Title: R Client for the VirusTotal API
Description: Use VirusTotal, a Google service that analyzes files and URLs
for viruses, worms, trojans etc., provides category of the content hosted by a
domain from a variety of prominent services, provides passive DNS information,
among other things. See <http://www.virustotal.com> for more information.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between virustotal versions 0.2.0 dated 2016-11-12 and 0.2.1 dated 2017-05-01
DESCRIPTION | 10 +-- MD5 | 61 ++++++++++----------- NEWS.md | 5 + R/add_comments.R | 13 ++-- R/domain_report.R | 9 +-- R/file_report.R | 25 +++++--- R/ip_report.R | 2 R/rescan_file.R | 19 +++--- R/scan_file.R | 7 +- R/scan_url.R | 13 ++-- R/set_key.R | 10 +-- R/url_report.R | 57 +++++++++++-------- R/virustotal.R | 98 ++++++++++++++++++---------------- build/vignette.rds |binary inst/doc/using_virustotal.html | 19 +++--- man/add_comments.Rd | 1 man/domain_report.Rd | 1 man/file_report.Rd | 1 man/ip_report.Rd | 1 man/rate_limit.Rd | 3 - man/rescan_file.Rd | 1 man/scan_file.Rd | 1 man/scan_url.Rd | 1 man/set_key.Rd | 1 man/url_report.Rd | 5 - man/virustotal-package.Rd | 3 - man/virustotal_GET.Rd | 1 man/virustotal_POST.Rd | 1 man/virustotal_check.Rd | 1 tests/testthat.R | 2 tests/testthat/test-data-structures.R | 41 +++++++------- tests/testthat/test-pkg-style.R |only 32 files changed, 216 insertions(+), 197 deletions(-)
Title: Load Census TIGER/Line Shapefiles into R
Description: Download TIGER/Line shapefiles from the United States Census Bureau
and load into R as 'SpatialDataFrame' or 'sf' objects.
Author: Kyle Walker [aut, cre],
Bob Rudis [ctb]
Maintainer: Kyle Walker <kyle.walker@tcu.edu>
Diff between tigris versions 0.3.3 dated 2016-07-06 and 0.5 dated 2017-05-01
DESCRIPTION | 16 - MD5 | 136 +++++----- NAMESPACE | 9 NEWS | 10 R/enumeration_units.R | 361 ++++++++++++++++++++++------- R/helpers.R | 334 ++++++++++++++++++++++---- R/landmarks.R | 59 +++- R/legislative.R | 90 ++++--- R/metro_areas.R | 179 ++++++++++---- R/national.R | 90 ++++++- R/native.R | 136 ++++++++-- R/places.R | 38 ++- R/pumas.R | 44 ++- R/states.R | 69 ++++- R/tigris-package.R | 4 R/transportation.R | 110 +++++++- R/water.R | 79 ++++-- R/zzz.R | 1 README.md | 22 - man/alaska_native_regional_corporations.Rd | 15 - man/area_water.Rd | 11 man/block_groups.Rd | 20 - man/blocks.Rd | 14 - man/coastline.Rd | 6 man/combined_statistical_areas.Rd | 16 - man/congressional_districts.Rd | 13 - man/core_based_statistical_areas.Rd | 16 - man/counties.Rd | 20 - man/county_subdivisions.Rd | 24 - man/divisions.Rd | 14 - man/filter_place.Rd | 2 man/filter_state.Rd | 2 man/fips_codes.Rd | 2 man/geo_join.Rd | 2 man/grep_place.Rd | 2 man/grep_state.Rd | 2 man/is_tigris.Rd | 2 man/landmarks.Rd | 11 man/linear_water.Rd | 11 man/list_counties.Rd | 2 man/list_places.Rd | 2 man/list_states.Rd | 2 man/lookup_code.Rd | 2 man/metro_divisions.Rd | 12 man/military.Rd | 9 man/nation.Rd | 14 - man/native_areas.Rd | 16 - man/new_england.Rd | 12 man/places.Rd | 20 - man/primary_roads.Rd | 14 - man/primary_secondary_roads.Rd | 13 - man/pumas.Rd | 20 - man/rails.Rd | 13 - man/rbind_tigris.Rd | 4 man/regions.Rd | 14 - man/roads.Rd | 13 - man/school_districts.Rd | 19 - man/state_legislative_districts.Rd | 12 man/states.Rd | 20 - man/tigris-exports.Rd | 2 man/tigris.Rd | 4 man/tigris_type.Rd | 2 man/tracts.Rd | 20 - man/tribal_block_groups.Rd | 15 - man/tribal_census_tracts.Rd | 15 - man/tribal_subdivisions_national.Rd | 10 man/urban_areas.Rd | 16 - man/voting_districts.Rd | 8 man/zctas.Rd | 20 - 69 files changed, 1627 insertions(+), 710 deletions(-)
Title: Fast FFT and DCT Based on the FFTW Library
Description: Provides a simple and efficient wrapper around the fastest
Fourier transform in the west (FFTW) <http://www.fftw.org/> library.
Author: Olaf Mersmann [aut],
Sebastian Krey [ctb],
Uwe Ligges [ctb, cre]
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between fftw versions 1.0-3 dated 2011-04-24 and 1.0-4 dated 2017-05-01
fftw-1.0-3/fftw/ChangeLog |only fftw-1.0-3/fftw/aclocal.m4 |only fftw-1.0-3/fftw/cleanup |only fftw-1.0-3/fftw/configure.ac |only fftw-1.0-3/fftw/inst |only fftw-1.0-3/fftw/src/build |only fftw-1.0-3/fftw/tests |only fftw-1.0-4/fftw/DESCRIPTION | 28 +- fftw-1.0-4/fftw/MD5 |only fftw-1.0-4/fftw/README.md |only fftw-1.0-4/fftw/configure | 551 ++++++++++++++++++++++--------------------- fftw-1.0-4/fftw/src/fftw.c | 111 ++++---- 12 files changed, 366 insertions(+), 324 deletions(-)
Title: A Collection of Robust Statistical Methods
Description: A collection of robust statistical methods based on Wilcox' WRS functions. It implements robust t-tests (independent and dependent samples), robust ANOVA (including between-within subject designs), quantile ANOVA, robust correlation, robust mediation, and nonparametric ANCOVA models based on robust location measures.
Author: Patrick Mair [cre, aut],
Rand Wilcox [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between WRS2 versions 0.9-1 dated 2016-08-13 and 0.9-2 dated 2017-05-01
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/Qanova.R | 2 +- R/med2way.R | 9 ++++++++- build/vignette.rds |binary inst/NEWS.Rd | 7 +++++++ inst/doc/WRS2.R | 23 ++++++++++++----------- inst/doc/WRS2.Rnw | 15 ++++++++------- inst/doc/WRS2.pdf |binary man/pbcor.Rd | 2 +- vignettes/WRS2.Rnw | 15 ++++++++------- 11 files changed, 59 insertions(+), 42 deletions(-)
Title: Manipulation of Microsoft Word and PowerPoint Documents
Description: Access and manipulate 'Microsoft Word' and 'Microsoft PowerPoint' documents from R.
The package focus on tabular and graphical reporting from R; it also provides two functions
that let users get document content into data objects. A set of functions
lets add and remove images, tables and paragraphs of text in new or existing documents.
When working with 'PowerPoint' presentations, slides can be added or removed; shapes inside
slides can also be added or removed. When working with 'Word' documents, a cursor can be
used to help insert or delete content at a specific location in the document. The package
does not require any installation of Microsoft product to be able to write Microsoft files.
Author: David Gohel [aut, cre]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between officer versions 0.1.2 dated 2017-04-29 and 0.1.3 dated 2017-05-01
DESCRIPTION | 8 ++++---- MD5 | 23 +++++++++++++---------- NAMESPACE | 2 +- NEWS | 10 ++++++++++ R/fortify_pptx.R | 32 ++++++++++++++++++++++++++++---- R/read_docx.R | 8 ++++++-- inst/doc/officer_reader.R | 2 +- inst/doc/officer_reader.Rmd | 4 +++- inst/doc/officer_reader.html | 12 ++++++++---- man/docx_dim.Rd | 2 +- man/media_extract.Rd |only vignettes/extract.png |only vignettes/image1.png |only vignettes/officer_reader.Rmd | 4 +++- 14 files changed, 78 insertions(+), 29 deletions(-)
Title: Simple and Canonical Correspondence Analysis
Description: Performs simple and canonical CA (covariates on rows/columns) on a two-way frequency table (with missings) by means of SVD. Different scaling methods (standard, centroid, Benzecri, Goodman) as well as various plots including confidence ellipsoids are provided.
Author: Patrick Mair [aut, cre], Jan De Leeuw [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between anacor versions 1.0-6 dated 2015-07-23 and 1.1-3 dated 2017-05-01
anacor-1.0-6/anacor/R/plot3d.anacor.R |only anacor-1.0-6/anacor/R/plot3dstatic.R |only anacor-1.0-6/anacor/R/plot3dstatic.anacor.R |only anacor-1.0-6/anacor/R/summary.anacor.R |only anacor-1.0-6/anacor/man/anacor-package.Rd |only anacor-1.1-3/anacor/DESCRIPTION | 14 +-- anacor-1.1-3/anacor/MD5 | 19 +--- anacor-1.1-3/anacor/NAMESPACE | 7 - anacor-1.1-3/anacor/R/anacor.R | 45 ++++++---- anacor-1.1-3/anacor/R/plot.anacor.R | 120 ++++++++++++++-------------- anacor-1.1-3/anacor/R/print.anacor.R | 15 ++- anacor-1.1-3/anacor/man/anacor.Rd | 34 +++---- anacor-1.1-3/anacor/man/plot.anacor.Rd | 46 ++++++---- 13 files changed, 158 insertions(+), 142 deletions(-)
Title: Weighted Generalized Estimating Equations and Model Selection
Description: Weighted generalized estimating equations (WGEE) is an extension of generalized linear models to longitudinal clustered data by incorporating the correlation within-cluster when data is missing at random (MAR). The parameters in mean, scale correlation structures are estimated based on quasi-likelihood. Multiple model selection criterion are provided for selection of mean model and working correlation structure based on WGEE/GEE.
Author: Cong Xu <congxu17@gmail.com>, Zheng Li <zheng.li@outlook.com>,
Ming Wang <mwang@phs.psu.edu>
Maintainer: Zheng Li <zheng.li@outlook.com>
Diff between wgeesel versions 1.0 dated 2017-04-21 and 1.1 dated 2017-05-01
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/QIC.gee.R | 15 +++++++-------- R/QICW.gee.R | 11 ++++++----- R/wgee.R | 20 ++++++++++++++++++-- man/MLIC.gee.Rd | 2 +- man/QIC.gee.Rd | 2 +- man/QICW.gee.Rd | 10 +++++----- man/wgee.Rd | 13 ++++++++----- man/wgeesel-package.Rd | 4 ++-- 10 files changed, 61 insertions(+), 42 deletions(-)
Title: 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra
Library
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 3.3.3). 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, Dirk Eddelbuettel, Romain Francois, and Yixuan Qiu;
the authors of Eigen for the included version of Eigen
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppEigen versions 0.3.2.9.1 dated 2017-03-15 and 0.3.3.3.0 dated 2017-05-01
RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/Array |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/Eigen2Support |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/LeastSquares |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/Cholesky/LLT_MKL.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/Core/Flagged.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/Core/Functors.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/Core/ProductBase.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/Core/products/CoeffBasedProduct.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixMatrixTriangular_MKL.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixMatrix_MKL.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixVector_MKL.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/Core/products/SelfadjointMatrixMatrix_MKL.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/Core/products/SelfadjointMatrixVector_MKL.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/Core/products/TriangularMatrixMatrix_MKL.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/Core/products/TriangularMatrixVector_MKL.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/Core/products/TriangularSolverMatrix_MKL.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/Eigen2Support |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/Eigenvalues/ComplexSchur_MKL.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/Eigenvalues/RealSchur_MKL.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_MKL.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/LU/Inverse.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/LU/PartialPivLU_MKL.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/QR/ColPivHouseholderQR_MKL.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/QR/HouseholderQR_MKL.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/SVD/JacobiSVD_MKL.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/misc/Solve.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/Eigen/src/misc/SparseSolve.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/unsupported/Eigen/SVD |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/unsupported/Eigen/src/IterativeSolvers/IncompleteCholesky.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/unsupported/Eigen/src/MatrixFunctions/MatrixFunctionAtomic.h |only RcppEigen-0.3.2.9.1/RcppEigen/inst/include/unsupported/Eigen/src/SVD |only RcppEigen-0.3.3.3.0/RcppEigen/ChangeLog | 62 RcppEigen-0.3.3.3.0/RcppEigen/DESCRIPTION | 29 RcppEigen-0.3.3.3.0/RcppEigen/MD5 | 787 +-- RcppEigen-0.3.3.3.0/RcppEigen/README.md | 2 RcppEigen-0.3.3.3.0/RcppEigen/build/vignette.rds |binary RcppEigen-0.3.3.3.0/RcppEigen/inst/NEWS.Rd | 15 RcppEigen-0.3.3.3.0/RcppEigen/inst/doc/RcppEigen-Introduction.pdf |binary RcppEigen-0.3.3.3.0/RcppEigen/inst/examples/lmBenchmark.R | 20 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/Cholesky | 17 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/CholmodSupport | 11 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/Core | 290 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/Eigen | 2 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/Eigenvalues | 15 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/Geometry | 61 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/Householder | 7 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/IterativeLinearSolvers | 24 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/Jacobi | 7 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/LU | 21 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/MetisSupport | 7 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/OrderingMethods | 7 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/PaStiXSupport | 12 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/PardisoSupport | 9 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/QR | 26 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/QtAlignedMalloc | 10 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/SPQRSupport | 9 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/SVD | 26 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/Sparse | 15 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/SparseCholesky | 2 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/SparseCore | 33 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/SparseLU | 3 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/SparseQR | 10 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/StdDeque | 2 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/StdList | 2 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/StdVector | 2 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/SuperLUSupport | 13 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/UmfPackSupport | 10 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Cholesky/LDLT.h | 268 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Cholesky/LLT.h | 168 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Cholesky/LLT_LAPACKE.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/CholmodSupport/CholmodSupport.h | 284 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Array.h | 144 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/ArrayBase.h | 70 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/ArrayWrapper.h | 145 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Assign.h | 540 -- RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/AssignEvaluator.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Assign_MKL.h | 254 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/BandMatrix.h | 61 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Block.h | 254 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/BooleanRedux.h | 42 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/CommaInitializer.h | 43 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/ConditionEstimator.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/CoreEvaluators.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/CoreIterators.h | 140 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/CwiseBinaryOp.h | 166 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/CwiseNullaryOp.h | 252 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/CwiseTernaryOp.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/CwiseUnaryOp.h | 111 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/CwiseUnaryView.h | 81 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/DenseBase.h | 388 + RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/DenseCoeffsBase.h | 279 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/DenseStorage.h | 442 + RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Diagonal.h | 66 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/DiagonalMatrix.h | 140 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/DiagonalProduct.h | 107 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Dot.h | 160 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/EigenBase.h | 46 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/ForceAlignedAccess.h | 24 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Fuzzy.h | 13 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/GeneralProduct.h | 493 -- RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/GenericPacketMath.h | 349 + RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/GlobalFunctions.h | 161 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/IO.h | 49 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Inverse.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Map.h | 110 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/MapBase.h | 100 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/MathFunctions.h | 835 +++ RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/MathFunctionsImpl.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Matrix.h | 241 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/MatrixBase.h | 313 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/NestByValue.h | 35 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/NoAlias.h | 62 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/NumTraits.h | 136 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/PermutationMatrix.h | 367 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/PlainObjectBase.h | 431 + RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Product.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/ProductEvaluators.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Random.h | 58 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Redux.h | 210 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Ref.h | 199 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Replicate.h | 95 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/ReturnByValue.h | 50 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Reverse.h | 209 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Select.h | 22 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/SelfAdjointView.h | 294 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/SelfCwiseBinaryOp.h | 174 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Solve.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/SolveTriangular.h | 77 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/SolverBase.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/StableNorm.h | 53 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Stride.h | 25 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Swap.h | 149 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Transpose.h | 185 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Transpositions.h | 248 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/TriangularMatrix.h | 1102 ++-- RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/VectorBlock.h | 27 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/VectorwiseOp.h | 339 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/Visitor.h | 77 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/arch/AVX |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/arch/AVX512 |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/arch/AltiVec/Complex.h | 354 + RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/arch/AltiVec/MathFunctions.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/arch/AltiVec/PacketMath.h | 794 ++- RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/arch/CUDA |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/Complex.h | 251 + RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/MathFunctions.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/PacketMath.h | 404 + RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/arch/SSE/Complex.h | 99 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/arch/SSE/MathFunctions.h | 113 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/arch/SSE/PacketMath.h | 416 + RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/arch/SSE/TypeCasting.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/arch/ZVector |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/functors |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/products/GeneralBlockPanelKernel.h | 2240 ++++++---- RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixMatrix.h | 373 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixMatrixTriangular.h | 138 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixMatrixTriangular_BLAS.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixMatrix_BLAS.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixVector.h | 305 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixVector_BLAS.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/products/Parallelizer.h | 69 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/products/SelfadjointMatrixMatrix.h | 335 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/products/SelfadjointMatrixMatrix_BLAS.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/products/SelfadjointMatrixVector.h | 123 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/products/SelfadjointMatrixVector_BLAS.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/products/SelfadjointProduct.h | 26 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/products/SelfadjointRank2Update.h | 8 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/products/TriangularMatrixMatrix.h | 138 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/products/TriangularMatrixMatrix_BLAS.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/products/TriangularMatrixVector.h | 174 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/products/TriangularMatrixVector_BLAS.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/products/TriangularSolverMatrix.h | 73 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/products/TriangularSolverMatrix_BLAS.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/products/TriangularSolverVector.h | 24 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/util/BlasUtil.h | 234 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/util/Constants.h | 160 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/util/DisableStupidWarnings.h | 31 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/util/ForwardDeclarations.h | 134 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/util/MKL_support.h | 50 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/util/Macros.h | 548 +- RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/util/Memory.h | 493 +- RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/util/Meta.h | 351 + RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h | 10 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/util/StaticAssert.h | 40 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Core/util/XprHelper.h | 582 ++ RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/ComplexEigenSolver.h | 25 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/ComplexSchur.h | 19 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/EigenSolver.h | 113 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h | 215 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h | 3 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/HessenbergDecomposition.h | 15 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/RealQZ.h | 46 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/RealSchur.h | 41 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h | 273 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/Tridiagonalization.h | 35 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Geometry/AlignedBox.h | 96 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Geometry/AngleAxis.h | 85 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Geometry/EulerAngles.h | 22 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Geometry/Homogeneous.h | 290 + RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Geometry/Hyperplane.h | 64 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Geometry/OrthoMethods.h | 58 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Geometry/ParametrizedLine.h | 60 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Geometry/Quaternion.h | 225 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Geometry/Rotation2D.h | 85 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Geometry/RotationBase.h | 48 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Geometry/Scaling.h | 38 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Geometry/Transform.h | 262 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Geometry/Translation.h | 60 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Geometry/Umeyama.h | 19 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Geometry/arch/Geometry_SSE.h | 56 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Householder/BlockHouseholder.h | 77 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Householder/Householder.h | 4 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Householder/HouseholderSequence.h | 56 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h | 114 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h | 97 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h | 137 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h | 138 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h | 342 + RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/Jacobi/Jacobi.h | 34 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/LU/Determinant.h | 2 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/LU/FullPivLU.h | 312 + RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/LU/InverseImpl.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/LU/PartialPivLU.h | 254 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/LU/PartialPivLU_LAPACKE.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/LU/arch/Inverse_SSE.h | 47 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/MetisSupport/MetisSupport.h | 18 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/OrderingMethods/Amd.h | 85 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/OrderingMethods/Eigen_Colamd.h | 412 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/OrderingMethods/Ordering.h | 51 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/PaStiXSupport/PaStiXSupport.h | 151 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/PardisoSupport/PardisoSupport.h | 230 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/QR/ColPivHouseholderQR.h | 283 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/QR/CompleteOrthogonalDecomposition.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/QR/FullPivHouseholderQR.h | 192 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/QR/HouseholderQR.h | 121 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/QR/HouseholderQR_LAPACKE.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h | 123 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SVD/BDCSVD.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SVD/JacobiSVD.h | 332 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SVD/JacobiSVD_LAPACKE.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SVD/SVDBase.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SVD/UpperBidiagonalization.h | 326 + RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCholesky/SimplicialCholesky.h | 272 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h | 34 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/AmbiVector.h | 98 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/CompressedStorage.h | 138 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h | 216 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/MappedSparseMatrix.h | 164 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseAssign.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseBlock.h | 1141 ++--- RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseColEtree.h | 44 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseCompressedBase.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseCwiseBinaryOp.h | 672 ++- RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseCwiseUnaryOp.h | 155 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseDenseProduct.h | 419 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseDiagonalProduct.h | 244 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseDot.h | 17 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseFuzzy.h | 29 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseMap.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseMatrix.h | 637 +- RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseMatrixBase.h | 269 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparsePermutation.h | 170 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseProduct.h | 291 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseRedux.h | 5 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseRef.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseSelfAdjointView.h | 556 +- RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseSolverBase.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseSparseProductWithPruning.h | 84 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseTranspose.h | 101 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseTriangularView.h | 250 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseUtil.h | 106 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseVector.h | 208 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseView.h | 228 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseCore/TriangularSolver.h | 117 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU.h | 223 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLUImpl.h | 10 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_Memory.h | 15 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_Structs.h | 3 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h | 69 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_Utils.h | 10 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_column_bmod.h | 7 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_column_dfs.h | 38 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h | 7 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_gemm_kernel.h | 93 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h | 21 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_kernel_bmod.h | 52 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_panel_bmod.h | 6 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_panel_dfs.h | 44 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_pivotL.h | 12 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_pruneL.h | 7 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_relax_snode.h | 12 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SparseQR/SparseQR.h | 187 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/StlSupport/StdDeque.h | 2 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/StlSupport/StdList.h | 4 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/StlSupport/StdVector.h | 5 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/StlSupport/details.h | 16 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/SuperLUSupport/SuperLUSupport.h | 209 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/UmfPackSupport/UmfPackSupport.h | 251 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/misc/Image.h | 2 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/misc/Kernel.h | 4 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/misc/RealSvd2x2.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/misc/blas.h | 422 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/misc/lapack.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/misc/lapacke.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/misc/lapacke_mangling.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/plugins/ArrayCwiseBinaryOps.h | 203 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/plugins/ArrayCwiseUnaryOps.h | 467 +- RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/plugins/BlockMethods.h | 1235 +++-- RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/plugins/CommonCwiseBinaryOps.h | 75 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/plugins/CommonCwiseUnaryOps.h | 199 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/plugins/MatrixCwiseBinaryOps.h | 29 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/Eigen/src/plugins/MatrixCwiseUnaryOps.h | 113 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/RcppEigenForward.h | 10 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/RcppEigenWrap.h | 44 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/AdolcForward | 2 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/AlignedVector3 | 38 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/CXX11 |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/EulerAngles |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/IterativeSolvers | 5 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/KroneckerProduct | 2 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/MPRealSupport | 104 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/MatrixFunctions | 76 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/OpenGLSupport | 20 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/SparseExtra | 3 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/SpecialFunctions |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/AutoDiff/AutoDiffJacobian.h | 49 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/AutoDiff/AutoDiffScalar.h | 222 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/Eigenvalues/ArpackSelfAdjointEigenSolver.h | 14 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/EulerAngles |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/IterativeSolvers/DGMRES.h | 57 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/IterativeSolvers/GMRES.h | 406 - RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/IterativeSolvers/IncompleteLU.h | 39 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/IterativeSolvers/MINRES.h | 84 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/IterativeSolvers/Scaling.h | 6 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h | 169 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/LevenbergMarquardt/LMcovar.h | 1 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/LevenbergMarquardt/LMpar.h | 2 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/LevenbergMarquardt/LMqrsolv.h | 9 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/LevenbergMarquardt/LevenbergMarquardt.h | 31 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/MatrixFunctions/MatrixExponential.h | 697 +-- RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/MatrixFunctions/MatrixFunction.h | 718 +-- RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/MatrixFunctions/MatrixLogarithm.h | 507 -- RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/MatrixFunctions/MatrixPower.h | 397 + RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/MatrixFunctions/MatrixSquareRoot.h | 450 -- RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/MatrixFunctions/StemFunction.h | 178 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/NonLinearOptimization/HybridNonLinearSolver.h | 4 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/NonLinearOptimization/LevenbergMarquardt.h | 25 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/Polynomials/PolynomialSolver.h | 33 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/Polynomials/PolynomialUtils.h | 2 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/Skyline/SkylineProduct.h | 6 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/SparseExtra/BlockSparseMatrix.h |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/SparseExtra/DynamicSparseMatrix.h | 71 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/SparseExtra/MarketIO.h | 21 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h | 43 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/SparseExtra/RandomSetter.h | 10 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/SpecialFunctions |only RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/Splines/Spline.h | 74 RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/Splines/SplineFitting.h | 274 + RcppEigen-0.3.3.3.0/RcppEigen/inst/include/unsupported/Eigen/src/Splines/SplineFwd.h | 3 RcppEigen-0.3.3.3.0/RcppEigen/inst/unitTests/runit.RcppEigen.R | 30 RcppEigen-0.3.3.3.0/RcppEigen/inst/unitTests/runit.sparse.R | 39 368 files changed, 26374 insertions(+), 18130 deletions(-)
Title: Accesses Google Maps APIs to Retrieve Data and Plot Maps
Description: Provides a mechanism to plot a Google Map from R and overlay
it with shapes and markers. Also provides access to Google Maps APIs,
including places, directions, roads, distances, geocoding, elevation and
timezone.
Author: David Cooley [aut, cre],
Paulo Barcelos [ctb] (Author of c++ decode_pl),
Rstudio [ctb] (Functions written for the Leaflet pacakge)
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between googleway versions 1.0.0 dated 2016-06-13 and 2.0.0 dated 2017-05-01
DESCRIPTION |only MD5 |only NAMESPACE |only R |only build |only data |only inst/doc/googleway-vignette.R | 10 inst/doc/googleway-vignette.Rmd |only inst/doc/googleway-vignette.html | 702 ++++++++++++++++++++++++++++++++++++++- inst/htmlwidgets |only man |only src |only tests |only vignettes |only 14 files changed, 704 insertions(+), 8 deletions(-)
Title: Fitting Frailty Models with the EM Algorithm
Description: Contains functions for fitting shared frailty models with a semi-parametric
baseline hazard with the Expectation-Maximization algorithm. Supported data formats
include clustered failures with left truncation and recurrent events in gap-time
or Andersen-Gill format. Several frailty distributions, such as the the gamma, positive stable
and the Power Variance Family are supported.
Author: Theodor Adrian Balan, Hein Putter
Maintainer: Theodor Adrian Balan <t.a.balan@lumc.nl>
Diff between frailtyEM versions 0.5.4 dated 2017-04-03 and 0.6.2 dated 2017-05-01
frailtyEM-0.5.4/frailtyEM/R/plot_methods.R |only frailtyEM-0.6.2/frailtyEM/DESCRIPTION | 14 frailtyEM-0.6.2/frailtyEM/MD5 | 50 + frailtyEM-0.6.2/frailtyEM/NAMESPACE | 21 frailtyEM-0.6.2/frailtyEM/NEWS.md | 53 ++ frailtyEM-0.6.2/frailtyEM/R/ca_test.R | 1 frailtyEM-0.6.2/frailtyEM/R/em_fit.R | 120 ---- frailtyEM-0.6.2/frailtyEM/R/emfrail.R | 340 ++++++++----- frailtyEM-0.6.2/frailtyEM/R/emfrail_arguments.R | 158 +++--- frailtyEM-0.6.2/frailtyEM/R/emfrail_aux.R | 3 frailtyEM-0.6.2/frailtyEM/R/ggplot_emfrail.R |only frailtyEM-0.6.2/frailtyEM/R/plot_emfrail.R |only frailtyEM-0.6.2/frailtyEM/R/predict.emfrail.R | 2 frailtyEM-0.6.2/frailtyEM/R/print.emfrail.R | 28 - frailtyEM-0.6.2/frailtyEM/R/print.emfrail_summary.R | 318 +++++++++--- frailtyEM-0.6.2/frailtyEM/R/summary.emfrail.R | 338 ++++++++++--- frailtyEM-0.6.2/frailtyEM/build/vignette.rds |binary frailtyEM-0.6.2/frailtyEM/inst/doc/frailtyEM_manual.R | 90 +-- frailtyEM-0.6.2/frailtyEM/inst/doc/frailtyEM_manual.Rnw | 377 ++++++++------- frailtyEM-0.6.2/frailtyEM/inst/doc/frailtyEM_manual.pdf |binary frailtyEM-0.6.2/frailtyEM/man/emfrail.Rd | 21 frailtyEM-0.6.2/frailtyEM/man/emfrail_control.Rd | 80 +-- frailtyEM-0.6.2/frailtyEM/man/emfrail_distribution.Rd | 4 frailtyEM-0.6.2/frailtyEM/man/ggplot_emfrail.Rd |only frailtyEM-0.6.2/frailtyEM/man/plot_emfrail.Rd | 8 frailtyEM-0.6.2/frailtyEM/man/summary.emfrail.Rd | 7 frailtyEM-0.6.2/frailtyEM/vignettes/frailtyEM_manual.Rnw | 377 ++++++++------- frailtyEM-0.6.2/frailtyEM/vignettes/mybib.bib | 159 +++--- 28 files changed, 1582 insertions(+), 987 deletions(-)
Title: Joint Modelling of Multivariate Longitudinal Data and
Time-to-Event Outcomes
Description: Fits the joint model proposed by Henderson and colleagues (2000)
<doi:10.1093/biostatistics/1.4.465>, but extended to the case of multiple
continuous longitudinal measures. The time-to-event data is modelled using a
Cox proportional hazards regression model with time-varying covariates. The
multiple longitudinal outcomes are modelled using a multivariate version of the
Laird and Ware linear mixed model. The association is captured by a multivariate
latent Gaussian process. The model is estimated using a Monte Carlo Expectation
Maximization algorithm. This project is funded by the Medical Research Council
(Grant number MR/M013227/1).
Author: Graeme L. Hickey [cre, aut],
Pete Philipson [aut],
Andrea Jorgensen [aut],
Ruwanthi Kolamunnage-Dona [aut],
Paula Williamson [ctb],
Dimitris Rizopoulos [ctb, dtc] (data/renal.rda, R/hessian.R, R/vcov.R)
Maintainer: Graeme L. Hickey <graeme.hickey@liverpool.ac.uk>
Diff between joineRML versions 0.2.1 dated 2017-04-25 and 0.2.2 dated 2017-05-01
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Title: Friendly R Startup Configuration
Description: Adds support for R startup configuration via '.Renviron.d' and '.Rprofile.d' directories in addition to '.Renviron' and '.Rprofile' files. This makes it possible to keep private / secret environment variables separate from other environment variables. It also makes it easier to share specific startup settings by simply copying a file to a directory.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between startup versions 0.5.0 dated 2017-02-12 and 0.6.0 dated 2017-05-01
DESCRIPTION | 8 +- MD5 | 60 +++++++++--------- NEWS | 95 ++++++++++++++++++---------- R/backup.R | 19 ++++- R/check.R | 39 +++++++---- R/debug.R | 17 +++-- R/files_apply.R | 40 ++++++------ R/filter_files.R | 161 ++++++++++++++++++++++++++++++++++++------------- R/find_files.R | 60 +++++++++++------- R/install.R | 104 ++++++++++++++++++++++++------- R/is_rstudio.R | 4 - R/is_wine.R | 4 - R/renviron_d.R | 9 +- R/rprofile_d.R | 17 +++-- R/startup.R | 49 +++++++++++--- R/sysinfo.R | 4 - README.md | 44 +++++++------ man/check.Rd | 13 ++- man/find_rprofile.Rd | 6 + man/find_rprofile_d.Rd | 12 ++- man/install.Rd | 30 +++++++-- man/is_rstudio.Rd | 4 - man/is_wine.Rd | 4 - man/startup.Rd | 36 +++++++--- tests/backup.R | 12 +-- tests/check.R | 9 +- tests/filter_files.R | 37 +++++++---- tests/install.R | 13 ++- tests/startup.R | 20 +++--- tests/sysinfo.R | 2 tests/unload.R | 1 31 files changed, 613 insertions(+), 320 deletions(-)
Title: Rolling Statistics
Description: Parallel functions for computing rolling statistics of time-series
data.
Author: Jason Foster
Maintainer: Jason Foster <jason.j.foster@gmail.com>
Diff between roll versions 1.0.6 dated 2016-09-19 and 1.0.7 dated 2017-05-01
DESCRIPTION | 10 MD5 | 39 +- NAMESPACE | 4 NEWS.md | 12 R/RcppExports.R | 26 + R/roll.R | 374 ++++++++++++++++++---------- README.md | 4 man/roll_cor.Rd | 30 +- man/roll_cov.Rd | 30 +- man/roll_eigen.Rd | 31 -- man/roll_lm.Rd | 31 -- man/roll_mean.Rd | 28 +- man/roll_pcr.Rd | 31 -- man/roll_prod.Rd |only man/roll_scale.Rd | 28 +- man/roll_sd.Rd | 28 +- man/roll_sum.Rd |only man/roll_var.Rd | 28 +- man/roll_vif.Rd | 31 -- src/RcppExports.cpp | 34 ++ src/init.c |only src/roll.cpp | 677 +++++++++++++++++++++++++++++++++++++++++----------- 22 files changed, 1005 insertions(+), 471 deletions(-)
Title: Regularized Autoregressive Hidden Semi Markov Model
Description: Fit Gaussian hidden Markov (or semi-Markov) models with / without autoregressive coefficients and with / without regularization. The fitting algorithm for the hidden Markov model is illustrated by Rabiner (1989) <doi:10.1109/5.18626>. The shrinkage estimation on the covariance matrices is based on the method by Ledoit et al. (2004) <doi:10.1016/S0047-259X(03)00096-4>. The shrinkage estimation on the autoregressive coefficients uses the elastic net shrinkage detailed in Zou et al. (2005) <doi:10.1111/j.1467-9868.2005.00503.x>.
Author: Zekun (Jack) Xu, Ye Liu
Maintainer: Zekun Xu <zekunxu@gmail.com>
Diff between rarhsmm versions 1.0.2 dated 2017-04-19 and 1.0.3 dated 2017-05-01
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/package.R | 4 ++-- data/finance.RData |binary man/package-rarhsmm.Rd | 4 ++-- 5 files changed, 13 insertions(+), 13 deletions(-)
Title: Dual-Agent Dose Escalation for Phase I Trials using the PIPE
Design
Description: Implements the Product of Independent beta Probabilities dose Escalation (PIPE) design for dual-agent Phase I trials as described in Mander AP, Sweeting MJ (2015) <DOI:10.1002/sim.6434>.
Author: Michael Sweeting
Maintainer: Michael Sweeting <mjs212@medschl.cam.ac.uk>
Diff between pipe.design versions 0.4 dated 2016-05-10 and 0.5 dated 2017-05-01
pipe.design-0.4/pipe.design/R/pipe.design_0.4.R |only pipe.design-0.5/pipe.design/DESCRIPTION | 8 pipe.design-0.5/pipe.design/MD5 | 13 pipe.design-0.5/pipe.design/NEWS | 5 pipe.design-0.5/pipe.design/R/pipe.design_0.5.R |only pipe.design-0.5/pipe.design/inst/shiny/shinyPIPE/rsconnect |only pipe.design-0.5/pipe.design/inst/shiny/shinyPIPE/server.R | 135 + pipe.design-0.5/pipe.design/inst/shiny/shinyPIPE/ui.R | 1062 ++++++++----- pipe.design-0.5/pipe.design/man/pipe.design.Rd | 42 9 files changed, 859 insertions(+), 406 deletions(-)
Title: Automatic Shift Detection using a Phylogenetic EM
Description: Implementation of the automatic shift detection method for
Brownian Motion (BM) or Ornstein–Uhlenbeck (OU) models of trait evolution on
phylogenies. Some tools to handle equivalent shifts configurations are also
available.
Author: Paul Bastide [aut, cre],
Mahendra Mariadassou [ctb]
Maintainer: Paul Bastide <paul.bastide@m4x.org>
Diff between PhylogeneticEM versions 1.0.0 dated 2017-01-31 and 1.0.1 dated 2017-05-01
DESCRIPTION | 8 MD5 | 288 +++++----- NAMESPACE | 2 NEWS.md |only R/E_step.R | 6 R/estimateEM.R | 4 R/generic_functions.R | 16 R/plot_functions.R | 44 + build/vignette.rds |binary inst/doc/tutorial.html | 16 man/PhyloEM.Rd | 1 man/add_complementary.Rd | 1 man/allocate_regimes_from_shifts.Rd | 1 man/allocate_shifts_from_regimes.Rd | 1 man/allocate_subset_node.simulate.Rd | 1 man/check.selection.strength.Rd | 1 man/check_data.Rd | 1 man/check_dimensions.Rd | 1 man/check_parsimony.Rd | 1 man/check_parsimony_clusters.Rd | 1 man/clusters_from_shifts.Rd | 1 man/compute_E.simple.Rd | 1 man/compute_actualization_matrix_ultrametric.Rd | 1 man/compute_betas_from_shifts.Rd | 1 man/compute_diff_exp.BM.Rd | 1 man/compute_dist_phy.Rd | 1 man/compute_expectations.BM.Rd | 1 man/compute_expectations.scOU.Rd | 1 man/compute_fixed_moments.Rd | 1 man/compute_gauss_lasso.Rd | 1 man/compute_log_likelihood.simple.Rd | 1 man/compute_mahalanobis_distance.simple.Rd | 1 man/compute_mean_variance.simple.Rd | 1 man/compute_residuals.simple.Rd | 1 man/compute_shifts_from_betas.Rd | 1 man/compute_state_filter.Rd | 1 man/compute_stationary_variance.Rd | 1 man/compute_sum_var_diff.Rd | 1 man/compute_times_ca.Rd | 1 man/compute_tree_correlations_matrix.BM.Rd | 1 man/compute_tree_correlations_matrix.scOU.Rd | 1 man/compute_var_M.BM.Rd | 1 man/compute_var_diff.BM.Rd | 1 man/compute_variance_covariance.BM.Rd | 1 man/compute_variance_covariance.OU.Rd | 1 man/compute_variance_covariance.scOU.Rd | 1 man/correspondenceEdges.Rd | 1 man/enlight.Rd | 2 man/enumerate_parsimony.Rd | 1 man/enumerate_tips_under_edges.Rd | 1 man/equivalent_shifts.Rd | 1 man/equivalent_shifts_edges.Rd | 1 man/equivalent_shifts_values.Rd | 1 man/estimate.alpha.Rd | 1 man/estimateEM.Rd | 1 man/extract.Rd | 1 man/extract.enumerate_parsimony.Rd | 1 man/extract.equivalent_shifts.Rd | 1 man/extract.parsimonyCost.Rd | 1 man/extract.parsimonyNumber.Rd | 1 man/extract.partitionsNumber.Rd | 1 man/extract.simul_process.Rd | 1 man/extract.variance_covariance.Rd | 1 man/find_grid_alpha.Rd | 13 man/find_independent_regression_vectors.glmnet_multivariate.Rd | 1 man/find_shift_values.Rd | 1 man/format_output.Rd | 1 man/get_variance_node.Rd | 1 man/go_back_to_original_process.Rd | 1 man/impute.data.Rphylopars.Rd | 1 man/imputed_traits.Rd | 2 man/incidence.matrix.Rd | 1 man/incidence.matrix.full.Rd | 1 man/incidence_matrix_actualization_factors.Rd | 1 man/init.EM.lasso.Rd | 1 man/init.allocate_regimes_from_shifts.Rd | 1 man/init.alpha.gamma.estimation.Rd | 1 man/init.compute_betas_from_shifts.Rd | 1 man/init.enumerate_parsimony.Rd | 1 man/init.incidence.matrix.Rd | 1 man/init.incidence.matrix.full.Rd | 1 man/init.parsimonyCost.Rd | 1 man/init.parsimonyNumber.Rd | 1 man/init.simulate.BM.Rd | 1 man/init.simulate.OU.Rd | 1 man/init.simulate.StateAndExp.Rd | 1 man/is.in.ranges.Rd | 1 man/lasso_regression_K_fixed.glmnet_multivariate.Rd | 1 man/log_likelihood.Rd | 4 man/matrix_of_possibles.Rd | 1 man/merge_complementary_vectors.Rd | 1 man/merge_params_independent.Rd | 1 man/model_selection.Rd | 2 man/monkeys.Rd | 1 man/optimize_costs_given_shift_position.OU.specialCase.Rd | 1 man/params_BM.Rd | 1 man/params_OU.Rd | 1 man/params_process.PhyloEM.Rd | 1 man/params_process.Rd | 1 man/params_process.character.Rd | 1 man/parsimonyCost.Rd | 1 man/parsimonyNumber.Rd | 1 man/partitionsNumber.Rd | 1 man/penalty_BaraudGiraudHuet_likelihood.Rd | 1 man/penalty_BirgeMassart_shape1.Rd | 1 man/penalty_BirgeMassart_shape2.Rd | 1 man/penalty_pBIC.Rd | 1 man/plot.PhyloEM.Rd | 12 man/plot.enumerate_parsimony.Rd | 1 man/plot.equivalent_shifts.Rd | 1 man/plot.params_process.Rd | 1 man/prod.index.Rd | 1 man/qr.solve_exact.Rd | 1 man/recursionDown.Rd | 1 man/residuals.PhyloEM.Rd | 1 man/sample_edges_intervals.Rd | 1 man/sample_shifts_edges.Rd | 1 man/scale_params.Rd | 1 man/segmentation.BM.Rd | 1 man/segmentation.OU.specialCase.lasso.Rd | 1 man/segmentation.OU.specialCase.same_shifts.Rd | 1 man/shifts.list_to_matrix.Rd | 1 man/shifts.list_to_vector.Rd | 1 man/shifts.matrix_to_list.Rd | 1 man/shifts.vector_to_list.Rd | 1 man/shifts_to_simmap.Rd | 1 man/simul_process.Rd | 4 man/simulate_internal.Rd | 1 man/split_params_independent.Rd | 1 man/sum.partitions.Rd | 1 man/sum.partitions.cardFixed.Rd | 1 man/sum.prod.comb.Rd | 1 man/sum.simplex.Rd | 1 man/test.root.state.Rd | 1 man/transform_branch_length.Rd | 1 man/transform_shifts_values.Rd | 1 man/update.allocate_regimes_from_shifts.Rd | 1 man/update.compute_betas_from_shifts.Rd | 1 man/update.enumerate_parsimony.Rd | 1 man/update.incidence.matrix.Rd | 1 man/update.incidence.matrix.full.Rd | 1 man/update.parsimonyCost.Rd | 1 man/update.parsimonyNumber.Rd | 1 man/update.partitionsNumber.gen.Rd | 1 man/wrapper_E_step.Rd | 1 src/init.c |only 146 files changed, 238 insertions(+), 313 deletions(-)
More information about PhylogeneticEM at CRAN
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Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modelling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 0.3.1 dated 2017-03-31 and 0.3.2 dated 2017-05-01
DESCRIPTION | 8 MD5 | 44 ++-- R/ANOVA.R | 5 R/ARMA.R | 86 ++++---- R/Binary_ANOVA.R | 2 R/Causation.R | 31 ++- R/Dependence.R | 9 R/Partition_Map.R | 158 ++++++++-------- R/Regression.R | 9 R/Seasonality_Test.R | 17 - R/Stack.R | 16 + build/vignette.rds |binary inst/doc/NNSvignette_Clustering_and_Regression.R | 2 inst/doc/NNSvignette_Clustering_and_Regression.Rmd | 4 inst/doc/NNSvignette_Clustering_and_Regression.html | 194 +++++++++++--------- inst/doc/NNSvignette_Forecasting.Rmd | 12 + inst/doc/NNSvignette_Forecasting.html | 22 +- man/NNS.ARMA.Rd | 27 ++ man/NNS.caus.Rd | 11 - man/NNS.part.Rd | 9 man/NNS.stack.Rd | 12 - vignettes/NNSvignette_Clustering_and_Regression.Rmd | 4 vignettes/NNSvignette_Forecasting.Rmd | 12 + 23 files changed, 409 insertions(+), 285 deletions(-)
Title: Fitting Structural Equation Mixture Models
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 <nora.umbach@web.de>
Diff between nlsem versions 0.7 dated 2017-01-02 and 0.8 dated 2017-05-01
ChangeLog | 6 ++++++ DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- inst/CITATION | 38 +++++++++++++++++++++++++++++--------- inst/doc/index.html |only inst/doc/nonlinear_SEM_in_R.pdf |binary man/em.Rd | 5 +++-- man/lav2nlsem.Rd | 5 +++++ man/nlsem-package.Rd | 12 +++++++----- man/qml.Rd | 7 ++++--- man/specify_sem.Rd | 6 ++++-- 11 files changed, 72 insertions(+), 34 deletions(-)
Title: Models Multivariate Cases Using Random Forests
Description: Models and predicts multiple output features in single random forest considering the
linear relation among the output features, see details in Rahman et al (2017)<doi:10.1093/bioinformatics/btw765>.
Author: Raziur Rahman
Maintainer: Raziur Rahman <razeeebuet@gmail.com>
Diff between MultivariateRandomForest versions 1.1.2 dated 2016-12-07 and 1.1.5 dated 2017-05-01
MultivariateRandomForest-1.1.2/MultivariateRandomForest/man/splitt.Rd |only MultivariateRandomForest-1.1.2/MultivariateRandomForest/src/Node_Cost_C.cpp |only MultivariateRandomForest-1.1.5/MultivariateRandomForest/DESCRIPTION | 15 - MultivariateRandomForest-1.1.5/MultivariateRandomForest/MD5 | 41 +-- MultivariateRandomForest-1.1.5/MultivariateRandomForest/NAMESPACE | 7 MultivariateRandomForest-1.1.5/MultivariateRandomForest/R/CrossValidation.R | 26 - MultivariateRandomForest-1.1.5/MultivariateRandomForest/R/Imputation.R | 19 - MultivariateRandomForest-1.1.5/MultivariateRandomForest/R/RcppExports.R | 6 MultivariateRandomForest-1.1.5/MultivariateRandomForest/R/build_forest_predict.R | 131 +++++----- MultivariateRandomForest-1.1.5/MultivariateRandomForest/R/build_single_tree.R | 31 -- MultivariateRandomForest-1.1.5/MultivariateRandomForest/R/predicting.R | 26 - MultivariateRandomForest-1.1.5/MultivariateRandomForest/R/single_tree_prediction.R | 25 - MultivariateRandomForest-1.1.5/MultivariateRandomForest/R/split_node.R | 45 --- MultivariateRandomForest-1.1.5/MultivariateRandomForest/man/CrossValidation.Rd | 3 MultivariateRandomForest-1.1.5/MultivariateRandomForest/man/Imputation.Rd | 1 MultivariateRandomForest-1.1.5/MultivariateRandomForest/man/build_forest_predict.Rd | 2 MultivariateRandomForest-1.1.5/MultivariateRandomForest/man/build_single_tree.Rd | 3 MultivariateRandomForest-1.1.5/MultivariateRandomForest/man/predicting.Rd | 9 MultivariateRandomForest-1.1.5/MultivariateRandomForest/man/single_tree_prediction.Rd | 1 MultivariateRandomForest-1.1.5/MultivariateRandomForest/man/split_node.Rd | 11 MultivariateRandomForest-1.1.5/MultivariateRandomForest/man/splitt2.Rd |only MultivariateRandomForest-1.1.5/MultivariateRandomForest/src/RcppExports.cpp | 24 - MultivariateRandomForest-1.1.5/MultivariateRandomForest/src/rcpp.cpp |only MultivariateRandomForest-1.1.5/MultivariateRandomForest/src/registerDynamicSymbol.cpp |only 24 files changed, 164 insertions(+), 262 deletions(-)
More information about MultivariateRandomForest at CRAN
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Title: Penalized Likelihood Estimation and Dynamic Prediction under the
Joint Frailty-Copula Models Between Tumour Progression and
Death for Meta-Analysis
Description: Perform the Cox regression and dynamic prediction methods under
the joint frailty-copula model between tumour progression and death for meta-analysis.
A penalized likelihood is employed for estimating model parameters, where the baseline hazard functions are approximated by smoothing splines.
The methods are applicable for meta-analytic data combining several studies.
The methods can analyze data having information on both terminal event time (e.g., time-to-death) and non-terminal event time (e.g., time-to-tumour progression).
See Emura et al. (2015) <doi:10.1177/0962280215604510> and
Emura et al. (2017) <doi:10.1177/0962280216688032> for details.
Survival data from ovarian cancer patients are also available.
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between joint.Cox versions 2.11 dated 2017-04-16 and 2.12 dated 2017-05-01
DESCRIPTION | 8 +++--- MD5 | 12 +++++----- R/jointCox.indep.reg.R | 49 ++++++++++++++++++++++-------------------- R/jointCox.reg.R | 53 +++++++++++++++++++++++++--------------------- man/joint.Cox-package.Rd | 4 +-- man/jointCox.indep.reg.Rd | 8 +++--- man/jointCox.reg.Rd | 8 +++--- 7 files changed, 75 insertions(+), 67 deletions(-)
Title: Convenient Data Exchange with Microsoft Excel
Description: Allows access to data in running instance of Microsoft Excel
(e. g. 'xl[a1] = xl[b2]*3' and so on). Graphics can be transferred with
'xl[a1] = current.graphics()'. There is an Excel workbook with examples of
calling R from Excel in the 'doc' folder. It tries to keep things as
simple as possible - there are no needs in any additional
installations besides R, only 'VBA' code in the Excel workbook.
Microsoft Excel is required for this package.
Author: Gregory Demin <excel.link.feedback@gmail.com>. To comply CRAN policy
includes source code from 'RDCOMClient' (http://www.omegahat.net/RDCOMClient) by
Duncan Temple Lang <duncan@wald.ucdavis.edu>.
Maintainer: Gregory Demin <excel.link.feedback@gmail.com>
Diff between excel.link versions 0.9.5 dated 2016-09-24 and 0.9.7 dated 2017-05-01
DESCRIPTION | 10 +- MD5 | 57 ++++++----- NAMESPACE | 18 +++ NEWS | 8 + R/0com.R | 24 ++-- R/excel.link.R | 2 R/utils.R | 10 +- R/xl.R | 107 +++++++++++++++++---- R/xl.bind.range.R | 37 ++++--- R/xl.constants.R |only R/xl.current.region.R | 19 ++- R/xl.workbooks.R | 21 +++- R/xl.write.R | 196 +++++++++++++++++++++++++++++++++++----- build/vignette.rds |binary inst/doc/CallingRFromExcel.html | 6 - man/RDCOMClient.Rd | 129 +++++++++++++------------- man/current.graphics.Rd | 1 man/excel.link.Rd | 2 man/xl.Rd | 60 ++++++++---- man/xl.bind.range.Rd | 39 +++---- man/xl.connect.table.Rd | 3 man/xl.current.region.Rd | 17 +-- man/xl.get.excel.Rd | 1 man/xl.index2address.Rd | 3 man/xl.property.Rd |only man/xl.read.file.Rd | 1 man/xl.sheet.add.Rd | 5 - man/xl.workbook.add.Rd | 12 +- man/xl.write.Rd | 5 - src/Makevars.win | 2 src/init.c |only 31 files changed, 547 insertions(+), 248 deletions(-)
Title: Time Series Clustering Along with Optimizations for the Dynamic
Time Warping Distance
Description: Time series clustering along with optimized techniques related
to the Dynamic Time Warping distance and its corresponding lower bounds.
Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole
clustering are available. Functionality can be easily extended with
custom distance measures and centroid definitions.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 3.1.2 dated 2017-04-01 and 3.2.0 dated 2017-05-01
DESCRIPTION | 17 MD5 | 147 +- NAMESPACE | 4 R/DBA.R | 409 +++---- R/GAK.R | 46 R/NCCc.R | 61 - R/SBD.R | 34 R/TADPole.R | 66 - R/as-methods.R |only R/compare-clusterings.R |only R/compute-envelop.R | 110 - R/create-dtwclust.R | 27 R/cvi.R | 327 ++--- R/dtw-basic.R | 444 +++---- R/dtw-lb.R | 39 R/dtw2.R | 114 -- R/dtwclust-classes.R | 480 ++++---- R/dtwclust-methods.R | 187 +-- R/dtwclust.R | 1799 +++++++++++++++----------------- R/lb-improved.R | 44 R/lb-keogh.R | 48 R/pkg.R | 377 +++--- R/reinterpolate.R | 8 R/shape-extraction.R | 267 ++-- R/tsclust-classes.R | 119 +- R/tsclust-controls.R | 334 ++--- R/tsclust-methods.R | 117 -- R/tsclust.R | 1655 ++++++++++++++--------------- R/uciCT.R | 8 R/utils.R | 54 R/zscore.R | 14 build/vignette.rds |binary inst/NEWS.Rd | 24 inst/comparison-examples.R |only inst/doc/dtwclust.Rnw | 19 inst/doc/dtwclust.pdf |binary man/DBA.Rd | 31 man/GAK.Rd | 40 man/NCCc.Rd | 7 man/SBD.Rd | 22 man/TADPole.Rd | 27 man/TSClusters-class.Rd | 120 +- man/as.matrix.Rd | 10 man/clusterSim.Rd | 4 man/compare_clusterings.Rd |only man/compare_clusterings_configs.Rd |only man/compute_envelop.Rd | 4 man/create_dtwclust.Rd | 24 man/cvi.Rd | 84 - man/dtw2.Rd | 12 man/dtw_basic.Rd | 22 man/dtw_lb.Rd | 27 man/dtwclust-class.Rd | 29 man/dtwclust-methods.Rd | 86 - man/dtwclust-package.Rd | 7 man/dtwclust.Rd | 538 ++++----- man/dtwclustControl-class.Rd | 76 - man/dtwclustFamily-class.Rd | 13 man/lb_improved.Rd | 34 man/lb_keogh.Rd | 40 man/pdc_configs.Rd |only man/randIndex.Rd | 4 man/reinterpolate.Rd | 8 man/shape_extraction.Rd | 25 man/tsclust-controls.Rd | 30 man/tsclust.Rd | 350 ++---- man/tsclustFamily-class.Rd | 13 man/tsclusters-methods.Rd | 117 -- man/uciCT.Rd | 8 man/zscore.Rd | 14 tests/testthat/regression/comparisons.R |only tests/testthat/regression/cvis.R | 56 tests/testthat/system/comparisons.R |only tests/testthat/test-01-unit.R | 1 tests/testthat/test-04-system.R | 17 tests/testthat/test-05-regression.R | 25 tests/testthat/unit/configs.R |only tests/testthat/unit/cvis.R | 18 vignettes/dtwclust.Rnw | 19 79 files changed, 4574 insertions(+), 4787 deletions(-)
Title: Double Hierarchical Generalized Linear Models
Description: Double hierarchical generalized linear models in which the mean, dispersion parameters for variance of random effects, and residual variance (overdispersion) can be further modeled as random-effect models.
Author: Youngjo Lee, Maengseok Noh
Maintainer: Maengseok Noh <msnoh@pknu.ac.kr>
Diff between dhglm versions 1.6 dated 2016-09-19 and 1.7 dated 2017-05-01
DESCRIPTION | 8 +- MD5 | 15 ++-- R/dhglmfit.R | 26 ++++++-- R/dhglmfit_run.R | 158 ++++++++++++++++++++++++++++++++++---------------- R/dhglmfit_run_sv.R |only R/plotdhglm.R | 12 +-- man/dhglm-package.Rd | 4 - man/dhglmfit.Rd | 18 +++-- man/residual.dhglm.Rd | 4 - 9 files changed, 162 insertions(+), 83 deletions(-)