Title: Bayesian Ordinal Analysis for State Trace Designs
Diff between StateTrace versions 1.0-2 dated 2012-01-03 and 1.0-4 dated 2012-05-04
Description: StateTrace automates many aspects of a state-trace
analysis of accuracy and other binary response data, including
implementing Bayesian methods quantifying evidence about the
outcomes of a state-trace experiment and the creation of
customisable graphs. It also offers users either a GUI or
non-GUI (i.e., command line input) implementation of the
contained functions
Author: Melissa Prince, Guy Hawkins, Jonathon Love, Andrew Heathcote
Maintainer: David Elliott
StateTrace-1.0-2/StateTrace/R/staGUI.r |only
StateTrace-1.0-4/StateTrace/DESCRIPTION | 16 +++++++++-----
StateTrace-1.0-4/StateTrace/MD5 | 12 +++++-----
StateTrace-1.0-4/StateTrace/R/staGUI.R |only
StateTrace-1.0-4/StateTrace/data/DFIE.txt.gz |binary
StateTrace-1.0-4/StateTrace/inst/doc/StateTrace.pdf |binary
StateTrace-1.0-4/StateTrace/man/001_StateTrace-package.rd | 4 +--
StateTrace-1.0-4/StateTrace/man/005_stFirst.rd | 10 ++++----
8 files changed, 24 insertions(+), 18 deletions(-)
Title: Rcpp integration for Armadillo templated linear algebra library
Diff between RcppArmadillo versions 0.3.0.2 dated 2012-04-19 and 0.3.0.3 dated 2012-05-04
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 3.0.3). 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 GNU LGPL version 3 or later, while
RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is
licenses under the GNU GPL version 2 or later, as is the rest
of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Romain Francois, Dirk Eddelbuettel and Doug Bates
ChangeLog | 12 ++++++++-
DESCRIPTION | 10 +++----
MD5 | 17 ++++++------
inst/NEWS | 10 +++++++
inst/examples/fastLm.r |only
inst/include/armadillo_bits/arma_version.hpp | 2 -
inst/include/armadillo_bits/auxlib_meat.hpp | 3 --
inst/include/armadillo_bits/fn_elem.hpp | 8 +++---
inst/include/armadillo_bits/op_htrans_meat.hpp | 2 -
inst/include/armadillo_bits/unwrap.hpp | 33 -------------------------
10 files changed, 42 insertions(+), 55 deletions(-)
Title: Analysis of evolutionary rates in an OU framework
Diff between OUwie versions 1.18 dated 2012-04-17 and 1.21 dated 2012-05-04
Description: Calculates and compares rate differences of continuous
character evolution under Brownian motion and a new set of
Ornstein-Uhlenbeck-based Hansen models that allow the strength
of selection and stochastic motion to vary across selective
regimes.
Author: Jeremy M. Beaulieu
Maintainer: Jeremy M. Beaulieu
DESCRIPTION | 18 +--
MD5 | 22 ++--
NAMESPACE | 2
R/OUwie.R | 15 +-
R/OUwie.contour.R | 25 ++--
R/OUwie.fixed.R | 4
R/OUwie.sim.R | 271 ++++++++++++++++++++++++++++++++-------------------
R/varcov.ou.R | 104 ++++++-------------
R/weight.mat.R | 89 ++++++----------
man/OUwie.Rd | 7 -
man/OUwie.contour.Rd | 12 +-
man/OUwie.sim.Rd | 9 -
12 files changed, 305 insertions(+), 273 deletions(-)
Title: MSeasy Tcl/Tk Graphical User Interface
Diff between MSeasyTkGUI versions 5.2 dated 2011-09-19 and 5.3 dated 2012-05-04
Description: A Tcl/Tk GUI for some basic functions in the MSeasy
package
Author: Yann Guitton
Maintainer: Yann Guitton
MSeasyTkGUI-5.2/MSeasyTkGUI/inst/doc/Manual_TkGUI.pdf |only
MSeasyTkGUI-5.3/MSeasyTkGUI/DESCRIPTION | 10 -
MSeasyTkGUI-5.3/MSeasyTkGUI/MD5 | 35 ++--
MSeasyTkGUI-5.3/MSeasyTkGUI/NAMESPACE |only
MSeasyTkGUI-5.3/MSeasyTkGUI/R/MSeasyTkGUI.R | 75 ++++++++--
MSeasyTkGUI-5.3/MSeasyTkGUI/R/dialog.MS.DataCreation.Agilent.R | 48 ++++--
MSeasyTkGUI-5.3/MSeasyTkGUI/R/dialog.MS.DataCreation.CDF.R | 51 ++++--
MSeasyTkGUI-5.3/MSeasyTkGUI/R/dialog.MS.DataCreation.user.R | 4
MSeasyTkGUI-5.3/MSeasyTkGUI/R/dialog.MS.aristo.R |only
MSeasyTkGUI-5.3/MSeasyTkGUI/R/dialog.MS.clust.R | 20 +-
MSeasyTkGUI-5.3/MSeasyTkGUI/R/dialog.MS.demon.R | 6
MSeasyTkGUI-5.3/MSeasyTkGUI/R/dialog.MS.msp.R |only
MSeasyTkGUI-5.3/MSeasyTkGUI/R/dialog.MS.nist.R |only
MSeasyTkGUI-5.3/MSeasyTkGUI/R/dialog.MS.step1.R | 21 +-
MSeasyTkGUI-5.3/MSeasyTkGUI/R/dialog.MS.step2.R | 4
MSeasyTkGUI-5.3/MSeasyTkGUI/R/dialog.MS.step3.R |only
MSeasyTkGUI-5.3/MSeasyTkGUI/R/zzz.R | 2
MSeasyTkGUI-5.3/MSeasyTkGUI/inst/doc/MSeasyTkGUI-manual.pdf |binary
MSeasyTkGUI-5.3/MSeasyTkGUI/inst/doc/Manual_TkGUI-5.3.pdf |only
MSeasyTkGUI-5.3/MSeasyTkGUI/man/MSeasyTkGUI-internals.Rd | 4
MSeasyTkGUI-5.3/MSeasyTkGUI/man/MSeasyTkGUI-package.Rd | 6
MSeasyTkGUI-5.3/MSeasyTkGUI/man/MSeasyTkGUI.Rd | 13 -
22 files changed, 203 insertions(+), 96 deletions(-)
Title: Preprocessing of Gas Chromatography-Mass Spectrometry (GC-MS)
data
Diff between MSeasy versions 5.2 dated 2011-09-19 and 5.3 dated 2012-05-04
Description: Package for the detection of molecules in complex mixtures
of compounds. It creates an initial_DATA matrix from several
GC-MS analyses by collecting and assembling the information
from chromatograms and mass spectra (\emph{MS.DataCreation}).It
tests for the best unsupervised clustering method to group
similar mass spectra into molecules (\emph{MS.test.clust}).It
runs the optimal unsupervised clustering method on the
initial_DATA matrix, identifies the optimal number of clusters,
produces different files for facilitating the quality control
and identification of putative molecules, and returns
fingerprinting or profiling matrices (\emph{MS.clust}).It
converts output files from \emph{MS.clust} for NIST mass
spectral library search and ARISTO webtool search
Author: Elodie Courtois, Yann Guitton, Florence Nicole
Maintainer:
MSeasy-5.2/MSeasy/R/MS.DataCreationCDF.R |only
MSeasy-5.2/MSeasy/inst/doc/Agilent_MSDataCreation/agilent1.D |only
MSeasy-5.2/MSeasy/inst/doc/Agilent_MSDataCreation/agilent2.D |only
MSeasy-5.2/MSeasy/man/MS.DataCreationCDF.Rd |only
MSeasy-5.3/MSeasy/DESCRIPTION | 30
MSeasy-5.3/MSeasy/MD5 | 46
MSeasy-5.3/MSeasy/NAMESPACE |only
MSeasy-5.3/MSeasy/R/MS.DataCreation.R | 1014 +++++++----
MSeasy-5.3/MSeasy/R/MS.clust.R | 34
MSeasy-5.3/MSeasy/R/MS.test.clust.R | 60
MSeasy-5.3/MSeasy/R/MSeasyToARISTO.R |only
MSeasy-5.3/MSeasy/R/MSeasyToMSP.R |only
MSeasy-5.3/MSeasy/R/SearchNIST.R |only
MSeasy-5.3/MSeasy/R/trans.ASCII.R | 25
MSeasy-5.3/MSeasy/inst/doc/Agilent_MSDataCreation/Agilent1.D |only
MSeasy-5.3/MSeasy/inst/doc/Agilent_MSDataCreation/Agilent2.D |only
MSeasy-5.3/MSeasy/inst/doc/MSeasy-manual.pdf |binary
MSeasy-5.3/MSeasy/inst/doc/Output_examples |only
MSeasy-5.3/MSeasy/man/ASCII_MSDataCreation.Rd | 2
MSeasy-5.3/MSeasy/man/Agilent_MSDataCreation.Rd | 4
MSeasy-5.3/MSeasy/man/Data_testclust.Rd | 2
MSeasy-5.3/MSeasy/man/MS.DataCreation.Rd | 122 -
MSeasy-5.3/MSeasy/man/MS.clust.Rd | 34
MSeasy-5.3/MSeasy/man/MS.test.clust.Rd | 18
MSeasy-5.3/MSeasy/man/MSeasy-package.Rd | 15
MSeasy-5.3/MSeasy/man/MSeasyToARISTO.Rd |only
MSeasy-5.3/MSeasy/man/MSeasyToMSP.Rd |only
MSeasy-5.3/MSeasy/man/SearchNIST.Rd |only
MSeasy-5.3/MSeasy/man/trans.ASCII.Rd | 8
29 files changed, 959 insertions(+), 455 deletions(-)
Title: Non-additive measure and integral manipulation functions
Diff between kappalab versions 0.4-5 dated 2012-02-29 and 0.4-6 dated 2012-05-04
Description: Kappalab, which stands for "laboratory for capacities", is
an S4 tool box for capacity (or non-additive measure, fuzzy
measure) and integral manipulation on a finite setting. It
contains routines for handling various types of set functions
such as games or capacities. It can be used to compute several
non-additive integrals: the Choquet integral, the Sugeno
integral, and the symmetric and asymmetric Choquet integrals.
An analysis of capacities in terms of decision behavior can be
performed through the computation of various indices such as
the Shapley value, the interaction index, the orness degree,
etc. The well-known Möbius transform, as well as other
equivalent representations of set functions can also be
computed. Kappalab further contains seven capacity
identification routines: three least squares based approaches,
a method based on linear programming, a maximum entropy like
method based on variance minimization, a minimum distance
approach and an unsupervised approach grounded on parametric
entropies. The functions contained in Kappalab can for instance
be used in the framework of multicriteria decision making or
cooperative game theory.
Author: Michel Grabisch, Ivan Kojadinovic, Patrick Meyer.
Maintainer: Ivan Kojadinovic
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
src/core.c | 8 +++++++-
3 files changed, 13 insertions(+), 7 deletions(-)
Title: A Parallel Simulation Framework
Diff between harvestr versions 0.1 dated 2012-03-13 and 0.3 dated 2012-05-04
Description: Functions for easy simulation and replicability.
Author: Andrew Redd
Maintainer: Andrew Redd
harvestr-0.1/harvestr/build.R |only
harvestr-0.1/harvestr/man/seed-funs.Rd |only
harvestr-0.3/harvestr/DESCRIPTION | 12 +--
harvestr-0.3/harvestr/MD5 | 39 +++++++-----
harvestr-0.3/harvestr/NAMESPACE | 1
harvestr-0.3/harvestr/NEWS | 20 ++++++
harvestr-0.3/harvestr/R/gather.R | 67 ++++++++++++++++-----
harvestr-0.3/harvestr/R/harvestr-package.R | 16 ++++-
harvestr-0.3/harvestr/R/utils.R |only
harvestr-0.3/harvestr/R/withseed.R | 8 +-
harvestr-0.3/harvestr/README.md | 66 ++++++++++----------
harvestr-0.3/harvestr/inst/doc |only
harvestr-0.3/harvestr/inst/examples |only
harvestr-0.3/harvestr/inst/tests/test-caching.R |only
harvestr-0.3/harvestr/inst/tests/test-gather.R | 33 ++++++++--
harvestr-0.3/harvestr/inst/tests/test-use_method.R |only
harvestr-0.3/harvestr/man/farm.Rd | 5 +
harvestr-0.3/harvestr/man/harvest.Rd | 5 +
harvestr-0.3/harvestr/man/harvestr.Rd | 16 +++++
harvestr-0.3/harvestr/man/reap.Rd | 9 +-
harvestr-0.3/harvestr/man/seed_funs.Rd |only
harvestr-0.3/harvestr/man/use_method.Rd |only
harvestr-0.3/harvestr/tests/test-parallel.R | 50 ++++++++-------
harvestr-0.3/harvestr/tests/testthat-package.R | 7 --
24 files changed, 242 insertions(+), 112 deletions(-)
Title: Estimation, simulation and visualization of Hierarchical
Archimedean Copulae (HAC)
Diff between HAC versions 0.2-0 dated 2012-04-20 and 0.2-1 dated 2012-05-04
Description: Package provides the estimation of the structure and the
parameters, simulation methods and structural plots of
high-dimensional Hierarchical Archimedean Copulae (HAC).
Author: Ostap Okhrin
Maintainer: Alexander Ristig
ChangeLog.txt | 12 ++++
DESCRIPTION | 10 ++--
MD5 | 26 +++++-----
NAMESPACE | 85 ++++++++++++++++++----------------
R/copula_cdf.r | 4 -
R/copula_estimate.r | 122 ++++++++++++++++++++++++++++++++++++++++---------
R/copula_functions.r | 74 +++++++++++++++++++++++++----
R/copula_pdf.r | 57 ++++++++++++++++++++--
R/copula_simulate.r | 10 ++--
man/Definitions.Rd | 5 +-
man/dHAC.Rd | 11 ++--
man/emp.copula.Rd | 22 ++------
man/estimate.copula.Rd | 13 ++++-
man/logLik.Rd |only
man/pairs.Rd |only
15 files changed, 325 insertions(+), 126 deletions(-)
Title: COSSO, adaptive COSSO, variable selection for nonparametric
smoothing spline models.
Diff between cosso versions 1.0-1 dated 2010-12-13 and 2.0-1 dated 2012-05-04
Description: COSSO is the short term for Component Selection and
Smoothing Operator. The new regularization method automatically
selects important function components by a soft-thresholding
penalty in the context of smoothing spline ANOVA models. The
details about the procedures are given in the paper by Lin and
Zhang (2007).
Author: Hao Helen Zhang
Maintainer: Chen-Yen Lin
cosso-1.0-1/cosso/R/cosso.R |only
cosso-1.0-1/cosso/man/compwt.rd |only
cosso-1.0-1/cosso/man/summary.cosso.rd |only
cosso-2.0-1/cosso/DESCRIPTION | 29 +++++++-----------
cosso-2.0-1/cosso/INDEX | 10 ++++--
cosso-2.0-1/cosso/MD5 |only
cosso-2.0-1/cosso/NAMESPACE |only
cosso-2.0-1/cosso/R/R.R |only
cosso-2.0-1/cosso/man/KQR.rd |only
cosso-2.0-1/cosso/man/KQRwt.rd |only
cosso-2.0-1/cosso/man/SSANOVAwt.rd |only
cosso-2.0-1/cosso/man/cosso-internal.Rd | 11 ++++++-
cosso-2.0-1/cosso/man/cosso.Rd | 50 +++++++++++++++-----------------
cosso-2.0-1/cosso/man/cosso.qr.Rd |only
cosso-2.0-1/cosso/man/plot.cosso.Rd | 31 +++++++++++--------
cosso-2.0-1/cosso/man/predict.cosso.Rd | 36 +++++++++++++----------
cosso-2.0-1/cosso/man/tune.cosso.Rd |only
cosso-2.0-1/cosso/man/tune.cosso.qr.rd |only
18 files changed, 92 insertions(+), 75 deletions(-)
Title: Data Analysis Using Regression and Multilevel/Hierarchical
Models
Diff between arm versions 1.5-03 dated 2012-03-03 and 1.5-04 dated 2012-05-04
Description: R functions for processing lm, glm, mer and polr outputs.
Author: Andrew Gelman
Maintainer: Yu-Sung Su
CHANGELOG | 4 ++++
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
man/bayesglm.Rd | 8 ++++++--
4 files changed, 17 insertions(+), 9 deletions(-)
Title: Dealing with very large datasets using BIRCH
Diff between birch versions 1.2-2 dated 2012-04-30 and 1.2-3 dated 2012-05-04
Description: birch is an implementation of the algorithms described in
Zhang et al (1997), and provides functions for creating
CF-trees, along with algorithms for dealing with some
combinatorial problems, such as covMcd and ltsReg. It is very
well suited for dealing with very large data sets, and does not
require that the data can fit in physical memory.
Author: Lysiane Charest, Justin Harrington, Matias Salibian-Barrera
Maintainer: Lysiane Charest
ChangeLog | 3 +++
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
src/ll_LeafNode.cc | 4 ++++
src/ll_Node.cc | 3 ++-
5 files changed, 17 insertions(+), 9 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-06-20 0.4
2011-04-01 0.3
2011-03-21 0.2
2011-03-18 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-10-16 1.5
2009-01-18 1.4
2007-11-09 1.3
2007-07-09 1.2
2003-12-11 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-02-07 0.1.0-03
2009-11-26 0.1.0-01
2009-11-22 0.0.3-05
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-04-27 2.0
2011-04-09 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-04-27 2.0
2011-04-09 1.0