Title: Similarity Regression Functions
Description: Functions for performing Bayesian `similarity regression', adapted to model the association between an HPO-encoded patient phenotype and binary genotype. A `no association' model is compared with one in which the log odds of having a rare genotype is linked to the semantic similarity between patient phenotype and a latent characteristic phenotype. The method estimates the probability of an association together with an HPO-coded phenotype characteristic of the disease.
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between SimReg versions 1.1 dated 2015-08-27 and 1.2 dated 2015-09-15
DESCRIPTION | 8 - MD5 | 36 +++---- R/functions.R | 43 ++++---- R/plots.R | 4 R/simReg.R | 42 +++++--- man/get.term.term.matrix.Rd | 6 + man/hpo.plot.marginal.freqs.Rd | 8 + man/sim.reg.Rd | 9 + man/sim.reg.full.summary.Rd | 4 src/Chain.cpp | 45 ++------- src/DeltaLikelihood.cpp | 32 +++--- src/DeltaLikelihood.h | 4 src/Likelihood.cpp | 7 - src/Likelihood.h | 4 src/RcppExports.cpp | 169 +++++++++++++++++++++------------- src/RcppExports.h | 11 +- src/State.cpp | 55 ++++++++--- src/State.h | 47 +++++++-- src/Update.cpp | 203 ++++++++++++++++++++++++++++++----------- 19 files changed, 474 insertions(+), 263 deletions(-)
Title: Image Registration Using the NiftyReg Library
Description: Provides an R interface to the NiftyReg image registration tools <http://sourceforge.net/projects/niftyreg/>. Linear and nonlinear registration are supported, in two and three dimensions.
Author: Jon Clayden, based on original code by Marc Modat, Pankaj Daga and others
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNiftyReg versions 1.1.5 dated 2015-09-03 and 2.0.0 dated 2015-09-15
RNiftyReg-1.1.5/RNiftyReg/inst/extdata/source.nii.gz |only RNiftyReg-1.1.5/RNiftyReg/inst/extdata/target.nii.gz |only RNiftyReg-1.1.5/RNiftyReg/man/convertAffine.Rd |only RNiftyReg-1.1.5/RNiftyReg/man/getDeformationField.Rd |only RNiftyReg-1.1.5/RNiftyReg/man/transformVoxelToWorld.Rd |only RNiftyReg-1.1.5/RNiftyReg/man/transformWithAffine.Rd |only RNiftyReg-1.1.5/RNiftyReg/man/transformWithControlPoints.Rd |only RNiftyReg-1.1.5/RNiftyReg/man/xformToAffine.Rd |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_KLdivergence.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_KLdivergence.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_aladin.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_aladin.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_blockMatching.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_blockMatching.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_f3d.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_f3d.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_f3d_sym.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_f3d_sym.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_femTransformation.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_femTransformation.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_globalTransformation.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_globalTransformation.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_localTransformation.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_localTransformation.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_localTransformation_be.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_localTransformation_jac.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_macros.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_maths.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_maths.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_mutualinformation.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_mutualinformation.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_resampling.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_resampling.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_ssd.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_ssd.h |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_tools.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/_reg_tools.h |only RNiftyReg-1.1.5/RNiftyReg/src/exit.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/exit.h |only RNiftyReg-1.1.5/RNiftyReg/src/index.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/index.h |only RNiftyReg-1.1.5/RNiftyReg/src/nifti1.h |only RNiftyReg-1.1.5/RNiftyReg/src/nifti1_io.c |only RNiftyReg-1.1.5/RNiftyReg/src/nifti1_io.h |only RNiftyReg-1.1.5/RNiftyReg/src/niftyreg.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/niftyreg.h |only RNiftyReg-1.1.5/RNiftyReg/src/print.cpp |only RNiftyReg-1.1.5/RNiftyReg/src/substitutions.h |only RNiftyReg-1.1.5/RNiftyReg/src/znzlib.c |only RNiftyReg-1.1.5/RNiftyReg/src/znzlib.h |only RNiftyReg-2.0.0/RNiftyReg/DESCRIPTION | 20 RNiftyReg-2.0.0/RNiftyReg/MD5 | 239 ++- RNiftyReg-2.0.0/RNiftyReg/NAMESPACE | 55 RNiftyReg-2.0.0/RNiftyReg/NEWS | 40 RNiftyReg-2.0.0/RNiftyReg/R/affine.R | 377 ++++- RNiftyReg-2.0.0/RNiftyReg/R/image.R |only RNiftyReg-2.0.0/RNiftyReg/R/nifti.R |only RNiftyReg-2.0.0/RNiftyReg/R/niftyreg.R | 725 +++++----- RNiftyReg-2.0.0/RNiftyReg/R/transform.R | 267 ++- RNiftyReg-2.0.0/RNiftyReg/R/xform.R | 110 + RNiftyReg-2.0.0/RNiftyReg/R/zzz.R | 12 RNiftyReg-2.0.0/RNiftyReg/README.md |only RNiftyReg-2.0.0/RNiftyReg/inst/extdata/affine.txt | 8 RNiftyReg-2.0.0/RNiftyReg/inst/extdata/control.nii.gz |only RNiftyReg-2.0.0/RNiftyReg/inst/extdata/epi_t2.nii.gz |only RNiftyReg-2.0.0/RNiftyReg/inst/extdata/flash_t1.nii.gz |only RNiftyReg-2.0.0/RNiftyReg/inst/extdata/house.png |only RNiftyReg-2.0.0/RNiftyReg/inst/extdata/house_colour.png |only RNiftyReg-2.0.0/RNiftyReg/inst/extdata/house_colour_large.jpg |only RNiftyReg-2.0.0/RNiftyReg/inst/extdata/mni_brain.nii.gz |only RNiftyReg-2.0.0/RNiftyReg/man/affine.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/applyTransform.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/buildAffine.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/composeTransforms.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/decomposeAffine.Rd | 69 RNiftyReg-2.0.0/RNiftyReg/man/deformationField.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/dumpNifti.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/forward.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/halfTransform.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/internalImage.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/invertAffine.Rd | 31 RNiftyReg-2.0.0/RNiftyReg/man/isImage.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/jacobian.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/ndim.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/niftyreg.Rd | 132 + RNiftyReg-2.0.0/RNiftyReg/man/niftyreg.linear.Rd | 165 +- RNiftyReg-2.0.0/RNiftyReg/man/niftyreg.nonlinear.Rd | 188 +- RNiftyReg-2.0.0/RNiftyReg/man/pixdim.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/readAffine.Rd | 47 RNiftyReg-2.0.0/RNiftyReg/man/readNifti.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/updateNifti.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/voxelToWorld.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/writeAffine.Rd | 28 RNiftyReg-2.0.0/RNiftyReg/man/writeNifti.Rd |only RNiftyReg-2.0.0/RNiftyReg/man/xform.Rd |only RNiftyReg-2.0.0/RNiftyReg/src/AffineMatrix.cpp |only RNiftyReg-2.0.0/RNiftyReg/src/AffineMatrix.h |only RNiftyReg-2.0.0/RNiftyReg/src/DeformationField.cpp |only RNiftyReg-2.0.0/RNiftyReg/src/DeformationField.h |only RNiftyReg-2.0.0/RNiftyReg/src/Makevars | 20 RNiftyReg-2.0.0/RNiftyReg/src/NiftiImage.cpp |only RNiftyReg-2.0.0/RNiftyReg/src/NiftiImage.h |only RNiftyReg-2.0.0/RNiftyReg/src/aladin.cpp |only RNiftyReg-2.0.0/RNiftyReg/src/aladin.h |only RNiftyReg-2.0.0/RNiftyReg/src/config.h |only RNiftyReg-2.0.0/RNiftyReg/src/f3d.cpp |only RNiftyReg-2.0.0/RNiftyReg/src/f3d.h |only RNiftyReg-2.0.0/RNiftyReg/src/main.cpp |only RNiftyReg-2.0.0/RNiftyReg/src/niftilib |only RNiftyReg-2.0.0/RNiftyReg/src/print.h | 29 RNiftyReg-2.0.0/RNiftyReg/src/reg-lib |only RNiftyReg-2.0.0/RNiftyReg/src/zlib |only RNiftyReg-2.0.0/RNiftyReg/src/znzlib |only RNiftyReg-2.0.0/RNiftyReg/tests |only 114 files changed, 1704 insertions(+), 858 deletions(-)
Title: Simulation and Estimation of Log-GARCH Models
Description: Simulation and estimation of univariate and multivariate log-GARCH models. The main functions of the package are: lgarchSim(), mlgarchSim(), lgarch() and mlgarch(). The first two functions simulate from a univariate and a multivariate log-GARCH model, respectively, whereas the latter two estimate a univariate and multivariate log-GARCH model, respectively.
Author: Genaro Sucarrat
Maintainer: Genaro Sucarrat <genaro.sucarrat@bi.no>
Diff between lgarch versions 0.5 dated 2014-09-01 and 0.6-2 dated 2015-09-15
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- NAMESPACE | 1 + NEWS | 25 +++++++++++++++++++++---- R/lgarch.R | 49 +++++++++++++++++++++++++++++++++++++++---------- R/lgarchSim.R | 4 ++-- R/rss.R | 11 ++++++++--- R/summary.lgarch.R | 3 ++- man/lgarch-package.Rd | 4 ++-- 9 files changed, 89 insertions(+), 36 deletions(-)
Title: Visualization and Imputation of Missing Values
Description: New tools for the visualization of missing
and/or imputed values are introduced, which can be used for exploring the data and the
structure of the missing and/or imputed values. Depending on this structure
of the missing values, the corresponding methods may help to identify the
mechanism generating the missing values and allows to explore the data
including missing values. In addition, the quality of imputation can be
visually explored using various univariate, bivariate, multiple and
multivariate plot methods. A graphical user interface available in the
separate package VIMGUI allows an easy handling of the implemented plot
methods.
Author: Matthias Templ, Andreas Alfons, Alexander Kowarik, Bernd Prantner
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between VIM versions 4.3.0 dated 2015-07-07 and 4.4.1 dated 2015-09-15
DESCRIPTION | 30 +++++++++++++++--------------- MD5 | 20 ++++++++++---------- NEWS | 3 +++ R/colormapMiss.R | 2 +- R/hotdeck.R | 17 +++++++++++++++-- data/SBS5242.rda |binary data/chorizonDL.rda |binary data/kola.background.rda |binary data/sleep.rda |binary data/tao.rda |binary data/testdata.RData |binary 11 files changed, 44 insertions(+), 28 deletions(-)
Title: Statistical Tools for Topological Data Analysis
Description: Tools for the statistical analysis of persistent homology and for density clustering. For that, this package provides an R interface for the efficient algorithms of the C++ libraries GUDHI, Dionysus, and PHAT.
Author: Brittany T. Fasy, Jisu Kim, Fabrizio Lecci, Clement Maria, Vincent Rouvreau. The included GUDHI is authored by Clement Maria, Dionysus by Dmitriy Morozov, and PHAT by Ulrich Bauer, Michael Kerber, and Jan Reininghaus.
Maintainer: Jisu Kim <jisuk1@andrew.cmu.edu>
Diff between TDA versions 1.3 dated 2014-12-22 and 1.4 dated 2015-09-15
TDA-1.3/TDA/R/ripsArbitDiag.R |only TDA-1.3/TDA/R/ripsL2Diag.R |only TDA-1.3/TDA/src/boost/aligned_storage.hpp |only TDA-1.3/TDA/src/boost/archive |only TDA-1.3/TDA/src/boost/array.hpp |only TDA-1.3/TDA/src/boost/assert.hpp |only TDA-1.3/TDA/src/boost/bind |only TDA-1.3/TDA/src/boost/bind.hpp |only TDA-1.3/TDA/src/boost/blank.hpp |only TDA-1.3/TDA/src/boost/blank_fwd.hpp |only TDA-1.3/TDA/src/boost/call_traits.hpp |only TDA-1.3/TDA/src/boost/checked_delete.hpp |only TDA-1.3/TDA/src/boost/compressed_pair.hpp |only TDA-1.3/TDA/src/boost/concept |only TDA-1.3/TDA/src/boost/concept_archetype.hpp |only TDA-1.3/TDA/src/boost/concept_check |only TDA-1.3/TDA/src/boost/concept_check.hpp |only TDA-1.3/TDA/src/boost/config |only TDA-1.3/TDA/src/boost/config.hpp |only TDA-1.3/TDA/src/boost/container |only TDA-1.3/TDA/src/boost/cstdint.hpp |only TDA-1.3/TDA/src/boost/current_function.hpp |only TDA-1.3/TDA/src/boost/detail |only TDA-1.3/TDA/src/boost/exception |only TDA-1.3/TDA/src/boost/foreach.hpp 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TDA-1.3/TDA/src/boost/multi_index/detail/do_not_copy_elements_tag.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/duplicates_iterator.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/has_tag.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/hash_index_args.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/hash_index_iterator.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/hash_index_node.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/header_holder.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/index_base.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/index_loader.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/index_matcher.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/index_node_base.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/index_saver.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/invariant_assert.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/is_index_list.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/iter_adaptor.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/modify_key_adaptor.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/msvc_index_specifier.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/no_duplicate_tags.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/node_type.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/ord_index_args.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/ord_index_node.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/ord_index_ops.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/prevent_eti.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/safe_ctr_proxy.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/safe_mode.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/scope_guard.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/seq_index_node.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/seq_index_ops.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/serialization_version.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/uintptr_type.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/unbounded.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/value_compare.hpp |only TDA-1.3/TDA/src/boost/multi_index/detail/vartempl_support.hpp |only TDA-1.3/TDA/src/boost/multi_index/global_fun.hpp |only TDA-1.3/TDA/src/boost/multi_index/hashed_index.hpp |only TDA-1.3/TDA/src/boost/multi_index/hashed_index_fwd.hpp |only TDA-1.3/TDA/src/boost/multi_index/identity.hpp |only TDA-1.3/TDA/src/boost/multi_index/identity_fwd.hpp |only TDA-1.3/TDA/src/boost/multi_index/indexed_by.hpp |only TDA-1.3/TDA/src/boost/multi_index/key_extractors.hpp |only TDA-1.3/TDA/src/boost/multi_index/mem_fun.hpp |only TDA-1.3/TDA/src/boost/multi_index/member.hpp |only TDA-1.3/TDA/src/boost/multi_index/ordered_index.hpp |only TDA-1.3/TDA/src/boost/multi_index/ordered_index_fwd.hpp |only TDA-1.3/TDA/src/boost/multi_index/safe_mode_errors.hpp |only TDA-1.3/TDA/src/boost/multi_index/sequenced_index.hpp |only TDA-1.3/TDA/src/boost/multi_index/sequenced_index_fwd.hpp |only TDA-1.3/TDA/src/boost/multi_index/tag.hpp |only TDA-1.3/TDA/src/boost/multi_index_container.hpp |only TDA-1.3/TDA/src/boost/multi_index_container_fwd.hpp |only TDA-1.3/TDA/src/boost/next_prior.hpp |only TDA-1.3/TDA/src/boost/noncopyable.hpp |only TDA-1.3/TDA/src/boost/none.hpp |only TDA-1.3/TDA/src/boost/none_t.hpp |only TDA-1.3/TDA/src/boost/operators.hpp |only TDA-1.3/TDA/src/boost/optional |only TDA-1.3/TDA/src/boost/optional.hpp |only TDA-1.3/TDA/src/boost/parameter |only TDA-1.3/TDA/src/boost/parameter.hpp |only TDA-1.3/TDA/src/boost/pending |only TDA-1.3/TDA/src/boost/pointee.hpp |only TDA-1.3/TDA/src/boost/pointer_cast.hpp |only TDA-1.3/TDA/src/boost/pointer_to_other.hpp |only TDA-1.3/TDA/src/boost/preprocessor |only TDA-1.3/TDA/src/boost/preprocessor.hpp |only TDA-1.3/TDA/src/boost/progress.hpp |only TDA-1.3/TDA/src/boost/property_map |only TDA-1.3/TDA/src/boost/range |only TDA-1.3/TDA/src/boost/range.hpp |only TDA-1.3/TDA/src/boost/ref.hpp |only 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TDA-1.4/TDA/R/siloF.R | 10 TDA-1.4/TDA/R/sphereUnif.R | 36 TDA-1.4/TDA/R/summary.diagram.R | 18 TDA-1.4/TDA/R/summary.maxPersistence.R | 23 TDA-1.4/TDA/R/torusUnif.R | 48 TDA-1.4/TDA/R/wasserstein.R | 61 TDA-1.4/TDA/build/vignette.rds |binary TDA-1.4/TDA/inst/doc/article.R | 912 +- TDA-1.4/TDA/inst/doc/article.Rnw | 448 - TDA-1.4/TDA/inst/doc/article.pdf |binary TDA-1.4/TDA/man/TDA-internal.Rd |only TDA-1.4/TDA/man/TDA-package.Rd | 8 TDA-1.4/TDA/man/alphaDiag.Rd |only TDA-1.4/TDA/man/bootstrapBand.Rd | 98 TDA-1.4/TDA/man/bootstrapDiagram.Rd | 129 TDA-1.4/TDA/man/bottleneck.Rd | 27 TDA-1.4/TDA/man/circleUnif.Rd | 6 TDA-1.4/TDA/man/clusterTree.Rd | 56 TDA-1.4/TDA/man/distFct.Rd | 30 TDA-1.4/TDA/man/dtm.Rd | 27 TDA-1.4/TDA/man/gridDiag.Rd | 162 TDA-1.4/TDA/man/hausdInterval.Rd | 59 TDA-1.4/TDA/man/kde.Rd | 73 TDA-1.4/TDA/man/kernelDist.Rd | 80 TDA-1.4/TDA/man/knnDE.Rd | 59 TDA-1.4/TDA/man/landscape.Rd | 63 TDA-1.4/TDA/man/maxPersistence.Rd | 160 TDA-1.4/TDA/man/multipBootstrap.Rd | 112 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Title: Clustering Mutations using High Throughput Sequencing (HTS) Data
Description: Using HTS data, clusters mutations in order to recreate putative clones from the data provided. It requires genotype at the location of the variant as well as the depth of coverage and number of reads supporting the mutation. Additional information may be provided, such as the contamination in the tumor sample. This package also provides a function QuantumCat() which simulates data obtained from tumor sequencing. Latest version can be found at github/DeveauP/QuantumClone .
Author: Paul Deveau [aut, cre]
Maintainer: Paul Deveau <paul.deveau@curie.fr>
Diff between QuantumClone versions 0.6.15 dated 2015-06-12 and 0.9.15 dated 2015-09-15
DESCRIPTION | 6 - MD5 | 76 +++++++-------- NAMESPACE | 32 +++--- R/EM.R | 29 ++++- R/QuantumClone_v3.R | 24 ++++ man/BIC_criterion.Rd | 36 +++---- man/CellularitiesFromFreq.Rd | 76 +++++++-------- man/Cluster_plot_from_cell.Rd | 92 +++++++++--------- man/EM.algo.Rd | 54 +++++----- man/EM_clustering.Rd | 68 ++++++------- man/From_freq_to_cell.Rd | 74 +++++++------- man/FullEM.Rd | 56 +++++------ man/Multitest.Rd | 116 +++++++++++------------ man/One_D_plot.Rd | 40 ++++---- man/One_step_clustering.Rd | 153 +++++++++++++++--------------- man/Patient_schrodinger_cellularities.Rd | 56 +++++------ man/Probability.to.belong.to.clone.Rd | 64 ++++++------ man/QuantumCat.Rd | 80 ++++++++-------- man/QuantumClone.Rd | 154 +++++++++++++++---------------- man/ThreeD_plot.Rd | 68 ++++++------- man/Tree_generation.Rd | 42 ++++---- man/add_leaf_list.Rd | 52 +++++----- man/create_priors.Rd | 40 ++++---- man/e.step.Rd | 48 ++++----- man/filter_on_fik.Rd | 36 +++---- man/find_x_position.Rd | 44 ++++---- man/hard.clustering.Rd | 36 +++---- man/is_included.Rd | 40 ++++---- man/list_prod.Rd | 46 ++++----- man/longueur.Rd | 40 ++++---- man/m.step.Rd | 60 ++++++------ man/manual_plot_trees.Rd | 48 ++++----- man/multiplot_trees.Rd | 44 ++++---- man/parallelEM.Rd | 66 ++++++------- man/phylo_tree_generation.Rd | 40 ++++---- man/plot_cell_from_Return_out.Rd | 44 ++++---- man/plot_with_margins_densities.Rd | 62 ++++++------ man/statistics_on_Multitest.Rd | 122 ++++++++++++------------ man/strcount.Rd | 42 ++++---- 39 files changed, 1171 insertions(+), 1135 deletions(-)
Title: Pathwise Calibrated Sparse Shooting Algorithm
Description: Implement the pathwise calibrated sparse shooting algorithm (PICASSO) for high dimensional regularized sparse linear regression, sparse logistic regression, and sparse undirected graphical model estimation. As a pathwise coordinate optimization algorithm, PICASSO exploits warm start initialization, active set updating, and strong rule for coordinate preselection to boost computation, and attains a linear convergence to a unique sparse local optimum with optimal statistical properties. Moreover, users can choose different regularizers, including L1, MCP, and SCAD regularizers. The computation is memory-optimized using the sparse matrix output.
Author: Xingguo Li, Tuo Zhao, and Han Liu
Maintainer: Xingguo Li <xingguo.leo@gmail.com>
Diff between picasso versions 0.3.0 dated 2014-10-18 and 0.4.7 dated 2015-09-15
picasso-0.3.0/picasso/R/glasso.R |only picasso-0.3.0/picasso/R/lasso.R |only picasso-0.3.0/picasso/R/logit.gr.orth.R |only picasso-0.3.0/picasso/R/mvr.orth.R |only picasso-0.3.0/picasso/R/picasso.mvr.R |only picasso-0.3.0/picasso/R/scio.R |only picasso-0.3.0/picasso/man/print.mvr.Rd |only picasso-0.3.0/picasso/src/mymath.c |only picasso-0.3.0/picasso/src/picasso_group_cyclic_orth.c |only picasso-0.3.0/picasso/src/picasso_group_greedy_orth.c |only picasso-0.3.0/picasso/src/picasso_group_prox_orth.c |only picasso-0.3.0/picasso/src/picasso_group_stoc_orth.c |only picasso-0.3.0/picasso/src/picasso_lasso_cyclic.c |only picasso-0.3.0/picasso/src/picasso_lasso_cyclic0.c |only picasso-0.3.0/picasso/src/picasso_lasso_greedy.c |only picasso-0.3.0/picasso/src/picasso_lasso_prox.c |only picasso-0.3.0/picasso/src/picasso_lasso_stoc.c |only picasso-0.3.0/picasso/src/picasso_logit_gr_cyclic_orth.c |only picasso-0.3.0/picasso/src/picasso_logit_gr_greedy_orth.c |only picasso-0.3.0/picasso/src/picasso_logit_gr_prox_orth.c |only picasso-0.3.0/picasso/src/picasso_logit_gr_stoc_orth.c |only picasso-0.3.0/picasso/src/picasso_mvr_cyclic_orth.c |only picasso-0.3.0/picasso/src/picasso_mvr_greedy_orth.c |only picasso-0.3.0/picasso/src/picasso_mvr_prox_orth.c |only picasso-0.3.0/picasso/src/picasso_mvr_stoc_orth.c |only picasso-0.3.0/picasso/src/picasso_scio_cyclic.c |only picasso-0.3.0/picasso/src/picasso_scio_greedy.c |only picasso-0.3.0/picasso/src/picasso_scio_prox.c |only picasso-0.3.0/picasso/src/picasso_scio_stoc.c |only picasso-0.4.7/picasso/DESCRIPTION | 13 picasso-0.4.7/picasso/MD5 | 62 -- picasso-0.4.7/picasso/NAMESPACE | 6 picasso-0.4.7/picasso/R/lasso.sc.cov.R |only picasso-0.4.7/picasso/R/lasso.sc.naive.R |only picasso-0.4.7/picasso/R/logit.R | 352 +++++++-------- picasso-0.4.7/picasso/R/picasso.R | 50 +- picasso-0.4.7/picasso/R/picasso.lasso.R | 305 +++--------- picasso-0.4.7/picasso/R/picasso.logit.R | 225 ++------- picasso-0.4.7/picasso/R/picasso.scio.R | 80 +-- picasso-0.4.7/picasso/R/scio.sc.R |only picasso-0.4.7/picasso/man/picasso-package.Rd | 6 picasso-0.4.7/picasso/man/picasso.Rd | 108 +--- picasso-0.4.7/picasso/man/predict.logit.Rd | 2 picasso-0.4.7/picasso/src/lambda_max.c |only picasso-0.4.7/picasso/src/mymath.h | 63 ++ picasso-0.4.7/picasso/src/mymath1.c |only picasso-0.4.7/picasso/src/picasso_lasso_sc_cov.c |only picasso-0.4.7/picasso/src/picasso_lasso_sc_naive.c |only picasso-0.4.7/picasso/src/picasso_logit_cyclic.c | 22 picasso-0.4.7/picasso/src/picasso_scio_sc.c |only picasso-0.4.7/picasso/src/standardize_design.c |only 51 files changed, 518 insertions(+), 776 deletions(-)
Title: Assessment of Stability of Individual Objects or Clusters in
Partitioning Solutions
Description: Allows one to assess the stability of individual objects, clusters and whole clustering solutions based on repeated runs of the K-means and K-medoids partitioning algorithms.
Author: Etienne Lord, Francois-Joseph Lapointe, and Vladimir Makarenkov
Maintainer: Etienne Lord <m.etienne.lord@gmail.com>
Diff between ClusterStability versions 1.0.0 dated 2015-09-14 and 1.0.1 dated 2015-09-15
ClusterStability-1.0.0/ClusterStability/src/Makevars |only ClusterStability-1.0.1/ClusterStability/DESCRIPTION | 10 +++++----- ClusterStability-1.0.1/ClusterStability/MD5 | 6 +++--- ClusterStability-1.0.1/ClusterStability/NEWS |only ClusterStability-1.0.1/ClusterStability/man/ClusterStability-package.Rd | 2 +- 5 files changed, 9 insertions(+), 9 deletions(-)
More information about ClusterStability at CRAN
Permanent link
Title: Bayesian Estimation of Incoherent Neutron Scattering Backgrounds
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 <av.gagin@gmail.com>
Diff between BBEST versions 0.1-4 dated 2015-04-06 and 0.1-5 dated 2015-09-15
DESCRIPTION | 10 MD5 | 6 NAMESPACE | 4 README.md | 704 ++++++++++++++++++++++++++++++------------------------------ 4 files changed, 363 insertions(+), 361 deletions(-)
Title: Visualizing Association Rules and Frequent Itemsets
Description: Extends package arules with various visualization techniques for association rules and itemsets. The package also includes several interactive visualizations for rule exploration.
Author: Michael Hahsler and Sudheer Chelluboina
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arulesViz versions 1.0-2 dated 2015-07-01 and 1.0-4 dated 2015-09-15
DESCRIPTION | 11 MD5 | 14 - R/AAA_helpers.R | 20 - R/graph.R | 6 R/groupedmatrix.R | 677 ++++++++++++++++++++++++------------------------- build/vignette.rds |binary inst/NEWS | 8 inst/doc/arulesViz.pdf |binary 8 files changed, 368 insertions(+), 368 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing,
manipulating and analyzing transaction data and patterns (frequent
itemsets and association rules). Also provides interfaces to
C implementations of the association mining algorithms Apriori and Eclat
by C. Borgelt.
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph],
Christian Borgelt [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arules versions 1.1-9 dated 2015-07-14 and 1.2-0 dated 2015-09-15
arules-1.1-9/arules/tests/associations.R |only arules-1.1-9/arules/tests/associations.Rout.save |only arules-1.1-9/arules/tests/extract.R |only arules-1.1-9/arules/tests/extract.Rout.save |only arules-1.1-9/arules/tests/interfaces.R |only arules-1.1-9/arules/tests/interfaces.Rout.save |only arules-1.1-9/arules/tests/itemMatrix.R |only arules-1.1-9/arules/tests/itemMatrix.Rout.save |only arules-1.1-9/arules/tests/matrix.R |only arules-1.1-9/arules/tests/matrix.Rout.save |only arules-1.1-9/arules/tests/measures.R |only arules-1.1-9/arules/tests/measures.Rout.save |only arules-1.1-9/arules/tests/sets.R |only arules-1.1-9/arules/tests/sets.Rout.save |only arules-1.1-9/arules/tests/transactions.R |only arules-1.1-9/arules/tests/transactions.Rout.save |only arules-1.2-0/arules/DESCRIPTION | 9 arules-1.2-0/arules/MD5 | 113 ++-- arules-1.2-0/arules/NAMESPACE | 11 arules-1.2-0/arules/R/AAADefs.R | 26 + arules-1.2-0/arules/R/AllClasses.R | 84 ++- arules-1.2-0/arules/R/Matrix.R | 34 - arules-1.2-0/arules/R/associations.R | 14 arules-1.2-0/arules/R/eclat.R | 6 arules-1.2-0/arules/R/inspect.R | 483 ++++++++++-------- arules-1.2-0/arules/R/is.superset.R | 11 arules-1.2-0/arules/R/itemCoding.R | 6 arules-1.2-0/arules/R/itemFrequency.R | 341 ++++++------- arules-1.2-0/arules/R/itemMatrix.R | 592 +++++++++++------------ arules-1.2-0/arules/R/itemsets.R | 30 - arules-1.2-0/arules/R/random.transactions.R | 10 arules-1.2-0/arules/R/read_write.R | 13 arules-1.2-0/arules/R/rules.R | 9 arules-1.2-0/arules/R/support.R | 200 ++++--- arules-1.2-0/arules/R/tidLists.R | 347 +++++++------ arules-1.2-0/arules/R/transactions.R | 97 ++- arules-1.2-0/arules/R/warm.R |only arules-1.2-0/arules/data/Adult.rda |binary arules-1.2-0/arules/data/Epub.rda |binary arules-1.2-0/arules/data/Groceries.rda |binary arules-1.2-0/arules/data/Income.rda |binary arules-1.2-0/arules/data/SunBai.rda |only arules-1.2-0/arules/data/datalist |only arules-1.2-0/arules/inst/NEWS | 41 + arules-1.2-0/arules/inst/doc/arules.R | 4 arules-1.2-0/arules/inst/doc/arules.Rnw | 8 arules-1.2-0/arules/inst/doc/arules.pdf |binary arules-1.2-0/arules/inst/tests |only arules-1.2-0/arules/man/SunBai.Rd |only arules-1.2-0/arules/man/associations-class.Rd | 6 arules-1.2-0/arules/man/hits.Rd |only arules-1.2-0/arules/man/inspect.Rd | 8 arules-1.2-0/arules/man/itemFrequency.Rd | 4 arules-1.2-0/arules/man/itemFrequencyPlot.Rd | 4 arules-1.2-0/arules/man/itemMatrix-class.Rd | 36 - arules-1.2-0/arules/man/random.transactions.Rd | 18 arules-1.2-0/arules/man/rules-class.Rd | 5 arules-1.2-0/arules/man/sort.Rd | 25 arules-1.2-0/arules/man/support.Rd | 8 arules-1.2-0/arules/man/tidLists-class.Rd | 44 + arules-1.2-0/arules/man/transactions-class.Rd | 18 arules-1.2-0/arules/man/weclat.Rd |only arules-1.2-0/arules/src/similarity.c |only arules-1.2-0/arules/src/warm.c |only arules-1.2-0/arules/tests/testthat.R |only arules-1.2-0/arules/vignettes/arules.Rnw | 8 66 files changed, 1506 insertions(+), 1167 deletions(-)
Title: Interpolation of Irregularly and Regularly Spaced Data
Description: Several cubic spline interpolation methods of H. Akima for irregular and
regular gridded data are available through this package, both for the bivariate case
(irregular data: ACM 526 and ACM 761, regular data: ACM 433) and univariate case (ACM 697).
Linear interpolation of irregular gridded data is also covered by reusing D. J. Renkas
triangulation code which is part of Akimas Fortran code.
Author: Hiroshi Akima [aut, cph] (Fortran code (TOMS 526, 761, 697 and 433)),
Albrecht Gebhardt [aut, cre, cph] (R port (interp* functions), bicubic*
functions),
Thomas Petzold [ctb, cph] (aspline function),
Martin Maechler [ctb, cph] (interp2xyz function + enhancements),
YYYY Association for Computing Machinery, Inc. [cph] (covers code from
TOMS 526, 761, 697 and 433)
Maintainer: Albrecht Gebhardt <albrecht.gebhardt@aau.at>
Diff between akima versions 0.5-11 dated 2013-09-16 and 0.5-12 dated 2015-09-15
akima-0.5-11/akima/ChangeLog |only akima-0.5-11/akima/PORTING |only akima-0.5-11/akima/src/ttidbs.f |only akima-0.5-12/akima/DESCRIPTION | 42 ++++++++++++++----- akima-0.5-12/akima/MD5 | 19 +++----- akima-0.5-12/akima/NAMESPACE | 9 ++++ akima-0.5-12/akima/R/interp.R | 82 +++++++++++++++++++++++++++----------- akima-0.5-12/akima/R/interpp.R | 44 +++++++++++++++++--- akima-0.5-12/akima/README | 76 ++++++++++++++++++++++++++++++++++- akima-0.5-12/akima/cleanup | 1 akima-0.5-12/akima/man/interp.Rd | 51 ++++++++++++++++++----- akima-0.5-12/akima/man/interpp.Rd | 80 +++++++++++++++++++++++++------------ 12 files changed, 315 insertions(+), 89 deletions(-)
Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in
tabular data such as primary and secondary cell suppression are covered in
this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@statistik.gv.at>
Diff between sdcTable versions 0.19.3 dated 2015-08-13 and 0.19.4 dated 2015-09-15
DESCRIPTION | 8 +++---- MD5 | 12 +++++----- R/export_functions.r | 49 +++++++++++-------------------------------- R/methods_class_sdcProblem.r | 3 +- build/vignette.rds |binary inst/doc/sdcTable.pdf |binary src/suppMultDimTable.cpp | 15 +++++++++---- 7 files changed, 36 insertions(+), 51 deletions(-)
Title: Interface to the 'Handsontable.js' Library
Description: An R interface to the 'Handsontable' JavaScript library, which is a
minimalist Excel-like data grid editor.
Author: Jonathan Owen [aut, cre, cph],
Jeff Allen [ctb],
Yihui Xie [ctb],
Enzo Martoglio [ctb],
Warpechowski Marcin [ctb, cph] (Handsontable.js library),
Handsoncode sp. z o.o. [ctb, cph] (Handsontable.js library),
Aisch Gregor [ctb, cph] (Chroma.js library),
Wood Tim [ctb, cph] (Moment.js library),
Chernev Iskren [ctb, cph] (Moment.js library),
Moment.js contributors [ctb, cph] (Moment.js library),
Bushell David [ctb, cph] (Pikaday.js library),
jQuery Foundation [ctb, cph] (jQuery.js library),
Splunk Inc [ctb, cph] (Sparkline.js library)
Maintainer: Jonathan Owen <jonathanro@gmail.com>
Diff between rhandsontable versions 0.2 dated 2015-08-25 and 0.2.1 dated 2015-09-15
DESCRIPTION | 6 MD5 | 31 +- NAMESPACE | 2 NEWS | 17 + R/misc.R | 12 - R/rhandsontable-package.R | 1 R/rhandsontable.R | 406 ++++++++++++++++++++++++-------------- build/vignette.rds |binary inst/doc/intro_rhandsontable.R | 39 +++ inst/doc/intro_rhandsontable.Rmd | 58 ++++- inst/doc/intro_rhandsontable.html | 154 +++++++++----- inst/htmlwidgets/rhandsontable.js | 127 ++--------- man/hot_col.Rd | 11 - man/hot_context_menu.Rd |only man/hot_table.Rd | 28 -- man/rhandsontable.Rd | 12 - vignettes/intro_rhandsontable.Rmd | 58 ++++- 17 files changed, 600 insertions(+), 362 deletions(-)
Title: Projection Pursuit Classification Tree Visualization
Description: Tools for exploring projection pursuit classification tree using
various projection pursuit indices.
Author: Eun-Kyung Lee
Maintainer: Eun-Kyung Lee <lee.eunk@gmail.com>
Diff between PPtreeViz versions 1.1.0 dated 2015-06-25 and 1.3.0 dated 2015-09-15
DESCRIPTION | 16 +++++++-------- MD5 | 46 ++++++++++++++++++++++----------------------- NAMESPACE | 1 R/Huberplot.R | 4 +-- R/LDAopt.R | 4 +-- R/PDAopt.R | 2 - R/PPclassNodeViz.R | 18 ++++++++++------- R/PPclassify.R | 7 +++--- R/PPoptViz.R | 6 ++--- R/PPtreeClass.R | 12 +++++------ R/plotPPtreeclass.R | 2 - R/predictPPtreeclass.R | 3 -- R/printPPtreeclass.R | 2 - man/Huber.plot.Rd | 4 +-- man/LDAopt.Rd | 4 +-- man/PDAopt.Rd | 2 - man/PP.Tree.class.Rd | 2 - man/PP.classify.Rd | 2 - man/PPclassNode.Viz.Rd | 2 - man/PPopt.Viz.Rd | 4 +-- man/plot.PPtreeclass.Rd | 2 - man/predict.PPtreeclass.Rd | 2 - man/print.PPtreeclass.Rd | 2 - src/PPoptimize.cpp | 4 +-- 24 files changed, 78 insertions(+), 75 deletions(-)
Title: Fitting Finite Mixture of Scale Mixture of Skew-Normal
Distributions
Description: Functions to fit finite mixture of scale mixture of
skew-normal (FM-SMSN) distributions.
Author: Marcos Prates [aut, cre, trl], Victor Lachos [aut], Celso Cabral [aut]
Maintainer: Marcos Prates <marcosop@est.ufmg.br>
Diff between mixsmsn versions 1.0-9 dated 2013-08-17 and 1.1-0 dated 2015-09-15
ChangeLog | 4 ++ DESCRIPTION | 18 ++++++----- MD5 | 14 ++++---- NAMESPACE | 8 ++++ R/dens.R | 98 ++++++++++++++++++++++++++++++------------------------------ R/gen.R | 40 ++++++++++++------------ R/mixsmsn.R | 26 +++++++-------- R/utils.R | 14 ++++---- 8 files changed, 118 insertions(+), 104 deletions(-)
Title: Tools for Data Handling and Analysis in Macroecology
Description: R functions for handling, processing, and analyzing geographic data on
species' distributions and environmental variables as well as species' description
and conservation information.
Author: Bruno Vilela & Fabricio Villalobos
Maintainer: Bruno Vilela <brunovilelasilva@hotmail.com>
Diff between letsR versions 2.1 dated 2015-04-16 and 2.2 dated 2015-09-15
letsR-2.1/letsR/man/letsR.Rd |only letsR-2.2/letsR/DESCRIPTION | 12 - letsR-2.2/letsR/MD5 | 134 ++++++++------- letsR-2.2/letsR/NAMESPACE | 19 ++ letsR-2.2/letsR/R/letsR-package.R | 15 + letsR-2.2/letsR/R/lets_correl.R | 6 letsR-2.2/letsR/R/lets_iucn_historic.R | 127 +++++++------- letsR-2.2/letsR/R/lets_iucncont.R | 8 letsR-2.2/letsR/R/lets_presab.R | 24 +- letsR-2.2/letsR/R/lets_presab_birds.R | 23 +- letsR-2.2/letsR/R/lets_presab_grid.R |only letsR-2.2/letsR/R/lets_presab_points.R | 3 letsR-2.2/letsR/R/lets_subsetPAM.R |only letsR-2.2/letsR/R/unicas.R | 2 letsR-2.2/letsR/README.md | 4 letsR-2.2/letsR/inst/CITATION |only letsR-2.2/letsR/man/IUCN.Rd | 2 letsR-2.2/letsR/man/PAM.Rd | 2 letsR-2.2/letsR/man/Phyllomedusa.Rd | 2 letsR-2.2/letsR/man/PresenceAbsence.Rd | 2 letsR-2.2/letsR/man/lets.addpoly.Rd | 2 letsR-2.2/letsR/man/lets.addvar.Rd | 2 letsR-2.2/letsR/man/lets.classvar.Rd | 2 letsR-2.2/letsR/man/lets.correl.Rd | 2 letsR-2.2/letsR/man/lets.distmat.Rd | 2 letsR-2.2/letsR/man/lets.field.Rd | 2 letsR-2.2/letsR/man/lets.gridirizer.Rd | 2 letsR-2.2/letsR/man/lets.iucn.Rd | 2 letsR-2.2/letsR/man/lets.iucn.ha.Rd | 2 letsR-2.2/letsR/man/lets.iucn.his.Rd | 2 letsR-2.2/letsR/man/lets.iucncont.Rd | 6 letsR-2.2/letsR/man/lets.maplizer.Rd | 2 letsR-2.2/letsR/man/lets.midpoint.Rd | 2 letsR-2.2/letsR/man/lets.overlap.Rd | 2 letsR-2.2/letsR/man/lets.pamcrop.Rd | 2 letsR-2.2/letsR/man/lets.presab.Rd | 17 + letsR-2.2/letsR/man/lets.presab.birds.Rd | 16 + letsR-2.2/letsR/man/lets.presab.grid.Rd |only letsR-2.2/letsR/man/lets.presab.points.Rd | 5 letsR-2.2/letsR/man/lets.rangesize.Rd | 2 letsR-2.2/letsR/man/lets.shFilter.Rd | 2 letsR-2.2/letsR/man/lets.subsetPAM.Rd |only letsR-2.2/letsR/man/lets.summarizer.Rd | 2 letsR-2.2/letsR/man/lets.transf.Rd | 2 letsR-2.2/letsR/man/letsR-package.Rd |only letsR-2.2/letsR/man/plot.PresenceAbsence.Rd | 2 letsR-2.2/letsR/man/print.PresenceAbsence.Rd | 2 letsR-2.2/letsR/man/print.summary.PresenceAbsence.Rd | 2 letsR-2.2/letsR/man/summary.PresenceAbsence.Rd | 2 letsR-2.2/letsR/man/temp.Rd | 2 letsR-2.2/letsR/tests/testthat/test-lets_addpoly.R | 4 letsR-2.2/letsR/tests/testthat/test-lets_addvar.R | 8 letsR-2.2/letsR/tests/testthat/test-lets_classvar.R | 6 letsR-2.2/letsR/tests/testthat/test-lets_correl.R | 7 letsR-2.2/letsR/tests/testthat/test-lets_distmat.R | 8 letsR-2.2/letsR/tests/testthat/test-lets_field.R | 12 - letsR-2.2/letsR/tests/testthat/test-lets_gridirizer.R | 2 letsR-2.2/letsR/tests/testthat/test-lets_iuccont.R |only letsR-2.2/letsR/tests/testthat/test-lets_iucn.R | 8 letsR-2.2/letsR/tests/testthat/test-lets_iucn_ha.R | 6 letsR-2.2/letsR/tests/testthat/test-lets_iucn_his.R | 6 letsR-2.2/letsR/tests/testthat/test-lets_maplizer.R | 6 letsR-2.2/letsR/tests/testthat/test-lets_midpoint.R | 4 letsR-2.2/letsR/tests/testthat/test-lets_overlap.R | 14 - letsR-2.2/letsR/tests/testthat/test-lets_pamcrop.R | 4 letsR-2.2/letsR/tests/testthat/test-lets_presab.R | 17 + letsR-2.2/letsR/tests/testthat/test-lets_presab_birds.R | 24 ++ letsR-2.2/letsR/tests/testthat/test-lets_presab_grid.R |only letsR-2.2/letsR/tests/testthat/test-lets_presab_points.R | 10 - letsR-2.2/letsR/tests/testthat/test-lets_rangesize.R | 14 - letsR-2.2/letsR/tests/testthat/test-lets_subsetPAM.R |only letsR-2.2/letsR/tests/testthat/test-lets_summarizer.R | 6 letsR-2.2/letsR/tests/testthat/test-lets_transf.R |only letsR-2.2/letsR/tests/testthat/test-printplotsummary.R |only 74 files changed, 385 insertions(+), 256 deletions(-)
Title: Sean Lahman's Baseball Database
Description: Provides the tables from Sean Lahman's Baseball Database as a set of R data.frames.
It uses the data on pitching, hitting and fielding performance and other tables
from 1871 through 2014, as recorded in the 2015 version of the database.
Author: Michael Friendly [aut], Dennis Murphy [ctb], Martin Monkman [ctb], Chris Dalzell [cre, ctb]
Maintainer: Chris Dalzell <cdalzell@gmail.com>
Diff between Lahman versions 3.0-1 dated 2014-09-13 and 4.0-1 dated 2015-09-15
Lahman-3.0-1/Lahman/R/sysdata.rda |only Lahman-3.0-1/Lahman/data/SchoolsPlayers.RData |only Lahman-3.0-1/Lahman/inst/scripts/README.md |only Lahman-3.0-1/Lahman/inst/scripts/lahmanData.R |only Lahman-3.0-1/Lahman/man/SchoolsPlayers.Rd |only Lahman-4.0-1/Lahman/DESCRIPTION | 29 ++-- Lahman-4.0-1/Lahman/MD5 | 128 ++++++++++----------- Lahman-4.0-1/Lahman/NEWS | 11 - Lahman-4.0-1/Lahman/R/Label.R | 2 Lahman-4.0-1/Lahman/R/battingStats.R | 2 Lahman-4.0-1/Lahman/README.md |only Lahman-4.0-1/Lahman/data/AllstarFull.RData |binary Lahman-4.0-1/Lahman/data/Appearances.RData |binary Lahman-4.0-1/Lahman/data/AwardsManagers.RData |binary Lahman-4.0-1/Lahman/data/AwardsPlayers.RData |binary Lahman-4.0-1/Lahman/data/AwardsShareManagers.RData |binary Lahman-4.0-1/Lahman/data/AwardsSharePlayers.RData |binary Lahman-4.0-1/Lahman/data/Batting.RData |binary Lahman-4.0-1/Lahman/data/BattingPost.RData |binary Lahman-4.0-1/Lahman/data/CollegePlaying.RData |only Lahman-4.0-1/Lahman/data/Fielding.RData |binary Lahman-4.0-1/Lahman/data/FieldingOF.RData |binary Lahman-4.0-1/Lahman/data/FieldingPost.RData |binary Lahman-4.0-1/Lahman/data/HallOfFame.RData |binary Lahman-4.0-1/Lahman/data/LahmanData.RData |binary Lahman-4.0-1/Lahman/data/Managers.RData |binary Lahman-4.0-1/Lahman/data/ManagersHalf.RData |binary Lahman-4.0-1/Lahman/data/Master.RData |binary Lahman-4.0-1/Lahman/data/Pitching.RData |binary Lahman-4.0-1/Lahman/data/PitchingPost.RData |binary Lahman-4.0-1/Lahman/data/Salaries.RData |binary Lahman-4.0-1/Lahman/data/Schools.RData |binary Lahman-4.0-1/Lahman/data/SeriesPost.RData |binary Lahman-4.0-1/Lahman/data/Teams.RData |binary Lahman-4.0-1/Lahman/data/TeamsFranchises.RData |binary Lahman-4.0-1/Lahman/data/TeamsHalf.RData |binary Lahman-4.0-1/Lahman/data/battingLabels.RData |binary Lahman-4.0-1/Lahman/data/datalist | 2 Lahman-4.0-1/Lahman/data/fieldingLabels.RData |binary Lahman-4.0-1/Lahman/data/pitchingLabels.RData |binary Lahman-4.0-1/Lahman/demo/batting-summstats.R | 4 Lahman-4.0-1/Lahman/inst/scripts/LahmanData.R |only Lahman-4.0-1/Lahman/inst/scripts/compress-data.R |only Lahman-4.0-1/Lahman/inst/scripts/readLahman.R | 97 ++++++++------- Lahman-4.0-1/Lahman/man/AllstarFull.Rd | 4 Lahman-4.0-1/Lahman/man/Appearances.Rd | 5 Lahman-4.0-1/Lahman/man/AwardsManagers.Rd | 4 Lahman-4.0-1/Lahman/man/AwardsPlayers.Rd | 6 Lahman-4.0-1/Lahman/man/AwardsShareManagers.Rd | 4 Lahman-4.0-1/Lahman/man/Batting.Rd | 8 - Lahman-4.0-1/Lahman/man/BattingPost.Rd | 4 Lahman-4.0-1/Lahman/man/CollegePlaying.Rd |only Lahman-4.0-1/Lahman/man/Fielding.Rd | 4 Lahman-4.0-1/Lahman/man/FieldingOF.Rd | 2 Lahman-4.0-1/Lahman/man/FieldingPost.Rd | 4 Lahman-4.0-1/Lahman/man/HallOfFame.Rd | 4 Lahman-4.0-1/Lahman/man/Label.Rd | 9 - Lahman-4.0-1/Lahman/man/Lahman-package.Rd | 10 - Lahman-4.0-1/Lahman/man/LahmanData.Rd | 4 Lahman-4.0-1/Lahman/man/Managers.Rd | 4 Lahman-4.0-1/Lahman/man/ManagersHalf.Rd | 2 Lahman-4.0-1/Lahman/man/Master.Rd | 8 - Lahman-4.0-1/Lahman/man/Pitching.Rd | 4 Lahman-4.0-1/Lahman/man/PitchingPost.Rd | 4 Lahman-4.0-1/Lahman/man/Salaries.Rd | 2 Lahman-4.0-1/Lahman/man/Schools.Rd | 35 +++-- Lahman-4.0-1/Lahman/man/SeriesPost.Rd | 4 Lahman-4.0-1/Lahman/man/Teams.Rd | 4 Lahman-4.0-1/Lahman/man/TeamsFranchises.Rd | 2 Lahman-4.0-1/Lahman/man/TeamsHalf.Rd | 2 70 files changed, 213 insertions(+), 205 deletions(-)
Title: Install Packages from Snapshots on the Checkpoint Server for
Reproducibility
Description: The goal of checkpoint is to solve the problem of package
reproducibility in R. Specifically, checkpoint allows you to install
packages as they existed on CRAN on a specific snapshot date as if you had
a CRAN time machine. To achieve reproducibility, the checkpoint() function
installs the packages required or called by your project and scripts to a
local library exactly as they existed at the specified point in time. Only
those packages are available to your project, thereby avoiding any package
updates that came later and may have altered your results. In this way,
anyone using checkpoint's checkpoint() can ensure the reproducibility of
your scripts or projects at any time. To create the snapshot archives, once
a day (at midnight UTC) Revolution Analytics refreshes the Austria CRAN mirror, on the "Managed
R Archived Network" server (http://mran.revolutionanalytics.com/).
Immediately after completion of the rsync mirror process, the process takes a
snapshot, thus creating the archive. Snapshot archives exist starting from
2014-09-17.
Author: Revolution Analytics
Maintainer: Andrie de Vries <adevries@microsoft.com>
Diff between checkpoint versions 0.3.10 dated 2015-04-27 and 0.3.15 dated 2015-09-15
checkpoint-0.3.10/checkpoint/tests/testthat/test-2-checkpoint.R |only checkpoint-0.3.15/checkpoint/DESCRIPTION | 12 checkpoint-0.3.15/checkpoint/MD5 | 38 +- checkpoint-0.3.15/checkpoint/NAMESPACE | 10 checkpoint-0.3.15/checkpoint/NEWS |only checkpoint-0.3.15/checkpoint/R/checkpoint-package.R | 10 checkpoint-0.3.15/checkpoint/R/checkpoint.R | 66 ++--- checkpoint-0.3.15/checkpoint/R/detach.R | 7 checkpoint-0.3.15/checkpoint/R/mranUrl.R |only checkpoint-0.3.15/checkpoint/R/scanRepoPackages.R | 50 ++- checkpoint-0.3.15/checkpoint/R/setSnapshot.R | 16 - checkpoint-0.3.15/checkpoint/build/vignette.rds |binary checkpoint-0.3.15/checkpoint/inst/examples/example_setSnapshot.R | 3 checkpoint-0.3.15/checkpoint/man/checkpoint-package.Rd | 4 checkpoint-0.3.15/checkpoint/man/checkpoint.Rd | 30 +- checkpoint-0.3.15/checkpoint/man/getValidSnapshots.Rd |only checkpoint-0.3.15/checkpoint/man/setSnapshot.Rd | 5 checkpoint-0.3.15/checkpoint/tests/test-all.R | 2 checkpoint-0.3.15/checkpoint/tests/testthat/test-0-snapshots.R | 100 +++++++ checkpoint-0.3.15/checkpoint/tests/testthat/test-1-scan.R | 129 +++++++--- checkpoint-0.3.15/checkpoint/tests/testthat/test-2-snapshot-dates.R |only checkpoint-0.3.15/checkpoint/tests/testthat/test-3-checkpoint.R |only checkpoint-0.3.15/checkpoint/vignettes/checkpoint.Rmd | 8 23 files changed, 345 insertions(+), 145 deletions(-)