Title: Function to create a random list for crossover studies
Diff between randomizeBE versions 0.1-3 dated 2012-08-10 and 0.2-1 dated 2012-09-20
Description: Contains a function to randomise subjects, patients in
groups of sequences (treatment sequences). If a blocksize is
given, the randomisation will be done within blocks. The
randomisation may be controlled by a Wald-Wolfowitz runs test.
The package is mainly intended for randomisation of
bioequivalence studies but may be used also for other clinical
crossover studies. Contains a helper function to get the
sequences of commonly used designs in BE studies.
Author: D. Labes
Maintainer: D. Labes
DESCRIPTION | 11 ++++++-----
MD5 | 10 ++++++----
NAMESPACE | 3 ++-
NEWS | 4 ++++
R/sequences.R |only
man/randomizeBE-package.Rd | 4 ++--
man/sequences.Rd |only
7 files changed, 20 insertions(+), 12 deletions(-)
Title: Data Analysis Using Regression and Multilevel/Hierarchical
Models
Diff between arm versions 1.5-05 dated 2012-06-05 and 1.5-06 dated 2012-09-20
Description: R functions for processing lm, glm, mer and polr outputs.
Author: Andrew Gelman
Maintainer: Yu-Sung Su
CHANGELOG | 4 ++
DESCRIPTION | 10 ++---
MD5 | 6 +--
R/bayesglm.R | 106 ++++++++++++++++++++++++++++++++---------------------------
4 files changed, 70 insertions(+), 56 deletions(-)
Title: Analysis of light based geolocator data
Diff between GeoLight versions 1.01 dated 2012-07-22 and 1.02 dated 2012-09-20
Description: The package provides basic functions for global
positioning based on light intensity measurements over time.
Positioning process includes the determination of sun events, a
discrimination of residency and movement periods, the
calibration of period-specific data and, finally, the
calculation of positions.
Author: Simeon Lisovski, Silke Bauer, Tamara Emmenegger
Maintainer: Simeon Lisovski
DESCRIPTION | 8 +-
MD5 | 12 +--
NEWS | 17 ++++
R/getElevation.R | 129 +++++++++++++++++++-----------------
R/lightFilter.R |only
R/twilightCalc.R | 169 ++++++++++++++++++++++++------------------------
man/GeoLight-package.Rd | 1
man/lightFilter.Rd |only
8 files changed, 182 insertions(+), 154 deletions(-)
Title: Training of neural networks
Diff between neuralnet versions 1.31 dated 2010-10-11 and 1.32 dated 2012-09-20
Description: Training of neural networks using backpropagation,
resilient backpropagation with (Riedmiller, 1994) or without
weight backtracking (Riedmiller and Braun, 1993) or the
modified globally convergent version by Anastasiadis et al.
(2005). The package allows flexible settings through
custom-choice of error and activation function. Furthermore,
the calculation of generalized weights (Intrator O & Intrator
N, 1993) is implemented.
Author: Stefan Fritsch, Frauke Guenther
Maintainer: Frauke Guenther
DESCRIPTION | 8 ++++----
MD5 |only
R/confidence.interval.r | 16 ++++++++--------
R/plot.nn.r | 10 +++-------
man/neuralnet-package.Rd | 4 ++--
man/neuralnet.Rd | 2 +-
man/plot.nn.Rd | 3 +--
neuralnet.tar |only
8 files changed, 19 insertions(+), 24 deletions(-)
Title: Time Frame coding kernel extensions
Diff between tframePlus versions 2012.4-2 dated 2012-05-02 and 2012.8-1 dated 2012-09-20
Description: Extensions and additional tframe utilities.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 9 +++++----
MD5 | 10 +++++-----
NAMESPACE | 2 ++
NEWS | 5 +++++
R/zoo.R | 18 ++++++++++++++++--
man/zoo.Rd | 4 ++++
6 files changed, 37 insertions(+), 11 deletions(-)
Title: Time Frame coding kernel
Diff between tframe versions 2012.4-2 dated 2012-05-02 and 2012.8-1 dated 2012-09-20
Description: The tframe package provides a kernel of functions for
programming time series methods in a way that is relatively
independently of the representation of time. It also provides
plotting, time windowing, and some other utility functions
which are specifically intended for time series. See the Guide
distributed as a vignette, or ?tframe.Intro for more details.
(User utilities other than the programming kernel have been
moved into package tfplot.)
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
NEWS | 4 ++++
inst/doc/Guide.Stex | 5 +----
vignettes/Guide.Stex | 5 +----
5 files changed, 15 insertions(+), 17 deletions(-)
Title: Time Frame User Utilities
Diff between tfplot versions 2012.4-1 dated 2012-04-10 and 2012.7-1 dated 2012-09-20
Description: Utilities in this package are for simple manipulation and
quick plotting of time series data. These utilities use the
tframe package which provides a programming kernel for time
series. Extension to tframe provided in tframePlus can also be
used. See the Guide vignette for examples.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
NEWS | 5 +++++
R/tfplot.R | 4 ++--
inst/doc/Guide.Stex | 4 +---
vignettes/Guide.Stex | 4 +---
6 files changed, 18 insertions(+), 17 deletions(-)
Title: Framework for the analysis of genomic prediction data using R
Diff between synbreed versions 0.9-3 dated 2012-05-25 and 0.9-4 dated 2012-09-20
Description: The package was developed within the Synbreed project for
synergistic plant and animal breeding (www.synbreed.tum.de). It
contains a collection of functions required for genomic
prediction in both plant and animal breeding. This covers data
processing, data visualization and analysis. All functions are
embedded within the framework of a single, unified data object.
The implementation is flexible with respect to a wide range of
data formats. This research was funded by the German Federal
Ministry of Education and Research (BMBF) within the
AgroClustEr Synbreed - Synergistic plant and animal breeding
(FKZ 0315528A).
Author: Valentin Wimmer, Theresa Albrecht, Hans-Juergen Auinger,
Chris-Carolin Schoen with contributions by Larry Schaeffer,
Malena Erbe, Ulrike Ober and Christian Reimer
Maintainer: Valentin Wimmer
synbreed-0.9-3/synbreed/R/Extract.relationshipMatrix.r |only
synbreed-0.9-4/synbreed/DESCRIPTION | 13 -
synbreed-0.9-4/synbreed/MD5 | 62 ++---
synbreed-0.9-4/synbreed/NEWS | 53 +++-
synbreed-0.9-4/synbreed/R/Extract.classes.r |only
synbreed-0.9-4/synbreed/R/LDDist.r | 34 ++
synbreed-0.9-4/synbreed/R/LDMap.r | 53 +++-
synbreed-0.9-4/synbreed/R/add.markers.r | 2
synbreed-0.9-4/synbreed/R/codeGeno.r | 13 -
synbreed-0.9-4/synbreed/R/create.gpData.r | 25 +-
synbreed-0.9-4/synbreed/R/crossVal.r | 86 ++++---
synbreed-0.9-4/synbreed/R/plot.LDdf.LDmat.r |only
synbreed-0.9-4/synbreed/R/plot.genMap.r | 22 +
synbreed-0.9-4/synbreed/R/plot.neighbourLD.r | 195 +++++++++--------
synbreed-0.9-4/synbreed/R/plot.pedigree.r | 4
synbreed-0.9-4/synbreed/R/plot.relationshipMatrix.r | 18 -
synbreed-0.9-4/synbreed/R/write.plink.r | 10
synbreed-0.9-4/synbreed/inst/CITATION | 50 ++--
synbreed-0.9-4/synbreed/inst/doc/figs/cattleHist.pdf |binary
synbreed-0.9-4/synbreed/inst/doc/figs/genMapCattle.pdf |binary
synbreed-0.9-4/synbreed/inst/doc/figs/genMapMaize.pdf |binary
synbreed-0.9-4/synbreed/inst/doc/figs/genMapMice.pdf |binary
synbreed-0.9-4/synbreed/inst/doc/figs/maizeHist.pdf |binary
synbreed-0.9-4/synbreed/inst/doc/figs/miceHist.pdf |binary
synbreed-0.9-4/synbreed/man/Extract.GenMap.Rd |only
synbreed-0.9-4/synbreed/man/LD.Rd | 5
synbreed-0.9-4/synbreed/man/LDDist.Rd | 19 +
synbreed-0.9-4/synbreed/man/LDMap.Rd | 18 +
synbreed-0.9-4/synbreed/man/plot.LDdf.Rd |only
synbreed-0.9-4/synbreed/man/plot.LDmat.Rd |only
synbreed-0.9-4/synbreed/man/plot.genMap.Rd | 16 +
synbreed-0.9-4/synbreed/man/plot.pedigree.Rd | 4
synbreed-0.9-4/synbreed/man/plot.relationshipMatrix.Rd | 2
synbreed-0.9-4/synbreed/man/plotNeighbourLD.Rd | 12 -
synbreed-0.9-4/synbreed/man/write.plink.Rd | 2
35 files changed, 450 insertions(+), 268 deletions(-)
Title: Steiner Tree Approach for Graph Analysis
Diff between SteinerNet versions 1.1 dated 2012-07-24 and 1.2 dated 2012-09-20
Description: A set of graph functions writen in R to find Steiner trees
on graphs. It provides tools for analysing Steiner tree
application on networks. It has applications in biological
pathway network analysis.
Author: Afshin Sadegh
Maintainer: Afshin Sadeghi
DESCRIPTION | 23
MD5 | 18
R/SteinerTree.r | 51 +
R/analysis.r | 20
R/simulations.r | 1051 ++++++++++++++++++++--------------------
inst/doc/SteinerNet.pdf |binary
man/generate_st_samples.Rd | 5
man/steiner_comparison_plots.Rd | 2
man/steiner_simulation.Rd | 5
man/steinertree.Rd | 57 +-
10 files changed, 632 insertions(+), 600 deletions(-)
Title: Least-squares means
Diff between lsmeans versions 0.99 dated 2012-08-27 and 0.99-80 dated 2012-09-20
Description: This package provides the function 'lsmeans' for
outputting so-called least-squares means for factor
combinations in an 'lm', 'lme', or 'lmer' object. It can also
compute contrasts or linear combinations of these least-squares
means, and several standard contrast families are provided.
Author: Russell V. Lenth
Maintainer: Russ Lenth
lsmeans-0.99-80/lsmeans/DESCRIPTION | 12
lsmeans-0.99-80/lsmeans/MD5 | 29 -
lsmeans-0.99-80/lsmeans/NAMESPACE | 2
lsmeans-0.99-80/lsmeans/R/KRstuff.R |only
lsmeans-0.99-80/lsmeans/R/lsmeans.R | 236 ++++++++--
lsmeans-0.99-80/lsmeans/inst/NEWS | 19
lsmeans-0.99-80/lsmeans/inst/doc/using-lsmeans.Rnw |only
lsmeans-0.99-80/lsmeans/inst/doc/using-lsmeans.pdf |only
lsmeans-0.99-80/lsmeans/lsmeans-Ex.R |only
lsmeans-0.99-80/lsmeans/man/lsmeans-package.Rd | 10
lsmeans-0.99-80/lsmeans/man/lsmeans.Rd | 88 ++-
lsmeans-0.99-80/lsmeans/vignettes/using-lsmeans-8-R-fig.pdf |only
lsmeans-0.99-80/lsmeans/vignettes/using-lsmeans-oats-intplot-fig.pdf |only
lsmeans-0.99-80/lsmeans/vignettes/using-lsmeans-typing-scatter-fig.pdf |only
lsmeans-0.99-80/lsmeans/vignettes/using-lsmeans-warp-intplot-fig.pdf |only
lsmeans-0.99-80/lsmeans/vignettes/using-lsmeans.Rnw |only
lsmeans-0.99/lsmeans/R/empty.cells.R |only
lsmeans-0.99/lsmeans/inst/doc/lsmeans.Rnw |only
lsmeans-0.99/lsmeans/inst/doc/lsmeans.pdf |only
lsmeans-0.99/lsmeans/man/empty.cells.Rd |only
lsmeans-0.99/lsmeans/vignettes/lsmeans-oats-intplot-fig.pdf |only
lsmeans-0.99/lsmeans/vignettes/lsmeans-typing-scatter-fig.pdf |only
lsmeans-0.99/lsmeans/vignettes/lsmeans-warp-intplot-fig.pdf |only
lsmeans-0.99/lsmeans/vignettes/lsmeans.Rnw |only
24 files changed, 310 insertions(+), 86 deletions(-)
Title: Read binary files saved by Igor Pro (including Neuromatic data)
Diff between IgorR versions 0.5-2 dated 2012-06-21 and 0.5-3 dated 2012-09-20
Description: This package provides function to read data from the Igor
Pro data analysis program by Wavemetrics. The data formats
supported are Igor packed experiment format (pxp) and Igor
binary wave (ibw). See: http://www.wavemetrics.com/ for
details. It also includes some functions to load special pxp
files produced by the Neuromatic/Nclamp packages for recording
and analysing neuronal data. See
http://www.neuromatic.thinkrandom.com/ for details.
Author: Greg Jefferis
Maintainer: Greg Jefferis
IgorR-0.5-2/IgorR/.gitignore |only
IgorR-0.5-2/IgorR/.project |only
IgorR-0.5-2/IgorR/gitwork.sh |only
IgorR-0.5-3/IgorR/DESCRIPTION | 8
IgorR-0.5-3/IgorR/MD5 | 13
IgorR-0.5-3/IgorR/NEWS | 4
IgorR-0.5-3/IgorR/R/ReadIgorBinary.R | 1054 ++++++++++++++--------------
IgorR-0.5-3/IgorR/R/ReadNclamp.R | 216 ++---
IgorR-0.5-3/IgorR/inst/tests/test-pxp.R | 12
IgorR-0.5-3/IgorR/man/SummariseSweepFile.Rd | 2
10 files changed, 656 insertions(+), 653 deletions(-)
Title: Dynamic Systems Estimation (time series package)
Diff between dse versions 2012.4-1 dated 2012-05-02 and 2012.6-1 dated 2012-09-20
Description: Package dse provides tools for multivariate, linear,
time-invariant, time series models. It includes ARMA and
state-space representations, and methods for converting between
them. It also includes simulation methods and several
estimation functions. The package has functions for looking at
model roots, stability, and forecasts at different horizons.
The ARMA model representaion is general, so that VAR, VARX,
ARIMA, ARMAX, ARIMAX can all be considered to be special cases.
Kalman filter and smoother estimates can be obtained from the
state space model, and state-space model reduction techniques
are implemented. An introduction and User's Guide is available
in a vignette.
Author: Paul Gilbert
Maintainer: Paul Gilbert
DESCRIPTION | 8 ++++----
MD5 | 20 ++++++++++----------
NEWS | 5 +++++
R/dse1.R | 36 ++++++++++++++++++++++--------------
data/eg1.DSE.data.diff.rda |binary
data/eg1.DSE.data.rda |binary
data/egJofF.1dec93.data.rda |binary
inst/doc/Guide.Stex | 4 +---
inst/doc/Guide.pdf |binary
man/stability.Rd | 14 +++++++++++---
vignettes/Guide.Stex | 4 +---
11 files changed, 54 insertions(+), 37 deletions(-)
Title: Companion to Applied Regression
Diff between car versions 2.0-13 dated 2012-08-28 and 2.0-14 dated 2012-09-20
Description: This package accompanies J. Fox and S. Weisberg, An R
Companion to Applied Regression, Second Edition, Sage, 2011.
Author: John Fox [aut, cre], Sanford Weisberg [aut], Douglas Bates
[ctb], David Firth [ctb], Michael Friendly [ctb], Gregor
Gorjanc [ctb], Spencer Graves [ctb], Richard Heiberger [ctb],
Rafael Laboissiere [ctb], Georges Monette [ctb], Henric Nilsson
[ctb], Derek Ogle [ctb], Brian Ripley [ctb], Achim Zeileis
[ctb]
Maintainer: John Fox
DESCRIPTION | 15 -
MD5 | 42 +--
NAMESPACE | 5
NEWS | 14 -
R/Ellipse.R | 9
R/ceresPlots.R | 31 +-
R/compareCoefs.R | 6
R/crPlots.R | 29 +-
R/linearHypothesis.R | 137 +++++-----
R/marginalModelPlot.R | 128 ++--------
R/residualPlots.R | 39 ---
R/scatterplot.R | 561 ++++++++++++++++++++------------------------
R/scatterplotMatrix.R | 431 ++++++++++++++-------------------
R/scatterplotSmoothers.R |only
man/Ellipses.Rd | 15 -
man/ScatterplotSmoothers.Rd |only
man/car-package.Rd | 70 ++---
man/ceresPlots.Rd | 14 -
man/crPlots.Rd | 16 -
man/marginalModelPlot.Rd | 59 +++-
man/residualPlots.Rd | 46 ++-
man/scatterplot.Rd | 97 ++++---
man/scatterplotMatrix.Rd | 263 ++++++++++----------
23 files changed, 974 insertions(+), 1053 deletions(-)
Title: Asymmetric Price Transmission (apt)
Diff between apt versions 1.1 dated 2012-03-31 and 1.2 dated 2012-09-20
Description: This package focuses on asymmetric price transmission
(APT) between two time series. It contains functions for linear
and nonlinear threshold cointegration, and furthermore,
symmetric and asymmetric error correction model.
Author: Changyou Sun
Maintainer: Changyou Sun
apt-1.1/apt/data/daCh.rda |only
apt-1.1/apt/data/daVi.rda |only
apt-1.1/apt/inst/doc/apt-manual.pdf |only
apt-1.1/apt/man/daCh.Rd |only
apt-1.1/apt/man/daVi.Rd |only
apt-1.2/apt/DESCRIPTION | 14 +--
apt-1.2/apt/MD5 | 71 +++++++---------
apt-1.2/apt/R/ciTarFit.R | 80 +++++++++---------
apt-1.2/apt/R/ciTarLag.R | 69 ++++++++--------
apt-1.2/apt/R/ciTarThd.R | 79 +++++++++---------
apt-1.2/apt/R/ecmAsyFit.R | 81 +++++++++---------
apt-1.2/apt/R/ecmAsyTest.R | 154 ++++++++++++++++++------------------
apt-1.2/apt/R/ecmDiag.R | 57 ++++++-------
apt-1.2/apt/R/ecmSymFit.R | 52 +++++-------
apt-1.2/apt/R/plot.ciTarLag.R | 18 +---
apt-1.2/apt/R/plot.ciTarThd.R | 25 ++---
apt-1.2/apt/R/print.ciTarFit.R | 38 +++-----
apt-1.2/apt/R/print.ecm.R | 43 ++++------
apt-1.2/apt/R/summary.ciTarFit.R | 79 ++++++++----------
apt-1.2/apt/R/summary.ecm.R | 48 +++++------
apt-1.2/apt/data/daVich.rda |binary
apt-1.2/apt/inst/doc/apt.Rnw | 4
apt-1.2/apt/man/apt-package.Rd | 8 -
apt-1.2/apt/man/ciTarFit.Rd | 33 -------
apt-1.2/apt/man/ciTarLag.Rd | 13 ---
apt-1.2/apt/man/ciTarThd.Rd | 39 ---------
apt-1.2/apt/man/daVich.Rd | 124 ++++++++++++++++++++++++++++
apt-1.2/apt/man/ecmAsyFit.Rd | 11 --
apt-1.2/apt/man/ecmAsyTest.Rd | 9 --
apt-1.2/apt/man/ecmDiag.Rd | 9 --
apt-1.2/apt/man/ecmSymFit.Rd | 6 -
apt-1.2/apt/man/plot.ciTarLag.Rd | 7 -
apt-1.2/apt/man/plot.ciTarThd.Rd | 5 -
apt-1.2/apt/man/print.ciTarFit.Rd | 4
apt-1.2/apt/man/print.ecm.Rd | 6 -
apt-1.2/apt/man/summary.ciTarFit.Rd | 8 -
apt-1.2/apt/man/summary.ecm.Rd | 7 -
apt-1.2/apt/vignettes/apt.Rnw | 4
apt-1.2/apt/vignettes/apt.bbl |only
apt-1.2/apt/vignettes/apt.blg |only
40 files changed, 576 insertions(+), 629 deletions(-)