Title: A fast solver for parameterized lp problems and constrained l1
minimization approach to sparse precision matrix estimation
Description: The package "fastclime" provides a method of recover the
precision matrix efficiently by applying parametric simplex
method. The computation is based on a linear optimization
solver. It also contains a generic LP solver and a parameterized LP solver using parametric simplex method.
Author: Haotian Pang, Han Liu and Robert Vanderbei
Maintainer: Haotian Pang
Diff between fastclime versions 1.2.1 dated 2013-09-28 and 1.2.2 dated 2013-09-29
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/fastclime.R | 4 ++-- R/fastclime.generator.R | 4 ++-- R/fastclime.plot.R | 4 ++-- R/fastclime.roc.R | 4 ++-- R/fastlp.R | 4 ++-- R/paralp.R | 4 ++-- inst/doc/vignette.pdf |binary src/paralp.c | 4 ++-- 10 files changed, 27 insertions(+), 27 deletions(-)
Title: TSdbi extension to connect to zip files
Description: Provides TSdbi package methods to retrieve time series data from
zipped, as if the files form a database.
Comprehensive examples of all the TS* packages is provided in the
vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert
Diff between TSzip versions 2012.8-1 dated 2012-10-01 and 2013.9-1 dated 2013-09-29
DESCRIPTION | 26 +++++++++++--------------- MD5 | 7 ++++--- NAMESPACE | 3 +++ NEWS | 8 ++++++++ build |only 5 files changed, 26 insertions(+), 18 deletions(-)
Title: TSdbi extension to connect to spreadsheets
Description: Provides TSdbi package methods to retrieve time series data from
spreadsheets, pretending the spreadsheet is a database.
Comprehensive examples of all the TS* packages is provided in the
vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert
Diff between TSxls versions 2012.8-1 dated 2012-10-01 and 2013.8-2 dated 2013-09-29
DESCRIPTION | 25 +++++++++++-------------- MD5 | 11 ++++++----- NAMESPACE | 3 +++ NEWS | 12 ++++++++++++ R/TSdbiMethods.R | 18 +++++++++++------- build |only man/TSdbiMethods.Rd | 4 +++- 7 files changed, 46 insertions(+), 27 deletions(-)
Title: TSdbi extensions for SQLite
Description: TSSQLite provides a SQLite interface for TSdbi.
Comprehensive examples of all the TS* packages is provided in the
vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert
Diff between TSSQLite versions 2012.8-1 dated 2012-10-01 and 2013.9-1 dated 2013-09-29
DESCRIPTION | 21 +++++++++------------ MD5 | 14 ++++++++------ NAMESPACE | 13 ++++++++----- NEWS | 8 ++++++++ R/TSdbiMethods.R | 20 ++++++++++---------- build |only inst/doc/Guide.Stex |only man/TSdbiMethods.Rd | 14 +++++++++++--- tests/RSQLite.R | 18 +++++++++++++----- 9 files changed, 67 insertions(+), 41 deletions(-)
Title: TSdbi extensions for PostgreSQL
Description: TSPostgreSQL provides a PostgreSQL interface for TSdbi.
Comprehensive examples of all the TS* packages is provided in the
vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert
Diff between TSPostgreSQL versions 2012.8-1 dated 2012-10-01 and 2013.9-1 dated 2013-09-29
DESCRIPTION | 19 ++++++++----------- MD5 | 12 +++++++----- NAMESPACE | 5 +++++ NEWS | 17 +++++++++++++++++ R/TSdbiMethods.R | 16 ++++++++-------- build |only inst/doc/Guide.Stex |only man/TSdbiMethods.Rd | 17 +++++++++++++---- 8 files changed, 58 insertions(+), 28 deletions(-)
Title: TSdbi extensions for ODBC
Description: TSodbc provides an ODBC interface for TSdbi.
Comprehensive examples of all the TS* packages is provided in the
vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert
Diff between TSodbc versions 2012.8-1 dated 2012-10-01 and 2013.9-1 dated 2013-09-29
DESCRIPTION | 22 +++++++++------------- MD5 | 12 +++++++----- NAMESPACE | 13 +++++++++---- NEWS | 8 ++++++++ R/TSdbiMethods.R | 16 ++++++++-------- build |only inst/doc/Guide.Stex |only man/TSdbiMethods.Rd | 17 +++++++++++++---- 8 files changed, 54 insertions(+), 34 deletions(-)
Title: TSdbi extensions for MySQL
Description: TSMySQL provides a MySQL interface for TSdbi.
Comprehensive examples of all the TS* packages is provided in the
vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert
Diff between TSMySQL versions 2012.8-1 dated 2012-10-02 and 2013.9-1 dated 2013-09-29
DESCRIPTION | 18 +++++++++--------- MD5 | 11 ++++++----- NAMESPACE | 14 ++++++++++---- NEWS | 15 +++++++++++++++ R/TSdbiMethods.R | 16 ++++++++-------- build |only man/TSdbiMethods.Rd | 18 +++++++++++++----- 7 files changed, 61 insertions(+), 31 deletions(-)
Title: TSdbi extensions for get.hist.quote
Description: Provides methods for generics in the TSdbi package to
retrieve data from historical quote URLs.
Comprehensive examples of all the TS* packages is provided in the
vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert
Diff between TShistQuote versions 2012.8-1 dated 2012-10-01 and 2013.9-1 dated 2013-09-29
DESCRIPTION | 23 ++++++++++------------- MD5 | 9 +++++---- NAMESPACE | 10 ++++++++-- NEWS | 10 ++++++++++ R/TSdbiMethods.R | 2 +- build |only 6 files changed, 34 insertions(+), 20 deletions(-)
Title: TSdbi extension to connect with getSymbols
Description: Provides methods for generics in the TSdbi package to
retrieve data with getSymbols, in particular from the Federal Reserve
FRED database.
Comprehensive examples of all the TS* packages is provided in the
vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert
Diff between TSgetSymbol versions 2012.8-1 dated 2012-10-01 and 2013.9-1 dated 2013-09-29
DESCRIPTION | 27 ++++++++++++--------------- MD5 | 9 +++++---- NAMESPACE | 9 +++++++-- NEWS | 11 +++++++++++ R/TSdbiMethods.R | 36 +++++++++++++----------------------- build |only 6 files changed, 48 insertions(+), 44 deletions(-)
Title: TSdbi extensions for fame
Description: TSfame provides a fame interface for TSdbi.
Comprehensive examples of all the TS* packages is provided in the
vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert
Diff between TSfame versions 2012.8-1 dated 2012-10-01 and 2013.8-2 dated 2013-09-29
DESCRIPTION | 25 +++++++++++-------------- MD5 | 8 +++++--- NAMESPACE | 16 ++++++++-------- NEWS | 13 +++++++++++++ build |only inst/doc/Guide.Stex |only 6 files changed, 37 insertions(+), 25 deletions(-)
Title: TSdbi (Time Series Database Interface)
Description: TSdbi provides a common interface to time series databases. The
objective is to define a standard interface so users can retrieve time
series data from various sources with a simple, common, set of
commands, and so programs can be written to be portable with respect
to the data source. The SQL implementations also provide a database
table design, so users needing to set up a time series database
have a reasonably complete way to do this easily. The interface
provides for a variety of options with respect to the representation
of time series in R. The interface, and the SQL implementations, also
handle vintages of time series data (sometime called editions or
realtime data). There is also a (not yet well tested) mechanism to
handle multilingual data documentation.
Comprehensive examples of all the TS* packages is provided in the
vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert
Diff between TSdbi versions 2013.3-1 dated 2013-03-28 and 2013.9-1 dated 2013-09-29
TSdbi-2013.3-1/TSdbi/R/TSquery.R |only TSdbi-2013.3-1/TSdbi/inst/TSsql |only TSdbi-2013.3-1/TSdbi/man/TSquery.Rd |only TSdbi-2013.3-1/TSdbi/man/dropTStable.Rd |only TSdbi-2013.3-1/TSdbi/man/internal.Rd |only TSdbi-2013.3-1/TSdbi/man/standardSQL.Rd |only TSdbi-2013.9-1/TSdbi/DESCRIPTION | 46 +- TSdbi-2013.9-1/TSdbi/MD5 | 26 - TSdbi-2013.9-1/TSdbi/NAMESPACE | 6 TSdbi-2013.9-1/TSdbi/NEWS | 14 TSdbi-2013.9-1/TSdbi/R/TSdbi.R | 491 ------------------------------ TSdbi-2013.9-1/TSdbi/build |only TSdbi-2013.9-1/TSdbi/man/TSdbi-package.Rd | 5 TSdbi-2013.9-1/TSdbi/man/TSget.Rd | 4 TSdbi-2013.9-1/TSdbi/man/TSput.Rd | 5 15 files changed, 59 insertions(+), 538 deletions(-)
Title: TSdbi Illustration
Description: TSdata illustrates the various TSdbi packages using time series
data from several sources. It also illustrates some simple time series
manipulation and plotting using packages tframe and tfplot.
Author: Paul Gilbert
Maintainer: Paul Gilbert
Diff between TSdata versions 2012.10-1 dated 2012-10-04 and 2013.9-1 dated 2013-09-29
DESCRIPTION | 27 - MD5 | 19 - NAMESPACE | 8 NEWS | 18 + inst/doc/Guide.Stex | 745 ++++++++++++++++++++++++++++++++-------------- inst/doc/Guide.bib |only inst/doc/Guide.pdf |binary inst/doc/GuideDevel.Stex | 23 - vignettes/Guide.Stex | 745 ++++++++++++++++++++++++++++++++-------------- vignettes/Guide.bib | 35 ++ vignettes/GuideDevel.Stex | 23 - 11 files changed, 1141 insertions(+), 502 deletions(-)
Title: TSdbi Comparison
Description: Utilities for comparing the equality of series on two databases.
Comprehensive examples of all the TS* packages is provided in the
vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert
Diff between TScompare versions 2013.3-1 dated 2013-03-28 and 2013.9-1 dated 2013-09-29
DESCRIPTION | 26 +++++++++++--------------- MD5 | 7 ++++--- NAMESPACE | 4 +++- NEWS | 10 ++++++++++ build |only 5 files changed, 28 insertions(+), 19 deletions(-)
Title: Programming with Big Data --- MPI Profiling Tools
Description: MPI profiling tools.
Author: Wei-Chen Chen [aut, cre],
Drew Schmidt [aut],
Gaurav Sehrawat [aut],
Pragneshkumar Patel [aut],
George Ostrouchov [aut]
Maintainer: Wei-Chen Chen
Diff between pbdPROF versions 0.1-0 dated 2013-08-01 and 0.2-0 dated 2013-09-29
pbdPROF-0.1-0/pbdPROF/INSTALL.win.bin |only pbdPROF-0.1-0/pbdPROF/INSTALL.win.src |only pbdPROF-0.1-0/pbdPROF/demo/allreduce.r |only pbdPROF-0.1-0/pbdPROF/demo/masterslavePI.r |only pbdPROF-0.1-0/pbdPROF/demo/svd.r |only pbdPROF-0.1-0/pbdPROF/inst/extdata/fpmpi.allreduce |only pbdPROF-0.1-0/pbdPROF/inst/extdata/fpmpi.masterslavePI |only pbdPROF-0.1-0/pbdPROF/inst/extdata/fpmpi.svd |only pbdPROF-0.1-0/pbdPROF/vignettes/include/06-debugging.tex |only pbdPROF-0.2-0/pbdPROF/ChangeLog | 10 pbdPROF-0.2-0/pbdPROF/DESCRIPTION | 14 pbdPROF-0.2-0/pbdPROF/INSTALL | 126 ++ pbdPROF-0.2-0/pbdPROF/MD5 | 98 - pbdPROF-0.2-0/pbdPROF/NAMESPACE | 21 pbdPROF-0.2-0/pbdPROF/R/00-classes.r | 6 pbdPROF-0.2-0/pbdPROF/R/01-generics.r | 8 pbdPROF-0.2-0/pbdPROF/R/grid_plotter.r |only pbdPROF-0.2-0/pbdPROF/R/parse.r | 53 pbdPROF-0.2-0/pbdPROF/R/plot.r | 581 ++++++++-- pbdPROF-0.2-0/pbdPROF/R/printing.r | 2 pbdPROF-0.2-0/pbdPROF/R/read.r | 11 pbdPROF-0.2-0/pbdPROF/README | 11 pbdPROF-0.2-0/pbdPROF/configure | 89 - pbdPROF-0.2-0/pbdPROF/configure.ac | 73 - pbdPROF-0.2-0/pbdPROF/data |only pbdPROF-0.2-0/pbdPROF/demo/00Index | 9 pbdPROF-0.2-0/pbdPROF/demo/allreduce.fpmpi.r |only pbdPROF-0.2-0/pbdPROF/demo/allreduce.mpip.r |only pbdPROF-0.2-0/pbdPROF/demo/masterslavePI.fpmpi.r |only pbdPROF-0.2-0/pbdPROF/demo/masterslavePI.mpip.r |only pbdPROF-0.2-0/pbdPROF/demo/svd.fpmpi.r |only pbdPROF-0.2-0/pbdPROF/demo/svd.mpip.r |only pbdPROF-0.2-0/pbdPROF/inst/doc/pbdPROF-guide.Rnw | 24 pbdPROF-0.2-0/pbdPROF/inst/doc/pbdPROF-guide.pdf |binary pbdPROF-0.2-0/pbdPROF/inst/extdata/allreduce.fpmpi |only pbdPROF-0.2-0/pbdPROF/inst/extdata/allreduce.mpip |only pbdPROF-0.2-0/pbdPROF/inst/extdata/masterslavePI.fpmpi |only pbdPROF-0.2-0/pbdPROF/inst/extdata/masterslavePI.mpip |only pbdPROF-0.2-0/pbdPROF/inst/extdata/svd.fpmpi |only pbdPROF-0.2-0/pbdPROF/inst/extdata/svd.mpip |only pbdPROF-0.2-0/pbdPROF/man/00_pbdPROF-package.Rd | 9 pbdPROF-0.2-0/pbdPROF/man/02_classes.Rd | 4 pbdPROF-0.2-0/pbdPROF/man/12_example.Rd | 19 pbdPROF-0.2-0/pbdPROF/man/aa_read_prof.Rd | 2 pbdPROF-0.2-0/pbdPROF/man/cc_plot.Rd | 16 pbdPROF-0.2-0/pbdPROF/man/zz_internal.Rd |only pbdPROF-0.2-0/pbdPROF/src/Makevars.in | 1 pbdPROF-0.2-0/pbdPROF/vignettes/include/00-acknowledgement.tex | 7 pbdPROF-0.2-0/pbdPROF/vignettes/include/00-copyright.tex | 5 pbdPROF-0.2-0/pbdPROF/vignettes/include/01-introduction.tex | 60 - pbdPROF-0.2-0/pbdPROF/vignettes/include/02-installation.tex | 222 +++ pbdPROF-0.2-0/pbdPROF/vignettes/include/03-testing.tex | 24 pbdPROF-0.2-0/pbdPROF/vignettes/include/04-example.tex | 367 +++++- pbdPROF-0.2-0/pbdPROF/vignettes/include/05-profiling.tex | 283 ++++ pbdPROF-0.2-0/pbdPROF/vignettes/include/06-plotting.tex |only pbdPROF-0.2-0/pbdPROF/vignettes/include/07-debugging.tex |only pbdPROF-0.2-0/pbdPROF/vignettes/include/pbdPROF.bib | 21 pbdPROF-0.2-0/pbdPROF/vignettes/include/pics/fpmpi.png |only pbdPROF-0.2-0/pbdPROF/vignettes/include/pics/fpmpi_pbdMPI_plot.jpeg |only pbdPROF-0.2-0/pbdPROF/vignettes/include/pics/mpip |only pbdPROF-0.2-0/pbdPROF/vignettes/include/style.tex | 8 pbdPROF-0.2-0/pbdPROF/vignettes/pbdPROF-guide.Rnw | 24 62 files changed, 1809 insertions(+), 399 deletions(-)
Title: Mixtures of von Mises-Fisher Distributions
Description: Fit and simulate mixtures of von Mises-Fisher distributions.
Author: Kurt Hornik [aut, cre],
Bettina Grün [aut]
Maintainer: Kurt Hornik
Diff between movMF versions 0.1-1 dated 2013-06-19 and 0.1-2 dated 2013-09-29
DESCRIPTION | 22 - MD5 | 23 - R/dmovMF.R | 2 R/movMF.R | 46 +++ build |only inst/NEWS.Rd | 13 - inst/doc/movMF.R | 189 +++++++++++++-- inst/doc/movMF.Rnw | 574 ++++++++++++++++++++++++++++++++-------------- inst/doc/movMF.pdf |binary man/movMF.Rd | 110 ++++++-- man/movMF_distribution.Rd | 6 vignettes/movMF.Rnw | 574 ++++++++++++++++++++++++++++++++-------------- vignettes/vMF.bib | 262 +++++++++++++------- 13 files changed, 1302 insertions(+), 519 deletions(-)
Title: Colocalisation tests of two genetic traits
Description: Performs the colocalisation tests described in Plagnol et al
(2009), Wallace et al (2013) and Giambartolomei et al (2013).
Author: Chris Wallace [aut, cre],
Claudia Giambartolomei [aut],
Vincent Plagnol [ctb]
Maintainer: Chris Wallace
Diff between coloc versions 2.3 dated 2013-09-25 and 2.3-1 dated 2013-09-29
ChangeLog | 6 ++++++ DESCRIPTION | 12 +++++++----- MD5 | 14 ++++++++------ NAMESPACE | 4 ++++ R/AllClasses.R | 20 ++++++++++---------- R/claudia.R | 6 ++++-- build |only inst/tests/test-abf.R | 16 ++++++++++++++++ inst/tests/test.txt |only 9 files changed, 55 insertions(+), 23 deletions(-)
Title: Rcpp integration for Armadillo templated linear algebra library
Description: R and Armadillo integration using Rcpp
Armadillo is a templated C++ linear algebra library (by Conrad Sanderson)
that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
A delayed evaluation approach is employed (during compile time) to combine
several operations into one, and to reduce (or eliminate) the need for
temporaries. This is accomplished through recursive templates and template
meta-programming.
This library is useful if C++ has been decided as the language of choice
(due to speed and/or integration capabilities), rather than another language.
The RcppArmadillo package includes the header files from the templated
Armadillo library (currently version 3.920.1). Thus users do not need to
install Armadillo itself in order to use RcppArmadillo.
This Armadillo integration provides a nice illustration of the
capabilities of the Rcpp package for seamless R and C++ integration.
Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
bindings/bridge to Armadillo) is licensed under the GNU GPL version 2
or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel
Diff between RcppArmadillo versions 0.3.910.0 dated 2013-08-15 and 0.3.920.1 dated 2013-09-29
RcppArmadillo-0.3.910.0/RcppArmadillo/inst/include/RcppArmadilloExtensions/spmat.h |only RcppArmadillo-0.3.910.0/RcppArmadillo/vignettes/Makefile |only RcppArmadillo-0.3.910.0/RcppArmadillo/vignettes/RcppArmadillo-intro.pdf |only RcppArmadillo-0.3.910.0/RcppArmadillo/vignettes/RcppArmadillo-unitTests.pdf |only RcppArmadillo-0.3.910.0/RcppArmadillo/vignettes/unitTests-results |only RcppArmadillo-0.3.920.1/RcppArmadillo/ChangeLog | 65 RcppArmadillo-0.3.920.1/RcppArmadillo/DESCRIPTION | 13 RcppArmadillo-0.3.920.1/RcppArmadillo/MD5 | 116 - RcppArmadillo-0.3.920.1/RcppArmadillo/cleanup | 1 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/NEWS.Rd | 24 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/doc/RcppArmadillo-intro.R |only RcppArmadillo-0.3.920.1/RcppArmadillo/inst/doc/RcppArmadillo-intro.Rnw |only RcppArmadillo-0.3.920.1/RcppArmadillo/inst/doc/RcppArmadillo-unitTests.R |only RcppArmadillo-0.3.920.1/RcppArmadillo/inst/doc/RcppArmadillo-unitTests.Rnw |only RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/RcppArmadillo.h | 1 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/RcppArmadilloAs.h |only RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/RcppArmadilloExtensions/sample.h | 51 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/RcppArmadilloForward.h | 18 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/RcppArmadilloWrap.h | 92 - RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo | 1 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/Col_bones.hpp | 22 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/Col_meat.hpp | 135 + RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/Cube_bones.hpp | 37 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/Cube_meat.hpp | 334 +++ RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/Mat_bones.hpp | 20 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/Mat_meat.hpp | 255 ++ RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/Row_bones.hpp | 20 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/Row_meat.hpp | 135 + RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/SpMat_bones.hpp | 14 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/SpMat_meat.hpp | 149 + RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/arma_config.hpp | 7 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/arma_ostream_bones.hpp | 6 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/arma_version.hpp | 6 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/arrayops_bones.hpp | 5 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/arrayops_meat.hpp | 20 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/debug.hpp | 1 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/diskio_meat.hpp | 10 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/eop_aux.hpp | 166 - RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/eop_core_bones.hpp | 1 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/eop_core_meat.hpp | 3 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/fn_dot.hpp | 24 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/fn_eig.hpp | 49 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/fn_elem.hpp | 27 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/fn_fft.hpp | 5 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/fn_fft2.hpp |only RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/fn_join.hpp | 28 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/forward_bones.hpp | 25 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/glue_join_bones.hpp | 7 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/glue_join_meat.hpp | 121 - RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/glue_kron_meat.hpp | 41 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/glue_times_bones.hpp | 3 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/mul_herk.hpp | 3 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/op_dot_bones.hpp | 12 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/op_dot_meat.hpp | 73 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/op_resize_meat.hpp | 22 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/span.hpp | 5 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/subview_bones.hpp | 7 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/subview_cube_bones.hpp | 1 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/subview_cube_meat.hpp | 32 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/include/armadillo_bits/subview_meat.hpp | 112 + RcppArmadillo-0.3.920.1/RcppArmadillo/inst/unitTests/cpp/armadillo.cpp | 62 RcppArmadillo-0.3.920.1/RcppArmadillo/inst/unitTests/runit.RcppArmadillo.R | 72 RcppArmadillo-0.3.920.1/RcppArmadillo/vignettes/RcppArmadillo-intro.Rnw | 882 ---------- RcppArmadillo-0.3.920.1/RcppArmadillo/vignettes/RcppArmadillo-unitTests.Rnw | 4 64 files changed, 2065 insertions(+), 1280 deletions(-)
Title: Seamless R and C++ Integration
Description: The Rcpp package provides R functions as well as a C++ library
which facilitate the integration of R and C++.
R data types (SEXP) are matched to C++ objects in a class hierarchy. All R
types are supported (vectors, functions, environment, etc ...) and each
type is mapped to a dedicated class. For example, numeric vectors are
represented as instances of the Rcpp::NumericVector class, environments are
represented as instances of Rcpp::Environment, functions are represented as
Rcpp::Function, etc ... The "Rcpp-introduction" vignette provides a good
entry point to Rcpp.
Conversion from C++ to R and back is driven by the templates Rcpp::wrap
and Rcpp::as which are highly flexible and extensible, as documented
in the "Rcpp-extending" vignette.
Rcpp also provides Rcpp modules, a framework that allows exposing
C++ functions and classes to the R level. The "Rcpp-modules" vignette
details the current set of features of Rcpp-modules.
Rcpp includes a concept called Rcpp sugar that brings many R functions
into C++. Sugar takes advantage of lazy evaluation and expression templates
to achieve great performance while exposing a syntax that is much nicer
to use than the equivalent low-level loop code. The "Rcpp-sugar" vignette
gives an overview of the feature.
Rcpp attributes provide a high-level syntax for declaring C++
functions as callable from R and automatically generating the code
required to invoke them. Attributes are intended to facilitate both
interactive use of C++ within R sessions as well as to support R
package development. Attributes are built on top of Rcpp modules and
their implementation is based on previous work in the inline package.
Many examples are included, and around 872 unit tests in 422 unit
test functions provide additional usage examples.
An earlier version of Rcpp, containing what we now call the 'classic Rcpp
API' was written during 2005 and 2006 by Dominick Samperi. This code has
been factored out of Rcpp into the package RcppClassic, and it is still
available for code relying on the older interface. New development should
always use this Rcpp package instead.
Additional documentation is available via the paper by Eddelbuettel and
Francois (2011, JSS) paper and the book by Eddelbuettel (2013, Springer);
see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel and Romain Francois, with contributions
by Douglas Bates, John Chambers and JJ Allaire
Maintainer: Dirk Eddelbuettel
Diff between Rcpp versions 0.10.4 dated 2013-06-24 and 0.10.5 dated 2013-09-29
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25 Rcpp-0.10.5/Rcpp/inst/include/Rcpp/config.h | 2 Rcpp-0.10.5/Rcpp/inst/include/Rcpp/internal/Exporter.h | 77 Rcpp-0.10.5/Rcpp/inst/include/Rcpp/internal/export.h | 40 Rcpp-0.10.5/Rcpp/inst/include/Rcpp/internal/wrap.h | 65 Rcpp-0.10.5/Rcpp/inst/include/Rcpp/is.h |only Rcpp-0.10.5/Rcpp/inst/include/Rcpp/longlong.h |only Rcpp-0.10.5/Rcpp/inst/include/Rcpp/macros/module.h | 38 Rcpp-0.10.5/Rcpp/inst/include/Rcpp/macros/preprocessor_generated.h | 332 Rcpp-0.10.5/Rcpp/inst/include/Rcpp/module/Module_generated_CppFunction.h |11607 ++++++++-- Rcpp-0.10.5/Rcpp/inst/include/Rcpp/module/Module_generated_CppMethod.h | 9102 +++++++ Rcpp-0.10.5/Rcpp/inst/include/Rcpp/module/Module_generated_Pointer_CppMethod.h | 9100 +++++++ Rcpp-0.10.5/Rcpp/inst/include/Rcpp/platform/compiler.h | 26 Rcpp-0.10.5/Rcpp/inst/include/Rcpp/sugar/functions/diff.h | 66 Rcpp-0.10.5/Rcpp/inst/include/Rcpp/sugar/functions/functions.h | 4 Rcpp-0.10.5/Rcpp/inst/include/Rcpp/sugar/functions/is_na.h | 23 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Rcpp-0.10.5/Rcpp/inst/unitTests/runit.Matrix.R | 292 Rcpp-0.10.5/Rcpp/inst/unitTests/runit.Module.R | 214 Rcpp-0.10.5/Rcpp/inst/unitTests/runit.RObject.R | 363 Rcpp-0.10.5/Rcpp/inst/unitTests/runit.Reference.R | 7 Rcpp-0.10.5/Rcpp/inst/unitTests/runit.S4.R | 4 Rcpp-0.10.5/Rcpp/inst/unitTests/runit.String.R | 5 Rcpp-0.10.5/Rcpp/inst/unitTests/runit.Vector.R | 1295 - Rcpp-0.10.5/Rcpp/inst/unitTests/runit.XPTr.R | 50 Rcpp-0.10.5/Rcpp/inst/unitTests/runit.as.R | 157 Rcpp-0.10.5/Rcpp/inst/unitTests/runit.environments.R | 152 Rcpp-0.10.5/Rcpp/inst/unitTests/runit.misc.R | 182 Rcpp-0.10.5/Rcpp/inst/unitTests/runit.modref.R | 80 Rcpp-0.10.5/Rcpp/inst/unitTests/runit.rmath.R | 498 Rcpp-0.10.5/Rcpp/inst/unitTests/runit.stats.R | 407 Rcpp-0.10.5/Rcpp/inst/unitTests/runit.sugar.R | 59 Rcpp-0.10.5/Rcpp/inst/unitTests/runit.support.R | 101 Rcpp-0.10.5/Rcpp/inst/unitTests/runit.wrap.R | 361 Rcpp-0.10.5/Rcpp/inst/unitTests/runit.wstring.R | 8 Rcpp-0.10.5/Rcpp/man/Rcpp-internal.Rd |only Rcpp-0.10.5/Rcpp/man/Rcpp.package.skeleton.Rd | 6 Rcpp-0.10.5/Rcpp/man/RcppLdFlags.Rd |only Rcpp-0.10.5/Rcpp/man/demangle.Rd |only Rcpp-0.10.5/Rcpp/man/pluginsAttribute.Rd | 3 Rcpp-0.10.5/Rcpp/man/setRcppClass.Rd | 6 Rcpp-0.10.5/Rcpp/man/sourceCpp.Rd | 20 Rcpp-0.10.5/Rcpp/src/Module.cpp | 102 Rcpp-0.10.5/Rcpp/src/api.cpp | 15 Rcpp-0.10.5/Rcpp/src/attributes.cpp | 47 Rcpp-0.10.5/Rcpp/vignettes |only 144 files changed, 36484 insertions(+), 5849 deletions(-)
Title: Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)
Description: A High-performance computing toolset for relatedness and principal component analysis of SNP data
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng
Diff between SNPRelate versions 0.9.17 dated 2013-09-05 and 0.9.18 dated 2013-09-29
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 5 +++++ R/IBD.r | 4 +++- R/SNPRelate_Main.r | 2 +- src/SNPRelate.cpp | 2 +- 6 files changed, 19 insertions(+), 12 deletions(-)
Title: Efficiently Read Sequence Data (VCF format, BCF format and METAL
format) into R
Description: Integrate sequencing data (VCF) or meta-analysis results in R
Author: Xiaowei Zhan
Maintainer: Xiaowei Zhan
Diff between seqminer versions 1.3 dated 2013-09-26 and 1.4 dated 2013-09-29
ChangeLog | 6 + DESCRIPTION | 6 - MD5 | 22 +++--- R/seqminer.R | 54 ++++++++++++++- inst/tests/testthat.R | 9 ++ inst/vcf/all.anno.filtered.extract.bcf.gz |only inst/vcf/all.anno.filtered.extract.bcf.gz.bci |only src/BCFReader.cpp | 2 src/VCFExtractor.h | 2 src/VCFHeader.h | 88 +++++++++++++++----------- src/VCFInputFile.cpp | 15 ++-- src/vcf2genoLoader.cpp | 4 - tests/tests.R | 1 13 files changed, 147 insertions(+), 62 deletions(-)