Title: SNP-set (Sequence) Kernel Association Test
Diff between SKAT versions 0.77 dated 2012-07-24 and 0.78 dated 2012-09-06
Description: Kernel based SNP set test
Author: Seunggeun Lee, Larisa Miropolsky and Micheal Wu
Maintainer: Seunggeun (Shawn) Lee
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
R/Function.R | 14 +++++++++-----
R/KMTest_Logistic_VarMatching.R | 4 ++++
R/KMTest_Optimal.R | 2 --
inst/doc/SKAT.pdf |binary
man/SKAT.rd | 7 ++++++-
7 files changed, 29 insertions(+), 18 deletions(-)
Title: Data for the synbreed package
Diff between synbreedData versions 1.1 dated 2012-03-14 and 1.3 dated 2012-09-06
Description: This package contains three data sets from cattle, maize
and mice to illustrate the functions in the synbreed R package.
All data sets are stored in the gpData format introduced in the
synbreed package. 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 Malena Erbe, Ulrike
Ober and Christian Reimer
Maintainer: Valentin Wimmer
synbreedData-1.1/synbreedData/data/cattle.R |only
synbreedData-1.1/synbreedData/data/maize.R |only
synbreedData-1.1/synbreedData/data/mice.R |only
synbreedData-1.1/synbreedData/inst |only
synbreedData-1.3/synbreedData/DESCRIPTION | 8 ++++----
synbreedData-1.3/synbreedData/MD5 | 12 ++++--------
synbreedData-1.3/synbreedData/data/cattle.RData |binary
synbreedData-1.3/synbreedData/data/maize.RData |binary
synbreedData-1.3/synbreedData/data/mice.RData |binary
9 files changed, 8 insertions(+), 12 deletions(-)
Title: Kernel smoothing
Diff between ks versions 1.8.8 dated 2012-05-25 and 1.8.9 dated 2012-09-06
Description: Kernel smoothers for univariate and multivariate data
Author: Tarn Duong
Maintainer: Tarn Duong
ks-1.8.8/ks/man/kde-test.Rd |only
ks-1.8.9/ks/CHANGELOG | 7 +
ks-1.8.9/ks/DESCRIPTION | 12 -
ks-1.8.9/ks/MD5 | 46 +++---
ks-1.8.9/ks/NAMESPACE | 4
ks-1.8.9/ks/R/binning.R | 101 +--------------
ks-1.8.9/ks/R/integrate-kde.R | 6
ks-1.8.9/ks/R/kda.R | 55 +++-----
ks-1.8.9/ks/R/kde-test.R | 242 ++++++++++++++++++++++++++++++++++++
ks-1.8.9/ks/R/normal.R | 40 ++++-
ks-1.8.9/ks/inst/doc/kde.pdf |binary
ks-1.8.9/ks/man/Hamise.mixt.Rd | 8 -
ks-1.8.9/ks/man/Hlscv.Rd | 3
ks-1.8.9/ks/man/Hpi.Rd | 5
ks-1.8.9/ks/man/Hscv.Rd | 2
ks-1.8.9/ks/man/dkde.Rd | 34 ++---
ks-1.8.9/ks/man/kda.Rd | 16 --
ks-1.8.9/ks/man/kda.kde.Rd |only
ks-1.8.9/ks/man/kde.Rd | 40 +----
ks-1.8.9/ks/man/kde.local.test.Rd |only
ks-1.8.9/ks/man/kde.test.Rd |only
ks-1.8.9/ks/man/ks-package.Rd | 7 -
ks-1.8.9/ks/man/plot.kda.kde.Rd |only
ks-1.8.9/ks/man/plot.kde.Rd | 94 ++-----------
ks-1.8.9/ks/man/plot.kde.loctest.Rd |only
ks-1.8.9/ks/man/plotmixt.Rd | 23 ++-
ks-1.8.9/ks/src/ks.c | 46 ++++++
27 files changed, 469 insertions(+), 322 deletions(-)
Title: A package for spatial visualization with Google Maps and
OpenStreetMap
Diff between ggmap versions 2.1 dated 2012-04-30 and 2.2 dated 2012-09-06
Description: ggmap allows for the easy visualization of spatial data
and models on top of Google Maps, OpenStreetMaps, Stamen Maps,
or CloudMade Maps using ggplot2.
Author: David Kahle
Maintainer: David Kahle
DESCRIPTION | 10 +++++-----
MD5 | 30 +++++++++++++++---------------
NAMESPACE | 10 +++++-----
NEWS | 14 ++++++++++++++
R/geocode.R | 6 ++++--
R/get_map.R | 5 +++++
R/ggmap.R | 46 +++++++++++++++++++++++-----------------------
R/mapdist.R | 5 +++--
R/qmplot.R | 10 +++++-----
R/revgeocode.R | 5 +++--
R/route.R | 5 +++--
R/theme_inset.R | 12 ++++++------
R/theme_nothing.R | 31 ++++++++++++-------------------
man/ggmap.Rd | 36 ++++++++++++++++++------------------
man/qmplot.Rd | 2 +-
man/theme_nothing.Rd | 2 +-
16 files changed, 123 insertions(+), 106 deletions(-)
Title: Estimation and simulation of the first-order Beta-t-EGARCH model
Diff between betategarch versions 1.2 dated 2012-06-04 and 1.3 dated 2012-09-06
Description: Estimation and simulation of the first-order Beta-t-EGARCH
model of Andrew Harvey. The two main functions are tegarch.sim
and tegarch.est. The former simulates a first order
Beta-t-EGARCH model whereas the latter estimates one. The other
functions are auxiliary functions called by tegarch.est, and
are not intended for the average user. However, for
completeness they are documented as well.
Author: Genaro Sucarrat
Maintainer: Genaro Sucarrat
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
R/betategarch-internal.R | 2 +-
man/betategarch-package.Rd | 8 ++++----
4 files changed, 13 insertions(+), 13 deletions(-)
Title: Spanish version of orloca package
Diff between orloca.es versions 3.2 dated 2010-05-26 and 4.0 dated 2012-09-06
Description: Version espanola del paquete orloca que trata el problema
de localizacion min-sum, tambien conocido como problema de
Fermat--Weber. El problema de localizacion min-sum busca un
punto tal que la suma ponderada de las distancias a los puntos
de demanda sea minima.
Author: Fernando Fernandez-Palacin
Maintainer: Manuel Munoz-Marquez
DESCRIPTION | 21 +++++++++++----------
MD5 |only
NAMESPACE |only
demo/orloca.R | 30 +++++++++++++++---------------
man/andalusia.Rd |only
man/as.Rd | 4 +++-
man/czsum.Rd | 4 ++--
man/loca.p.Rd | 3 ++-
man/orloca.es-package.Rd | 12 +++++++-----
man/plot.loca.p.Rd | 15 +++++++++++++--
man/plot.zsum.Rd | 17 ++++++++++++-----
man/zsum.Rd | 18 +++++++++++++++++-
man/zsuml2.Rd | 3 ++-
man/zsuml2min.Rd | 22 +++++-----------------
man/zsumlp.Rd | 37 +++++++++++++++++++++----------------
man/zsumlpmin.Rd | 10 ++++------
man/zsummin.Rd | 24 +++++++++++++++---------
17 files changed, 129 insertions(+), 91 deletions(-)
Title: Rcpp integration for Armadillo templated linear algebra library
Diff between RcppArmadillo versions 0.3.2.4 dated 2012-07-12 and 0.3.4.0 dated 2012-09-06
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 3.4.0). 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
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
RcppArmadillo-0.3.2.4/RcppArmadillo/inst/NEWS |only
RcppArmadillo-0.3.4.0/RcppArmadillo/ChangeLog | 33
RcppArmadillo-0.3.4.0/RcppArmadillo/DESCRIPTION | 12
RcppArmadillo-0.3.4.0/RcppArmadillo/MD5 | 188 -
RcppArmadillo-0.3.4.0/RcppArmadillo/R/fastLm.R | 26
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/NEWS.Rd |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/doc/RcppArmadillo-intro.pdf |binary
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/doc/RcppArmadillo-unitTests.pdf |binary
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/doc/unitTests-results/RcppArmadillo-unitTests.html | 10
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/doc/unitTests-results/RcppArmadillo-unitTests.txt | 38
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo | 61
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/Col_bones.hpp | 3
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/Col_meat.hpp | 134
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/Cube_meat.hpp | 24
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/Mat_bones.hpp | 19
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/Mat_meat.hpp | 387 +-
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/Row_bones.hpp | 3
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/Row_meat.hpp | 120
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/SpBase_bones.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/SpBase_meat.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/SpCol_bones.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/SpCol_meat.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/SpGlue_bones.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/SpGlue_meat.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/SpMat_bones.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/SpMat_iterators_meat.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/SpMat_meat.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/SpOp_bones.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/SpOp_meat.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/SpProxy.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/SpRow_bones.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/SpRow_meat.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/SpSubview_bones.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/SpSubview_iterators_meat.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/SpSubview_meat.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/SpValProxy_bones.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/SpValProxy_meat.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/access.hpp | 11
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/arma_config.hpp | 15
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/arma_ostream_bones.hpp | 6
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/arma_ostream_meat.hpp | 254 +
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/arma_version.hpp | 6
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/arrayops_bones.hpp | 10
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/arrayops_meat.hpp | 87
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/auxlib_bones.hpp | 9
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/auxlib_meat.hpp | 434 ++
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/config.hpp | 8
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/diskio_bones.hpp | 49
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/diskio_meat.hpp | 1619 +++++++++-
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/eGlue_meat.hpp | 6
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/eop_aux.hpp | 154
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_accu.hpp | 38
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_as_scalar.hpp | 18
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_conv_to.hpp | 108
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_dot.hpp | 124
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_elem.hpp | 12
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_max.hpp | 62
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_min.hpp | 61
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_n_unique.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_qr.hpp | 31
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_speye.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_spones.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_sprandn.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_sprandu.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_strans.hpp | 16
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_sum.hpp | 62
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_svd.hpp | 24
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_trace.hpp | 35
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_trans.hpp | 72
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/forward_bones.hpp | 31
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/gemm.hpp | 27
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/hdf5_misc.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/lapack_bones.hpp | 18
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/lapack_wrapper.hpp | 65
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/memory.hpp | 35
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/op_dot_bones.hpp | 3
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/op_dot_meat.hpp | 36
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/op_htrans_meat.hpp | 1
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/op_sort_bones.hpp | 7
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/op_sort_meat.hpp | 14
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/op_strans_meat.hpp | 1
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/operator_div.hpp | 205 +
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/operator_minus.hpp | 96
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/operator_ostream.hpp | 20
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/operator_plus.hpp | 84
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/operator_schur.hpp | 199 +
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/operator_times.hpp | 328 ++
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/podarray_bones.hpp | 5
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/podarray_meat.hpp | 48
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/restrictors.hpp | 8
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/spglue_minus_bones.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/spglue_minus_meat.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/spglue_plus_bones.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/spglue_plus_meat.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/spglue_times_bones.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/spglue_times_meat.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/spop_htrans_bones.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/spop_htrans_meat.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/spop_max_bones.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/spop_max_meat.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/spop_min_bones.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/spop_min_meat.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/spop_misc_bones.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/spop_misc_meat.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/spop_strans_bones.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/spop_strans_meat.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/spop_sum_bones.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/spop_sum_meat.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/subview_bones.hpp | 6
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/subview_each_bones.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/subview_each_meat.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/subview_elem2_bones.hpp | 2
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/subview_elem2_meat.hpp | 2
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/subview_meat.hpp | 50
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/traits.hpp | 92
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/typedef.hpp | 32
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/include/armadillo_bits/unwrap_spmat.hpp |only
RcppArmadillo-0.3.4.0/RcppArmadillo/inst/unitTests/runit.fastLm.R | 66
RcppArmadillo-0.3.4.0/RcppArmadillo/man/RcppArmadillo-package.Rd | 4
119 files changed, 5285 insertions(+), 589 deletions(-)
Title: General Frailty models using a semi_parametrical penalized
likelihood estimation or a parametrical estimation
Diff between frailtypack versions 2.2-24 dated 2012-07-25 and 2.2-25 dated 2012-09-06
Description: Frailtypack now fits several classes of frailty models
using a penalized likelihood estimation on the hazard function
but also a parametrical estimation. 1) A shared gamma frailty
model and Cox proportional hazard model. Clustered and
recurrent survival times can be studied (the
Andersen-Gill(1982) approach has been implemented for recurrent
events). An automatic choice of the smoothing parameter is
possible using an approximated cross-validation procedure. 2)
Additive frailty models for proportional hazard models with two
correlated random effects (intercept random effect with random
slope). 3) Nested frailty models for hierarchically clustered
data (with 2 levels of clustering) by including two iid gamma
random effects. 4) Joint frailty models in the context of joint
modelling of recurrent events with terminal event. Prediction
values are available. Left truncated, right-censored data,
interval-censored data (only for Cox proportional hazard and
shared frailty model) and strata (max=2) are allowed. The
package includes concordance measures for Cox proportional
hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Amadou Diakite and Alexandre Laurent
Maintainer: Virginie Rondeau
DESCRIPTION | 8 ++++----
MD5 | 10 ++++++----
NEWS | 5 +++++
data/diabetes.rda |only
man/SurvIC.Rd | 24 +++++++++++++++++++++++-
man/diabetes.Rd |only
man/frailtypack-package.Rd | 6 +++---
7 files changed, 41 insertions(+), 12 deletions(-)
Title: Pretty descriptive stats.
Diff between prettyR versions 2.0-4 dated 2012-01-22 and 2.0-5 dated 2012-09-06
Description: Functions for conventionally formatted descriptive stats,
and to format R output as HTML.
Author: Jim Lemon
Maintainer: Jim Lemon
DESCRIPTION | 8 ++++----
MD5 | 16 ++++++++--------
NEWS | 5 +++++
R/delim.table.R | 2 +-
R/describe.R | 13 ++++++++++---
R/htmlize.R | 9 +++++----
R/rep_n_stack.R | 48 ++++++++++++++++++++++++++++++++++--------------
man/delim.table.Rd | 14 ++++++++++++--
man/rep_n_stack.Rd | 9 +++++++++
9 files changed, 88 insertions(+), 36 deletions(-)
Title: Estimating the proportion of true null hypotheses for FDR
Diff between pi0 versions 1.3-200 dated 2012-01-17 and 1.3-250 dated 2012-09-06
Description: This package implements method(s) to (approximately
unbiasedly) estimate the proportion of true null hypotheses,
i.e., the pi0, when a very large number of hypotheses are
simultaneously tested, especially for the purpose of (local)
false discovery rate control for microarray data. It also
contains functions to estimate the distribution of
noncentrality parameters from a large number of parametric
tests.
Author: Long Qu
Maintainer: Long Qu
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/int.nct.R | 2 +-
man/pi0-package.Rd | 4 ++--
4 files changed, 10 insertions(+), 10 deletions(-)
Title: Statistical analysis for Methylation-sensitive Amplification
Polymorphism data
Diff between msap versions 0.1-2 dated 2012-06-26 and 1.0 dated 2012-09-06
Description: Statistical Analyses of Methylation-sensitive
Amplification Polymorphism (MSAP) assays.
Author: Andres Perez-Figueroa
Maintainer: Andres Perez-Figueroa
DESCRIPTION | 16 +++----
MD5 | 12 +++--
R/msap.R | 118 ++++++++++++++++++++++++++++++++++++++---------------
R/segShannon.R |only
inst/doc/msap.Rnw | 57 ++++++++++++++++++++-----
man/msap.Rd | 8 +++
vignettes/msap.Rnw | 57 ++++++++++++++++++++-----
vignettes/msap.dvi |only
8 files changed, 196 insertions(+), 72 deletions(-)
Title: Gaussian Copula Marginal Regression
Diff between gcmr versions 0.5.0 dated 2012-09-03 and 0.5.1 dated 2012-09-06
Description: likelihood inference in Gaussian copula marginal
regression models
Author: Guido Masarotto and Cristiano Varin
Maintainer: Cristiano Varin
DESCRIPTION | 6 +++---
MD5 | 6 +++---
NEWS | 7 ++++---
R/gcmr.R | 11 ++++++-----
4 files changed, 16 insertions(+), 14 deletions(-)
Title: Spherical k-Means Clustering
Diff between skmeans versions 0.2-2 dated 2012-06-04 and 0.2-3 dated 2012-09-06
Description: Algorithms to compute spherical k-means partitions.
Features several methods, including a genetic and a fixed-point
algorithm and an interface to the CLUTO vcluster program.
Author: Kurt Hornik [aut, cre], Ingo Feinerer [aut], Martin Kober [aut]
Maintainer: Kurt Hornik
DESCRIPTION | 8 ++++----
MD5 | 5 +++--
R/skmeans.R | 3 +--
inst/CITATION |only
4 files changed, 8 insertions(+), 8 deletions(-)
Title: Rcmdr plugin for quality control course
Diff between RcmdrPlugin.qual versions 2.2.1 dated 2012-04-01 and 2.2.2 dated 2012-09-06
More information about RcmdrPlugin.qual at CRAN
Description: This package provides an Rcmdr "plug-in" based on the
Quality control class Stat 4300
Author: Erin Hodgess
Maintainer: Erin Hodgess
DESCRIPTION | 10 +++++-----
MD5 | 2 +-
2 files changed, 6 insertions(+), 6 deletions(-)
Permanent link
Title: Nonlinear least squares examples from NIST
Diff between NISTnls versions 0.9-12 dated 2009-02-11 and 0.9-13 dated 2012-09-06
Description: Datasets for testing nonlinear regression routines.
Author: original from National Institutes for Standards and Technology
(NIST) http://www.itl.nist.gov/div898/strd/nls/nls_main.shtml R
port by Douglas Bates
Maintainer: Douglas Bates
NISTnls-0.9-12/NISTnls/R |only
NISTnls-0.9-12/NISTnls/data/Bennett5.tab |only
NISTnls-0.9-12/NISTnls/data/Chwirut1.tab |only
NISTnls-0.9-12/NISTnls/data/Chwirut2.tab |only
NISTnls-0.9-12/NISTnls/data/DanielWood.tab |only
NISTnls-0.9-12/NISTnls/data/ENSO.tab |only
NISTnls-0.9-12/NISTnls/data/Eckerle4.tab |only
NISTnls-0.9-12/NISTnls/data/Gauss1.tab |only
NISTnls-0.9-12/NISTnls/data/Gauss2.tab |only
NISTnls-0.9-12/NISTnls/data/Gauss3.tab |only
NISTnls-0.9-12/NISTnls/data/Hahn1.tab |only
NISTnls-0.9-12/NISTnls/data/Kirby2.tab |only
NISTnls-0.9-12/NISTnls/data/Lanczos1.tab |only
NISTnls-0.9-12/NISTnls/data/Lanczos2.tab |only
NISTnls-0.9-12/NISTnls/data/Lanczos3.tab |only
NISTnls-0.9-12/NISTnls/data/MGH09.tab |only
NISTnls-0.9-12/NISTnls/data/MGH10.tab |only
NISTnls-0.9-12/NISTnls/data/MGH17.tab |only
NISTnls-0.9-12/NISTnls/data/Misra1a.tab |only
NISTnls-0.9-12/NISTnls/data/Misra1b.tab |only
NISTnls-0.9-12/NISTnls/data/Misra1c.tab |only
NISTnls-0.9-12/NISTnls/data/Misra1d.tab |only
NISTnls-0.9-12/NISTnls/data/Nelson.tab |only
NISTnls-0.9-12/NISTnls/data/Ratkowsky2.tab |only
NISTnls-0.9-12/NISTnls/data/Ratkowsky3.tab |only
NISTnls-0.9-12/NISTnls/data/Roszman1.tab |only
NISTnls-0.9-12/NISTnls/data/Thurber.tab |only
NISTnls-0.9-13/NISTnls/ChangeLog | 9 +++++++--
NISTnls-0.9-13/NISTnls/DESCRIPTION | 20 +++++++++++---------
NISTnls-0.9-13/NISTnls/MD5 |only
NISTnls-0.9-13/NISTnls/NAMESPACE |only
NISTnls-0.9-13/NISTnls/README.md |only
NISTnls-0.9-13/NISTnls/data/Bennett5.tab.gz |only
NISTnls-0.9-13/NISTnls/data/Chwirut1.tab.gz |only
NISTnls-0.9-13/NISTnls/data/Chwirut2.tab.gz |only
NISTnls-0.9-13/NISTnls/data/DanielWood.tab.gz |only
NISTnls-0.9-13/NISTnls/data/ENSO.tab.gz |only
NISTnls-0.9-13/NISTnls/data/Eckerle4.tab.gz |only
NISTnls-0.9-13/NISTnls/data/Gauss1.tab.gz |only
NISTnls-0.9-13/NISTnls/data/Gauss2.tab.gz |only
NISTnls-0.9-13/NISTnls/data/Gauss3.tab.gz |only
NISTnls-0.9-13/NISTnls/data/Hahn1.tab.gz |only
NISTnls-0.9-13/NISTnls/data/Kirby2.tab.gz |only
NISTnls-0.9-13/NISTnls/data/Lanczos1.tab.gz |only
NISTnls-0.9-13/NISTnls/data/Lanczos2.tab.gz |only
NISTnls-0.9-13/NISTnls/data/Lanczos3.tab.gz |only
NISTnls-0.9-13/NISTnls/data/MGH09.tab.gz |only
NISTnls-0.9-13/NISTnls/data/MGH10.tab.gz |only
NISTnls-0.9-13/NISTnls/data/MGH17.tab.gz |only
NISTnls-0.9-13/NISTnls/data/Misra1a.tab.gz |only
NISTnls-0.9-13/NISTnls/data/Misra1b.tab.gz |only
NISTnls-0.9-13/NISTnls/data/Misra1c.tab.gz |only
NISTnls-0.9-13/NISTnls/data/Misra1d.tab.gz |only
NISTnls-0.9-13/NISTnls/data/Nelson.tab.gz |only
NISTnls-0.9-13/NISTnls/data/Ratkowsky2.tab.gz |only
NISTnls-0.9-13/NISTnls/data/Ratkowsky3.tab.gz |only
NISTnls-0.9-13/NISTnls/data/Roszman1.tab.gz |only
NISTnls-0.9-13/NISTnls/data/Thurber.tab.gz |only
58 files changed, 18 insertions(+), 11 deletions(-)
Title: Multivariate Meta-Analysis Using Sarmanov Beta Prior
Distributions
Diff between mmeta versions 1.01 dated 2012-08-16 and 1.02 dated 2012-09-06
Description: This package implements a novel bivariate meta-analysis
using Sarmanov beta prior distributions.
Author: Sheng Luo, Yong Chen, Haitao Chu, Xiao Su
Maintainer: Xiao Su
DESCRIPTION | 8 ++++----
MD5 | 20 ++++++++++----------
man/colorectal.Rd | 2 +-
man/diabetes.Rd | 2 +-
man/multipletables.rd | 2 +-
man/plot.singletable.rd | 2 +-
man/singletable.Rd | 2 +-
man/summary.multipletables.rd | 2 +-
man/summary.singletable.rd | 2 --
man/withdrawal.Rd | 2 +-
man/xtable.multipletables.rd | 2 +-
11 files changed, 22 insertions(+), 24 deletions(-)
Title: Builds and analyses Integral Projection Models (IPMs).
Diff between IPMpack versions 1.4 dated 2012-08-18 and 1.5 dated 2012-09-06
Description: IPMpack takes demographic vital rates and (optionally)
environmental data to build integral projection models. A
number of functional forms for growth and survival can be
incorporated, as well as a range of reproductive strategies.
The package also includes a suite of diagnostic routines,
provides classic matrix model output (e.g., lambda,
elasticities, sensitivities), and produces post-hoc metrics
(e.g., passage time and life expectancy).
Author: CJE Metcalf, SM McMahon, R Salguero-Gomez, E Jongejans
Maintainer: Sean McMahon
IPMpack-1.4/IPMpack/data/datalist |only
IPMpack-1.4/IPMpack/man/sensParamsDiscrete.Rd |only
IPMpack-1.5/IPMpack/DESCRIPTION | 8
IPMpack-1.5/IPMpack/MD5 | 80 +
IPMpack-1.5/IPMpack/R/IPMpack-Base.r | 659 +++++++++++++---
IPMpack-1.5/IPMpack/R/IPMpack-Impl.r | 619 ++++++++++++---
IPMpack-1.5/IPMpack/R/IPMpack-Util.r | 114 ++
IPMpack-1.5/IPMpack/data/cryptaDataCovSubset.csv.gz |binary
IPMpack-1.5/IPMpack/data/hyperDataCovSubset.csv.gz |binary
IPMpack-1.5/IPMpack/inst/doc/IPMpack_Vignette.Rnw | 61 -
IPMpack-1.5/IPMpack/inst/doc/IPMpack_Vignette.pdf |binary
IPMpack-1.5/IPMpack/man/convergeLambda.Rd | 2
IPMpack-1.5/IPMpack/man/convertGrowthObjIncrTruncObj.Rd | 4
IPMpack-1.5/IPMpack/man/createCompoundCmatrix.Rd | 5
IPMpack-1.5/IPMpack/man/createCompoundFmatrix.Rd | 7
IPMpack-1.5/IPMpack/man/createCompoundPmatrix.Rd | 6
IPMpack-1.5/IPMpack/man/createIPMCmatrix.Rd | 6
IPMpack-1.5/IPMpack/man/createIPMFmatrix.Rd | 19
IPMpack-1.5/IPMpack/man/createIPMPmatrix.Rd | 15
IPMpack-1.5/IPMpack/man/createIntegerFmatrix.Rd |only
IPMpack-1.5/IPMpack/man/cryptaDataCovSubset.csv.Rd | 24
IPMpack-1.5/IPMpack/man/diagnosticsPmatrix.Rd | 20
IPMpack-1.5/IPMpack/man/discreteTrans-class.Rd | 3
IPMpack-1.5/IPMpack/man/discreteTransInteger-class.Rd |only
IPMpack-1.5/IPMpack/man/fecObj-class.Rd | 2
IPMpack-1.5/IPMpack/man/fecObjInteger-class.Rd |only
IPMpack-1.5/IPMpack/man/getIPMoutputDirect.Rd | 55 +
IPMpack-1.5/IPMpack/man/getListRegObjects.Rd | 23
IPMpack-1.5/IPMpack/man/growth-methods.Rd | 11
IPMpack-1.5/IPMpack/man/growthObjNegBin-class.Rd |only
IPMpack-1.5/IPMpack/man/hyperDataSubset.csv.Rd | 143 +--
IPMpack-1.5/IPMpack/man/makeClonalObj.Rd | 4
IPMpack-1.5/IPMpack/man/makeDiscreteTrans.Rd | 33
IPMpack-1.5/IPMpack/man/makeDiscreteTransInteger.Rd |only
IPMpack-1.5/IPMpack/man/makeFecObj.Rd | 8
IPMpack-1.5/IPMpack/man/makeFecObjInteger.Rd |only
IPMpack-1.5/IPMpack/man/makeGrowthObj.Rd | 6
IPMpack-1.5/IPMpack/man/makePostFecObjs.Rd | 4
IPMpack-1.5/IPMpack/man/meanLifeExpect.Rd | 6
IPMpack-1.5/IPMpack/man/picGrow.Rd | 10
IPMpack-1.5/IPMpack/man/picSurv.Rd | 5
IPMpack-1.5/IPMpack/man/sensParams.Rd | 12
IPMpack-1.5/IPMpack/man/succisaDataSubset.csv.Rd | 2
IPMpack-1.5/IPMpack/vignettes/IPMpack_Vignette.Rnw | 61 -
IPMpack-1.5/IPMpack/vignettes/Rd.sty |only
IPMpack-1.5/IPMpack/vignettes/inconsolata.sty |only
46 files changed, 1555 insertions(+), 482 deletions(-)
Title: Hybrid index estimation
Diff between HIest versions 1.0 dated 2012-05-18 and 2.0 dated 2012-09-06
Description: Uses likelihood to estimate ancestry and heterozygosity.
Evaluates simple hybrid classifications (parentals, F1, F2,
backcrosses). Estimates genomic clines.
Author: Ben Fitzpatrick
Maintainer:
DESCRIPTION | 9 +-
MD5 | 24 +++---
R/Cline.fit.R | 198 +++++++++++++++++++++++++++++++++++++--------------
R/Cline.plot.R | 157 ++++++++++++++++++++++++++++------------
R/LongX2.R |only
R/gcline.fn.R | 72 +++++++++++++++---
R/spatial.AD.R |only
R/spatial.HZ.R |only
man/Bluestone.Rd | 2
man/Cline.fit.Rd | 33 +-------
man/Cline.plot.Rd | 10 --
man/HIest-package.Rd | 6 +
man/gcline.fn.Rd | 16 ++--
man/longX2.Rd |only
man/spatial.AD.Rd |only
man/spatial.HZ.Rd |only
16 files changed, 361 insertions(+), 166 deletions(-)
Title: Finite Moment Stable Distributions
Diff between FMStable versions 0.1-1 dated 2012-08-15 and 0.1-2 dated 2012-09-06
Description: This package implements some basic procedures for dealing
with log maximally skew stable distributions, which are also
called finite moment log stable distributions.
Author: Geoff Robinson
Maintainer: Geoff Robinson
DESCRIPTION | 8 +-
MD5 | 13 ++--
R/functions.R | 167 +++++++++++++++++++++++++++++++++++-----------------
inst |only
man/Estable.Rd | 7 +-
man/FMstable.Rd | 4 -
man/optionValues.Rd | 8 ++
src/FMStable.c | 24 +++----
8 files changed, 153 insertions(+), 78 deletions(-)
Title: Dirichlet Regression in R
Diff between DirichletReg versions 0.3-0 dated 2011-10-27 and 0.4-0 dated 2012-09-06
Description: Implements the Dirichlet Regression in R
Author: Marco J. Maier
Maintainer: Marco J. Maier
DirichletReg-0.3-0/DirichletReg/.Rinstignore |only
DirichletReg-0.3-0/DirichletReg/R/getdata.R |only
DirichletReg-0.3-0/DirichletReg/R/prep_formula.R |only
DirichletReg-0.3-0/DirichletReg/R/starplot.R |only
DirichletReg-0.3-0/DirichletReg/inst/doc/DirichletReg-vig.bib |only
DirichletReg-0.3-0/DirichletReg/inst/doc/Z.cls |only
DirichletReg-0.3-0/DirichletReg/inst/doc/_compile.bat |only
DirichletReg-0.3-0/DirichletReg/inst/doc/jss.bst |only
DirichletReg-0.4-0/DirichletReg/DESCRIPTION | 30
DirichletReg-0.4-0/DirichletReg/MD5 | 96 +-
DirichletReg-0.4-0/DirichletReg/NAMESPACE | 45 -
DirichletReg-0.4-0/DirichletReg/NEWS | 17
DirichletReg-0.4-0/DirichletReg/R/AIC.DirichletRegModel.R | 8
DirichletReg-0.4-0/DirichletReg/R/DR_LL_alt.R | 20
DirichletReg-0.4-0/DirichletReg/R/DR_LL_common.R | 10
DirichletReg-0.4-0/DirichletReg/R/DR_data.R | 105 +--
DirichletReg-0.4-0/DirichletReg/R/DirichReg.R | 183 ++++-
DirichletReg-0.4-0/DirichletReg/R/DirichReg_fit.R | 12
DirichletReg-0.4-0/DirichletReg/R/anova.DirichletRegModel.R | 2
DirichletReg-0.4-0/DirichletReg/R/coef.DirichletRegModel.R | 5
DirichletReg-0.4-0/DirichletReg/R/confint.DirichletRegModel.R | 24
DirichletReg-0.4-0/DirichletReg/R/coord.trafo.R | 2
DirichletReg-0.4-0/DirichletReg/R/get_starting_values.R | 26
DirichletReg-0.4-0/DirichletReg/R/plot.DirichletRegData.R | 71 +-
DirichletReg-0.4-0/DirichletReg/R/plot_DRdata_3d.R | 43 -
DirichletReg-0.4-0/DirichletReg/R/plot_DRdata_4d.R | 13
DirichletReg-0.4-0/DirichletReg/R/predict.DirichletRegModel.R | 24
DirichletReg-0.4-0/DirichletReg/R/print.DirichletRegConfint.R | 22
DirichletReg-0.4-0/DirichletReg/R/print.DirichletRegData.R | 20
DirichletReg-0.4-0/DirichletReg/R/print.DirichletRegModel.R | 20
DirichletReg-0.4-0/DirichletReg/R/summary.DirichletRegData.R |only
DirichletReg-0.4-0/DirichletReg/R/summary.DirichletRegModel.R | 30
DirichletReg-0.4-0/DirichletReg/R/sysdata.rda |binary
DirichletReg-0.4-0/DirichletReg/R/update.DirichletRegModel.R |only
DirichletReg-0.4-0/DirichletReg/R/vcov.DirichletRegModel.R | 4
DirichletReg-0.4-0/DirichletReg/R/zzz.R | 14
DirichletReg-0.4-0/DirichletReg/data/ArcticLake.RData |binary
DirichletReg-0.4-0/DirichletReg/data/BloodSamples.RData |binary
DirichletReg-0.4-0/DirichletReg/data/GlacialTills.RData |binary
DirichletReg-0.4-0/DirichletReg/data/ReadingSkills.RData |only
DirichletReg-0.4-0/DirichletReg/data/Rocks.RData |binary
DirichletReg-0.4-0/DirichletReg/inst/CITATION | 20
DirichletReg-0.4-0/DirichletReg/inst/doc/DirichletReg-vig.Rnw | 333 +++++-----
DirichletReg-0.4-0/DirichletReg/inst/doc/DirichletReg-vig.pdf |binary
DirichletReg-0.4-0/DirichletReg/man/ArcticLake.Rd | 12
DirichletReg-0.4-0/DirichletReg/man/BloodSamples.Rd | 15
DirichletReg-0.4-0/DirichletReg/man/DR_data.Rd | 77 +-
DirichletReg-0.4-0/DirichletReg/man/Dirichlet.Rd | 2
DirichletReg-0.4-0/DirichletReg/man/DirichletRegModel.Rd | 59 -
DirichletReg-0.4-0/DirichletReg/man/GlacialTills.Rd | 4
DirichletReg-0.4-0/DirichletReg/man/ReadingSkills.Rd |only
DirichletReg-0.4-0/DirichletReg/man/Rocks.Rd | 11
DirichletReg-0.4-0/DirichletReg/man/anova.DirichletRegModel.Rd | 25
DirichletReg-0.4-0/DirichletReg/man/dirichreg.Rd | 155 ++--
DirichletReg-0.4-0/DirichletReg/man/plot.DirichletRegData.Rd | 45 -
DirichletReg-0.4-0/DirichletReg/vignettes |only
56 files changed, 935 insertions(+), 669 deletions(-)
Title: Core methods and classes used by aroma.* packages part of The
Aroma Framework
Diff between aroma.core versions 2.5.0 dated 2012-03-26 and 2.6.0 dated 2012-09-06
Description: This package contains core methods and classes used by
higher-level aroma.* packages part of the Aroma Project, e.g.
aroma.affymetrix and aroma.cn. Its API should be considered to
be in alpha and beta versions, and is mostly of interest to
developers.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
aroma.core-2.5.0/aroma.core/R/weightedMad.R |only
aroma.core-2.5.0/aroma.core/man/weightedMad.Rd |only
aroma.core-2.6.0/aroma.core/DESCRIPTION | 27
aroma.core-2.6.0/aroma.core/MD5 | 115 +-
aroma.core-2.6.0/aroma.core/NAMESPACE | 11
aroma.core-2.6.0/aroma.core/R/AromaCellCpgFile.R | 2
aroma.core-2.6.0/aroma.core/R/AromaCellPositionFile.R | 2
aroma.core-2.6.0/aroma.core/R/AromaMicroarrayTabularBinaryFile.R | 2
aroma.core-2.6.0/aroma.core/R/AromaRepository.R | 530 ++++++++--
aroma.core-2.6.0/aroma.core/R/AromaTransform.R | 2
aroma.core-2.6.0/aroma.core/R/AromaUnitCallSet.R | 2
aroma.core-2.6.0/aroma.core/R/AromaUnitPscnBinaryFile.R |only
aroma.core-2.6.0/aroma.core/R/AromaUnitPscnBinarySet.R |only
aroma.core-2.6.0/aroma.core/R/AromaUnitSignalBinaryFile.R | 33
aroma.core-2.6.0/aroma.core/R/AromaUnitTabularBinaryFile.R | 2
aroma.core-2.6.0/aroma.core/R/AromaUnitTotalCnBinaryFile.R | 26
aroma.core-2.6.0/aroma.core/R/AromaUnitTotalCnBinarySet.exportAromaUnitPscnBinarySet.R |only
aroma.core-2.6.0/aroma.core/R/AromaUnitTotalCnBinarySet.exportTotalCnRatioSet.R | 4
aroma.core-2.6.0/aroma.core/R/ChromosomeExplorer.R | 2
aroma.core-2.6.0/aroma.core/R/CopyNumberChromosomalModel.R | 33
aroma.core-2.6.0/aroma.core/R/CopyNumberSegmentationModel.R | 2
aroma.core-2.6.0/aroma.core/R/Image.EXTS.R | 12
aroma.core-2.6.0/aroma.core/R/PairedPSCNData.PLOT.R |only
aroma.core-2.6.0/aroma.core/R/RasterImage.R | 17
aroma.core-2.6.0/aroma.core/R/RawGenomicSignals.R | 4
aroma.core-2.6.0/aroma.core/R/UnitAnnotationDataFile.R | 2
aroma.core-2.6.0/aroma.core/R/colBinnedSmoothing.R | 39
aroma.core-2.6.0/aroma.core/R/findAnnotationData.R | 30
aroma.core-2.6.0/aroma.core/R/findPngDevice.R | 4
aroma.core-2.6.0/aroma.core/R/fitWHRCModel.matrix.R | 33
aroma.core-2.6.0/aroma.core/R/fitWRMA.matrix.R | 20
aroma.core-2.6.0/aroma.core/R/norm2d.matrix.R | 6
aroma.core-2.6.0/aroma.core/R/smoothWRMA.matrix.R | 4
aroma.core-2.6.0/aroma.core/R/smoothWSA.matrix.R | 9
aroma.core-2.6.0/aroma.core/R/zzz.R | 6
aroma.core-2.6.0/aroma.core/incl/999.missingdocs.txt | 23
aroma.core-2.6.0/aroma.core/incl/colBinnedSmoothing.Rex | 16
aroma.core-2.6.0/aroma.core/inst/NEWS | 97 +
aroma.core-2.6.0/aroma.core/man/AbstractCNData.Rd | 2
aroma.core-2.6.0/aroma.core/man/AbstractPSCNData.Rd | 2
aroma.core-2.6.0/aroma.core/man/AromaRepository.Rd |only
aroma.core-2.6.0/aroma.core/man/AromaTabularBinaryFile.Rd | 2
aroma.core-2.6.0/aroma.core/man/AromaTabularBinarySet.Rd | 2
aroma.core-2.6.0/aroma.core/man/AromaUnitCallFile.Rd | 2
aroma.core-2.6.0/aroma.core/man/AromaUnitFracBCnBinaryFile.Rd | 2
aroma.core-2.6.0/aroma.core/man/AromaUnitGenotypeCallFile.Rd | 2
aroma.core-2.6.0/aroma.core/man/AromaUnitPscnBinaryFile.Rd |only
aroma.core-2.6.0/aroma.core/man/AromaUnitPscnBinarySet.Rd |only
aroma.core-2.6.0/aroma.core/man/AromaUnitSignalBinaryFile.Rd | 3
aroma.core-2.6.0/aroma.core/man/AromaUnitSignalBinarySet.Rd | 2
aroma.core-2.6.0/aroma.core/man/AromaUnitTotalCnBinaryFile.Rd | 7
aroma.core-2.6.0/aroma.core/man/AromaUnitTotalCnBinarySet.Rd | 1
aroma.core-2.6.0/aroma.core/man/AromaUnitTypesFile.Rd | 2
aroma.core-2.6.0/aroma.core/man/BinnedScatter.Rd | 2
aroma.core-2.6.0/aroma.core/man/ChromosomeExplorer.Rd | 2
aroma.core-2.6.0/aroma.core/man/CopyNumberChromosomalModel.Rd | 6
aroma.core-2.6.0/aroma.core/man/Non-documented_objects.Rd | 26
aroma.core-2.6.0/aroma.core/man/PairedPSCNData.Rd | 1
aroma.core-2.6.0/aroma.core/man/colBinnedSmoothing.matrix.Rd | 30
aroma.core-2.6.0/aroma.core/man/downloadChipTypeFile.AromaRepository.Rd |only
aroma.core-2.6.0/aroma.core/man/downloadFile.AromaRepository.Rd |only
aroma.core-2.6.0/aroma.core/man/findAnnotationData.Rd | 6
aroma.core-2.6.0/aroma.core/man/listFiles.AromaRepository.Rd |only
aroma.core-2.6.0/aroma.core/man/plotTracks.PairedPSCNData.Rd |only
aroma.core-2.6.0/aroma.core/tests/RawCopyNumbers.R | 31
65 files changed, 1005 insertions(+), 245 deletions(-)
Title: Analysis of large Affymetrix microarray data sets
Diff between aroma.affymetrix versions 2.5.0 dated 2012-03-26 and 2.6.0 dated 2012-09-06
More information about aroma.affymetrix at CRAN
Description: This package implements classes for files and sets of
files for various Affymetrix file formats, e.g.
AffymetrixCdfFile, AffymetrixCelFile, and AffymetrixCelSet.
These are designed to be memory efficient but still being fast.
The idea is to keep all data on file and only read data into
memory when needed. Clever caching mechanisms are used to
minimize the overhead of data IO. All of the above is hidden
in the package API and for the developer (and the end user),
the data is queried as if it lives in memory. With this design
it is only the diskspace that limits the number of arrays that
can be analyzed. To install, do:
source("http://www.aroma-project.org/hbLite.R");
hbInstall("aroma.affymetrix").
Author: Henrik Bengtsson, James Bullard, Kasper Hansen, Pierre Neuvial,
Elizabeth Purdom, Mark Robinson, Ken Simpson
Maintainer: Henrik Bengtsson
aroma.affymetrix-2.5.0/aroma.affymetrix/R/readCdfDataFrame.R |only
aroma.affymetrix-2.5.0/aroma.affymetrix/inst/buildScripts/chipTypes/MoGene-1_0-st-v1/.Rhistory |only
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aroma.affymetrix-2.5.0/aroma.affymetrix/inst/testScripts/replication/chipTypes/HG-U133_Plus_2/extractAffyBatch.R |only
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aroma.affymetrix-2.5.0/aroma.affymetrix/inst/testScripts/system/chipTypes/Hs_PromPR_v02/test20090629,MatSmoothing.R |only
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aroma.affymetrix-2.6.0/aroma.affymetrix/DESCRIPTION | 26
aroma.affymetrix-2.6.0/aroma.affymetrix/MD5 | 356 ++++---
aroma.affymetrix-2.6.0/aroma.affymetrix/R/006.fixVarArgs.R | 11
aroma.affymetrix-2.6.0/aroma.affymetrix/R/AffyGenePDInfo.writeCdf.R | 21
aroma.affymetrix-2.6.0/aroma.affymetrix/R/AffymetrixCelSet.convertToUnique.R | 59 +
aroma.affymetrix-2.6.0/aroma.affymetrix/R/AffymetrixPgfFile.R |only
aroma.affymetrix-2.6.0/aroma.affymetrix/R/AromaChipTypeAnnotationFile.R | 5
aroma.affymetrix-2.6.0/aroma.affymetrix/R/ChipEffectSet.STATS.R | 24
aroma.affymetrix-2.6.0/aroma.affymetrix/R/CrlmmModel.R | 29
aroma.affymetrix-2.6.0/aroma.affymetrix/R/ExonRmaPlm.R | 2
aroma.affymetrix-2.6.0/aroma.affymetrix/R/HetLogAddPlm.R | 16
aroma.affymetrix-2.6.0/aroma.affymetrix/R/MatSmoothing.R | 13
aroma.affymetrix-2.6.0/aroma.affymetrix/R/ProbeLevelModel.R | 2
aroma.affymetrix-2.6.0/aroma.affymetrix/R/RmaPlm.R | 205 ----
aroma.affymetrix-2.6.0/aroma.affymetrix/R/SnpChipEffectSet.extractAlleleSet.R | 4
aroma.affymetrix-2.6.0/aroma.affymetrix/R/SnpChipEffectSet.extractSnpCnvQSet.R | 6
aroma.affymetrix-2.6.0/aroma.affymetrix/R/SnpChipEffectSet.extractSnpQSet.R | 4
aroma.affymetrix-2.6.0/aroma.affymetrix/R/bpmapCluster2Cdf.R | 457 +++++++---
aroma.affymetrix-2.6.0/aroma.affymetrix/R/doCRMAv1.R | 15
aroma.affymetrix-2.6.0/aroma.affymetrix/R/doCRMAv2.R | 95 ++
aroma.affymetrix-2.6.0/aroma.affymetrix/incl/999.missingdocs.txt | 15
aroma.affymetrix-2.6.0/aroma.affymetrix/inst/NEWS | 103 ++
aroma.affymetrix-2.6.0/aroma.affymetrix/inst/testScripts/addons |only
aroma.affymetrix-2.6.0/aroma.affymetrix/inst/testScripts/archive |only
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aroma.affymetrix-2.6.0/aroma.affymetrix/inst/testScripts/downloadUtils.R |only
aroma.affymetrix-2.6.0/aroma.affymetrix/inst/testScripts/installUtils.R |only
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aroma.affymetrix-2.6.0/aroma.affymetrix/man/Non-documented_objects.Rd | 16
aroma.affymetrix-2.6.0/aroma.affymetrix/man/ProbeLevelModel.Rd | 2
aroma.affymetrix-2.6.0/aroma.affymetrix/man/RmaPlm.Rd | 2
aroma.affymetrix-2.6.0/aroma.affymetrix/man/bpmapCluster2Cdf.Rd | 23
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aroma.affymetrix-2.6.0/aroma.affymetrix/man/getFitUnitGroupFunction.HetLogAddPlm.Rd | 2
aroma.affymetrix-2.6.0/aroma.affymetrix/man/getFitUnitGroupFunction.RmaPlm.Rd | 2
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269 files changed, 1035 insertions(+), 534 deletions(-)
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