Title: R interface to the iPlant Discovery Environment
Diff between rPlant versions 2.1 dated 2013-02-07 and 2.3 dated 2013-03-12
Description: rPlant is an R interface to the the many computational
resources iPlant offers through their RESTful application
programming interface. Currently, rPlant functions interact
with the iPlant foundational API, the Taxonomic Name Resolution
Service API, and the Phylotastic Taxosaurus API. Before using
rPlant, users will have to register with the iPlant
Collaborative.
http://www.iplantcollaborative.org/discover/discovery-environment
Author: Barb Banbury
Maintainer: Barb Banbury
DESCRIPTION | 23 +++++---
MD5 | 36 ++++++-------
R/GetCitations.R | 2
R/RunClustal.R | 5 +
R/RunMafft.R | 5 +
R/RunMuscle.R | 5 +
R/RunParsdna.R | 7 +-
R/RunParsprotein.R | 7 +-
R/RunQuicktree.R | 6 +-
R/RunRAxMLdna.R | 55 ++++++++++----------
R/RunRAxMLprotein.R | 12 ++--
R/TNRS.R | 50 +++++++++++-------
R/rPlant.R | 133 ++++++++++++++++++++++++++++++-------------------
data/ex.lp.fasta.rda |binary
man/RunClustal.Rd | 2
man/RunMafft.Rd | 2
man/RunQuicktree.Rd | 2
man/RunRAxMLdna.Rd | 6 +-
man/RunRAxMLprotein.Rd | 4 +
19 files changed, 218 insertions(+), 144 deletions(-)
Title: Rcpp integration for Armadillo templated linear algebra library
Diff between RcppArmadillo versions 0.3.800.0 dated 2013-03-02 and 0.3.800.1 dated 2013-03-12
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 3.800.1). 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
ChangeLog | 22 ++
DESCRIPTION | 10 -
MD5 | 20 +-
inst/NEWS.Rd | 12 +
inst/include/RcppArmadilloExtensions |only
inst/include/armadillo_bits/arma_version.hpp | 2
inst/include/armadillo_bits/diskio_meat.hpp | 22 +-
inst/include/armadillo_bits/gemv.hpp | 143 ++++++++++++---
inst/unitTests/cpp |only
inst/unitTests/runit.RcppArmadillo.R | 245 ++-------------------------
inst/unitTests/runit.sample.R |only
tests/doRUnit.R | 7
12 files changed, 211 insertions(+), 272 deletions(-)
Title: Programming with Big Data -- Base Wrappers for Distributed
Matrices
Diff between pbdBASE versions 0.1-1 dated 2012-11-30 and 0.2-0 dated 2013-03-12
Description: pbdBASE gives higher packages, like pbdDMAT, access to
low-level scalable Fortran routines. The package consists of a
set of ScaLAPACK wrappers, as well as a host of new C and
Fortran code.
Author: Drew Schmidt [aut, cre], Wei-Chen Chen [aut], George Ostrouchov
[aut], Pragneshkumar Patel [aut]
Maintainer: Drew Schmidt
pbdBASE-0.1-1/pbdBASE/R/00-ddmatrix_class.R |only
pbdBASE-0.1-1/pbdBASE/R/01-ddmatrix_s4.R |only
pbdBASE-0.1-1/pbdBASE/R/utility.R |only
pbdBASE-0.1-1/pbdBASE/R/utility_ddmatrix.R |only
pbdBASE-0.1-1/pbdBASE/R/wrappers_pblas_level3.R |only
pbdBASE-0.1-1/pbdBASE/R/z_methods_ddmatrix.R |only
pbdBASE-0.1-1/pbdBASE/data/control.rda |only
pbdBASE-0.1-1/pbdBASE/man/00_zz_dmatclass.Rd |only
pbdBASE-0.1-1/pbdBASE/man/ac_control.Rd |only
pbdBASE-0.1-1/pbdBASE/man/ba_distrib.Rd |only
pbdBASE-0.1-1/pbdBASE/man/baa_print.Rd |only
pbdBASE-0.1-1/pbdBASE/man/bab_summary.Rd |only
pbdBASE-0.1-1/pbdBASE/man/bb_asddm.Rd |only
pbdBASE-0.1-1/pbdBASE/man/bc_asmat.Rd |only
pbdBASE-0.1-1/pbdBASE/man/ca_dimensions.Rd |only
pbdBASE-0.1-1/pbdBASE/man/ea_type.Rd |only
pbdBASE-0.1-1/pbdBASE/man/eb_nas.Rd |only
pbdBASE-0.1-1/pbdBASE/man/ec_comparators.Rd |only
pbdBASE-0.1-1/pbdBASE/man/sa_extract.Rd |only
pbdBASE-0.1-1/pbdBASE/man/sb_insert.Rd |only
pbdBASE-0.1-1/pbdBASE/man/ua_bind.Rd |only
pbdBASE-0.1-1/pbdBASE/src/base_scalapack_utility_fort.c |only
pbdBASE-0.1-1/pbdBASE/src/base_variance.c |only
pbdBASE-0.1-1/pbdBASE/src/par_selection.f |only
pbdBASE-0.1-1/pbdBASE/src/scalapack_utility_cpp.cpp |only
pbdBASE-0.1-1/pbdBASE/src/selection.f |only
pbdBASE-0.1-1/pbdBASE/src/variance.f |only
pbdBASE-0.2-0/pbdBASE/COPYING | 711 +++++-----
pbdBASE-0.2-0/pbdBASE/ChangeLog | 23
pbdBASE-0.2-0/pbdBASE/DESCRIPTION | 27
pbdBASE-0.2-0/pbdBASE/MD5 | 113 -
pbdBASE-0.2-0/pbdBASE/NAMESPACE | 27
pbdBASE-0.2-0/pbdBASE/R/get_conf.r | 2
pbdBASE-0.2-0/pbdBASE/R/get_lib.r | 2
pbdBASE-0.2-0/pbdBASE/R/lm.R | 284 ---
pbdBASE-0.2-0/pbdBASE/R/misc.r |only
pbdBASE-0.2-0/pbdBASE/R/pkg_blacs_apts.r |only
pbdBASE-0.2-0/pbdBASE/R/utility_blacs.R | 224 ---
pbdBASE-0.2-0/pbdBASE/R/utility_scalapack.R | 139 +
pbdBASE-0.2-0/pbdBASE/R/wrappers_blacs.r |only
pbdBASE-0.2-0/pbdBASE/R/wrappers_misc.r |only
pbdBASE-0.2-0/pbdBASE/R/wrappers_pblas.R |only
pbdBASE-0.2-0/pbdBASE/R/wrappers_plinalg.r |only
pbdBASE-0.2-0/pbdBASE/R/wrappers_putil.R |only
pbdBASE-0.2-0/pbdBASE/R/wrappers_scalapack.R | 391 +++--
pbdBASE-0.2-0/pbdBASE/R/zzz.r | 28
pbdBASE-0.2-0/pbdBASE/configure | 16
pbdBASE-0.2-0/pbdBASE/configure.ac | 23
pbdBASE-0.2-0/pbdBASE/data/conflicts.OK.rda |binary
pbdBASE-0.2-0/pbdBASE/data/envir.rda |binary
pbdBASE-0.2-0/pbdBASE/demo/example1.r | 9
pbdBASE-0.2-0/pbdBASE/inst/CITATION | 4
pbdBASE-0.2-0/pbdBASE/inst/doc/pbdBASE-guide.Rnw | 3
pbdBASE-0.2-0/pbdBASE/inst/doc/pbdBASE-guide.pdf |binary
pbdBASE-0.2-0/pbdBASE/inst/doc/pbdBASE-include/00-acknowledgement.tex | 4
pbdBASE-0.2-0/pbdBASE/inst/doc/pbdBASE-include/01-copyright.tex |only
pbdBASE-0.2-0/pbdBASE/man/aa_initgrid.Rd | 31
pbdBASE-0.2-0/pbdBASE/man/ba_a_ownership.Rd | 19
pbdBASE-0.2-0/pbdBASE/man/zz_base.internal.Rd | 81 -
pbdBASE-0.2-0/pbdBASE/src/Makevars.in | 40
pbdBASE-0.2-0/pbdBASE/src/Makevars.win | 9
pbdBASE-0.2-0/pbdBASE/src/auxil.f |only
pbdBASE-0.2-0/pbdBASE/src/base_global.h | 15
pbdBASE-0.2-0/pbdBASE/src/base_lm.c | 133 -
pbdBASE-0.2-0/pbdBASE/src/base_mpi_blac.c | 161 +-
pbdBASE-0.2-0/pbdBASE/src/base_pblas_level3.c | 10
pbdBASE-0.2-0/pbdBASE/src/base_scalapack.c | 262 ++-
pbdBASE-0.2-0/pbdBASE/src/base_scalapack_utility.c |only
pbdBASE-0.2-0/pbdBASE/src/export_blacs |only
pbdBASE-0.2-0/pbdBASE/src/install.libs.R |only
pbdBASE-0.2-0/pbdBASE/src/lm.f | 3
pbdBASE-0.2-0/pbdBASE/src/mpi_blacs.f | 8
pbdBASE-0.2-0/pbdBASE/src/other.c |only
pbdBASE-0.2-0/pbdBASE/src/secret |only
74 files changed, 1406 insertions(+), 1396 deletions(-)
Title: Model the spectral response of a closed water-well to harmonic
strains at seismic frequencies.
Diff between kitagawa versions 1.0-1 dated 2012-10-26 and 1.1-1 dated 2013-03-12
Description: Provides tools to calculate what the theoretical
hydrodynamic response will be for borehole strain and
fluid-pressure (water height) measurements of seismic waves,
for a given set of aquifer parameters. The calculations are
based on the model presented by Kitagawa et al (2011); hence,
the name of the package.
Author: Andrew J Barbour
Maintainer: Andrew J Barbour
kitagawa-1.0-1/kitagawa/NEWS |only
kitagawa-1.1-1/kitagawa/DESCRIPTION | 12 +++++++-----
kitagawa-1.1-1/kitagawa/MD5 | 10 ++++++----
kitagawa-1.1-1/kitagawa/R/well_response.R | 8 ++++++++
kitagawa-1.1-1/kitagawa/R/zzz.R |only
kitagawa-1.1-1/kitagawa/README.md | 4 ++--
kitagawa-1.1-1/kitagawa/WISHLIST |only
kitagawa-1.1-1/kitagawa/inst |only
8 files changed, 23 insertions(+), 11 deletions(-)
Title: Utility functions for working with Random Number Generators
Diff between rngtools versions 1.1 dated 2012-12-10 and 1.2 dated 2013-03-12
Description: This package contains a set of functions for working with
Random Number Generators (RNGs). In particular, it defines a
generic S4 framework for getting/setting the current RNG, or
RNG data that are embedded into objects for reproducibility.
Notably, convenient default methods greatly facilitate the way
current RNG settings can be changed.
Author: Renaud Gaujoux
Maintainer: Renaud Gaujoux
DESCRIPTION | 9 ++--
MD5 | 16 +++----
R/RNG.R | 20 ++++----
inst/doc/rngtools-unitTests.Rnw | 28 ++++++------
inst/doc/rngtools-unitTests.pdf |binary
man/rng.Rd | 6 +-
vignettes/Makefile | 4 -
vignettes/rngtools-unitTests.Rnw | 28 ++++++------
vignettes/vignette.mk | 87 +++++++++++++++++++--------------------
9 files changed, 100 insertions(+), 98 deletions(-)
Title: Seamless Interface to Octave -- and Matlab
Diff between RcppOctave versions 0.8.12 dated 2012-12-17 and 0.9 dated 2013-03-12
Description: Direct interface to Octave. The primary goal is to
facilitate the port of Matlab/Octave scripts to R. The package
enables to call any Octave functions from R and as well as
browsing their documentation, passing variables between R and
Octave, using R core RNGs in Octave, which ensure stochastic
computations are also reproducible.
Author: Renaud Gaujoux
Maintainer: Renaud Gaujoux
RcppOctave-0.8.12/RcppOctave/inst/unitTests/_runit.module.R |only
RcppOctave-0.9/RcppOctave/DESCRIPTION | 11 -
RcppOctave-0.9/RcppOctave/MD5 | 85 +++++-----
RcppOctave-0.9/RcppOctave/NAMESPACE | 5
RcppOctave-0.9/RcppOctave/R/Octave-class.R | 38 ++++
RcppOctave-0.9/RcppOctave/R/OctaveFunction-class.R | 41 +++-
RcppOctave-0.9/RcppOctave/R/base-functions.R | 55 +++++-
RcppOctave-0.9/RcppOctave/R/eval.R | 6
RcppOctave-0.9/RcppOctave/R/package.R | 27 ++-
RcppOctave-0.9/RcppOctave/build/RcppOctave.pdf |binary
RcppOctave-0.9/RcppOctave/configure | 38 ++--
RcppOctave-0.9/RcppOctave/configure.in | 18 +-
RcppOctave-0.9/RcppOctave/demo/00Index | 3
RcppOctave-0.9/RcppOctave/demo/gamma.R |only
RcppOctave-0.9/RcppOctave/demo/gibbs.R |only
RcppOctave-0.9/RcppOctave/demo/timerng.R |only
RcppOctave-0.9/RcppOctave/inst/REFERENCES.bib | 36 +++-
RcppOctave-0.9/RcppOctave/inst/doc/RcppOctave-unitTests.Rnw | 37 ++--
RcppOctave-0.9/RcppOctave/inst/doc/RcppOctave-unitTests.pdf |binary
RcppOctave-0.9/RcppOctave/inst/doc/RcppOctave.pdf |binary
RcppOctave-0.9/RcppOctave/inst/unitTests/runit.OctaveFunction.R |only
RcppOctave-0.9/RcppOctave/inst/unitTests/runit.eval.R | 4
RcppOctave-0.9/RcppOctave/man-roxygen/OctaveDoc.R | 2
RcppOctave-0.9/RcppOctave/man/Octave-class.Rd | 5
RcppOctave-0.9/RcppOctave/man/OctaveFunction-class.Rd | 22 +-
RcppOctave-0.9/RcppOctave/man/OctaveInterface.Rd | 38 ++++
RcppOctave-0.9/RcppOctave/man/o_addpath.Rd | 3
RcppOctave-0.9/RcppOctave/man/o_assign.Rd | 3
RcppOctave-0.9/RcppOctave/man/o_clear.Rd | 3
RcppOctave-0.9/RcppOctave/man/o_eval.Rd | 3
RcppOctave-0.9/RcppOctave/man/o_exist.Rd |only
RcppOctave-0.9/RcppOctave/man/o_help.Rd | 28 ++-
RcppOctave-0.9/RcppOctave/man/o_load.Rd | 3
RcppOctave-0.9/RcppOctave/man/o_rexp.Rd | 3
RcppOctave-0.9/RcppOctave/man/o_rgamma.Rd | 3
RcppOctave-0.9/RcppOctave/man/o_rnorm.Rd | 3
RcppOctave-0.9/RcppOctave/man/o_runif.Rd | 3
RcppOctave-0.9/RcppOctave/man/o_source.Rd | 3
RcppOctave-0.9/RcppOctave/man/o_version.Rd | 12 +
RcppOctave-0.9/RcppOctave/man/o_who.Rd | 3
RcppOctave-0.9/RcppOctave/man/o_whos.Rd | 3
RcppOctave-0.9/RcppOctave/src/Makevars.in | 2
RcppOctave-0.9/RcppOctave/src/modules/Rrng.cc | 2
RcppOctave-0.9/RcppOctave/staticdocs |only
RcppOctave-0.9/RcppOctave/vignettes/Makefile | 4
RcppOctave-0.9/RcppOctave/vignettes/RcppOctave-unitTests.Rnw | 37 ++--
RcppOctave-0.9/RcppOctave/vignettes/src/RcppOctave.Rnw | 7
47 files changed, 418 insertions(+), 181 deletions(-)
Title: Estimating regional trends of a prevalence from a DHS
Diff between prevR versions 2.1 dated 2012-06-20 and 2.2 dated 2013-03-12
Description: This package performs spatial estimation of a prevalence
surface or a relative risks surface, using data from a
Demographic and Health Survey (DHS) or an analog survey.
Author: Joseph Larmarange - CEPED (Universite Paris Descartes Ined IRD)
IRD, with fundings from ANRS and IRD, and technical support
from LYSIS (info@lysis-consultants.fr)
Maintainer: Joseph Larmarange
DESCRIPTION | 13 +++++----
MD5 | 34 ++++++++++++-------------
NAMESPACE | 11 +++++---
R/as.SpatialGrid.prevR.r | 1
R/import.dhs.prevR.r | 32 ------------------------
R/krige.prevR.r | 2 -
R/summary.prevR.r | 8 ++++--
inst/doc/prevR-FR.pdf |binary
inst/doc/prevR-FR.rnw | 9 ++++--
man/as.data.frame.prevR.Rd | 14 ++++++----
man/prevR-class.Rd | 8 +++---
man/prevR-package.Rd | 4 +--
man/print-prevR-method.Rd | 6 +++-
man/rings-prevR-method.Rd | 4 +--
man/show-prevR-method.Rd | 6 +++-
man/summary-prevR-method.Rd | 16 +++++++++---
prevR-Ex.R | 58 ++++++++++++++++++++++++++------------------
vignettes/prevR-FR.rnw | 9 ++++--
18 files changed, 125 insertions(+), 110 deletions(-)
Title: Meta-Analysis with R
Diff between meta versions 2.1-4 dated 2012-11-29 and 2.2-0 dated 2013-03-12
Description: Fixed and random effects meta-analysis. Functions for
tests of bias, forest and funnel plot.
Author: Guido Schwarzer
Maintainer: Guido Schwarzer
DESCRIPTION | 9 +++++----
MD5 | 14 +++++++-------
NEWS | 21 ++++++++++++++++++++-
R/forest.meta.R | 18 +++++++++++++++++-
R/meta-internal.R | 13 ++++++++-----
R/metabin.R | 24 +++++++++++++++++-------
man/metabin.Rd | 2 +-
man/metaprop.Rd | 2 +-
8 files changed, 76 insertions(+), 27 deletions(-)
Title: Calculate solutions to Kelvin differential equation using Bessel
functions.
Diff between kelvin versions 1.1-0 dated 2012-09-27 and 1.2-1 dated 2013-03-12
Description: Uses Bessel functions to calculate the analytic solutions
to the Kelvin differential equation, namely the primary (Be)
and complementary (Ke) complex functions.
Author: Andrew J Barbour
Maintainer: Andrew J Barbour
kelvin-1.1-0/kelvin/NEWS |only
kelvin-1.1-0/kelvin/R/Kelvin.R |only
kelvin-1.2-1/kelvin/DESCRIPTION | 21 +++++++++++----------
kelvin-1.2-1/kelvin/MD5 | 12 ++++++------
kelvin-1.2-1/kelvin/R/Keir.R | 1 +
kelvin-1.2-1/kelvin/R/kelvin-package.R | 5 +----
kelvin-1.2-1/kelvin/R/zzz.R |only
kelvin-1.2-1/kelvin/inst |only
kelvin-1.2-1/kelvin/man/Keir.Rd | 1 +
9 files changed, 20 insertions(+), 20 deletions(-)
Title: Generic Reproducible Parallel Backend for foreach Loops
Diff between doRNG versions 1.5 dated 2012-11-07 and 1.5.3 dated 2013-03-12
Description: This package provides functions to perform reproducible
parallel foreach loops, using independent random streams as
generated by L'Ecuyer's combined multiple-recursive generator
[L'Ecuyer (1999)]. It enables to easily convert standard
%dopar% loops into fully reproducible loops, independently of
the number of workers, the task scheduling strategy, or the
chosen parallel environment and associated foreach backend.
Author: Renaud Gaujoux
Maintainer: Renaud Gaujoux
DESCRIPTION | 12
MD5 | 22
R/doRNG.R | 963 ++++++++++++++++----------------
inst/doc/doRNG-unitTests.Rnw | 31 -
inst/doc/doRNG-unitTests.pdf |binary
inst/doc/doRNG.pdf |binary
inst/unitTests/runit.dorng.R | 490 ++++++++--------
man/doRNG.Rd | 6
man/doRNGversion.Rd | 3
vignettes/Makefile | 6
vignettes/doRNG-unitTests.Rnw | 31 -
vignettes/src/doRNG.Rnw | 1235 ++++++++++++++++++++----------------------
12 files changed, 1405 insertions(+), 1394 deletions(-)
Title: file-based access to large matrices stored on HDD in binary
format
Diff between DatABEL versions 0.9-2 dated 2010-10-20 and 0.9-4 dated 2013-03-12
Description: a package providing an interface to the C++ FILEVECTOR
library facilitating analysis of large (giga- to tera-bytes)
matrices; matrix storage is organized in a way that either
columns or rows are quickly accessible; primarily aimed to
support genome-wide association analyses e.g. using GenABEL,
MixABEL and ProbABEL
Author: Yurii Aulchenko, Stepan Yakovenko, Erik Roos, Marcel Kempenaar
Maintainer: Yurii Aulchenko
DatABEL-0.9-2/DatABEL/tests |only
DatABEL-0.9-4/DatABEL/CHANGES.LOG | 19 +-
DatABEL-0.9-4/DatABEL/DESCRIPTION | 26 +--
DatABEL-0.9-4/DatABEL/MD5 |only
DatABEL-0.9-4/DatABEL/R/DatABEL-package.R | 7
DatABEL-0.9-4/DatABEL/R/apply2dfo.R | 12 +
DatABEL-0.9-4/DatABEL/R/apply2dfo_util.R | 5
DatABEL-0.9-4/DatABEL/R/checkPackageVersionOnCRAN.R |only
DatABEL-0.9-4/DatABEL/R/databel2matrix.R | 27 +--
DatABEL-0.9-4/DatABEL/R/databel_class.R | 26 ++-
DatABEL-0.9-4/DatABEL/R/matrix2databel.R | 8
DatABEL-0.9-4/DatABEL/R/text2databel.R | 12 -
DatABEL-0.9-4/DatABEL/R/zzz.R | 131 ++++++++-------
DatABEL-0.9-4/DatABEL/inst/doc/intro_DatABEL.Rnw |only
DatABEL-0.9-4/DatABEL/inst/doc/intro_DatABEL.pdf |binary
DatABEL-0.9-4/DatABEL/man/DatABEL-package.Rd | 34 ++--
DatABEL-0.9-4/DatABEL/man/apply2dfo.Rd | 78 +++++----
DatABEL-0.9-4/DatABEL/man/databel-class.Rd | 4
DatABEL-0.9-4/DatABEL/man/databel.Rd | 29 ++-
DatABEL-0.9-4/DatABEL/man/databel2matrix.Rd | 35 ++--
DatABEL-0.9-4/DatABEL/man/databel2text.Rd | 37 ++--
DatABEL-0.9-4/DatABEL/man/extract_text_file_columns.Rd | 27 ++-
DatABEL-0.9-4/DatABEL/man/get_temporary_file_name.Rd | 23 +-
DatABEL-0.9-4/DatABEL/man/make_empty_fvf.Rd | 44 +++--
DatABEL-0.9-4/DatABEL/man/matrix2databel.Rd | 48 +++--
DatABEL-0.9-4/DatABEL/man/process_lm_output.Rd | 52 +++---
DatABEL-0.9-4/DatABEL/man/text2databel.Rd | 142 ++++++++++-------
DatABEL-0.9-4/DatABEL/src/AbstractMatrix_R.cpp | 6
DatABEL-0.9-4/DatABEL/src/FilteredMatrix_R.cpp | 4
DatABEL-0.9-4/DatABEL/src/dautil.cpp | 1
DatABEL-0.9-4/DatABEL/vignettes |only
31 files changed, 524 insertions(+), 313 deletions(-)
Title: Diagnostics plots for Bicluster Data
Diff between BcDiag versions 1.0.1 dated 2013-01-13 and 1.0.2 dated 2013-03-12
Description: This package provides Diagnostic tools based on two way
anova and median polish residual plots for Bicluster output
obtained from packages; "biclust" by Kaiser et al.(2008),"isa2"
by Csardi et al. (2010) and "fabia" by Hochreiter et al.
(2010). Moreover, It provides visualization tools for bicluster
output and corresponding non bicluster rows or columns
outcomes. It has also extended the idea of Kaiser et al.(2008)
which is, extracting bicluster output in a text format, by
adding by adding two bicluster methods from fabia and isa2 r
packages.
Author: Aregay Mengsteab, Martin Otava, Tatsiana Khamiakova
Maintainer: Aregay Mengsteab
DESCRIPTION | 29 ++++++++++++++++-------------
MD5 | 6 +++---
man/exploreBic.Rd | 6 +++---
man/exploreOnlybic.Rd | 6 +++---
4 files changed, 25 insertions(+), 22 deletions(-)
Title: classes and methods for spatial data
Diff between sp versions 1.0-5 dated 2012-12-21 and 1.0-6 dated 2013-03-12
Description: A package that provides classes and methods for spatial
data. The classes document where the spatial location
information resides, for 2D or 3D data. Utility functions are
provided, e.g. for plotting data as maps, spatial selection, as
well as methods for retrieving coordinates, for subsetting,
print, summary, etc.
Author: Edzer Pebesma [aut, cre], Roger Bivand [aut], Barry Rowlingson
[ctb], Virgilio Gomez-Rubio [ctb]
Maintainer: Edzer Pebesma
sp-1.0-5/sp/ChangeLog |only
sp-1.0-6/sp/DESCRIPTION | 9
sp-1.0-6/sp/MD5 | 70
sp-1.0-6/sp/NAMESPACE | 18
sp-1.0-6/sp/R/CRS-methods.R | 5
sp-1.0-6/sp/R/Class-SpatialPolygons.R | 8
sp-1.0-6/sp/R/SpatialPolygons-methods.R | 8
sp-1.0-6/sp/R/SpatialPolygonsDataFrame-methods.R | 10
sp-1.0-6/sp/R/chfids.R | 2
sp-1.0-6/sp/R/image.R | 4
sp-1.0-6/sp/R/loadmeuse.R | 53
sp-1.0-6/sp/R/over.R | 64
sp-1.0-6/sp/R/overlay.R | 4
sp-1.0-6/sp/R/point.in.polygon.R | 14
sp-1.0-6/sp/R/spplot.R | 123
sp-1.0-6/sp/R/zerodist.R | 4
sp-1.0-6/sp/demo/00Index | 1
sp-1.0-6/sp/demo/gallery.R | 2
sp-1.0-6/sp/demo/meuse.R |only
sp-1.0-6/sp/inst/ChangeLog | 107
sp-1.0-6/sp/inst/doc/intro_sp.pdf |binary
sp-1.0-6/sp/inst/doc/over.Rnw | 22
sp-1.0-6/sp/inst/doc/over.pdf |binary
sp-1.0-6/sp/man/CRS-class.Rd | 1
sp-1.0-6/sp/man/SpatialPixels-class.Rd | 4
sp-1.0-6/sp/man/as.SpatialPolygons.GridTopology.Rd | 5
sp-1.0-6/sp/man/image.Rd | 2
sp-1.0-6/sp/man/loadmeuse.Rd | 23
sp-1.0-6/sp/man/mapasp.Rd | 13
sp-1.0-6/sp/man/over.Rd | 6
sp-1.0-6/sp/man/overlay-methods.Rd | 2
sp-1.0-6/sp/man/overlay.Rd | 4
sp-1.0-6/sp/man/spplot.Rd | 5
sp-1.0-6/sp/man/spsample.Rd | 37
sp-1.0-6/sp/tests/Examples/sp-Ex.Rout.save | 3940 ---------------------
sp-1.0-6/sp/tests/fail1.Rout.save | 5
sp-1.0-6/sp/x |only
sp-1.0-6/sp/xx |only
38 files changed, 505 insertions(+), 4070 deletions(-)
Title: Tools for mapping multiple complex traits
Diff between qtlmt versions 0.1-2 dated 2011-07-04 and 0.1-3 dated 2013-03-12
Description: This software provides tools for joint analysis of
multiple traits in a backcross (BC) or recombinant inbred lines
(RIL) population. It can be used to select an optimal subset of
traits for multiple-trait mapping, analyze multiple traits via
the SURE model, which can associate different QTL with
different traits, and perform multiple-trait composite
multiple-interval mapping.
Author: Riyan Cheng
Maintainer: Riyan Cheng
ChangeLog | 4 +++-
DESCRIPTION | 18 ++++++++++--------
MD5 |only
R/zzz.R | 9 +++++----
data/etrait.RData |binary
src/qtlmt.cc | 39 ++++++++++++++++++---------------------
src/qtlmt.h | 1 +
7 files changed, 37 insertions(+), 34 deletions(-)
Title: Package development utilities
Diff between pkgmaker versions 0.10.1 dated 2012-12-07 and 0.14 dated 2013-03-12
Description: This package provides some low-level utilities to use for
package development. It currently provides managers for
multiple package specific options and registries, vignette,
unit test and bibtex related utilities. It serves as a base
package for packages like NMF, RcppOctave, doRNG, and as an
incubator package for other general purposes utilities, that
will eventually be packaged separately. It is still under
heavy development and changes in the interface(s) are more than
likely to happen.
Author: Renaud Gaujoux
Maintainer: Renaud Gaujoux
pkgmaker-0.10.1/pkgmaker/man/cite.Rd |only
pkgmaker-0.14/pkgmaker/DESCRIPTION | 22
pkgmaker-0.14/pkgmaker/MD5 | 66
pkgmaker-0.14/pkgmaker/NAMESPACE | 14
pkgmaker-0.14/pkgmaker/R/bibtex.R | 13
pkgmaker-0.14/pkgmaker/R/devutils.R | 972 ++++++-----
pkgmaker-0.14/pkgmaker/R/graphics.R | 13
pkgmaker-0.14/pkgmaker/R/is.R | 43
pkgmaker-0.14/pkgmaker/R/namespace.R | 303 +--
pkgmaker-0.14/pkgmaker/R/options.R | 51
pkgmaker-0.14/pkgmaker/R/package-extra.R | 244 +-
pkgmaker-0.14/pkgmaker/R/packages.R | 613 ++++---
pkgmaker-0.14/pkgmaker/R/registry.R | 742 +++++++-
pkgmaker-0.14/pkgmaker/R/unitTests.R | 2
pkgmaker-0.14/pkgmaker/R/utils.R | 2
pkgmaker-0.14/pkgmaker/R/vignette.R | 1335 ++++++++--------
pkgmaker-0.14/pkgmaker/inst/doc/pkgmaker-unitTests.Rnw | 23
pkgmaker-0.14/pkgmaker/inst/doc/pkgmaker-unitTests.pdf |binary
pkgmaker-0.14/pkgmaker/inst/vignette.mk | 89 -
pkgmaker-0.14/pkgmaker/man/R.exec.Rd | 6
pkgmaker-0.14/pkgmaker/man/alphacol.Rd | 11
pkgmaker-0.14/pkgmaker/man/citecmd.Rd |only
pkgmaker-0.14/pkgmaker/man/dot-packageMetaRegistry.Rd |only
pkgmaker-0.14/pkgmaker/man/fix_registry.Rd |only
pkgmaker-0.14/pkgmaker/man/isCRANcheck.Rd |only
pkgmaker-0.14/pkgmaker/man/is_something.Rd | 31
pkgmaker-0.14/pkgmaker/man/local-options.Rd |only
pkgmaker-0.14/pkgmaker/man/namespace.Rd | 13
pkgmaker-0.14/pkgmaker/man/packageExtra.Rd | 92 -
pkgmaker-0.14/pkgmaker/man/quickinstall.Rd | 26
pkgmaker-0.14/pkgmaker/man/regfetch.Rd | 50
pkgmaker-0.14/pkgmaker/man/registry.Rd | 127 +
pkgmaker-0.14/pkgmaker/man/setupPackageOptions.Rd | 2
pkgmaker-0.14/pkgmaker/man/vignette.Rd | 20
pkgmaker-0.14/pkgmaker/man/write.bib.Rd | 2
pkgmaker-0.14/pkgmaker/vignettes/Makefile | 6
pkgmaker-0.14/pkgmaker/vignettes/pkgmaker-unitTests.Rnw | 23
37 files changed, 2980 insertions(+), 1976 deletions(-)
Title: Estimation of the effective dimension reduction (EDR) space
Diff between EDR versions 0.6-4 dated 2010-04-07 and 0.6-5 dated 2013-03-12
Description: The package contains R-functions to estimate the effective
dimension reduction space in multi-index regression models.
Author: Joerg Polzehl
Maintainer: Joerg Polzehl
DESCRIPTION | 20 ++++++++++----------
MD5 |only
R/edr.r | 9 +++++++--
man/edr.R.Rd | 2 +-
man/plot.edr.Rd | 2 +-
man/predict.edr.Rd | 2 +-
man/print.edr.Rd | 2 +-
man/summary.edr.Rd | 2 +-
8 files changed, 22 insertions(+), 17 deletions(-)
Title: Low-level R to Java interface
Diff between rJava versions 0.9-3 dated 2011-12-11 and 0.9-4 dated 2013-03-12
Description: Low-level interface to Java VM very much like .C/.Call and
friends. Allows creation of objects, calling methods and
accessing fields.
Author: Simon Urbanek
Maintainer: Simon Urbanek
rJava-0.9-3/rJava/inst/jri |only
rJava-0.9-4/rJava/DESCRIPTION | 10
rJava-0.9-4/rJava/MD5 | 104 ++---
rJava-0.9-4/rJava/NAMESPACE | 2
rJava-0.9-4/rJava/NEWS | 18
rJava-0.9-4/rJava/R/call.R | 8
rJava-0.9-4/rJava/R/windows/FirstLib.R | 7
rJava-0.9-4/rJava/R/with.R | 18
rJava-0.9-4/rJava/R/zzz.R.in | 1
rJava-0.9-4/rJava/inst/java/RJavaArrayTools.class |binary
rJava-0.9-4/rJava/inst/java/RJavaArrayTools.java | 59 ++
rJava-0.9-4/rJava/inst/javadoc/ArrayDimensionException.html | 4
rJava-0.9-4/rJava/inst/javadoc/ArrayWrapper.html | 4
rJava-0.9-4/rJava/inst/javadoc/ArrayWrapper_Test.html | 4
rJava-0.9-4/rJava/inst/javadoc/DummyPoint.html | 4
rJava-0.9-4/rJava/inst/javadoc/FlatException.html | 4
rJava-0.9-4/rJava/inst/javadoc/NotAnArrayException.html | 4
rJava-0.9-4/rJava/inst/javadoc/NotComparableException.html | 4
rJava-0.9-4/rJava/inst/javadoc/ObjectArrayException.html | 4
rJava-0.9-4/rJava/inst/javadoc/PrimitiveArrayException.html | 4
rJava-0.9-4/rJava/inst/javadoc/RJavaArrayIterator.html | 4
rJava-0.9-4/rJava/inst/javadoc/RJavaArrayTools.ArrayDimensionMismatchException.html | 4
rJava-0.9-4/rJava/inst/javadoc/RJavaArrayTools.html | 199 +++++++++-
rJava-0.9-4/rJava/inst/javadoc/RJavaArrayTools_Test.html | 4
rJava-0.9-4/rJava/inst/javadoc/RJavaClassLoader.html | 4
rJava-0.9-4/rJava/inst/javadoc/RJavaComparator.html | 4
rJava-0.9-4/rJava/inst/javadoc/RJavaImport.html | 4
rJava-0.9-4/rJava/inst/javadoc/RJavaTools.html | 4
rJava-0.9-4/rJava/inst/javadoc/RJavaTools_Test.DummyNonStaticClass.html | 4
rJava-0.9-4/rJava/inst/javadoc/RJavaTools_Test.TestException.html | 4
rJava-0.9-4/rJava/inst/javadoc/RJavaTools_Test.html | 4
rJava-0.9-4/rJava/inst/javadoc/RectangularArrayBuilder.html | 4
rJava-0.9-4/rJava/inst/javadoc/RectangularArrayBuilder_Test.html | 4
rJava-0.9-4/rJava/inst/javadoc/RectangularArrayExamples.html | 4
rJava-0.9-4/rJava/inst/javadoc/RectangularArraySummary.html | 4
rJava-0.9-4/rJava/inst/javadoc/TestException.html | 4
rJava-0.9-4/rJava/inst/javadoc/allclasses-frame.html | 4
rJava-0.9-4/rJava/inst/javadoc/allclasses-noframe.html | 4
rJava-0.9-4/rJava/inst/javadoc/constant-values.html | 32 +
rJava-0.9-4/rJava/inst/javadoc/deprecated-list.html | 4
rJava-0.9-4/rJava/inst/javadoc/help-doc.html | 4
rJava-0.9-4/rJava/inst/javadoc/index-all.html | 31 +
rJava-0.9-4/rJava/inst/javadoc/index.html | 2
rJava-0.9-4/rJava/inst/javadoc/overview-tree.html | 4
rJava-0.9-4/rJava/inst/javadoc/package-frame.html | 4
rJava-0.9-4/rJava/inst/javadoc/package-summary.html | 4
rJava-0.9-4/rJava/inst/javadoc/package-tree.html | 4
rJava-0.9-4/rJava/inst/javadoc/serialized-form.html | 4
rJava-0.9-4/rJava/jri/src/rjava.c | 2
rJava-0.9-4/rJava/src/Rglue.c | 7
rJava-0.9-4/rJava/src/java/RJavaArrayTools.class |binary
rJava-0.9-4/rJava/src/java/RJavaArrayTools.java | 59 ++
rJava-0.9-4/rJava/src/rJava.h | 2
53 files changed, 539 insertions(+), 154 deletions(-)
Title: An R package to assist in the workflow of writing academic
articles and other reports
Diff between reports versions 0.1.1 dated 2013-03-11 and 0.1.2 dated 2013-03-12
Description: reports is a package that assists in writing reports and
presentations by providing a frame work that brings together
existing R, LaTeX/.docx and Pandoc tools. The package is
designed to be used with RStudio, MiKTex/Tex Live/LibreOffice,
knitr, knitcitations, Pandoc and pander. The user will want to
download these free programs/packages to maximize the
effectiveness of the reports package. Functions with two
letter names are general text formatting functions for copying
text from articles for inclusion as a citation.
Author: Tyler Rinker
Maintainer: Tyler Rinker
reports-0.1.1/reports/man/install_pandoc.Rd |only
reports-0.1.2/reports/DESCRIPTION | 12 +-
reports-0.1.2/reports/MD5 | 57 ++++------
reports-0.1.2/reports/NAMESPACE | 1
reports-0.1.2/reports/NEWS | 26 ++++
reports-0.1.2/reports/R/CA.R | 9 +
reports-0.1.2/reports/R/GQ.R | 27 +++-
reports-0.1.2/reports/R/LL.R | 9 +
reports-0.1.2/reports/R/US.R | 9 +
reports-0.1.2/reports/R/doc_temp.R | 10 -
reports-0.1.2/reports/R/html5.R | 6 -
reports-0.1.2/reports/R/install_pandoc.R | 28 ++--
reports-0.1.2/reports/R/new_report.R | 3
reports-0.1.2/reports/R/reports-package.R | 6 -
reports-0.1.2/reports/R/reveal.js.R | 20 ++-
reports-0.1.2/reports/R/tex2docx.R | 5
reports-0.1.2/reports/README.md | 16 +-
reports-0.1.2/reports/inst/CITATION | 4
reports-0.1.2/reports/inst/extdata/doc_library/basic_web/DESCRIPTION | 8 -
reports-0.1.2/reports/inst/extdata/docs/example.bib | 4
reports-0.1.2/reports/man/CA.Rd | 4
reports-0.1.2/reports/man/GQ.Rd | 13 +-
reports-0.1.2/reports/man/LL.Rd | 4
reports-0.1.2/reports/man/US.Rd | 4
reports-0.1.2/reports/man/doc_temp.Rd | 6 -
reports-0.1.2/reports/man/html5.Rd | 8 -
reports-0.1.2/reports/man/reports.Rd | 13 +-
reports-0.1.2/reports/man/reveal.js.Rd | 6 -
reports-0.1.2/reports/man/tex2docx.Rd | 5
reports-0.1.2/reports/man/themes.Rd | 2
30 files changed, 210 insertions(+), 115 deletions(-)
Title: Flexible Pair-Copula Estimation in D-vines using Bivariate
Penalized Splines
Diff between penDvine versions 0.2 dated 2012-07-23 and 0.2.2 dated 2013-03-12
Description: Flexible Pair-Copula Estimation in D-vines using Bivariate
Penalized Splines.
Author: Christian Schellhase
Maintainer: Christian Schellhase
DESCRIPTION | 21 +++++++------
MD5 | 74 ++++++++++++++++++++++++------------------------
NAMESPACE | 2 -
R/Dvine.r | 73 ++++++++++++++++++++++++-----------------------
R/cal.Dvine.r | 2 -
R/cond.cop.r | 14 +++++----
R/distr.func.help.r | 14 +++++----
R/eval.paircopula.r | 2 -
R/int.bernstein.help.r | 2 -
R/int.bspline.help.r | 4 +-
R/int.bspline2.r | 11 +++++--
R/marg.likelihood.r | 9 +++--
R/my.bspline.r | 1
R/my.loop.r | 3 +
R/new.lambda.r | 21 ++++++++++---
R/order.Dvine.r | 29 +++++++++++-------
R/paircopula.R | 26 +++++++++-------
R/pen.matrix.r | 4 +-
R/plot.paircopula.r | 2 -
R/start.valgrid.r | 4 +-
man/Derv1.Rd | 5 +--
man/Derv2.Rd | 4 --
man/Dvine.Rd | 8 +++--
man/bernstein.Rd | 3 -
man/cal.Dvine.Rd | 6 +--
man/cond.cop.Rd | 8 ++---
man/f.hat.val.Rd | 4 +-
man/marg.likelihood.Rd | 5 ---
man/my.IC.Rd | 3 -
man/my.loop.Rd | 5 +--
man/new.weights.Rd | 6 +--
man/order.Dvine.Rd | 4 --
man/paircopula.Rd | 12 ++++---
man/pen.log.like.Rd | 4 +-
man/pen.matrix.Rd | 4 --
man/penDvine-package.Rd | 20 ++++++------
man/plot.paircopula.Rd | 5 +--
man/sim.Dvine.Rd | 5 +--
38 files changed, 224 insertions(+), 205 deletions(-)
Title: Comparing correlations
Diff between cocor versions 0.01-2 dated 2013-02-21 and 0.01-3 dated 2013-03-12
Description: This package provides functions to compare two
correlations based on either dependent or independent groups.
Author: Birk Diedenhofen
Maintainer: Birk Diedenhofen
cocor-0.01-2/cocor/LICENSE |only
cocor-0.01-3/cocor/ChangeLog | 4
cocor-0.01-3/cocor/DESCRIPTION | 8 -
cocor-0.01-3/cocor/MD5 | 13 +-
cocor-0.01-3/cocor/R/cocor-package.R | 4
cocor-0.01-3/cocor/inst/CITATION | 4
cocor-0.01-3/cocor/inst/tests/test.r | 180 ++++++++++++++++----------------
cocor-0.01-3/cocor/man/cocor-package.Rd | 4
8 files changed, 110 insertions(+), 107 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-04-04 1.5-1
2010-04-04 1.1-11
2010-03-20 1.1-8
2010-03-16 1.1-7
2010-01-15 1.1-6
2009-10-05 1.1-5
2009-09-19 1.1-3
2009-08-31 1.1-2
2009-08-27 1.1-1
2009-01-16 0.9-7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-01-31 1.0.0
Title: Presmoothed Estimation in Survival Analysis
Diff between survPresmooth versions 1.1-5 dated 2013-01-09 and 1.1-6 dated 2013-03-12
Description: Presmoothed estimators of survival, density, cumulative
and non-cumulative hazard functions with right-censored
survival data
Author: Ignacio Lopez de Ullibarri and Maria Amalia Jacome
Maintainer: Ignacio Lopez de Ullibarri
ChangeLog | 10 +++++++++-
DESCRIPTION | 9 +++++----
MD5 | 4 ++--
3 files changed, 16 insertions(+), 7 deletions(-)
Title: raster: Geographic data analysis and modeling
Diff between raster versions 2.0-41 dated 2012-12-24 and 2.1-12 dated 2013-03-12
Description: Reading, writing, manipulating, analyzing and modeling of
gridded spatial data. The package implements basic and
high-level functions and processing of very large files is
supported.
Author: Robert J. Hijmans & Jacob van Etten
Maintainer: Robert J. Hijmans
ChangeLog | 17 +++++
DESCRIPTION | 13 +---
MD5 | 150 ++++++++++++++++++++++++------------------------
R/GDALtransient.R | 26 ++++++--
R/adjacency.R | 7 +-
R/aggregate.R | 9 ++
R/artith.R | 27 +++++---
R/as.data.frame.R | 10 ++-
R/as.matrix.R | 7 ++
R/barplot.R | 9 ++
R/click.R | 52 +++++++++++++++-
R/coerce.R | 3
R/crop.R | 4 -
R/depracated.R | 81 -------------------------
R/extractPolygons.R | 26 +++++---
R/gdal.R | 61 +------------------
R/image.R | 10 +--
R/indexReplace.R | 24 ++++---
R/indexReplaceBrick.R | 26 ++++----
R/kernelDens.R |only
R/math.R | 10 +--
R/names.R | 10 +++
R/netCDFread.R | 24 +++++++
R/netCDFreadCells.R | 28 ++++++--
R/netCDFtoRasterCD.R | 11 +--
R/netCDFtoRasterGMT.R |only
R/netCDFtoStack.R | 9 +-
R/plot.R | 14 ++--
R/plotCT.R | 18 +++++
R/plotExent.R | 4 -
R/plotRGB.R | 15 +---
R/plotRaster.R | 2
R/pointdistance.R | 17 ++++-
R/projectRaster.R | 24 +++++--
R/rasterFromFile.R | 7 +-
R/rasterFromGDAL.R | 17 ++++-
R/rasterFromXYZ.R | 12 ++-
R/rasterOptions.R | 67 ++++++++++-----------
R/rasterizePoints.R | 32 +++-------
R/rasterizePolygons.R | 9 +-
R/ratify.R | 25 ++------
R/rotate.R | 16 ++++-
R/setExtent.R | 65 +++++++++-----------
R/show.R | 23 +++----
R/shp.R | 31 ++++++---
R/stackQuick.R | 12 ++-
R/text.R | 6 +
R/update.R | 2
R/writeStartStopGDAL.R | 2
R/xyCell.R | 16 ++---
R/zonal.R | 137 +++++++++++++++++++++++++++++++++++++++++++
R/zoom.R | 2
R/zzz.R | 12 ++-
inst/doc/Raster.Rnw | 3
inst/doc/Raster.pdf |binary
inst/doc/functions.pdf |binary
inst/doc/rasterfile.pdf |binary
man/adjacency.Rd | 28 --------
man/adjacent.Rd | 11 +++
man/as.matrix.Rd | 2
man/click.Rd | 9 +-
man/compare.Rd | 28 +++-----
man/factor.Rd | 6 -
man/image.Rd | 2
man/names.Rd | 7 +-
man/obsolete.Rd | 11 ---
man/plot.Rd | 8 +-
man/plotRGB.Rd | 10 ++-
man/programming.Rd | 4 -
man/raster-package.Rd | 2
man/rasterOptions.Rd | 5 -
man/rasterize.Rd | 2
man/shp.Rd | 4 -
man/terrain.Rd | 2
man/xyFromCell.Rd | 13 ++--
man/zonal.Rd | 7 +-
src/terrain.c | 11 +--
77 files changed, 812 insertions(+), 604 deletions(-)
Title: Fractional Gaussian Noise and hyperbolic decay time series model
fitting
Diff between FGN versions 2.0-1 dated 2012-12-13 and 2.0-4 dated 2013-03-12
Description: Exact MLE and Whittle MLE estimation for various
hyperbolic decay time series models.
Author: A.I. McLeod and Justin Veenstra
Maintainer: A.I. McLeod
DESCRIPTION | 21 +++++++++++----------
MD5 | 40 ++++++++++++++++++++++++++++++++--------
NAMESPACE | 4 ++++
NEWS | 9 ++++++---
R/ARToPacf.R |only
R/InvertibleQ.R |only
R/PacfToAR.R |only
R/WLoglikelihood.R |only
R/earfima.R |only
R/sdfPLA.R | 1 +
R/sdfarma.R |only
R/sdfhd.R |only
R/tacf.R |only
R/warfima.R |only
data/NileFlowCMS.rda |binary
data/NileMin.rda |binary
data/SeriesB.rda |only
data/globtp.rda |only
inst/doc/v23i05.pdf |binary
man/ARToPacf.Rd |only
man/FGN-package.Rd | 10 +++++-----
man/InvertibleQ.Rd |only
man/PacfToAR.Rd |only
man/SeriesB.Rd |only
man/WLoglikelihood.Rd |only
man/earfima.Rd |only
man/globtp.Rd |only
man/sdfarma.Rd |only
man/sdfhd.Rd |only
man/tacvfARFIMA.Rd |only
man/warfima.Rd |only
src |only
32 files changed, 59 insertions(+), 26 deletions(-)
Title: Batch Effects Removal
Diff between ber versions 3.0 dated 2012-03-22 and 4.0 dated 2013-03-12
Description: The functions in this package remove batch effects from
microarrary normalized data. The expression levels of the genes
are represented in a matrix where rows correspond to
independent samples and columns to genes (variables). The
batches are represented by categorical variables (objects of
class factor). When further covariates of interest are
available they can be used to remove efficiently the batch
effects and adjust the data.
Author: Marco Giordan
Maintainer: Marco Giordan
DESCRIPTION | 13 +-
MD5 | 20 ++--
NAMESPACE | 11 ++
R/ber.r | 101 +++++++++++----------
R/ber_bg.r | 235 ++++++++++++++++---------------------------------
man/ber.Rd | 19 +--
man/ber_bg.Rd | 19 +--
man/combat_np.Rd | 18 +--
man/combat_p.Rd | 17 +--
man/mean_centering.Rd | 9 -
man/standardization.Rd | 9 -
11 files changed, 197 insertions(+), 274 deletions(-)
Title: A collection of methods for singular spectrum analysis
Diff between Rssa versions 0.9.8 dated 2012-12-11 and 0.9.9 dated 2013-03-12
Description: This package provides various Singular Spectrum Analysis
routines.
Author: Anton Korobeynikov
Maintainer: Anton Korobeynikov
DESCRIPTION | 11 +
MD5 | 59 +++++----
NAMESPACE | 12 +
R/cadzow.R |only
R/common.R | 30 ++--
R/forecast.R | 232 +++++++++++++++++-------------------
R/hankel.R | 144 +++++++++++-----------
R/hbhankel.R | 24 +--
R/hmatr.R | 24 +--
R/parest.R | 58 +++++----
R/plot.R | 4
R/ssa.R | 84 ++++++++-----
R/toeplitz.R | 52 +++++---
R/wcor.R | 24 +--
inst/extdata |only
inst/tests |only
man/bforecast.Rd | 28 ++--
man/cadzow.Rd |only
man/forecast.Rd | 30 ++--
man/hankel.Rd | 5
man/lrr.Rd | 13 +-
man/parest.Rd | 24 ++-
man/reconstruct.Rd | 8 -
man/rforecast.Rd | 10 +
man/toeplitz.Rd | 5
man/vforecast.Rd | 12 +
src/fft_plan.h |only
src/hankel.c | 335 ++++++++++++++++++++++++++++++++++++++++++++---------
src/toeplitz.c | 44 +++---
tests |only
30 files changed, 794 insertions(+), 478 deletions(-)
Title: Programming with Big Data -- Scalable Linear Algebra Packages
Diff between pbdSLAP versions 0.1-4 dated 2013-02-15 and 0.1-5 dated 2013-03-12
Description: pbdSLAP utilizes scalable linear algebra packages mainly
including BLACS, PBLAS, and ScaLAPACK in double precision via
pbdMPI based on ScaLAPACK version 2.0.2.
Author: Wei-Chen Chen [aut, cre], Drew Schmidt [aut], George Ostrouchov
[aut], Pragneshkumar Patel [aut]
Maintainer: Wei-Chen Chen
ChangeLog | 3 +++
DESCRIPTION | 11 ++++++-----
MD5 | 8 ++++----
inst/doc/pbdSLAP-guide.pdf |binary
src/install.libs.R | 3 ++-
5 files changed, 15 insertions(+), 10 deletions(-)
Title: Programming with Big Data -- Interface to MPI
Diff between pbdMPI versions 0.1-4 dated 2013-02-14 and 0.1-5 dated 2013-03-12
Description: pbdMPI provides an efficient interface to MPI by utilizing
S4 classes and methods with a focus on Single Program/Multiple
Data (SPMD) parallel programming style, which is intended for
batch parallel execution.
Author: Wei-Chen Chen [aut, cre], George Ostrouchov [aut], Drew Schmidt
[aut], Pragneshkumar Patel [aut], Hao Yu [aut]
Maintainer: Wei-Chen Chen
pbdMPI-0.1-4/pbdMPI/R/comm_any_all.r |only
pbdMPI-0.1-5/pbdMPI/ChangeLog | 5 +++
pbdMPI-0.1-5/pbdMPI/DESCRIPTION | 9 +++---
pbdMPI-0.1-5/pbdMPI/MD5 | 32 +++++++++++++-----------
pbdMPI-0.1-5/pbdMPI/NAMESPACE | 5 +++
pbdMPI-0.1-5/pbdMPI/R/comm_errors.r |only
pbdMPI-0.1-5/pbdMPI/R/comm_tool.r |only
pbdMPI-0.1-5/pbdMPI/R/zzz.r.in | 1
pbdMPI-0.1-5/pbdMPI/configure | 7 +++--
pbdMPI-0.1-5/pbdMPI/configure.ac | 7 +++--
pbdMPI-0.1-5/pbdMPI/data/control.r | 3 +-
pbdMPI-0.1-5/pbdMPI/demo/any_all.r | 2 -
pbdMPI-0.1-5/pbdMPI/inst/doc/pbdMPI-guide.pdf |binary
pbdMPI-0.1-5/pbdMPI/man/11_d.control.Rd | 1
pbdMPI-0.1-5/pbdMPI/man/xx_comm_any_all.Rd | 6 ++--
pbdMPI-0.1-5/pbdMPI/man/xx_comm_stop_warning.Rd |only
pbdMPI-0.1-5/pbdMPI/src/Rinlinedfuns.h |only
pbdMPI-0.1-5/pbdMPI/src/comm_api.h | 4 +++
pbdMPI-0.1-5/pbdMPI/src/comm_errors.c |only
pbdMPI-0.1-5/pbdMPI/src/install.libs.R | 3 +-
20 files changed, 56 insertions(+), 29 deletions(-)
Title: Sample Size Estimation Functions for Studies of Interobserver
Agreement
Diff between kappaSize versions 1.0 dated 2012-03-06 and 1.1 dated 2013-03-12
Description: This package contains basic tools for the purpose of
sample size estimation in studies of interobserver/interrater
agreement (reliability). This package contains sample size
estimation functions for both the power-based and confidence
interval-based methods, with binary or multinomial outcomes and
two through six raters.
Author: Michael A Rotondi
Maintainer: Michael A Rotondi
DESCRIPTION | 11 ++++++-----
MD5 | 26 +++++++++++++-------------
R/CI3Cats.R | 2 +-
R/CI4Cats.R | 2 +-
R/CI5Cats.R | 2 +-
R/CIBinary.R | 2 +-
R/FixedN3Cats.R | 2 +-
R/FixedN4Cats.R | 2 +-
R/FixedN5Cats.R | 2 +-
R/FixedNBinary.R | 2 +-
R/power3Cats.R | 2 +-
R/power4Cats.R | 4 ++--
R/power5Cats.R | 4 ++--
R/powerBinary.R | 2 +-
14 files changed, 33 insertions(+), 32 deletions(-)
Title: GUI for DErivatives in R
Diff between GUIDE versions 0.99.2 dated 2013-03-11 and 0.99.5 dated 2013-03-12
Description: GUI for DErivatives in R
Author: S Subramanian
Maintainer: S Subramanian
DESCRIPTION | 8 +--
MD5 | 102 +++++++++++++++++++++---------------------
R/BinomTree.R | 6 +-
R/JDPaths.R | 4 -
R/Premium3D.R | 5 --
R/basicpayoffs.R | 4 -
R/blackscholes.R | 2
R/bondchange.R | 2
R/bondconv.R | 4 -
R/bonddur.R | 6 +-
R/bondprice.R | 4 -
R/calcgreeks.R | 4 -
R/cdswap.R | 2
R/curswapvalue.R | 2
R/durcoupon.R | 4 -
R/durmaturity.R | 6 +-
R/forwardcommodity.R | 26 +++++-----
R/forwardcurrency.R | 22 ++++-----
R/forwardstock.R | 27 +++++------
R/fra.R | 8 +--
R/fravalue.R | 8 +--
R/futurescommodity.R | 26 +++++-----
R/futurescurrency.R | 23 ++++-----
R/futuresstock.R | 22 ++++-----
R/fv.R | 4 -
R/fvann.R | 6 +-
R/greekneutrality.R | 16 +++---
R/impvol.R | 13 ++---
R/irswapvalue.R | 14 ++---
R/pricematurity.R | 2
R/priceyield.R | 8 +--
R/pv.R | 3 -
R/pvann.R | 4 -
R/rate.R | 9 +--
R/reversebutterfly.R | 8 +--
R/reversestrangle.R | 6 +-
R/stockTimeGreeks.R | 7 +-
R/straddle.R | 6 +-
R/strangle.R | 6 +-
R/strap.R | 8 +--
R/strip.R | 7 +-
R/trading.menu.R | 4 -
R/var1stock.R | 14 ++---
R/var2stocks.R | 22 ++++-----
R/varbehavior.R | 17 +++----
inst/doc/A_guide_to_GUIDE.pdf |binary
man/forwardcommodity.Rd | 6 +-
man/forwardcurrency.Rd | 2
man/forwardstock.Rd | 2
man/futurescommodity.Rd | 5 --
man/futurescurrency.Rd | 2
man/futuresstock.Rd | 2
52 files changed, 262 insertions(+), 268 deletions(-)
Title: memory-efficient storage of large data on disk and fast access
functions
Diff between ff versions 2.2-10 dated 2012-11-06 and 2.2-11 dated 2013-03-12
Description: The ff package provides data structures that are stored on
disk but behave (almost) as if they were in RAM by
transparently mapping only a section (pagesize) in main memory
- the effective virtual memory consumption per ff object. ff
supports R's standard atomic data types 'double', 'logical',
'raw' and 'integer' and non-standard atomic types boolean (1
bit), quad (2 bit unsigned), nibble (4 bit unsigned), byte (1
byte signed with NAs), ubyte (1 byte unsigned), short (2 byte
signed with NAs), ushort (2 byte unsigned), single (4 byte
float with NAs). For example 'quad' allows efficient storage of
genomic data as an 'A','T','G','C' factor. The unsigned types
support 'circular' arithmetic. There is also support for
close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date'
and custom close-to-atomic types. ff not only has native
C-support for vectors, matrices and arrays with flexible
dimorder (major column-order, major row-order and
generalizations for arrays). There is also a ffdf class not
unlike data.frames and import/export filters for csv files. ff
objects store raw data in binary flat files in native encoding,
and complement this with metadata stored in R as physical and
virtual attributes. ff objects have well-defined hybrid copying
semantics, which gives rise to certain performance improvements
through virtualization. ff objects can be stored and reopened
across R sessions. ff files can be shared by multiple ff R
objects (using different data en/de-coding schemes) in the same
process or from multiple R processes to exploit parallelism. A
wide choice of finalizer options allows to work with
'permanent' files as well as creating/removing 'temporary' ff
files completely transparent to the user. On certain
OS/Filesystem combinations, creating the ff files works without
notable delay thanks to using sparse file allocation. Several
access optimization techniques such as Hybrid Index
Preprocessing and Virtualization are implemented to achieve
good performance even with large datasets, for example virtual
matrix transpose without touching a single byte on disk.
Further, to reduce disk I/O, 'logicals' and non-standard data
types get stored native and compact on binary flat files i.e.
logicals take up exactly 2 bits to represent TRUE, FALSE and
NA. Beyond basic access functions, the ff package also
provides compatibility functions that facilitate writing code
for ff and ram objects and support for batch processing on ff
objects (e.g. as.ram, as.ff, ffapply). ff interfaces closely
with functionality from package 'bit': chunked looping, fast
bit operations and coercions between different objects that can
store subscript information ('bit', 'bitwhich', ff 'boolean',
ri range index, hi hybrid index). This allows to work
interactively with selections of large datasets and quickly
modify selection criteria. Further high-performance
enhancements can be made available upon request.
Author: Daniel Adler
Maintainer: Jens Oehlschlägel
DESCRIPTION | 11
LICENSE | 2
MD5 | 22
NEWS | 15
R/ff.R | 98 -
R/ffbit.R | 4
R/ffdf.R | 27
R/ordermerge.R | 2354 ++++++++++++++++++++++----------------------
R/vmode.R | 38
R/zzz.R | 101 +
man/open.ff.rd | 5
src/utk_platform_macros.hpp | 4
12 files changed, 1355 insertions(+), 1326 deletions(-)