | 21 +
man/shinyUI.Rd | 8
man/sliderInput.Rd | 6
man/tabPanel.Rd | 2
man/tableOutput.Rd | 51 +-
man/textInput.Rd | 6
man/updateSliderInput.Rd | 49 +-
58 files changed, 896 insertions(+), 686 deletions(-)
Title: Tools to Manage a Parametric Function that Describes Phenology
Diff between phenology versions 4.0 dated 2014-10-05 and 4.0.4 dated 2015-02-10
Description: Functions to fit and test the phenology of species based on counts. The package includes also several useful more general functions.
Author: Marc Girondot
Maintainer: Marc Girondot
DESCRIPTION | 11 +--
MD5 | 148 +++++++++++++++++++++----------------------
NAMESPACE | 3
NEWS | 8 ++
R/MHalgoGen.R | 34 ++++++++-
R/add_phenology.R | 14 +++-
R/barplot_errbar.R | 1
R/format_par.R | 53 ++++-----------
R/insidesearch.R |only
R/phenology-package.R | 6 -
R/plot.phenology.R | 1
R/plot.phenologymap.R | 25 +------
R/plot_errbar.R | 3
R/print.phenologyout.R | 6 +
R/read_phenology.R | 46 +++++++++----
man/BE_to_LBLE.Rd | 3
man/ChangeCoordinate.Rd | 3
man/Gratiot.Rd | 3
man/LBLE_to_BE.Rd | 3
man/LBLE_to_L.Rd | 3
man/L_to_LBLE.Rd | 3
man/MinBMinE_to_Min.Rd | 3
man/ScalePreviousPlot.Rd | 3
man/adapt_parameters.Rd | 3
man/add_SD.Rd | 3
man/add_phenology.Rd | 3
man/as.mcmc.mcmcComposite.Rd | 3
man/as.par.mcmcComposite.Rd | 3
man/asc.Rd | 3
man/barplot_errbar.Rd | 3
man/chr.Rd | 3
man/clean.knitr.Rd | 3
man/compare_AIC.Rd | 3
man/compassRose2.Rd | 3
man/convert.tz.Rd | 3
man/extract_result.Rd | 3
man/fit_phenology.Rd | 3
man/getTide.Rd | 3
man/growlnotify.Rd | 3
man/ind_long_lat.Rd | 3
man/insidesearch.Rd |only
man/likelihood_phenology.Rd | 3
man/local.search.Rd | 3
man/logLik.phenology.Rd | 3
man/map.scale2.Rd | 3
man/map_Gratiot.Rd | 3
man/map_phenology.Rd | 3
man/moon_phase.Rd | 3
man/par_init.Rd | 3
man/phenology-package.Rd | 9 +-
man/phenology.Rd | 3
man/phenology_MHmcmc.Rd | 3
man/phenology_MHmcmc_p.Rd | 3
man/plot.mcmcComposite.Rd | 3
man/plot.phenology.Rd | 3
man/plot.phenologymap.Rd | 7 --
man/plot_add.Rd | 3
man/plot_delta.Rd | 3
man/plot_errbar.Rd | 3
man/plot_phi.Rd | 3
man/print.phenology.Rd | 3
man/print.phenologymap.Rd | 3
man/print.phenologyout.Rd | 3
man/read_folder.Rd | 3
man/remove_site.Rd | 3
man/result_Gratiot.Rd | 3
man/result_Gratiot1.Rd | 3
man/result_Gratiot2.Rd | 3
man/result_Gratiot_Flat.Rd | 3
man/result_Gratiot_mcmc.Rd | 3
man/shift_sinusoid.Rd | 3
man/summary.mcmcComposite.Rd | 3
man/summary.phenology.Rd | 3
man/summary.phenologymap.Rd | 3
man/summary.phenologyout.Rd | 3
man/toggle_Min_PMin.Rd | 3
76 files changed, 317 insertions(+), 232 deletions(-)
Title: Multiple Imputation for Multivariate Panel or Clustered Data
Diff between pan versions 0.9 dated 2013-09-27 and 1.3 dated 2015-02-10
Description: Multiple imputation for multivariate panel or clustered data.
Author: Original by Joseph L. Schafer
Maintainer: Jing hua Zhao
pan-0.9/pan/.Rinstignore |only
pan-0.9/pan/INDEX |only
pan-0.9/pan/LICENSE |only
pan-0.9/pan/inst/doc/pan-tr.R |only
pan-1.3/pan/ChangeLog | 14 ++++++++++++++
pan-1.3/pan/DESCRIPTION | 16 ++++++++--------
pan-1.3/pan/MD5 | 20 +++++++++-----------
pan-1.3/pan/build |only
pan-1.3/pan/inst/doc/pan-tr.Rnw | 6 +++---
pan-1.3/pan/inst/doc/pan-tr.pdf |binary
pan-1.3/pan/man/ecme.Rd | 9 ++++++---
pan-1.3/pan/man/pan.Rd | 9 ++++++---
pan-1.3/pan/src/pan.f | 4 ++--
pan-1.3/pan/vignettes/pan-tr.Rnw | 6 +++---
14 files changed, 51 insertions(+), 33 deletions(-)
Title: Optimal k-Means Clustering for One-Dimensional Data
Diff between Ckmeans.1d.dp versions 3.3.0 dated 2015-02-09 and 3.3.1 dated 2015-02-10
Description: A dynamic programming algorithm for optimal one-dimensional k-means clustering. The algorithm minimizes the sum of squares of within-cluster distances. As an alternative to the standard heuristic k-means algorithm, this algorithm guarantees optimality and repeatability.
Author: Joe Song and Haizhou Wang
Maintainer: Joe Song
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NEWS | 5 +++++
src/Ckmeans.1d.dp.cpp | 2 +-
4 files changed, 13 insertions(+), 8 deletions(-)
Title: Markov-Switching, Bayesian, Vector Autoregression Models
Diff between MSBVAR versions 0.9-1 dated 2014-07-25 and 0.9-2 dated 2015-02-10
Description: Provides methods for estimating frequentist and
Bayesian Vector Autoregression (VAR) models and Markov-switching
Bayesian VAR (MSBVAR). Functions for reduced
form and structural VAR models are also available. Includes
methods for the generating posterior inferences for these models,
forecasts, impulse responses (using likelihood-based error bands),
and forecast error decompositions. Also includes utility functions
for plotting forecasts and impulse responses, and generating draws
from Wishart and singular multivariate normal densities. Current
version includes functionality to build and evaluate models with
Markov switching.
Author: Patrick Brandt [aut, cre],
W. Ryan Davis [ctb]
Maintainer: Patrick Brandt
DESCRIPTION | 12 ++++++------
LICENSE | 4 ++--
MD5 | 25 +++++++++++++------------
NAMESPACE | 6 ++++++
R/zzz.R | 2 +-
README | 11 +++++++----
man/BCFdata.Rd | 12 ++++++------
man/IsraelPalestineConflict.Rd | 2 +-
man/hc.forecast.Rd | 2 +-
man/uc.forecast.Rd | 2 +-
src/FFBS.f | 8 ++++----
src/MSBVARfun.cpp | 3 ++-
src/utils.f | 38 ++++++++++++++++++++++++++++----------
src/wrapper.c |only
14 files changed, 78 insertions(+), 49 deletions(-)
Title: Marker-Based Estimation of Heritability Using Individual Plant
or Plot Data
Diff between heritability versions 1.0 dated 2014-11-07 and 1.1 dated 2015-02-10
Description: Implements marker-based estimation of heritability when observations on genetically identical replicates are available. These can be either observations on individual plants or plot-level data in a field trial. Heritability can then be estimated using a mixed model for the individual plant or plot data. For comparison, also mixed-model based estimation using genotypic means and estimation of repeatability with ANOVA are implemented. For illustration the package contains several datasets for the model species Arabidopsis thaliana.
Author: Willem Kruijer, with a contribution from Ian White (the internal function pin). Contains data collected by Padraic Flood and Rik Kooke.
Maintainer: Willem Kruijer
DESCRIPTION | 14 +++++++-------
MD5 | 30 +++++++++++++++---------------
NAMESPACE | 1 +
R/AI_algorithm.R | 24 ++++++++++++------------
R/AI_algorithm_weights.r | 26 +++++++++++++-------------
R/marker_h2_means.r | 21 +++++++++++++++++++--
man/BT_LW_H.Rd | 4 ++--
man/K_arabidopsis.Rd | 3 ---
man/R_matrix.Rd | 4 ++--
man/floweringTime.Rd | 4 ++--
man/heritability-package.Rd | 6 +++---
man/leafArea.Rd | 4 ++--
man/marker_h2.Rd | 8 ++++----
man/marker_h2_means.Rd | 14 +++++++-------
man/means_floweringTime.Rd | 4 ++--
man/repeatability.Rd | 7 +++----
16 files changed, 94 insertions(+), 80 deletions(-)
Title: Time Series Analysis and Computational Finance
Diff between tseries versions 0.10-32 dated 2013-05-13 and 0.10-33 dated 2015-02-10
Description: Time series analysis and computational finance.
Author: Adrian Trapletti [aut],
Kurt Hornik [aut, cre],
Blake LeBaron [ctb] (BDS test code)
Maintainer: Kurt Hornik
ChangeLog | 7 ++++++
DESCRIPTION | 26 ++++++++++++----------
MD5 | 22 +++++++++----------
R/finance.R | 60 ++++++++++++++++++++--------------------------------
data/NelPlo.rda |binary
data/USeconomic.rda |binary
data/bev.rda |binary
data/camp.rda |binary
data/ice.river.rda |binary
data/nino.rda |binary
data/tcm.rda |binary
data/tcmd.rda |binary
12 files changed, 56 insertions(+), 59 deletions(-)
Title: Imperialist Competitive Algorithm
Diff between ICAFF versions 1.0 dated 2015-02-01 and 1.0.1 dated 2015-02-10
Description: Imperialist Competitive Algorithm (ICA)
Author: Farimah Houshmand, Farzad Eskandari Ph.D.
Maintainer: Farimah Houshmand
ICAFF-1.0.1/ICAFF/DESCRIPTION | 30 +
ICAFF-1.0.1/ICAFF/MD5 | 17 -
ICAFF-1.0.1/ICAFF/NAMESPACE | 6
ICAFF-1.0.1/ICAFF/R/ICA.R | 544 ++++++++++++++---------------------
ICAFF-1.0.1/ICAFF/R/ICAFF-internal.R | 251 ++++++++--------
ICAFF-1.0.1/ICAFF/R/coef.ICA.R |only
ICAFF-1.0.1/ICAFF/R/plot.ICA.R |only
ICAFF-1.0.1/ICAFF/R/print.ICA.R |only
ICAFF-1.0.1/ICAFF/R/summary.ICA.R |only
ICAFF-1.0.1/ICAFF/man/ICA.Rd | 184 +++++++----
ICAFF-1.0.1/ICAFF/man/plot.ICA.Rd |only
ICAFF-1.0/ICAFF/R/cost.R |only
ICAFF-1.0/ICAFF/man/ICAFF-package.Rd |only
13 files changed, 497 insertions(+), 535 deletions(-)
Title: Soft Clustering Algorithms
Diff between SoftClustering versions 0.14.02 dated 2014-02-17 and 1.1502 dated 2015-02-10
More information about SoftClustering at CRAN
Description: It contains soft clustering algorithms, in particular approaches derived from rough set theory: Lingras & West original rough k-means, Peters' refined rough k-means, and PI rough k-means. It also contains classic k-means and a corresponding illustrative demo.
Author: G. Peters (Ed.)
Maintainer: G. Peters
SoftClustering-0.14.02/SoftClustering/R/RoughClustering_01402.r |only
SoftClustering-0.14.02/SoftClustering/data/DemoDataC2D2a.txt.gz |only
SoftClustering-1.1502/SoftClustering/DESCRIPTION | 9 -
SoftClustering-1.1502/SoftClustering/MD5 | 39 +++--
SoftClustering-1.1502/SoftClustering/NAMESPACE | 4
SoftClustering-1.1502/SoftClustering/R/HardkMeansDemo.r |only
SoftClustering-1.1502/SoftClustering/R/RoughClustering.r |only
SoftClustering-1.1502/SoftClustering/data/DemoDataC2D2a.txt |only
SoftClustering-1.1502/SoftClustering/data/initMeansC2D2a.txt |only
SoftClustering-1.1502/SoftClustering/data/initMeansC3D2a.txt |only
SoftClustering-1.1502/SoftClustering/data/initMeansC4D2a.txt |only
SoftClustering-1.1502/SoftClustering/data/initMeansC5D2a.txt |only
SoftClustering-1.1502/SoftClustering/man/DemoDataC2D2a.Rd | 2
SoftClustering-1.1502/SoftClustering/man/HardKMeans.Rd | 36 +---
SoftClustering-1.1502/SoftClustering/man/HardKMeansDemo.Rd |only
SoftClustering-1.1502/SoftClustering/man/RoughKMeans_LW.Rd | 72 +++------
SoftClustering-1.1502/SoftClustering/man/RoughKMeans_PE.Rd | 57 ++-----
SoftClustering-1.1502/SoftClustering/man/RoughKMeans_PI.Rd | 52 ++----
SoftClustering-1.1502/SoftClustering/man/RoughKMeans_SHELL.Rd | 77 +++-------
SoftClustering-1.1502/SoftClustering/man/createLowerMShipMatrix.Rd | 7
SoftClustering-1.1502/SoftClustering/man/datatypeInteger.Rd |only
SoftClustering-1.1502/SoftClustering/man/initMeansC2D2a.Rd |only
SoftClustering-1.1502/SoftClustering/man/initMeansC3D2a.Rd |only
SoftClustering-1.1502/SoftClustering/man/initMeansC4D2a.Rd |only
SoftClustering-1.1502/SoftClustering/man/initMeansC5D2a.Rd |only
SoftClustering-1.1502/SoftClustering/man/initializeMeansMatrix.Rd | 14 -
SoftClustering-1.1502/SoftClustering/man/normalizeMatrix.Rd | 14 -
SoftClustering-1.1502/SoftClustering/man/plotRoughKMeans.Rd | 23 +-
28 files changed, 154 insertions(+), 252 deletions(-)
Permanent link
Title: R Individual Specialization (RInSp)
Diff between RInSp versions 1.1 dated 2015-02-04 and 1.2 dated 2015-02-10
Description: Functions to calculate several ecological indices of individual and population niche width
(Araujo's E, clustering and pairwise similarity among individuals, IS, Petraitis' W, and Roughgarden's
WIC/TNW) to assess individual specialization based on data of resource use. Resource use can be
quantified by counts of categories, measures of mass/lenght or proportions. Monte Carlo resampling
procedures are available for hypothesis testing against multinomial null models.
Author: Dr. Nicola Zaccarelli, Dr. Giorgio Mancinelli, and Prof. Dan Bolnick
Maintainer: Dr. Nicola Zaccarelli
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
man/RInSp-package.Rd | 6 +++---
src/Emc.c | 7 +++----
src/MCprocedure.c | 12 ++++++------
src/PSicalc.c | 14 +++++++-------
src/WTcMC.c | 17 +++++++++--------
src/WTdMC.c | 11 ++++++-----
8 files changed, 45 insertions(+), 44 deletions(-)
Title: Rough - Enhanced - Bayesian Finite Mixture Modeling
Diff between rebmix versions 2.6.2 dated 2014-09-05 and 2.7.0 dated 2015-02-10
Description: R functions for random univariate and multivariate finite mixture generation, number of components, component weights and component parameters estimation, printing and plotting of finite mixtures, bootstrapping and class membership prediction. Variables can be either continuous or discrete, may follow normal, lognormal, Weibull, gamma, binomial, Poisson or Dirac parametric families and should be independent within components.
Author: Marko Nagode [aut, cre]
Maintainer: Marko Nagode
rebmix-2.6.2/rebmix/R/boot.R |only
rebmix-2.6.2/rebmix/R/predict.list.R |only
rebmix-2.6.2/rebmix/man/boot.Rd |only
rebmix-2.6.2/rebmix/man/predict.list.Rd |only
rebmix-2.7.0/rebmix/DESCRIPTION | 10
rebmix-2.7.0/rebmix/MD5 | 120 +++---
rebmix-2.7.0/rebmix/NAMESPACE | 56 ---
rebmix-2.7.0/rebmix/R/IC.R | 188 +---------
rebmix-2.7.0/rebmix/R/RCLSMIX.R |only
rebmix-2.7.0/rebmix/R/REBMIX.R | 108 +++---
rebmix-2.7.0/rebmix/R/RNGMIX.R | 2
rebmix-2.7.0/rebmix/R/boot.REBMIX.R |only
rebmix-2.7.0/rebmix/R/defaults.R | 2
rebmix-2.7.0/rebmix/R/densKNearestNeighbour.x.R | 17
rebmix-2.7.0/rebmix/R/densKNearestNeighbour.xy.R | 20 -
rebmix-2.7.0/rebmix/R/densParzenWindow.x.R | 19 -
rebmix-2.7.0/rebmix/R/densParzenWindow.xy.R | 18 -
rebmix-2.7.0/rebmix/R/dist.x.R | 20 -
rebmix-2.7.0/rebmix/R/dist.xy.R | 24 +
rebmix-2.7.0/rebmix/R/kseq.R | 8
rebmix-2.7.0/rebmix/R/plot.REBMIX.R | 123 ++++--
rebmix-2.7.0/rebmix/build/vignette.rds |binary
rebmix-2.7.0/rebmix/data/adult.rda |binary
rebmix-2.7.0/rebmix/data/galaxy.rda |binary
rebmix-2.7.0/rebmix/data/truck.rda |binary
rebmix-2.7.0/rebmix/data/weibull.rda |binary
rebmix-2.7.0/rebmix/data/weibullnormal.rda |binary
rebmix-2.7.0/rebmix/data/wine.rda |binary
rebmix-2.7.0/rebmix/demo/rebmix.truck.R | 2
rebmix-2.7.0/rebmix/demo/rebmix.weibullnormal.R | 2
rebmix-2.7.0/rebmix/inst/NEWS.Rd | 22 +
rebmix-2.7.0/rebmix/inst/doc/rebmix.Rnw | 16
rebmix-2.7.0/rebmix/inst/doc/rebmix.pdf |binary
rebmix-2.7.0/rebmix/man/AIC.Rd | 12
rebmix-2.7.0/rebmix/man/AWE.Rd | 4
rebmix-2.7.0/rebmix/man/BIC.Rd | 4
rebmix-2.7.0/rebmix/man/CLC.Rd | 4
rebmix-2.7.0/rebmix/man/HQC.Rd | 4
rebmix-2.7.0/rebmix/man/ICL.Rd | 4
rebmix-2.7.0/rebmix/man/ICLBIC.Rd | 4
rebmix-2.7.0/rebmix/man/MDL.Rd | 9
rebmix-2.7.0/rebmix/man/PC.Rd | 4
rebmix-2.7.0/rebmix/man/PRD.Rd | 4
rebmix-2.7.0/rebmix/man/RCLSMIX.Rd |only
rebmix-2.7.0/rebmix/man/REBMIX.Rd | 52 +-
rebmix-2.7.0/rebmix/man/SSE.Rd | 4
rebmix-2.7.0/rebmix/man/boot.REBMIX.Rd |only
rebmix-2.7.0/rebmix/man/coef.REBMIX.Rd | 3
rebmix-2.7.0/rebmix/man/dfmix.Rd | 1
rebmix-2.7.0/rebmix/man/kseq.Rd | 2
rebmix-2.7.0/rebmix/man/logL.Rd | 4
rebmix-2.7.0/rebmix/man/pfmix.Rd | 1
rebmix-2.7.0/rebmix/man/plot.REBMIX.Rd | 9
rebmix-2.7.0/rebmix/man/print.REBMIX.Rd | 5
rebmix-2.7.0/rebmix/man/print.RNGMIX.Rd | 1
rebmix-2.7.0/rebmix/man/print.boot.REBMIX.Rd | 3
rebmix-2.7.0/rebmix/man/summary.REBMIX.Rd | 3
rebmix-2.7.0/rebmix/man/summary.boot.REBMIX.Rd | 3
rebmix-2.7.0/rebmix/src/Makevars | 2
rebmix-2.7.0/rebmix/src/Rrebmix.c | 58 +--
rebmix-2.7.0/rebmix/src/rebmixf.c | 408 +++++++++++++++--------
rebmix-2.7.0/rebmix/src/rebmixf.h | 38 +-
rebmix-2.7.0/rebmix/src/rngmixf.c | 2
rebmix-2.7.0/rebmix/vignettes/algorithm.pdf |binary
rebmix-2.7.0/rebmix/vignettes/rebmix.Rnw | 16
65 files changed, 783 insertions(+), 662 deletions(-)
Title: Linear Mixed Models
Diff between lmm versions 0.9 dated 2013-12-10 and 1.0 dated 2015-02-10
Description: Some improved procedures for linear mixed models.
Author: Original by Joseph L. Schafer
Maintainer: Jing hua Zhao
lmm-0.9/lmm/.Rinstignore |only
lmm-0.9/lmm/LICENSE |only
lmm-0.9/lmm/inst/doc/lmm-tr.R |only
lmm-1.0/lmm/ChangeLog | 8 +++++++-
lmm-1.0/lmm/DESCRIPTION | 16 ++++++++--------
lmm-1.0/lmm/MD5 | 11 +++++------
lmm-1.0/lmm/build |only
lmm-1.0/lmm/inst/doc/lmm-tr.pdf |binary
lmm-1.0/lmm/src/lmm.f | 6 +++---
9 files changed, 23 insertions(+), 18 deletions(-)
Title: Linear Group Fixed Effects
Diff between lfe versions 1.8-1441 dated 2014-12-25 and 2.0-1570 dated 2015-02-10
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.
Includes support for instrumental variables, conditional F statistics for weak instruments,
robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure
DESCRIPTION | 14
MD5 | 130 +-
NAMESPACE | 12
NEWS |only
R/bccorr.R | 277 ++++--
R/btrap.R | 21
R/compfactor.R | 1
R/condfstat.R |only
R/felm.R | 1103 +++++++++++--------------
R/felm.old.R |only
R/generics.R |only
R/getfe.R | 4
R/kaczmarz.R | 40
R/oldfelm.R | 1027 ++++++++++++++++++++---
R/utils.R | 245 -----
R/waldtest.R |only
build/autoconf/install-sh | 668 ++++++++++-----
configure | 20
configure.ac | 2
exec/lfescript | 111 +-
inst/CITATION | 13
inst/doc/CHANGELOG | 33
inst/doc/identification.R | 54 -
inst/doc/identification.Rnw | 2
inst/doc/identification.pdf |binary
inst/doc/index.html | 60 -
inst/doc/lfeguide.txt | 40
inst/doc/lfehow.R | 20
inst/doc/lfehow.pdf |binary
inst/doc/speed.R | 10
inst/doc/speed.pdf |binary
man/bccorr.Rd | 4
man/btrap.Rd | 6
man/condfstat.Rd |only
man/demeanlist.Rd | 3
man/felm.Rd | 104 +-
man/fevcov.Rd | 58 -
man/getfe.Rd | 7
man/is.estimable.Rd | 7
man/kaczmarz.Rd | 3
man/lfe-package.Rd | 31
man/summary.felm.Rd | 43
man/varvars.Rd | 3
man/waldtest.Rd |only
src/Makevars.in | 2
src/Makevars.win | 3
src/demean.c |only
src/factor.c |only
src/kaczmarz.c |only
src/lfe.c | 1888 -------------------------------------------
src/lfe.h |only
src/utils.c |only
tests/anomalies.R |only
tests/anomalies.Rout.save |only
tests/bctest.Rout.save | 6
tests/cluster.R | 6
tests/cluster.Rout.save | 72 -
tests/comparelm.Rout.save | 13
tests/degenerate.Rout.save | 17
tests/efcheck.Rout.save | 10
tests/fourfac.Rout.save | 10
tests/interact.Rout.save | 821 +++++++++---------
tests/ivtest.R | 26
tests/ivtest.Rout.save | 144 +--
tests/lfetest.Rout.save | 6
tests/mlhs.R |only
tests/mlhs.Rout.save |only
tests/multiway.R | 14
tests/multiway.Rout.save | 92 --
tests/naomit.Rout.save | 9
tests/nonest.Rout.save | 10
tests/onefac.Rout.save | 6
tests/verify.Rout.save | 13
vignettes/identification.Rnw | 2
74 files changed, 3175 insertions(+), 4171 deletions(-)
Title: Numerical Calibration of Proxy-Climate Relationships
Diff between treeclim versions 1.0.10 dated 2015-01-19 and 1.0.11 dated 2015-02-10
Description: Bootstrapped response and correlation functions,
seasonal correlations and evaluation of reconstruction
skills for use in dendroclimatology and dendroecology
Author: Christian Zang [aut, cre, cph, trl],
Franco Biondi [ctb, cph]
Maintainer: Christian Zang
DESCRIPTION | 8
MD5 | 37 +--
R/exclude_from.R | 94 ++++----
R/skills.R | 544 +++++++++++++++++++++++++-------------------------
R/zzz.R | 38 +--
README.md |only
inst/Changelog | 3
man/dcc.Rd | 478 +++++++++++++++++++++----------------------
man/g_test.Rd | 128 +++++------
man/init_boot_data.Rd | 52 ++--
man/norw015.Rd | 56 ++---
man/norway_prec.Rd | 48 ++--
man/norway_temp.Rd | 48 ++--
man/seascorr.Rd | 278 ++++++++++++-------------
man/skills.Rd | 212 +++++++++----------
man/spain_prec.Rd | 48 ++--
man/spain_temp.Rd | 48 ++--
man/tc_correlation.Rd | 52 ++--
man/tc_mfunc.Rd | 76 +++---
man/tc_response.Rd | 50 ++--
20 files changed, 1151 insertions(+), 1147 deletions(-)
Title: Fitting Structural Equation Mixture Models
Diff between nlsem versions 0.1 dated 2014-12-19 and 0.2 dated 2015-02-10
Description: Estimation of structural equation models with nonlinear effects
and underlying nonnormal distributions.
Author: Nora Umbach [aut, cre],
Katharina Naumann [aut],
David Hoppe [aut],
Holger Brandt [aut],
Augustin Kelava [ctb],
Bernhard Schmitz [ctb]
Maintainer: Nora Umbach
DESCRIPTION | 9 +-
MD5 | 38 +++++------
NAMESPACE | 1
R/em.R | 50 ++++++++-------
R/lms.R | 4 -
R/model.R | 38 ++++++++---
R/s3generics.R | 65 ++++++++++++--------
R/semm.R | 15 ++--
man/anova.Rd | 2
man/as.data.frame.Rd | 4 -
man/count_free_parameters.Rd | 4 -
man/create_sem.Rd | 9 +-
man/em.Rd | 139 ++++++++-----------------------------------
man/fill_model.Rd | 8 +-
man/nlsem-package.Rd | 52 ++++++++--------
man/simulate.Rd | 17 ++---
man/specify_sem.Rd | 32 ++++-----
man/summary.Rd | 15 ----
tests/tests_for_model.R | 17 +----
tests/tests_for_semm.R | 42 ------------
20 files changed, 229 insertions(+), 332 deletions(-)
Title: A Collection of Statistical Tools for Biologists
Diff between asbio versions 1.1-1 dated 2014-09-06 and 1.1-5 dated 2015-02-10
Description: Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL.
Author: Ken Aho
Maintainer: Ken Aho
DESCRIPTION | 12 -
MD5 | 72 +++++------
NAMESPACE | 19 ++-
R/Bayes.disc.r | 5
R/Venn.R | 10 -
R/anm.ExpDesign.r | 6
R/bplot.r | 4
R/ci.prat.ak.R | 309 +++++++++++++++++++++++++++++--------------------
R/ci.prat.r | 4
R/huber.NR.R | 2
R/loess.surf.R | 3
R/loglik.norm.plot.r | 2
R/one.sample.t.R | 21 ++-
R/one.sample.z.R | 11 +
R/pairw.anova.R | 2
R/qq.Plot.R | 6
R/r.bw.R | 2
R/r.dist.r | 4
R/samp.dist.snap.tck.r | 2
R/samp.dist.tck.r | 2
R/see.regression.tck.r | 12 -
R/see.smooth.tck.r | 4
R/shade.r | 8 +
build/vignette.rds |binary
man/anm.loglik.rd | 2
man/bvn.plot.rd | 2
man/ci.prat.ak.Rd | 5
man/ci.prat.rd | 2
man/heart.rd | 4
man/huber.NR.Rd | 4
man/huber.mu.rd | 4
man/huber.one.step.rd | 4
man/one.sample.t.rd | 6
man/one.sample.z.Rd | 7 -
man/paik.rd | 2
man/r.dist.rd | 4
man/shade.norm.Rd | 5
37 files changed, 339 insertions(+), 234 deletions(-)
Title: Using V-algorithm and Newton-Raphson Method to Obtain
Multiple-objective Optimal Design
Diff between VNM versions 2.0 dated 2014-10-31 and 4.0 dated 2015-02-09
Description: Using V-algorithm and Newton-Raphson method to obtain multiple-objective optimal design for estimating the shape of dose-response, the ED50 (the dose producing an effect midway between the expected responses at the extreme doses) and the MED (the minimum effective dose level) for the 2,3,4-parameter logistic models and for evaluating its efficiencies for the three objectives.
Author: Seung Won Hyun, Weng Kee Wong, and Yarong Yang
Maintainer: Yarong Yang
DESCRIPTION | 14 +++---
MD5 | 34 +++++++++-----
NAMESPACE | 14 +++++-
R/AllClasses.R |only
R/Deff.R | 109 +++++++++++++++++++++++++++++++++-------------
R/MOPT.R | 113 +++++++++++++++++++++++++++++++++++++-----------
R/S.Weight.R | 95 ++++++++++++++++++++++++++++------------
R/ceff1.R | 104 ++++++++++++++++++++++++++++++++------------
R/ceff2.R | 114 ++++++++++++++++++++++++++++++++++++-------------
R/plot-methods.R |only
R/summary-methods.R |only
man/Deff.Rd | 8 +--
man/MOPT.Rd | 10 ++--
man/OPT-class.Rd |only
man/PAR-class.Rd |only
man/S.Weight.Rd | 2
man/SW-class.Rd |only
man/VNM-package.Rd | 12 ++---
man/ceff1.Rd | 11 ++--
man/ceff2.Rd | 8 +--
man/plot-methods.Rd |only
man/summary-methods.Rd |only
22 files changed, 464 insertions(+), 184 deletions(-)
Title: Penalized Semiparametric Bayesian Cox Models with Shrinkage and
Grouping Priors
Diff between psbcGroup versions 1.0 dated 2013-04-05 and 1.1 dated 2015-02-09
Description: The package provides algorithms for fitting penalized semiparametric Bayesian Cox (PSBC) models with shrinkage and grouping priors.
Author: Kyu Ha Lee, Sounak Chakraborty, (Tony) Jianguo Sun
Maintainer: Kyu Ha Lee
DESCRIPTION | 17 ++++++++---------
MD5 | 18 +++++++++---------
NAMESPACE | 5 +++++
R/psbcEN.R | 1 -
R/psbcFL.R | 2 +-
R/psbcGL.R | 1 -
man/psbcEN.Rd | 22 +++++++++++++---------
man/psbcFL.Rd | 21 ++++++++++++---------
man/psbcGL.Rd | 25 +++++++++++++++----------
man/psbcGroup.Rd | 15 ++++++++-------
10 files changed, 71 insertions(+), 56 deletions(-)
Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Diff between nat versions 1.5.12 dated 2014-08-21 and 1.6.4 dated 2015-02-09
Description: NeuroAnatomy Toolbox (nat) is a reboot of the AnalysisSuite
(see https://github.com/jefferis/nat.as) bundle of R code that we have
been using for a number of years to analyse and visualise 3D biological
image data, especially traced neurons. The nat package is considerably
cleaner, properly documented and provides all of the core 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 (via the nat.nblast extension
package).
Author: Greg Jefferis and James Manton
Maintainer: Greg Jefferis
nat-1.5.12/nat/man/amiralandmark-io.Rd |only
nat-1.5.12/nat/man/cmtklandmarks.Rd |only
nat-1.5.12/nat/tests/testthat/test-amiralandmarks-io.R |only
nat-1.6.4/nat/DESCRIPTION | 46 -
nat-1.6.4/nat/MD5 | 346 +++++-----
nat-1.6.4/nat/NAMESPACE | 38 -
nat-1.6.4/nat/NEWS | 70 ++
nat-1.6.4/nat/R/amiralandmarks-io.R | 129 +++
nat-1.6.4/nat/R/amiramesh-io.R | 72 +-
nat-1.6.4/nat/R/cmtk-reformat.R | 58 +
nat-1.6.4/nat/R/cmtk.R | 17
nat-1.6.4/nat/R/cmtk_io.R | 91 +-
nat-1.6.4/nat/R/dotprops.R | 14
nat-1.6.4/nat/R/hxsurf.R | 5
nat-1.6.4/nat/R/im3d.R | 99 ++
nat-1.6.4/nat/R/nat-package.R | 4
nat-1.6.4/nat/R/ndigest.R | 12
nat-1.6.4/nat/R/neuron-io-amira.R | 28
nat-1.6.4/nat/R/neuron-io-fiji.R |only
nat-1.6.4/nat/R/neuron-io-neuroml.R |only
nat-1.6.4/nat/R/neuron-io.R | 284 ++++++--
nat-1.6.4/nat/R/neuron-plot.R | 21
nat-1.6.4/nat/R/neuron.R | 228 +++---
nat-1.6.4/nat/R/neuronlist.R | 225 +++++-
nat-1.6.4/nat/R/neuronlist_sets.R |only
nat-1.6.4/nat/R/ngraph.R | 85 +-
nat-1.6.4/nat/R/nrrd-io.R | 20
nat-1.6.4/nat/R/seglist.R | 46 -
nat-1.6.4/nat/R/vaa3draw-io.R | 40 -
nat-1.6.4/nat/R/xform.R | 53 +
nat-1.6.4/nat/R/xformimage.R |only
nat-1.6.4/nat/R/xformpoints.R | 8
nat-1.6.4/nat/R/zzz.R | 39 +
nat-1.6.4/nat/README.md | 5
nat-1.6.4/nat/man/Cell07PNs.Rd | 3
nat-1.6.4/nat/man/affmat2cmtkparams.Rd | 3
nat-1.6.4/nat/man/all.equal.dotprops.Rd | 3
nat-1.6.4/nat/man/all.equal.im3d.Rd | 21
nat-1.6.4/nat/man/all.equal.neuron.Rd | 31
nat-1.6.4/nat/man/amiramesh-io.Rd | 5
nat-1.6.4/nat/man/amiratype.Rd | 5
nat-1.6.4/nat/man/as.im3d.Rd | 36 -
nat-1.6.4/nat/man/as.mesh3d.Rd | 3
nat-1.6.4/nat/man/as.neuronlist.Rd | 5
nat-1.6.4/nat/man/as.neuronlist.neuronlistfh.Rd | 3
nat-1.6.4/nat/man/boundingbox.Rd | 31
nat-1.6.4/nat/man/c.neuronlist.Rd | 3
nat-1.6.4/nat/man/clampmax.Rd | 3
nat-1.6.4/nat/man/cmtk.bindir.Rd | 5
nat-1.6.4/nat/man/cmtk.call.Rd | 5
nat-1.6.4/nat/man/cmtk.dof2mat.Rd | 3
nat-1.6.4/nat/man/cmtk.extract_affine.Rd |only
nat-1.6.4/nat/man/cmtk.mat2dof.Rd | 3
nat-1.6.4/nat/man/cmtk.reformatx.Rd | 42 -
nat-1.6.4/nat/man/cmtk.statistics.Rd | 3
nat-1.6.4/nat/man/cmtk.targetvolume.Rd | 18
nat-1.6.4/nat/man/cmtk.version.Rd | 3
nat-1.6.4/nat/man/cmtkparams2affmat.Rd | 11
nat-1.6.4/nat/man/cmtkreg.Rd | 3
nat-1.6.4/nat/man/cmtkreglist.Rd | 10
nat-1.6.4/nat/man/coord2ind.Rd | 3
nat-1.6.4/nat/man/dotprops-arithmetic.Rd | 3
nat-1.6.4/nat/man/dotprops.Rd | 21
nat-1.6.4/nat/man/fileformats.Rd | 71 +-
nat-1.6.4/nat/man/find.neuron.Rd | 8
nat-1.6.4/nat/man/find.soma.Rd |only
nat-1.6.4/nat/man/flip.Rd | 3
nat-1.6.4/nat/man/graph.nodes.Rd | 3
nat-1.6.4/nat/man/im3d-coords.Rd | 6
nat-1.6.4/nat/man/im3d-io.Rd | 15
nat-1.6.4/nat/man/im3d.Rd | 6
nat-1.6.4/nat/man/image.im3d.Rd | 27
nat-1.6.4/nat/man/imexpand.grid.Rd | 6
nat-1.6.4/nat/man/imscalebar.Rd | 3
nat-1.6.4/nat/man/imslice.Rd | 6
nat-1.6.4/nat/man/ind2coord.Rd | 3
nat-1.6.4/nat/man/intersect.Rd |only
nat-1.6.4/nat/man/is.amiramesh.Rd | 17
nat-1.6.4/nat/man/is.fijitraces.Rd |only
nat-1.6.4/nat/man/is.neuroml.Rd |only
nat-1.6.4/nat/man/is.neuronlist.Rd | 3
nat-1.6.4/nat/man/is.nrrd.Rd | 10
nat-1.6.4/nat/man/is.swc.Rd |only
nat-1.6.4/nat/man/is.vaa3draw.Rd | 11
nat-1.6.4/nat/man/kcs20.Rd | 3
nat-1.6.4/nat/man/materials.Rd | 3
nat-1.6.4/nat/man/mirror.Rd | 3
nat-1.6.4/nat/man/nat-internal.Rd | 3
nat-1.6.4/nat/man/nat-package.Rd | 10
nat-1.6.4/nat/man/ndigest.Rd | 16
nat-1.6.4/nat/man/neuron-arithmetic.Rd | 3
nat-1.6.4/nat/man/neuron.Rd | 13
nat-1.6.4/nat/man/neuronlist-arithmetic.Rd | 3
nat-1.6.4/nat/man/neuronlist-dataframe-methods.Rd | 15
nat-1.6.4/nat/man/neuronlist.Rd | 3
nat-1.6.4/nat/man/neuronlistfh.Rd | 9
nat-1.6.4/nat/man/ngraph.Rd | 81 +-
nat-1.6.4/nat/man/nlapply.Rd | 10
nat-1.6.4/nat/man/nlscan.Rd |only
nat-1.6.4/nat/man/nopen3d.Rd | 3
nat-1.6.4/nat/man/normalise_swc.Rd |only
nat-1.6.4/nat/man/npop3d.Rd | 3
nat-1.6.4/nat/man/nrrd.voxdims.Rd | 3
nat-1.6.4/nat/man/origin.Rd | 6
nat-1.6.4/nat/man/pan3d.Rd | 3
nat-1.6.4/nat/man/plot.neuron.Rd | 3
nat-1.6.4/nat/man/plot.neuronlist.Rd | 18
nat-1.6.4/nat/man/plot3d.boundingbox.Rd | 3
nat-1.6.4/nat/man/plot3d.dotprops.Rd | 3
nat-1.6.4/nat/man/plot3d.hxsurf.Rd | 3
nat-1.6.4/nat/man/plot3d.neuron.Rd | 10
nat-1.6.4/nat/man/plot3d.neuronlist.Rd | 18
nat-1.6.4/nat/man/pointsinside.Rd | 3
nat-1.6.4/nat/man/potential_synapses.Rd | 11
nat-1.6.4/nat/man/projection.Rd | 6
nat-1.6.4/nat/man/prune.Rd | 3
nat-1.6.4/nat/man/read.cmtk.Rd | 7
nat-1.6.4/nat/man/read.cmtkreg.Rd | 10
nat-1.6.4/nat/man/read.hxsurf.Rd | 10
nat-1.6.4/nat/man/read.landmarks.Rd |only
nat-1.6.4/nat/man/read.morphml.Rd |only
nat-1.6.4/nat/man/read.neuron.Rd | 39 +
nat-1.6.4/nat/man/read.neuron.fiji.Rd |only
nat-1.6.4/nat/man/read.neuron.neuroml.Rd |only
nat-1.6.4/nat/man/read.neuron.swc.Rd | 6
nat-1.6.4/nat/man/read.neuronlistfh.Rd | 3
nat-1.6.4/nat/man/read.neurons.Rd | 26
nat-1.6.4/nat/man/read.nrrd.Rd | 7
nat-1.6.4/nat/man/read.vaa3draw.Rd | 3
nat-1.6.4/nat/man/remotesync.Rd | 7
nat-1.6.4/nat/man/resample.Rd | 20
nat-1.6.4/nat/man/rootpoints.Rd | 3
nat-1.6.4/nat/man/scale.dotprops.Rd | 3
nat-1.6.4/nat/man/scale.neuron.Rd | 3
nat-1.6.4/nat/man/seglengths.Rd | 3
nat-1.6.4/nat/man/seglist.Rd | 3
nat-1.6.4/nat/man/seglist2swc.Rd | 39 -
nat-1.6.4/nat/man/segmentgraph.Rd | 3
nat-1.6.4/nat/man/setdiff.Rd |only
nat-1.6.4/nat/man/spine.Rd | 16
nat-1.6.4/nat/man/sub-.neuronlistfh.Rd | 3
nat-1.6.4/nat/man/sub2ind.Rd | 3
nat-1.6.4/nat/man/subset.dotprops.Rd | 3
nat-1.6.4/nat/man/subset.hxsurf.Rd | 3
nat-1.6.4/nat/man/subset.neuronlist.Rd | 3
nat-1.6.4/nat/man/threshold.Rd | 10
nat-1.6.4/nat/man/union.Rd |only
nat-1.6.4/nat/man/unmask.Rd | 12
nat-1.6.4/nat/man/voxdims.Rd | 6
nat-1.6.4/nat/man/write.amiramesh.Rd | 13
nat-1.6.4/nat/man/write.cmtk.Rd | 7
nat-1.6.4/nat/man/write.cmtkreg.Rd | 7
nat-1.6.4/nat/man/write.hxsurf.Rd | 5
nat-1.6.4/nat/man/write.neuron.Rd | 14
nat-1.6.4/nat/man/write.neuronlistfh.Rd | 3
nat-1.6.4/nat/man/write.neurons.Rd | 41 -
nat-1.6.4/nat/man/write.nrrd.Rd | 3
nat-1.6.4/nat/man/xform.Rd | 29
nat-1.6.4/nat/man/xformimage.Rd |only
nat-1.6.4/nat/man/xformpoints.Rd | 3
nat-1.6.4/nat/man/xyzmatrix.Rd | 3
nat-1.6.4/nat/tests/testthat/test-.neuron-io-remote-nocran.R |only
nat-1.6.4/nat/tests/testthat/test-amiramesh-io.R | 23
nat-1.6.4/nat/tests/testthat/test-cmtk-reformat.R | 29
nat-1.6.4/nat/tests/testthat/test-cmtk.R | 1
nat-1.6.4/nat/tests/testthat/test-hxsurf.R | 7
nat-1.6.4/nat/tests/testthat/test-im3d.R | 16
nat-1.6.4/nat/tests/testthat/test-landmarks-io.R |only
nat-1.6.4/nat/tests/testthat/test-ndigest.R | 3
nat-1.6.4/nat/tests/testthat/test-neuroml-io.R |only
nat-1.6.4/nat/tests/testthat/test-neuron-fiji-io.R |only
nat-1.6.4/nat/tests/testthat/test-neuron-io.R | 63 +
nat-1.6.4/nat/tests/testthat/test-neuron.R | 33
nat-1.6.4/nat/tests/testthat/test-neuronlist.R | 34
nat-1.6.4/nat/tests/testthat/test-ngraph.R | 23
nat-1.6.4/nat/tests/testthat/test-nrrd-io.R | 10
nat-1.6.4/nat/tests/testthat/test-seglist.R | 7
nat-1.6.4/nat/tests/testthat/test-xform.R | 22
nat-1.6.4/nat/tests/testthat/test-xformimage.R |only
nat-1.6.4/nat/tests/testthat/testdata/amira/landmarks.am |only
nat-1.6.4/nat/tests/testthat/testdata/landmarks |only
nat-1.6.4/nat/tests/testthat/testdata/neuroml |only
nat-1.6.4/nat/tests/testthat/testdata/neuroml2 |only
nat-1.6.4/nat/tests/testthat/testdata/neuron/MultiplePathsJoinedToMainPath.traces |only
nat-1.6.4/nat/tests/testthat/testdata/neuron/SequentiallyBranchingTrace.traces |only
nat-1.6.4/nat/tests/testthat/testdata/neuron/SinglePath.traces |only
nat-1.6.4/nat/tests/testthat/testdata/neuron/fitted.traces |only
nat-1.6.4/nat/tests/testthat/testdata/neuron/unfitted.swc |only
nat-1.6.4/nat/tests/testthat/testdata/nrrd/FCWB_2um_mask.nrrd |only
nat-1.6.4/nat/tests/testthat/testdata/nrrd/JFRC2-444_mask.nrrd |only
190 files changed, 2452 insertions(+), 1044 deletions(-)
Title: Tools for Data Handling and Analysis in Macroecology
Diff between letsR versions 1.0 dated 2014-05-19 and 2.0 dated 2015-02-09
Description: Includes R functions for handling and analyzing geographic data, mainly
species' geographic distributions (in ESRI shapefile format) and
environmental variables (in raster format), as well as species' information
related to their description (e.g. taxonomy and year of description) and
conservation status (e.g. category of threat, population trend) as provided
by the IUCN's RedList database. The package includes functions to create
presence-absence matrices based on species distributions and user-defined
grid systems, from which several other functions could be applied to
generate, for example, species richness rasters and maps, and geographical
midpoints of species. In addition, it provides a function to create spatial
correlograms of variables, based on the Moran's I index, under the
equiprobable or equidistant criterion to define distance classes.
Author: Bruno Vilela & Fabricio Villalobos
Maintainer: Bruno Vilela
letsR-1.0/letsR/R/Data_PAM.R |only
letsR-1.0/letsR/R/Data_Phyllomedusa.R |only
letsR-1.0/letsR/R/Data_temp.R |only
letsR-1.0/letsR/R/lets.correl.R |only
letsR-1.0/letsR/R/lets_cont.R |only
letsR-1.0/letsR/R/lets_iun_habitats.R |only
letsR-1.0/letsR/man/letsR.Rd |only
letsR-2.0/letsR/DESCRIPTION | 16 -
letsR-2.0/letsR/MD5 | 116 ++++++-----
letsR-2.0/letsR/NAMESPACE | 20 +-
letsR-2.0/letsR/R/Data_iucn.R | 32 +++
letsR-2.0/letsR/R/letsR-package.R | 12 -
letsR-2.0/letsR/R/lets_addpoly.R | 74 ++++---
letsR-2.0/letsR/R/lets_addvar.R | 8
letsR-2.0/letsR/R/lets_classvar.R |only
letsR-2.0/letsR/R/lets_correl.R |only
letsR-2.0/letsR/R/lets_distmat.R |only
letsR-2.0/letsR/R/lets_field.R | 19 +
letsR-2.0/letsR/R/lets_gridirizer.R |only
letsR-2.0/letsR/R/lets_iucn.R | 7
letsR-2.0/letsR/R/lets_iucn_habitats.R |only
letsR-2.0/letsR/R/lets_iucn_historic.R | 7
letsR-2.0/letsR/R/lets_iucncont.R |only
letsR-2.0/letsR/R/lets_maplizer.R | 8
letsR-2.0/letsR/R/lets_midpoint.R | 12 -
letsR-2.0/letsR/R/lets_overlap.R |only
letsR-2.0/letsR/R/lets_pamcrop.R |only
letsR-2.0/letsR/R/lets_presab.R | 188 +++++++++++++------
letsR-2.0/letsR/R/lets_presab_birds.R | 145 ++++++++++----
letsR-2.0/letsR/R/lets_presab_points.R |only
letsR-2.0/letsR/R/lets_rangesize.R |only
letsR-2.0/letsR/R/lets_shpfilter.R | 4
letsR-2.0/letsR/R/lets_summaryze.R |only
letsR-2.0/letsR/R/plot_PresenceAbsence.R | 14 -
letsR-2.0/letsR/R/print_PresenceAbsence.R | 2
letsR-2.0/letsR/R/print_summary_PresenceAbsence.R | 4
letsR-2.0/letsR/R/removecells.R | 2
letsR-2.0/letsR/R/removesp.R | 2
letsR-2.0/letsR/R/summary_PresenceAbsence.R | 2
letsR-2.0/letsR/R/unicas.R | 2
letsR-2.0/letsR/README.md | 41 ++--
letsR-2.0/letsR/data/temp.rda |binary
letsR-2.0/letsR/man/PAM.Rd | 8
letsR-2.0/letsR/man/Phyllomedusa.Rd | 9
letsR-2.0/letsR/man/iucn.Rd | 7
letsR-2.0/letsR/man/lets.addpoly.Rd | 23 +-
letsR-2.0/letsR/man/lets.addvar.Rd | 21 +-
letsR-2.0/letsR/man/lets.classvar.Rd |only
letsR-2.0/letsR/man/lets.correl.Rd | 39 +--
letsR-2.0/letsR/man/lets.distmat.Rd |only
letsR-2.0/letsR/man/lets.field.Rd | 37 +--
letsR-2.0/letsR/man/lets.gridirizer.Rd |only
letsR-2.0/letsR/man/lets.iucn.Rd | 26 +-
letsR-2.0/letsR/man/lets.iucn.ha.Rd | 23 +-
letsR-2.0/letsR/man/lets.iucn.his.Rd | 27 +-
letsR-2.0/letsR/man/lets.iucncont.Rd | 19 +
letsR-2.0/letsR/man/lets.maplizer.Rd | 22 +-
letsR-2.0/letsR/man/lets.midpoint.Rd | 19 -
letsR-2.0/letsR/man/lets.overlap.Rd |only
letsR-2.0/letsR/man/lets.pamcrop.Rd |only
letsR-2.0/letsR/man/lets.presab.Rd | 136 +++++--------
letsR-2.0/letsR/man/lets.presab.birds.Rd | 117 +++--------
letsR-2.0/letsR/man/lets.presab.points.Rd |only
letsR-2.0/letsR/man/lets.rangesize.Rd |only
letsR-2.0/letsR/man/lets.shFilter.Rd | 50 ++---
letsR-2.0/letsR/man/lets.summarizer.Rd |only
letsR-2.0/letsR/man/lets.transf.Rd | 12 -
letsR-2.0/letsR/man/plot.PresenceAbsence.Rd | 17 -
letsR-2.0/letsR/man/print.PresenceAbsence.Rd | 7
letsR-2.0/letsR/man/print.summary.PresenceAbsence.Rd | 7
letsR-2.0/letsR/man/summary.PresenceAbsence.Rd | 7
letsR-2.0/letsR/man/temp.Rd | 11 -
72 files changed, 758 insertions(+), 623 deletions(-)
Title: K-Sample Rank Tests and their Combinations
Diff between kSamples versions 1.0 dated 2012-08-31 and 1.0.1 dated 2015-02-09
Description: Compares k samples using the Anderson-Darling test,
Kruskal-Wallis type tests with different rank score criteria,
and Steel's multiple comparison test. It computes asymptotic,
simulated or (limited) exact P-values, all valid under
randomization, with or without ties, or conditionally under
random sampling from populations, given the observed tie
pattern. Except for Steel's test it also combines these tests
across several blocks of samples. Also analyzed are 2 x t
contingency tables and their blocked combinations using the
Kruskal-Wallis criterion. Steel's test is inverted to provide
simultaneous confidence bounds for shift parameters. A
plotting function shows that asymptotic approximations for
small sample sizes provide only very limited utility when
comparing tail probabilities with those obtained via simulation
or exact calculations.
Author: Fritz Scholz [aut, cre],
Angie Zhu [aut]
Maintainer: Fritz Scholz
kSamples-1.0.1/kSamples/DESCRIPTION | 18 ++++++++++--------
kSamples-1.0.1/kSamples/MD5 | 9 ++++-----
kSamples-1.0.1/kSamples/NAMESPACE | 6 +++++-
kSamples-1.0.1/kSamples/R/qn.test.R | 2 +-
kSamples-1.0.1/kSamples/man/kSamples-package.Rd | 4 ++--
kSamples-1.0/kSamples/man/print.kSamples.Rd |only
6 files changed, 22 insertions(+), 17 deletions(-)
Title: Meta-Analysis of Diagnostic Test Accuracy when Reference Test is
Imperfect
Diff between HSROC versions 2.1.7 dated 2013-08-22 and 2.1.8 dated 2015-02-09
Description: Implements a model for joint meta-analysis of sensitivity and specificity of the diagnostic test under evaluation, while taking into account the possibly imperfect sensitivity and specificity of the reference test. This hierarchical model accounts for both within and between study variability. Estimation is carried out using a Bayesian approach, implemented via a Gibbs sampler. The model can be applied in situations where more than one reference test is used in the selected studies.
Author: Ian Schiller and Nandini Dendukuri
Maintainer: Ian Schiller
HSROC-2.1.7/HSROC/inst/doc/Tutorial.R |only
HSROC-2.1.8/HSROC/DESCRIPTION | 16 ++++++++--------
HSROC-2.1.8/HSROC/MD5 | 16 ++++++++--------
HSROC-2.1.8/HSROC/NAMESPACE | 2 +-
HSROC-2.1.8/HSROC/NEWS | 9 ++++++++-
HSROC-2.1.8/HSROC/R/HSROC-internal.R | 2 +-
HSROC-2.1.8/HSROC/build |only
HSROC-2.1.8/HSROC/data/In.house.rda |binary
HSROC-2.1.8/HSROC/data/MRI.rda |binary
HSROC-2.1.8/HSROC/inst/doc/Tutorial.pdf |binary
10 files changed, 26 insertions(+), 19 deletions(-)
Title: Redraw Base Graphics Using grid Graphics
Diff between gridGraphics versions 0.1-2 dated 2014-11-26 and 0.1-3 dated 2015-02-09
Description: Functions to convert a page of plots drawn with the
graphics package into identical output drawn with the grid package.
The result looks like the original graphics-based plot, but consists
of grid grobs and viewports that can then be manipulated with
grid functions (e.g., edit grobs and revisit viewports).
Author: Paul Murrell [cre, aut]
Maintainer: Paul Murrell
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/par.R | 3 +++
inst/NEWS.Rd | 8 ++++++++
4 files changed, 18 insertions(+), 7 deletions(-)
Title: The Complex Multivariate Gaussian Distribution
Diff between cmvnorm versions 1.0 dated 2014-09-09 and 1.0-1 dated 2015-02-09
Description: Various utilities for the complex multivariate Gaussian distribution.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin
DESCRIPTION | 10 -
MD5 | 16 -
build/vignette.rds |binary
inst/doc/complicator.R | 59 ++++--
inst/doc/complicator.Rnw | 374 ++++++++++++++++++++++++++---------------
inst/doc/complicator.pdf |binary
man/corr_complex.Rd | 65 +++++--
vignettes/complex_gaussian.bib | 48 +++++
vignettes/complicator.Rnw | 374 ++++++++++++++++++++++++++---------------
9 files changed, 641 insertions(+), 305 deletions(-)
Title: Semiparametric Bivariate Probit Modelling
Diff between SemiParBIVProbit versions 3.2-13.2 dated 2015-01-15 and 3.3 dated 2015-02-09
More information about SemiParBIVProbit at CRAN
Description: Routine for fitting bivariate models for binary responses with semiparametric predictors (including linear and nonlinear effects) in the presence of correlated error equations, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra
Maintainer: Giampiero Marra
ChangeLog | 6 +
DESCRIPTION | 8 -
MD5 | 82 +++++++++---------
NAMESPACE | 24 ++++-
R/AT.r | 119 +++++++++++++-------------
R/BCDF.r |only
R/BiCDF.r |only
R/LM.bpm.r | 22 ++--
R/S.m.r | 50 ++++-------
R/SemiParBIVProbit.fit.R | 8 -
R/SemiParBIVProbit.fit.post.r | 124 +++++++++++++++++----------
R/SemiParBIVProbit.fit1.R | 14 ++-
R/SemiParBIVProbit.r | 165 +++++++++++++++++++++++++++----------
R/adjCov.r | 10 +-
R/adjCovSD.r | 6 +
R/bprobgHs.r | 65 +++++++++++---
R/bprobgHsPL.r | 11 +-
R/bprobgHsPO.r | 60 ++++++++++---
R/bprobgHsSS.r | 95 ++++++++++++++-------
R/copgHs.r | 65 ++------------
R/est.prev.r | 6 +
R/gt.bpm.R | 2
R/pen.r | 90 ++++++++++++--------
R/penPL.r | 8 -
R/plot.SemiParBIVProbit.r | 11 +-
R/predict.SemiParBIVProbit.r | 14 ++-
R/print.SemiParBIVProbit.r | 47 ++++++----
R/print.summary.SemiParBIVProbit.r | 87 ++++++++++++-------
R/sem.checks.r | 2
R/startSS.r | 6 -
R/summary.SemiParBIVProbit.r | 150 +++++++++++++++++----------------
man/BCDF.Rd |only
man/BiCDF.Rd |only
man/LM.bpm.Rd | 5 -
man/S.m.Rd | 2
man/SemiParBIVProbit-package.Rd | 7 +
man/SemiParBIVProbit.Rd | 59 +++++++++----
man/SemiParBIVProbit.fit1.Rd | 2
man/SemiParBIVProbitObject.Rd | 11 +-
man/bprobgHs.Rd | 2
man/bprobgHsPL.Rd | 4
man/bprobgHsPO.Rd | 2
man/bprobgHsSS.Rd | 4
man/est.prev.Rd | 2
44 files changed, 880 insertions(+), 577 deletions(-)
Permanent link
Title: Optimal k-Means Clustering for One-Dimensional Data
Diff between Ckmeans.1d.dp versions 3.02 dated 2014-03-30 and 3.3.0 dated 2015-02-09
Description: A dynamic programming algorithm for optimal one-dimensional k-means clustering. The algorithm minimizes the sum of squares of within-cluster distances. As an alternative to the standard heuristic k-means algorithm, this algorithm guarantees optimality and repeatability.
Author: Joe Song and Haizhou Wang
Maintainer: Joe Song
DESCRIPTION | 13 +--
MD5 | 16 ++--
NAMESPACE | 3
NEWS |only
R/Ckmeans.1d.dp.R | 25 ++++--
inst/CITATION | 12 +--
man/Ckmeans.1d.dp.Rd | 29 ++++---
man/print.Ckmeans.1d.dp.Rd | 10 +-
src/Ckmeans.1d.dp.cpp | 178 +++++++++++++++------------------------------
tests |only
10 files changed, 124 insertions(+), 162 deletions(-)
Title: SNPs Enrichment Analysis
Diff between snpEnrichment versions 1.6.0 dated 2014-11-04 and 1.6.3 dated 2015-02-09
Description: Implements classes and methods for large scale SNP enrichment analysis (e.g. SNPs associated with genes expression in a GWAS signal).
Author: Mickael Canouil [aut, cre],
Loic Yengo [ctb]
Maintainer: Mickael Canouil
ChangeLog | 15 +++++++++++++++
DESCRIPTION | 16 ++++++++--------
MD5 | 12 ++++++------
R/Global.R | 2 +-
R/chromosome.R | 2 +-
R/enrichment.R | 7 ++++---
data/toyEnrichment.RData |binary
7 files changed, 35 insertions(+), 19 deletions(-)
Title: R Interface to the Pushbullet Messaging Service
Diff between RPushbullet versions 0.1.1 dated 2014-11-04 and 0.2.0 dated 2015-02-09
Description: An R interface to the Pushbullet messaging service which
provides fast and efficient notifications (and file transfer) between
computers, phones and tablets. An account has to be registered at the site
http://www.pushbullet.com site to obtain a (free) API key.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 51 +++++++++++++++++++++
DESCRIPTION | 20 ++++----
MD5 | 19 ++++---
NAMESPACE | 4 +
R/init.R | 99 ++++++++++++++++++++++++++---------------
R/pushes.R | 82 ++++++++++++++++++++++------------
README.md | 43 +++++++++++++++--
inst |only
man/pbGetDevices.Rd | 3 -
man/pbPost.Rd | 14 ++++-
tests/simpleTests.R | 125 ++++++++++++++++++++++++++++++++++++++++++++++++----
11 files changed, 359 insertions(+), 101 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Diff between openair versions 1.1-3 dated 2015-01-27 and 1.1-5 dated 2015-02-09
Description: Tools to analyse, interpret and understand air
pollution data. Data are typically hourly time series
and both monitoring data and dispersion model output
can be analysed. Many functions can also be applied to
other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw
DESCRIPTION | 14
MD5 | 83 ++--
NAMESPACE | 9
R/TaylorDiagram.R | 4
R/TheilSen.R | 10
R/aqStats.R | 303 ++++++--------
R/calcPercentile.R | 6
R/calendarPlot.R | 22 -
R/checkPrep.R | 27 -
R/conditionalEval.R | 14
R/conditionalQuantile.R | 6
R/cutData.R | 68 +--
R/importAURN.R | 2
R/importAURNCsv.R | 2
R/importAirbase.R | 2
R/importKCL.R | 14
R/importSAQN.R | 2
R/importTraj.R | 2
R/kernelExceed.R | 2
R/linearRelation.R | 20
R/modStats.R | 22 -
R/percentileRose.R | 20
R/polarAnnulus.R | 4
R/polarCluster.R | 2
R/polarFreq.R | 2
R/polarPlot.R | 977 +++++++++++++++++++++++------------------------
R/quickText.R | 9
R/scatterPlot.R | 104 ++---
R/smoothTrend.R | 8
R/summaryPlot.R | 33 +
R/timeAverage.R | 993 ++++++++++++++++++++++++------------------------
R/timePlot.R | 8
R/timeProp.R | 12
R/timeVariation.R | 56 +-
R/trajCluster.R | 4
R/trajLevel.R | 33 -
R/utilities.R | 113 +++--
R/windRose.R | 35 -
README.md | 12
man/aqStats.Rd | 5
man/scatterPlot.Rd | 4
src/Cquantile.cpp |only
src/rolling.cpp | 124 ++---
43 files changed, 1634 insertions(+), 1558 deletions(-)
Title: Generalized Method of Moments and Generalized Empirical
Likelihood
Diff between gmm versions 1.5-0 dated 2013-12-11 and 1.5-1 dated 2015-02-09
Description: It is a complete suite to estimate models based on moment
conditions. It includes the two step Generalized method of
moments (GMM) of Hansen(1982), the iterated GMM and continuous
updated estimator (CUE) of Hansen-Eaton-Yaron(1996) and several
methods that belong to the Generalized Empirical Likelihood
(GEL) family of estimators, as presented by Smith(1997),
Kitamura(1997), Newey-Smith(2004) and Anatolyev(2005).
Author: Pierre Chausse
Maintainer: Pierre Chausse
DESCRIPTION | 12 +++----
MD5 | 24 +++++++--------
NAMESPACE | 2 -
NEWS | 6 +++
R/Methods.gmm.R | 28 +++++++++++++----
R/getModel.R | 5 +--
R/gmm.R | 43 ++++++++++++++++++++-------
R/momentEstim.R | 21 ++++++-------
build/vignette.rds |binary
inst/doc/gmm_with_R.R | 74 ++++++++++++++++++++++++-----------------------
inst/doc/gmm_with_R.pdf |binary
inst/doc/gmm_with_R.rnw | 4 ++
vignettes/gmm_with_R.rnw | 4 ++
13 files changed, 138 insertions(+), 85 deletions(-)
Title: Dirichlet Regression in R
Diff between DirichletReg versions 0.6-1 dated 2014-12-10 and 0.6-2 dated 2015-02-09
Description: Implements Dirichlet regression models in R.
Author: Marco Johannes Maier [cre, aut]
Maintainer: Marco Johannes Maier
DESCRIPTION | 15
MD5 | 32 -
NEWS | 9
R/plot_DRdata_3d.R | 2
R/sysdata.rda |binary
build/partial.rdb |binary
build/vignette.rds |binary
data/ArcticLake.RData |binary
data/BloodSamples.RData |binary
data/GlacialTills.RData |binary
data/ReadingSkills.RData |binary
data/Rocks.RData |binary
inst/CITATION | 5
inst/NEWS.Rd | 6
inst/NEWS.pdf |binary
inst/doc/DirichletReg-vig.R | 824 +++++++++++++++++++++---------------------
inst/doc/DirichletReg-vig.pdf |binary
17 files changed, 452 insertions(+), 441 deletions(-)
Title: Computation of Bayes Factors for Common Designs
Diff between BayesFactor versions 0.9.10-1 dated 2015-02-04 and 0.9.10-2 dated 2015-02-09
Description: A suite of functions for computing
various Bayes factors for simple designs, including contingency tables,
one- and two-sample designs, one-way designs, general ANOVA designs, and
linear regression.
Author: Richard D. Morey [aut, cre],
Jeffrey N. Rouder [aut],
Tahira Jamil [ctb]
Maintainer: Richard D. Morey
DESCRIPTION | 10 +++++-----
MD5 | 20 ++++++++++----------
NEWS | 5 +++++
R/BayesFactorPCL-package.R | 3 +--
R/aaGenerics.R | 2 +-
build/vignette.rds |binary
inst/doc/compare_lme4.html | 14 +++++++-------
inst/doc/manual.html | 2 +-
inst/doc/priors.html | 2 +-
man/BayesFactor-package.Rd | 5 +----
man/grapes-termin-grapes.Rd | 4 ++--
11 files changed, 34 insertions(+), 33 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Diff between vardpoor versions 0.2.4 dated 2015-01-04 and 0.2.6 dated 2015-02-09
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks
DESCRIPTION | 12 ++++++------
MD5 | 26 +++++++++++++-------------
R/vardcros.R | 2 +-
R/vardom.R | 6 +++---
R/vardomh.R | 18 ++++++++++++------
R/variance_est.R | 2 +-
R/varpoord.R | 44 +++++++++++++++++++++++++-------------------
inst/CITATION | 4 ++--
inst/NEWS | 11 ++++++++++-
man/vardchanges.Rd | 2 +-
man/vardcros.Rd | 3 ++-
man/vardom.Rd | 2 +-
man/vardomh.Rd | 2 +-
man/vardpoor-package.Rd | 4 ++--
14 files changed, 80 insertions(+), 58 deletions(-)
Title: Excursion Sets and Contour Credibility Regions for Random Fields
Diff between excursions versions 2.0.6 dated 2015-02-02 and 2.0.16 dated 2015-02-09
Description: Functions that compute probabilistic excursion sets, contour credibility regions, contour avoiding regions, and simultaneous confidence bands for latent gaussian random processes and fields. The package also contains functions that calculate these quantities for models estimated with the INLA package.
Author: David Bolin
Maintainer: David Bolin
DESCRIPTION | 12 ++--
MD5 | 41 +++++++-------
NAMESPACE | 7 ++
R/geometry.R | 12 ++--
R/utils.R | 68 ++++++++++++++++++-----
man/continuous.Rd | 12 ++--
man/contourmap.colors.Rd | 4 -
man/contourmap.inla.Rd | 4 -
man/excursions.inla.Rd | 4 -
man/excursions.variances.Rd | 4 -
man/require.nowarnings.Rd |only
man/simconf.inla.Rd | 4 -
man/tricontour.Rd | 2
man/tricontourmap.Rd | 10 +--
src/Makevars | 6 --
src/integration.cpp | 78 +++++++++++++++++++++++++++
tests/testthat/helper-data.R | 6 --
tests/testthat/test.contourmap.R | 6 +-
tests/testthat/test.contourmap.inla.R | 2
tests/testthat/test.excursions.R | 97 ++++++++++++++++------------------
tests/testthat/test.excursions.inla.R | 2
tests/testthat/test.integration.R | 37 ++++++++----
22 files changed, 275 insertions(+), 143 deletions(-)
Title: Transcription Factor Binding Site Identification Tool
Diff between rtfbs versions 0.3.3 dated 2015-01-13 and 0.3.4 dated 2015-02-09
Description: RTFBS identifies and scores possible Transcription Factor
Binding Sites and allows for FDR analysis and pruning. It supports
splitting of sequences based on size or a specified GFF, grouping
by G+C content, and specification of Markov model order. The heavy
lifting is done in C while all results are made available via R.
Author: Nicholas Peterson, Andre Martins, Melissa Hubisz, and Adam
Siepel
Maintainer: Melissa Hubisz
DESCRIPTION | 10 -
MD5 | 20 +--
configure | 31 +++--
configure.ac | 8 -
inst/doc/vignette.pdf |binary
man/rtfbs-package.Rd | 8 -
src/Makevars.in | 108 +++++++++----------
src/Makevars.win | 108 +++++++++----------
src/fit_column.c | 14 ++
src/fit_feature.c | 4
src/maf.c | 274 +++++++++++++++++++++++++-------------------------
11 files changed, 302 insertions(+), 283 deletions(-)
Title: Local Average Response Functions for Instrumental Variable
Estimation of Treatment Effects
Diff between LARF versions 1.2 dated 2014-09-28 and 1.3 dated 2015-02-09
Description: Provides instrumental variable estimation of treatment effects when both the endogenous treatment and its instrument are binary. Applicable to both binary and continuous outcomes.
Author: Weihua An and Xuefu Wang, Indiana University Bloomington
Maintainer: Weihua An
DESCRIPTION | 8 +--
MD5 | 12 +++-
NAMESPACE | 7 ++
R/larf.R | 120 ++++++++++++++++++++++++++-----------------------
R/npse.R |only
man/Generate.Powers.Rd |only
man/cvlm.Rd |only
man/larf.Rd | 4 -
man/npse.Rd |only
9 files changed, 86 insertions(+), 65 deletions(-)
Title: Entrez in R
Diff between rentrez versions 0.3.1 dated 2014-09-24 and 0.4 dated 2015-02-08
Description: Rentrez provides an R interact to the NCBI's EUtils API allowing
users to search databases like genbank and pubmed, process the resulting
files and pull data into their R sessions.
Author: David Winter [aut, cre],
Scott Chamberlain [ctb]
Maintainer: David Winter
rentrez-0.3.1/rentrez/R/make_entrez_query.r |only
rentrez-0.3.1/rentrez/R/set_globals.r |only
rentrez-0.3.1/rentrez/man/entrez_email.Rd |only
rentrez-0.4/rentrez/DESCRIPTION | 8
rentrez-0.4/rentrez/MD5 | 64 +++--
rentrez-0.4/rentrez/NAMESPACE | 16 +
rentrez-0.4/rentrez/NEWS | 47 ++-
rentrez-0.4/rentrez/R/base.r |only
rentrez-0.4/rentrez/R/entrez_citmatch.r |only
rentrez-0.4/rentrez/R/entrez_fetch.r | 6
rentrez-0.4/rentrez/R/entrez_global_query.r | 6
rentrez-0.4/rentrez/R/entrez_info.r |only
rentrez-0.4/rentrez/R/entrez_link.r | 25 +-
rentrez-0.4/rentrez/R/entrez_post.r | 2
rentrez-0.4/rentrez/R/entrez_search.r | 84 ++++---
rentrez-0.4/rentrez/R/entrez_summary.r | 196 ++++++++++++----
rentrez-0.4/rentrez/build/vignette.rds |binary
rentrez-0.4/rentrez/inst/doc/rentrez_tutorial.R | 21 +
rentrez-0.4/rentrez/inst/doc/rentrez_tutorial.Rmd | 57 +++-
rentrez-0.4/rentrez/inst/doc/rentrez_tutorial.html | 249 +++++++++++++--------
rentrez-0.4/rentrez/man/entrez_citmatch.Rd |only
rentrez-0.4/rentrez/man/entrez_db_links.Rd |only
rentrez-0.4/rentrez/man/entrez_db_searchable.Rd |only
rentrez-0.4/rentrez/man/entrez_db_summary.Rd |only
rentrez-0.4/rentrez/man/entrez_dbs.Rd |only
rentrez-0.4/rentrez/man/entrez_fetch.Rd | 13 -
rentrez-0.4/rentrez/man/entrez_global_query.Rd | 11
rentrez-0.4/rentrez/man/entrez_info.Rd |only
rentrez-0.4/rentrez/man/entrez_link.Rd | 29 +-
rentrez-0.4/rentrez/man/entrez_post.Rd | 9
rentrez-0.4/rentrez/man/entrez_search.Rd | 38 ++-
rentrez-0.4/rentrez/man/entrez_summary.Rd | 36 ++-
rentrez-0.4/rentrez/man/parse_pubmed_xml.Rd | 3
rentrez-0.4/rentrez/man/rentrez.Rd | 3
rentrez-0.4/rentrez/tests/testthat/test_citmatch.r |only
rentrez-0.4/rentrez/tests/testthat/test_fetch.r | 26 +-
rentrez-0.4/rentrez/tests/testthat/test_info.r |only
rentrez-0.4/rentrez/tests/testthat/test_search.r | 9
rentrez-0.4/rentrez/tests/testthat/test_webenv.r | 2
rentrez-0.4/rentrez/vignettes/rentrez_tutorial.Rmd | 57 +++-
40 files changed, 686 insertions(+), 331 deletions(-)
Title: Identifying Functional Polymorphisms
Diff between IFP versions 0.1.1 dated 2015-01-10 and 0.1.2 dated 2015-02-08
Description: A suite for identifying causal models using relative concordances and identifying causal polymorphisms in case-control genetic association data, especially with large controls re-sequenced data.
Author: Leeyoung Park
Maintainer: Leeyoung Park
DESCRIPTION | 6 +++---
MD5 | 10 +++++-----
R/drgen.gm.R | 4 ++--
R/drggn.gm.R | 2 +-
R/drgn.gm.R | 2 +-
man/iter.mcmc.Rd | 16 +++++++++++++++-
6 files changed, 27 insertions(+), 13 deletions(-)
Title: Geostatistical Analysis and Design of Optimal Spatial Sampling
Networks
Diff between geospt versions 1.0-0 dated 2014-10-08 and 1.0-1 dated 2015-02-08
Description: Estimation of the variogram through trimmed mean, radial basis
functions (optimization, prediction and cross-validation), summary
statistics from cross-validation, pocket plot, and design of
optimal sampling networks through sequential and simultaneous
points methods.
Author: Carlos Melo
Maintainer: Alí Santacruz
DESCRIPTION | 23 ++----
MD5 | 26 +++---
NAMESPACE | 3
R/graph.rbf.R | 186 +++++++++++++++++++++++---------------------------
R/rbf.R | 74 ++++++++-----------
R/rbf.tcv.R | 5 +
man/RBF.phi.Rd | 2
man/criterio.cv.Rd | 2
man/est.variograms.Rd | 6 -
man/geospt-package.Rd | 7 -
man/graph.rbf.Rd | 30 ++++----
man/rbf.cv.Rd | 2
man/rbf.cv1.Rd | 6 -
man/rbf.tcv.Rd | 2
14 files changed, 180 insertions(+), 194 deletions(-)
Title: Bradley-Terry Models
Diff between BradleyTerry2 versions 1.0-5 dated 2014-06-16 and 1.0-6 dated 2015-02-08
Description: Specify and fit the Bradley-Terry model, including structured versions in which the parameters are related to explanatory variables through a linear predictor and versions with contest-specific effects, such as a home advantage.
Author: Heather Turner and David Firth
Maintainer: Heather Turner
BradleyTerry2-1.0-5/BradleyTerry2/data/springall.txt.gz |only
BradleyTerry2-1.0-6/BradleyTerry2/DESCRIPTION | 10 -
BradleyTerry2-1.0-6/BradleyTerry2/MD5 | 52 +++++-----
BradleyTerry2-1.0-6/BradleyTerry2/NAMESPACE | 1
BradleyTerry2-1.0-6/BradleyTerry2/R/BTabilities.R | 46 +++++---
BradleyTerry2-1.0-6/BradleyTerry2/R/BTm.R | 5
BradleyTerry2-1.0-6/BradleyTerry2/R/BTm.setup.R | 4
BradleyTerry2-1.0-6/BradleyTerry2/R/Diff.R | 15 ++
BradleyTerry2-1.0-6/BradleyTerry2/R/model.matrix.BTm.R |only
BradleyTerry2-1.0-6/BradleyTerry2/build/vignette.rds |binary
BradleyTerry2-1.0-6/BradleyTerry2/data/CEMS.rda |binary
BradleyTerry2-1.0-6/BradleyTerry2/data/chameleons.rda |binary
BradleyTerry2-1.0-6/BradleyTerry2/data/citations.rda |binary
BradleyTerry2-1.0-6/BradleyTerry2/data/icehockey.rda |binary
BradleyTerry2-1.0-6/BradleyTerry2/data/seeds.rda |binary
BradleyTerry2-1.0-6/BradleyTerry2/data/sound.fields.rda |binary
BradleyTerry2-1.0-6/BradleyTerry2/data/springall.rda |binary
BradleyTerry2-1.0-6/BradleyTerry2/inst/NEWS | 16 +++
BradleyTerry2-1.0-6/BradleyTerry2/inst/doc/BradleyTerry.R | 12 +-
BradleyTerry2-1.0-6/BradleyTerry2/inst/doc/BradleyTerry.Rnw | 29 +++--
BradleyTerry2-1.0-6/BradleyTerry2/inst/doc/BradleyTerry.pdf |binary
BradleyTerry2-1.0-6/BradleyTerry2/man/BTm.Rd | 11 +-
BradleyTerry2-1.0-6/BradleyTerry2/man/CEMS.Rd | 4
BradleyTerry2-1.0-6/BradleyTerry2/man/flatlizards.Rd | 4
BradleyTerry2-1.0-6/BradleyTerry2/man/football.Rd | 10 +
BradleyTerry2-1.0-6/BradleyTerry2/tests/flatlizards.Rout.save | 11 +-
BradleyTerry2-1.0-6/BradleyTerry2/tests/predict.Rout.save | 11 +-
BradleyTerry2-1.0-6/BradleyTerry2/vignettes/BradleyTerry.Rnw | 29 +++--
28 files changed, 168 insertions(+), 102 deletions(-)
More information about nestedRanksTest at CRAN
Permanent link
Title: Causal Effect Estimation and Diagnostics with Support Vector
Machines
Diff between SVMMatch versions 1.0 dated 2015-02-07 and 1.1 dated 2015-02-08
Description: Causal effect estimation in observational data often requires identifying a set of untreated observations that are comparable to some treated group of interest. This package provides a suite of functions for identifying such a set of observations and for implementing standard and new diagnostics tools. The primary function, svmmatch(), uses support vector machines to identify a region of common support between treatment and control groups. A sensitivity analysis, balance checking, and assessment of the region of overlap between treated and control groups is included. The Bayesian implementation allows for recovery of uncertainty estimates for the treatment effect and all other parameters.
Author: Marc Ratkovic
Maintainer: Marc Ratkovic
DESCRIPTION | 9 +++++----
MD5 | 8 +++++---
NEWS |only
man/LaLonde.Rd | 2 +-
src/Makevars | 2 +-
src/Makevars.win |only
6 files changed, 12 insertions(+), 9 deletions(-)
Title: Rcpp Integration for MLPACK Library
Diff between RcppMLPACK versions 1.0.10 dated 2014-12-21 and 1.0.10-2 dated 2015-02-08
Description: MLPACK is an intuitive, fast, scalable C++ machine learning
library, meant to be a machine learning analog to LAPACK. It
aims to implement a wide array of machine learning methods
and function as a Swiss army knife for machine learning
researchers: MLPACK is from http://www.mlpack.org/: sources are included in the package.
Author: Qiang Kou, Ryan Curtin
Maintainer: Qiang Kou
DESCRIPTION | 9 +++++----
MD5 | 6 +++---
inst/doc/RcppMLPACK-intro.pdf |binary
src/mlpack/core/tree/cosine_tree/cosine_tree.cpp | 2 +-
4 files changed, 9 insertions(+), 8 deletions(-)
Title: Practical Numerical Math Functions
Diff between pracma versions 1.7.9 dated 2014-11-15 and 1.8.3 dated 2015-02-08
Description:
Functions from numerical analysis and linear algebra, numerical
optimization, differential equations, plus some special functions.
Uses Matlab function names where appropriate to simplify porting.
Author: Hans Werner Borchers
Maintainer: Hans W. Borchers
pracma-1.7.9/pracma/R/runstest.R |only
pracma-1.7.9/pracma/man/runstest.Rd |only
pracma-1.8.3/pracma/DESCRIPTION | 14 +++----
pracma-1.8.3/pracma/MD5 | 54 ++++++++++++++---------------
pracma-1.8.3/pracma/NEWS | 34 +++++++++++++-----
pracma-1.8.3/pracma/R/circlefit.R | 16 +++++---
pracma-1.8.3/pracma/R/hurst.R | 5 ++
pracma-1.8.3/pracma/R/sumalt.R |only
pracma-1.8.3/pracma/man/agmean.Rd | 16 ++++++++
pracma-1.8.3/pracma/man/cd.Rd | 1
pracma-1.8.3/pracma/man/circlefit.Rd | 13 ++++--
pracma-1.8.3/pracma/man/clear.Rd | 1
pracma-1.8.3/pracma/man/clenshaw_curtis.Rd | 4 +-
pracma-1.8.3/pracma/man/ellip.Rd | 2 -
pracma-1.8.3/pracma/man/eta.Rd | 2 -
pracma-1.8.3/pracma/man/fresnel.Rd | 2 -
pracma-1.8.3/pracma/man/gammainc.Rd | 2 -
pracma-1.8.3/pracma/man/gammaz.Rd | 2 -
pracma-1.8.3/pracma/man/hadamard.Rd | 2 -
pracma-1.8.3/pracma/man/hankel.Rd | 2 -
pracma-1.8.3/pracma/man/hilb.Rd | 2 -
pracma-1.8.3/pracma/man/lambertW.Rd | 2 -
pracma-1.8.3/pracma/man/moler.Rd | 2 -
pracma-1.8.3/pracma/man/nile.Rd | 5 --
pracma-1.8.3/pracma/man/pascal.Rd | 2 -
pracma-1.8.3/pracma/man/rosser.Rd | 2 -
pracma-1.8.3/pracma/man/sumalt.Rd |only
pracma-1.8.3/pracma/man/vander.Rd | 2 -
pracma-1.8.3/pracma/man/wilkinson.Rd | 2 -
pracma-1.8.3/pracma/man/zeta.Rd | 2 -
30 files changed, 119 insertions(+), 74 deletions(-)
Title: Benchmark for the CEC 2005 Special Session on Real-Parameter
Optimization
Diff between cec2005benchmark versions 1.0.3 dated 2013-03-20 and 1.0.4 dated 2015-02-08
More information about cec2005benchmark at CRAN
Description: This package is a wrapper for the C implementation of the 25 benchmark functions for the CEC 2005 Special Session on Real-Parameter Optimization. The original C code by Santosh Tiwari and related documentation are available at http://www.ntu.edu.sg/home/EPNSugan/index_files/CEC-05/CEC05.htm.
Author: Yasser Gonzalez-Fernandez [aut, cre],
Marta Soto [aut]
Maintainer: Yasser Gonzalez-Fernandez
DESCRIPTION | 25 ++++++++-----------
MD5 | 58 +++++++++++++++++++++++-----------------------
NEWS | 12 ++++++---
inst/CITATION | 27 ++++++++++-----------
man/cec2005benchmark.Rd | 9 +++----
man/cec2005benchmark1.Rd | 9 +++----
man/cec2005benchmark10.Rd | 9 +++----
man/cec2005benchmark11.Rd | 9 +++----
man/cec2005benchmark12.Rd | 9 +++----
man/cec2005benchmark13.Rd | 9 +++----
man/cec2005benchmark14.Rd | 9 +++----
man/cec2005benchmark15.Rd | 9 +++----
man/cec2005benchmark16.Rd | 9 +++----
man/cec2005benchmark17.Rd | 9 +++----
man/cec2005benchmark18.Rd | 9 +++----
man/cec2005benchmark19.Rd | 9 +++----
man/cec2005benchmark2.Rd | 9 +++----
man/cec2005benchmark20.Rd | 9 +++----
man/cec2005benchmark21.Rd | 9 +++----
man/cec2005benchmark22.Rd | 9 +++----
man/cec2005benchmark23.Rd | 9 +++----
man/cec2005benchmark24.Rd | 9 +++----
man/cec2005benchmark25.Rd | 9 +++----
man/cec2005benchmark3.Rd | 9 +++----
man/cec2005benchmark4.Rd | 9 +++----
man/cec2005benchmark5.Rd | 9 +++----
man/cec2005benchmark6.Rd | 9 +++----
man/cec2005benchmark7.Rd | 9 +++----
man/cec2005benchmark8.Rd | 11 ++++----
man/cec2005benchmark9.Rd | 9 +++----
30 files changed, 192 insertions(+), 166 deletions(-)
Permanent link
Title: Technology Forecasting using DEA
Diff between TFDEA versions 0.9.5 dated 2014-10-01 and 0.9.8 dated 2015-02-07
Description: The package implements the TFDEA algorithm for technology forecasting.
It enables to estimate the arrival and/or capabilities of future technologies.
It also implements DEA (Data Envelopment Analysis) that can employ not only basic models
but also alternate model(s) to deal with infeasibility.
In addition, the package includes some standard technology forecasting data sets.
Author: Tom Shott [aut, cre],
Dong-Joon Lim [aut]
Maintainer: Tom Shott
ChangeLog |only
DESCRIPTION | 25 +-
MD5 | 26 +-
R/DEA.R | 49 ++--
R/SDEA.R | 55 ++---
R/TFDEA.R | 17 -
R/dea_common.R |only
R/dea_internal.R | 483 ++++++++++++++++++-----------------------------
R/fast_internal.R |only
R/sdea_internal.R |only
R/utility.R | 230 ++++++++++++++++------
data/wireless_2012.RData |only
man/DEA.Rd | 2
man/SDEA.Rd | 45 ++--
man/TFDEA.Rd | 2
man/fighter_jet.Rd | 16 +
man/wireless_2012.Rd |only
17 files changed, 494 insertions(+), 456 deletions(-)
Title: Stochastic Newton Sampler (SNS)
Diff between sns versions 0.9.1 dated 2014-08-30 and 1.0.0 dated 2015-02-07
Description: Stochastic Newton Sampler (SNS) is a Metropolis-Hastings-based, Markov Chain Monte Carlo sampler for twice differentiable, log-concave probability densities where the proposal density function is a multivariate Gaussian resulting from a second-order Taylor-series expansion of log-density around the current point. The mean of the Gaussian proposal is the full Newton-Raphson step from the current point. A boolean flag allows for switching from SNS to Newton-Raphson optimization (by choosing the mean of proposal function as next point). This can be used during burn-in to get close to the mode of the pdf (which is unique due to concavity). For high-dimensional densities, mixing can be improved via 'state space partitioning' strategy, in which SNS is applied to disjoint subsets of state space, wrapped in a Gibbs cycle.
Author: Alireza S. Mahani, Asad Hasan, Marshall Jiang, Mansour T.A. Sharabiani
Maintainer: Alireza Mahani
sns-0.9.1/sns/R/bayesGLM.R |only
sns-0.9.1/sns/R/expand.1par.R |only
sns-0.9.1/sns/man/bayesGLM.Rd |only
sns-1.0.0/sns/ChangeLog |only
sns-1.0.0/sns/DESCRIPTION | 15 +-
sns-1.0.0/sns/MD5 | 33 +++--
sns-1.0.0/sns/NAMESPACE | 13 +-
sns-1.0.0/sns/R/ess.R | 100 ++++-----------
sns-1.0.0/sns/R/sns.R | 219 +++++++++++++++-------------------
sns-1.0.0/sns/R/sns.methods.R | 249 ++++++++++++++++++++++++++++++++++-----
sns-1.0.0/sns/R/zzz.R | 3
sns-1.0.0/sns/build |only
sns-1.0.0/sns/inst |only
sns-1.0.0/sns/man/ess.Rd | 35 +----
sns-1.0.0/sns/man/plot.sns.Rd |only
sns-1.0.0/sns/man/predict.sns.Rd |only
sns-1.0.0/sns/man/sns.Rd | 73 +++++++----
sns-1.0.0/sns/man/sns.part.Rd |only
sns-1.0.0/sns/man/summary.sns.Rd |only
sns-1.0.0/sns/vignettes |only
20 files changed, 453 insertions(+), 287 deletions(-)
Title: Parametric and semi-parametric analysis of semi-competing risks
data
Diff between SemiCompRisks versions 1.0 dated 2013-12-21 and 2.0 dated 2015-02-07
Description: This package contains algorithms to perform various types of parametric and semi-parametric analyses of semi-competing risks data. We also provide functions to fit survival regression models to univariate time-to-event outcome.
Author: Kyu Ha Lee and Sebastien Haneuse
Maintainer: Kyu Ha Lee
DESCRIPTION | 12
MD5 | 101
NAMESPACE | 9
R/BayesID.R | 357 ++-
R/BayesIDcor.R |only
R/BayesSurv.R | 18
R/BayesSurvcor.R |only
R/ehr.R | 4
R/methods.R | 2003 ++++++++++++++++-
R/simSurv.R | 2
data/BMT.rda |binary
data/scrCorData.rda |only
data/scrData.rda |binary
data/survData.rda |binary
man/BayesID.Rd | 61
man/BayesIDcor.Rd |only
man/BayesSurv.Rd | 55
man/BayesSurvcor.Rd |only
man/SemiCompRisks-package.Rd | 29
man/ehr.Rd | 10
man/methods.Rd | 23
man/scrCorData.Rd |only
man/simID.Rd | 12
man/simSurv.Rd | 12
src/BpeDpCorScr.c |only
src/BpeDpCorScr.h |only
src/BpeDpCorScrSM.c |only
src/BpeDpCorScrSM.h |only
src/BpeDpCorScrSM_Updates.c |only
src/BpeDpCorScr_Updates.c |only
src/BpeDpCorSurv.c |only
src/BpeDpCorSurv.h |only
src/BpeDpCorSurv_Updates.c |only
src/BpeMvnCorScr.c |only
src/BpeMvnCorScr.h |only
src/BpeMvnCorScrSM.c |only
src/BpeMvnCorScrSM.h |only
src/BpeMvnCorScrSM_Updates.c |only
src/BpeMvnCorScr_Updates.c |only
src/BpeMvnCorSurv.c |only
src/BpeMvnCorSurv.h |only
src/BpeMvnCorSurv_Updates.c |only
src/BpeScr.c | 156 -
src/BpeScrSM.c | 201 -
src/BpeScrSM_Updates.c | 758 ------
src/BpeScr_Updates.c | 723 ------
src/BpeSurv.c | 302 --
src/BpeSurv_Updates.c | 348 ---
src/BweibCorSurv.c |only
src/BweibCorSurv.h |only
src/BweibCorSurv_Updates.c |only
src/BweibDpCorScr.c |only
src/BweibDpCorScr.h |only
src/BweibDpCorScrSM.c |only
src/BweibDpCorScrSM.h |only
src/BweibDpCorScrSM_Updates.c |only
src/BweibDpCorScr_Updates.c |only
src/BweibDpCorSurv.c |only
src/BweibDpCorSurv.h |only
src/BweibDpCorSurv_Updates.c |only
src/BweibMvnCorScr.c |only
src/BweibMvnCorScr.h |only
src/BweibMvnCorScrSM.c |only
src/BweibMvnCorScrSM.h |only
src/BweibMvnCorScrSM_Updates.c |only
src/BweibMvnCorScr_Updates.c |only
src/BweibScr.c | 19
src/BweibScrSM.c |only
src/BweibScrSM.h |only
src/BweibScrSM_Updates.c |only
src/BweibScr_Updates.c | 9
src/BweibSurv.c | 20
src/BweibSurv_Updates.c | 3
src/Utilities.c | 4597 ++++++++++++++++++++++++++++++++++++++++-
74 files changed, 7080 insertions(+), 2764 deletions(-)
Title: R Interface to FOAAS
Diff between rfoaas versions 0.1.1 dated 2015-01-11 and 0.1.3 dated 2015-02-07
Description: R access to the FOAAS (F... Off As A Service) web service is provided.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 23 +++++++++++
DESCRIPTION | 12 +++---
MD5 | 12 +++---
R/foaas.R | 84 ++++++++++++++++++++++++-------------------
README.md | 2 -
man/rfoaas-package.Rd | 80 +++++++++++++++++++++++++---------------
tests/runTestsAgainstFOAAS.R | 1
7 files changed, 133 insertions(+), 81 deletions(-)
Title: Recommender System using Matrix Factorization
Diff between recosystem versions 0.2.4 dated 2014-09-13 and 0.2.5 dated 2015-02-07
Description: This package is an R wrapper of the libmf library
(http://www.csie.ntu.edu.tw/~cjlin/libmf/) for recommender
system using matrix factorization. It is typically used to
approximate an incomplete matrix using the product of two
matrices in a latent space. Other common names for this task
include "collaborative filtering", "matrix completion",
"matrix recovery", etc.
Author: Yixuan Qiu, Chih-Jen Lin, Yu-Chin Juan, Yong Zhuang,
Wei-Sheng Chin and other contributors. See file AUTHORS for
details.
Maintainer: Yixuan Qiu
DESCRIPTION | 8 -
MD5 | 25 ++-
R/RecoSys.R | 112 ++++++++++++++---
README.md |only
build/vignette.rds |binary
inst/NEWS.Rd | 6
inst/doc/introduction.Rmd | 11 -
inst/doc/introduction.html | 296 +++++++++++++++++++++++----------------------
man/Reco.Rd | 12 +
man/convert.Rd | 7 -
man/output.Rd |only
man/predict.Rd | 11 -
man/train.Rd | 7 -
src/output.cpp |only
vignettes/introduction.Rmd | 11 -
15 files changed, 305 insertions(+), 201 deletions(-)
Title: H2O R Interface
Diff between h2o versions 2.8.1.1 dated 2014-10-27 and 2.8.4.4 dated 2015-02-07
Description: R scripting functionality for H2O, the open source
math engine for big data that computes parallel distributed
machine learning algorithms such as generalized linear models,
gradient boosting machines, random forests, and neural networks
(deep learning) within various cluster environments.
Author: Anqi Fu [aut], Spencer Aiello [aut], Ariel Rao [aut],
Amy Wang [aut], Tom Kraljevic [aut], and Petr Maj [ctb]
with contributions from the H2O team
Maintainer: Tom Kraljevic
h2o-2.8.1.1/h2o/man/ddply.H2OParsedData.Rd |only
h2o-2.8.4.4/h2o/DESCRIPTION | 28 -
h2o-2.8.4.4/h2o/MD5 | 89 ++--
h2o-2.8.4.4/h2o/NAMESPACE | 45 +-
h2o-2.8.4.4/h2o/R/Algorithms.R | 543 +++++++++++++++----------
h2o-2.8.4.4/h2o/R/Classes.R | 223 ++++++++--
h2o-2.8.4.4/h2o/R/Internal.R | 34 +
h2o-2.8.4.4/h2o/R/ParseImport.R | 171 +++++--
h2o-2.8.4.4/h2o/R/Wrapper.R | 38 +
h2o-2.8.4.4/h2o/R/models.R | 5
h2o-2.8.4.4/h2o/demo/h2o.kmeans.R | 3
h2o-2.8.4.4/h2o/inst/branch.txt | 2
h2o-2.8.4.4/h2o/inst/buildnum.txt | 2
h2o-2.8.4.4/h2o/man/H2OGapStatModel-class.Rd |only
h2o-2.8.4.4/h2o/man/H2OPerfModel-class.Rd | 1
h2o-2.8.4.4/h2o/man/H2ORawData-class.Rd | 2
h2o-2.8.4.4/h2o/man/data.frameORnull-class.Rd |only
h2o-2.8.4.4/h2o/man/h2o-package.Rd | 23 -
h2o-2.8.4.4/h2o/man/h2o.SpeeDRF.Rd | 13
h2o-2.8.4.4/h2o/man/h2o.addFunction.Rd | 4
h2o-2.8.4.4/h2o/man/h2o.coxph.Rd | 24 -
h2o-2.8.4.4/h2o/man/h2o.createFrame.Rd | 99 ++--
h2o-2.8.4.4/h2o/man/h2o.ddply.Rd |only
h2o-2.8.4.4/h2o/man/h2o.deeplearning.Rd | 13
h2o-2.8.4.4/h2o/man/h2o.gains.Rd |only
h2o-2.8.4.4/h2o/man/h2o.gapStatistic.Rd | 32 -
h2o-2.8.4.4/h2o/man/h2o.gbm.Rd | 23 -
h2o-2.8.4.4/h2o/man/h2o.getTimezone.Rd |only
h2o-2.8.4.4/h2o/man/h2o.glm.Rd | 324 +++++++-------
h2o-2.8.4.4/h2o/man/h2o.importFile.Rd | 7
h2o-2.8.4.4/h2o/man/h2o.importFolder.Rd | 7
h2o-2.8.4.4/h2o/man/h2o.importHDFS.Rd | 7
h2o-2.8.4.4/h2o/man/h2o.importURL.Rd | 9
h2o-2.8.4.4/h2o/man/h2o.init.Rd | 8
h2o-2.8.4.4/h2o/man/h2o.interaction.Rd |only
h2o-2.8.4.4/h2o/man/h2o.kmeans.Rd | 2
h2o-2.8.4.4/h2o/man/h2o.listTimezones.Rd |only
h2o-2.8.4.4/h2o/man/h2o.makeGLMModel.Rd |only
h2o-2.8.4.4/h2o/man/h2o.naiveBayes.Rd | 2
h2o-2.8.4.4/h2o/man/h2o.order.Rd |only
h2o-2.8.4.4/h2o/man/h2o.parseRaw.Rd | 6
h2o-2.8.4.4/h2o/man/h2o.pcr.Rd | 2
h2o-2.8.4.4/h2o/man/h2o.performance.Rd | 4
h2o-2.8.4.4/h2o/man/h2o.predict.Rd | 13
h2o-2.8.4.4/h2o/man/h2o.randomForest.Rd | 18
h2o-2.8.4.4/h2o/man/h2o.removeVecs.Rd |only
h2o-2.8.4.4/h2o/man/h2o.saveAll.Rd | 2
h2o-2.8.4.4/h2o/man/h2o.saveModel.Rd | 2
h2o-2.8.4.4/h2o/man/h2o.setTimezone.Rd |only
h2o-2.8.4.4/h2o/man/h2o.uploadFile.Rd | 5
h2o-2.8.4.4/h2o/man/plot.H2OGapStatModel.Rd |only
h2o-2.8.4.4/h2o/man/rbind.H2OParsedData.Rd |only
h2o-2.8.4.4/h2o/man/summary.H2OGapStatModel.Rd |only
53 files changed, 1187 insertions(+), 648 deletions(-)
Title: Finding Heterogeneous Treatment Effects
Diff between FindIt versions 0.3 dated 2013-02-01 and 0.4 dated 2015-02-07
Description: FindIt implements the heterogeneous
treatment effect estimation procedure proposed by Imai and
Ratkovic (2013). The proposed method is applicable, for
example, when selecting a small number of most (or least)
efficacious treatments from a large number of alternative
treatments as well as when identifying subsets of the
population who benefit (or are harmed by) a treatment of
interest. The method adapts the Support Vector Machine
classifier by placing separate LASSO constraints over the
pre-treatment parameters and causal heterogeneity parameters of
interest. This allows for the qualitative distinction between
causal and other parameters, thereby making the variable
selection suitable for the exploration of causal heterogeneity.
Author: Naoki Egami
Maintainer: Naoki Egami
FindIt-0.3/FindIt/ChangeLog |only
FindIt-0.4/FindIt/DESCRIPTION | 21
FindIt-0.4/FindIt/MD5 | 15
FindIt-0.4/FindIt/NAMESPACE | 6
FindIt-0.4/FindIt/R/SVMHet.R | 3275 ++++++++++++++++++++++++----
FindIt-0.4/FindIt/man/FindIt.Rd | 282 +-
FindIt-0.4/FindIt/man/MakeAllWay.Rd | 25
FindIt-0.4/FindIt/man/MakeTwoWay.Rd | 20
FindIt-0.4/FindIt/man/Predict.FindIt.Rd |only
FindIt-0.4/FindIt/man/plot.PredictFindIt.Rd |only
10 files changed, 3138 insertions(+), 506 deletions(-)
Title: Difference Metrics for Comparing Pairs of Maps
Diff between diffeR versions 0.0-1 dated 2014-11-29 and 0.0-2 dated 2015-02-07
Description: Difference metrics for comparing pairs of maps representing real or categorical variables at original and multiple resolutions.
Author: Robert Gilmore Pontius Jr.
Maintainer: Alí Santacruz
DESCRIPTION | 8 +++----
MD5 | 47 +++++++++++++++++++++++--------------------
NAMESPACE | 4 ++-
R/crosstabm.R | 27 +++++++++++++++---------
R/differenceMR.R | 4 +--
R/overallComponentsPlot.R |only
R/sample2pop.R |only
demo/00Index | 1
demo/diffMetrics.R |only
man/MAD.Rd | 2 -
man/composite.Rd | 6 ++---
man/crosstabm.Rd | 21 +++++++++++++++----
man/diffTablej.Rd | 9 ++++++--
man/diffeR-package.Rd | 4 +--
man/differenceMR.Rd | 12 ++++++++--
man/exchangeDij.Rd | 4 +--
man/exchangeDj.Rd | 4 +--
man/overallAllocD.Rd | 4 +--
man/overallComponentsPlot.Rd |only
man/overallDiff.Rd | 4 +--
man/overallDiffCatj.Rd | 4 +--
man/overallExchangeD.Rd | 4 +--
man/overallQtyD.Rd | 4 +--
man/overallShiftD.Rd | 4 +--
man/quantityDj.Rd | 4 +--
man/sample2pop.Rd |only
man/shiftDj.Rd | 4 +--
27 files changed, 112 insertions(+), 73 deletions(-)
Title: Multiple Choice Test Evaluation
Diff between klausuR versions 0.12-5 dated 2012-03-11 and 0.12-10 dated 2015-02-07
Description: A set of functions designed to quickly generate results of a
multiple choice test. Generates detailed global results, lists for
anonymous feedback and personalised result feedback (in LaTeX and/or PDF
format), as well as item statistics like Cronbach's alpha or disciminatory
power. klausuR also includes a plugin for the R GUI and IDE RKWard,
providing dialogs for its basic features. To use them, install RKWard from
http://rkward.sf.net (plugins are detected automatically). Due to some
restrictions on CRAN, the full package sources are only available from the
project homepage.
Author: m.eik michalke [aut, cre]
Maintainer: m.eik michalke
klausuR-0.12-10/klausuR/ChangeLog | 227 +-
klausuR-0.12-10/klausuR/DESCRIPTION | 48
klausuR-0.12-10/klausuR/MD5 | 102 -
klausuR-0.12-10/klausuR/NAMESPACE | 17
klausuR-0.12-10/klausuR/R/00_class_01_klausuR.test.R |only
klausuR-0.12-10/klausuR/R/00_class_02_klausuR.R |only
klausuR-0.12-10/klausuR/R/00_class_03_klausuR.answ.R |only
klausuR-0.12-10/klausuR/R/00_class_04_klausuR.mult.R |only
klausuR-0.12-10/klausuR/R/01_method_plot.klausuR.R |only
klausuR-0.12-10/klausuR/R/01_method_show.klausuR.R |only
klausuR-0.12-10/klausuR/R/01_method_sort.klausuR.R |only
klausuR-0.12-10/klausuR/R/compare.R | 548 +++---
klausuR-0.12-10/klausuR/R/grand.table.R | 158 +
klausuR-0.12-10/klausuR/R/klausuR-internal.R | 1150 ++++++++-----
klausuR-0.12-10/klausuR/R/klausuR-internal.roxy.all.R | 56
klausuR-0.12-10/klausuR/R/klausuR-package.R | 18
klausuR-0.12-10/klausuR/R/klausur.R | 637 ++++---
klausuR-0.12-10/klausuR/R/klausur.data.R | 276 +--
klausuR-0.12-10/klausuR/R/klausur.gen.R | 63
klausuR-0.12-10/klausuR/R/klausur.gen.corr.R | 64
klausuR-0.12-10/klausuR/R/klausur.gen.marks.R | 356 ++--
klausuR-0.12-10/klausuR/R/klausur.mufo.R | 265 +--
klausuR-0.12-10/klausuR/R/klausur.report.R | 1180 +++++++-------
klausuR-0.12-10/klausuR/R/nret.rescale.R | 106 -
klausuR-0.12-10/klausuR/R/nret.translator.R | 430 ++---
klausuR-0.12-10/klausuR/data/antworten.mufo.rda |binary
klausuR-0.12-10/klausuR/data/antworten.rda |binary
klausuR-0.12-10/klausuR/inst/CITATION | 22
klausuR-0.12-10/klausuR/inst/NEWS.Rd | 250 ++
klausuR-0.12-10/klausuR/inst/rkward/plugins/test_data.xml | 2
klausuR-0.12-10/klausuR/man/antworten.Rd | 9
klausuR-0.12-10/klausuR/man/antworten.mufo.Rd | 9
klausuR-0.12-10/klausuR/man/compare.Rd | 112 -
klausuR-0.12-10/klausuR/man/grand.table.Rd | 61
klausuR-0.12-10/klausuR/man/klausuR-class.Rd | 56
klausuR-0.12-10/klausuR/man/klausuR-package.Rd | 43
klausuR-0.12-10/klausuR/man/klausuR.answ-class.Rd | 70
klausuR-0.12-10/klausuR/man/klausuR.mult-class.Rd | 25
klausuR-0.12-10/klausuR/man/klausuR.test-class.Rd | 26
klausuR-0.12-10/klausuR/man/klausur.Rd | 415 ++--
klausuR-0.12-10/klausuR/man/klausur.data.Rd | 258 +--
klausuR-0.12-10/klausuR/man/klausur.gen.Rd | 29
klausuR-0.12-10/klausuR/man/klausur.gen.corr.Rd | 49
klausuR-0.12-10/klausuR/man/klausur.gen.marks.Rd | 149 -
klausuR-0.12-10/klausuR/man/klausur.mufo.Rd | 171 --
klausuR-0.12-10/klausuR/man/klausur.report.Rd | 237 +-
klausuR-0.12-10/klausuR/man/nret.rescale.Rd | 43
klausuR-0.12-10/klausuR/man/nret.translator.Rd | 160 -
klausuR-0.12-10/klausuR/man/plot-methods.Rd | 71
klausuR-0.12-10/klausuR/man/show-methods.Rd | 35
klausuR-0.12-10/klausuR/man/sort-methods.Rd | 41
klausuR-0.12-10/klausuR/man/spss.data.Rd | 6
klausuR-0.12-5/klausuR/R/klausuR-class.R |only
klausuR-0.12-5/klausuR/R/klausuR.answ-class.R |only
klausuR-0.12-5/klausuR/R/klausuR.mult-class.R |only
klausuR-0.12-5/klausuR/R/klausuR.test-class.R |only
klausuR-0.12-5/klausuR/R/plot.klausuR.R |only
klausuR-0.12-5/klausuR/R/show.klausuR.R |only
klausuR-0.12-5/klausuR/R/sort.klausuR.R |only
59 files changed, 4387 insertions(+), 3663 deletions(-)
Title: Advanced Tables for Markdown/HTML
Diff between htmlTable versions 1.0 dated 2014-12-21 and 1.1 dated 2015-02-07
Description: Tables with state of the art layout containing
row spanners, column spanners, table spanners, zebra striping,
and more. While allowing advanced layout the underlying CSS structure is
simple in order to maximize compatibility with MS Word/LibreOffice.
The package also contains a few text formatting functions that help outputting
text compatible with HTML/LaTeX.
Author: Max Gordon
Maintainer: Max Gordon
DESCRIPTION | 20
MD5 | 89
NAMESPACE | 5
NEWS | 17
R/htmlTable.R | 297 -
R/htmlTable_helpers.R | 82
R/htmlTable_render.R |only
R/txtFrmt.R | 22
README.md |only
build/vignette.rds |binary
inst/doc/general.R |only
inst/doc/general.Rmd |only
inst/doc/general.html |only
inst/doc/tables.R | 16
inst/doc/tables.Rmd | 16
inst/doc/tables.html | 6350 ++++++++++++------------
man/SCB.Rd | 3
man/htmlTable.Rd | 111
man/outputInt.Rd | 3
man/prAddCells.Rd | 3
man/prAddSemicolon2StrEnd.Rd | 3
man/prAttr4RgroupAdd.Rd |only
man/prGetAlign.Rd | 3
man/prGetCgroupHeader.Rd | 7
man/prGetRgroupLine.Rd |only
man/prGetRowlabelPos.Rd | 3
man/prGetStyle.Rd | 3
man/prGetThead.Rd |only
man/prMergeClr.Rd | 3
man/prPrepareAlign.Rd | 7
man/prPrepareCgroup.Rd | 20
man/prPrepareColors.Rd | 9
man/prPrepareCss.Rd | 7
man/prSkipRownames.Rd | 3
man/prTblNo.Rd | 3
man/pvalueFormatter.Rd | 3
man/splitLines4Table.Rd | 3
man/tblNoLast.Rd | 4
man/tblNoNext.Rd | 4
man/txtInt.Rd | 3
man/txtMergeLines.Rd | 3
man/txtPval.Rd | 3
man/txtRound.Rd | 11
tests/testthat/test-htmlTable.R | 77
tests/testthat/test-htmlTable_rgroup_tspanner.R |only
tests/testthat/test-htmlTable_total.R |only
tests/testthat/test-txtFrmt.R | 48
tests/visual_tests/htmlTable_markdown.Rmd | 2
tests/visual_tests/pandoc_test.Rmd |only
tests/visual_tests/pandoc_v1.13_bug.md |only
vignettes/general.Rmd |only
vignettes/tables.Rmd | 16
52 files changed, 3872 insertions(+), 3410 deletions(-)
Title: Random name generating function and data set
Diff between randomNames versions 0.0-6 dated 2013-01-21 and 0.0-8 dated 2015-02-07
Description: Function to generate random gender and ethnicity correct first and/or last names. Names are chosen proportionally based upon their probability of appearing in a large scale data base of real names.
Author: Damian W. Betebenner
Maintainer: Damian W. Betebenner
DESCRIPTION | 14 ++++++--------
MD5 | 13 +++++++------
R/randomNames.R | 4 ++--
data/datalist |only
data/randomNamesData.rda |binary
inst/CITATION | 8 ++++----
inst/NEWS | 4 ++++
man/randomNames-package.Rd | 8 ++++----
8 files changed, 27 insertions(+), 24 deletions(-)
Title: Flexible Mediation Analysis using Natural Effect Models
Diff between medflex versions 0.4.0 dated 2014-12-11 and 0.5-0 dated 2015-02-07
Description: medflex allows to run flexible mediation analyses using natural
effect models as described in Lange, Vansteelandt and Bekaert (2012),
Vansteelandt, Bekaert and Lange (2012) and Loeys, Moerkerke, De Smet,
Buysse, Steen and Vansteelandt (2013).
Author: Johan Steen [aut, cre],
Tom Loeys [aut],
Beatrijs Moerkerke [aut],
Stijn Vansteelandt [aut],
Joris Meys [ctb] (technical support),
Theis Lange [ctb] (valuable suggestions)
Maintainer: Johan Steen
DESCRIPTION | 17 -
MD5 | 63 +++--
NAMESPACE | 18 +
NEWS |only
R/UPBdata_descr.R | 21 +
R/neImpute.R | 88 +++++---
R/neLht.R | 403 +++++++++++++++++++++++++++----------
R/neModel.R | 510 ++++++++++++++++++++++++++++++++++++------------
R/neWeight.R | 125 +++++++----
R/terms-expand.R | 14 -
R/utils.R | 61 ++++-
R/zzz.R |only
data/UPBdata.rda |binary
inst/CITATION | 5
inst/doc |only
man/UPBdata.Rd | 22 +-
man/expData.Rd | 5
man/neImpute.Rd | 5
man/neImpute.default.Rd | 58 +++--
man/neImpute.formula.Rd | 23 +-
man/neLht-methods.Rd | 34 +--
man/neLht.Rd | 75 ++++++-
man/neModel-methods.Rd | 60 +++--
man/neModel.Rd | 147 +++++++++----
man/neWeight.Rd | 5
man/neWeight.default.Rd | 67 +++---
man/neWeight.formula.Rd | 23 +-
man/plot.neLht.Rd | 29 +-
man/plot.neModel.Rd | 30 +-
man/weights.expData.Rd |only
vignettes |only
31 files changed, 1339 insertions(+), 569 deletions(-)
Title: Least-Squares Means
Diff between lsmeans versions 2.14 dated 2015-01-06 and 2.15 dated 2015-02-07
Description: Obtain least-squares means for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of least-squares means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell V. Lenth [aut], Maxime Hervé [ctb]
Maintainer: Russ Lenth
DESCRIPTION | 10 ++---
MD5 | 35 +++++++++---------
NAMESPACE | 5 +-
R/aovlist-support.R | 2 -
R/helpers.R | 84 +++++++++++++++++++++++++--------------------
R/lsmeans.R | 12 +++---
R/ordinal-support.R | 32 ++++++++++-------
R/ref.grid.R | 4 +-
R/rms-support.R |only
R/summary.R | 67 +++++++++++++++++++----------------
inst/NEWS | 8 ++++
inst/doc/extending.R | 6 +--
inst/doc/extending.pdf |binary
inst/doc/extending.rnw | 8 ++--
inst/doc/using-lsmeans.pdf |binary
man/extending.Rd | 40 ++++++++-------------
man/models.Rd | 26 ++++++++++++-
tests/tests1.Rout.save | 11 +++--
vignettes/extending.rnw | 8 ++--
19 files changed, 206 insertions(+), 152 deletions(-)
Title: Explorer of World Population Prospects
Diff between wppExplorer versions 1.4-0 dated 2014-08-22 and 1.5-0 dated 2015-02-07
Description: A shiny interface for exploring data in wpp2008-wpp2012 packages.
Author: Hana Sevcikova
Maintainer: Hana Sevcikova
ChangeLog | 6 ++++++
DESCRIPTION | 8 ++++----
MD5 | 18 +++++++++---------
R/global.R | 17 +++++++++--------
R/wpp.R | 17 ++++++++++++++++-
inst/explore/server.R | 6 +++---
inst/explore/ui.R | 2 +-
man/wpp.indicator.Rd | 4 +++-
man/wppExplorer-package.Rd | 4 ++--
tests/test_functions.R | 2 +-
10 files changed, 54 insertions(+), 30 deletions(-)
Title: Linked Micromap Plots
Diff between micromap versions 1.9.1 dated 2015-01-26 and 1.9.2 dated 2015-02-06
Description: This group of functions simplifies the creation of linked micromap
plots.
Author: Quinn Payton [aut],
Tony Olsen [aut],
Marc Weber [ctb],
Michael McManus [ctb],
Tom Kincaid [cre, ctb]
Maintainer: Tom Kincaid
DESCRIPTION | 12 ++++++------
MD5 | 8 ++++----
NAMESPACE | 6 +++---
inst/NEWS.Rd | 16 ++++++++++++++++
inst/doc/CHANGES.pdf |binary
5 files changed, 29 insertions(+), 13 deletions(-)
Title: Bayesian Estimation of Incoherent Neutron Scattering Backgrounds
Diff between BBEST versions 0.1-1 dated 2014-12-05 and 0.1-2 dated 2015-02-06
Description: We implemented a Bayesian-statistics approach for
subtraction of incoherent scattering from neutron total-scattering data.
In this approach, the estimated background signal associated with
incoherent scattering maximizes the posterior probability, which combines
the likelihood of this signal in reciprocal and real spaces with the prior
that favors smooth lines.
Author: Anton Gagin and Igor Levin with contributions from Charles R. Hogg III
Maintainer: Anton Gagin
DESCRIPTION | 6 -
MD5 | 16 +-
R/fits.R | 23 ++++
R/plot.R | 6 -
R/uncertainty.R | 1
README.md | 272 +++++++++++++++++++++++++++++++++++++++++++++++-
inst/gui/help/help.html | 6 +
inst/gui/server.R | 3
inst/gui/ui.R | 9 +
9 files changed, 324 insertions(+), 18 deletions(-)
Title: Variance Component Models
Diff between varComp versions 0.1-317 dated 2013-08-31 and 0.1-360 dated 2015-02-06
Description: Variance component models: REML estimation, testing fixed effect contrasts through Satterthwaite or Kenward-Roger methods, testing the nullity of variance components through (linear or quadratic) score tests or likelihood ratio tests.
Author: Long Qu (long.qu@wright.edu)
Maintainer: Long Qu
varComp-0.1-317/varComp/man/char2list.Rd |only
varComp-0.1-360/varComp/DESCRIPTION | 10 ++---
varComp-0.1-360/varComp/MD5 | 37 +++++++++----------
varComp-0.1-360/varComp/NAMESPACE | 2 -
varComp-0.1-360/varComp/R/KR.varComp.R | 3 +
varComp-0.1-360/varComp/R/p.value.R | 2 -
varComp-0.1-360/varComp/R/print.varComp.test.R | 2 -
varComp-0.1-360/varComp/R/varComp-utilities.R | 2 +
varComp-0.1-360/varComp/R/varComp.LinScore.SSAS155.R | 6 +--
varComp-0.1-360/varComp/R/varComp.LinScore.test.R | 2 -
varComp-0.1-360/varComp/R/varComp.R | 21 +++++++---
varComp-0.1-360/varComp/R/varComp.RLRT.test.R | 2 -
varComp-0.1-360/varComp/R/varComp.VM03.test.R | 6 +--
varComp-0.1-360/varComp/R/varComp.test.R | 4 +-
varComp-0.1-360/varComp/man/logLik.varComp.Rd | 2 -
varComp-0.1-360/varComp/man/varComp-package.Rd | 6 +--
varComp-0.1-360/varComp/man/varComp.Rd | 4 +-
varComp-0.1-360/varComp/man/varComp.control.Rd | 2 -
varComp-0.1-360/varComp/man/varComp.test.Rd | 2 -
varComp-0.1-360/varComp/man/varComp.test.control.Rd | 10 ++---
20 files changed, 68 insertions(+), 57 deletions(-)
Title: Genetic Analysis of Populations With Mixed Reproduction
Diff between poppr versions 1.1.3 dated 2015-02-03 and 1.1.4 dated 2015-02-06
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the adegenet package.
Author: Zhian N. Kamvar [cre, aut],
Javier F. Tabima [aut],
Niklaus J. Grunwald [ths]
Maintainer: Zhian N. Kamvar
DESCRIPTION | 6 ++--
MD5 | 38 +++++++++++++++---------------
NEWS | 11 ++++++--
inst/doc/algo.Rnw | 2 -
inst/doc/algo.pdf |binary
inst/doc/poppr_manual.Rnw | 2 -
inst/doc/poppr_manual.pdf |binary
tests/testthat/test-values.R | 2 -
vignettes/algo.Rnw | 2 -
vignettes/figure/Aeut_MLG_Ahena-1.pdf |binary
vignettes/figure/Aeut_MLG_black-1.pdf |binary
vignettes/figure/Aeut_MLG_title-1.pdf |binary
vignettes/figure/bd_histogram-1.pdf |binary
vignettes/figure/ex_data_picture-1.pdf |binary
vignettes/figure/initializing_poppr-1.pdf |binary
vignettes/figure/mlgbarplot-1.pdf |binary
vignettes/figure/mlgrareplot-1.pdf |binary
vignettes/figure/subnor-1.pdf |binary
vignettes/figure/unnamed-chunk-3-1.pdf |binary
vignettes/poppr_manual.Rnw | 2 -
20 files changed, 35 insertions(+), 30 deletions(-)
Title: Wegener Center Climate Uncertainty Explorer
Diff between wux versions 1.2-2 dated 2014-11-24 and 1.2-3 dated 2015-02-06
Description: Methods to calculate and interpret climate change signals and time series from climate multi-model ensembles. Climate model output in binary NetCDF format is read in and aggregated over a specified region to a data.frame for statistical analysis. Global circulation models (GCMs), as the CMIP5 or CMIP3 simulations, can be read in the same way as Regional Climate Models (RCMs), as e.g. the CORDEX or ENSEMBLES simulations.
Author: Thomas Mendlik [aut, cre], Georg Heinrich [aut], Armin Leuprecht [aut], Andreas Gobiet [ths]
Maintainer: Thomas Mendlik
DESCRIPTION | 20 ++++++++++++++------
MD5 | 18 +++++++++---------
R/AnovaReconstruct.R | 14 +++++++-------
R/PlotFunctions.R | 12 ++++++------
R/models2wuxSubregions.R | 6 +++---
R/summaryWux.R | 6 +++---
data/modelinput_test.rda |binary
data/userinput_CMIP5_changesignal.rda |binary
data/userinput_CMIP5_timeseries.rda |binary
man/models2wux.Rd | 2 +-
10 files changed, 43 insertions(+), 35 deletions(-)
Title: n-gram Text Regression, aka Concise Comparative Summarization
Diff between textreg versions 0.1.1 dated 2015-02-02 and 0.1.2 dated 2015-02-06
Description: Function for sparse regression on raw text, regressing a labeling
vector onto a feature space consisting of all possible phrases.
Author: Luke Miratrix
Maintainer: Luke Miratrix
DESCRIPTION | 9
MD5 | 45 +
NAMESPACE | 3
R/cross_validation_code.R | 311 ++++++------
R/package_and_data_documentation.R | 11
R/textreg.R | 628 +++++++++++++++----------
R/vizualize_phrases.R | 3
build |only
inst/doc/bathtub_vignette.R |only
inst/doc/bathtub_vignette.Rnw |only
inst/doc/bathtub_vignette.pdf |binary
inst/testthat/test-Lq.R | 2
inst/testthat/test-build.corpus.R |only
inst/testthat/test-cross-validation.R | 8
inst/testthat/test-find-threshold-C.R | 2
inst/testthat/test-ngram-call-basics.R | 1
man/build.corpus.Rd |only
man/cpp_build.corpus.Rd |only
man/cpp_textreg.Rd | 7
man/is.textreg.corpus.Rd |only
man/print.textreg.corpus.Rd |only
man/textreg-package.Rd | 10
src/RcppExports.cpp |only
src/textreg.cpp | 808 ++++++++++++++++++++-------------
vignettes |only
25 files changed, 1094 insertions(+), 754 deletions(-)
Title: basic tools for the analysis of disease outbreaks.
Diff between OutbreakTools versions 0.1-11 dated 2014-08-11 and 0.1-12 dated 2015-02-06
Description: basic tools for the analysis of disease outbreaks.
Author: The Hackout team (In alphabetic order: David Aanensen, Marc Baguelin, Paul Birrell, Simon Cauchemez, Anton Camacho, Caroline Colijn, Anne Cori, Xavier Didelot, Ken Eames, Christophe Fraser, Simon Frost, Niel Hens, Joseph Hugues, Thibaut Jombart, Lulla Opatowski, Oliver Ratmann, Samuel Soubeyrand, Marc Suchard, Jacco Wallinga, Rolf Ypma)
Maintainer: Thibaut Jombart
ChangeLog | 17 ++-
DESCRIPTION | 12 +-
MD5 | 36 +++---
NAMESPACE | 2
R/get.incidence.R | 4
R/importFromJSON.R | 126 +++++++++++++++++++++--
R/obkData_basics.R | 11 ++
R/plotggphy.R | 15 ++
R/utils.R | 33 +++++-
build/vignette.rds |binary
data/FluH1N1pdm2009.RData |binary
data/HorseFlu.RData |binary
data/HorseFluRaw.RData |binary
data/ToyOutbreak.RData |binary
data/ToyOutbreakRaw.RData |binary
inst/doc/OutbreakTools.R | 243 +++++++++++++++------------------------------
inst/doc/OutbreakTools.pdf |binary
man/ToyOutbreak.Rd | 9 -
man/ToyOutbreakRaw.Rd | 6 -
19 files changed, 298 insertions(+), 216 deletions(-)
Title: Engle-Granger Cointegration Models
Diff between egcm versions 1.0.2 dated 2014-03-28 and 1.0.6 dated 2015-02-06
Description: This package provides an easy-to-use implementation of the Engle-Granger
two-step procedure for identifying pairs of cointegrated series. It is geared towards
the analysis of pairs of securities. Summary and plot functions are provided,
and the package is able to fetch closing prices of securities from Yahoo.
A variety of unit root tests are supported, and an improved unit root test is included.
Author: Matthew Clegg [aut, cre, cph]
Maintainer: Matthew Clegg
egcm-1.0.2/egcm/tests/tests.Rout.save |only
egcm-1.0.6/egcm/CHANGELOG |only
egcm-1.0.6/egcm/DESCRIPTION | 19 +++---
egcm-1.0.6/egcm/MD5 | 29 ++++-----
egcm-1.0.6/egcm/NAMESPACE | 5 -
egcm-1.0.6/egcm/R/egcm.R | 106 +++++++++++++++++++---------------
egcm-1.0.6/egcm/R/egcm_extras.R | 91 ++++++++++++++++++++++++++++-
egcm-1.0.6/egcm/R/init.R | 4 -
egcm-1.0.6/egcm/README.md | 2
egcm-1.0.6/egcm/TODO | 13 ++--
egcm-1.0.6/egcm/man/allpairs.egcm.Rd |only
egcm-1.0.6/egcm/man/egcm-package.Rd | 9 +-
egcm-1.0.6/egcm/man/egcm.Rd | 25 ++++----
egcm-1.0.6/egcm/man/rar1.Rd | 2
egcm-1.0.6/egcm/man/ur_power.Rd | 22 +++----
egcm-1.0.6/egcm/man/yegcm.Rd | 5 +
egcm-1.0.6/egcm/tests/tests.R | 9 ++
17 files changed, 232 insertions(+), 109 deletions(-)
Title: Robust estimation of the generalized log gamma model.
Diff between robustloggamma versions 0.4-28 dated 2013-12-19 and 0.4-31 dated 2015-02-06
More information about robustloggamma at CRAN
Description: Robust estimation of the generalized log gamma model is provided using Quantile Tau estimator and Weighted Likelihood estimator.
Author: Claudio Agostinelli
Maintainer: Claudio Agostinelli
DESCRIPTION | 11 ++--
MD5 | 44 +++++++++--------
NAMESPACE | 2
R/ScoresAndDerivatives.R | 35 ++++++++++----
R/WLfunctions.R | 8 ++-
R/loggammarob.R | 45 ++++++++++--------
README | 2
data/alcoa.rda |binary
data/drg2000.rda |binary
data/sqrtloggamma.rda |binary
man/LogGammaDist.Rd | 7 ++
src/ploggamma.f |only
src/regtau.f | 65 +++++++++++++-------------
src/wrapper.c |only
tests/QTau-savedvalues.R | 14 ++---
tests/WL-savedvalues.R | 72 ++++++++++++++---------------
tests/WQTau-savedvalues.R | 52 ++++++++++-----------
tests/loggammarob-QTau.R | 7 +-
tests/loggammarob-WL.R | 9 +--
tests/loggammarob-WQTau.R | 6 +-
tests/loggammarob-oneWL.R | 8 +--
tests/oneWL-savedvalues.R | 76 +++++++++++++++---------------
tests/sumWL-savedvalues.R | 102 ++++++++++++++++++++---------------------
tests/sumoneWL-savedvalues.R | 106 +++++++++++++++++++++----------------------
24 files changed, 351 insertions(+), 320 deletions(-)
Permanent link
Title: Multivariate Normal Mixture Models and Mixtures of Generalized
Linear Mixed Models Including Model Based Clustering
Diff between mixAK versions 3.8 dated 2014-09-03 and 3.10 dated 2015-02-06
Description: This package contains a mixture of statistical methods including the MCMC methods to analyze normal mixtures. Additionally, model based clustering methods are implemented to perform classification based on (multivariate) longitudinal (or otherwise correlated) data. The basis for such clustering is a mixture of multivariate generalized linear mixed models.
Author: Arnošt Komárek
Maintainer: Arnošt Komárek
mixAK-3.10/mixAK/DESCRIPTION | 12 ++--
mixAK-3.10/mixAK/MD5 | 18 +++---
mixAK-3.10/mixAK/NAMESPACE | 52 +++++++++++++++++-
mixAK-3.10/mixAK/NEWS | 6 ++
mixAK-3.10/mixAK/data/Acidity.rda |binary
mixAK-3.10/mixAK/data/Enzyme.rda |binary
mixAK-3.10/mixAK/data/Galaxy.rda |binary
mixAK-3.10/mixAK/inst/CITATION | 5 -
mixAK-3.10/mixAK/inst/doc/CITATION_includeMethodology |only
mixAK-3.10/mixAK/man/NMixRelabel.Rd | 4 -
mixAK-3.8/mixAK/inst/CITATION_includeMethodology |only
11 files changed, 76 insertions(+), 21 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining
Diff between FactoMineR versions 1.28 dated 2014-12-12 and 1.29 dated 2015-02-06
Description: Exploratory data analysis methods such as principal component methods and clustering
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson
DESCRIPTION | 15 +-
MD5 | 38 ++---
NAMESPACE | 37 +++++
R/HCPC.R | 25 ++-
R/plot.HCPC.R | 2
R/plot.spMCA.R | 8 +
R/plotellipses.r | 4
R/spMCA.R | 108 +++++++++--------
R/summary.CA.r | 7 +
inst/doc/FactoMineR.pdf |binary
inst/doc/clustering_and_pricipal_component_methods.pdf |binary
man/CaGalt.Rd | 2
man/coord.ellipse.Rd | 2
man/health.Rd | 4
man/plot.HCPC.Rd | 2
man/plot.MCA.Rd | 6
man/plot.MFA.Rd | 27 ++++
man/plot.catdes.Rd | 2
man/spMCA.Rd | 14 +-
man/tea.Rd | 2
20 files changed, 205 insertions(+), 100 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-06-01 1.4.6
2014-01-07 1.4.5
2012-10-12 1.4.4
2012-09-29 1.4.3
2012-08-13 1.4.2
2012-07-17 1.4.1
2012-06-13 1.4.0
2012-01-23 1.3.5
2011-08-23 1.3.4
2011-04-13 1.3.3
2010-09-08 1.3.2
2010-09-06 1.3.1
2010-07-06 1.3
Title: Regularized Principal Component Analysis for Spatial Data
Diff between SpatPCA versions 1.0 dated 2015-01-23 and 1.0.0.1 dated 2015-02-06
Description: This package provides regularized principal component
analysis incorporating smoothness, sparseness and orthogonality of
eigenfunctions by using alternating direction method of multipliers (ADMM)
algorithm.
Author: Wen-Ting Wang and Hsin-Cheng Huang
Maintainer: Wen-Ting Wang
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
man/SpatPCA-package.Rd | 4 ++--
src/RcppExports.cpp | 8 ++++----
src/rcpp_SpatPCA.cpp | 43 ++++++++++++++++++++++++++-----------------
5 files changed, 40 insertions(+), 31 deletions(-)
Title: Text mining of PubMed Abstracts
Diff between pubmed.mineR versions 1.0.3 dated 2014-12-26 and 1.0.3.1 dated 2015-02-06
Description: Text mining of PubMed Abstracts (text and XML) from http://www.ncbi.nlm.nih.gov/pubmed.
Author: Jyoti Sharma, S.Ramachandran, Ab Rauf Shah
Maintainer: S. Ramachandran
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
NAMESPACE | 2 +-
3 files changed, 7 insertions(+), 7 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-01-16 1.2
2014-02-21 1.1
2011-08-15 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-01-10 0.6.0
2013-09-18 0.5.0
2013-04-15 0.4.1
2013-04-13 0.4.0
2012-12-18 0.3-0
2012-10-11 0.2-0
2012-09-23 0.1-56
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-22 1.1.0
2013-12-17 1.0.24
2013-11-18 1.0.6
2013-07-09 0.10.0
2013-04-18 0.9.1
2013-01-24 0.8-0
2012-10-26 0.7-0
2012-08-23 0.6-0
2012-05-20 0.5-0
2012-04-21 0.4-0
2012-03-31 0.3-3
2012-03-09 0.2-1
2012-02-14 0.1-24
2012-02-14 0.1-25
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-05-31 1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-18 0.7.0
2013-10-21 0.6.0
2013-04-14 0.5.0
2013-01-23 0.4-0
2012-12-17 0.3-0
2012-11-13 0.2-0
2012-10-13 0.1-0
Title: Zebra-Striped Tables in LaTeX and HTML Formats
Diff between ztable versions 0.1.3 dated 2015-01-18 and 0.1.4 dated 2015-02-06
Description: Makes zebra-striped tables (tables with alternating row colors)
in LaTeX and HTML formats easily from a data.frame, matrix, lm, aov, anova,
glm, coxph, mytable and cbind.mytable objects.
Author: Keon-Woong Moon [aut, cre]
Maintainer: Keon-Woong Moon
DESCRIPTION | 17
MD5 | 45
NAMESPACE | 14
NEWS | 15
R/print.ztable.html.R | 533 +
R/ztable.R | 463 -
R/ztable.cbind.mytable.R |only
R/ztable.mytable.R |only
R/ztable2.R | 342
R/zzz.R | 5
README.md | 9199 +++++++++++++++-------
inst/doc/ztable.R | 141
inst/doc/ztable.Rmd | 210
inst/doc/ztable.html |18158 ++++++++++++++++++++++++++++++--------------
man/addSubColNames.Rd |only
man/extractAlign.Rd |only
man/getNewSpanCol.Rd |only
man/getNewSpanRow.Rd |only
man/getspanRowData.Rd |only
man/getspanRowLength.Rd |only
man/isGroupCol.Rd |only
man/isspanCol.Rd |only
man/isspanRow.Rd |only
man/printRowGroup.Rd |only
man/spanCol.Rd |only
man/spanColWidth.Rd |only
man/spanRow.Rd |only
man/tr.Rd |only
man/tr2.Rd |only
man/vline2align.Rd |only
man/vlines.Rd |only
man/ztable.cbind.mytable.Rd |only
man/ztable.mytable.Rd |only
vignettes/ztable.Rmd | 210
34 files changed, 20537 insertions(+), 8815 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-06-01 1.0
2010-10-01 0.92
2010-09-09 0.91
2010-07-24 0.90
2010-04-29 0.85
2010-04-06 0.80
2009-12-30 0.45
2009-12-28 0.4
2009-05-29 0.3
2009-03-02 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-19 1.1
2013-11-10 1.0
More information about SimilarityMeasures at CRAN
Permanent link
Title: R interface to X-13ARIMA-SEATS
Diff between seasonal versions 0.70.1 dated 2014-10-02 and 0.80.0 dated 2015-02-06
Description: seasonal is an easy-to-use R-interface to X-13ARIMA-SEATS, the
newest seasonal adjustment software by the US Census Bureau. It offers full
access to almost all options and outputs of X-13, including X-11 and SEATS,
automatic ARIMA model search, outlier detection and support for user
defined holiday variables, such as Chinese New Year or Indian Diwali. It
also includes a Shiny-based graphical user interface. Seasonal does not
contain the binaries of X-13, which must be installed separately. See the
README file or the vignette for installation notes.
Author: Christoph Sax
Maintainer: Christoph Sax
seasonal-0.70.1/seasonal/R/deprecated.R |only
seasonal-0.70.1/seasonal/data/chcpi.RData |only
seasonal-0.70.1/seasonal/man/seasonal-deprecated.Rd |only
seasonal-0.80.0/seasonal/DESCRIPTION | 20 -
seasonal-0.80.0/seasonal/MD5 | 89 ++---
seasonal-0.80.0/seasonal/NAMESPACE | 2
seasonal-0.80.0/seasonal/NEWS | 25 +
seasonal-0.80.0/seasonal/R/checkX13.R | 65 +++-
seasonal-0.80.0/seasonal/R/defunct.R |only
seasonal-0.80.0/seasonal/R/detect.R | 33 +-
seasonal-0.80.0/seasonal/R/diagnostics.R | 7
seasonal-0.80.0/seasonal/R/genhol.R | 49 ++-
seasonal-0.80.0/seasonal/R/outlier.R | 6
seasonal-0.80.0/seasonal/R/read_series.R | 4
seasonal-0.80.0/seasonal/R/seas.R | 130 ++++++--
seasonal-0.80.0/seasonal/R/seasonal-package.R | 57 +++
seasonal-0.80.0/seasonal/R/spclist.R | 36 +-
seasonal-0.80.0/seasonal/R/static.R | 4
seasonal-0.80.0/seasonal/R/summary.R | 33 +-
seasonal-0.80.0/seasonal/README.md | 320 +++++++++++++++++---
seasonal-0.80.0/seasonal/build/vignette.rds |binary
seasonal-0.80.0/seasonal/data/holiday.RData |binary
seasonal-0.80.0/seasonal/data/seasonal.RData |only
seasonal-0.80.0/seasonal/demo/seas.R | 2
seasonal-0.80.0/seasonal/inst/doc/seas.Rnw | 4
seasonal-0.80.0/seasonal/inst/doc/seas.pdf |binary
seasonal-0.80.0/seasonal/man/SPECS.Rd | 5
seasonal-0.80.0/seasonal/man/checkX13.Rd | 3
seasonal-0.80.0/seasonal/man/cpi.Rd | 11
seasonal-0.80.0/seasonal/man/easter.Rd | 17 -
seasonal-0.80.0/seasonal/man/exp.Rd | 8
seasonal-0.80.0/seasonal/man/final.Rd | 3
seasonal-0.80.0/seasonal/man/genhol.Rd | 49 ++-
seasonal-0.80.0/seasonal/man/identify.seas.Rd | 3
seasonal-0.80.0/seasonal/man/iip.Rd |only
seasonal-0.80.0/seasonal/man/inspect.Rd | 7
seasonal-0.80.0/seasonal/man/na.x13.Rd | 3
seasonal-0.80.0/seasonal/man/out.Rd | 3
seasonal-0.80.0/seasonal/man/outlier.Rd | 3
seasonal-0.80.0/seasonal/man/plot.seas.Rd | 7
seasonal-0.80.0/seasonal/man/qs.Rd | 3
seasonal-0.80.0/seasonal/man/seas.Rd | 19 -
seasonal-0.80.0/seasonal/man/seasonal-defunct.Rd |only
seasonal-0.80.0/seasonal/man/seasonal-package.Rd | 3
seasonal-0.80.0/seasonal/man/series.Rd | 3
seasonal-0.80.0/seasonal/man/static.Rd | 3
seasonal-0.80.0/seasonal/man/summary.seas.Rd | 34 +-
seasonal-0.80.0/seasonal/vignettes/README.tex | 287 +++++++++++++----
seasonal-0.80.0/seasonal/vignettes/seas.Rnw | 4
49 files changed, 1035 insertions(+), 329 deletions(-)
Title: An interface to the Nexus Class Library
Diff between rncl versions 0.2.0 dated 2014-12-02 and 0.2.2 dated 2015-02-06
Description: An interface to the Nexus Class Library which allows parsing
of NEXUS, Newick and other phylogenetic tree file formats. It provides
elements of the file that can be used to build phylogenetic objects
such as ape's phylo or phylobase's phylo4(d).
Author: Francois Michonneau [aut, cre],
Ben Bolker [aut],
Mark Holder [aut],
Paul Lewis [aut],
Brian O'Meara [aut]
Maintainer: Francois Michonneau
DESCRIPTION | 18 +++++++++---------
MD5 | 10 +++++-----
NAMESPACE | 2 +-
R/rncl.R | 4 ++--
man/read_nexus_phylo.Rd | 3 ++-
man/rncl.Rd | 7 ++++---
6 files changed, 23 insertions(+), 21 deletions(-)
Title: Nearest-neighbor Classification with Categorical Variables
Diff between knncat versions 1.2.1 dated 2015-01-24 and 1.2.2 dated 2015-02-06
Description: Scale categorical variables in such a way as
to make NN classification as accurate as possible. The code also
handles continuous variables and prior probabilities, and does
intelligent variable selection and estimation of both error rates
and the right number of NN's.
Author: Sam Buttrey
Maintainer: Sam Buttrey
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
src/dsort.c | 3 ++-
src/ords.c | 3 ++-
4 files changed, 11 insertions(+), 9 deletions(-)
Title: Targeted Learning of a NP Importance of a Continuous Exposure
Diff between tmle.npvi versions 0.8.1 dated 2014-02-08 and 0.9.3 dated 2015-02-05
Description: Targeted minimum loss estimation (TMLE) of a non-parametric variable importance measure of a continuous exposure 'X' on an outcome 'Y', taking baseline covariates 'W' into account.
Author: Antoine Chambaz, Pierre Neuvial
Maintainer: Pierre Neuvial
tmle.npvi-0.8.1/tmle.npvi/man/SL.DSA.2.Rd |only
tmle.npvi-0.8.1/tmle.npvi/man/SL.DSA.Rd |only
tmle.npvi-0.8.1/tmle.npvi/man/predict.SL.DSA.Rd |only
tmle.npvi-0.8.1/tmle.npvi/man/tmle.npvi.Rd |only
tmle.npvi-0.9.3/tmle.npvi/DESCRIPTION | 18
tmle.npvi-0.9.3/tmle.npvi/MD5 | 77 ++-
tmle.npvi-0.9.3/tmle.npvi/NAMESPACE | 34 +
tmle.npvi-0.9.3/tmle.npvi/R/NPVI.R | 112 +++++
tmle.npvi-0.9.3/tmle.npvi/R/NPVI.update.R | 32 -
tmle.npvi-0.9.3/tmle.npvi/R/NPVI.updatePsi.R | 6
tmle.npvi-0.9.3/tmle.npvi/R/SuperLearning.R |only
tmle.npvi-0.9.3/tmle.npvi/R/estimateDevG.R | 3
tmle.npvi-0.9.3/tmle.npvi/R/estimateDevMu.R | 2
tmle.npvi-0.9.3/tmle.npvi/R/estimateDevTheta.R | 2
tmle.npvi-0.9.3/tmle.npvi/R/estimateG.R | 2
tmle.npvi-0.9.3/tmle.npvi/R/estimateMuAux.R | 2
tmle.npvi-0.9.3/tmle.npvi/R/estimateTheta.R | 2
tmle.npvi-0.9.3/tmle.npvi/R/getSample.R | 8
tmle.npvi-0.9.3/tmle.npvi/R/mu.R | 26 +
tmle.npvi-0.9.3/tmle.npvi/R/pcor.R | 3
tmle.npvi-0.9.3/tmle.npvi/R/simulateData.R | 33 +
tmle.npvi-0.9.3/tmle.npvi/R/simulateParsimoniouslyXgivenW.R | 214 ++++-------
tmle.npvi-0.9.3/tmle.npvi/R/simulateParsimoniouslyYgivenXW.R | 122 ++----
tmle.npvi-0.9.3/tmle.npvi/R/theta.R | 131 ++++--
tmle.npvi-0.9.3/tmle.npvi/R/tmle.npvi.R | 103 ++++-
tmle.npvi-0.9.3/tmle.npvi/R/validateArgumentObs.R | 2
tmle.npvi-0.9.3/tmle.npvi/build/vignette.rds |binary
tmle.npvi-0.9.3/tmle.npvi/data/datalist |only
tmle.npvi-0.9.3/tmle.npvi/data/learningLib.rda |binary
tmle.npvi-0.9.3/tmle.npvi/data/superLearningLib.rda |binary
tmle.npvi-0.9.3/tmle.npvi/data/tcga2012brca.rda |only
tmle.npvi-0.9.3/tmle.npvi/inst/NEWS | 93 +---
tmle.npvi-0.9.3/tmle.npvi/inst/doc/tmle-npvi.R | 109 +++--
tmle.npvi-0.9.3/tmle.npvi/inst/doc/tmle-npvi.Rnw | 110 +++++
tmle.npvi-0.9.3/tmle.npvi/inst/doc/tmle-npvi.pdf |binary
tmle.npvi-0.9.3/tmle.npvi/inst/testScripts |only
tmle.npvi-0.9.3/tmle.npvi/man/getPValue.NPVI.Rd |only
tmle.npvi-0.9.3/tmle.npvi/man/getPValue.matrix.Rd |only
tmle.npvi-0.9.3/tmle.npvi/man/getSample.Rd | 8
tmle.npvi-0.9.3/tmle.npvi/man/tcga2012brca.Rd |only
tmle.npvi-0.9.3/tmle.npvi/man/tmle.npvi..Rd |only
tmle.npvi-0.9.3/tmle.npvi/vignettes/tmle-npvi.Rnw | 110 +++++
42 files changed, 876 insertions(+), 488 deletions(-)
Title: Table Monster
Diff between TableMonster versions 1.1 dated 2014-07-21 and 1.2 dated 2015-02-05
Description: Provides a user friendly interface to generation of booktab style
tables using xtable.
Author: Grant Izmirlian Jr
Maintainer: Grant Izmirlian Jr
DESCRIPTION | 6 +++---
MD5 | 6 +++---
R/TableMonster.R | 31 ++++++++++++++++++++++++++++---
man/print.TableMonster.Rd | 8 +++++++-
4 files changed, 41 insertions(+), 10 deletions(-)
Title: Multivariate Normal Functions for Sparse Covariance and
Precision Matrices.
Diff between sparseMVN versions 0.1.0 dated 2013-11-05 and 0.2.0 dated 2015-02-05
Description: Computes multivariate normal (MVN) densities, and
samples from MVN distributions, when the covariance or
precision matrix is sparse.
Author: Michael Braun [aut, cre, cph]
Maintainer: Michael Braun
sparseMVN-0.1.0/sparseMVN/R/demo_funcs.R |only
sparseMVN-0.1.0/sparseMVN/R/mvnSparse.R |only
sparseMVN-0.1.0/sparseMVN/demo |only
sparseMVN-0.1.0/sparseMVN/inst/doc/sparseMVN-vignette.Rnw |only
sparseMVN-0.1.0/sparseMVN/inst/doc/sparseMVN-vignette.pdf |only
sparseMVN-0.1.0/sparseMVN/inst/examples/tables.R |only
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sparseMVN-0.1.0/sparseMVN/vignettes/sparseMVN-vignette.Rnw |only
sparseMVN-0.2.0/sparseMVN/DESCRIPTION | 26 +
sparseMVN-0.2.0/sparseMVN/MD5 | 36 +-
sparseMVN-0.2.0/sparseMVN/NAMESPACE | 7
sparseMVN-0.2.0/sparseMVN/NEWS | 18 +
sparseMVN-0.2.0/sparseMVN/R/rmvn-sparse.R |only
sparseMVN-0.2.0/sparseMVN/R/sparseMVN-package.R |only
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sparseMVN-0.2.0/sparseMVN/man/sparseMVN-package.Rd | 33 +-
sparseMVN-0.2.0/sparseMVN/tests |only
sparseMVN-0.2.0/sparseMVN/vignettes/sparseMVN-demo.Rmd |only
sparseMVN-0.2.0/sparseMVN/vignettes/sparseMVN.bib | 171 +++++++++----
sparseMVN-0.2.0/sparseMVN/vignettes/timing.Rmd |only
sparseMVN-0.2.0/sparseMVN/vignettes/timing.html |only
29 files changed, 189 insertions(+), 102 deletions(-)
Title: R Interface to EPP-lab, a Java Program for Exploratory
Projection Pursuit
Diff between REPPlab versions 0.9 dated 2014-09-05 and 0.9.1 dated 2015-02-05
Description: An R Interface to EPP-lab v1.0. EPP-lab is a Java program for projection pursuit using genetic algorithms written by Alain Berro and S. Larabi Marie-Sainte and is included in the package.
Author: Daniel Fischer, Alain Berro, Klaus Nordhausen, Anne Ruiz-Gazen
Maintainer: Daniel Fischer
DESCRIPTION | 16 ++++++++--------
MD5 | 6 +++---
inst/ChangeLog | 4 ++++
man/REPPlab-package.Rd | 10 +++++-----
4 files changed, 20 insertions(+), 16 deletions(-)
Title: PANIC Tests of Nonstationarity
Diff between PANICr versions 0.0.0.2 dated 2014-10-24 and 0.0.0.5 dated 2015-02-05
Description: This package contains a methodology that makes use of the factor
structure of large dimensional panels to understand the nature of
nonstationarity inherent in data. This is referred to as PANIC - Panel
Analysis of Nonstationarity in Idiosyncratic and Common Components. PANIC
(2004) includes valid pooling methods that allow panel unit root tests
tests to be constructed. PANIC (2004) can detect whether the
nonstationarity in a series is pervasive, or variable specific, or both.
PANIC (2010) includes the Panel Modified Sargan-Bhargava test, three models
for a Moon and Perron style test, and a bias correction for the
idiosyncratic unit root test of PANIC (2004). The PANIC model approximates
the number of factors based on Bai and Ng (2002).
Author: Steve Bronder
Maintainer: Steve Bronder
PANICr-0.0.0.2/PANICr/inst/doc/PANICr.R |only
PANICr-0.0.0.2/PANICr/vignettes/NIPAagg1.rda |only
PANICr-0.0.0.2/PANICr/vignettes/NIPAagg2.rda |only
PANICr-0.0.0.2/PANICr/vignettes/NIPAagg3.rda |only
PANICr-0.0.0.5/PANICr/DESCRIPTION | 19
PANICr-0.0.0.5/PANICr/MD5 | 106 +--
PANICr-0.0.0.5/PANICr/R/MCMCfacstuffzzz.R | 306 ++++-----
PANICr-0.0.0.5/PANICr/R/MCMCpanic10.R | 875 +++++++++++----------------
PANICr-0.0.0.5/PANICr/R/NIPAagg1.R | 26
PANICr-0.0.0.5/PANICr/R/NIPAagg2.R | 28
PANICr-0.0.0.5/PANICr/R/NIPAagg3.R | 26
PANICr-0.0.0.5/PANICr/R/adf04.r | 158 ++--
PANICr-0.0.0.5/PANICr/R/adf10.r | 166 ++---
PANICr-0.0.0.5/PANICr/R/adfc2.R | 22
PANICr-0.0.0.5/PANICr/R/adfnc.R | 22
PANICr-0.0.0.5/PANICr/R/adfp.r | 178 ++---
PANICr-0.0.0.5/PANICr/R/cPANIC.r | 412 ++++++------
PANICr-0.0.0.5/PANICr/R/coint0.R | 22
PANICr-0.0.0.5/PANICr/R/getnfac.r | 318 ++++-----
PANICr-0.0.0.5/PANICr/R/glsd.r | 116 +--
PANICr-0.0.0.5/PANICr/R/lagn.R | 78 +-
PANICr-0.0.0.5/PANICr/R/lm1.R | 22
PANICr-0.0.0.5/PANICr/R/minindc.r | 56 -
PANICr-0.0.0.5/PANICr/R/mydiff.r | 66 +-
PANICr-0.0.0.5/PANICr/R/myols.r | 30
PANICr-0.0.0.5/PANICr/R/nuisance.r | 114 +--
PANICr-0.0.0.5/PANICr/R/nw.r | 146 ++--
PANICr-0.0.0.5/PANICr/R/panic10b.r | 737 +++++++++++-----------
PANICr-0.0.0.5/PANICr/R/pc.R | 80 +-
PANICr-0.0.0.5/PANICr/R/pool10.r | 92 +-
PANICr-0.0.0.5/PANICr/R/poolcoint.R | 94 +-
PANICr-0.0.0.5/PANICr/R/s2ar.r | 174 ++---
PANICr-0.0.0.5/PANICr/R/trimr.r | 92 +-
PANICr-0.0.0.5/PANICr/README.md | 18
PANICr-0.0.0.5/PANICr/build/vignette.rds |binary
PANICr-0.0.0.5/PANICr/inst/doc/PANICr.Rmd | 127 ---
PANICr-0.0.0.5/PANICr/inst/doc/PANICr.html | 497 +--------------
PANICr-0.0.0.5/PANICr/man/MCMCpanic04.Rd | 17
PANICr-0.0.0.5/PANICr/man/MCMCpanic10.Rd | 148 ++--
PANICr-0.0.0.5/PANICr/man/NIPAagg1.Rd | 26
PANICr-0.0.0.5/PANICr/man/NIPAagg2.Rd | 26
PANICr-0.0.0.5/PANICr/man/NIPAagg3.Rd | 26
PANICr-0.0.0.5/PANICr/man/adf.Rd | 50 -
PANICr-0.0.0.5/PANICr/man/adfc2.Rd | 18
PANICr-0.0.0.5/PANICr/man/adfnc.Rd | 18
PANICr-0.0.0.5/PANICr/man/coint0.Rd | 18
PANICr-0.0.0.5/PANICr/man/getnfac.Rd | 94 +-
PANICr-0.0.0.5/PANICr/man/lm1.Rd | 18
PANICr-0.0.0.5/PANICr/man/mydiff.Rd | 40 -
PANICr-0.0.0.5/PANICr/man/nuisance.Rd | 50 -
PANICr-0.0.0.5/PANICr/man/panic04.Rd | 85 +-
PANICr-0.0.0.5/PANICr/man/panic10.Rd | 26
PANICr-0.0.0.5/PANICr/man/pool.Rd | 42 -
PANICr-0.0.0.5/PANICr/man/s2ar.Rd | 72 +-
PANICr-0.0.0.5/PANICr/man/trimr.Rd | 42 -
PANICr-0.0.0.5/PANICr/vignettes/PANICr.Rmd | 127 ---
56 files changed, 2671 insertions(+), 3495 deletions(-)
Title: Symbolic Differentiation
Diff between Deriv versions 1.0 dated 2014-12-23 and 2.0 dated 2015-02-05
Description: Compared to R functions deriv() and D(), Deriv() admits
user-defined function as well as function substitution
in arguments of functions to be differentiated.
Author: Andrew Clausen [aut],
Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol
DESCRIPTION | 23 +
MD5 | 24 +
NAMESPACE | 2
NEWS | 33 ++
R/Deriv.R | 495 ++++++++++++++++----------------------
R/Simplify.R | 660 +++++++++++++++++++++++++++++++++++++++++++--------
README.md | 23 +
inst |only
man/Deriv-package.Rd | 60 +---
man/Deriv.Rd | 102 ++++---
man/Simplify.Rd |only
man/format1.Rd |only
tests |only
13 files changed, 932 insertions(+), 490 deletions(-)
Title: Default Bayesian Hypothesis Tests for Correlation, Partial
Correlation, and Mediation
Diff between BayesMed versions 1.0 dated 2014-01-28 and 1.0.1 dated 2015-02-05
Description: Default Bayesian hypothesis tests for correlation, partial correlation, and mediation
Author: Michele B. Nuijten, Ruud Wetzels, Dora Matzke, Conor V. Dolan, and Eric-Jan Wagenmakers
Maintainer: Michele B. Nuijten
BayesMed-1.0.1/BayesMed/DESCRIPTION | 12 ++++-----
BayesMed-1.0.1/BayesMed/MD5 | 29 +++++++++++-------------
BayesMed-1.0.1/BayesMed/R/print.jzs_med.R |only
BayesMed-1.0.1/BayesMed/man/BayesMed-package.Rd | 25 ++++++++++++++------
BayesMed-1.0.1/BayesMed/man/Firefighters.Rd | 7 ++++-
BayesMed-1.0.1/BayesMed/man/jzs_cor.Rd | 2 -
BayesMed-1.0.1/BayesMed/man/jzs_corSD.Rd | 2 -
BayesMed-1.0.1/BayesMed/man/jzs_med.Rd | 2 -
BayesMed-1.0.1/BayesMed/man/jzs_medSD.Rd | 2 -
BayesMed-1.0.1/BayesMed/man/jzs_partcor.Rd | 2 -
BayesMed-1.0.1/BayesMed/man/jzs_partcorSD.Rd | 2 -
BayesMed-1.0.1/BayesMed/man/plot.CI.Rd | 6 ++--
BayesMed-1.0.1/BayesMed/man/plot.JZSMed.Rd | 4 +--
BayesMed-1.0.1/BayesMed/man/plot.rjags.Rd | 10 ++++----
BayesMed-1.0.1/BayesMed/man/print.jzs_med.Rd |only
BayesMed-1.0/BayesMed/R/print.JZSMedSD.R |only
BayesMed-1.0/BayesMed/README.md |only
BayesMed-1.0/BayesMed/man/print.JZSMed.Rd |only
18 files changed, 58 insertions(+), 47 deletions(-)
Title: SciViews GUI API - Functions to interface with Komodo Edit/IDE
Diff between svKomodo versions 0.9-62 dated 2014-03-02 and 0.9-63 dated 2015-02-05
Description: Functions to manage the GUI client, like Komodo with the
SciViews-K extension
Author: Philippe Grosjean [aut, cre]
Maintainer: Philippe Grosjean
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
NEWS | 6 ++++++
R/svKomodo-internal.R | 20 +++++++++++++++-----
inst/NEWS.Rd | 8 +++++++-
man/svKomodo-package.Rd | 4 ++--
6 files changed, 39 insertions(+), 17 deletions(-)
Title: Meta-Analysis of Diagnostic Accuracy
Diff between mada versions 0.5.6 dated 2014-07-23 and 0.5.7 dated 2015-02-05
Description: Provides functions for diagnostic meta-analysis. Next to basic analysis and visualization the bivariate Model of Reitsma et al. (2005) that is equivalent to the HSROC of Rutter&Gatsonis (2001) can be fitted. A new approach based to diagnostic meta-analysis of Holling et al. (2012) is also available. Standard methods like summary, plot and so on are provided.
Author: Philipp Doebler
Maintainer: Philipp Doebler
DESCRIPTION | 17 +++-----
MD5 | 30 +++++++--------
NAMESPACE | 8 ++++
R/reitsma.R | 56 ++++++++++++++++++++++++++++-
R/rsSROC.R | 2 -
build/vignette.rds |binary
data/AuditC.rda |binary
data/Dementia.rda |binary
data/IAQ.rda |binary
data/SAQ.rda |binary
data/smoking.rda |binary
inst/doc/mada.R | 97 +++++++++++++++++++++++++++++----------------------
inst/doc/mada.Rnw | 32 +++++++++++++---
inst/doc/mada.pdf |binary
man/reitsma-class.Rd | 5 ++
vignettes/mada.Rnw | 32 +++++++++++++---
16 files changed, 196 insertions(+), 83 deletions(-)
Title: Simulation of Longitudinal Data
Diff between mlxR versions 2.1.0 dated 2015-01-12 and 2.1.1 dated 2015-02-05
Description: Simulation and visualization of complex
models for longitudinal data. The models are encoded using the model coding
language Mlxtran, automatically converted into C++ codes, compiled on the
fly and linked to R using the Rcpp package. That allows one to implement
very easily complex ODE-based models and complex statistical models,
including mixed effects models, for continuous, count, categorical, and
time-to-event data.
Author: Marc Lavielle [aut, cre],
Romain Francois [aut],
Fazia Bellal [ctb]
Maintainer: Marc Lavielle
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/convertmlx.R | 10 ++++++++--
R/initMlxLibrary.R | 14 +++++++++-----
4 files changed, 24 insertions(+), 14 deletions(-)
Title: Interval Testing Procedure for Functional Data
Diff between fdatest versions 2.0 dated 2014-11-24 and 2.1 dated 2015-02-05
Description: Implementation of the Interval Testing Procedure for functional data in different frameworks (i.e., one or two-population frameworks, functional linear models) by means of different basis expansions (i.e., B-spline, Fourier, and phase-amplitude Fourier). The current version of the package requires functional data evaluated on a uniform grid; it automatically projects each function on a chosen functional basis; it performs the entire family of multivariate tests; and, finally, it provides the matrix of the p-values of the previous tests and the vector of the corrected p-values. The functional basis, the coupled or uncoupled scenario, and the kind of test can be chosen by the user. The package provides also a plotting function creating a graphical output of the procedure: the p-value heat-map, the plot of the corrected p-values, and the plot of the functional data.
Author: Alessia Pini, Simone Vantini
Maintainer: Alessia Pini
DESCRIPTION | 14 ++---
MD5 | 48 +++++++++---------
NAMESPACE | 8 +++
NEWS |only
R/ITPaovbspline.R | 115 ++++++++++++++++++++++---------------------
R/ITPimage.R | 23 +++++---
R/ITPlmbspline.R | 124 +++++++++++++++--------------------------------
R/fdatest_2.1-internal.R |only
R/plot.ITP1.R | 4 -
R/plot.ITP2.R | 8 +--
data/NASAtemp.rda |binary
man/ITP1bspline.Rd | 5 +
man/ITP1fourier.Rd | 6 +-
man/ITP2bspline.Rd | 14 ++---
man/ITP2fourier.Rd | 8 +--
man/ITP2pafourier.Rd | 7 +-
man/ITPaovbspline.Rd | 7 +-
man/ITPimage.Rd | 21 +------
man/ITPlmbspline.Rd | 8 +--
man/fdatest-package.Rd | 53 +++++++++++++++-----
man/plot.ITP1.Rd | 11 ----
man/plot.ITP2.Rd | 10 ---
man/plot.ITPaov.Rd | 8 +--
man/plot.ITPlm.Rd | 9 +--
man/summary.ITPaov.Rd | 13 ++--
man/summary.ITPlm.Rd | 13 ++--
26 files changed, 259 insertions(+), 278 deletions(-)
Title: Survival Regression with Smoothed Error Distribution
Diff between smoothSurv versions 1.3-2 dated 2013-06-12 and 1.5 dated 2015-02-05
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 | 22 +++++++++---------
MD5 | 30 +++++++++++++-----------
NAMESPACE | 9 ++++---
NEWS | 10 ++++++++
R/confint.smoothSurvReg.R |only
R/estimTdiff.R | 50 ++++++++++++++++++++++++++++++-----------
R/fdensity.smoothSurvReg.R | 4 +--
R/hazard.smoothSurvReg.R | 4 +--
R/print.estimTdiff.R | 29 +++++++++++++----------
R/smoothSurvReg.R | 45 +++++++++++++++++++++++-------------
R/survfit.smoothSurvReg.R | 4 +--
inst/CITATION | 5 +---
man/confint.smoothSurvReg.Rd |only
man/fdensity.smoothSurvReg.Rd | 6 +++-
man/hazard.smoothSurvReg.Rd | 5 +++-
man/residuals.smoothSurvReg.Rd | 2 -
man/survfit.smoothSurvReg.Rd | 5 +++-
17 files changed, 145 insertions(+), 85 deletions(-)
Title: Estimation, Simulation and Visualization of Hierarchical
Archimedean Copulae (HAC)
Diff between HAC versions 1.0-1 dated 2014-08-13 and 1.0-2 dated 2015-02-05
Description: Package provides the estimation of the structure and the parameters, sampling methods and structural plots of Hierarchical Archimedean Copulae (HAC).
Author: Ostap Okhrin
Maintainer: Alexander Ristig
DESCRIPTION | 16 ++++++++--------
MD5 | 14 +++++++-------
NAMESPACE | 4 +---
R/estimate.r | 36 +++++++++++++++++++++++++++++++-----
build/vignette.rds |binary
inst/ChangeLog | 8 ++++++++
inst/doc/HAC.pdf |binary
man/estimate.copula.Rd | 2 +-
8 files changed, 56 insertions(+), 24 deletions(-)
Title: Bayesian Survival Regression with Flexible Error and Random
Effects Distributions
Diff between bayesSurv versions 2.3-1 dated 2014-08-09 and 2.4 dated 2015-02-05
Description: Later
Author: Arnošt Komárek
Maintainer: Arnošt Komárek
CHANGES | 4 ++++
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
inst/CITATION | 5 ++---
4 files changed, 13 insertions(+), 10 deletions(-)
Title: Phylogenetic Tools for comparative biology (and other things)
Diff between phytools versions 0.4-31 dated 2014-08-26 and 0.4-45 dated 2015-02-05
Description: phytools provides various functions for phylogenetic analysis,
mostly relevant to comparative biology.
Author: Liam J. Revell
Maintainer: Liam J. Revell
phytools-0.4-31/phytools/man/repPhylo.Rd |only
phytools-0.4-45/phytools/DESCRIPTION | 10
phytools-0.4-45/phytools/MD5 | 294 +++++++++---------
phytools-0.4-45/phytools/NAMESPACE | 19 -
phytools-0.4-45/phytools/R/densityMap.R | 17 -
phytools-0.4-45/phytools/R/fancyTree.R | 9
phytools-0.4-45/phytools/R/fitPagel.R |only
phytools-0.4-45/phytools/R/locate.fossil.R |only
phytools-0.4-45/phytools/R/locate.yeti.R | 123 ++++++-
phytools-0.4-45/phytools/R/pbtree.R | 7
phytools-0.4-45/phytools/R/phenogram.R | 15
phytools-0.4-45/phytools/R/plotSimmap.R | 138 +++++---
phytools-0.4-45/phytools/R/read.newick.R | 48 +-
phytools-0.4-45/phytools/R/sim.history.R | 27 +
phytools-0.4-45/phytools/R/utilities.R | 85 ++++-
phytools-0.4-45/phytools/R/writeAncestors.R | 13
phytools-0.4-45/phytools/man/add.arrow.Rd |only
phytools-0.4-45/phytools/man/add.color.bar.Rd | 3
phytools-0.4-45/phytools/man/add.everywhere.Rd | 3
phytools-0.4-45/phytools/man/add.random.Rd | 3
phytools-0.4-45/phytools/man/add.simmap.legend.Rd | 3
phytools-0.4-45/phytools/man/add.species.to.genus.Rd | 3
phytools-0.4-45/phytools/man/allFurcTrees.Rd | 2
phytools-0.4-45/phytools/man/anc.Bayes.Rd | 3
phytools-0.4-45/phytools/man/anc.ML.Rd | 5
phytools-0.4-45/phytools/man/anc.trend.Rd | 3
phytools-0.4-45/phytools/man/ancThresh.Rd | 4
phytools-0.4-45/phytools/man/applyBranchLengths.Rd | 3
phytools-0.4-45/phytools/man/ave.rates.Rd | 3
phytools-0.4-45/phytools/man/bind.tip.Rd | 3
phytools-0.4-45/phytools/man/bmPlot.Rd | 4
phytools-0.4-45/phytools/man/branching.diffusion.Rd | 3
phytools-0.4-45/phytools/man/brownie.lite.Rd | 2
phytools-0.4-45/phytools/man/brownieREML.Rd | 6
phytools-0.4-45/phytools/man/cladelabels.Rd | 4
phytools-0.4-45/phytools/man/collapse.to.star.Rd | 3
phytools-0.4-45/phytools/man/contMap.Rd | 6
phytools-0.4-45/phytools/man/countSimmap.Rd | 3
phytools-0.4-45/phytools/man/densityMap.Rd | 6
phytools-0.4-45/phytools/man/describe.simmap.Rd | 3
phytools-0.4-45/phytools/man/di2multi.simmap.Rd | 3
phytools-0.4-45/phytools/man/drop.clade.Rd | 3
phytools-0.4-45/phytools/man/drop.leaves.Rd | 3
phytools-0.4-45/phytools/man/drop.tip.contMap.Rd | 3
phytools-0.4-45/phytools/man/drop.tip.simmap.Rd | 3
phytools-0.4-45/phytools/man/estDiversity.Rd | 2
phytools-0.4-45/phytools/man/evol.rate.mcmc.Rd | 2
phytools-0.4-45/phytools/man/evol.vcv.Rd | 2
phytools-0.4-45/phytools/man/evolvcv.lite.Rd | 2
phytools-0.4-45/phytools/man/exhaustiveMP.Rd | 2
phytools-0.4-45/phytools/man/expm.Rd | 3
phytools-0.4-45/phytools/man/export.as.xml.Rd | 4
phytools-0.4-45/phytools/man/fancyTree.Rd | 3
phytools-0.4-45/phytools/man/fastAnc.Rd | 3
phytools-0.4-45/phytools/man/fastBM.Rd | 3
phytools-0.4-45/phytools/man/fastMRCA.Rd | 3
phytools-0.4-45/phytools/man/findMRCA.Rd | 3
phytools-0.4-45/phytools/man/fitBayes.Rd | 2
phytools-0.4-45/phytools/man/fitDiversityModel.Rd | 2
phytools-0.4-45/phytools/man/fitPagel.Rd |only
phytools-0.4-45/phytools/man/gammatest.Rd | 2
phytools-0.4-45/phytools/man/genSeq.Rd | 3
phytools-0.4-45/phytools/man/getCladesofSize.Rd | 3
phytools-0.4-45/phytools/man/getDescendants.Rd | 3
phytools-0.4-45/phytools/man/getExtant.Rd | 3
phytools-0.4-45/phytools/man/getSisters.Rd | 3
phytools-0.4-45/phytools/man/getStates.Rd | 3
phytools-0.4-45/phytools/man/ladderize.simmap.Rd |only
phytools-0.4-45/phytools/man/lambda.transform.Rd | 3
phytools-0.4-45/phytools/man/likMlambda.Rd | 3
phytools-0.4-45/phytools/man/locate.fossil.Rd |only
phytools-0.4-45/phytools/man/locate.yeti.Rd | 8
phytools-0.4-45/phytools/man/ls.tree.Rd | 3
phytools-0.4-45/phytools/man/ltt.Rd | 2
phytools-0.4-45/phytools/man/ltt95.Rd | 3
phytools-0.4-45/phytools/man/make.era.map.Rd | 3
phytools-0.4-45/phytools/man/make.simmap.Rd | 6
phytools-0.4-45/phytools/man/map.overlap.Rd | 3
phytools-0.4-45/phytools/man/map.to.singleton.Rd | 3
phytools-0.4-45/phytools/man/matchNodes.Rd | 3
phytools-0.4-45/phytools/man/mergeMappedStates.Rd | 3
phytools-0.4-45/phytools/man/midpoint.root.Rd | 8
phytools-0.4-45/phytools/man/minRotate.Rd | 3
phytools-0.4-45/phytools/man/minSplit.Rd | 2
phytools-0.4-45/phytools/man/mrp.supertree.Rd | 10
phytools-0.4-45/phytools/man/multi.mantel.Rd | 2
phytools-0.4-45/phytools/man/multiC.Rd | 3
phytools-0.4-45/phytools/man/multiRF.Rd | 7
phytools-0.4-45/phytools/man/nodeHeights.Rd | 3
phytools-0.4-45/phytools/man/optim.phylo.ls.Rd | 4
phytools-0.4-45/phytools/man/orderMappedEdge.Rd | 3
phytools-0.4-45/phytools/man/paintSubTree.Rd | 3
phytools-0.4-45/phytools/man/paste.tree.Rd | 3
phytools-0.4-45/phytools/man/pbtree.Rd | 3
phytools-0.4-45/phytools/man/pgls.Ives.Rd | 4
phytools-0.4-45/phytools/man/phenogram.Rd | 11
phytools-0.4-45/phytools/man/phyl.RMA.Rd | 3
phytools-0.4-45/phytools/man/phyl.cca.Rd | 4
phytools-0.4-45/phytools/man/phyl.pairedttest.Rd | 4
phytools-0.4-45/phytools/man/phyl.pca.Rd | 4
phytools-0.4-45/phytools/man/phyl.resid.Rd | 6
phytools-0.4-45/phytools/man/phyl.vcv.Rd | 3
phytools-0.4-45/phytools/man/phylANOVA.Rd | 2
phytools-0.4-45/phytools/man/phylo.to.map.Rd | 3
phytools-0.4-45/phytools/man/phylo.toBackbone.Rd | 3
phytools-0.4-45/phytools/man/phyloDesign.Rd | 3
phytools-0.4-45/phytools/man/phylomorphospace.Rd | 6
phytools-0.4-45/phytools/man/phylomorphospace3d.Rd | 4
phytools-0.4-45/phytools/man/phylosig.Rd | 9
phytools-0.4-45/phytools/man/phytools-package.Rd | 2
phytools-0.4-45/phytools/man/plot.backbonePhylo.Rd | 3
phytools-0.4-45/phytools/man/plotBranchbyTrait.Rd | 3
phytools-0.4-45/phytools/man/plotSimmap.Rd | 6
phytools-0.4-45/phytools/man/plotThresh.Rd | 5
phytools-0.4-45/phytools/man/plotTree.Rd | 5
phytools-0.4-45/phytools/man/plotTree.wBars.Rd | 3
phytools-0.4-45/phytools/man/print.backbonePhylo.Rd | 3
phytools-0.4-45/phytools/man/ratebystate.Rd | 3
phytools-0.4-45/phytools/man/rateshift.Rd | 3
phytools-0.4-45/phytools/man/read.newick.Rd | 3
phytools-0.4-45/phytools/man/read.simmap.Rd | 6
phytools-0.4-45/phytools/man/reorder.backbonePhylo.Rd | 3
phytools-0.4-45/phytools/man/reorderSimmap.Rd | 3
phytools-0.4-45/phytools/man/rep.phylo.Rd |only
phytools-0.4-45/phytools/man/reroot.Rd | 4
phytools-0.4-45/phytools/man/rerootingMethod.Rd | 7
phytools-0.4-45/phytools/man/rescaleSimmap.Rd | 3
phytools-0.4-45/phytools/man/rotateNodes.Rd | 3
phytools-0.4-45/phytools/man/roundBranches.Rd | 3
phytools-0.4-45/phytools/man/roundPhylogram.Rd | 3
phytools-0.4-45/phytools/man/rstate.Rd | 3
phytools-0.4-45/phytools/man/sampleFrom.Rd | 3
phytools-0.4-45/phytools/man/setMap.Rd | 5
phytools-0.4-45/phytools/man/sim.corrs.Rd | 5
phytools-0.4-45/phytools/man/sim.history.Rd | 8
phytools-0.4-45/phytools/man/sim.ratebystate.Rd | 3
phytools-0.4-45/phytools/man/sim.rates.Rd | 3
phytools-0.4-45/phytools/man/skewers.Rd | 2
phytools-0.4-45/phytools/man/splitTree.Rd | 3
phytools-0.4-45/phytools/man/splitplotTree.Rd | 3
phytools-0.4-45/phytools/man/starTree.Rd | 3
phytools-0.4-45/phytools/man/strahlerNumber.Rd | 3
phytools-0.4-45/phytools/man/threshBayes.Rd | 7
phytools-0.4-45/phytools/man/threshDIC.Rd | 5
phytools-0.4-45/phytools/man/threshState.Rd | 5
phytools-0.4-45/phytools/man/to.matrix.Rd | 3
phytools-0.4-45/phytools/man/treeSlice.Rd | 3
phytools-0.4-45/phytools/man/untangle.Rd | 3
phytools-0.4-45/phytools/man/vcvPhylo.Rd | 3
phytools-0.4-45/phytools/man/write.simmap.Rd | 4
phytools-0.4-45/phytools/man/writeAncestors.Rd | 3
phytools-0.4-45/phytools/man/writeNexus.Rd | 3
152 files changed, 941 insertions(+), 339 deletions(-)
Title: Knockoff Filter
Diff between knockoff versions 0.1.1 dated 2014-12-20 and 0.2 dated 2015-02-05
Description: The knockoff filter is a procedure for controlling the false
discovery rate (FDR) when performing variable selection. For more information,
see the website below and the accompanying paper.
Author: Rina Foygel Barber, Emmanuel Candes, Evan Patterson
Maintainer: Evan Patterson
DESCRIPTION | 13 ++++---
MD5 | 52 +++++++++++++++-------------
NAMESPACE | 2 -
NEWS |only
R/create.R | 21 +++++------
R/knockoff.R | 12 ++++--
R/stats_lasso.R | 26 +++++++++-----
R/util.R | 15 ++++++++
build/vignette.rds |binary
inst/doc/intro.R | 5 ++
inst/doc/intro.Rmd | 10 +++++
inst/doc/intro.html | 10 ++++-
inst/doc/sdp.Rmd | 14 +++++--
inst/doc/sdp.html | 13 ++++---
man/fs.Rd | 3 +
man/knockoff.Rd | 3 +
man/knockoff.create.Rd | 7 ++-
man/knockoff.filter.Rd | 10 +++--
man/knockoff.stat.fs.Rd | 3 +
man/knockoff.stat.lasso.Rd | 24 +++++++++---
man/knockoff.threshold.Rd | 3 +
man/lasso_max_lambda.Rd | 3 +
tests/testthat/InputStreamByteWrapper.class |only
tests/testthat/MatlabServer.m |only
tests/testthat/matlab_compat.R | 4 +-
tests/testthat/test_create.R | 34 +++++++++++++++---
tests/testthat/test_util.R |only
vignettes/intro.Rmd | 10 +++++
vignettes/sdp.Rmd | 14 +++++--
29 files changed, 221 insertions(+), 90 deletions(-)
Title: Package to fit spatial data in gamlss
Diff between gamlss.spatial versions 0.1 dated 2014-02-21 and 0.2 dated 2015-02-05
More information about gamlss.spatial at CRAN
Description: Spatial models in gamlss
Author: Fernanda De Bastiani, Mikis Stasinopoulos,
Maintainer: Fernanda De Bastiani
DESCRIPTION | 10
MD5 | 8
NAMESPACE | 11 -
R/extraFunctions.R | 537 ++++++++++++++++++++++++++---------------------------
R/mrf-for-gamlss.R | 5
5 files changed, 287 insertions(+), 284 deletions(-)
Permanent link
Title: Probabilistic Population Projection
Diff between bayesPop versions 5.2-1 dated 2014-11-20 and 5.2-2 dated 2015-02-05
Description: The package allows to generate population projections for all countries of the world using several probabilistic components, such as total fertility rate (TFR) and life expectancy.
Author: Hana Sevcikova, Adrian Raftery
Maintainer: Hana Sevcikova
ChangeLog | 4 ++++
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/get_outputs.R | 4 ++--
man/bayesPop-package.Rd | 7 ++++---
5 files changed, 18 insertions(+), 13 deletions(-)
Title: Replication Interval Functions
Diff between replicationInterval versions 0.2 dated 2014-10-24 and 0.3 dated 2015-02-04
More information about replicationInterval at CRAN
Description: A common problem faced by journal reviewers and authors is the
question of whether the results of a replication study are consistent with
the original published study. One solution to this problem is to examine
the effect size from the published study and generate the range of effect
sizes that could reasonably be obtained (due to random sampling) in a
replication attempt (i.e., calculate a replication interval). If a
replication effect size falls outside the replication interval then that
value could not have occurred to due the effects of sampling error alone.
Alternatively, if a replication effect size falls within the replication
interval then the replication results could have reasonably occurred due to
the effects of sampling error alone. This package has functions that
calculate the replication interval for two different types of effect sizes,
namely correlation (i.e., r) and the standardized mean difference
(i.e., d-value).
Author: David Stanley
Maintainer: David Stanley
DESCRIPTION | 10 +--
MD5 | 10 +--
R/replicationInterval.R | 102 +++++++++++++++++++++++--------------
man/replicationInterval-package.Rd | 8 +-
man/ri.d.Rd | 8 ++
man/ri.r.Rd | 5 +
6 files changed, 91 insertions(+), 52 deletions(-)
Permanent link
Title: Mark-Recapture Distance Sampling
Diff between mrds versions 2.1.10 dated 2014-09-27 and 2.1.12 dated 2015-02-04
Description: Animal abundance estimation via conventional, multiple covariate
and mark-recapture distance sampling (CDS/MCDS/MRDS). Detection function
fitting is performed via maximum likelihood. Also included are diagnostics
and plotting for fitted detection functions. Abundance estimation is via a
Horvitz-Thompson-like estimator.
Author: Jeff Laake
Maintainer: David Miller
DESCRIPTION | 27 -
MD5 | 58 +--
NEWS | 569 ++++++++++++++++++-------------------
R/ddf.R | 125 +++-----
R/ddf.trial.R | 4
R/detfct.R | 24 -
R/detfct.fit.opt.R | 85 +++--
R/dht.R | 13
R/flpt.lnl.r | 4
R/gstdint.R | 129 ++++++--
R/integratepdf.r | 73 +++-
R/mrds-package.R | 335 ++++++++++++---------
R/pdot.dsr.integrate.logistic.R | 26 +
R/predict.ds.R | 22 -
R/setcov.R | 36 --
R/varn.R | 194 +++++-------
README.md | 2
data/book.tee.data.rda |binary
man/ddf.Rd | 125 +++-----
man/detfct.fit.opt.Rd | 9
man/dht.Rd | 2
man/distpdf.Rd | 24 -
man/gstdint.Rd | 4
man/integratepdf.Rd | 2
man/lfbcvi.Rd | 109 ++++---
man/lfgcwa.Rd | 215 ++++++++-----
man/pdot.dsr.integrate.logistic.Rd | 10
man/predict.ds.Rd | 21 -
man/stake77.Rd | 8
man/varn.Rd | 28 -
30 files changed, 1209 insertions(+), 1074 deletions(-)
Title: Distance Sampling Detection Function and Abundance Estimation
Diff between Distance versions 0.9.2 dated 2014-09-15 and 0.9.3 dated 2015-02-04
Description: A simple way of fitting detection functions to distance sampling
data for both line and point transects. Adjustment term selection, left and
right truncation as well as monotonicity constraints and binning are
supported. Abundance and density estimates can also be calculated (via a
Horvitz-Thompson-like estimator) if survey area information is provided.
Author: David Lawrence Miller
Maintainer: David Lawrence Miller
Distance-0.9.2/Distance/tests |only
Distance-0.9.3/Distance/DESCRIPTION | 22 -
Distance-0.9.3/Distance/MD5 | 47 +-
Distance-0.9.3/Distance/NAMESPACE | 2
Distance-0.9.3/Distance/NEWS | 8
Distance-0.9.3/Distance/R/Distance-package.R | 2
Distance-0.9.3/Distance/R/checkdata.R | 13
Distance-0.9.3/Distance/R/create.bins.R | 5
Distance-0.9.3/Distance/R/ds.R | 4
Distance-0.9.3/Distance/R/plot.dsmodel.R | 2
Distance-0.9.3/Distance/R/print.dsmodel.R | 2
Distance-0.9.3/Distance/R/print.summary.dsmodel.R | 2
Distance-0.9.3/Distance/R/summary.dsmodel.R | 2
Distance-0.9.3/Distance/man/Distance-package.Rd | 24 -
Distance-0.9.3/Distance/man/checkdata.Rd | 17
Distance-0.9.3/Distance/man/create.bins.Rd | 13
Distance-0.9.3/Distance/man/ds.Rd | 374 +++++++------------
Distance-0.9.3/Distance/man/flatfile.Rd | 29 -
Distance-0.9.3/Distance/man/minke.Rd | 22 -
Distance-0.9.3/Distance/man/plot.dsmodel.Rd | 10
Distance-0.9.3/Distance/man/print.dsmodel.Rd | 12
Distance-0.9.3/Distance/man/print.summary.dsmodel.Rd | 13
Distance-0.9.3/Distance/man/summary.dsmodel.Rd | 13
23 files changed, 261 insertions(+), 377 deletions(-)
Title: Trust Region Optimization for Nonlinear Functions with Sparse
Hessians
Diff between trustOptim versions 0.8.4.1 dated 2014-09-27 and 0.8.5 dated 2015-02-04
Description: Trust region algorithm for nonlinear optimization. Efficient when the Hessian of the objective function is sparse (i.e., relatively few nonzero cross-partial derivatives).
Author: Michael Braun [aut, cre, cph]
Maintainer: Michael Braun
trustOptim-0.8.4.1/trustOptim/R/hbc_funcs.R |only
trustOptim-0.8.4.1/trustOptim/R/logit.R |only
trustOptim-0.8.4.1/trustOptim/R/rosen_funcs.R |only
trustOptim-0.8.4.1/trustOptim/R/vech.R |only
trustOptim-0.8.4.1/trustOptim/demo |only
trustOptim-0.8.4.1/trustOptim/inst/doc/trustOptim.Rnw |only
trustOptim-0.8.4.1/trustOptim/inst/doc/trustOptim.pdf |only
trustOptim-0.8.4.1/trustOptim/man/demo_funcs_hbc.Rd |only
trustOptim-0.8.4.1/trustOptim/man/inv.vech.Rd |only
trustOptim-0.8.4.1/trustOptim/man/logit.Rd |only
trustOptim-0.8.4.1/trustOptim/man/rosen.Rd |only
trustOptim-0.8.4.1/trustOptim/man/vech.Rd |only
trustOptim-0.8.4.1/trustOptim/vignettes/trustOptim.Rnw |only
trustOptim-0.8.5/trustOptim/DESCRIPTION | 31 -
trustOptim-0.8.5/trustOptim/MD5 | 63 +-
trustOptim-0.8.5/trustOptim/NAMESPACE | 18
trustOptim-0.8.5/trustOptim/NEWS | 121 +++--
trustOptim-0.8.5/trustOptim/R/RcppExports.R |only
trustOptim-0.8.5/trustOptim/R/binary-data.R |only
trustOptim-0.8.5/trustOptim/R/binary.R |only
trustOptim-0.8.5/trustOptim/R/callTrust.R | 36 -
trustOptim-0.8.5/trustOptim/build/vignette.rds |binary
trustOptim-0.8.5/trustOptim/data |only
trustOptim-0.8.5/trustOptim/inst/doc/trustOptim-demo.R |only
trustOptim-0.8.5/trustOptim/inst/doc/trustOptim-demo.Rmd |only
trustOptim-0.8.5/trustOptim/inst/doc/trustOptim-demo.html |only
trustOptim-0.8.5/trustOptim/inst/doc/trustOptim-quick.R |only
trustOptim-0.8.5/trustOptim/inst/doc/trustOptim-quick.Rmd |only
trustOptim-0.8.5/trustOptim/inst/doc/trustOptim-quick.html |only
trustOptim-0.8.5/trustOptim/inst/include/CG-base.h | 7
trustOptim-0.8.5/trustOptim/inst/include/CG-quasi.h | 2
trustOptim-0.8.5/trustOptim/inst/include/CG-sparse.h | 2
trustOptim-0.8.5/trustOptim/inst/include/Rfunc.cpp | 2
trustOptim-0.8.5/trustOptim/inst/include/RfuncHess.cpp | 2
trustOptim-0.8.5/trustOptim/inst/include/common_R.hpp | 4
trustOptim-0.8.5/trustOptim/man/binary-data.Rd |only
trustOptim-0.8.5/trustOptim/man/binary.Rd |only
trustOptim-0.8.5/trustOptim/man/trust.optim.Rd | 24 -
trustOptim-0.8.5/trustOptim/man/trustOptim.Rd | 3
trustOptim-0.8.5/trustOptim/src/Makevars | 5
trustOptim-0.8.5/trustOptim/src/RcppExports.cpp |only
trustOptim-0.8.5/trustOptim/src/trustOptim.cpp | 245 +++++------
trustOptim-0.8.5/trustOptim/tests |only
trustOptim-0.8.5/trustOptim/vignettes/trustOptim-demo.Rmd |only
trustOptim-0.8.5/trustOptim/vignettes/trustOptim-quick.Rmd |only
trustOptim-0.8.5/trustOptim/vignettes/trustOptim.bib | 281 +++----------
46 files changed, 350 insertions(+), 496 deletions(-)
Title: Read and Analyze PLEXOS Solutions
Diff between rplexos versions 0.12 dated 2015-01-27 and 0.12.1 dated 2015-02-04
Description: Efficiently read and analyze PLEXOS solutions by converting them
into SQLite databases that can be easily queried. It supports collation of
solutions that may have been divided into different time partitions,
as well as the comparison across different scenarios.
Author: Eduardo Ibanez [aut, cre],
Marcin Kalicinski [ctb] (for the included RapidXml source),
National Renewable Energy Laboratory [cph]
Maintainer: Eduardo Ibanez
DESCRIPTION | 20 ++++++++++---------
MD5 | 40 +++++++++++++++++++--------------------
R/plexos_open.R | 18 ++++++++---------
R/process_folder.R | 3 ++
R/process_input.R | 26 ++++++++++++++++++++++++-
R/process_solution.R | 4 +--
R/query.R | 5 ++++
inst/web/index.html | 21 ++++++++++----------
inst/web/is_sample_stats.html | 19 ++++++------------
inst/web/list_folders.html | 13 +++---------
inst/web/plexos_close.html | 11 ++--------
inst/web/plexos_open.html | 19 ++++++++++--------
inst/web/process_folder.html | 43 +++++++++++++++++++++++-------------------
inst/web/query_config.html | 11 ++--------
inst/web/query_log.html | 11 ++--------
inst/web/query_master.html | 27 ++++++++++++++------------
inst/web/query_property.html | 11 ++--------
inst/web/rplexos.html | 13 +++---------
inst/web/valid_columns.html | 11 ++--------
man/plexos_open.Rd | 4 +++
man/process_folder.Rd | 3 ++
21 files changed, 173 insertions(+), 160 deletions(-)
Title: Distance and Similarity Measures
Diff between proxy versions 0.4-13 dated 2014-09-22 and 0.4-14 dated 2015-02-04
Description: Provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.
Author: David Meyer [aut, cre],
Christian Buchta [aut]
Maintainer: David Meyer
DESCRIPTION | 8 ++++----
MD5 | 30 +++++++++++++++---------------
NAMESPACE | 2 +-
R/dissimilarities.R | 31 +++++++++++++++++++++++++++++++
R/dist.R | 4 ++++
R/similarities.R | 30 ------------------------------
build/vignette.rds |binary
inst/NEWS.Rd | 5 +++++
inst/doc/overview.pdf |binary
man/dist.Rd | 1 +
tests/apply.Rout.save | 10 +++++++---
tests/distance.Rout.save | 12 ++++++++----
tests/distcalls.R | 6 +++++-
tests/distcalls.Rout.save | 25 ++++++++++++++++---------
tests/registry.Rout.save | 14 ++++++++++----
tests/util.Rout.save | 14 ++++++++++----
16 files changed, 117 insertions(+), 75 deletions(-)
Title: General Package for Meta-Analysis
Diff between meta versions 4.0-3 dated 2015-01-07 and 4.1-0 dated 2015-02-04
Description: User-friendly general package providing standard methods for meta-analysis:
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from RevMan 5;
- prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression (if R package metafor is installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer
DESCRIPTION | 12 ++++----
MD5 | 36 +++++++++++++-------------
NAMESPACE | 4 ++
NEWS | 47 ++++++++++++++++++++++++++++++++++
R/catmeth.R | 19 +++++++++++++
R/chklevel.R | 2 -
R/forest.meta.R | 3 +-
R/meta-internal.R | 4 ++
R/metacont.R | 67 ++++++++++++++++++++++++++++++++++++++++---------
R/metagen.R | 5 +--
R/paulemandel.R | 11 +++++++-
R/print.meta.R | 4 ++
R/print.summary.meta.R | 8 ++++-
R/setchar.R | 2 -
R/settings.meta.R | 16 +++++++++++
R/summary.meta.R | 2 +
R/update.meta.R | 3 ++
man/metacont.Rd | 67 ++++++++++++++++++++++++++++++++++++++++++++-----
man/update.meta.Rd | 15 ++++++++++
19 files changed, 271 insertions(+), 56 deletions(-)
Title: Numerical Estimation of Sparse Hessians
Diff between sparseHessianFD versions 0.1.1 dated 2013-11-06 and 0.2.0 dated 2015-02-04
More information about sparseHessianFD at CRAN
Description: Computes Hessian of a scalar-valued function, and returns it in
sparse Matrix format, using ACM TOMS Algorithm 636. The user must supply the objective function, the
gradient, and the row and column indices of the non-zero elements of the
lower triangle of the Hessian (i.e., the sparsity structure must be known
in advance). The algorithm exploits this sparsity, so Hessians can be
computed quickly even when the number of arguments to the objective
functions is large. This package is intended to be useful for numeric
optimization (e.g., with the trustOptim package) or in simulation (e.g.,
the sparseMVN package). The underlying algorithm is ACM TOMS Algorithm 636,
written by Coleman, Garbow and More (ACM Transactions on Mathematical
Software, 11:4, Dec. 1985).
Author: R interface code by Michael Braun
Original Fortran code by Thomas F. Coleman, Burton S. Garbow and
Jorge J. More.
Maintainer: Michael Braun
sparseHessianFD-0.1.1/sparseHessianFD/R/classes.R |only
sparseHessianFD-0.1.1/sparseHessianFD/R/wrappers.R |only
sparseHessianFD-0.1.1/sparseHessianFD/inst/doc/sparseHessianFD.Rnw |only
sparseHessianFD-0.1.1/sparseHessianFD/inst/doc/sparseHessianFD.pdf |only
sparseHessianFD-0.1.1/sparseHessianFD/inst/examples/ex_funcs.R |only
sparseHessianFD-0.1.1/sparseHessianFD/inst/examples/example.R |only
sparseHessianFD-0.1.1/sparseHessianFD/inst/include/Rfunc.cpp |only
sparseHessianFD-0.1.1/sparseHessianFD/inst/include/common_R.hpp |only
sparseHessianFD-0.1.1/sparseHessianFD/inst/include/exceptions.hpp |only
sparseHessianFD-0.1.1/sparseHessianFD/man/Coord.to.Sym.Pattern.Matrix.Rd |only
sparseHessianFD-0.1.1/sparseHessianFD/man/Sym.CSC.to.Matrix.Rd |only
sparseHessianFD-0.1.1/sparseHessianFD/man/newSparseHessian.Rd |only
sparseHessianFD-0.1.1/sparseHessianFD/man/sparseHessianObj-class.Rd |only
sparseHessianFD-0.1.1/sparseHessianFD/man/wrappers.Rd |only
sparseHessianFD-0.1.1/sparseHessianFD/src/Rinterface.cpp |only
sparseHessianFD-0.1.1/sparseHessianFD/vignettes/sparseHessianFD.Rnw |only
sparseHessianFD-0.1.1/sparseHessianFD/vignettes/sparseHessianFD.bib |only
sparseHessianFD-0.2.0/sparseHessianFD/DESCRIPTION | 48 +++--
sparseHessianFD-0.2.0/sparseHessianFD/MD5 | 64 ++++---
sparseHessianFD-0.2.0/sparseHessianFD/NAMESPACE | 18 +-
sparseHessianFD-0.2.0/sparseHessianFD/NEWS | 39 ++++
sparseHessianFD-0.2.0/sparseHessianFD/R/binary-data.R |only
sparseHessianFD-0.2.0/sparseHessianFD/R/binary.R |only
sparseHessianFD-0.2.0/sparseHessianFD/R/deprecated.R |only
sparseHessianFD-0.2.0/sparseHessianFD/R/matrices.R | 84 +++++-----
sparseHessianFD-0.2.0/sparseHessianFD/R/sparseHessianFD-class.R |only
sparseHessianFD-0.2.0/sparseHessianFD/R/sparseHessianFD-new.R |only
sparseHessianFD-0.2.0/sparseHessianFD/R/sparseHessianFD.R |only
sparseHessianFD-0.2.0/sparseHessianFD/build/vignette.rds |binary
sparseHessianFD-0.2.0/sparseHessianFD/data |only
sparseHessianFD-0.2.0/sparseHessianFD/inst/CITATION |only
sparseHessianFD-0.2.0/sparseHessianFD/inst/Rfunc_old.cpp |only
sparseHessianFD-0.2.0/sparseHessianFD/inst/doc/sparseHessianFD.R |only
sparseHessianFD-0.2.0/sparseHessianFD/inst/doc/sparseHessianFD.Rmd |only
sparseHessianFD-0.2.0/sparseHessianFD/inst/doc/sparseHessianFD.html |only
sparseHessianFD-0.2.0/sparseHessianFD/inst/examples/ex2.R |only
sparseHessianFD-0.2.0/sparseHessianFD/inst/include/except.h |only
sparseHessianFD-0.2.0/sparseHessianFD/inst/include/func.h |only
sparseHessianFD-0.2.0/sparseHessianFD/man/Coord.to.Pattern.Matrix.Rd | 46 ++---
sparseHessianFD-0.2.0/sparseHessianFD/man/Matrix.to.Coord.Rd | 31 +--
sparseHessianFD-0.2.0/sparseHessianFD/man/binary-data.Rd |only
sparseHessianFD-0.2.0/sparseHessianFD/man/binary.Rd |only
sparseHessianFD-0.2.0/sparseHessianFD/man/sparseHessianFD-class.Rd |only
sparseHessianFD-0.2.0/sparseHessianFD/man/sparseHessianFD-deprecated.Rd |only
sparseHessianFD-0.2.0/sparseHessianFD/man/sparseHessianFD-package.Rd | 69 +++-----
sparseHessianFD-0.2.0/sparseHessianFD/man/sparseHessianFD.new.Rd |only
sparseHessianFD-0.2.0/sparseHessianFD/src/FDHS-DSSM.c | 6
sparseHessianFD-0.2.0/sparseHessianFD/src/Makevars | 6
sparseHessianFD-0.2.0/sparseHessianFD/src/Makevars.win | 7
sparseHessianFD-0.2.0/sparseHessianFD/src/rcpp_module.cpp |only
sparseHessianFD-0.2.0/sparseHessianFD/tests |only
sparseHessianFD-0.2.0/sparseHessianFD/vignettes/sparseHessianFD.Rmd |only
52 files changed, 236 insertions(+), 182 deletions(-)
Permanent link
Title: Extract Statistics from Articles and Recompute P Values
Diff between statcheck versions 1.0.0 dated 2014-11-20 and 1.0.1 dated 2015-02-04
Description: Extract statistics from articles and recompute p values.
Author: Sacha Epskamp
Maintainer: Michele B. Nuijten
DESCRIPTION | 10 +--
MD5 | 8 +-
R/htmlImport.R | 2
R/statcheck.R | 32 +++++++++--
man/statcheck.Rd | 151 +++++++++++++++++++++++++++++++++++++------------------
5 files changed, 138 insertions(+), 65 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Diff between netmeta versions 0.6-0 dated 2014-07-29 and 0.7-0 dated 2015-02-04
Description: Network meta-analysis following methods by Rücker (2012) and Krahn et al. (2013)
Author: Gerta Rücker [aut],
Guido Schwarzer [aut, cre],
Ulrike Krahn [aut],
Jochem König [aut]
Maintainer: Guido Schwarzer
DESCRIPTION | 14 +++---
MD5 | 47 ++++++++++++++--------
NAMESPACE | 6 ++
NEWS | 85 +++++++++++++++++++++++++++++++++++++++++
R/chklist.R |only
R/decomp.tau.R | 2
R/forest.netmeta.R | 29 +++++---------
R/netgraph.R | 73 +++++++++++++++--------------------
R/netheat.R | 19 +++++++--
R/netmeta.R | 88 ++++++++++++++++++-------------------------
R/nma.krahn.R | 14 +++---
R/nma.ruecker.R | 2
R/pairwise.R |only
R/print.decomp.design.R | 14 +++---
R/print.netmeta.R | 11 +++--
R/print.summary.netmeta.R | 48 +++++++++++++++++++----
R/setref.R |only
R/setseq.R |only
R/stress.R | 2
R/summary.netmeta.R | 3 +
R/tau.within.R | 7 ++-
data/dietaryfat.csv.gz |only
data/parkinson.csv.gz |only
data/smokingcessation.csv.gz |only
man/dietaryfat.Rd |only
man/netgraph.Rd | 14 +++---
man/netmeta.Rd | 2
man/pairwise.Rd |only
man/parkinson.Rd |only
man/smokingcessation.Rd |only
30 files changed, 306 insertions(+), 174 deletions(-)
Title: Plot rpart Models. An Enhanced Version of plot.rpart
Diff between rpart.plot versions 1.5.1 dated 2014-12-14 and 1.5.2 dated 2015-02-04
Description: Plot rpart models. Extends plot.rpart and text.rpart in
the rpart package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow
DESCRIPTION | 6 +++---
MD5 | 14 +++++++-------
NEWS | 4 ++++
R/layout.R | 4 ++--
R/lib.R | 26 +++++++++++---------------
inst/doc/prp.pdf |binary
inst/slowtests/test.prp.R | 11 +++++++++++
inst/slowtests/test.prp.Rout.save | 13 ++++++++++++-
8 files changed, 50 insertions(+), 28 deletions(-)
Title: R Individual Specialization (RInSp)
Diff between RInSp versions 1.0 dated 2013-07-26 and 1.1 dated 2015-02-04
Description: Functions to calculate several ecological indices of individual and population niche width
(Araujo's E, clustering and pairwise similarity among individuals, IS, Petraitis' W, and Roughgarden's
WIC/TNW) to assess individual specialization based on data of resource use. Resource use can be
quantified by counts of categories, measures of mass/lenght or proportions. Monte Carlo resampling
procedures are available for hypothesis testing against multinomial null models.
Author: Dr. Nicola Zaccarelli, Dr. Giorgio Mancinelli, and Prof. Dan Bolnick
Maintainer: Dr. Nicola Zaccarelli
DESCRIPTION | 21 +--
MD5 | 30 ++--
R/Eindex.R | 319 ++++++++++++++++++++++++++-------------------------
R/like.Wi.R | 8 -
inst/citation | 39 +++---
man/Eindex.Rd | 185 +++++++++++++++--------------
man/Emc.Rd | 2
man/RInSp-package.Rd | 18 ++
man/like.Wi.Rd | 107 ++++++++---------
man/overlap.Rd | 18 +-
man/sumMC.RInSp.Rd | 2
src/Emc.c | 61 +++++----
src/MCprocedure.c | 19 +--
src/PSicalc.c | 14 +-
src/WTcMC.c | 17 +-
src/WTdMC.c | 15 +-
16 files changed, 465 insertions(+), 410 deletions(-)
Title: Miscellaneous Useful Functions
Diff between miscFuncs versions 1.2-6 dated 2014-07-23 and 1.2-7 dated 2015-02-04
Description: LaTeX tables, Kalman filter, web scraping, development tools,
relative risk, odds ratio
Author: Benjamin M. Taylor
Maintainer: Benjamin M. Taylor
DESCRIPTION | 8 +++----
MD5 | 48 +++++++++++++++++++++++------------------------
NAMESPACE | 2 -
build/vignette.rds |binary
inst/doc/miscFuncs.Rtex | 6 ++++-
inst/doc/miscFuncs.pdf |binary
man/EKFadvance.Rd | 3 +-
man/KFadvance.Rd | 3 +-
man/KFadvanceAR2.Rd | 3 +-
man/KFtemplates.Rd | 3 +-
man/bin.Rd | 3 +-
man/generic.Rd | 3 +-
man/getstrbetween.Rd | 3 +-
man/getwikicoords.Rd | 3 +-
man/latexformat.Rd | 3 +-
man/latextable.Rd | 3 +-
man/method.Rd | 3 +-
man/print22.Rd | 3 +-
man/roxbc.Rd | 3 +-
man/roxbuild.Rd | 3 +-
man/roxtext.Rd | 3 +-
man/timeop.Rd | 3 +-
man/twotwoinfo.Rd | 3 +-
man/vdc.Rd | 3 +-
vignettes/miscFuncs.Rtex | 6 ++++-
25 files changed, 75 insertions(+), 49 deletions(-)
Title: Multivariable Fractional Polynomials
Diff between mfp versions 1.5.0 dated 2014-10-02 and 1.5.1 dated 2015-02-04
Description: Fractional polynomials are used to represent curvature in regression models. A key reference is Royston and Altman, 1994.
Author: original by Gareth Ambler
Maintainer: Stephan Luecke
mfp-1.5.0/mfp/Changelog |only
mfp-1.5.0/mfp/inst/doc/mfp.R |only
mfp-1.5.0/mfp/inst/doc/mfp.Rnw |only
mfp-1.5.0/mfp/inst/doc/mfp.pdf |only
mfp-1.5.0/mfp/vignettes/mfp.Rnw |only
mfp-1.5.0/mfp/vignettes/mfp.bib |only
mfp-1.5.1/mfp/ChangeLog |only
mfp-1.5.1/mfp/DESCRIPTION | 8
mfp-1.5.1/mfp/MD5 | 20 -
mfp-1.5.1/mfp/build/vignette.rds |binary
mfp-1.5.1/mfp/data/bodyfat.rda |binary
mfp-1.5.1/mfp/inst/doc/mfp_vignette.R |only
mfp-1.5.1/mfp/inst/doc/mfp_vignette.Rnw |only
mfp-1.5.1/mfp/inst/doc/mfp_vignette.pdf |only
mfp-1.5.1/mfp/man/mfp.Rd | 316 +++++++++++++++----------------
mfp-1.5.1/mfp/vignettes/mfp_vignette.Rnw |only
mfp-1.5.1/mfp/vignettes/mfp_vignette.bib |only
17 files changed, 172 insertions(+), 172 deletions(-)
Title: Log-Gaussian Cox Process
Diff between lgcp versions 1.3-7 dated 2015-01-24 and 1.3-8 dated 2015-02-04
Description: Spatial and spatio-temporal modelling of point patterns using the
log-Gaussian Cox process. Bayesian inference for spatial, spatiotemporal,
multivariate and aggregated point processes using Markov chain Monte Carlo.
Author: B. M. Taylor, T. M. Davies, B. S. Rowlingson, P. J. Diggle. Additional
code contributions from E. Pebesma.
Maintainer: Benjamin M. Taylor
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
build/vignette.rds |binary
inst/doc/lgcp.Rnw | 8 ++++++--
inst/doc/lgcp.pdf |binary
vignettes/lgcp.Rnw | 8 ++++++--
6 files changed, 21 insertions(+), 13 deletions(-)
Title: Quasi-Periodic Time Series Characteristics
Diff between Tides versions 1.0 dated 2013-08-29 and 1.1 dated 2015-02-04
Description: Calculate Characteristics of Qasi-Periodic Time Series, e.g. Estuarine Water Levels.
Author: Tom Cox
Maintainer: Tom Cox
Tides-1.0/Tides/doc |only
Tides-1.1/Tides/ChangeLog |only
Tides-1.1/Tides/DESCRIPTION | 16 ++++-----
Tides-1.1/Tides/MD5 | 43 +++++++++---------------
Tides-1.1/Tides/R/Tides.R | 49 ++++++++++++++++++++++------
Tides-1.1/Tides/data/data.rda |binary
Tides-1.1/Tides/data/example.RData |binary
Tides-1.1/Tides/inst |only
Tides-1.1/Tides/man/IF.Rd | 2 -
Tides-1.1/Tides/man/IT.Rd | 2 -
Tides-1.1/Tides/man/TidalCharacteristics.Rd | 4 +-
Tides-1.1/Tides/man/Tides.Rd | 6 +--
Tides-1.1/Tides/man/extrema.Rd | 2 -
Tides-1.1/Tides/man/gapsts.Rd | 2 -
Tides-1.1/Tides/man/plot.Tides.Rd | 2 -
Tides-1.1/Tides/man/print.Tides.Rd | 2 -
Tides-1.1/Tides/vignettes |only
17 files changed, 74 insertions(+), 56 deletions(-)
Title: Build Regular Expressions in a Human Readable Way
Diff between rebus versions 0.0-4 dated 2015-01-21 and 0.0-5 dated 2015-02-04
Description: Build regular expressions piece by piece using human readable code.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton
DESCRIPTION | 8 ++++----
MD5 | 9 +++++----
NEWS | 2 ++
R/number_range.R | 28 +++++++++++++++++++++++-----
inst/tests/test-number_range.R |only
man/number_range.Rd | 4 ++++
6 files changed, 38 insertions(+), 13 deletions(-)
Title: Collection of Genetic Data Analysis Tools
Diff between GeneticTools versions 0.3 dated 2014-08-06 and 0.3.1 dated 2015-02-04
Description: A loose collection of tools for the analysis of gene expression and genotype data, currently with main focus on eQTL and MDR analysis.
Author: Daniel Fischer
Maintainer: Daniel Fischer
GeneticTools |only
1 file changed
Title: Readable Check Functions to Ensure Code Integrity
Diff between assertive versions 0.1-8 dated 2013-10-13 and 0.2-1 dated 2015-02-04
Description: Lots of is_* functions to check the state of your variables,
and assert_* functions to throw errors if they aren't in the right form.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton
assertive-0.1-8/assertive/man/is_R.Rd |only
assertive-0.1-8/assertive/man/is_ex_file.Rd |only
assertive-0.1-8/assertive/man/is_hex_colour.Rd |only
assertive-0.2-1/assertive/DESCRIPTION | 41
assertive-0.2-1/assertive/MD5 | 320 ++-
assertive-0.2-1/assertive/NAMESPACE | 145 +
assertive-0.2-1/assertive/NEWS | 7
assertive-0.2-1/assertive/R/are-same.R |only
assertive-0.2-1/assertive/R/assert-are-same.R |only
assertive-0.2-1/assertive/R/assert-is-a-type.R | 12
assertive-0.2-1/assertive/R/assert-is-connection.R | 117 +
assertive-0.2-1/assertive/R/assert-is-empty-scalar.R | 21
assertive-0.2-1/assertive/R/assert-is-file.R | 38
assertive-0.2-1/assertive/R/assert-is-in-range.R | 54
assertive-0.2-1/assertive/R/assert-is-na-nan-null.R | 32
assertive-0.2-1/assertive/R/assert-is-other.R | 92 +
assertive-0.2-1/assertive/R/assert-is-reflection.R | 63
assertive-0.2-1/assertive/R/assert-is-string-uk.R | 140 -
assertive-0.2-1/assertive/R/assert-is-string.R | 112 +
assertive-0.2-1/assertive/R/assert-is-type.R | 12
assertive-0.2-1/assertive/R/assert-r-has-capability.R |only
assertive-0.2-1/assertive/R/assertive-package.R | 17
assertive-0.2-1/assertive/R/has.R | 165 +
assertive-0.2-1/assertive/R/internal.R | 234 ++
assertive-0.2-1/assertive/R/is-a-type.R | 43
assertive-0.2-1/assertive/R/is-connection.R | 267 ++-
assertive-0.2-1/assertive/R/is-empty-scalar.R | 146 +
assertive-0.2-1/assertive/R/is-file.R | 157 +
assertive-0.2-1/assertive/R/is-in-range.R | 17
assertive-0.2-1/assertive/R/is-na-nan-null.R | 141 +
assertive-0.2-1/assertive/R/is-other.R | 112 -
assertive-0.2-1/assertive/R/is-real-imaginary.R | 23
assertive-0.2-1/assertive/R/is-reflection.R | 273 ++-
assertive-0.2-1/assertive/R/is-string-uk.R | 92 -
assertive-0.2-1/assertive/R/is-string-us.R | 85
assertive-0.2-1/assertive/R/is-string.R | 426 +++-
assertive-0.2-1/assertive/R/is-time.R | 30
assertive-0.2-1/assertive/R/is-true-false.R | 70
assertive-0.2-1/assertive/R/is-type.R | 102 -
assertive-0.2-1/assertive/R/r-has-capability.R |only
assertive-0.2-1/assertive/R/utils.R | 350 +++-
assertive-0.2-1/assertive/R/zzz.R | 2
assertive-0.2-1/assertive/inst/tests/test-has.R | 513 +++--
assertive-0.2-1/assertive/inst/tests/test-internal.R | 85
assertive-0.2-1/assertive/inst/tests/test-is-a-type.R | 401 ++--
assertive-0.2-1/assertive/inst/tests/test-is-atomic-recursive-vector.R | 226 +-
assertive-0.2-1/assertive/inst/tests/test-is-connection.R | 266 ++-
assertive-0.2-1/assertive/inst/tests/test-is-empty-scalar.R | 173 --
assertive-0.2-1/assertive/inst/tests/test-is-file.R | 131 -
assertive-0.2-1/assertive/inst/tests/test-is-in-range.R | 294 +--
assertive-0.2-1/assertive/inst/tests/test-is-na-nan-null.R | 64
assertive-0.2-1/assertive/inst/tests/test-is-other.R | 130 -
assertive-0.2-1/assertive/inst/tests/test-is-real-imaginary.R | 77
assertive-0.2-1/assertive/inst/tests/test-is-reflection.R | 313 ++-
assertive-0.2-1/assertive/inst/tests/test-is-string-uk.R | 862 +++-------
assertive-0.2-1/assertive/inst/tests/test-is-string-us.R | 114 -
assertive-0.2-1/assertive/inst/tests/test-is-string.R | 473 ++---
assertive-0.2-1/assertive/inst/tests/test-is-time.R | 38
assertive-0.2-1/assertive/inst/tests/test-is-true-false.R | 111 -
assertive-0.2-1/assertive/inst/tests/test-is-type.R | 735 +++-----
assertive-0.2-1/assertive/inst/tests/test-is-valid-variable-name.R | 174 --
assertive-0.2-1/assertive/inst/tests/test-r-has-capabilities.R |only
assertive-0.2-1/assertive/inst/tests/test-utils.R |only
assertive-0.2-1/assertive/man/DIM.Rd |only
assertive-0.2-1/assertive/man/are_identical.Rd |only
assertive-0.2-1/assertive/man/are_same_length.Rd |only
assertive-0.2-1/assertive/man/as.character.file.Rd |only
assertive-0.2-1/assertive/man/assert_engine.Rd | 32
assertive-0.2-1/assertive/man/assertive.Rd | 30
assertive-0.2-1/assertive/man/bapply.Rd | 22
assertive-0.2-1/assertive/man/call_and_name.Rd | 25
assertive-0.2-1/assertive/man/cause.Rd | 17
assertive-0.2-1/assertive/man/character_to_list_of_integer_vectors.Rd | 13
assertive-0.2-1/assertive/man/coerce_to.Rd | 34
assertive-0.2-1/assertive/man/create_regex.Rd | 31
assertive-0.2-1/assertive/man/d.Rd | 24
assertive-0.2-1/assertive/man/dont_stop.Rd |only
assertive-0.2-1/assertive/man/false.Rd | 16
assertive-0.2-1/assertive/man/get_name_in_parent.Rd | 11
assertive-0.2-1/assertive/man/has_any_attributes.Rd | 17
assertive-0.2-1/assertive/man/has_arg.Rd | 25
assertive-0.2-1/assertive/man/has_attributes.Rd | 27
assertive-0.2-1/assertive/man/has_cols.Rd | 28
assertive-0.2-1/assertive/man/has_dims.Rd | 20
assertive-0.2-1/assertive/man/has_duplicates.Rd | 28
assertive-0.2-1/assertive/man/has_names.Rd | 46
assertive-0.2-1/assertive/man/has_terms.Rd | 22
assertive-0.2-1/assertive/man/is2.Rd | 34
assertive-0.2-1/assertive/man/is_S4.Rd | 25
assertive-0.2-1/assertive/man/is_array.Rd | 31
assertive-0.2-1/assertive/man/is_atomic.Rd | 36
assertive-0.2-1/assertive/man/is_batch_mode.Rd | 21
assertive-0.2-1/assertive/man/is_cas_number.Rd | 42
assertive-0.2-1/assertive/man/is_character.Rd | 87 -
assertive-0.2-1/assertive/man/is_class.Rd | 24
assertive-0.2-1/assertive/man/is_complex.Rd | 38
assertive-0.2-1/assertive/man/is_connection.Rd | 177 +-
assertive-0.2-1/assertive/man/is_credit_card_number.Rd | 40
assertive-0.2-1/assertive/man/is_data.frame.Rd | 22
assertive-0.2-1/assertive/man/is_date_string.Rd | 31
assertive-0.2-1/assertive/man/is_debugged.Rd | 22
assertive-0.2-1/assertive/man/is_dir.Rd | 19
assertive-0.2-1/assertive/man/is_divisible_by.Rd |only
assertive-0.2-1/assertive/man/is_email_address.Rd | 61
assertive-0.2-1/assertive/man/is_empty.Rd | 111 +
assertive-0.2-1/assertive/man/is_empty_file.Rd |only
assertive-0.2-1/assertive/man/is_empty_model.Rd | 31
assertive-0.2-1/assertive/man/is_environment.Rd | 21
assertive-0.2-1/assertive/man/is_error_free.Rd | 15
assertive-0.2-1/assertive/man/is_executable_file.Rd |only
assertive-0.2-1/assertive/man/is_existing.Rd | 55
assertive-0.2-1/assertive/man/is_existing_file.Rd | 24
assertive-0.2-1/assertive/man/is_factor.Rd | 25
assertive-0.2-1/assertive/man/is_finite.Rd | 56
assertive-0.2-1/assertive/man/is_function.Rd | 34
assertive-0.2-1/assertive/man/is_hex_color.Rd |only
assertive-0.2-1/assertive/man/is_honorific.Rd | 35
assertive-0.2-1/assertive/man/is_in_past.Rd | 41
assertive-0.2-1/assertive/man/is_in_range.Rd | 126 -
assertive-0.2-1/assertive/man/is_inherited_from.Rd |only
assertive-0.2-1/assertive/man/is_integer.Rd | 40
assertive-0.2-1/assertive/man/is_ip_address.Rd | 31
assertive-0.2-1/assertive/man/is_isbn_code.Rd | 39
assertive-0.2-1/assertive/man/is_language.Rd | 53
assertive-0.2-1/assertive/man/is_leaf.Rd | 18
assertive-0.2-1/assertive/man/is_library.Rd | 23
assertive-0.2-1/assertive/man/is_list.Rd | 22
assertive-0.2-1/assertive/man/is_loaded.Rd | 27
assertive-0.2-1/assertive/man/is_logical.Rd | 38
assertive-0.2-1/assertive/man/is_na.Rd | 31
assertive-0.2-1/assertive/man/is_nan.Rd | 36
assertive-0.2-1/assertive/man/is_null.Rd | 26
assertive-0.2-1/assertive/man/is_numeric.Rd | 38
assertive-0.2-1/assertive/man/is_on_os_path.Rd | 23
assertive-0.2-1/assertive/man/is_qr.Rd | 22
assertive-0.2-1/assertive/man/is_r.Rd |only
assertive-0.2-1/assertive/man/is_raster.Rd | 25
assertive-0.2-1/assertive/man/is_raw.Rd | 39
assertive-0.2-1/assertive/man/is_real.Rd | 33
assertive-0.2-1/assertive/man/is_relistable.Rd | 26
assertive-0.2-1/assertive/man/is_single_character.Rd |only
assertive-0.2-1/assertive/man/is_symmetric_matrix.Rd | 28
assertive-0.2-1/assertive/man/is_table.Rd | 21
assertive-0.2-1/assertive/man/is_true.Rd | 79
assertive-0.2-1/assertive/man/is_ts.Rd | 29
assertive-0.2-1/assertive/man/is_uk_car_licence.Rd | 43
assertive-0.2-1/assertive/man/is_uk_national_insurance_number.Rd | 35
assertive-0.2-1/assertive/man/is_uk_postcode.Rd | 39
assertive-0.2-1/assertive/man/is_uk_telephone_number.Rd | 35
assertive-0.2-1/assertive/man/is_unsorted.Rd | 49
assertive-0.2-1/assertive/man/is_us_telephone_number.Rd | 41
assertive-0.2-1/assertive/man/is_us_zip_code.Rd | 56
assertive-0.2-1/assertive/man/is_valid_r_code.Rd | 14
assertive-0.2-1/assertive/man/is_valid_variable_name.Rd | 50
assertive-0.2-1/assertive/man/is_whole_number.Rd | 41
assertive-0.2-1/assertive/man/is_windows.Rd | 76
assertive-0.2-1/assertive/man/is_xxx_for_decimal_point.Rd | 49
assertive-0.2-1/assertive/man/locale_categories.Rd | 17
assertive-0.2-1/assertive/man/matches_regex.Rd | 25
assertive-0.2-1/assertive/man/merge.list.Rd |only
assertive-0.2-1/assertive/man/merge_dots_with_list.Rd | 28
assertive-0.2-1/assertive/man/modal_value.Rd | 12
assertive-0.2-1/assertive/man/n_elements.Rd |only
assertive-0.2-1/assertive/man/na.Rd | 16
assertive-0.2-1/assertive/man/parenthesise.Rd |only
assertive-0.2-1/assertive/man/print_and_capture.Rd |only
assertive-0.2-1/assertive/man/r_can_compile_code.Rd |only
assertive-0.2-1/assertive/man/r_has_jpeg_capability.Rd |only
assertive-0.2-1/assertive/man/recycle.Rd |only
assertive-0.2-1/assertive/man/set_cause.Rd |only
assertive-0.2-1/assertive/man/strip_attributes.Rd | 10
assertive-0.2-1/assertive/man/strip_invalid_chars.Rd | 37
assertive-0.2-1/assertive/man/sys_get_locale.Rd | 23
assertive-0.2-1/assertive/man/truncate.Rd |only
assertive-0.2-1/assertive/man/use_first.Rd | 18
assertive-0.2-1/assertive/man/warn_about_file.access_under_windows.Rd |only
assertive-0.2-1/assertive/tests |only
177 files changed, 7432 insertions(+), 4919 deletions(-)
Title: A GAMLSS Add-on Package For Fitting Mixture Distributions
Diff between gamlss.mx versions 4.2-7 dated 2014-01-18 and 4.3-1 dated 2015-02-04
Description: The main purpose of this package is to allow fitting of
mixture distributions with GAMLSS models.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
DESCRIPTION | 13 +--
MD5 | 14 +--
NAMESPACE | 8 +-
R/gamlssMX-10-11-07.R | 189 ++++++++++++++++++++++++++++----------------------
R/gamlssNP.R | 132 ++++++++++++++++++----------------
data/brains.rda |binary
data/enzyme.rda |binary
man/dMX.Rd | 92 ++++++++++++------------
8 files changed, 240 insertions(+), 208 deletions(-)
Title: Demos for GAMLSS
Diff between gamlss.demo versions 4.2-7 dated 2014-01-11 and 4.3-1 dated 2015-02-04
Description: Demos for smoothing and gamlss.family distributions.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
gamlss.demo-4.2-7/gamlss.demo/R/LocalSmother.r |only
gamlss.demo-4.3-1/gamlss.demo/DESCRIPTION | 14 -
gamlss.demo-4.3-1/gamlss.demo/MD5 | 31 +-
gamlss.demo-4.3-1/gamlss.demo/NAMESPACE | 19 -
gamlss.demo-4.3-1/gamlss.demo/R/DPO.R |only
gamlss.demo-4.3-1/gamlss.demo/R/Demo_All_Distibutions.r | 46 +--
gamlss.demo-4.3-1/gamlss.demo/R/LocalRegressionDemo.R |only
gamlss.demo-4.3-1/gamlss.demo/R/LocalSmother.R |only
gamlss.demo-4.3-1/gamlss.demo/R/PSPlay_bsplines.R | 2
gamlss.demo-4.3-1/gamlss.demo/R/PSPlay_discrete.r | 90 +++----
gamlss.demo-4.3-1/gamlss.demo/R/PSPlay_psplines.r | 162 +++++++-------
gamlss.demo-4.3-1/gamlss.demo/R/demoDist.R | 6
gamlss.demo-4.3-1/gamlss.demo/R/demoPsplines.R | 92 +++----
gamlss.demo-4.3-1/gamlss.demo/R/gamlss_demo.R | 155 ++++++-------
gamlss.demo-4.3-1/gamlss.demo/R/movMean.R |only
gamlss.demo-4.3-1/gamlss.demo/man/Locmean.Rd |only
gamlss.demo-4.3-1/gamlss.demo/man/demo.BetaSplines.Rd | 16 -
gamlss.demo-4.3-1/gamlss.demo/man/demo.LocalRegression.Rd |only
gamlss.demo-4.3-1/gamlss.demo/man/demo.Locmean.Rd | 2
gamlss.demo-4.3-1/gamlss.demo/man/demo.NO.Rd | 2
20 files changed, 324 insertions(+), 313 deletions(-)
Title: Partial Autoregression
Diff between partialAR versions 1.0.3 dated 2015-01-28 and 1.0.5 dated 2015-02-04
Description: Fits time series models which consist of a sum of a permanent and a transient component.
Author: Matthew Clegg [aut, cre, cph]
Maintainer: Matthew Clegg
DESCRIPTION | 12 ++++++-----
MD5 | 20 +++++++++---------
R/RcppExports.R | 4 +++
R/lr.R | 39 +++++++++++++++++++----------------
R/lrdata.R | 4 +--
R/lrtables.R | 24 +++++++++++-----------
man/fit.par.Rd | 1
man/partialAR-package.Rd | 2 -
src/RcppExports.cpp | 17 +++++++++++++++
src/cfit.cc | 51 ++++++++++++++++++++++-------------------------
tests/tests.R | 6 +++++
11 files changed, 105 insertions(+), 75 deletions(-)
Title: Machine Learning in R
Diff between mlr versions 2.2 dated 2014-10-29 and 2.3 dated 2015-02-04
Description: Interface to a large number of classification and regression
techniques, including machine-readable parameter descriptions. There is
also an experimental extension for survival analysis, clustering and
general, example-specific cost-sensitive learning. Generic resampling,
including cross-validation, bootstrapping and subsampling. Hyperparameter
tuning with modern optimization techniques, for single- and multi-objective
problems. Filter and wrapper methods for feature selection. Extension of
basic learners with additional operations common in machine learning, also
allowing for easy nested resampling. Most operations can be parallelized.
Author: Bernd Bischl [aut, cre],
Michel Lang [aut],
Jakob Richter [aut],
Jakob Bossek [aut],
Leonard Judt [aut],
Tobias Kuehn [aut],
Erich Studerus [aut],
Lars Kotthoff [aut]
Maintainer: Bernd Bischl
mlr-2.2/mlr/R/RLearner_classif_plsDA.R |only
mlr-2.2/mlr/R/RLearner_cluster_DBScan.R |only
mlr-2.2/mlr/R/ResampleDescs.R |only
mlr-2.2/mlr/R/getBaggingModels.R |only
mlr-2.2/mlr/R/getFailuremodelMsg.R |only
mlr-2.2/mlr/man/getBaggingModels.Rd |only
mlr-2.2/mlr/man/getCostSensClassifModel.Rd |only
mlr-2.2/mlr/man/getCostSensRegrModels.Rd |only
mlr-2.2/mlr/man/getCostSensWeightedPairsModels.Rd |only
mlr-2.2/mlr/tests/run-imbal.R |only
mlr-2.2/mlr/tests/run-resample.R |only
mlr-2.2/mlr/tests/testthat/helper_fix_packages.R |only
mlr-2.2/mlr/tests/testthat/test_base_confMatrix.R |only
mlr-2.2/mlr/tests/testthat/test_base_convertColumnNames.R |only
mlr-2.2/mlr/tests/testthat/test_base_toString.R |only
mlr-2.2/mlr/tests/testthat/test_classif_hda.R |only
mlr-2.2/mlr/tests/testthat/test_classif_loclda.R |only
mlr-2.2/mlr/tests/testthat/test_classif_plsDA.R |only
mlr-2.2/mlr/tests/testthat/test_cluster_DBScan.R |only
mlr-2.2/mlr/tests/testthat/test_featsel_extra_FilterWrapper.R |only
mlr-2.2/mlr/tests/testthat/test_imbal_OverBagging.R |only
mlr-2.2/mlr/tests/testthat/test_imbal_overundersample.R |only
mlr-2.2/mlr/tests/testthat/test_imbal_smote.R |only
mlr-2.2/mlr/tests/testthat/test_imbal_weightedclasses.R |only
mlr-2.2/mlr/tests/testthat/test_regr_logicreg.R |only
mlr-2.2/mlr/tests/testthat/test_resample_b632.R |only
mlr-2.2/mlr/tests/testthat/test_resample_b632plus.R |only
mlr-2.2/mlr/tests/testthat/test_resample_bs.R |only
mlr-2.2/mlr/tests/testthat/test_resample_convenience.R |only
mlr-2.2/mlr/tests/testthat/test_resample_cv.R |only
mlr-2.2/mlr/tests/testthat/test_resample_extra_bs.R |only
mlr-2.2/mlr/tests/testthat/test_resample_extra_cv.R |only
mlr-2.2/mlr/tests/testthat/test_resample_extra_repcv.R |only
mlr-2.2/mlr/tests/testthat/test_resample_extra_subsample.R |only
mlr-2.2/mlr/tests/testthat/test_resample_holdout.R |only
mlr-2.2/mlr/tests/testthat/test_resample_loo.R |only
mlr-2.2/mlr/tests/testthat/test_resample_makeResampleDesc.R |only
mlr-2.2/mlr/tests/testthat/test_resample_repcv.R |only
mlr-2.2/mlr/tests/testthat/test_resample_stratify.R |only
mlr-2.2/mlr/tests/testthat/test_resample_subsample.R |only
mlr-2.2/mlr/tests/testthat/test_resample_weights.R |only
mlr-2.2/mlr/tests/testthat/test_tune_TuneWrapper.R |only
mlr-2.3/mlr/DESCRIPTION | 33
mlr-2.3/mlr/MD5 | 917 +++++-----
mlr-2.3/mlr/NAMESPACE | 150 +
mlr-2.3/mlr/NEWS | 63
mlr-2.3/mlr/R/Aggregation.R | 2
mlr-2.3/mlr/R/BaggingWrapper.R | 45
mlr-2.3/mlr/R/BaseEnsemble_operators.R | 7
mlr-2.3/mlr/R/BaseWrapper.R | 61
mlr-2.3/mlr/R/BaseWrapper_operators.R | 2
mlr-2.3/mlr/R/BenchmarkResult_operators.R | 25
mlr-2.3/mlr/R/ChainModel.R | 9
mlr-2.3/mlr/R/CostSensClassifWrapper.R | 36
mlr-2.3/mlr/R/CostSensRegrWrapper.R | 45
mlr-2.3/mlr/R/CostSensWeightedPairsLearner.R | 46
mlr-2.3/mlr/R/DownsampleWrapper.R | 6
mlr-2.3/mlr/R/FailureModel.R | 14
mlr-2.3/mlr/R/FeatSelControl.R | 29
mlr-2.3/mlr/R/FeatSelControlExhaustive.R | 7
mlr-2.3/mlr/R/FeatSelControlGA.R | 17
mlr-2.3/mlr/R/FeatSelControlRandom.R | 6
mlr-2.3/mlr/R/FeatSelControlSequential.R | 10
mlr-2.3/mlr/R/FeatSelResult.R | 21
mlr-2.3/mlr/R/FeatSelWrapper.R | 2
mlr-2.3/mlr/R/Filter.R | 27
mlr-2.3/mlr/R/FilterWrapper.R | 18
mlr-2.3/mlr/R/HomogeneousEnsemble.R |only
mlr-2.3/mlr/R/Impute.R | 4
mlr-2.3/mlr/R/ImputeWrapper.R | 5
mlr-2.3/mlr/R/Learner.R | 12
mlr-2.3/mlr/R/Learner_properties.R | 15
mlr-2.3/mlr/R/Measure.R | 40
mlr-2.3/mlr/R/Measure_custom_resampled.R | 8
mlr-2.3/mlr/R/Measure_make_cost.R | 5
mlr-2.3/mlr/R/ModelMultiplexer.R | 27
mlr-2.3/mlr/R/MulticlassWrapper.R | 22
mlr-2.3/mlr/R/NoFeaturesModel.R | 21
mlr-2.3/mlr/R/OptControl.R | 13
mlr-2.3/mlr/R/OptResult.R | 3
mlr-2.3/mlr/R/OptWrapper.R | 14
mlr-2.3/mlr/R/OverBaggingWrapper.R | 8
mlr-2.3/mlr/R/OverUndersampleWrapper.R | 6
mlr-2.3/mlr/R/Prediction.R | 26
mlr-2.3/mlr/R/PreprocWrapper.R | 3
mlr-2.3/mlr/R/PreprocWrapperCaret.R |only
mlr-2.3/mlr/R/RLearner.R | 4
mlr-2.3/mlr/R/RLearner_classif_LiblineaRBinary.R | 2
mlr-2.3/mlr/R/RLearner_classif_LiblineaRLogReg.R | 14
mlr-2.3/mlr/R/RLearner_classif_ada.R | 4
mlr-2.3/mlr/R/RLearner_classif_bartMachine.R | 20
mlr-2.3/mlr/R/RLearner_classif_bdk.R |only
mlr-2.3/mlr/R/RLearner_classif_binomial.R |only
mlr-2.3/mlr/R/RLearner_classif_blackboost.R | 6
mlr-2.3/mlr/R/RLearner_classif_extraTrees.R |only
mlr-2.3/mlr/R/RLearner_classif_gbm.R | 4
mlr-2.3/mlr/R/RLearner_classif_glmboost.R | 36
mlr-2.3/mlr/R/RLearner_classif_glmnet.R | 22
mlr-2.3/mlr/R/RLearner_classif_lda.R | 10
mlr-2.3/mlr/R/RLearner_classif_logreg.R | 9
mlr-2.3/mlr/R/RLearner_classif_lqa.R | 16
mlr-2.3/mlr/R/RLearner_classif_mda.R | 3
mlr-2.3/mlr/R/RLearner_classif_plr.R | 9
mlr-2.3/mlr/R/RLearner_classif_probit.R |only
mlr-2.3/mlr/R/RLearner_classif_qda.R | 10
mlr-2.3/mlr/R/RLearner_classif_randomForestSRC.R | 7
mlr-2.3/mlr/R/RLearner_classif_rrlda.R | 2
mlr-2.3/mlr/R/RLearner_classif_sda.R | 2
mlr-2.3/mlr/R/RLearner_classif_xgboost.R |only
mlr-2.3/mlr/R/RLearner_classif_xyf.R |only
mlr-2.3/mlr/R/RLearner_regr_bartMachine.R |only
mlr-2.3/mlr/R/RLearner_regr_bcart.R |only
mlr-2.3/mlr/R/RLearner_regr_bdk.R |only
mlr-2.3/mlr/R/RLearner_regr_bgp.R |only
mlr-2.3/mlr/R/RLearner_regr_bgpllm.R |only
mlr-2.3/mlr/R/RLearner_regr_blm.R |only
mlr-2.3/mlr/R/RLearner_regr_brnn.R |only
mlr-2.3/mlr/R/RLearner_regr_btgp.R |only
mlr-2.3/mlr/R/RLearner_regr_btgpllm.R |only
mlr-2.3/mlr/R/RLearner_regr_btlm.R |only
mlr-2.3/mlr/R/RLearner_regr_crs.R | 6
mlr-2.3/mlr/R/RLearner_regr_cubist.R |only
mlr-2.3/mlr/R/RLearner_regr_elmNN.R |only
mlr-2.3/mlr/R/RLearner_regr_extraTrees.R |only
mlr-2.3/mlr/R/RLearner_regr_gbm.R | 2
mlr-2.3/mlr/R/RLearner_regr_glmnet.R | 16
mlr-2.3/mlr/R/RLearner_regr_km.R | 8
mlr-2.3/mlr/R/RLearner_regr_laGP.R |only
mlr-2.3/mlr/R/RLearner_regr_mob.R | 8
mlr-2.3/mlr/R/RLearner_regr_randomForestSRC.R | 7
mlr-2.3/mlr/R/RLearner_regr_xgboost.R |only
mlr-2.3/mlr/R/RLearner_regr_xyf.R |only
mlr-2.3/mlr/R/RLearner_surv_CoxBoost.R | 24
mlr-2.3/mlr/R/RLearner_surv_cvglmnet.R | 18
mlr-2.3/mlr/R/RLearner_surv_glmboost.R | 58
mlr-2.3/mlr/R/RLearner_surv_glmnet.R | 18
mlr-2.3/mlr/R/RLearner_surv_optimCoxBoostPenalty.R | 50
mlr-2.3/mlr/R/RLearner_surv_penalized.R | 16
mlr-2.3/mlr/R/RLearner_surv_randomForestSRC.R | 17
mlr-2.3/mlr/R/RLearner_surv_rpart.R |only
mlr-2.3/mlr/R/ResampleDesc.R | 84
mlr-2.3/mlr/R/ResampleInstance.R | 30
mlr-2.3/mlr/R/ResampleResult.R |only
mlr-2.3/mlr/R/SMOTEWrapper.R | 3
mlr-2.3/mlr/R/Task_operators.R | 47
mlr-2.3/mlr/R/TuneControl.R | 37
mlr-2.3/mlr/R/TuneControlCMAES.R | 7
mlr-2.3/mlr/R/TuneControlGenSA.R | 7
mlr-2.3/mlr/R/TuneControlGrid.R | 8
mlr-2.3/mlr/R/TuneControlIrace.R | 7
mlr-2.3/mlr/R/TuneControlMBO.R | 14
mlr-2.3/mlr/R/TuneControlRandom.R | 7
mlr-2.3/mlr/R/TuneMultiCritControl.R | 8
mlr-2.3/mlr/R/TuneMultiCritControlGrid.R | 4
mlr-2.3/mlr/R/TuneMultiCritControlNSGA2.R | 4
mlr-2.3/mlr/R/TuneMultiCritControlRandom.R | 4
mlr-2.3/mlr/R/TuneMultiCritResult.R | 3
mlr-2.3/mlr/R/TuneResult.R | 12
mlr-2.3/mlr/R/TuneWrapper.R | 18
mlr-2.3/mlr/R/WeightedClassesWrapper.R | 4
mlr-2.3/mlr/R/WrappedModel.R | 64
mlr-2.3/mlr/R/aggregations.R | 62
mlr-2.3/mlr/R/asROCRPrediction.R | 9
mlr-2.3/mlr/R/benchmark.R | 5
mlr-2.3/mlr/R/checkPrediction.R |only
mlr-2.3/mlr/R/checkTunerParset.R | 4
mlr-2.3/mlr/R/configureMlr.R | 18
mlr-2.3/mlr/R/convertX.R | 1
mlr-2.3/mlr/R/evalOptimizationState.R | 47
mlr-2.3/mlr/R/filterFeatures.R | 14
mlr-2.3/mlr/R/fixDataForLearner.R |only
mlr-2.3/mlr/R/getConfMatrix.R | 45
mlr-2.3/mlr/R/getFilterValues.R | 2
mlr-2.3/mlr/R/getHyperPars.R | 1
mlr-2.3/mlr/R/helpers.R | 34
mlr-2.3/mlr/R/isFailureModel.R | 40
mlr-2.3/mlr/R/joinClassLevels.R | 4
mlr-2.3/mlr/R/listLearners.R | 5
mlr-2.3/mlr/R/logFunOpt.R |only
mlr-2.3/mlr/R/measures.R | 512 +++--
mlr-2.3/mlr/R/mergeSmallFactorLevels.R | 2
mlr-2.3/mlr/R/normalizeFeatures.R | 2
mlr-2.3/mlr/R/performance.R | 53
mlr-2.3/mlr/R/plotFilterValues.R | 1
mlr-2.3/mlr/R/plotLearnerPrediction.R | 29
mlr-2.3/mlr/R/plotROCRCurves.R |only
mlr-2.3/mlr/R/plotThreshVsPerf.R | 9
mlr-2.3/mlr/R/plotTuneMultiCritResult.R | 1
mlr-2.3/mlr/R/plotViperCharts.R |only
mlr-2.3/mlr/R/predict.R | 5
mlr-2.3/mlr/R/predictLearner.R | 1
mlr-2.3/mlr/R/removeConstantFeatures.R | 3
mlr-2.3/mlr/R/resample.R | 65
mlr-2.3/mlr/R/selectFeatures.R | 5
mlr-2.3/mlr/R/selectFeaturesExhaustive.R | 7
mlr-2.3/mlr/R/selectFeaturesGA.R | 4
mlr-2.3/mlr/R/selectFeaturesRandom.R | 11
mlr-2.3/mlr/R/selectFeaturesSequential.R | 4
mlr-2.3/mlr/R/setHyperPars.R | 23
mlr-2.3/mlr/R/setPredictThreshold.R |only
mlr-2.3/mlr/R/setThreshold.R | 3
mlr-2.3/mlr/R/smote.R | 6
mlr-2.3/mlr/R/summarizeColumns.R | 20
mlr-2.3/mlr/R/train.R | 5
mlr-2.3/mlr/R/tuneCMAES.R | 5
mlr-2.3/mlr/R/tuneGenSA.R | 6
mlr-2.3/mlr/R/tuneIrace.R | 9
mlr-2.3/mlr/R/tuneMBO.R | 23
mlr-2.3/mlr/R/tuneMultiCritNSGA2.R | 2
mlr-2.3/mlr/R/tuneParams.R | 2
mlr-2.3/mlr/R/tuneParamsMultiCrit.R | 2
mlr-2.3/mlr/R/tuneThreshold.R | 5
mlr-2.3/mlr/R/utils_opt.R | 32
mlr-2.3/mlr/R/zzz.R | 2
mlr-2.3/mlr/man/Aggregation.Rd | 14
mlr-2.3/mlr/man/BenchmarkResult.Rd | 3
mlr-2.3/mlr/man/FailureModel.Rd | 3
mlr-2.3/mlr/man/FeatSelControl.Rd | 33
mlr-2.3/mlr/man/FeatSelResult.Rd | 6
mlr-2.3/mlr/man/FilterValues.Rd | 3
mlr-2.3/mlr/man/LearnerProperties.Rd | 14
mlr-2.3/mlr/man/Prediction.Rd | 3
mlr-2.3/mlr/man/RLearner.Rd | 3
mlr-2.3/mlr/man/ResamplePrediction.Rd | 4
mlr-2.3/mlr/man/ResampleResult.Rd |only
mlr-2.3/mlr/man/Task.Rd | 3
mlr-2.3/mlr/man/TaskDesc.Rd | 3
mlr-2.3/mlr/man/TuneControl.Rd | 38
mlr-2.3/mlr/man/TuneMultiCritControl.Rd | 17
mlr-2.3/mlr/man/TuneMultiCritResult.Rd | 3
mlr-2.3/mlr/man/TuneResult.Rd | 6
mlr-2.3/mlr/man/aggregations.Rd | 45
mlr-2.3/mlr/man/agri.task.Rd | 3
mlr-2.3/mlr/man/analyzeFeatSelResult.Rd | 3
mlr-2.3/mlr/man/asROCRPrediction.Rd | 14
mlr-2.3/mlr/man/bc.task.Rd | 3
mlr-2.3/mlr/man/benchmark.Rd | 8
mlr-2.3/mlr/man/bh.task.Rd | 3
mlr-2.3/mlr/man/capLargeValues.Rd | 3
mlr-2.3/mlr/man/configureMlr.Rd | 12
mlr-2.3/mlr/man/costiris.task.Rd | 3
mlr-2.3/mlr/man/createDummyFeatures.Rd | 3
mlr-2.3/mlr/man/crossover.Rd | 3
mlr-2.3/mlr/man/downsample.Rd | 3
mlr-2.3/mlr/man/dropFeatures.Rd | 3
mlr-2.3/mlr/man/estimateResidualVariance.Rd | 3
mlr-2.3/mlr/man/filterFeatures.Rd | 8
mlr-2.3/mlr/man/getBMRAggrPerformances.Rd | 5
mlr-2.3/mlr/man/getBMRFeatSelResults.Rd | 5
mlr-2.3/mlr/man/getBMRFilteredFeatures.Rd | 5
mlr-2.3/mlr/man/getBMRLearnerIds.Rd | 10
mlr-2.3/mlr/man/getBMRPerformances.Rd | 3
mlr-2.3/mlr/man/getBMRPredictions.Rd | 5
mlr-2.3/mlr/man/getBMRTaskIds.Rd | 3
mlr-2.3/mlr/man/getBMRTuneResults.Rd | 5
mlr-2.3/mlr/man/getConfMatrix.Rd | 6
mlr-2.3/mlr/man/getFailureModelMsg.Rd | 3
mlr-2.3/mlr/man/getFeatSelResult.Rd | 3
mlr-2.3/mlr/man/getFilterValues.Rd | 3
mlr-2.3/mlr/man/getFilteredFeatures.Rd | 3
mlr-2.3/mlr/man/getHomogeneousEnsembleModels.Rd |only
mlr-2.3/mlr/man/getHyperPars.Rd | 10
mlr-2.3/mlr/man/getLearnerModel.Rd | 3
mlr-2.3/mlr/man/getMlrOptions.Rd | 3
mlr-2.3/mlr/man/getParamSet.Rd | 10
mlr-2.3/mlr/man/getProbabilities.Rd | 9
mlr-2.3/mlr/man/getStackedBaseLearnerPredictions.Rd | 3
mlr-2.3/mlr/man/getTaskCosts.Rd | 10
mlr-2.3/mlr/man/getTaskData.Rd | 10
mlr-2.3/mlr/man/getTaskDescription.Rd |only
mlr-2.3/mlr/man/getTaskFeatureNames.Rd | 13
mlr-2.3/mlr/man/getTaskFormula.Rd | 14
mlr-2.3/mlr/man/getTaskId.Rd |only
mlr-2.3/mlr/man/getTaskNFeats.Rd | 9
mlr-2.3/mlr/man/getTaskTargetNames.Rd |only
mlr-2.3/mlr/man/getTaskTargets.Rd | 8
mlr-2.3/mlr/man/getTaskType.Rd |only
mlr-2.3/mlr/man/getTuneResult.Rd | 3
mlr-2.3/mlr/man/imputations.Rd | 3
mlr-2.3/mlr/man/impute.Rd | 3
mlr-2.3/mlr/man/iris.task.Rd | 3
mlr-2.3/mlr/man/isFailureModel.Rd | 3
mlr-2.3/mlr/man/joinClassLevels.Rd | 3
mlr-2.3/mlr/man/learnerArgsToControl.Rd | 3
mlr-2.3/mlr/man/learners.Rd | 3
mlr-2.3/mlr/man/listFilterMethods.Rd | 3
mlr-2.3/mlr/man/listLearners.Rd | 3
mlr-2.3/mlr/man/listMeasures.Rd | 3
mlr-2.3/mlr/man/lung.task.Rd | 3
mlr-2.3/mlr/man/makeAggregation.Rd | 3
mlr-2.3/mlr/man/makeBaggingWrapper.Rd | 6
mlr-2.3/mlr/man/makeCostMeasure.Rd | 35
mlr-2.3/mlr/man/makeCostSensClassifWrapper.Rd | 6
mlr-2.3/mlr/man/makeCostSensRegrWrapper.Rd | 6
mlr-2.3/mlr/man/makeCostSensWeightedPairsWrapper.Rd | 5
mlr-2.3/mlr/man/makeCustomResampledMeasure.Rd | 53
mlr-2.3/mlr/man/makeDownsampleWrapper.Rd | 4
mlr-2.3/mlr/man/makeFeatSelWrapper.Rd | 4
mlr-2.3/mlr/man/makeFilter.Rd | 3
mlr-2.3/mlr/man/makeFilterWrapper.Rd | 9
mlr-2.3/mlr/man/makeFixedHoldoutInstance.Rd | 3
mlr-2.3/mlr/man/makeImputeMethod.Rd | 3
mlr-2.3/mlr/man/makeImputeWrapper.Rd | 4
mlr-2.3/mlr/man/makeLearner.Rd | 23
mlr-2.3/mlr/man/makeMeasure.Rd | 65
mlr-2.3/mlr/man/makeModelMultiplexer.Rd | 3
mlr-2.3/mlr/man/makeModelMultiplexerParamSet.Rd | 3
mlr-2.3/mlr/man/makeMulticlassWrapper.Rd | 4
mlr-2.3/mlr/man/makeOverBaggingWrapper.Rd | 6
mlr-2.3/mlr/man/makePreprocWrapper.Rd | 4
mlr-2.3/mlr/man/makePreprocWrapperCaret.Rd |only
mlr-2.3/mlr/man/makeResampleDesc.Rd | 23
mlr-2.3/mlr/man/makeResampleInstance.Rd | 4
mlr-2.3/mlr/man/makeSMOTEWrapper.Rd | 4
mlr-2.3/mlr/man/makeStackedLearner.Rd | 3
mlr-2.3/mlr/man/makeTuneWrapper.Rd | 4
mlr-2.3/mlr/man/makeUndersampleWrapper.Rd | 4
mlr-2.3/mlr/man/makeWeightedClassesWrapper.Rd | 4
mlr-2.3/mlr/man/makeWrappedModel.Rd | 3
mlr-2.3/mlr/man/measures.Rd | 96 +
mlr-2.3/mlr/man/mergeSmallFactorLevels.Rd | 3
mlr-2.3/mlr/man/mtcars.task.Rd | 3
mlr-2.3/mlr/man/normalizeFeatures.Rd | 3
mlr-2.3/mlr/man/oversample.Rd | 3
mlr-2.3/mlr/man/performance.Rd | 36
mlr-2.3/mlr/man/pid.task.Rd | 3
mlr-2.3/mlr/man/plotFilterValues.Rd | 3
mlr-2.3/mlr/man/plotLearnerPrediction.Rd | 9
mlr-2.3/mlr/man/plotROCRCurves.Rd |only
mlr-2.3/mlr/man/plotThreshVsPerf.Rd | 3
mlr-2.3/mlr/man/plotTuneMultiCritResult.Rd | 3
mlr-2.3/mlr/man/plotViperCharts.Rd |only
mlr-2.3/mlr/man/predict.WrappedModel.Rd | 9
mlr-2.3/mlr/man/predictLearner.Rd | 3
mlr-2.3/mlr/man/reimpute.Rd | 3
mlr-2.3/mlr/man/removeConstantFeatures.Rd | 3
mlr-2.3/mlr/man/removeHyperPars.Rd | 13
mlr-2.3/mlr/man/resample.Rd | 91
mlr-2.3/mlr/man/selectFeatures.Rd | 3
mlr-2.3/mlr/man/setAggregation.Rd | 3
mlr-2.3/mlr/man/setHyperPars.Rd | 13
mlr-2.3/mlr/man/setHyperPars2.Rd | 3
mlr-2.3/mlr/man/setId.Rd | 14
mlr-2.3/mlr/man/setPredictThreshold.Rd |only
mlr-2.3/mlr/man/setPredictType.Rd | 18
mlr-2.3/mlr/man/setThreshold.Rd | 6
mlr-2.3/mlr/man/showHyperPars.Rd | 10
mlr-2.3/mlr/man/smote.Rd | 3
mlr-2.3/mlr/man/sonar.task.Rd | 3
mlr-2.3/mlr/man/subsetTask.Rd | 10
mlr-2.3/mlr/man/summarizeColumns.Rd | 3
mlr-2.3/mlr/man/summarizeLevels.Rd | 3
mlr-2.3/mlr/man/train.Rd | 3
mlr-2.3/mlr/man/trainLearner.Rd | 3
mlr-2.3/mlr/man/tuneParams.Rd | 3
mlr-2.3/mlr/man/tuneParamsMultiCrit.Rd | 3
mlr-2.3/mlr/man/tuneThreshold.Rd | 3
mlr-2.3/mlr/man/wpbc.task.Rd | 3
mlr-2.3/mlr/tests/run-classif.R | 2
mlr-2.3/mlr/tests/run-cluster.R | 2
mlr-2.3/mlr/tests/run-featsel.R | 2
mlr-2.3/mlr/tests/run-learners.R | 2
mlr-2.3/mlr/tests/run-parallel.R | 7
mlr-2.3/mlr/tests/run-regr.R | 2
mlr-2.3/mlr/tests/run-stack.R | 2
mlr-2.3/mlr/tests/run-surv.R | 2
mlr-2.3/mlr/tests/run-tune.R | 2
mlr-2.3/mlr/tests/testthat/Rplots.pdf |binary
mlr-2.3/mlr/tests/testthat/helper_helpers.R | 16
mlr-2.3/mlr/tests/testthat/helper_mock_learners.R | 25
mlr-2.3/mlr/tests/testthat/helper_objects.R | 10
mlr-2.3/mlr/tests/testthat/test_base_BaggingWrapper.R | 14
mlr-2.3/mlr/tests/testthat/test_base_BaseWrapper.R | 3
mlr-2.3/mlr/tests/testthat/test_base_MulticlassWrapper.R | 8
mlr-2.3/mlr/tests/testthat/test_base_PreprocWrapperCaret.R |only
mlr-2.3/mlr/tests/testthat/test_base_TuneWrapper.R |only
mlr-2.3/mlr/tests/testthat/test_base_aggregations.R | 8
mlr-2.3/mlr/tests/testthat/test_base_benchmark.R | 8
mlr-2.3/mlr/tests/testthat/test_base_blocking.R | 51
mlr-2.3/mlr/tests/testthat/test_base_clustering.R | 2
mlr-2.3/mlr/tests/testthat/test_base_configureMlr.R | 5
mlr-2.3/mlr/tests/testthat/test_base_costsens.R | 2
mlr-2.3/mlr/tests/testthat/test_base_dropFeatures.R | 4
mlr-2.3/mlr/tests/testthat/test_base_estimateResidualVariance.R | 2
mlr-2.3/mlr/tests/testthat/test_base_getConfMatrix.R |only
mlr-2.3/mlr/tests/testthat/test_base_getHyperPars.R |only
mlr-2.3/mlr/tests/testthat/test_base_getParamSet.R |only
mlr-2.3/mlr/tests/testthat/test_base_helpers.R | 9
mlr-2.3/mlr/tests/testthat/test_base_hyperpars.R | 67
mlr-2.3/mlr/tests/testthat/test_base_imbal_overbagging.R |only
mlr-2.3/mlr/tests/testthat/test_base_imbal_overundersample.R |only
mlr-2.3/mlr/tests/testthat/test_base_imbal_smote.R |only
mlr-2.3/mlr/tests/testthat/test_base_imbal_weightedclasses.R |only
mlr-2.3/mlr/tests/testthat/test_base_impute.R | 24
mlr-2.3/mlr/tests/testthat/test_base_measures.R | 14
mlr-2.3/mlr/tests/testthat/test_base_performance.R | 22
mlr-2.3/mlr/tests/testthat/test_base_plotViperCharts.R |only
mlr-2.3/mlr/tests/testthat/test_base_predict.R | 27
mlr-2.3/mlr/tests/testthat/test_base_resample.R | 6
mlr-2.3/mlr/tests/testthat/test_base_resample_b632.R |only
mlr-2.3/mlr/tests/testthat/test_base_resample_b632plus.R |only
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mlr-2.3/mlr/tests/testthat/test_base_resample_convenience.R |only
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mlr-2.3/mlr/tests/testthat/test_base_resample_loo.R |only
mlr-2.3/mlr/tests/testthat/test_base_resample_makeResampleDesc.R |only
mlr-2.3/mlr/tests/testthat/test_base_resample_repcv.R |only
mlr-2.3/mlr/tests/testthat/test_base_resample_stratify.R |only
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mlr-2.3/mlr/tests/testthat/test_base_resample_weights.R |only
mlr-2.3/mlr/tests/testthat/test_base_rocr.R | 17
mlr-2.3/mlr/tests/testthat/test_base_selectFeatures.R |only
mlr-2.3/mlr/tests/testthat/test_base_summarizeColumns.R | 14
mlr-2.3/mlr/tests/testthat/test_base_tuning.R | 53
mlr-2.3/mlr/tests/testthat/test_classif_IBk.R | 8
mlr-2.3/mlr/tests/testthat/test_classif_J48.R | 67
mlr-2.3/mlr/tests/testthat/test_classif_JRip.R | 67
mlr-2.3/mlr/tests/testthat/test_classif_LiblineaRBinary.R | 4
mlr-2.3/mlr/tests/testthat/test_classif_LiblineaRLogReg.R | 10
mlr-2.3/mlr/tests/testthat/test_classif_LiblineaRMultiClass.R | 10
mlr-2.3/mlr/tests/testthat/test_classif_OneR.R | 62
mlr-2.3/mlr/tests/testthat/test_classif_PART.R | 7
mlr-2.3/mlr/tests/testthat/test_classif_ada.R | 10
mlr-2.3/mlr/tests/testthat/test_classif_bartMachine.R | 12
mlr-2.3/mlr/tests/testthat/test_classif_bdk.R |only
mlr-2.3/mlr/tests/testthat/test_classif_binomial.R |only
mlr-2.3/mlr/tests/testthat/test_classif_blackboost.R | 24
mlr-2.3/mlr/tests/testthat/test_classif_boost.R | 20
mlr-2.3/mlr/tests/testthat/test_classif_cforest.R | 18
mlr-2.3/mlr/tests/testthat/test_classif_ctree.R | 12
mlr-2.3/mlr/tests/testthat/test_classif_extraTrees.R |only
mlr-2.3/mlr/tests/testthat/test_classif_fnn.R | 15
mlr-2.3/mlr/tests/testthat/test_classif_gbm.R | 68
mlr-2.3/mlr/tests/testthat/test_classif_geoDA.R | 20
mlr-2.3/mlr/tests/testthat/test_classif_glmboost.R | 56
mlr-2.3/mlr/tests/testthat/test_classif_glmnet.R | 19
mlr-2.3/mlr/tests/testthat/test_classif_kknn.R | 6
mlr-2.3/mlr/tests/testthat/test_classif_knn.R | 14
mlr-2.3/mlr/tests/testthat/test_classif_ksvm.R | 60
mlr-2.3/mlr/tests/testthat/test_classif_lda.R | 6
mlr-2.3/mlr/tests/testthat/test_classif_linDA.R | 20
mlr-2.3/mlr/tests/testthat/test_classif_lqa.R | 14
mlr-2.3/mlr/tests/testthat/test_classif_lssvm.R | 50
mlr-2.3/mlr/tests/testthat/test_classif_mda.R | 72
mlr-2.3/mlr/tests/testthat/test_classif_multinom.R | 54
mlr-2.3/mlr/tests/testthat/test_classif_naiveBayes.R | 10
mlr-2.3/mlr/tests/testthat/test_classif_nnet.R | 8
mlr-2.3/mlr/tests/testthat/test_classif_plr.R | 8
mlr-2.3/mlr/tests/testthat/test_classif_plsdaCaret.R | 4
mlr-2.3/mlr/tests/testthat/test_classif_probit.R |only
mlr-2.3/mlr/tests/testthat/test_classif_qda.R | 15
mlr-2.3/mlr/tests/testthat/test_classif_quaDA.R | 28
mlr-2.3/mlr/tests/testthat/test_classif_randomForest.R | 8
mlr-2.3/mlr/tests/testthat/test_classif_randomForestSRC.R | 10
mlr-2.3/mlr/tests/testthat/test_classif_rda.R | 76
mlr-2.3/mlr/tests/testthat/test_classif_rpart.R | 12
mlr-2.3/mlr/tests/testthat/test_classif_rrlda.R | 10
mlr-2.3/mlr/tests/testthat/test_classif_sda.R | 6
mlr-2.3/mlr/tests/testthat/test_classif_svm.R | 34
mlr-2.3/mlr/tests/testthat/test_classif_xgboost.R |only
mlr-2.3/mlr/tests/testthat/test_classif_xyf.R |only
mlr-2.3/mlr/tests/testthat/test_cluster_EM.R | 36
mlr-2.3/mlr/tests/testthat/test_cluster_FarthestFirst.R | 6
mlr-2.3/mlr/tests/testthat/test_cluster_SimpleKMeans.R | 6
mlr-2.3/mlr/tests/testthat/test_cluster_XMeans.R | 6
mlr-2.3/mlr/tests/testthat/test_cluster_cmeans.R | 10
mlr-2.3/mlr/tests/testthat/test_cluster_kmeans.R | 6
mlr-2.3/mlr/tests/testthat/test_featsel_FilterWrapper.R | 4
mlr-2.3/mlr/tests/testthat/test_featsel_filterFeatures.R | 4
mlr-2.3/mlr/tests/testthat/test_featsel_selectFeatures.R | 77
mlr-2.3/mlr/tests/testthat/test_learners_all.R | 43
mlr-2.3/mlr/tests/testthat/test_learners_classiflabelswitch.R |only
mlr-2.3/mlr/tests/testthat/test_parallel_all.R | 48
mlr-2.3/mlr/tests/testthat/test_regr_IBk.R | 6
mlr-2.3/mlr/tests/testthat/test_regr_bartMachine.R |only
mlr-2.3/mlr/tests/testthat/test_regr_bcart.R |only
mlr-2.3/mlr/tests/testthat/test_regr_bdk.R |only
mlr-2.3/mlr/tests/testthat/test_regr_bgp.R |only
mlr-2.3/mlr/tests/testthat/test_regr_bgpllm.R |only
mlr-2.3/mlr/tests/testthat/test_regr_blackboost.R | 47
mlr-2.3/mlr/tests/testthat/test_regr_blm.R |only
mlr-2.3/mlr/tests/testthat/test_regr_brnn.R |only
mlr-2.3/mlr/tests/testthat/test_regr_btgp.R |only
mlr-2.3/mlr/tests/testthat/test_regr_btgpllm.R |only
mlr-2.3/mlr/tests/testthat/test_regr_btlm.R |only
mlr-2.3/mlr/tests/testthat/test_regr_cforest.R | 14
mlr-2.3/mlr/tests/testthat/test_regr_crs.R | 14
mlr-2.3/mlr/tests/testthat/test_regr_ctree.R | 8
mlr-2.3/mlr/tests/testthat/test_regr_cubist.R |only
mlr-2.3/mlr/tests/testthat/test_regr_earth.R | 40
mlr-2.3/mlr/tests/testthat/test_regr_elmNN.R |only
mlr-2.3/mlr/tests/testthat/test_regr_extraTrees.R |only
mlr-2.3/mlr/tests/testthat/test_regr_fnn.R | 16
mlr-2.3/mlr/tests/testthat/test_regr_gbm.R | 48
mlr-2.3/mlr/tests/testthat/test_regr_glmnet.R | 8
mlr-2.3/mlr/tests/testthat/test_regr_kknn.R | 63
mlr-2.3/mlr/tests/testthat/test_regr_km.R | 10
mlr-2.3/mlr/tests/testthat/test_regr_ksvm.R | 4
mlr-2.3/mlr/tests/testthat/test_regr_laGP.R |only
mlr-2.3/mlr/tests/testthat/test_regr_lm.R | 10
mlr-2.3/mlr/tests/testthat/test_regr_mob.R | 6
mlr-2.3/mlr/tests/testthat/test_regr_penalized_lasso.R | 70
mlr-2.3/mlr/tests/testthat/test_regr_penalized_ridge.R | 66
mlr-2.3/mlr/tests/testthat/test_regr_plsr.R | 36
mlr-2.3/mlr/tests/testthat/test_regr_randomForest.R | 6
mlr-2.3/mlr/tests/testthat/test_regr_randomForestSRC.R | 10
mlr-2.3/mlr/tests/testthat/test_regr_rpart.R | 16
mlr-2.3/mlr/tests/testthat/test_regr_rsm.R | 6
mlr-2.3/mlr/tests/testthat/test_regr_svm.R | 6
mlr-2.3/mlr/tests/testthat/test_regr_xgboost.R |only
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mlr-2.3/mlr/tests/testthat/test_stack.R | 6
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mlr-2.3/mlr/tests/testthat/test_surv_cforest.R | 17
mlr-2.3/mlr/tests/testthat/test_surv_coxph.R | 10
mlr-2.3/mlr/tests/testthat/test_surv_cvglmnet.R | 21
mlr-2.3/mlr/tests/testthat/test_surv_glmboost.R | 20
mlr-2.3/mlr/tests/testthat/test_surv_glmnet.R | 16
mlr-2.3/mlr/tests/testthat/test_surv_penalized.R | 8
mlr-2.3/mlr/tests/testthat/test_surv_randomForestSRC.R | 6
mlr-2.3/mlr/tests/testthat/test_tune_ModelMultiplexer.R | 18
mlr-2.3/mlr/tests/testthat/test_tune_tuneIraceR.R | 9
mlr-2.3/mlr/tests/testthat/test_tune_tuneMBO.R | 3
mlr-2.3/mlr/tests/testthat/test_tune_tuneParamsMultiCrit.R | 2
525 files changed, 4390 insertions(+), 2921 deletions(-)
Title: Linear Predictive Models Based on the LIBLINEAR C/C++ Library
Diff between LiblineaR versions 1.80-10 dated 2014-09-16 and 1.94-2 dated 2015-02-04
Description: A wrapper around the LIBLINEAR C/C++ library for
machine learning (available at http://www.csie.ntu.edu.tw/~cjlin/liblinear).
LIBLINEAR is a simple library for solving large-scale regularized linear
classification and regression. It currently supports L2-regularized
classification (such as logistic regression, L2-loss linear SVM and L1-loss
linear SVM) as well as L1-regularized classification (such as L2-loss linear
SVM and logistic regression) and L2-regularized support vector regression
(with L1- or L2-loss). The main features of LiblineaR include multi-class
classification (one-vs-the rest, and Crammer & Singer method), cross
validation for model selection, probability estimates (logistic regression
only) or weights for unbalanced data. The estimation of the models is
particularly fast as compared to other libraries.
Author: Thibault Helleputte
Maintainer: Thibault Helleputte
LiblineaR-1.80-10/LiblineaR/man/LiblineaR-package.Rd |only
LiblineaR-1.94-2/LiblineaR/DESCRIPTION | 28
LiblineaR-1.94-2/LiblineaR/MD5 | 33
LiblineaR-1.94-2/LiblineaR/NEWS | 28
LiblineaR-1.94-2/LiblineaR/R/LiblineaR.R | 493 +++++++--
LiblineaR-1.94-2/LiblineaR/R/heuristicC.R | 76 +
LiblineaR-1.94-2/LiblineaR/R/predict.R | 132 +-
LiblineaR-1.94-2/LiblineaR/README | 50
LiblineaR-1.94-2/LiblineaR/inst/CITATION | 9
LiblineaR-1.94-2/LiblineaR/man/LiblineaR.Rd | 322 +++---
LiblineaR-1.94-2/LiblineaR/man/heuristicC.Rd | 71 -
LiblineaR-1.94-2/LiblineaR/man/predict.LiblineaR.Rd | 168 +--
LiblineaR-1.94-2/LiblineaR/src/linear.cpp | 960 ++++++++++++++-----
LiblineaR-1.94-2/LiblineaR/src/linear.h | 16
LiblineaR-1.94-2/LiblineaR/src/predictLinear.c | 136 +-
LiblineaR-1.94-2/LiblineaR/src/trainLinear.c | 304 +++---
LiblineaR-1.94-2/LiblineaR/src/tron.cpp | 11
LiblineaR-1.94-2/LiblineaR/tests |only
18 files changed, 1949 insertions(+), 888 deletions(-)
Title: A Genetic Algorithm for Fixed-Size Subset Selection
Diff between kofnGA versions 1.0 dated 2014-09-24 and 1.1 dated 2015-02-04
Description: Function kofnGA uses a genetic algorithm to choose a subset of a
fixed size k from the integers 1:n, such that a user-supplied objective function
is minimized at that subset. The selection step is done by tournament selection
based on ranks, and elitism may be used to retain a portion of the best solutions
from one generation to the next.
Author: Mark A. Wolters
Maintainer: Mark A. Wolters
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
NAMESPACE | 6 +++++-
inst/CITATION | 4 ++--
man/kofnGA-package.Rd | 6 +++---
man/kofnGA.Rd | 4 +++-
6 files changed, 22 insertions(+), 16 deletions(-)
Title: Categorical Bayesian Network Inference
Diff between catnet versions 1.14.5 dated 2014-12-09 and 1.14.8 dated 2015-02-04
Description: Structure learning and parameter estimation of discrete Bayesian networks using likelihood-based criteria. Exhaustive search for fixed node orders and stochastic search of optimal orders via simulated annealing algorithm are implemented.
Author: Nikolay Balov, Peter Salzman
Maintainer: Nikolay Balov
DESCRIPTION | 8 +--
MD5 | 10 ++--
src/catnet_class.h | 122 ++++++++++++++++++++++++++++++---------------------
src/catnet_search2.h | 10 ++--
src/problist.h | 12 ++++-
src/rcatnet.cpp | 7 ++
6 files changed, 105 insertions(+), 64 deletions(-)
Title: Computation of Bayes Factors for Common Designs
Diff between BayesFactor versions 0.9.10 dated 2015-02-01 and 0.9.10-1 dated 2015-02-04
Description: A suite of functions for computing
various Bayes factors for simple designs, including contingency tables,
one- and two-sample designs, one-way designs, general ANOVA designs, and
linear regression.
Author: Richard D. Morey [aut, cre],
Jeffrey N. Rouder [aut],
Tahira Jamil [ctb]
Maintainer: Richard D. Morey
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
NEWS | 5 +++++
R/BayesFactorPCL-package.R | 2 +-
inst/doc/compare_lme4.html | 10 +++++-----
inst/doc/manual.html | 2 +-
inst/doc/priors.html | 2 +-
src/logSummaryStats.cpp | 2 +-
8 files changed, 25 insertions(+), 20 deletions(-)
Title: Traveling Salesperson Problem (TSP)
Diff between TSP versions 1.0-9 dated 2014-07-16 and 1.0-10 dated 2015-02-03
Description: Basic infrastructure and some algorithms for the traveling
salesperson problem (also traveling salesman problem; TSP).
The package provides some simple algorithms and
an interface to Concorde, the currently fastest TSP solver. Concorde
itself is not included in the package and has to be obtained separately.
Author: Michael Hahsler [aut, cre, cph],
Kurt Hornik [aut, cph]
Maintainer: Michael Hahsler
DESCRIPTION | 12 +++++------
MD5 | 44 ++++++++++++++++++++---------------------
R/ATSP.R | 2 -
R/TSP.R | 3 +-
R/cut_tour.R | 1
R/tsp_concorde.R | 26 +++++++++++++-----------
build/vignette.rds |binary
data/USCA312.rda |binary
data/USCA312_map.rda |binary
data/USCA50.rda |binary
inst/NEWS | 5 ++++
inst/doc/TSP.pdf |binary
man/ATSP.Rd | 1
man/Concorde.Rd | 10 +++++----
man/TOUR.Rd | 1
man/TSP.Rd | 1
man/TSPLIB.Rd | 3 +-
man/USCA312.Rd | 1
man/cut_tour.Rd | 1
man/insert_dummy.Rd | 1
man/reformulate_ATSP_as_TSP.Rd | 1
man/solve_TSP.Rd | 1
man/tour_length.Rd | 1
23 files changed, 68 insertions(+), 47 deletions(-)
Title: Quasi Variances for Factor Effects in Statistical Models
Diff between qvcalc versions 0.8-8 dated 2012-06-05 and 0.8-9 dated 2015-02-03
Description: Functions to compute quasi variances and associated measures of approximation error
Author: David Firth
Maintainer: David Firth
qvcalc-0.8-8/qvcalc/INDEX |only
qvcalc-0.8-9/qvcalc/DESCRIPTION | 19 +++++++++----------
qvcalc-0.8-9/qvcalc/MD5 | 11 +++++------
qvcalc-0.8-9/qvcalc/R/qvcalc.R | 8 +++++++-
qvcalc-0.8-9/qvcalc/man/plot.qv.Rd | 5 ++++-
qvcalc-0.8-9/qvcalc/man/qvcalc.Rd | 17 +++++++++--------
qvcalc-0.8-9/qvcalc/man/worstErrors.Rd | 2 +-
7 files changed, 35 insertions(+), 27 deletions(-)
Title: Combination of Factorial Methods and Cluster Analysis
Diff between FactoClass versions 1.1.0 dated 2013-07-18 and 1.1.1 dated 2015-02-03
Description: Multivariate exploration of a data table with factorial
analysis and cluster methods.
Author: Campo Elias Pardo
Maintainer: Campo Elias Pardo
FactoClass-1.1.0/FactoClass/FactoClass-Ex.R |only
FactoClass-1.1.1/FactoClass/DESCRIPTION | 8
FactoClass-1.1.1/FactoClass/MD5 | 17 -
FactoClass-1.1.1/FactoClass/NAMESPACE | 25 +
FactoClass-1.1.1/FactoClass/R/plot.dudi.R | 351 ++++++++++++--------------
FactoClass-1.1.1/FactoClass/R/plotfp.R | 288 ++++++++++-----------
FactoClass-1.1.1/FactoClass/R/stableclus.R | 218 ++++++++--------
FactoClass-1.1.1/FactoClass/man/Bogota.Rd | 30 +-
FactoClass-1.1.1/FactoClass/man/plotfp.Rd | 115 ++++----
FactoClass-1.1.1/FactoClass/man/stableclus.Rd | 112 ++++----
10 files changed, 590 insertions(+), 574 deletions(-)
More information about AncestryMapper at CRAN
Permanent link
Title: R Commander Plug-in for the survival Package
Diff between RcmdrPlugin.survival versions 1.0-4 dated 2013-01-17 and 1.0-5 dated 2015-02-03
More information about RcmdrPlugin.survival at CRAN
Description: This package provides an R Commander plug-in for the survival
package, with dialogs for Cox models, parametric survival regression models,
estimation of survival curves, and testing for differences in survival
curves, along with data-management facilities and a variety of tests,
diagnostics and graphs.
Author: John Fox
Maintainer: John Fox
RcmdrPlugin.survival-1.0-4/RcmdrPlugin.survival/man/anova.coxph.Rd |only
RcmdrPlugin.survival-1.0-4/RcmdrPlugin.survival/man/survQuantiles.Rd |only
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/DESCRIPTION | 20 +-
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/MD5 | 26 +--
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/NAMESPACE | 8 -
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/R/CoxModel.R | 4
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/R/Survdiff.R | 2
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/R/Survfit.R | 6
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/R/misc.R | 12 -
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/R/quantile.survfit.R | 76 +++++-----
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/R/survregModel.R | 4
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/R/unfold.R | 2
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/inst/CHANGES | 6
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/inst/etc/menus.txt | 5
RcmdrPlugin.survival-1.0-5/RcmdrPlugin.survival/man/RcmdrPlugin.survival-package.Rd | 4
15 files changed, 91 insertions(+), 84 deletions(-)
Permanent link
Title: Genetic Analysis of Populations With Mixed Reproduction
Diff between poppr versions 1.1.2 dated 2014-07-29 and 1.1.3 dated 2015-02-03
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the adegenet package.
Author: Zhian N. Kamvar [cre, aut],
Javier F. Tabima [aut],
Niklaus J. Grunwald [ths]
Maintainer: Zhian N. Kamvar
DESCRIPTION | 29 ++-
MD5 | 222 +++++++++++++++--------------
NAMESPACE | 2
NEWS | 19 ++
R/Index_calculations.r | 8 -
R/amova.r | 14 -
R/bruvo.r | 99 +++++++-----
R/data_subset.r | 40 ++++-
R/distances.r | 29 ++-
R/file_handling.r | 5
R/internal.r | 38 +++-
R/methods.r | 3
R/mlg.r | 5
R/poppr.R | 2
R/sandbox.r | 24 +--
R/visualizations.r | 172 ++++++++++++++--------
R/zzz.r | 2
README.md | 16 --
build/vignette.rds |binary
data/Aeut.rda |binary
data/Pinf.rda |binary
data/monpop.rda |binary
data/partial_clone.rda |binary
inst/doc/algo.R | 4
inst/doc/algo.Rnw | 27 +++
inst/doc/algo.pdf |binary
inst/doc/poppr_manual.R | 36 ++--
inst/doc/poppr_manual.Rnw | 48 +++---
inst/doc/poppr_manual.pdf |binary
man/Aeut.Rd | 3
man/Pinf.Rd | 3
man/aboot.Rd | 13 +
man/bootgen-class.Rd | 3
man/bootgen-methods.Rd | 10 -
man/bruvo.boot.Rd | 3
man/bruvo.dist.Rd | 95 ++++++------
man/bruvo.msn.Rd | 3
man/bruvomat-class.Rd | 3
man/bruvomat-methods.Rd | 3
man/clonecorrect.Rd | 3
man/coercion-methods.Rd | 3
man/diss.dist.Rd | 3
man/genclone-class.Rd | 3
man/genclone-method.Rd | 7
man/genetic_distance.Rd | 3
man/genind2genalex.Rd | 3
man/genotype_curve.Rd | 3
man/getfile.Rd | 3
man/greycurve.Rd | 3
man/hierarchy-methods.Rd | 3
man/ia.Rd | 9 -
man/info_table.Rd | 9 -
man/informloci.Rd | 3
man/is.genclone.Rd | 3
man/locus_table.Rd | 3
man/missingno.Rd | 3
man/mlg.Rd | 15 +
man/monpop.Rd | 3
man/partial_clone.Rd | 3
man/plot_poppr_msn.Rd | 127 +++++++++-------
man/poppr-package.Rd | 5
man/poppr.Rd | 3
man/poppr.all.Rd | 3
man/poppr.amova.Rd | 5
man/poppr.msn.Rd | 14 +
man/popsub.Rd | 3
man/population-methods.Rd | 3
man/private_alleles.Rd | 5
man/read.genalex.Rd | 3
man/recode_polyploids.Rd | 5
man/shufflepop.Rd | 3
man/splitcombine.Rd | 7
src/poppr_distance.c | 2
tests/testthat/test-amova.R | 19 ++
tests/testthat/test-colors.R |only
tests/testthat/test-distpop.R | 7
tests/testthat/test-import.R |only
tests/testthat/test-values.R | 30 +++
vignettes/algo-concordance.tex | 2
vignettes/algo.Rnw | 27 +++
vignettes/figure/Aeut_MLG_Ahena-1.pdf |only
vignettes/figure/Aeut_MLG_Ahena.pdf |binary
vignettes/figure/Aeut_MLG_Ahena1.pdf |only
vignettes/figure/Aeut_MLG_Ahena2.pdf |only
vignettes/figure/Aeut_MLG_black-1.pdf |only
vignettes/figure/Aeut_MLG_black.pdf |binary
vignettes/figure/Aeut_MLG_title-1.pdf |only
vignettes/figure/Aeut_MLG_title.pdf |binary
vignettes/figure/bd_histogram-1.pdf |only
vignettes/figure/bd_histogram.pdf |binary
vignettes/figure/bruvo_msn.pdf |binary
vignettes/figure/bruvo_tree.pdf |binary
vignettes/figure/ex_data_picture-1.pdf |only
vignettes/figure/ex_data_picture.pdf |binary
vignettes/figure/ggplotchart.pdf |binary
vignettes/figure/greycurve_normal.pdf |binary
vignettes/figure/greycurve_small_heavy.pdf |binary
vignettes/figure/greywidth_inverse.pdf |binary
vignettes/figure/greywidth_large_heavy.pdf |binary
vignettes/figure/initializing_poppr-1.pdf |only
vignettes/figure/initializing_poppr.pdf |binary
vignettes/figure/mantel.pdf |binary
vignettes/figure/mlgbarplot-1.pdf |only
vignettes/figure/mlgbarplot.pdf |binary
vignettes/figure/mlgrareplot-1.pdf |only
vignettes/figure/mlgrareplot.pdf |binary
vignettes/figure/popcompare_bruvo2.pdf |binary
vignettes/figure/poppr_msn_fig.pdf |binary
vignettes/figure/subnor-1.pdf |only
vignettes/figure/subnor.pdf |binary
vignettes/figure/unnamed-chunk-3-1.pdf |only
vignettes/figure/unnamed-chunk-3.pdf |binary
vignettes/figure/unnamed-chunk-4.pdf |binary
vignettes/figure/unnamed-chunk-5.pdf |binary
vignettes/figure/unnamed-chunk-6.pdf |binary
vignettes/figure/unnamed-chunk-7.pdf |binary
vignettes/figure/unnamed-chunk-8.pdf |only
vignettes/figure/unnamed-chunk-9.pdf |only
vignettes/poppr_manual-concordance.tex | 4
vignettes/poppr_manual.Rnw | 48 +++---
120 files changed, 862 insertions(+), 534 deletions(-)
Title: Confidence Intervals with Poisson Double Sampling
Diff between poisDoubleSamp versions 1.0 dated 2015-02-02 and 1.1 dated 2015-02-03
More information about poisDoubleSamp at CRAN
Description: Functions to create confidence intervals for ratios of Poisson
rates under misclassification using double sampling.
Author: David Kahle [aut, cre],
Phil Young [aut],
Dean Young [aut]
Maintainer: David Kahle
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
src/unNormedMargLogLikeCpp.cpp | 4 ++--
src/unNormedMargLogLikeMaxLogTermCpp.cpp | 8 ++++----
4 files changed, 13 insertions(+), 13 deletions(-)
Permanent link
Title: Tools for Reading and Handling Spatial Objects
Diff between maptools versions 0.8-30 dated 2014-06-05 and 0.8-34 dated 2015-02-03
Description: Set of tools for manipulating and reading geographic data, in particular ESRI shapefiles; C code used from shapelib. It includes binary access to GSHHG shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as PBSmapping, spatstat, maps, RArcInfo, Stata tmap, WinBUGS, Mondrian, and others.
Author: Roger Bivand [cre, aut],
Nicholas Lewin-Koh [aut],
Edzer Pebesma [ctb],
Eric Archer [ctb],
Adrian Baddeley [ctb],
Hans-Jörg Bibiko [ctb],
Steven Brey [ctb],
Jonathan Callahan [ctb],
German Carrillo [ctb],
Stéphane Dray [ctb],
David Forrest [ctb],
Michael Friendly [ctb],
Patrick Giraudoux [ctb],
Duncan Golicher [ctb],
Virgilio Gómez Rubio [ctb],
Patrick Hausmann [ctb],
Karl Ove Hufthammer [ctb],
Thomas Jagger [ctb],
Sebastian Luque [ctb],
Don MacQueen [ctb],
Andrew Niccolai [ctb],
Edzer Pebesma [ctb],
Oscar Perpiñán Lamigueiro [ctb],
Tom Short [ctb],
Greg Snow [ctb],
Ben Stabler [ctb],
Murray Stokely [ctb],
Rolf Turner [ctb]
Maintainer: Roger Bivand
ChangeLog | 872 ++++++++++++++++++++++++++++++++++++++++++
DESCRIPTION | 12
MD5 | 54 +-
R/DP.R | 6
R/Rgshhs.R | 14
R/SP2owin.R | 14
R/checkHoles.R | 36 +
R/nowrapRecenter.R | 26 -
R/point_line_distance.R | 10
R/sp2pbs.R | 26 -
R/sp_spat1.R | 12
R/spatstat1.R | 95 ++--
R/spmaps.R | 16
R/union.R | 16
build/vignette.rds |binary
inst/ChangeLog | 872 ++++++++++++++++++++++++++++++++++++++++++
inst/doc/combine_maptools.pdf |binary
man/GE_SpatialGrid.Rd | 4
man/SpatialLines2PolySet.Rd | 5
man/dotsInPolys.Rd | 3
man/map2SpatialPolygons.Rd | 3
man/readGPS.Rd | 32 -
man/readSplus.Rd | 2
man/sp2WB.Rd | 4
man/sp2tmap.Rd | 2
man/symbolsInPolys.Rd | 3
src/Rgshhs.c | 10
src/shapefil.h | 14
28 files changed, 1983 insertions(+), 180 deletions(-)
Title: Leveraging Learning to Automatically Manage Algorithms
Diff between llama versions 0.8 dated 2015-01-31 and 0.8.1 dated 2015-02-03
Description: Provides functionality to train and evaluate algorithm selection models for portfolios.
Author: Lars Kotthoff [aut,cre],
Bernd Bischl [aut],
Barry Hurley [ctb],
Talal Rahwan [ctb]
Maintainer: Lars Kotthoff
DESCRIPTION | 8 +++----
MD5 | 38 +++++++++++++++++------------------
R/helpers.R | 6 +++++
inst/manual/llama.pdf |binary
man/analysis.Rd | 2 -
man/classify.Rd | 2 -
man/classifyPairs.Rd | 2 -
man/cluster.Rd | 2 -
man/imputeCensored.Rd | 2 -
man/llama-package.Rd | 2 -
man/misc.Rd | 2 -
man/misclassificationPenalties.Rd | 2 -
man/normalize.Rd | 2 -
man/parscores.Rd | 2 -
man/plot.Rd | 2 -
man/regression.Rd | 2 -
man/regressionPairs.Rd | 2 -
man/successes.Rd | 2 -
tests/testthat/helper_mockLearners.R | 6 ++---
tests/testthat/test.satsolvers.R | 14 ++++++------
20 files changed, 53 insertions(+), 47 deletions(-)
More information about RPPairwiseDesign at CRAN
Permanent link
Title: Relative Contribution of Effects in a Regression Model
Diff between relimp versions 1.0-3 dated 2011-10-17 and 1.0-4 dated 2015-02-03
Description: Functions to facilitate inference on the relative importance of predictors in a linear or generalized linear model, and a couple of useful Tcl/Tk widgets.
Author: David Firth with contributions from Heather Turner
Maintainer: David Firth
DESCRIPTION | 17 +--
MD5 | 13 +-
NAMESPACE | 2
R/Tcl-utilities.R |only
R/pickFrom.R | 165 ++++++++++++++++++-----------------
R/relimp.R | 40 ++++----
R/showData.R | 249 +++++++++++++++++++++++++++---------------------------
man/relimp.Rd | 5 -
8 files changed, 250 insertions(+), 241 deletions(-)
Title: R Commander
Diff between Rcmdr versions 2.1-5 dated 2014-12-10 and 2.1-6 dated 2015-02-03
Description:
A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre],
Milan Bouchet-Valat [aut],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ctb],
Kosar Karimi Pour [ctb],
G. Jay Kerns [ctb],
Renaud Lancelot [ctb],
Matthieu Lesnoff [ctb],
Uwe Ligges [ctb],
Samir Messad [ctb],
Martin Maechler [ctb],
Robert Muenchen [ctb],
Duncan Murdoch [ctb],
Erich Neuwirth [ctb],
Dan Putler [ctb],
Brian Ripley [ctb],
Miroslav Ristic [ctb],
Peter Wolf [ctb],
Kevin Wright [ctb]
Maintainer: John Fox
DESCRIPTION | 13
MD5 | 14
NAMESPACE | 10
NEWS | 4
R/model-menu.R | 6
R/utilities.R | 5994 +++++++++++++++++++++++++--------------------------
man/Confint.Rd | 10
man/Rcmdr-package.Rd | 4
8 files changed, 3043 insertions(+), 3012 deletions(-)
Title: Helpers for Parameters in Black-Box Optimization, Tuning and
Machine Learning.
Diff between ParamHelpers versions 1.4 dated 2014-10-10 and 1.5 dated 2015-02-03
Description: Functions for parameter descriptions and operations in black-box optimization, tuning
and machine learning. Parameters can be described (type, constraints, defaults, etc.),
combined to parameter sets and can in general be programmed on.
A useful OptPath object (archive) to log function evaluations is also provided.
Author: Bernd Bischl [aut, cre],
Michel Lang [aut],
Jakob Bossek [aut],
Daniel Horn [aut]
Maintainer: Bernd Bischl
DESCRIPTION | 19 +--
MD5 | 142 +++++++++++++--------------
NAMESPACE | 2
NEWS | 6 -
R/OptPath.R | 7 -
R/OptPath_getter.R | 2
R/OptPath_setter.R | 3
R/ParamSet.R | 8 -
R/aParam.R | 4
R/convertParamSetToIrace.R | 4
R/generateDesign.R | 2
R/getDefaults.R | 21 ++-
R/isMissingValue.R | 3
R/removeMissingValues.R | 4
man/LearnerParam.Rd | 3
man/OptPath.Rd | 5
man/Param.Rd | 3
man/addOptPathEl.Rd | 6 -
man/as.data.frame.OptPathDF.Rd | 3
man/convertParamSetToIrace.Rd | 3
man/dfRowsToList.Rd | 3
man/discreteNameToValue.Rd | 3
man/discreteValueToName.Rd | 3
man/dropParams.Rd | 3
man/extractParamSetFromSooFunction.Rd | 3
man/filterParams.Rd | 3
man/generateDesign.Rd | 3
man/generateGridDesign.Rd | 3
man/generateRandomDesign.Rd | 3
man/getDefaults.Rd | 11 +-
man/getLower.Rd | 3
man/getOptPathBestIndex.Rd | 3
man/getOptPathCol.Rd | 3
man/getOptPathCols.Rd | 3
man/getOptPathDOB.Rd | 3
man/getOptPathEOL.Rd | 3
man/getOptPathEl.Rd | 3
man/getOptPathErrorMessages.Rd | 3
man/getOptPathExecTimes.Rd | 3
man/getOptPathLength.Rd | 3
man/getOptPathParetoFront.Rd | 3
man/getOptPathX.Rd | 3
man/getOptPathY.Rd | 3
man/getParamIds.Rd | 3
man/getParamLengths.Rd | 3
man/getParamNr.Rd | 3
man/getParamTypeCounts.Rd | 3
man/getParamTypes.Rd | 3
man/hasFiniteBoxConstraints.Rd | 3
man/hasForbidden.Rd | 3
man/hasRequires.Rd | 3
man/hasTrafo.Rd | 3
man/hasType.Rd | 3
man/isEmpty.Rd | 3
man/isFeasible.Rd | 3
man/isForbidden.Rd | 3
man/isType.Rd | 3
man/makeParamSet.Rd | 3
man/paramValueToString.Rd | 3
man/removeMissingValues.Rd | 3
man/repairPoint.Rd | 3
man/sampleValue.Rd | 3
man/sampleValues.Rd | 3
man/setOptPathElDOB.Rd | 3
man/setOptPathElEOL.Rd | 3
man/setValueCNames.Rd | 3
man/trafoOptPath.Rd | 3
man/trafoValue.Rd | 3
tests/testthat/test_OptPath.R | 6 -
tests/testthat/test_convertParamSetToIrace.R | 16 ++-
tests/testthat/test_generateDesign.R | 11 +-
tests/testthat/test_getDefaults.R | 15 ++
72 files changed, 278 insertions(+), 172 deletions(-)
Title: Numerical Methods and Optimization in Finance
Diff between NMOF versions 0.34-0 dated 2014-11-05 and 0.34-1 dated 2015-02-03
Description: Functions, examples and data from the book
'Numerical Methods and Optimization in Finance' by M.
Gilli, D. Maringer and E. Schumann. The package provides
implementations of several optimisation heuristics, such as
Differential Evolution, Genetic Algorithms and Threshold
Accepting. There are also functions for the valuation of
financial instruments, such as bonds and options, and
functions that help with stochastic simulations.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann
DESCRIPTION | 8
MD5 | 65 ++---
build/vignette.rds |binary
inst/NMOFex/NMOFman.R | 538 +++++++++++++++++++++++-----------------------
inst/doc/An_overview.R | 14 -
inst/doc/An_overview.Rnw | 3
inst/doc/An_overview.pdf |binary
inst/doc/DEnss.R | 60 ++---
inst/doc/DEnss.Rnw | 5
inst/doc/DEnss.pdf |binary
inst/doc/LSselect.R | 24 +-
inst/doc/LSselect.Rnw | 3
inst/doc/LSselect.pdf |binary
inst/doc/NMOF.bib |only
inst/doc/PSlms.R | 20 -
inst/doc/PSlms.Rnw | 2
inst/doc/PSlms.pdf |binary
inst/doc/TAportfolio.R | 40 +--
inst/doc/TAportfolio.Rnw | 5
inst/doc/TAportfolio.pdf |binary
inst/doc/qTableEx.Rnw | 2
inst/doc/qTableEx.pdf |binary
inst/doc/repair.R | 30 +-
inst/doc/repair.Rnw | 4
inst/doc/repair.pdf |binary
inst/doc/vectorise.pdf |binary
inst/unitTests/report.txt | 26 +-
vignettes/.install_extras |only
vignettes/An_overview.Rnw | 3
vignettes/DEnss.Rnw | 5
vignettes/LSselect.Rnw | 3
vignettes/PSlms.Rnw | 2
vignettes/TAportfolio.Rnw | 5
vignettes/qTableEx.Rnw | 2
vignettes/repair.Rnw | 4
35 files changed, 451 insertions(+), 422 deletions(-)
Title: Nested Association Mapping analysis
Diff between NAM versions 1.0.2.1 dated 2015-01-24 and 1.0.2.2 dated 2015-02-03
Description: Package designed for association studies in nested association mapping (NAM) panels, but it also can handle biparental and random populations. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML.
Author: Alencar Xavier, William Muir, Katy Rainey, Tiago Pimenta, Qishan Wang, Shizhong Xu.
Maintainer: Alencar Xavier
DESCRIPTION | 10 +++++-----
MD5 | 9 +++++----
R/gwas.R | 9 +++++----
R/gwas2.R |only
man/NAM-package.Rd | 6 +++---
man/gwas.Rd | 3 +++
6 files changed, 21 insertions(+), 16 deletions(-)
Title: Miscellaneous Functions from M. Kohl
Diff between MKmisc versions 0.96 dated 2013-11-17 and 0.97 dated 2015-02-03
Description: Miscellaneous Functions from M. Kohl
Author: Matthias Kohl [aut, cre]
Maintainer: Matthias Kohl
DESCRIPTION | 15 ++--
MD5 | 18 ++--
NAMESPACE | 1
NEWS | 9 ++
R/or2rr.R |only
R/quantileCI.R | 11 ++
R/repMeans.R | 182 +++++++++++++++++++++++--------------------------
inst/CITATION | 16 +---
man/0MKmisc-package.Rd | 6 -
man/or2rr.Rd |only
man/quantileCI.Rd | 19 +++--
11 files changed, 146 insertions(+), 131 deletions(-)
Title: Distributions To Be Used For GAMLSS Modelling
Diff between gamlss.dist versions 4.3-1 dated 2014-09-17 and 4.3-4 dated 2015-02-03
Description: This package contains the distributions for GAMLSS
modelling.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
gamlss.dist-4.3-1/gamlss.dist/R/WA1.R |only
gamlss.dist-4.3-1/gamlss.dist/R/WARING.r |only
gamlss.dist-4.3-4/gamlss.dist/DESCRIPTION | 10
gamlss.dist-4.3-4/gamlss.dist/MD5 | 26
gamlss.dist-4.3-4/gamlss.dist/NAMESPACE | 3
gamlss.dist-4.3-4/gamlss.dist/R/BEOI.r | 550 +++++++-------
gamlss.dist-4.3-4/gamlss.dist/R/BEZI.r | 544 ++++++-------
gamlss.dist-4.3-4/gamlss.dist/R/DoublePoisson-30-12-14.R |only
gamlss.dist-4.3-4/gamlss.dist/R/NO.r | 280 +++----
gamlss.dist-4.3-4/gamlss.dist/R/WARING_BOB.r |only
gamlss.dist-4.3-4/gamlss.dist/R/ZAGA.R | 10
gamlss.dist-4.3-4/gamlss.dist/R/make-link-gamlss-4-4-13.R | 344 ++++----
gamlss.dist-4.3-4/gamlss.dist/man/DPO.Rd |only
gamlss.dist-4.3-4/gamlss.dist/man/WARING.Rd | 132 +--
gamlss.dist-4.3-4/gamlss.dist/man/ZAGA.Rd | 227 ++---
gamlss.dist-4.3-4/gamlss.dist/src/dDPOgetC5_C.c |only
gamlss.dist-4.3-4/gamlss.dist/src/tofyHead.h | 2
17 files changed, 1071 insertions(+), 1057 deletions(-)
Title: Tools for Analysis of Diversity and Similarity in Biological
Systems
Diff between divo versions 0.1 dated 2015-01-29 and 0.1.1 dated 2015-02-03
Description: A set of tools for empirical analysis of diversity (a number and frequency of different types in population) and similarity (a number and frequency of shared types in two populations) in biological or ecological systems.
Author: Maciej Pietrzak, Michal Seweryn, Grzegorz Rempala
Maintainer: Maciej Pietrzak
DESCRIPTION | 8 ++---
MD5 | 15 +++++----
R/divo.R | 72 +++++++++++++++++++++++++++++++++-------------
inst/DivO_DP.py | 54 +++++++++++++++++++---------------
inst/DivO_EnvCheck.py |only
inst/DivO_Overlap.py | 13 +++-----
inst/doc/divo-Manual.Rnw | 2 -
inst/doc/divo-Manual.pdf |binary
vignettes/divo-Manual.Rnw | 2 -
9 files changed, 101 insertions(+), 65 deletions(-)
Title: Documentation for Packages distr, distrEx, distrSim, distrTEst,
distrTeach, distrMod, and distrEllipse
Diff between distrDoc versions 2.5 dated 2013-09-13 and 2.5.1 dated 2015-02-03
Description: provides documentation in form of a common vignette to packages distr, distrEx,
distrMod, distrSim, distrTEst, distrTeach, and distrEllipse
Author: Florian Camphausen [ctb] (contributed as student to the documented
packages in the initial phase --2005),
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Thomas Stabla [ctb] (contributed as student to the documented packages
in the initial phase --2005)
Maintainer: Peter Ruckdeschel
DESCRIPTION | 31 ++++++++++++++++++++-----------
MD5 | 15 ++++++++-------
build |only
inst/CITATION | 22 +++++++++++++++++++++-
inst/NEWS | 9 +++++++++
inst/doc/distr.R | 3 ++-
inst/doc/distr.Rnw | 10 ++++++----
inst/doc/distr.pdf |binary
vignettes/distr.Rnw | 10 ++++++----
9 files changed, 72 insertions(+), 28 deletions(-)
Title: Global Value Chains Decomposition (Wang-Wei-Zhu and Leontief)
Diff between decompr versions 2.0 dated 2015-01-27 and 2.1.0 dated 2015-02-03
Description: Two Global Value Chains decompositions are implemented. Firstly,
the Wang-Wei-Zhu (Wang, Wei, and Zhu 2013) algorithm splits bilateral gross
exports into 16 value added components. Secondly, the Leontief decomposition
(default) derives the value added origin of exports by country and
industry, which is also based on Wang, Wei, and Zhu (2013).
Author: Bastiaan Quast [aut, cre],
Fei Wang [aut],
Victor Kummritz [aut]
Maintainer: Bastiaan Quast
DESCRIPTION | 8 +++----
MD5 | 19 +++++++++---------
NAMESPACE | 1
NEWS | 26 +++++++++++++++++-------
R/decomp.R | 10 ++++++++-
R/leontief.R | 51 ++++++++++++++++++++++++++++++++++++++++++++++---
README.md | 26 +++++++-----------------
man/decomp.Rd | 4 +--
man/kung_fu.Rd | 4 +--
man/leontief.Rd | 2 -
man/leontief_output.Rd |only
11 files changed, 103 insertions(+), 48 deletions(-)
Title: GAMLSS Utilities
Diff between gamlss.util versions 4.2-7 dated 2013-07-03 and 4.3-2 dated 2015-02-03
Description: Extra Functions For GAMLSS And Others Models
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
gamlss.util-4.2-7/gamlss.util/R/createLags.R |only
gamlss.util-4.2-7/gamlss.util/R/flexDist.r |only
gamlss.util-4.2-7/gamlss.util/R/movMean.R |only
gamlss.util-4.2-7/gamlss.util/R/penLS.R |only
gamlss.util-4.2-7/gamlss.util/man/Locmean.Rd |only
gamlss.util-4.2-7/gamlss.util/man/flexDist.Rd |only
gamlss.util-4.2-7/gamlss.util/man/penLS.Rd |only
gamlss.util-4.3-2/gamlss.util/DESCRIPTION | 20
gamlss.util-4.3-2/gamlss.util/MD5 | 29 -
gamlss.util-4.3-2/gamlss.util/NAMESPACE | 56 +-
gamlss.util-4.3-2/gamlss.util/R/PenRegQ.R | 28 -
gamlss.util-4.3-2/gamlss.util/R/centiles-ts.R | 289 +++++++-------
gamlss.util-4.3-2/gamlss.util/R/garmaFit.R | 166 +++++---
gamlss.util-4.3-2/gamlss.util/R/plotSimpleGamlss-3-7-13.R | 7
gamlss.util-4.3-2/gamlss.util/R/scattersmooth.r | 257 ++++++------
gamlss.util-4.3-2/gamlss.util/man/garmaFit.Rd | 6
gamlss.util-4.3-2/gamlss.util/man/penReg.Rd | 26 -
gamlss.util-4.3-2/gamlss.util/man/plotSimpleGamlss.Rd | 2
gamlss.util-4.3-2/gamlss.util/man/scattersmooth.Rd | 28 +
19 files changed, 486 insertions(+), 428 deletions(-)
Title: Generating and fitting truncated (gamlss.family) distributions
Diff between gamlss.tr versions 4.2-7 dated 2014-01-18 and 4.3-1 dated 2015-02-03
Description: This is an add on package to GAMLSS. The purpose of this
package is to allow users to defined truncated distributions in
GAMLSS models. The main function gen.trun() generates truncated
version of an existing GAMLSS family distribution.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
NAMESPACE | 4 +++-
man/fitTail.Rd | 3 ++-
4 files changed, 13 insertions(+), 10 deletions(-)
Title: Generalised Additive Models for Location Scale and Shape.
Diff between gamlss versions 4.3-1 dated 2014-09-17 and 4.3-4 dated 2015-02-03
Description: The Library For Fitting GAMLSS Models
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
gamlss-4.3-1/gamlss/R/SUMMARY-15-06-13.R |only
gamlss-4.3-1/gamlss/R/gamlss-01-05-13.R |only
gamlss-4.3-1/gamlss/R/vcoc-gamlss-03-10-13.R |only
gamlss-4.3-4/gamlss/DESCRIPTION | 10
gamlss-4.3-4/gamlss/MD5 | 47 +--
gamlss-4.3-4/gamlss/NAMESPACE | 1
gamlss-4.3-4/gamlss/R/SUMMARY.R |only
gamlss-4.3-4/gamlss/R/cubicSplines-10-08-12.R | 184 +++++------
gamlss-4.3-4/gamlss/R/extra.R | 119 ++++---
gamlss-4.3-4/gamlss/R/gamlss.R |only
gamlss-4.3-4/gamlss/R/lms.R | 6
gamlss-4.3-4/gamlss/R/lo_new.R | 18 -
gamlss-4.3-4/gamlss/R/lpred.R | 332 ++++++++++-----------
gamlss-4.3-4/gamlss/R/pb_03-02-2014.R | 14
gamlss-4.3-4/gamlss/R/pb_new.R |only
gamlss-4.3-4/gamlss/R/predict.gamlss.R | 2
gamlss-4.3-4/gamlss/R/pvc.R | 17 -
gamlss-4.3-4/gamlss/R/qstats-29-12-12.R | 13
gamlss-4.3-4/gamlss/R/quantSheets.R | 19 -
gamlss-4.3-4/gamlss/R/stepGAIC-03-10-13..R | 19 +
gamlss-4.3-4/gamlss/R/term-plot.R | 402 ++++++++++++++++++--------
gamlss-4.3-4/gamlss/R/vcov-gamlss.R |only
gamlss-4.3-4/gamlss/inst/doc/NEWS.txt | 44 ++
gamlss-4.3-4/gamlss/man/Q.stats.Rd | 102 +++---
gamlss-4.3-4/gamlss/man/gamlss.ps.Rd | 4
gamlss-4.3-4/gamlss/man/ps.Rd | 13
gamlss-4.3-4/gamlss/man/summary.gamlss.Rd | 6
gamlss-4.3-4/gamlss/man/term.plot.Rd | 66 ++--
28 files changed, 850 insertions(+), 588 deletions(-)
Title: Miscellaneous Helper Functions for B. Bischl
Diff between BBmisc versions 1.8 dated 2014-10-30 and 1.9 dated 2015-02-03
Description: Miscellaneous helper functions for and from B. Bischl and
some other guys at TU Dortmund, mainly for package development.
Author: Bernd Bischl [aut, cre],
Michel Lang [aut],
Jakob Bossek [aut],
Daniel Horn [aut],
Jakob Richter [aut]
Maintainer: Bernd Bischl
DESCRIPTION | 10 -
MD5 | 215 +++++++++++++++++-----------------
NAMESPACE | 3
NEWS | 35 +++--
R/load2.R | 2
R/mapValues.R |only
R/messagef.R | 10 -
R/normalize.R | 11 +
R/optimizeSubInts.R | 21 ++-
R/pause.R | 2
R/requirePackages.R | 60 ++++++---
R/save2.R | 2
R/setClasses.R | 2
man/addClasses.Rd | 3
man/argsAsNamedList.Rd | 3
man/asMatrixCols.Rd | 3
man/asQuoted.Rd | 3
man/binPack.Rd | 3
man/btwn.Rd | 3
man/cFactor.Rd | 3
man/catf.Rd | 3
man/checkArg.Rd | 3
man/checkListElementClass.Rd | 3
man/chunk.Rd | 3
man/clipString.Rd | 3
man/coalesce.Rd | 3
man/collapse.Rd | 3
man/collapsef.Rd | 3
man/computeMode.Rd | 3
man/convertDataFrameCols.Rd | 3
man/convertInteger.Rd | 3
man/convertIntegers.Rd | 3
man/convertListOfRowsToDataFrame.Rd | 3
man/convertMatrixType.Rd | 3
man/convertRowsToList.Rd | 3
man/convertToShortString.Rd | 3
man/dapply.Rd | 3
man/deprecated.Rd | 3
man/do.call2.Rd | 3
man/dropNamed.Rd | 3
man/ensureVector.Rd | 3
man/explode.Rd | 3
man/extractSubList.Rd | 3
man/filterNull.Rd | 3
man/getAttributeNames.Rd | 3
man/getClass1.Rd | 3
man/getFirst.Rd | 3
man/getMaxIndex.Rd | 3
man/getMaxIndexOfRows.Rd | 3
man/getOperatingSystem.Rd | 3
man/getRelativePath.Rd | 3
man/getUnixTime.Rd | 3
man/getUsedFactorLevels.Rd | 3
man/hasAttributes.Rd | 3
man/insert.Rd | 3
man/is.error.Rd | 3
man/isDirectory.Rd | 3
man/isEmptyDirectory.Rd | 3
man/isExpensiveExampleOk.Rd | 3
man/isFALSE.Rd | 3
man/isProperlyNamed.Rd | 3
man/isScalarNA.Rd | 3
man/isScalarValue.Rd | 3
man/isSubset.Rd | 3
man/isSuperset.Rd | 3
man/isValidName.Rd | 3
man/itostr.Rd | 3
man/lib.Rd | 3
man/load2.Rd | 3
man/lsort.Rd | 3
man/makeDataFrame.Rd | 3
man/makeFileCache.Rd | 3
man/makeProgressBar.Rd | 3
man/makeS3Obj.Rd | 3
man/makeSimpleFileLogger.Rd | 3
man/mapValues.Rd |only
man/messagef.Rd | 8 -
man/namedList.Rd | 3
man/names2.Rd | 3
man/nin.Rd | 3
man/normalize.Rd | 5
man/optimizeSubInts.Rd | 6
man/pause.Rd | 3
man/printStrToChar.Rd | 3
man/printToChar.Rd | 3
man/rangeVal.Rd | 3
man/requirePackages.Rd | 26 ++--
man/rowLapply.Rd | 3
man/save2.Rd | 3
man/seq_row.Rd | 3
man/setAttribute.Rd | 3
man/setClasses.Rd | 3
man/setRowNames.Rd | 3
man/setValue.Rd | 3
man/sortByCol.Rd | 3
man/splitPath.Rd | 3
man/splitTime.Rd | 3
man/stopf.Rd | 3
man/strrepeat.Rd | 3
man/suppressAll.Rd | 3
man/symdiff.Rd | 3
man/system3.Rd | 3
man/toRangeStr.Rd | 3
man/vlapply.Rd | 3
man/warningf.Rd | 3
man/which.first.Rd | 3
tests/testthat/test_mapValues.R |only
tests/testthat/test_normalize.R | 14 ++
tests/testthat/test_optimizeSubInts.R | 6
tests/testthat/test_requirePackages.R | 25 ++-
110 files changed, 447 insertions(+), 280 deletions(-)
Title: Multinomial Processing Tree (MPT) Models
Diff between mpt versions 0.5-0 dated 2014-10-06 and 0.5-1 dated 2015-02-03
Description: Fitting and testing multinomial processing tree models, a class
of statistical models for categorical data. The parameters are the link
probabilities of a tree-like graph and represent the latent cognitive
processing steps executed to arrive at observable response categories
(Batchelder & Riefer, 1999; Erdfelder et al., 2009; Riefer &
Batchelder, 1988).
Author: Florian Wickelmaier [aut, cre],
Achim Zeileis [aut]
Maintainer: Florian Wickelmaier
ChangeLog | 14 +++++++++-----
DESCRIPTION | 8 ++++----
MD5 | 24 +++++++++++++-----------
R/mpt.R | 13 +++++++------
R/mptspec.R | 47 +++++++++++++++++++++++++++++++++++++----------
data/proact.rda |binary
data/prospecMemory.rda |only
data/recogROC.rda |binary
data/retroact.rda |binary
man/mpt.Rd | 5 +++--
man/mptEM.Rd | 18 +++++++++---------
man/mptspec.Rd | 8 ++++++++
man/prospecMemory.Rd |only
man/simulate.mpt.Rd | 2 +-
14 files changed, 91 insertions(+), 48 deletions(-)
Title: Metapopulation and Landscape Simulation
Diff between MetaLandSim versions 0.1 dated 2014-11-09 and 0.2 dated 2015-02-03
Description: Tools to generate random landscape graphs, evaluate species
occurrence in dynamic landscapes, simulate future landscape occupation and
evaluate range expansion when new empty patches are available (e.g. as a
result of climate change).
Author: Frederico Mestre, Fernando Canovas, Ricardo Pita, Antonio Mira, Pedro
Beja.
Maintainer: Frederico Mestre
MetaLandSim-0.1/MetaLandSim/R/manage.simulations.R |only
MetaLandSim-0.1/MetaLandSim/man/manage.simulations.Rd |only
MetaLandSim-0.2/MetaLandSim/DESCRIPTION | 8 -
MetaLandSim-0.2/MetaLandSim/MD5 | 43 +++++-----
MetaLandSim-0.2/MetaLandSim/NAMESPACE | 4
MetaLandSim-0.2/MetaLandSim/R/manage_expansion_sim.R |only
MetaLandSim-0.2/MetaLandSim/R/manage_landscape_sim.R |only
MetaLandSim-0.2/MetaLandSim/build/vignette.rds |binary
MetaLandSim-0.2/MetaLandSim/data/cabrera.rda |binary
MetaLandSim-0.2/MetaLandSim/data/datalist | 1
MetaLandSim-0.2/MetaLandSim/data/landscape_change.rda |binary
MetaLandSim-0.2/MetaLandSim/data/mc_df.rda |binary
MetaLandSim-0.2/MetaLandSim/data/occ.landscape.rda |binary
MetaLandSim-0.2/MetaLandSim/data/occ.landscape2.rda |binary
MetaLandSim-0.2/MetaLandSim/data/param1.rda |binary
MetaLandSim-0.2/MetaLandSim/data/param2.rda |only
MetaLandSim-0.2/MetaLandSim/data/rg_exp.rda |binary
MetaLandSim-0.2/MetaLandSim/data/rland.rda |binary
MetaLandSim-0.2/MetaLandSim/inst/CITATION |only
MetaLandSim-0.2/MetaLandSim/inst/doc/MetaLandSim.pdf |binary
MetaLandSim-0.2/MetaLandSim/inst/doc/landscape_simulation.pdf |binary
MetaLandSim-0.2/MetaLandSim/inst/doc/range_expansion.pdf |binary
MetaLandSim-0.2/MetaLandSim/man/MetaLandSim-package.Rd | 39 +++++++--
MetaLandSim-0.2/MetaLandSim/man/iterate.graph.Rd | 8 -
MetaLandSim-0.2/MetaLandSim/man/manage_expansion_sim.Rd |only
MetaLandSim-0.2/MetaLandSim/man/manage_landscape_sim.Rd |only
MetaLandSim-0.2/MetaLandSim/man/param2.Rd |only
27 files changed, 68 insertions(+), 35 deletions(-)
Title: Fitting an interval response variable using gamlss.family
distributions
Diff between gamlss.cens versions 4.2.7 dated 2014-01-11 and 4.3.1 dated 2015-02-03
Description: This is an add on package to GAMLSS. The purpose of this
package is to allow users to fit interval response variables in
GAMLSS models. The main function gen.cens() generates a
censored version of an existing GAMLSS family distribution.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
NAMESPACE | 42 +++++++++++++++++++++---------------------
data/lip.rda |binary
4 files changed, 29 insertions(+), 29 deletions(-)
Title: GAMLSS Extra Additive terms
Diff between gamlss.add versions 4.3-0 dated 2014-06-03 and 4.3-3 dated 2015-02-03
Description: Extra additive terms for GAMLSS models.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
DESCRIPTION | 13 ++---
MD5 | 16 +++---
NAMESPACE | 13 +++--
R/freeKnots-18-06-13.R | 2
R/gam_gamlss.R | 13 +++--
R/nnet_gamlss.R | 28 +++++++----
R/plotNN.R |only
R/tree_gamlss.R | 23 ++++++---
man/gamlss.ga.Rd | 118 ++++++++++++++++++++++++-------------------------
man/plotNN.Rd |only
10 files changed, 128 insertions(+), 98 deletions(-)
Title: DetMCD Algorithm (Robust and Deterministic Estimation of
Location and Scatter)
Diff between DetMCD versions 0.0.1 dated 2014-10-21 and 0.0.2 dated 2015-02-03
Description: DetMCD is a new algorithm for robust and deterministic estimation of location and scatter. The benefits of robust and deterministic estimation are explained in Hubert, M., Rousseeuw, P.J. and Verdonck, T. (2012),"A deterministic algorithm for robust location and scatter", Journal of Computational and Graphical Statistics, Volume 21, Number 3, Pages 618--637.
Author: Vakili Kaveh [aut, cre],
Mia Hubert [ths]
Maintainer: Vakili Kaveh
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
NAMESPACE | 4 +---
R/DetMCD.R | 3 ++-
4 files changed, 11 insertions(+), 12 deletions(-)
Title: N-Gram Analysis of Biological Sequences
Diff between biogram versions 1.0 dated 2014-12-19 and 1.1 dated 2015-02-03
Description: Tools for extraction and analysis of various
n-grams (sequences of n items) derived from biological sequences (proteins
or nucleic acids). To deal with the dimensionality of the n-gram data,
biogram uses QuiPT (quick permutation test) for fast feature-filtering.
Author: Michal Burdukiewicz [cre, aut],
Piotr Sobczyk [aut],
Chris Lauber [aut]
Maintainer: Michal Burdukiewicz
biogram-1.0/biogram/man/data_sample.Rd |only
biogram-1.0/biogram/man/prepare_data.Rd |only
biogram-1.0/biogram/tests/testthat/test_quit_consistency.R |only
biogram-1.1/biogram/CHANGELOG |only
biogram-1.1/biogram/DESCRIPTION | 7
biogram-1.1/biogram/MD5 | 80 ++++----
biogram-1.1/biogram/NAMESPACE | 10 -
biogram-1.1/biogram/R/biogram.R | 89 +++++----
biogram-1.1/biogram/R/check_criterion.R | 2
biogram-1.1/biogram/R/check_ngrams.R |only
biogram-1.1/biogram/R/count_multigrams.R | 36 ++-
biogram-1.1/biogram/R/count_ngrams.R | 61 ++++--
biogram-1.1/biogram/R/criterion_distribution.R | 32 +--
biogram-1.1/biogram/R/data_manipulation.R | 112 ++++++------
biogram-1.1/biogram/R/decode_ngrams.R |only
biogram-1.1/biogram/R/feature_test_class.R |only
biogram-1.1/biogram/R/information_gain.R | 24 +-
biogram-1.1/biogram/R/ngrams.R | 11 -
biogram-1.1/biogram/R/position_ngrams.R |only
biogram-1.1/biogram/R/test_features.R | 98 +++++++---
biogram-1.1/biogram/R/utilities.R | 1
biogram-1.1/biogram/README.md | 13 +
biogram-1.1/biogram/inst |only
biogram-1.1/biogram/man/biogram-package.Rd | 92 +++++----
biogram-1.1/biogram/man/calc_ig.Rd | 8
biogram-1.1/biogram/man/calc_ig_single.Rd | 5
biogram-1.1/biogram/man/count_multigrams.Rd | 43 ++--
biogram-1.1/biogram/man/count_ngrams.Rd | 61 ++++--
biogram-1.1/biogram/man/create_feature_target.Rd | 3
biogram-1.1/biogram/man/create_ngrams.Rd | 16 +
biogram-1.1/biogram/man/criterion_distribution.Rd | 9
biogram-1.1/biogram/man/criterions.Rd | 3
biogram-1.1/biogram/man/cut.feature_test.Rd |only
biogram-1.1/biogram/man/decode_ngrams.Rd |only
biogram-1.1/biogram/man/degenerate.Rd | 3
biogram-1.1/biogram/man/fast_crosstable.Rd | 3
biogram-1.1/biogram/man/feature_test.Rd |only
biogram-1.1/biogram/man/get_ngrams_ind.Rd | 3
biogram-1.1/biogram/man/human_cleave.Rd | 3
biogram-1.1/biogram/man/is_ngram.Rd |only
biogram-1.1/biogram/man/l2n.Rd | 3
biogram-1.1/biogram/man/n2l.Rd | 3
biogram-1.1/biogram/man/position_ngrams.Rd |only
biogram-1.1/biogram/man/print.feature_test.Rd |only
biogram-1.1/biogram/man/seq2ngrams.Rd | 6
biogram-1.1/biogram/man/summary.feature_test.Rd |only
biogram-1.1/biogram/man/test_features.Rd | 49 +++--
biogram-1.1/biogram/tests/testthat/test_count_ngrams.R | 76 ++++----
biogram-1.1/biogram/tests/testthat/test_position_ngrams.R |only
biogram-1.1/biogram/tests/testthat/test_quipt_consistency.R |only
50 files changed, 580 insertions(+), 385 deletions(-)
Title: Embedded JavaScript Engine
Diff between V8 versions 0.4 dated 2015-01-12 and 0.5 dated 2015-02-03
Description: V8 is Google's open source, high performance JavaScript engine. It
is written in C++ and implements ECMAScript as specified in ECMA-262, 5th
edition. In addition, this package implements typed arrays as specified in
ECMA 6 in order to support high performance computing and libraries compiled
with emscripten.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
DESCRIPTION | 14
MD5 | 37 -
R/RcppExports.R | 12
R/V8.R | 7
configure | 6
inst/doc/npm.R | 2
inst/doc/npm.Rmd | 2
inst/doc/npm.html | 11
inst/doc/v8_intro.R | 22
inst/doc/v8_intro.Rmd | 20
inst/doc/v8_intro.html | 28
inst/js/crossfilter.js |only
inst/js/underscore.js | 1414 -------------------------------------------------
man/new_context.Rd | 5
src/RcppExports.cpp | 48 +
src/V8.cpp | 63 ++
src/v8_typed_array.cpp |only
src/v8_typed_array.h |only
tools/v8-3.14.5.rb | 5
vignettes/npm.Rmd | 2
vignettes/v8_intro.Rmd | 20
21 files changed, 238 insertions(+), 1480 deletions(-)
Title: Seawater Carbonate Chemistry
Diff between seacarb versions 3.0.5 dated 2015-01-12 and 3.0.6 dated 2015-02-03
Description: Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Author: Jean-Pierre Gattuso [aut, cre, cph],
Jean-Marie Epitalon [aut],
Heloise Lavigne [aut],
James Orr [ctb],
Bernard Gentili [ctb],
Andreas Hofmann [ctb],
Aurélien Proye [ctb],
Karline Soetaert [ctb],
James Rae [ctb]
Maintainer: Jean-Pierre Gattuso
ChangeLog | 6 ++-
DESCRIPTION | 8 ++--
MD5 | 26 ++++++-------
R/buffer.R | 19 ++++-----
R/carb.R | 112 ++++++++++++++++++++++++++++++++++++++-------------------
man/Om.Rd | 4 +-
man/buffer.Rd | 2 -
man/buffesm.Rd | 2 -
man/carb.Rd | 16 +++++---
man/oa.Rd | 2 -
man/pCa.Rd | 2 -
man/pTA.Rd | 2 -
man/pgas.Rd | 2 -
man/pmix.Rd | 2 -
14 files changed, 125 insertions(+), 80 deletions(-)
Title: Whole Genome Average Interval Mapping for QTL Detection using
Mixed Models
Diff between wgaim versions 1.4-5 dated 2015-01-31 and 1.4-6 dated 2015-02-03
Description: This package integrates sophisticated mixed modelling methods with a whole genome approach to detecting significant QTL in linkage maps.
Author: Julian Taylor
Maintainer: Julian Taylor
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/wgaim8.R | 9 +++++----
inst/doc/wgaim.pdf |binary
4 files changed, 12 insertions(+), 11 deletions(-)
Title: Simulation and Analysis of Random Fields
Diff between RandomFields versions 3.0.60 dated 2015-01-28 and 3.0.62 dated 2015-02-03
Description: Simulation of Gaussian and extreme value random fields;
conditional simulation; kriging; maximum likelihood estimation
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather
DESCRIPTION | 6
MD5 | 79 +++++-----
NAMESPACE | 8 +
R/Methods-RFsp.R | 18 ++
R/RC_GLOBALS.R | 3
R/RFempvario-Methods-plots.R | 2
R/RFgui.R | 4
R/RMmodels-Methods-plots.R | 11 -
R/RMmodelsSpecial.R | 4
R/convert.R | 21 +-
R/getNset.R | 37 +++++
R/rf-plots.R | 6
man/CoordinateSystems.Rd | 50 +++++-
man/RFgridDataFrame-class.Rd | 6
man/RFpar.Rd |only
man/RFpointsDataFrame-class.Rd | 6
man/RFspatialGridDataFrame-class.Rd | 6
man/RFspatialPointsDataFrame-class.Rd | 6
man/RandomFields.Rd | 1
man/plot-method.Rd | 4
src/Coordinate_systems.cc | 67 ++-------
src/Coordinate_systems.h | 13 -
src/Huetchen.cc | 2
src/InternalCov.cc | 17 +-
src/KeyInfo.cc | 245 ++++++++++++++++------------------
src/Makevars.in | 2
src/Primitive.cc | 97 ++++++++-----
src/RF.h | 150 ++++++++++++--------
src/auxiliary.cc | 2
src/basic.h | 3
src/circulant.cc | 2
src/extremes.cc | 4
src/families.cc | 7
src/getNset.cc | 7
src/initNerror.cc | 16 +-
src/operator.cc | 2
src/plusmalS.cc | 193 +++++++++++++++++++-------
src/primitive.h | 10 -
src/rf_interfaces.cc | 22 +--
src/startGetNset.cc | 16 +-
src/variogramAndCo.cc | 16 +-
41 files changed, 690 insertions(+), 481 deletions(-)
Title: Analyzing RNA Sequence Count Tables Using Quasi-likelihood
Diff between QuasiSeq versions 1.0-5 dated 2015-01-05 and 1.0-6 dated 2015-02-03
Description: Identify differentially expressed genes in RNA-seq count data using quasi-Poisson or quasi-negative binomial models with QL, QLShrink and QLSpline methods (Lund, Nettleton, McCarthy, and Smyth, 2012).
Author: Steve Lund
Maintainer: Steve Lund
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/QL.results.R | 2 +-
3 files changed, 7 insertions(+), 7 deletions(-)
Title: Evaluation of Diversity in Nucleotide Libraries
Diff between peptider versions 0.1.6 dated 2014-12-03 and 0.1.7 dated 2015-02-03
Description: Functions for evaluating diversity in peptide libraries, including
NNN, NNB, NNK/S, and 20/20 schemes. This includes expected coverage,
relative efficiency, and functional diversity of the library.
Author: Heike Hofmann, Eric Hare, ggobi Foundation
Maintainer: Eric Hare
DESCRIPTION | 10 +++----
MD5 | 56 ++++++++++++++++++++++----------------------
NAMESPACE | 2 -
R/peptider.r | 45 +++++++++++++++++++----------------
R/tabulate.r | 8 +++---
data/schemes.rda |binary
man/BLOSUM80.Rd | 3 +-
man/codons.Rd | 3 +-
man/coverage.Rd | 5 ++-
man/detect.Rd | 3 +-
man/diversity.Rd | 3 +-
man/efficiency.Rd | 5 ++-
man/encodingReduce.Rd | 3 +-
man/genNeighbors.Rd | 5 ++-
man/genNeighbors_reduced.Rd | 5 ++-
man/generateCustom.Rd | 5 ++-
man/generateCustomLib.Rd | 5 ++-
man/generateCustomNei.Rd | 5 ++-
man/generateCustomProbs.Rd | 5 ++-
man/getChoices.Rd | 3 +-
man/getCounts.Rd | 3 +-
man/getNeighbors.Rd | 3 +-
man/getNofNeighbors.Rd | 3 +-
man/libBuild.Rd | 3 +-
man/libscheme.Rd | 5 ++-
man/makowski.Rd | 5 ++-
man/ppeptide.Rd | 3 +-
man/scheme.Rd | 3 +-
man/schemes.Rd | 11 ++++----
29 files changed, 123 insertions(+), 95 deletions(-)
Title: Unified interface to Some Popular Parallelization Back-ends for
Interactive Usage and Package Development
Diff between parallelMap versions 1.1 dated 2014-07-03 and 1.2 dated 2015-02-03
Description: Map over lists in parallel. Supports local, multicore, mpi
and BatchJobs mode. Allows "tagging" of the parallel operation
with a level name that can be later selected by the user to
switch on parallel execution for exactly this operation.
Author: Bernd Bischl
Maintainer: Bernd Bischl
parallelMap-1.1/parallelMap/man/parallelShowRegisteredLevels.Rd |only
parallelMap-1.2/parallelMap/DESCRIPTION | 16 -
parallelMap-1.2/parallelMap/MD5 | 71 ++++---
parallelMap-1.2/parallelMap/NAMESPACE | 6
parallelMap-1.2/parallelMap/NEWS | 8
parallelMap-1.2/parallelMap/R/autodetectCpus.R | 20 +-
parallelMap-1.2/parallelMap/R/batchjobs.R | 36 ----
parallelMap-1.2/parallelMap/R/displayErrorMessages.R | 15 -
parallelMap-1.2/parallelMap/R/getExtraPackages.R | 15 -
parallelMap-1.2/parallelMap/R/getOption.R | 4
parallelMap-1.2/parallelMap/R/logging.R | 2
parallelMap-1.2/parallelMap/R/makeMulticoreCluster.R |only
parallelMap-1.2/parallelMap/R/mclapply_fixed.R | 70 ++++---
parallelMap-1.2/parallelMap/R/parallelApply.R | 6
parallelMap-1.2/parallelMap/R/parallelExport.R | 15 -
parallelMap-1.2/parallelMap/R/parallelLibrary.R | 35 ++-
parallelMap-1.2/parallelMap/R/parallelMap.R | 89 ++++------
parallelMap-1.2/parallelMap/R/parallelRegisterLevels.R | 62 +++++-
parallelMap-1.2/parallelMap/R/parallelSource.R | 35 ++-
parallelMap-1.2/parallelMap/R/parallelStart.R | 59 ++++--
parallelMap-1.2/parallelMap/R/parallelStop.R | 13 -
parallelMap-1.2/parallelMap/R/utils.R | 10 -
parallelMap-1.2/parallelMap/R/zzz.R | 5
parallelMap-1.2/parallelMap/man/parallelExport.Rd | 15 -
parallelMap-1.2/parallelMap/man/parallelGetRegisteredLevels.Rd |only
parallelMap-1.2/parallelMap/man/parallelLapply.Rd | 15 -
parallelMap-1.2/parallelMap/man/parallelLibrary.Rd | 5
parallelMap-1.2/parallelMap/man/parallelMap.Rd | 5
parallelMap-1.2/parallelMap/man/parallelRegisterLevels.Rd | 27 ++-
parallelMap-1.2/parallelMap/man/parallelShowOptions.Rd | 3
parallelMap-1.2/parallelMap/man/parallelSource.Rd | 5
parallelMap-1.2/parallelMap/man/parallelStart.Rd | 11 -
parallelMap-1.2/parallelMap/man/parallelStop.Rd | 3
parallelMap-1.2/parallelMap/tests/testthat/helpers.R | 4
parallelMap-1.2/parallelMap/tests/testthat/test_autodetectCpus.R |only
parallelMap-1.2/parallelMap/tests/testthat/test_batchjobs.R | 20 --
parallelMap-1.2/parallelMap/tests/testthat/test_multicore.R | 2
parallelMap-1.2/parallelMap/tests/testthat/test_registerLevels.R | 32 ++-
parallelMap-1.2/parallelMap/tests/testthat/test_stopWithJobErrorMessages.R |only
39 files changed, 403 insertions(+), 336 deletions(-)
Title: Matrix eQTL: Ultra fast eQTL analysis via large matrix
operations
Diff between MatrixEQTL versions 2.1.0 dated 2014-02-25 and 2.1.1 dated 2015-02-03
Description: Matrix eQTL is designed for fast eQTL analysis on large datasets.
Matrix eQTL can test for association between genotype and gene expression using linear regression
with either additive or ANOVA genotype effects.
The models can include covariates to account for factors
as population stratification, gender, and clinical variables.
It also supports models with heteroscedastic and/or correlated errors,
false discovery rate estimation and separate treatment of local (cis) and distant (trans) eQTLs.
Author: Andrey Shabalin
Maintainer: Andrey Shabalin
MatrixEQTL-2.1.0/MatrixEQTL/demo/a.nocvrt.R |only
MatrixEQTL-2.1.0/MatrixEQTL/demo/b.cvrt.R |only
MatrixEQTL-2.1.0/MatrixEQTL/demo/c.weights.R |only
MatrixEQTL-2.1.0/MatrixEQTL/demo/d.ANOVA.R |only
MatrixEQTL-2.1.0/MatrixEQTL/demo/d.ANOVA5.R |only
MatrixEQTL-2.1.0/MatrixEQTL/demo/e.interaction.R |only
MatrixEQTL-2.1.1/MatrixEQTL/DESCRIPTION | 9
MatrixEQTL-2.1.1/MatrixEQTL/MD5 | 38 ++-
MatrixEQTL-2.1.1/MatrixEQTL/R/Matrix_eQTL_engine.R | 170 +++++++----------
MatrixEQTL-2.1.1/MatrixEQTL/demo/00Index | 6
MatrixEQTL-2.1.1/MatrixEQTL/demo/a.nocvrt.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/b.cvrt.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/c.weights.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/d.ANOVA.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/d.ANOVA5.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/e.interaction.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/p.hist.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/q.qqplot.r |only
MatrixEQTL-2.1.1/MatrixEQTL/demo/sample.cis.r | 6
MatrixEQTL-2.1.1/MatrixEQTL/inst/CITATION | 2
MatrixEQTL-2.1.1/MatrixEQTL/man/MatrixEQTL-package.Rd | 2
MatrixEQTL-2.1.1/MatrixEQTL/man/MatrixEQTL_cis_code.Rd | 4
MatrixEQTL-2.1.1/MatrixEQTL/man/Matrix_eQTL_main.Rd | 2
MatrixEQTL-2.1.1/MatrixEQTL/man/modelANOVA.Rd | 15 +
MatrixEQTL-2.1.1/MatrixEQTL/man/modelLINEAR.Rd | 6
MatrixEQTL-2.1.1/MatrixEQTL/man/modelLINEAR_CROSS.Rd | 5
MatrixEQTL-2.1.1/MatrixEQTL/man/plot.MatrixEQTL.Rd | 5
27 files changed, 131 insertions(+), 139 deletions(-)
Title: Functions to Create and Manipulate Discrete Random Variables
Diff between discreteRV versions 1.1.3 dated 2014-12-03 and 1.1.4 dated 2015-02-03
Description: discreteRV implements a set of functions that allow computations
involving discrete random variables. It uses a syntax which is familiar to
that which is used in mathematical statistics and probability courses.
Author: Andreas Buja
Maintainer: Eric Hare
DESCRIPTION | 12 ++++----
MD5 | 60 +++++++++++++++++++++----------------------
NAMESPACE | 3 +-
R/discreteRV-Probabilities.r | 31 ++++++++++++----------
man/Conditional.Rd | 3 +-
man/E.Rd | 3 +-
man/KURT.Rd | 3 +-
man/P.Rd | 3 +-
man/Prop.Rd | 3 +-
man/SD.Rd | 3 +-
man/SKEW.Rd | 3 +-
man/SofI.Rd | 3 +-
man/SofIID.Rd | 3 +-
man/V.Rd | 3 +-
man/as.RV.Rd | 3 +-
man/grapes-AND-grapes.Rd | 3 +-
man/grapes-OR-grapes.Rd | 3 +-
man/grapes-in-grapes.Rd | 3 +-
man/make.RV.Rd | 17 +++++++-----
man/margins.Rd | 3 +-
man/mult.Rd | 3 +-
man/multN.Rd | 3 +-
man/outcomes.Rd | 3 +-
man/plot.RV.Rd | 3 +-
man/plot.RVsim.Rd | 3 +-
man/print.RV.Rd | 3 +-
man/probs.Rd | 3 +-
man/props.Rd | 3 +-
man/qqnorm.RV.Rd | 3 +-
man/rsim.Rd | 3 +-
man/skewSim.Rd | 3 +-
31 files changed, 117 insertions(+), 84 deletions(-)
Title: Cross-Entropy Clustering
Diff between CEC versions 0.9.2 dated 2014-11-15 and 0.9.3 dated 2015-02-03
Description: Cross-Entropy Clustering (CEC) divides the data into Gaussian type clusters. It performs the automatic reduction of unnecessary clusters, while at the same time allows the simultaneous use of various type Gaussian mixture models.
Author: Konrad Kamieniecki [aut, cre], Przemyslaw Spurek [ctb]
Maintainer: Konrad Kamieniecki
CEC-0.9.2/CEC/R/initcenters.R |only
CEC-0.9.2/CEC/README.md |only
CEC-0.9.2/CEC/man/initcenters.Rd |only
CEC-0.9.3/CEC/DESCRIPTION | 8
CEC-0.9.3/CEC/MD5 | 31
CEC-0.9.3/CEC/NAMESPACE | 2
CEC-0.9.3/CEC/R/cec.R | 82
CEC-0.9.3/CEC/R/cec.plot.cost.function.R |only
CEC-0.9.3/CEC/R/init.centers.R |only
CEC-0.9.3/CEC/R/model.covariance.R |only
CEC-0.9.3/CEC/data/fourGaussians.rda |only
CEC-0.9.3/CEC/data/mixShapes.rda |only
CEC-0.9.3/CEC/inst/cec_tests/cec1.dp | 2481 --
CEC-0.9.3/CEC/inst/cec_tests/clustering.test.R | 9
CEC-0.9.3/CEC/inst/cec_tests/energy.calculation.test.mouseset3d.R | 22
CEC-0.9.3/CEC/inst/cec_tests/mouse3d.data |11330 +++-------
CEC-0.9.3/CEC/man/cec.Rd | 38
CEC-0.9.3/CEC/man/fourGaussians.Rd |only
CEC-0.9.3/CEC/man/init.centers.Rd |only
CEC-0.9.3/CEC/man/mixShapes.Rd |only
CEC-0.9.3/CEC/src/Makevars | 2
CEC-0.9.3/CEC/src/cec.c | 13
22 files changed, 4765 insertions(+), 9253 deletions(-)
More information about poisDoubleSamp at CRAN
Permanent link
Title: Compute the Personalized Activity Index Based on a Negative
Binomial Model
Diff between lmeNB versions 1.2 dated 2014-01-24 and 1.3 dated 2015-02-02
Description: The functions in this package implement the safety monitoring procedures proposed in the paper titled "Detection of unusual increases in MRI lesion counts in individual multiple sclerosis patients" by Zhao, Y., Li, D.K.B., Petkau, A.J., Riddehough, A., Traboulsee, A., published in Journal of the American Statistical Association in 2013. The procedure first models longitudinally collected count variables with a negative binomial mixed-effect regression model. To account for the correlation among repeated measures from the same patient, the model has subject-specific random intercept, which can be modelled with a gamma or log-normal distributions. One can also choose the semi-parametric option which does not assume any distribution for the random effect. These mixed-effect models could be useful beyond the application of the safety monitoring. The maximum likelihood methods are used to estimate the unknown fixed effect parameters of the model. Based on the fitted model, the personalized activity index is computed for each patient. Lastly, this package is companion to R package lmeNBBayes, which contains the functions to compute the Personalized Activity Index in Bayesian framework.
Author: Yinshan Zhao and Yumi Kondo (with contributions from Steven G. Johnson, Rudolf Schuerer and Brian Gough on the integration subroutines)
Maintainer: Yumi Kondo
lmeNB-1.2/lmeNB/man/mle_a3_fun.Rd |only
lmeNB-1.2/lmeNB/man/mle_ar1_fun.Rd |only
lmeNB-1.2/lmeNB/man/mle_ar1_non3.Rd |only
lmeNB-1.2/lmeNB/man/mle_fun.Rd |only
lmeNB-1.3/lmeNB/DESCRIPTION | 29
lmeNB-1.3/lmeNB/MD5 | 36 -
lmeNB-1.3/lmeNB/NAMESPACE | 13
lmeNB-1.3/lmeNB/R/AR1models.R | 1016 ++++------------------------
lmeNB-1.3/lmeNB/R/CPI.R | 794 ++++++++--------------
lmeNB-1.3/lmeNB/R/INDmodels.R | 1269 +++++++++++++++++++++++-------------
lmeNB-1.3/lmeNB/R/Simulation.R | 20
lmeNB-1.3/lmeNB/R/oldCode.R |only
lmeNB-1.3/lmeNB/man/CP_se.Rd | 101 +-
lmeNB-1.3/lmeNB/man/RElmeNB.Rd |only
lmeNB-1.3/lmeNB/man/fitParaAR1.Rd |only
lmeNB-1.3/lmeNB/man/fitParaIND.Rd |only
lmeNB-1.3/lmeNB/man/fitSemiAR1.Rd |only
lmeNB-1.3/lmeNB/man/fitSemiIND.Rd |only
lmeNB-1.3/lmeNB/man/index_batch.Rd | 163 +++-
lmeNB-1.3/lmeNB/man/jCP_ar1.Rd | 111 +--
lmeNB-1.3/lmeNB/man/lmeNB.Rd | 474 +++++++++----
lmeNB-1.3/lmeNB/man/rNBME_R.Rd | 107 ---
lmeNB-1.3/lmeNB/src |only
23 files changed, 1882 insertions(+), 2251 deletions(-)
Title: Excursion Sets and Contour Credibility Regions for Random Fields
Diff between excursions versions 1.1-20140610 dated 2014-06-11 and 2.0.6 dated 2015-02-02
Description: Functions that compute probabilistic excursion sets, contour credibility regions, contour avoiding regions, and simultaneous confidence bands for latent gaussian random processes and fields. The package also contains functions that calculate these quantities for models estimated with the INLA package.
Author: David Bolin
Maintainer: David Bolin
excursions-1.1-20140610/excursions/R/excursions.int.R |only
excursions-1.1-20140610/excursions/R/excursions.simconf.R |only
excursions-1.1-20140610/excursions/inst/doc/copying/AMD.txt |only
excursions-1.1-20140610/excursions/inst/doc/copying/CHOLMOD.txt |only
excursions-1.1-20140610/excursions/inst/doc/copying/COLAMD.txt |only
excursions-1.1-20140610/excursions/man/excursions.int.Rd |only
excursions-1.1-20140610/excursions/man/excursions.simconf.Rd |only
excursions-1.1-20140610/excursions/src/AMD |only
excursions-1.1-20140610/excursions/src/CHOLMOD |only
excursions-1.1-20140610/excursions/src/COLAMD |only
excursions-1.1-20140610/excursions/src/Makefile |only
excursions-1.1-20140610/excursions/src/Makefile.win |only
excursions-1.1-20140610/excursions/src/excursions.cpp |only
excursions-1.1-20140610/excursions/src/gaussint.cpp |only
excursions-1.1-20140610/excursions/src/install.libs.R |only
excursions-1.1-20140610/excursions/src/utils.cpp |only
excursions-1.1-20140610/excursions/src/utils.h |only
excursions-1.1-20140610/excursions/src/xerbla.c |only
excursions-2.0.6/excursions/DESCRIPTION | 30
excursions-2.0.6/excursions/MD5 | 194 ----
excursions-2.0.6/excursions/NAMESPACE | 22
excursions-2.0.6/excursions/R/contourmap.R |only
excursions-2.0.6/excursions/R/contourmap.inla.R |only
excursions-2.0.6/excursions/R/contourutil.R |only
excursions-2.0.6/excursions/R/excursions.R | 406 +++-----
excursions-2.0.6/excursions/R/excursions.inla.R | 446 +++++----
excursions-2.0.6/excursions/R/gaussint.R |only
excursions-2.0.6/excursions/R/geometry.R |only
excursions-2.0.6/excursions/R/inlautils.R |only
excursions-2.0.6/excursions/R/simconf.R |only
excursions-2.0.6/excursions/R/simconf.inla.R |only
excursions-2.0.6/excursions/R/simconf.mixture.R |only
excursions-2.0.6/excursions/R/utils.R | 374 ++++++-
excursions-2.0.6/excursions/README.md |only
excursions-2.0.6/excursions/inst/CITATION |only
excursions-2.0.6/excursions/inst/COPYRIGHTS | 18
excursions-2.0.6/excursions/man/continuous.Rd |only
excursions-2.0.6/excursions/man/contourmap.Rd |only
excursions-2.0.6/excursions/man/contourmap.colors.Rd |only
excursions-2.0.6/excursions/man/contourmap.inla.Rd |only
excursions-2.0.6/excursions/man/excursions.Rd | 72 -
excursions-2.0.6/excursions/man/excursions.inla.Rd | 105 +-
excursions-2.0.6/excursions/man/excursions.variances.Rd |only
excursions-2.0.6/excursions/man/gaussint.Rd |only
excursions-2.0.6/excursions/man/simconf.Rd |only
excursions-2.0.6/excursions/man/simconf.inla.Rd |only
excursions-2.0.6/excursions/man/simconf.mixture.Rd |only
excursions-2.0.6/excursions/man/tricontour.Rd |only
excursions-2.0.6/excursions/man/tricontourmap.Rd |only
excursions-2.0.6/excursions/src/Makevars |only
excursions-2.0.6/excursions/src/RngStream.c | 120 +-
excursions-2.0.6/excursions/src/RngStream.h | 6
excursions-2.0.6/excursions/src/integration.cpp | 481 +++++-----
excursions-2.0.6/excursions/src/qinv.cpp |only
excursions-2.0.6/excursions/src/reordering.cpp |only
excursions-2.0.6/excursions/tests |only
56 files changed, 1264 insertions(+), 1010 deletions(-)
Title: Sample Size Estimation Functions for Cluster Randomized Trials
Diff between CRTSize versions 0.3 dated 2013-12-18 and 0.4 dated 2015-02-02
Description: This package contains basic tools for the purpose of sample size estimation in cluster (group) randomized trials. The package contains traditional power-based methods, empirical smoothing (Rotondi and Donner, 2009), and updated meta-analysis techniques (Rotondi and Donner, 2012).
Author: Michael A Rotondi
Maintainer: Michael A Rotondi
DESCRIPTION | 8
MD5 | 12
NAMESPACE | 22 +
R/n4incidence.R | 6
R/n4means.R | 4
R/n4meansMeta.R | 754 ++++++++++++++++++++++++++++----------------------------
R/n4props.R | 4
7 files changed, 415 insertions(+), 395 deletions(-)
Title: Simulation of Event Histories for Multi-state Models
Diff between simMSM versions 1.1.2 dated 2015-01-12 and 1.1.4 dated 2015-02-02
Description: Simulation of event histories with possibly non-linear baseline hazard rate functions, non-linear (time-varying) covariate effect functions, and dependencies on the past of the history. Random generation of event histories is performed using inversion sampling on the cumulative all-cause hazard rate functions.
Author: Holger Reulen
Maintainer: Holger Reulen
simMSM-1.1.2/simMSM/man/allcausehr.Rd |only
simMSM-1.1.2/simMSM/man/cumallcausehr.Rd |only
simMSM-1.1.2/simMSM/man/hr.Rd |only
simMSM-1.1.2/simMSM/man/meancentering.Rd |only
simMSM-1.1.2/simMSM/man/simCR.Rd |only
simMSM-1.1.2/simMSM/man/simEBMT.Rd |only
simMSM-1.1.2/simMSM/man/simMSM-package.Rd |only
simMSM-1.1.2/simMSM/man/simexit.Rd |only
simMSM-1.1.2/simMSM/man/simexitinner.Rd |only
simMSM-1.1.2/simMSM/man/simsinglehistory.Rd |only
simMSM-1.1.2/simMSM/man/simto.Rd |only
simMSM-1.1.2/simMSM/man/unirootf.Rd |only
simMSM-1.1.4/simMSM/DESCRIPTION | 11 +-
simMSM-1.1.4/simMSM/MD5 | 51 ++++-----
simMSM-1.1.4/simMSM/NAMESPACE | 10 +
simMSM-1.1.4/simMSM/R/TraFromMpl.R |only
simMSM-1.1.4/simMSM/R/allcausehr.R | 5
simMSM-1.1.4/simMSM/R/cumallcausehr.R | 4
simMSM-1.1.4/simMSM/R/mplskeleton.R |only
simMSM-1.1.4/simMSM/R/plotbe.R |only
simMSM-1.1.4/simMSM/R/plotcph.R |only
simMSM-1.1.4/simMSM/R/plotnae.R |only
simMSM-1.1.4/simMSM/R/pmeskeleton.R |only
simMSM-1.1.4/simMSM/R/simCR.R | 4
simMSM-1.1.4/simMSM/R/simEBMT.R | 3
simMSM-1.1.4/simMSM/R/simeventhistories.R | 123 ++++++++++++++++++++---
simMSM-1.1.4/simMSM/R/simexit.R | 21 +--
simMSM-1.1.4/simMSM/R/simexitinner.R | 19 ---
simMSM-1.1.4/simMSM/R/simsinglehistory.R | 58 +++++++++-
simMSM-1.1.4/simMSM/R/simto.R | 10 -
simMSM-1.1.4/simMSM/R/tolongformat.R |only
simMSM-1.1.4/simMSM/R/unirootf.R | 4
simMSM-1.1.4/simMSM/man/mplskeleton.Rd |only
simMSM-1.1.4/simMSM/man/plotbe.Rd |only
simMSM-1.1.4/simMSM/man/plotcph.Rd |only
simMSM-1.1.4/simMSM/man/plotnae.Rd |only
simMSM-1.1.4/simMSM/man/pmeskeleton.Rd |only
simMSM-1.1.4/simMSM/man/simeventhistories.Rd | 144 ++++++++++++++++++---------
simMSM-1.1.4/simMSM/man/tolongformat.Rd |only
39 files changed, 323 insertions(+), 144 deletions(-)
Title: Data Structures and Algorithms for Relations
Diff between relations versions 0.6-3 dated 2014-04-02 and 0.6-4 dated 2015-02-02
Description: Data structures and algorithms for k-ary relations with
arbitrary domains, featuring relational algebra, predicate functions,
and fitters for consensus relations.
Author: David Meyer [aut],
Kurt Hornik [aut, cre],
Christian Buchta [ctb]
Maintainer: Kurt Hornik
DESCRIPTION | 6 ++--
MD5 | 28 ++++++++++-----------
build/vignette.rds |binary
data/Cetacea.rda |binary
data/Felines.rda |binary
data/SVM_Benchmarking_Classification.rda |binary
data/SVM_Benchmarking_Classification_Consensus.rda |binary
data/SVM_Benchmarking_Regression.rda |binary
data/SVM_Benchmarking_Regression_Consensus.rda |binary
inst/doc/relations.R | 1
inst/doc/relations.Rnw | 2 -
inst/doc/relations.pdf |binary
man/Felines.Rd | 2 -
man/algebra.Rd | 2 -
vignettes/relations.Rnw | 2 -
15 files changed, 22 insertions(+), 21 deletions(-)
Title: Cluster ensembles
Diff between clue versions 0.3-48 dated 2014-04-02 and 0.3-49 dated 2015-02-02
Description: CLUster Ensembles
Author: Kurt Hornik [aut, cre],
Walter Böhm [ctb]
Maintainer: Kurt Hornik
DESCRIPTION | 6 +++---
MD5 | 32 ++++++++++++++++----------------
build/vignette.rds |binary
data/CKME.rda |binary
data/Cassini.rda |binary
data/GVME.rda |binary
data/GVME_Consensus.rda |binary
data/Kinship82.rda |binary
data/Kinship82_Consensus.rda |binary
data/Phonemes.rda |binary
inst/doc/clue.R | 1 +
inst/doc/clue.Rnw | 4 ++--
inst/doc/clue.pdf |binary
man/cl_bag.Rd | 2 +-
man/cl_dissimilarity.Rd | 7 +++----
vignettes/clue.Rnw | 4 ++--
vignettes/cluster.bib | 14 +++++++++++++-
17 files changed, 41 insertions(+), 29 deletions(-)
Title: Toolkit for Weighting and Analysis of Nonequivalent Groups
Diff between twang versions 1.4-0 dated 2014-03-18 and 1.4-9.3 dated 2015-02-02
Description: This package offers functions for propensity score
estimating and weighting, nonresponse weighting, and diagnosis
of the weights. This package was originally developed by Drs.
Ridgeway, McCaffrey, and Morral. Burgette, Griffin and
McCaffrey updated the package during 2011-2015.
Author: Greg Ridgeway, Dan McCaffrey, Andrew Morral, Beth Ann, Lane Burgette
Maintainer: Lane Burgette
twang-1.4-0/twang/R/ksStatTrueMN.R |only
twang-1.4-0/twang/R/plot.mnps.old.R |only
twang-1.4-9.3/twang/DESCRIPTION | 16
twang-1.4-9.3/twang/MD5 | 73
twang-1.4-9.3/twang/NAMESPACE | 2
twang-1.4-9.3/twang/R/bal.stat.R | 6
twang-1.4-9.3/twang/R/bal.table.R | 102
twang-1.4-9.3/twang/R/boxplot.mnps.R | 41
twang-1.4-9.3/twang/R/desc.wts.R | 4
twang-1.4-9.3/twang/R/diag.plot.color.R | 2
twang-1.4-9.3/twang/R/displayPlots.R |only
twang-1.4-9.3/twang/R/makeWeightsMNPS.R | 2
twang-1.4-9.3/twang/R/mnps2.R | 19
twang-1.4-9.3/twang/R/pairwiseComparison.R | 6
twang-1.4-9.3/twang/R/plot.mnps.2.R |only
twang-1.4-9.3/twang/R/plot.mnps.R | 384 ++-
twang-1.4-9.3/twang/R/plotTruePairs.R |only
twang-1.4-9.3/twang/R/print.summary.mnps.R | 28
twang-1.4-9.3/twang/R/ps.summary.new2.R | 6
twang-1.4-9.3/twang/R/summary.mnps.R | 54
twang-1.4-9.3/twang/R/summary.ps.R | 31
twang-1.4-9.3/twang/build/vignette.rds |binary
twang-1.4-9.3/twang/data/AOD.RData |binary
twang-1.4-9.3/twang/data/egsingle.RData |binary
twang-1.4-9.3/twang/data/lalonde.RData |binary
twang-1.4-9.3/twang/data/lindner.RData |binary
twang-1.4-9.3/twang/data/raceprofiling.RData |binary
twang-1.4-9.3/twang/inst/doc/mnps.R | 157 -
twang-1.4-9.3/twang/inst/doc/mnps.pdf |binary
twang-1.4-9.3/twang/inst/doc/mnps.rnw | 434 ++-
twang-1.4-9.3/twang/inst/doc/twang.R | 189 -
twang-1.4-9.3/twang/inst/doc/twang.pdf |binary
twang-1.4-9.3/twang/inst/doc/twang.rnw | 3418 +++++++++++++--------------
twang-1.4-9.3/twang/man/bal.stat.Rd | 5
twang-1.4-9.3/twang/man/bal.table.Rd | 14
twang-1.4-9.3/twang/man/boxplot.mnps.Rd | 7
twang-1.4-9.3/twang/man/desc.wts.Rd | 7
twang-1.4-9.3/twang/man/plot.mnps.Rd | 25
twang-1.4-9.3/twang/vignettes/mnps.rnw | 434 ++-
twang-1.4-9.3/twang/vignettes/twang.rnw | 3418 +++++++++++++--------------
40 files changed, 4874 insertions(+), 4010 deletions(-)
Title: Data Visualization for Statistics in Social Science
Diff between sjPlot versions 1.6.5 dated 2014-12-15 and 1.6.8 dated 2015-02-02
Description: Collection of several plotting and table output functions for
visualizing data, and utility functions.
Author: Daniel Lüdecke
Maintainer: Daniel Lüdecke
sjPlot-1.6.5/sjPlot/man/sjp.glm.ma.Rd |only
sjPlot-1.6.5/sjPlot/man/sjp.lm.ma.Rd |only
sjPlot-1.6.5/sjPlot/man/sjp.lm1.Rd |only
sjPlot-1.6.5/sjPlot/man/sjp.reglin.Rd |only
sjPlot-1.6.5/sjPlot/man/sjp.vif.Rd |only
sjPlot-1.6.8/sjPlot/DESCRIPTION | 10
sjPlot-1.6.8/sjPlot/MD5 | 189 -
sjPlot-1.6.8/sjPlot/NAMESPACE | 189 -
sjPlot-1.6.8/sjPlot/NEWS | 24
sjPlot-1.6.8/sjPlot/R/helpfunctions.R | 957 ++++----
sjPlot-1.6.8/sjPlot/R/sjImportSPSS.R | 802 +++----
sjPlot-1.6.8/sjPlot/R/sjPlotAncovaLSMeans.R | 714 +++---
sjPlot-1.6.8/sjPlot/R/sjPlotCorr.R | 697 +++---
sjPlot-1.6.8/sjPlot/R/sjPlotGLME.R | 292 ++
sjPlot-1.6.8/sjPlot/R/sjPlotGroupFrequencies.R | 2487 +++++++++++------------
sjPlot-1.6.8/sjPlot/R/sjPlotInteractions.R | 6
sjPlot-1.6.8/sjPlot/R/sjPlotLikert.R | 4
sjPlot-1.6.8/sjPlot/R/sjPlotLinreg.R | 535 ++--
sjPlot-1.6.8/sjPlot/R/sjPlotLinregMultiple.R | 831 +++----
sjPlot-1.6.8/sjPlot/R/sjPlotOdds.R | 1570 +++++++-------
sjPlot-1.6.8/sjPlot/R/sjPlotOddsMultiple.R | 1
sjPlot-1.6.8/sjPlot/R/sjPlotScatter.R | 2
sjPlot-1.6.8/sjPlot/R/sjPlotSetTheme.R | 7
sjPlot-1.6.8/sjPlot/R/sjRecode.R | 21
sjPlot-1.6.8/sjPlot/R/sjStatistics.R | 70
sjPlot-1.6.8/sjPlot/R/sjTabCorr.R | 5
sjPlot-1.6.8/sjPlot/R/sjTabFrequencies.R | 1287 ++++++-----
sjPlot-1.6.8/sjPlot/R/sjTabGrpmean.R | 6
sjPlot-1.6.8/sjPlot/R/sjTabLinReg.R | 75
sjPlot-1.6.8/sjPlot/R/sjTabOdds.R | 20
sjPlot-1.6.8/sjPlot/R/sjTabPropTable.R | 1642 +++++++--------
sjPlot-1.6.8/sjPlot/README.md | 39
sjPlot-1.6.8/sjPlot/man/efc.Rd | 92
sjPlot-1.6.8/sjPlot/man/sj.setGeomColors.Rd | 52
sjPlot-1.6.8/sjPlot/man/sjPlot-package.Rd | 4
sjPlot-1.6.8/sjPlot/man/sjc.cluster.Rd | 180 -
sjPlot-1.6.8/sjPlot/man/sjc.dend.Rd | 104
sjPlot-1.6.8/sjPlot/man/sjc.elbow.Rd | 76
sjPlot-1.6.8/sjPlot/man/sjc.grpdisc.Rd | 110 -
sjPlot-1.6.8/sjPlot/man/sjc.kgap.Rd | 134 -
sjPlot-1.6.8/sjPlot/man/sjc.qclus.Rd | 386 +--
sjPlot-1.6.8/sjPlot/man/sji.SPSS.Rd | 102
sjPlot-1.6.8/sjPlot/man/sji.convertToLabel.Rd | 80
sjPlot-1.6.8/sjPlot/man/sji.convertToValue.Rd | 78
sjPlot-1.6.8/sjPlot/man/sji.getValueLabels.Rd | 94
sjPlot-1.6.8/sjPlot/man/sji.getVariableLabels.Rd | 92
sjPlot-1.6.8/sjPlot/man/sji.setValueLabels.Rd | 96
sjPlot-1.6.8/sjPlot/man/sji.setVariableLabels.Rd | 124 -
sjPlot-1.6.8/sjPlot/man/sji.viewSPSS.Rd | 248 +-
sjPlot-1.6.8/sjPlot/man/sjp.chi2.Rd | 122 -
sjPlot-1.6.8/sjPlot/man/sjp.corr.Rd | 248 +-
sjPlot-1.6.8/sjPlot/man/sjp.emm.int.Rd | 270 +-
sjPlot-1.6.8/sjPlot/man/sjp.glm.Rd | 384 +--
sjPlot-1.6.8/sjPlot/man/sjp.glmer.Rd | 410 +--
sjPlot-1.6.8/sjPlot/man/sjp.glmm.Rd | 325 +--
sjPlot-1.6.8/sjPlot/man/sjp.int.Rd | 450 ++--
sjPlot-1.6.8/sjPlot/man/sjp.likert.Rd | 442 ++--
sjPlot-1.6.8/sjPlot/man/sjp.lm.Rd | 370 ++-
sjPlot-1.6.8/sjPlot/man/sjp.lmer.Rd | 369 +--
sjPlot-1.6.8/sjPlot/man/sjp.lmm.Rd | 311 +-
sjPlot-1.6.8/sjPlot/man/sjp.pca.Rd | 288 +-
sjPlot-1.6.8/sjPlot/man/sjp.scatter.Rd | 2
sjPlot-1.6.8/sjPlot/man/sjp.stackfrq.Rd | 360 +--
sjPlot-1.6.8/sjPlot/man/sjs.aov1.levene.Rd | 56
sjPlot-1.6.8/sjPlot/man/sjs.chi2.gof.Rd | 78
sjPlot-1.6.8/sjPlot/man/sjs.cramer.Rd | 54
sjPlot-1.6.8/sjPlot/man/sjs.cronbach.Rd | 60
sjPlot-1.6.8/sjPlot/man/sjs.etasq.Rd | 100
sjPlot-1.6.8/sjPlot/man/sjs.mic.Rd | 98
sjPlot-1.6.8/sjPlot/man/sjs.mwu.Rd | 114 -
sjPlot-1.6.8/sjPlot/man/sjs.phi.Rd | 54
sjPlot-1.6.8/sjPlot/man/sjs.reliability.Rd | 178 -
sjPlot-1.6.8/sjPlot/man/sjs.se.Rd | 42
sjPlot-1.6.8/sjPlot/man/sjs.stdb.Rd | 88
sjPlot-1.6.8/sjPlot/man/sjs.table.values.Rd | 80
sjPlot-1.6.8/sjPlot/man/sjt.corr.Rd | 358 +--
sjPlot-1.6.8/sjPlot/man/sjt.df.Rd | 290 +-
sjPlot-1.6.8/sjPlot/man/sjt.frq.Rd | 440 ++--
sjPlot-1.6.8/sjPlot/man/sjt.glm.Rd | 508 ++--
sjPlot-1.6.8/sjPlot/man/sjt.grpmean.Rd | 155 -
sjPlot-1.6.8/sjPlot/man/sjt.itemanalysis.Rd | 392 +--
sjPlot-1.6.8/sjPlot/man/sjt.lm.Rd | 552 ++---
sjPlot-1.6.8/sjPlot/man/sjt.pca.Rd | 354 +--
sjPlot-1.6.8/sjPlot/man/sjt.stackfrq.Rd | 386 +--
sjPlot-1.6.8/sjPlot/man/sjt.xtab.Rd | 446 ++--
sjPlot-1.6.8/sjPlot/man/sju.adjustPlotRange.y.Rd | 90
sjPlot-1.6.8/sjPlot/man/sju.dicho.Rd | 78
sjPlot-1.6.8/sjPlot/man/sju.groupString.Rd | 98
sjPlot-1.6.8/sjPlot/man/sju.groupVar.Rd | 132 -
sjPlot-1.6.8/sjPlot/man/sju.groupVarLabels.Rd | 150 -
sjPlot-1.6.8/sjPlot/man/sju.mean.n.Rd | 80
sjPlot-1.6.8/sjPlot/man/sju.recode.Rd | 48
sjPlot-1.6.8/sjPlot/man/sju.recodeTo.Rd | 96
sjPlot-1.6.8/sjPlot/man/sju.setNA.Rd | 62
sjPlot-1.6.8/sjPlot/man/sju.strpos.Rd | 138 -
sjPlot-1.6.8/sjPlot/man/sju.weight.Rd | 78
sjPlot-1.6.8/sjPlot/man/sju.weight2.Rd | 90
sjPlot-1.6.8/sjPlot/man/sju.wordwrap.Rd | 56
98 files changed, 12740 insertions(+), 12224 deletions(-)
Title: Improved Access for Blind Users
Diff between BrailleR versions 0.11 dated 2014-09-27 and 0.16.1 dated 2015-02-02
Description: Blind users do not have access to the graphical output from R without printing the content of graph windows to an embosser of some kind. This is not as immediate as is required for efficient access to statistical output. The functions here are created so that blind people can make even better use of R.
Author: A. Jonathan R. Godfrey [aut, cre], Greg Snow [ctb], Paul Murrell [ctb], Yihui Xie [ctb]
Maintainer: A. Jonathan R. Godfrey
DESCRIPTION | 12 -
MD5 | 58 +++++----
NAMESPACE | 9 +
R/DataViewer.R |only
R/MaskedFunctions.R | 9 -
R/OneFactor.R |only
R/Options.R |only
R/UniDesc.R | 125 ++++++++++++-------
R/VIMethod.R | 146 ++++++++++++++++++-----
R/WhereXY.R | 28 ++--
R/zzz.R |only
build/vignette.rds |binary
inst/CITATION | 4
inst/Sound |only
inst/doc/BrailleRManual.html | 44 ++++--
inst/doc/Ex1histograms.html | 110 ++++++++---------
inst/doc/Ex2BasicNumerical.html | 59 +++++----
inst/doc/Ex3UnivariateDescription.R | 4
inst/doc/Ex3UnivariateDescription.html | 24 ++-
inst/doc/Ex3UnivariateDescription.rmd | 10 -
inst/doc/Ex4SingleResponseOneGroupingFactor.R |only
inst/doc/Ex4SingleResponseOneGroupingFactor.html |only
inst/doc/Ex4SingleResponseOneGroupingFactor.rmd |only
man/BrailleR-package.Rd | 10 -
man/DataViewer.Rd |only
man/OneFactor.Rd |only
man/Options.Rd |only
man/R2txtJG.Rd | 12 -
man/UniDesc.Rd | 22 +--
man/VI.Rd | 23 ++-
man/WhereXY.Rd | 12 +
man/boxplot.Rd | 17 +-
man/hist.Rd | 15 +-
man/unfinished.Rd | 3
vignettes/Ex3UnivariateDescription.rmd | 10 -
vignettes/Ex4SingleResponseOneGroupingFactor.rmd |only
36 files changed, 480 insertions(+), 286 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-22 1.1
2014-08-09 1.0
Title: n-gram Text Regression, aka Concise Comparative Summarization
Diff between textreg versions 0.1 dated 2014-12-04 and 0.1.1 dated 2015-02-02
Description: Function for sparse regression on raw text, regressing a labeling
vector onto a feature space consisting of all possible phrases.
Author: Luke Miratrix
Maintainer: Luke Miratrix
DESCRIPTION | 6 +++---
MD5 | 4 ++--
src/textreg.cpp | 15 +++++++++------
3 files changed, 14 insertions(+), 11 deletions(-)
Title: STRUctural Modeling of Latent Variables for General Pedigree
Diff between strum versions 0.5 dated 2014-12-10 and 0.5.1 dated 2015-02-02
Description: This package implements a broad class of latent variable and structural equation models for general pedigree data.
Author: Nathan Morris [aut, cre],
Yeunjoo Song [aut],
Stephen Cahn [ctb]
Maintainer: Nathan Morris
DESCRIPTION | 6 +++---
MD5 | 4 ++--
src/computeLLDeriv.cpp | 4 ++--
3 files changed, 7 insertions(+), 7 deletions(-)
Title: Royston's H Test: Multivariate Normality Test
Diff between royston versions 1.1 dated 2015-01-16 and 1.2 dated 2015-02-02
Description: Performs a multivariate normality test based on Royston's H test
Author: Selcuk Korkmaz
Maintainer: Selcuk Korkmaz
royston-1.1/royston/data |only
royston-1.1/royston/man/a.Rd |only
royston-1.2/royston/DESCRIPTION | 11 ++++++-----
royston-1.2/royston/MD5 | 10 +++++-----
royston-1.2/royston/R/royston.test.R | 1 -
royston-1.2/royston/R/welcome.R |only
royston-1.2/royston/inst |only
royston-1.2/royston/man/royston-package.Rd | 2 --
8 files changed, 11 insertions(+), 13 deletions(-)
Title: A Google Analytics API client for R
Diff between RGA versions 0.1.4 dated 2014-12-19 and 0.2 dated 2015-02-02
Description: Provides functions for accessing and retrieving data from the
Google Analytics APIs (https://developers.google.com/analytics/). Supports
OAuth 2.0 authorization. Package provides access to the Management, Core
Reporting, Multi-Channel Funnels Reporting, Real Time Reporting and
Metadata APIs. Access to all the Google Analytics accounts which the user
has access to. Auto-pagination to return more than 10,000 rows of the
results by combining multiple data requests. Also package provides
shiny app to explore the core reporting API dimensions and metrics.
Author: Artem Klevtsov [aut, cre],
Philipp Upravitelev [ctb],
Olga Shramko [ctb]
Maintainer: Artem Klevtsov
RGA-0.1.4/RGA/R/data.R |only
RGA-0.1.4/RGA/R/get-mgmt.R |only
RGA-0.1.4/RGA/R/get-pages.R |only
RGA-0.1.4/RGA/R/list-mgmt.R |only
RGA-0.1.4/RGA/R/onload.R |only
RGA-0.1.4/RGA/R/sysdata.rda |only
RGA-0.1.4/RGA/man/dims_mets.Rd |only
RGA-0.1.4/RGA/man/get_firstdate.Rd |only
RGA-0.2/RGA/DESCRIPTION | 24 +-
RGA-0.2/RGA/MD5 | 115 ++++++++----
RGA-0.2/RGA/NAMESPACE | 29 ++-
RGA-0.2/RGA/R/accounts.R |only
RGA-0.2/RGA/R/auth.R | 30 +--
RGA-0.2/RGA/R/convert.R | 110 ++++++------
RGA-0.2/RGA/R/custom.R |only
RGA-0.2/RGA/R/experiments.R |only
RGA-0.2/RGA/R/filters.R |only
RGA-0.2/RGA/R/first-date.R |only
RGA-0.2/RGA/R/ga.R |only
RGA-0.2/RGA/R/get-data.R | 23 ++
RGA-0.2/RGA/R/goals.R |only
RGA-0.2/RGA/R/mcf.R |only
RGA-0.2/RGA/R/metadata.R |only
RGA-0.2/RGA/R/mgmt.R |only
RGA-0.2/RGA/R/package.R | 33 ++-
RGA-0.2/RGA/R/profiles.R |only
RGA-0.2/RGA/R/query.R | 31 +--
RGA-0.2/RGA/R/report.R | 231 ++-----------------------
RGA-0.2/RGA/R/request.R | 93 +++-------
RGA-0.2/RGA/R/rt.R |only
RGA-0.2/RGA/R/segments.R |only
RGA-0.2/RGA/R/shiny.R | 41 ++--
RGA-0.2/RGA/R/unsampled.R |only
RGA-0.2/RGA/R/url.R | 72 ++------
RGA-0.2/RGA/R/utils.R | 61 +++++-
RGA-0.2/RGA/R/webproperties.R |only
RGA-0.2/RGA/R/zzz.R | 4
RGA-0.2/RGA/README.md | 268 +-----------------------------
RGA-0.2/RGA/build |only
RGA-0.2/RGA/data |only
RGA-0.2/RGA/inst |only
RGA-0.2/RGA/man/RGA.Rd | 37 +++-
RGA-0.2/RGA/man/authorize.Rd | 20 +-
RGA-0.2/RGA/man/dimsmets.Rd |only
RGA-0.2/RGA/man/firstdate.Rd |only
RGA-0.2/RGA/man/ga.Rd | 40 ++--
RGA-0.2/RGA/man/get_experiment.Rd |only
RGA-0.2/RGA/man/get_filter.Rd |only
RGA-0.2/RGA/man/get_ga.Rd | 22 +-
RGA-0.2/RGA/man/get_goal.Rd | 40 ++--
RGA-0.2/RGA/man/get_mcf.Rd | 19 +-
RGA-0.2/RGA/man/get_profile.Rd | 46 ++---
RGA-0.2/RGA/man/get_rt.Rd | 18 --
RGA-0.2/RGA/man/get_unsampled_report.Rd |only
RGA-0.2/RGA/man/get_webproperty.Rd | 44 ++--
RGA-0.2/RGA/man/list_accounts.Rd | 30 +--
RGA-0.2/RGA/man/list_custom_sources.Rd |only
RGA-0.2/RGA/man/list_experiments.Rd |only
RGA-0.2/RGA/man/list_filters.Rd |only
RGA-0.2/RGA/man/list_goals.Rd | 45 +----
RGA-0.2/RGA/man/list_metadata.Rd |only
RGA-0.2/RGA/man/list_profiles.Rd | 42 +---
RGA-0.2/RGA/man/list_segments.Rd | 31 +--
RGA-0.2/RGA/man/list_unsampled_reports.Rd |only
RGA-0.2/RGA/man/list_webproperties.Rd | 39 ++--
RGA-0.2/RGA/tests |only
RGA-0.2/RGA/vignettes |only
67 files changed, 640 insertions(+), 998 deletions(-)
Title: Metropolis Sampler and Supporting Functions for Estimating
Animal Movement from Archival Tags and Satellite Fixes
Diff between tripEstimation versions 0.0-41 dated 2013-07-10 and 0.0-42 dated 2015-02-02
More information about tripEstimation at CRAN
Description: Data handling and estimation functions for animal movement
estimation from archival or satellite tags. Helper functions are included
for making image summaries binned by time interval from MCMC simulations of
point data.
Author: Michael D. Sumner [aut, cre],
Simon Wotherspoon [ctb]
Maintainer: Michael D. Sumner
DESCRIPTION | 17 ++++++++++-------
MD5 | 10 +++++-----
NEWS | 4 ++++
README.md | 5 +----
TODO | 9 +++++++--
inst/CITATION | 16 +++++++++++-----
6 files changed, 38 insertions(+), 23 deletions(-)
Permanent link
Title: Linkage Map Construction using the MSTmap Algorithm
Diff between ASMap versions 0.3-2 dated 2014-10-13 and 0.3-3 dated 2015-02-02
Description: Functions for (A)ccurate and (S)peedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred R/qtl objects. This includes extremely fast linkage map clustering and optimal marker ordering using MSTmap (see Wu et al.,2008).
Author: Julian Taylor
Maintainer: Julian Taylor
DESCRIPTION | 10 ++--
MD5 | 10 ++--
R/mstmap9.R | 106 +++++++++++++++++++++++++++++++++++++++++++----
man/ASMap-package.Rd | 2
man/mstmap.cross.Rd | 2
man/mstmap.data.frame.Rd | 4 -
6 files changed, 111 insertions(+), 23 deletions(-)
Title: The Analysis of Biological Data
Diff between abd versions 0.2-6 dated 2014-03-31 and 0.2-7 dated 2015-02-02
Description: The abd package contains data sets and sample code for The
Analysis of Biological Data by Michael Whitlock and Dolph Schluter (2009;
Roberts & Company Publishers).
Author: Kevin M. Middleton
Maintainer: Kevin M. Middleton
DESCRIPTION | 13 -
MD5 | 310 +++++++++++++++++++++----------------------
NAMESPACE | 3
R/abdData.R | 63 ++++----
R/datasets.R | 261 ++++++------------------------------
R/histochart.R | 7
R/themes.R | 2
man/AlgaeCO2.Rd | 18 +-
man/Antilles.Rd | 15 +-
man/Aspirin.Rd | 16 +-
man/BeeGenes.Rd | 16 +-
man/BeeLifespans.Rd | 10 -
man/Beetles.Rd | 14 -
man/BirdSexRatio.Rd | 10 -
man/Blackbirds.Rd | 16 +-
man/BodyFatHeatLoss.Rd | 13 -
man/BrainExpression.Rd | 17 +-
man/BrookTrout.Rd | 26 +--
man/Cavalry.Rd | 19 +-
man/Chickadees.Rd | 17 +-
man/ChimpBrains.Rd | 9 -
man/Cichlids.Rd | 19 +-
man/CichlidsGnRH.Rd | 17 +-
man/Clearcuts.Rd | 16 +-
man/CocaineDopamine.Rd | 20 +-
man/Convictions.Rd | 15 --
man/ConvictionsAndIncome.Rd | 15 +-
man/Crickets.Rd | 13 -
man/DEET.Rd | 15 --
man/DaphniaLongevity.Rd | 14 -
man/DaphniaResistance.Rd | 17 +-
man/DayOfBirth.Rd | 15 +-
man/DesertBirds.Rd | 16 +-
man/Dioecy.Rd | 11 -
man/Dolphins.Rd | 17 +-
man/DungBeetles.Rd | 18 +-
man/Earthworms.Rd | 16 +-
man/Earwigs.Rd | 19 +-
man/Eelgrass.Rd | 20 +-
man/ElVerde.Rd | 13 -
man/ElectricFish.Rd | 16 +-
man/EndangeredSpecies.Rd | 13 -
man/FingerRatio.Rd | 17 +-
man/Fireflies.Rd | 18 +-
man/FireflyFlash.Rd | 14 -
man/FlyTestes.Rd | 17 +-
man/FlycatcherPatch.Rd | 14 -
man/GeneRegulation.Rd | 14 -
man/GlidingSnakes.Rd | 16 +-
man/GodwitArrival.Rd | 15 +-
man/Grassland.Rd | 16 +-
man/GreatTitMalaria.Rd | 14 -
man/Greenspace.Rd | 15 --
man/Guppies.Rd | 18 +-
man/Hemoglobin.Rd | 18 +-
man/HippocampusLesions.Rd | 14 -
man/HornedLizards.Rd | 16 +-
man/HumanBodyTemp.Rd | 21 +-
man/HumanGeneLengths.Rd | 65 ++-------
man/Hurricanes.Rd | 18 +-
man/Iguanas.Rd | 16 +-
man/IntertidalAlgae.Rd | 14 -
man/JetLagKnees.Rd | 14 +
man/KenyaFinches.Rd | 17 +-
man/LanguageBrains.Rd | 16 +-
man/LarvalFish.Rd | 15 --
man/Lefthanded.Rd | 15 +-
man/LionCubs.Rd | 13 -
man/LionNoses.Rd | 14 -
man/LiverPreparation.Rd | 18 +-
man/LizardBite.Rd | 29 +---
man/LizardSprint.Rd | 24 +--
man/Lobsters.Rd | 16 +-
man/LodgepolePines.Rd | 21 +-
man/LupusMice.Rd | 14 -
man/Lynx.Rd | 12 -
man/MarineReserve.Rd | 15 --
man/MassExtinctions.Rd | 12 -
man/MoleRats.Rd | 20 +-
man/Mosquitoes.Rd | 17 +-
man/MouseEmpathy.Rd | 16 +-
man/NeanderthalBrains.Rd | 12 -
man/NematodeLifespan.Rd | 19 +-
man/NeotropicalTrees.Rd | 21 +-
man/Newts.Rd | 19 +-
man/NoSmokingDay.Rd | 17 +-
man/NorthSeaCod.Rd | 18 +-
man/OstrichTemp.Rd | 23 +--
man/Penguins.Rd | 16 +-
man/PlantPersistence.Rd | 14 -
man/Pollen.Rd | 14 -
man/Powerball.Rd | 12 -
man/PrimateMetabolism.Rd | 12 -
man/PrimateWBC.Rd | 11 -
man/ProgesteroneExercise.Rd | 18 +-
man/Pseudoscorpions.Rd | 20 +-
man/Pufferfish.Rd | 22 +--
man/Rattlesnakes.Rd | 16 +-
man/Rigormortis.Rd | 13 -
man/RopeTrick.Rd | 16 +-
man/SagebrushCrickets.Rd | 17 +-
man/SalmonColor.Rd | 20 +-
man/Seedlings.Rd | 6
man/Selection.Rd | 18 +-
man/SexualSelection.Rd | 21 +-
man/ShadParasites.Rd | 14 -
man/ShrinkingSeals.Rd | 16 +-
man/ShuttleDisaster.Rd | 22 +--
man/Silversword.Rd | 14 -
man/SleepAndPerformance.Rd | 15 +-
man/SockeyeFemales.Rd | 17 +-
man/Sparrows.Rd | 17 +-
man/SpiderColonies.Rd | 15 --
man/SpiderSpeed.Rd | 20 +-
man/Stalkies1.Rd | 9 -
man/Stalkies2.Rd | 16 +-
man/SticklebackPlates.Rd | 32 ++--
man/SticklebackPreference.Rd | 19 +-
man/Sumo.Rd | 11 -
man/SyrupSwimming.Rd | 17 +-
man/TeenDeaths.Rd | 15 --
man/Telomeres.Rd | 18 +-
man/TimeOfDeath.Rd | 14 -
man/Toads.Rd | 9 -
man/Tobacco.Rd | 16 +-
man/Tobacco2.Rd | 18 +-
man/ToothAge.Rd | 15 +-
man/TreeSeedlings.Rd | 16 +-
man/Trematodes.Rd | 15 +-
man/Trillium.Rd | 15 +-
man/Truffles.Rd | 20 +-
man/TsetseLearning.Rd | 16 +-
man/TwoKids.Rd | 13 -
man/VampireBites.Rd | 9 -
man/VasopressinVoles.Rd | 20 +-
man/Vines.Rd | 16 +-
man/VoleDispersal.Rd | 12 -
man/WalkingStickFemurs.Rd | 17 +-
man/WalkingStickHeads.Rd | 20 +-
man/WeddellSeals.Rd | 19 +-
man/WillsDebates.Rd | 9 -
man/WillsPresidents.Rd | 11 -
man/WolfTeeth.Rd | 18 +-
man/Wolves.Rd | 17 +-
man/WorldCup.Rd | 5
man/WrasseSexes.Rd | 6
man/YeastGenes.Rd | 12 -
man/ZebraFinchBeaks.Rd | 17 +-
man/ZebraFinches.Rd | 17 +-
man/ZooMortality.Rd | 13 -
man/Zooplankton.Rd | 19 +-
man/abd-package.Rd | 30 ++--
man/abdData.Rd | 45 ++----
man/dataInfo.Rd | 9 -
man/histochart.Rd | 32 +---
man/themes.Rd | 28 +--
156 files changed, 1455 insertions(+), 1693 deletions(-)
Title: Bayesian Inference for Zero/One Inflated Beta Regression
Diff between zoib versions 1.0 dated 2014-06-04 and 1.1 dated 2015-02-01
Description: zoib fits beta regression and zero or one inflated beta regression and obtains Bayesian Inference of the model via the Markov Chain Monte Carlo approach implemented in JAGS
Author: Fang Liu
Maintainer: Fang Liu
zoib-1.0/zoib/tests/eg1-Gas.R |only
zoib-1.0/zoib/tests/eg2-Bivariate.R |only
zoib-1.1/zoib/DESCRIPTION | 10 -
zoib-1.1/zoib/MD5 | 74 ++++++-------
zoib-1.1/zoib/R/check.psrf.R | 42 ++++---
zoib-1.1/zoib/R/joint.2z.R | 2
zoib-1.1/zoib/R/sep.2z.R | 15 ++
zoib-1.1/zoib/R/sep.2z0.R | 17 ++-
zoib-1.1/zoib/R/sep.2z01.R | 16 ++
zoib-1.1/zoib/R/sep.2z1.R | 15 ++
zoib-1.1/zoib/R/zoib.R | 72 ++++++++++---
zoib-1.1/zoib/data/BiRepeated.rda |binary
zoib-1.1/zoib/inst/bugs/fixed.bug | 2
zoib-1.1/zoib/inst/bugs/fixed0.bug | 4
zoib-1.1/zoib/inst/bugs/fixed01.bug | 5
zoib-1.1/zoib/inst/bugs/fixed1.bug | 4
zoib-1.1/zoib/inst/bugs/joint_1z.bug | 21 ++-
zoib-1.1/zoib/inst/bugs/joint_1z0.bug | 7 -
zoib-1.1/zoib/inst/bugs/joint_1z01.bug | 4
zoib-1.1/zoib/inst/bugs/joint_1z1.bug | 6 -
zoib-1.1/zoib/inst/bugs/joint_2z.bug | 2
zoib-1.1/zoib/inst/bugs/joint_2z0.bug | 2
zoib-1.1/zoib/inst/bugs/joint_2z01.bug | 4
zoib-1.1/zoib/inst/bugs/joint_2z1.bug | 6 -
zoib-1.1/zoib/inst/bugs/sep_1z.bug | 6 -
zoib-1.1/zoib/inst/bugs/sep_1z0.bug | 6 -
zoib-1.1/zoib/inst/bugs/sep_1z01.bug | 4
zoib-1.1/zoib/inst/bugs/sep_1z1.bug | 6 -
zoib-1.1/zoib/inst/bugs/sep_2z.bug | 4
zoib-1.1/zoib/inst/bugs/sep_2z0.bug | 4
zoib-1.1/zoib/inst/bugs/sep_2z01.bug | 4
zoib-1.1/zoib/inst/bugs/sep_2z1.bug | 2
zoib-1.1/zoib/man/AlcoholUse.Rd | 31 +++--
zoib-1.1/zoib/man/BiRepeated.Rd | 50 ++++++---
zoib-1.1/zoib/man/GasolineYield.Rd | 67 +++++++++---
zoib-1.1/zoib/man/check.psrf.Rd | 4
zoib-1.1/zoib/man/zoib-package.Rd | 19 +--
zoib-1.1/zoib/man/zoib.Rd | 180 ++++++++++-----------------------
zoib-1.1/zoib/tests/test1.R |only
zoib-1.1/zoib/tests/test2.R |only
40 files changed, 427 insertions(+), 290 deletions(-)
Title: Multivariate Constructs
Diff between multicon versions 1.5 dated 2015-01-08 and 1.6 dated 2015-02-01
Description: Includes functions designed to examine relationships among multivariate constructs (e.g., personality). This includes functions for profile (within-person) analysis, dealing with large numbers of analyses, lens model analyses, and structural summary methods for data with circumplex structure. The package also includes functions for graphically comparing and displaying group means.
Author: Ryne A. Sherman
Maintainer: Ryne A. Sherman
DESCRIPTION | 8 ++++----
MD5 | 24 +++++++++++++++++-------
NAMESPACE | 8 ++++++++
R/diffPlot.formula.r | 2 +-
R/partwhole.R | 3 +--
R/tContrast.R |only
R/tContrast.default.R |only
R/tContrast.formula.R |only
R/winvar.r |only
R/yuenContrast.default.r |only
R/yuenContrast.formula.r |only
R/yuenContrast.r |only
man/diffPlot.Rd | 7 +++----
man/multicon-package.Rd | 4 ++--
man/partwhole.Rd | 4 ++--
man/tContrast.Rd |only
man/winvar.rd |only
man/yuenContrast.rd |only
18 files changed, 38 insertions(+), 22 deletions(-)
Title: Companion to Applied Regression
Diff between car versions 2.0-22 dated 2014-11-18 and 2.0-24 dated 2015-02-01
Description:
This package accompanies J. Fox and S. Weisberg, An R Companion to Applied Regression,
Second Edition, Sage, 2011.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Daniel Adler [ctb],
Douglas Bates [ctb],
Gabriel Baud-Bovy [ctb],
Steve Ellison [ctb],
David Firth [ctb],
Michael Friendly [ctb],
Gregor Gorjanc [ctb],
Spencer Graves [ctb],
Richard Heiberger [ctb],
Rafael Laboissiere [ctb],
Georges Monette [ctb],
Duncan Murdoch [ctb],
Henric Nilsson [ctb],
Derek Ogle [ctb],
Brian Ripley [ctb],
William Venables [ctb],
Achim Zeileis [ctb],
R-Core [ctb]
Maintainer: John Fox
DESCRIPTION | 19
MD5 | 146 ++--
NAMESPACE | 6
NEWS | 22
R/Anova.R | 12
R/Boot.R | 31
R/bootCase.R | 7
R/linearHypothesis.R | 1429 ++++++++++++++++++++++----------------------
R/marginalModelPlot.R | 4
R/mcPlots.R | 4
R/scatterplotSmoothers.R | 72 +-
R/subsets.R | 14
R/utility-functions.R | 6
R/vif.R | 4
build/vignette.rds |binary
data/AMSsurvey.rda |binary
data/Adler.rda |binary
data/Angell.rda |binary
data/Anscombe.rda |binary
data/Baumann.rda |binary
data/Bfox.rda |binary
data/Blackmore.rda |binary
data/Burt.rda |binary
data/CanPop.rda |binary
data/Chile.rda |binary
data/Chirot.rda |binary
data/Cowles.rda |binary
data/Davis.rda |binary
data/DavisThin.rda |binary
data/Depredations.rda |binary
data/Duncan.rda |binary
data/Ericksen.rda |binary
data/Florida.rda |binary
data/Freedman.rda |binary
data/Friendly.rda |binary
data/Ginzberg.rda |binary
data/Greene.rda |binary
data/Guyer.rda |binary
data/Hartnagel.rda |binary
data/Highway1.rda |binary
data/KosteckiDillon.rda |binary
data/Leinhardt.rda |binary
data/Mandel.rda |binary
data/Migration.rda |binary
data/Moore.rda |binary
data/Mroz.rda |binary
data/OBrienKaiser.rda |binary
data/Ornstein.rda |binary
data/Pottery.rda |binary
data/Prestige.rda |binary
data/Quartet.rda |binary
data/Robey.rda |binary
data/SLID.rda |binary
data/Sahlins.rda |binary
data/Salaries.rda |binary
data/Soils.rda |binary
data/States.rda |binary
data/Transact.rda |binary
data/UN.rda |binary
data/USPop.rda |binary
data/Vocab.rda |binary
data/WeightLoss.rda |binary
data/Womenlf.rda |binary
data/Wong.rda |only
data/Wool.rda |binary
inst/doc/embedding.pdf |binary
man/AMSsurvey.Rd | 88 +-
man/Florida.Rd | 4
man/ScatterplotSmoothers.Rd | 17
man/Soils.Rd | 2
man/UN.Rd | 2
man/Wong.Rd |only
man/car-package.Rd | 8
man/marginalModelPlot.Rd | 40 -
man/subsets.Rd | 14
75 files changed, 1005 insertions(+), 946 deletions(-)
Title: Regional frequency analysis using L-moments
Diff between lmomRFA versions 3.0 dated 2014-01-15 and 3.0-1 dated 2015-02-01
Description: Functions for regional frequency analysis using the methods
of J. R. M. Hosking and J. R. Wallis (1997), "Regional frequency analysis:
an approach based on L-moments".
Author: J. R. M. Hosking
Maintainer: J. R. M. Hosking
DESCRIPTION | 10 ++--
MD5 | 48 ++++++++++-----------
NEWS | 7 ++-
R/lmomRFA.r | 8 ---
data/Appalach.rda |binary
data/Cascades.rda |binary
data/Maxwind.rda |binary
man/cluagg.Rd | 2
man/cluinf.Rd | 2
man/clukm.Rd | 2
man/evplot.rfd.Rd | 2
man/lmomRFA-package.Rd | 2
man/regavlmom.Rd | 2
man/regdata.Rd | 2
man/regfit.Rd | 2
man/reglmr.Rd | 2
man/regquant.Rd | 2
man/regquantbounds.Rd | 2
man/regsamlmu.Rd | 2
man/regsimh.Rd | 2
man/regsimq.Rd | 2
man/regtst.Rd | 2
man/sitequant.Rd | 2
man/summary.regtst.Rd | 2
src/lmomRFA.f | 108 ++++++++-----------------------------------------
25 files changed, 72 insertions(+), 143 deletions(-)
Title: L-moments
Diff between lmom versions 2.4 dated 2014-03-24 and 2.5 dated 2015-02-01
Description: Functions related to L-moments: computation of L-moments
and trimmed L-moments of distributions and data samples; parameter
estimation; L-moment ratio diagram; plot vs. quantiles of an
extreme-value distribution.
Author: J. R. M. Hosking
Maintainer: J. R. M. Hosking
DESCRIPTION | 10 +--
MD5 | 28 ++++----
NEWS | 21 ++++++
R/lmom.r | 53 +++++++++-------
man/evplot.Rd | 13 +--
man/lmom-package.Rd | 2
man/lmr-functions.Rd | 3
man/lmrd.Rd | 8 +-
man/lmrdpoints.Rd | 2
man/lmrp.Rd | 15 +---
man/pel-functions.Rd | 2
man/pelp.Rd | 2
man/samlmu.Rd | 2
src/lmoments.f | 166 ++++++++-------------------------------------------
src/samlm.f | 30 +++++----
15 files changed, 138 insertions(+), 219 deletions(-)
Title: Composite-Likelihood Based Analysis of Random Fields
Diff between CompRandFld versions 1.0.3-3 dated 2015-01-15 and 1.0.3-4 dated 2015-02-01
Description: A set of procedures for the analysis of Random Fields using likelihood and non-standard likelihood methods is provided. Spatial analysis often involves dealing with large dataset. Therefore even simple studies may be too computationally demanding. Composite likelihood inference is emerging as a useful tool for mitigating such computational problems. This methodology shows satisfactory results when compared with other techniques such as the tapering method. Moreover, composite likelihood (and related quantities) have some useful properties similar to those of the standard likelihood.
Author: Simone Padoan[aut, cre]
Maintainer: Simone Padoan
DESCRIPTION | 20 ++---
MD5 | 57 ++++++++--------
NAMESPACE | 4 +
R/Covmatrix.r | 4 -
inst/CITATION |only
man/CheckCorrModel.Rd | 3
man/CheckInput.Rd | 3
man/CheckLikelihood.Rd | 2
man/CheckModel.Rd | 2
man/CheckType.Rd | 3
man/CheckVarType.Rd | 3
man/CompLikelihood.Rd | 2
man/CorrelationParam.Rd | 4 -
man/Covariogram.Rd | 5 +
man/Covmatrix.Rd | 60 +++++++++--------
man/Dist2Dist.Rd | 4 -
man/EVariogram.Rd | 6 +
man/FitComposite.Rd | 22 +++---
man/FitGev.Rd | 3
man/GevLogLik.Rd | 3
man/HypoTest.Rd | 9 +-
man/InitParam.Rd | 7 +-
man/Kri.Rd | 103 ++++++++++++++----------------
man/Likelihood.Rd | 2
man/MomEst.Rd | 2
man/NuisanceParam.Rd | 3
man/RFsim.Rd | 8 +-
man/WLeastSquare.Rd | 10 +-
man/WlsInit.Rd | 2
src/Utility.c | 164 ++++++++++++++++++++++++++----------------------
30 files changed, 274 insertions(+), 246 deletions(-)
Title: Variance Dispersion, Fraction of Design Space Plots, Designs,
and Contour Plots
Diff between VdgRsm versions 1.3 dated 2014-11-29 and 1.4 dated 2015-02-01
Description: This package creates variance dispersion graphs (VDGs), fraction of design space (FDS) plots, and contour of SPVs for second-order model designs in spherical or cuboidal regions. The package also generates some response surface designs.
Author: Patchanok Srisuradetchai, John J. Borkowski
Maintainer: Patchanok Srisuradetchai
VdgRsm-1.3/VdgRsm/man/VdgRsm-package.Rd |only
VdgRsm-1.4/VdgRsm/DESCRIPTION | 20
VdgRsm-1.4/VdgRsm/MD5 | 13
VdgRsm-1.4/VdgRsm/NAMESPACE | 10
VdgRsm-1.4/VdgRsm/R/VdgRsm.R | 757 ++++++++++++++++++++++++++++----
VdgRsm-1.4/VdgRsm/man/Borkowski2003.Rd | 10
VdgRsm-1.4/VdgRsm/man/VdgRsm.Rd |only
VdgRsm-1.4/VdgRsm/man/cpv.Rd | 16
VdgRsm-1.4/VdgRsm/man/spvcontour.Rd |only
9 files changed, 721 insertions(+), 105 deletions(-)
Title: Geographically-Weighted Models
Diff between GWmodel versions 1.2-3 dated 2014-05-12 and 1.2-5 dated 2015-02-01
Description: In GWmodel, we introduce techniques from a particular branch of spatial statistics,termed geographically-weighted (GW) models. GW models suit situations when data are not described well by some global model, but where there are spatial regions where a suitably localised calibration provides a better description. GWmodel includes functions to calibrate: GW summary statistics, GW principal components analysis, GW discriminant analysis and various forms of GW regression; some of which are provided in basic and robust (outlier resistant) forms.
Author: Binbin Lu[aut], Paul Harris[aut], Martin Charlton[aut], Chris Brunsdon[aut], Tomoki Nakaya[aut], Isabella Gollini[ctb]
Maintainer: Binbin Lu
DESCRIPTION | 23 ++++----
MD5 | 116 +++++++++++++++++++++++----------------------
NAMESPACE | 3 -
R/LocalsummaryStatistics.r | 1
R/gw.weight.r | 90 +++++++++++++++++++++++++---------
R/gwr.basic.r | 83 --------------------------------
R/gwr.t.adjust.r | 12 +++-
R/minkovski.approach.r |only
R/zzz.r | 2
inst |only
man/EWHP.Rd | 4 -
man/EWOutline.rd | 2
man/GWmodel-package.Rd | 21 ++++----
man/LondonBorough.rd | 2
man/LondonHP.Rd | 11 +---
man/bw.ggwr.Rd | 2
man/bw.gwda.rd | 2
man/bw.gwpca.rd | 2
man/bw.gwr.Rd | 2
man/bw.gwr.lcr.rd | 2
man/check.components.rd | 2
man/ggwr.cv.Rd | 2
man/ggwr.cv.contrib.Rd | 2
man/glyph.plot.rd | 2
man/gw.dist.Rd | 2
man/gw.pcplot.rd | 9 +--
man/gwda.rd | 2
man/gwpca.cv.Rd | 2
man/gwpca.cv.contrib.Rd | 2
man/gwpca.rd | 20 +++----
man/gwr.basic.rd | 10 +--
man/gwr.collin.diagno.Rd | 2
man/gwr.cv.Rd | 2
man/gwr.cv.contrib.Rd | 2
man/gwr.generalised.Rd | 4 -
man/gwr.hetero.rd | 2
man/gwr.lcr.cv.Rd | 2
man/gwr.lcr.cv.contrib.Rd | 2
man/gwr.lcr.rd | 10 +--
man/gwr.mixed.rd | 2
man/gwr.predict.Rd | 2
man/gwr.robust.Rd | 2
man/gwr.t.adjust.rd | 2
man/gwss.rd | 2
man/mink.approach.rd |only
man/mink.matrixview.rd |only
man/model.selection.gwr.Rd | 8 +--
man/model.sort.gwr.Rd | 2
man/model.view.gwr.rd | 2
man/montecarlo.gwpca.1.rd | 2
man/montecarlo.gwpca.2.rd | 2
man/montecarlo.gwr.Rd | 2
man/montecarlo.gwss.Rd | 2
man/plot.mcsims.rd | 2
man/print.ggwrm.Rd | 2
man/print.gwrm.Rd | 3 -
man/print.gwrm.lcr.rd | 2
man/print.gwrm.pred.rd | 2
man/print.gwss.Rd | 2
man/writeGWR.Rd | 2
man/writeGWR.shp.Rd | 2
61 files changed, 236 insertions(+), 272 deletions(-)
Title: Differential Functioning of Items and Tests
Diff between DFIT versions 1.0-1 dated 2014-07-15 and 1.0-2 dated 2015-02-01
Description: A set of functions to perform Raju, van der Linden and Fleer's
(1995) Differential Functioning of Items and Tests (DFIT) analyses. It includes
functions to use the Monte Carlo Item Parameter Replication approach
(Oshima, Raju, & Nanda, 2006) for obtaining the associated statistical
significance tests cut-off points. They may also be used for a priori and
post-hoc power calculations.
Author: Victor H. Cervantes
Maintainer: Victor H. Cervantes
DESCRIPTION | 15 +++++++--------
MD5 | 6 +++---
NEWS | 3 +++
inst/CITATION | 2 +-
4 files changed, 14 insertions(+), 12 deletions(-)
Title: A Connection Interface to Libcurl
Diff between curl versions 0.4 dated 2015-01-08 and 0.5 dated 2015-02-01
Description: The curl() function provides a drop-in replacement for base url()
with better performance and support for http 2.0, ssl (https://, ftps://),
gzip, deflate and other libcurl goodies. This interface is implemented
using the RConnection API in order to support incremental processing of
both binary and text streams. If you are looking for a more-user-friendly
http client, try the RCurl or httr packages instead.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
DESCRIPTION | 13 +++++++------
MD5 | 10 +++++-----
NEWS | 3 +++
configure | 5 +++--
src/curl.c | 12 ++++++++++--
src/utils.c | 4 ++++
6 files changed, 32 insertions(+), 15 deletions(-)
Title: Business Days Calculations and Utilities
Diff between bizdays versions 0.1.5 dated 2014-06-16 and 0.2.1 dated 2015-02-01
Description: Business days calculations based on a list of holidays and
nonworking weekdays. Quite useful for fixed income and derivatives pricing.
Author: Wilson Freitas
Maintainer: Wilson Freitas
bizdays-0.1.5/bizdays/man/add.bizdays.Rd |only
bizdays-0.2.1/bizdays/DESCRIPTION | 17
bizdays-0.2.1/bizdays/MD5 | 40 -
bizdays-0.2.1/bizdays/NAMESPACE | 41 -
bizdays-0.2.1/bizdays/NEWS | 28
bizdays-0.2.1/bizdays/R/R-bizdays-package.r | 35 -
bizdays-0.2.1/bizdays/R/calendar.R | 733 +++++++++++++----------
bizdays-0.2.1/bizdays/README.md | 56 +
bizdays-0.2.1/bizdays/inst/tests/test-bizdays.R | 7
bizdays-0.2.1/bizdays/inst/tests/test-calendar.R | 28
bizdays-0.2.1/bizdays/man/Calendar.Rd | 77 +-
bizdays-0.2.1/bizdays/man/adjust.date.Rd | 63 -
bizdays-0.2.1/bizdays/man/bizdays-package.Rd |only
bizdays-0.2.1/bizdays/man/bizdays.Rd | 82 +-
bizdays-0.2.1/bizdays/man/bizdays.options.Rd | 33 -
bizdays-0.2.1/bizdays/man/bizdayse.Rd | 87 +-
bizdays-0.2.1/bizdays/man/bizseq.Rd | 44 -
bizdays-0.2.1/bizdays/man/bizyears.Rd | 71 +-
bizdays-0.2.1/bizdays/man/bizyearse.Rd |only
bizdays-0.2.1/bizdays/man/holidaysANBIMA.Rd | 5
bizdays-0.2.1/bizdays/man/is.bizday.Rd | 47 -
bizdays-0.2.1/bizdays/man/offset.Rd |only
bizdays-0.2.1/bizdays/vignettes |only
23 files changed, 884 insertions(+), 610 deletions(-)
Title: MA Birk's Functions
Diff between birk versions 1.2 dated 2014-11-07 and 1.3.0 dated 2015-02-01
Description: This is a compilation of functions that I found useful to make. It currently includes a unit of measurement conversion function, a Q10 calculator for temperature dependence of chemical and biological rates, and some miscellaneous wrapper functions to make R code shorter and faster to write.
Author: Matthew A. Birk
Maintainer: Matthew A. Birk
birk-1.2/birk/man/birk-package.Rd |only
birk-1.3.0/birk/DESCRIPTION | 19 ++---
birk-1.3.0/birk/MD5 | 26 ++++--
birk-1.3.0/birk/NAMESPACE | 9 ++
birk-1.3.0/birk/NEWS |only
birk-1.3.0/birk/R/Q10calc.R |only
birk-1.3.0/birk/R/birk.R |only
birk-1.3.0/birk/R/conv_unit.R | 117 +++++++++++++++++++++++++------
birk-1.3.0/birk/R/geom_mean.R | 23 +++++-
birk-1.3.0/birk/R/range_seq.R |only
birk-1.3.0/birk/R/se.R | 18 ++++
birk-1.3.0/birk/man/Q10calc.Rd |only
birk-1.3.0/birk/man/birk.Rd |only
birk-1.3.0/birk/man/conv_unit.Rd | 90 +++++++++++------------
birk-1.3.0/birk/man/conv_unit_options.Rd | 46 +++++++-----
birk-1.3.0/birk/man/geom_mean.Rd | 33 ++++++--
birk-1.3.0/birk/man/range_seq.Rd |only
birk-1.3.0/birk/man/se.Rd | 27 +++++--
18 files changed, 286 insertions(+), 122 deletions(-)
Title: Data Generation with Binary and Continuous Non-normal Components
Diff between BinNonNor versions 1.0 dated 2014-12-16 and 1.1 dated 2015-02-01
Description: Generation of multiple binary and continuous non-normal variables simultaneously
given the marginal characteristics and association structure based on the methodology
proposed by Demirtas et al. (2012).
Author: Gul Inan, Hakan Demirtas
Maintainer: Gul Inan
DESCRIPTION | 8 +--
MD5 | 38 +++++++-------
R/Int.Corr.NN.R | 10 +--
R/Tetra.Corr.BB.R | 10 +--
R/correlation.bound.check.R | 3 -
R/fleishman.coef.R | 3 -
R/gen.Bin.NonNor.R | 14 ++---
R/overall.corr.mat.R | 1
man/BinNonNor-package.Rd | 4 -
man/Biserial.Corr.BN.Rd | 9 +++
man/Int.Corr.NN.Rd | 2
man/Tetra.Corr.BB.Rd | 2
man/correlation.bound.check.Rd | 21 ++++++-
man/correlation.limits.Rd | 14 +++--
man/fleishman.coef.Rd | 13 ++--
man/gen.Bin.NonNor.Rd | 95 +++++++++++++++++++++---------------
man/overall.corr.mat.Rd | 11 +++-
man/validation.bin.Rd | 22 +++++---
man/validation.corr.Rd | 27 ++++++----
man/validation.skewness.kurtosis.Rd | 26 ++++++---
20 files changed, 207 insertions(+), 126 deletions(-)
Title: Computation of Bayes Factors for Common Designs
Diff between BayesFactor versions 0.9.9 dated 2014-10-22 and 0.9.10 dated 2015-02-01
Description: A suite of functions for computing
various Bayes factors for simple designs, including contingency tables,
one- and two-sample designs, one-way designs, general ANOVA designs, and
linear regression.
Author: Richard D. Morey [aut, cre],
Jeffrey N. Rouder [aut],
Tahira Jamil [ctb]
Maintainer: Richard D. Morey
BayesFactor-0.9.10/BayesFactor/DESCRIPTION | 12
BayesFactor-0.9.10/BayesFactor/MD5 | 127 +++++-----
BayesFactor-0.9.10/BayesFactor/NAMESPACE | 3
BayesFactor-0.9.10/BayesFactor/NEWS | 9
BayesFactor-0.9.10/BayesFactor/R/BayesFactorPCL-package.R | 4
BayesFactor-0.9.10/BayesFactor/R/RcppExports.R | 16 +
BayesFactor-0.9.10/BayesFactor/R/anovaBF.R | 2
BayesFactor-0.9.10/BayesFactor/R/common.R | 24 -
BayesFactor-0.9.10/BayesFactor/R/contingency-utility.R | 2
BayesFactor-0.9.10/BayesFactor/R/generalTest-utility.R | 12
BayesFactor-0.9.10/BayesFactor/R/generalTestBF.R | 2
BayesFactor-0.9.10/BayesFactor/R/logMean.R | 16 -
BayesFactor-0.9.10/BayesFactor/R/meta-ttest-utility.R | 12
BayesFactor-0.9.10/BayesFactor/R/meta.ttestBF.R | 2
BayesFactor-0.9.10/BayesFactor/R/methods-BFBayesFactor.R | 2
BayesFactor-0.9.10/BayesFactor/R/methods-BFlinearModel-compare.R | 75 +++--
BayesFactor-0.9.10/BayesFactor/R/nWayAOV-utility.R | 8
BayesFactor-0.9.10/BayesFactor/R/nWayAOV.R | 2
BayesFactor-0.9.10/BayesFactor/R/oneWayAOV_Fstat.R | 18 -
BayesFactor-0.9.10/BayesFactor/R/proportion-utility.R | 6
BayesFactor-0.9.10/BayesFactor/R/ttestBF.R | 2
BayesFactor-0.9.10/BayesFactor/R/ttest_tstat.R | 7
BayesFactor-0.9.10/BayesFactor/build/vignette.rds |binary
BayesFactor-0.9.10/BayesFactor/inst/doc/compare_lme4.html | 76 ++---
BayesFactor-0.9.10/BayesFactor/inst/doc/manual.html | 88 +++---
BayesFactor-0.9.10/BayesFactor/inst/doc/priors.html | 42 +--
BayesFactor-0.9.10/BayesFactor/man/BFBayesFactor-class.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/BFBayesFactorList-class.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/BFInfo.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/BFManual.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/BayesFactor-package.Rd | 7
BayesFactor-0.9.10/BayesFactor/man/anovaBF.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/as.BFBayesFactor.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/compare-methods.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/contingencyTableBF.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/enumerateGeneralModels.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/extractBF-methods.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/generalTestBF.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/grapes-same-grapes.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/grapes-termin-grapes.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/linearReg.R2stat.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/lmBF.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/logMeanExpLogs.Rd | 12
BayesFactor-0.9.10/BayesFactor/man/meta.ttestBF.Rd | 5
BayesFactor-0.9.10/BayesFactor/man/model-classes.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/model.matrix-methods.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/nWayAOV.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/oneWayAOV.Fstat.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/options-BayesFactor.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/plot.BFBayesFactor.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/plot.BFBayesFactorTop.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/posterior-methods.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/proportionBF.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/puzzles.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/raceDolls.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/recompute-methods.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/regressionBF.Rd | 3
BayesFactor-0.9.10/BayesFactor/man/ttest.tstat.Rd | 5
BayesFactor-0.9.10/BayesFactor/man/ttestBF.Rd | 5
BayesFactor-0.9.10/BayesFactor/src/BFPCL.h | 18 -
BayesFactor-0.9.10/BayesFactor/src/RcppExports.cpp | 62 ++++
BayesFactor-0.9.10/BayesFactor/src/bfcommon.h | 11
BayesFactor-0.9.10/BayesFactor/src/logRepresentedReal.cpp |only
BayesFactor-0.9.10/BayesFactor/src/logRepresentedReal.h |only
BayesFactor-0.9.10/BayesFactor/src/logSummaryStats.cpp |only
BayesFactor-0.9.10/BayesFactor/src/logUtility.cpp |only
BayesFactor-0.9.9/BayesFactor/src/logMean.c |only
67 files changed, 446 insertions(+), 332 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-09 2014.4-1
2013-09-29 2013.9-1