Mon, 01 May 2017

Package virustotal updated to version 0.2.1 with previous version 0.2.0 dated 2016-11-12

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(-)

More information about virustotal at CRAN
Permanent link

Package tigris updated to version 0.5 with previous version 0.3.3 dated 2016-07-06

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(-)

More information about tigris at CRAN
Permanent link

Package fftw updated to version 1.0-4 with previous version 1.0-3 dated 2011-04-24

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(-)

More information about fftw at CRAN
Permanent link

Package WRS2 updated to version 0.9-2 with previous version 0.9-1 dated 2016-08-13

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(-)

More information about WRS2 at CRAN
Permanent link

Package officer updated to version 0.1.3 with previous version 0.1.2 dated 2017-04-29

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(-)

More information about officer at CRAN
Permanent link

New package MHTmult with initial version 0.1.0
Package: MHTmult
Type: Package
Title: Multiple Hypotheses Testing for Multiple Families/Groups Structure
Version: 0.1.0
Author: Yalin Zhu, Wenge Guo
Maintainer: Yalin Zhu <yalin.zhu@outlook.com>
BugReports: https://github.com/allenzhuaz/MHTmult/issues
Description: A Comprehensive tool for almost all existing multiple testing methods for multiple families. The package summarizes the existing methods for multiple families multiple testing procedures (MTPs) such as double FDR, group Benjamini-Hochberg (GBH) procedure and average FDR controlling procedure. The package also provides some novel multiple testing procedures using selective inference idea.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: TRUE
Suggests: structSSI, MHTdiscrete, FixSeqMTP
NeedsCompilation: yes
Packaged: 2017-05-01 15:51:11 UTC; yalinzhu
Repository: CRAN
Date/Publication: 2017-05-01 16:21:02 UTC

More information about MHTmult at CRAN
Permanent link

New package cfa with initial version 0.10-0
Package: cfa
Description: Analysis of configuration frequencies for simple and repeated measures, multiple-samples CFA, hierarchical CFA, bootstrap CFA, functional CFA, Kieser-Victor CFA, and Lindner's test using a conventional and an accelerated algorithm.
Title: Configural Frequency Analysis (CFA)
Version: 0.10-0
Date: 2017-04-29
Authors@R: c(person("Patrick", "Mair", role = c("aut", "cre"), email = "mair@fas.harvard.edu"), person("Stefan", "Funke", role = "aut"), person("Joachim", "Harloff", role = "ctb"), person("Alexander", "von Eye", role = "ctb"))
Depends: R (>= 3.0.1)
Suggests: parallel
License: GPL (>= 2)
NeedsCompilation: yes
LazyData: true
Packaged: 2017-04-29 20:15:58 UTC; patrick
Author: Patrick Mair [aut, cre], Stefan Funke [aut], Joachim Harloff [ctb], Alexander von Eye [ctb]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Repository: CRAN
Date/Publication: 2017-05-01 16:18:32 UTC

More information about cfa at CRAN
Permanent link

Package anacor updated to version 1.1-3 with previous version 1.0-6 dated 2015-07-23

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(-)

More information about anacor at CRAN
Permanent link

Package wgeesel updated to version 1.1 with previous version 1.0 dated 2017-04-21

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(-)

More information about wgeesel at CRAN
Permanent link

New package rwunderground with initial version 0.1.6
Package: rwunderground
Type: Package
Title: R Interface to Weather Underground API
Version: 0.1.6
Date: 2017-05-01
Author: Alex Shum <alex@ALShum.com>
Maintainer: Eric Hare <eric@omnianalytics.io>
Description: Tools for getting historical weather information and forecasts from wunderground.com. Historical weather and forecast data includes, but is not limited to, temperature, humidity, windchill, wind speed, dew point, heat index. Additionally, the weather underground weather API also includes information on sunrise/sunset, tidal conditions, satellite/webcam imagery, weather alerts, hurricane alerts and historical high/low temperatures.
URL: https://github.com/ALShum/rwunderground, http://www.wunderground.com/weather/api
BugReports: https://github.com/alshum/rwunderground/issues
License: GPL (>= 2)
Imports: httr, dplyr, countrycode
LazyData: TRUE
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-05-01 12:50:34 UTC; erichare
X-CRAN-Comment: Archived on 2017-03-26 as check problems were not corrected despite reminders.
Repository: CRAN
Date/Publication: 2017-05-01 15:59:42 UTC

More information about rwunderground at CRAN
Permanent link

Package RcppEigen updated to version 0.3.3.3.0 with previous version 0.3.2.9.1 dated 2017-03-15

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(-)

More information about RcppEigen at CRAN
Permanent link

Package googleway updated to version 2.0.0 with previous version 1.0.0 dated 2016-06-13

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(-)

More information about googleway at CRAN
Permanent link

Package frailtyEM updated to version 0.6.2 with previous version 0.5.4 dated 2017-04-03

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(-)

More information about frailtyEM at CRAN
Permanent link

Package joineRML updated to version 0.2.2 with previous version 0.2.1 dated 2017-04-25

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

 joineRML-0.2.1/joineRML/inst/doc/technical.ltx                                                              |only
 joineRML-0.2.1/joineRML/man/initsSurv.Rd                                                                    |only
 joineRML-0.2.1/joineRML/man/initsSurv_unbalanced.Rd                                                         |only
 joineRML-0.2.1/joineRML/vignettes/joineRML_cache/html/hvd_model_boot_f450182d26c4fe8447b1a85588ff46ea.RData |only
 joineRML-0.2.1/joineRML/vignettes/joineRML_cache/html/hvd_model_boot_f450182d26c4fe8447b1a85588ff46ea.rdb   |only
 joineRML-0.2.1/joineRML/vignettes/joineRML_cache/html/hvd_model_boot_f450182d26c4fe8447b1a85588ff46ea.rdx   |only
 joineRML-0.2.1/joineRML/vignettes/joineRML_cache/html/joineRML_c93014128247f4f1d85a458110b8bff3.RData       |only
 joineRML-0.2.1/joineRML/vignettes/joineRML_cache/html/joineRML_c93014128247f4f1d85a458110b8bff3.rdb         |only
 joineRML-0.2.1/joineRML/vignettes/joineRML_cache/html/joineRML_c93014128247f4f1d85a458110b8bff3.rdx         |only
 joineRML-0.2.1/joineRML/vignettes/joineRML_cache/html/joineR_16041b81b92a58932ff851f9a55e0ae5.RData         |only
 joineRML-0.2.1/joineRML/vignettes/joineRML_cache/html/joineR_16041b81b92a58932ff851f9a55e0ae5.rdb           |only
 joineRML-0.2.1/joineRML/vignettes/joineRML_cache/html/joineR_16041b81b92a58932ff851f9a55e0ae5.rdx           |only
 joineRML-0.2.1/joineRML/vignettes/joineRML_files                                                            |only
 joineRML-0.2.1/joineRML/vignettes/technical.ltx                                                             |only
 joineRML-0.2.2/joineRML/DESCRIPTION                                                                         |   14 
 joineRML-0.2.2/joineRML/MD5                                                                                 |  134 +--
 joineRML-0.2.2/joineRML/NEWS.md                                                                             |   12 
 joineRML-0.2.2/joineRML/R/bootSE.R                                                                          |    8 
 joineRML-0.2.2/joineRML/R/confint.mjoint.R                                                                  |    8 
 joineRML-0.2.2/joineRML/R/epileptic.qol.R                                                                   |   11 
 joineRML-0.2.2/joineRML/R/fitted.mjoint.R                                                                   |    4 
 joineRML-0.2.2/joineRML/R/fixef.mjoint.R                                                                    |    4 
 joineRML-0.2.2/joineRML/R/formula.mjoint.R                                                                  |    8 
 joineRML-0.2.2/joineRML/R/heart.valve.R                                                                     |   27 
 joineRML-0.2.2/joineRML/R/initsSurv.R                                                                       |   16 
 joineRML-0.2.2/joineRML/R/joineRML.R                                                                        |   12 
 joineRML-0.2.2/joineRML/R/logLik.mjoint.R                                                                   |    5 
 joineRML-0.2.2/joineRML/R/mjoint.R                                                                          |   61 -
 joineRML-0.2.2/joineRML/R/mjoint.object.R                                                                   |    4 
 joineRML-0.2.2/joineRML/R/pbc2.R                                                                            |    4 
 joineRML-0.2.2/joineRML/R/plot.mjoint.R                                                                     |    2 
 joineRML-0.2.2/joineRML/R/plot.ranef.mjoint.R                                                               |    4 
 joineRML-0.2.2/joineRML/R/plotConvergence.R                                                                 |   16 
 joineRML-0.2.2/joineRML/R/ranef.mjoint.R                                                                    |    4 
 joineRML-0.2.2/joineRML/R/renal.R                                                                           |    8 
 joineRML-0.2.2/joineRML/R/residuals.mjoint.R                                                                |    4 
 joineRML-0.2.2/joineRML/R/sampleData.R                                                                      |    2 
 joineRML-0.2.2/joineRML/R/simData.R                                                                         |   28 
 joineRML-0.2.2/joineRML/README.md                                                                           |   35 
 joineRML-0.2.2/joineRML/build/vignette.rds                                                                  |binary
 joineRML-0.2.2/joineRML/inst/doc/joineRML.R                                                                 |   11 
 joineRML-0.2.2/joineRML/inst/doc/joineRML.Rmd                                                               |   34 
 joineRML-0.2.2/joineRML/inst/doc/joineRML.html                                                              |  364 ++--------
 joineRML-0.2.2/joineRML/inst/doc/technical.Rnw                                                              |only
 joineRML-0.2.2/joineRML/inst/doc/technical.pdf                                                              |binary
 joineRML-0.2.2/joineRML/man/bootSE.Rd                                                                       |   44 -
 joineRML-0.2.2/joineRML/man/confint.mjoint.Rd                                                               |    8 
 joineRML-0.2.2/joineRML/man/epileptic.qol.Rd                                                                |   10 
 joineRML-0.2.2/joineRML/man/fitted.mjoint.Rd                                                                |    4 
 joineRML-0.2.2/joineRML/man/fixef.mjoint.Rd                                                                 |    4 
 joineRML-0.2.2/joineRML/man/formula.mjoint.Rd                                                               |    8 
 joineRML-0.2.2/joineRML/man/heart.valve.Rd                                                                  |   27 
 joineRML-0.2.2/joineRML/man/joineRML.Rd                                                                     |   12 
 joineRML-0.2.2/joineRML/man/logLik.mjoint.Rd                                                                |    5 
 joineRML-0.2.2/joineRML/man/mjoint.Rd                                                                       |   61 -
 joineRML-0.2.2/joineRML/man/mjoint.object.Rd                                                                |    4 
 joineRML-0.2.2/joineRML/man/pbc2.Rd                                                                         |    4 
 joineRML-0.2.2/joineRML/man/plot.mjoint.Rd                                                                  |    2 
 joineRML-0.2.2/joineRML/man/plot.ranef.mjoint.Rd                                                            |    4 
 joineRML-0.2.2/joineRML/man/plotConvergence.Rd                                                              |   16 
 joineRML-0.2.2/joineRML/man/ranef.mjoint.Rd                                                                 |    4 
 joineRML-0.2.2/joineRML/man/renal.Rd                                                                        |    8 
 joineRML-0.2.2/joineRML/man/residuals.mjoint.Rd                                                             |    4 
 joineRML-0.2.2/joineRML/man/sampleData.Rd                                                                   |    2 
 joineRML-0.2.2/joineRML/man/simData.Rd                                                                      |   26 
 joineRML-0.2.2/joineRML/man/summary.mjoint.Rd                                                               |    2 
 joineRML-0.2.2/joineRML/vignettes/joineRML.Rmd                                                              |   34 
 joineRML-0.2.2/joineRML/vignettes/joineRML_cache/html/__packages                                            |   12 
 joineRML-0.2.2/joineRML/vignettes/joineRML_cache/html/hvd_model_fit_4c7e505dd19c268aea1f99aee071cc94.RData  |binary
 joineRML-0.2.2/joineRML/vignettes/joineRML_cache/html/hvd_model_fit_4c7e505dd19c268aea1f99aee071cc94.rdb    |binary
 joineRML-0.2.2/joineRML/vignettes/joineRML_cache/html/hvd_model_fit_4c7e505dd19c268aea1f99aee071cc94.rdx    |binary
 joineRML-0.2.2/joineRML/vignettes/joineRML_cache/html/joineRML_99311e8db628fe71216e242a3e88a9eb.RData       |only
 joineRML-0.2.2/joineRML/vignettes/joineRML_cache/html/joineRML_99311e8db628fe71216e242a3e88a9eb.rdb         |only
 joineRML-0.2.2/joineRML/vignettes/joineRML_cache/html/joineRML_99311e8db628fe71216e242a3e88a9eb.rdx         |only
 joineRML-0.2.2/joineRML/vignettes/joineRML_cache/html/joineR_614bf2d80922aa5f35d5dcaffbb8e1c2.RData         |only
 joineRML-0.2.2/joineRML/vignettes/joineRML_cache/html/joineR_614bf2d80922aa5f35d5dcaffbb8e1c2.rdb           |only
 joineRML-0.2.2/joineRML/vignettes/joineRML_cache/html/joineR_614bf2d80922aa5f35d5dcaffbb8e1c2.rdx           |only
 joineRML-0.2.2/joineRML/vignettes/technical.Rnw                                                             |only
 78 files changed, 440 insertions(+), 709 deletions(-)

More information about joineRML at CRAN
Permanent link

Package startup updated to version 0.6.0 with previous version 0.5.0 dated 2017-02-12

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(-)

More information about startup at CRAN
Permanent link

Package roll updated to version 1.0.7 with previous version 1.0.6 dated 2016-09-19

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(-)

More information about roll at CRAN
Permanent link

Package rarhsmm updated to version 1.0.3 with previous version 1.0.2 dated 2017-04-19

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(-)

More information about rarhsmm at CRAN
Permanent link

Package pipe.design updated to version 0.5 with previous version 0.4 dated 2016-05-10

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(-)

More information about pipe.design at CRAN
Permanent link

Package PhylogeneticEM updated to version 1.0.1 with previous version 1.0.0 dated 2017-01-31

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
Permanent link

Package NNS updated to version 0.3.2 with previous version 0.3.1 dated 2017-03-31

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(-)

More information about NNS at CRAN
Permanent link

Package nlsem updated to version 0.8 with previous version 0.7 dated 2017-01-02

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(-)

More information about nlsem at CRAN
Permanent link

Package MultivariateRandomForest updated to version 1.1.5 with previous version 1.1.2 dated 2016-12-07

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
Permanent link

Package joint.Cox updated to version 2.12 with previous version 2.11 dated 2017-04-16

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(-)

More information about joint.Cox at CRAN
Permanent link

Package excel.link updated to version 0.9.7 with previous version 0.9.5 dated 2016-09-24

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(-)

More information about excel.link at CRAN
Permanent link

Package dtwclust updated to version 3.2.0 with previous version 3.1.2 dated 2017-04-01

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(-)

More information about dtwclust at CRAN
Permanent link

Package dhglm updated to version 1.7 with previous version 1.6 dated 2016-09-19

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(-)

More information about dhglm at CRAN
Permanent link

New package angstroms with initial version 0.0.1
Package: angstroms
Title: Tools for 'ROMS' the Regional Ocean Modeling System
Version: 0.0.1
Authors@R: person("Michael D.","Sumner", role = c("aut", "cre"), email = "mdsumner@gmail.com")
Description: Helper functions for working with Regional Ocean Modeling System 'ROMS' output. See <https://www.myroms.org/> for more information about 'ROMS'.
Depends: R (>= 3.3.0), raster
License: GPL-3
LazyData: true
Imports: nabor, ncdf4, proj4, sp, spbabel
RoxygenNote: 6.0.1
Suggests: testthat, covr
URL: https://github.com/mdsumner/angstroms
BugReports: https://github.com/mdsumner/angstroms/issues
NeedsCompilation: no
Packaged: 2017-05-01 02:42:30 UTC; mdsumner
Author: Michael D. Sumner [aut, cre]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Repository: CRAN
Date/Publication: 2017-05-01 10:35:22 UTC

More information about angstroms at CRAN
Permanent link


Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.