Title: Estimate a Log-Concave Probability Density from iid Observations
Diff between logcondens versions 2.0.1 dated 2010-11-19 and 2.0.2 dated 2011-02-24
Description: Given independent and identically distributed observations
X(1), ..., X(n), this package allows to compute the maximum
likelihood estimator (MLE) of a density as well as a smoothed
version of it under the assumption that the density is
log-concave, see Rufibach (2007) and Duembgen and Rufibach
(2009). The main function of the package is 'logConDens' that
allows computation of the log-concave MLE and its smoothed
version. In addition, we provide functions to compute (1) the
value of the density and distribution function estimates (MLE
and smoothed) at a given point (2) the characterizing functions
of the estimator, (3) to sample from the estimated
distribution, (5) to compute a two-sample permutation test
based on log-concave densities, (6) the ROC curve based on
log-concave estimates within cases and controls. Finally, three
datasets that have been used to illustrate log-concave density
estimation are made available.
Author: Kaspar Rufibach
Maintainer: Kaspar Rufibach
logcondens-2.0.1/logcondens/inst/doc/Rplots.pdf |only
logcondens-2.0.2/logcondens/DESCRIPTION | 17 +++++++++--------
logcondens-2.0.2/logcondens/NEWS | 5 +++++
logcondens-2.0.2/logcondens/R/ROCx.r |only
logcondens-2.0.2/logcondens/R/logConROC.R |only
logcondens-2.0.2/logcondens/data/pancreas.rda |only
logcondens-2.0.2/logcondens/inst/doc/logcondens.Rnw | 4 +++-
logcondens-2.0.2/logcondens/inst/doc/logcondens.pdf |binary
logcondens-2.0.2/logcondens/inst/doc/plots |only
logcondens-2.0.2/logcondens/man/ROCx.Rd |only
logcondens-2.0.2/logcondens/man/logConROC.Rd |only
logcondens-2.0.2/logcondens/man/logcondens-package.Rd | 15 +++++++++++++--
logcondens-2.0.2/logcondens/man/pancreas.Rd |only
13 files changed, 30 insertions(+), 11 deletions(-)
Title: Independent Factor Analysis
Diff between ifa versions 5.0 dated 2007-07-09 and 6.0 dated 2011-02-24
Description: The package performes Independent Factor Analysis
Author: Cinzia Viroli
Maintainer: Cinzia Viroli
DESCRIPTION | 27 +++++++++++++++------------
R/ifa.aic.R | 4 ++--
R/ifa.em.R | 2 +-
man/ifa.aic.Rd | 2 +-
man/ifa.bic.Rd | 2 +-
man/ifa.em.Rd | 13 +++++--------
src/ifaem.f90 | 9 ++-------
7 files changed, 27 insertions(+), 32 deletions(-)
Title: Restricted MLE for Functional Principal Components Analysis
Diff between fpca versions 0.1-1 dated 2008-03-24 and 0.2-1 dated 2011-02-24
Description: A geometric approach to MLE for functional principal
components
Author: Jie Peng
Maintainer: Jie Peng
fpca-0.1-1/fpca/INDEX |only
fpca-0.1-1/fpca/data/example.rda |only
fpca-0.1-1/fpca/man/example.Rd |only
fpca-0.2-1/fpca/DESCRIPTION | 20 +-
fpca-0.2-1/fpca/NAMESPACE | 4
fpca-0.2-1/fpca/R/fpca_func.R | 11 -
fpca-0.2-1/fpca/R/fpca_pred.r |only
fpca-0.2-1/fpca/R/fpca_score.r |only
fpca-0.2-1/fpca/R/functions_EM.R | 27 ++-
fpca-0.2-1/fpca/R/functions_GenData.R | 4
fpca-0.2-1/fpca/R/functions_Optimization.R | 8
fpca-0.2-1/fpca/data/easy.rda |only
fpca-0.2-1/fpca/data/prac.rda |only
fpca-0.2-1/fpca/man/easy.Rd |only
fpca-0.2-1/fpca/man/fpca.Rd | 19 +-
fpca-0.2-1/fpca/man/fpca.mle.Rd | 242 ++++++++++++++++++++---------
fpca-0.2-1/fpca/man/fpca.pred.rd |only
fpca-0.2-1/fpca/man/fpca.score.rd |only
fpca-0.2-1/fpca/man/prac.Rd |only
19 files changed, 229 insertions(+), 106 deletions(-)
Title: A Suite of S-Plus Functions Implementing Smoothing Splines
Diff between assist versions 3.1 dated 2010-09-15 and 3.1.1 dated 2011-02-24
Description: ASSIST, see manual
Author: Yuedong Wang
Maintainer: Chunlei Ke
assist-3.1.1/assist/DESCRIPTION | 6
assist-3.1.1/assist/INDEX | 206 ++++++++++++++-------------
assist-3.1.1/assist/R/assist.R | 4
assist-3.1.1/assist/man/intervals.nnr.rd | 2
assist-3.1.1/assist/man/intervals.slm.rd | 2
assist-3.1.1/assist/man/intervals.snm.rd | 2
assist-3.1.1/assist/man/intervals.snr.rd | 2
assist-3.1.1/assist/man/plot.bCI.rd | 2
assist-3.1.1/assist/man/plot.ssr.rd | 2
assist-3.1.1/assist/man/print.anova.ssr.rd | 2
assist-3.1.1/assist/man/print.summary.nnr.rd | 2
assist-3.1.1/assist/man/print.summary.slm.rd | 2
assist-3.1.1/assist/man/print.summary.snm.rd | 2
assist-3.1.1/assist/man/print.summary.snr.rd | 2
assist-3.1.1/assist/man/print.summary.ssr.rd | 2
assist-3.1.1/assist/man/ultra.rd | 4
assist-3.1.1/assist/src/kernel.c | 72 +++++++++
assist-3.1/assist/src/monotone.c |only
18 files changed, 198 insertions(+), 118 deletions(-)
Title: Seamless R and C++ Integration
Diff between Rcpp versions 0.9.1 dated 2011-02-14 and 0.9.2 dated 2011-02-24
Description: The Rcpp package provides a C++ library which facilitates
the integration of R and C++.
R data types (SEXP) are matched to C++ objects in a class hierarchy.
All R types are supported (vectors, functions, environment, etc
...) and each type is mapped to a dedicated class. For
example, numeric vectors are represented as instances of the
Rcpp::NumericVector class, environments are represented as
instances of Rcpp::Environment, functions are represented as
Rcpp::Function, etc ... The "Rcpp-introduction" vignette
provides a good entry point to Rcpp.
Conversion from C++ to R and back is driven by the templates Rcpp::wrap
and Rcpp::as which are highly flexible and extensible, as
documented in the "Rcpp-extending" vignette.
Rcpp also provides Rcpp modules, a framework that allows exposing C++
functions and classes to the R level. The "Rcpp-modules"
vignette details the current set of features of Rcpp-modules.
Rcpp includes a concept called Rcpp sugar that brings many R functions
into C++. Sugar takes advantage of lazy evaluation and
expression templates to achieve great performance while
exposing a syntax that is much nicer to use than the equivalent
low-level loop code. The "Rcpp-sugar" vignette gives an
overview of the feature.
Several examples are included, and 753 unit tests in 335 unit test
functions provide additional usage examples.
An earlier version of Rcpp, containing what we now call the 'classic
Rcpp API' was written during 2005 and 2006 by Dominick Samperi.
This code has been factored out of Rcpp into the package
RcppClassic and it is still available for code relying on this
interface. New development should use this package instead.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by
Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel and Romain Francois
ChangeLog | 65 +++++++++++++-----
DESCRIPTION | 8 +-
inst/NEWS | 15 ++++
inst/THANKS | 3
inst/doc/Rcpp-FAQ.pdf |binary
inst/doc/Rcpp-FAQ/Rcpp-FAQ.Rnw | 88 +++++++++++++++++++++++++
inst/doc/Rcpp-extending.pdf |binary
inst/doc/Rcpp-introduction.pdf |binary
inst/doc/Rcpp-modules.pdf |binary
inst/doc/Rcpp-package.pdf |binary
inst/doc/Rcpp-quickref.pdf |binary
inst/doc/Rcpp-sugar.pdf |binary
inst/doc/Rcpp-unitTests.pdf |binary
inst/doc/Rcpp.bib | 23 +++++-
inst/doc/unitTests-results/Rcpp-unitTests.html | 6 -
inst/doc/unitTests-results/Rcpp-unitTests.txt | 50 +++++++-------
inst/include/Rcpp/Module.h | 23 +++---
inst/include/Rcpp/config.h | 2
inst/include/RcppCommon.h | 14 +++
inst/unitTests/runit.Module.client.package.R | 10 ++
20 files changed, 243 insertions(+), 64 deletions(-)
Title: Model diagnostics for population pharmacokinetic models
Diff between PKgraph versions 1.2 dated 2010-12-02 and 1.3 dated 2011-02-24
Description: PKgraph provides a graphical user interface for population
pharmacokinetic model diagnosis. It also provides an integrated
and comprehensive platform for the analysis of pharmacokinetic
data including exploratory data analysis, goodness of model
fit, model validation and model comparison. Results from a
variety of modeling fitting software, including NONMEM,
Monolix, SAS and R, can be used. PKgraph is programmed in R,
and uses the R packages lattice, ggplot2 for static graphics,
and rggobi for interactive graphics.
Author: Xiaoyong Sun
Maintainer: Xiaoyong Sun
DESCRIPTION | 10 -
R/PKgraphlayout.r | 2
R/function.r | 47 ++++-----
R/functionOK.r | 24 ++++
inst/doc/PKgraph.pdf |binary
inst/doc/PKgraph.rnw | 246 ++++++++++++++++++++++++++++++++++++++-----------
inst/doc/PKgraph.tex | 246 ++++++++++++++++++++++++++++++++++++++-----------
inst/doc/inputData.pdf |only
8 files changed, 443 insertions(+), 132 deletions(-)
Title: Sparse and Dense Matrix Classes and Methods
Diff between Matrix versions 0.999375-46 dated 2010-12-15 and 0.999375-47 dated 2011-02-24
Description: Classes and methods for dense and sparse matrices and
operations on them using Lapack and SuiteSparse.
Author: Douglas Bates
Maintainer: Doug and Martin
ChangeLog | 65 ++++++++++++++++++++-
DESCRIPTION | 10 +--
NAMESPACE | 2
R/AllClass.R | 28 ++++++++-
R/Auxiliaries.R | 2
R/CHMfactor.R | 14 ----
R/Ops.R | 5 -
R/Tsparse.R | 39 +++++++-----
R/lMatrix.R | 13 +---
R/nearPD.R | 1
R/pMatrix.R | 5 +
R/spModels.R | 10 ---
R/sparseMatrix.R | 4 -
R/sparseVector.R | 40 ++++++++++---
inst/doc/Comparisons.pdf |binary
inst/doc/Design-issues.pdf |binary
inst/doc/Intro2Matrix.pdf |binary
inst/doc/Introduction.pdf |binary
inst/doc/sparseModels.Rnw | 36 ++++++-----
inst/doc/sparseModels.pdf |binary
inst/test-tools.R | 13 +++-
man/LU-class.Rd | 27 +++++---
man/formatSparseM.Rd | 14 +++-
man/lu.Rd | 14 ++--
man/pMatrix-class.Rd | 2
man/printSpMatrix.Rd | 34 ++++++++---
man/sparse.model.matrix.Rd | 1
man/sparseVector-class.Rd | 14 +++-
man/symmpart.Rd | 17 +++--
src/Csparse.c | 3
src/Mutils.c | 62 +++++---------------
src/Mutils.h | 24 +++----
src/Tsparse.c | 11 +--
src/chm_common.c | 36 ++++++-----
src/cs_utils.c | 12 +--
src/dgCMatrix.c | 8 +-
src/dgeMatrix.c | 7 +-
src/factorizations.c | 111 +++++++++++++++++++++++++++---------
src/t_Matrix_rle.c | 2
tests/bind.R | 5 +
tests/bind.Rout.save | 19 ++++--
tests/factorizing.R | 18 +++--
tests/indexing.R | 59 +++++++++++++++----
tests/indexing.Rout.save | 136 +++++++++++++++++++++++++++++++--------------
44 files changed, 612 insertions(+), 311 deletions(-)