Author: Peter K Dunn
Diff between tweedie versions 1.6.7 dated 2009-06-30 and 1.6.8 dated 2009-07-18
Title: Tweedie exponential family models
Description: Maximum likelihood computations for Tweedie families.
CHANGE.log | 4 +
DESCRIPTION | 8 +--
R/tweedie.R | 18 +++----
man/dtweedie.Rd | 2
man/tweedie-package.Rd | 4 -
src/tweedie.f | 116 ++++++++++++++++++++++++-------------------------
6 files changed, 78 insertions(+), 74 deletions(-)
Author: Antonio Fabio Di Narzo, Jose Luis Aznarte, Matthieu Stigler
Title: Time series analysis based on dynamical systems theory
Description: Time series analysis based on dynamical systems theory
Diff between tsDyn versions 0.6-1 dated 2009-02-24 and 0.7 dated 2009-07-18
tsDyn-0.6-1/tsDyn/inst/doc/.build.timestamp |only tsDyn-0.6-1/tsDyn/inst/doc/tsDyn.R |only tsDyn-0.6-1/tsDyn/inst/doc/tsDyn.tex |only tsDyn-0.7/tsDyn/DESCRIPTION | 14 tsDyn-0.7/tsDyn/NAMESPACE | 46 + tsDyn-0.7/tsDyn/R/BBCtest.R |only tsDyn-0.7/tsDyn/R/HanSeo_TVECM.R |only tsDyn-0.7/tsDyn/R/KapShinTest.R |only tsDyn-0.7/tsDyn/R/TVAR.sim.R |only tsDyn-0.7/tsDyn/R/TVAR_LRtest.R |only tsDyn-0.7/tsDyn/R/TVARestim.R |only tsDyn-0.7/tsDyn/R/TVECM.R |only tsDyn-0.7/tsDyn/R/TVECM.sim.R |only tsDyn-0.7/tsDyn/R/TVECMSeoTest.R |only tsDyn-0.7/tsDyn/R/aar.R | 1 tsDyn-0.7/tsDyn/R/lineVar.R |only tsDyn-0.7/tsDyn/R/linear.R | 56 + tsDyn-0.7/tsDyn/R/lstar.R | 20 tsDyn-0.7/tsDyn/R/misc.R | 213 ++++++ tsDyn-0.7/tsDyn/R/miscSETAR.R |only tsDyn-0.7/tsDyn/R/nlVar-methods.R |only tsDyn-0.7/tsDyn/R/nlar-methods.R | 59 + tsDyn-0.7/tsDyn/R/nnet.R | 1 tsDyn-0.7/tsDyn/R/resVar.R |only tsDyn-0.7/tsDyn/R/selectSETAR.R |only tsDyn-0.7/tsDyn/R/setar.R | 856 ++++++++++++++++++---------- tsDyn-0.7/tsDyn/R/setar.sim.R |only tsDyn-0.7/tsDyn/R/setarTest.R |only tsDyn-0.7/tsDyn/R/star.R | 250 ++++---- tsDyn-0.7/tsDyn/data |only tsDyn-0.7/tsDyn/inst/CITATION | 21 tsDyn-0.7/tsDyn/inst/ChangeLog | 25 tsDyn-0.7/tsDyn/inst/doc/tsDyn.Stex | 11 tsDyn-0.7/tsDyn/inst/doc/tsDyn.pdf |binary tsDyn-0.7/tsDyn/man/.Rd2dvi20266 |only tsDyn-0.7/tsDyn/man/BBCTest.Rd |only tsDyn-0.7/tsDyn/man/BIC.Rd |only tsDyn-0.7/tsDyn/man/DataIIPUs.Rd |only tsDyn-0.7/tsDyn/man/DataUsUnemp.Rd |only tsDyn-0.7/tsDyn/man/KapShinTest.Rd |only tsDyn-0.7/tsDyn/man/MakeThSpec.Rd |only tsDyn-0.7/tsDyn/man/TVAR.LRtest.Rd |only tsDyn-0.7/tsDyn/man/TVAR.Rd |only tsDyn-0.7/tsDyn/man/TVAR.sim.Rd |only tsDyn-0.7/tsDyn/man/TVECM.Rd |only tsDyn-0.7/tsDyn/man/TVECM.SeoTest.Rd |only tsDyn-0.7/tsDyn/man/TVECM.sim.Rd |only tsDyn-0.7/tsDyn/man/addRegime.Rd | 3 tsDyn-0.7/tsDyn/man/extendBoot.Rd |only tsDyn-0.7/tsDyn/man/lineVar.Rd |only tsDyn-0.7/tsDyn/man/linear.Rd | 4 tsDyn-0.7/tsDyn/man/nlar-methods.Rd | 3 tsDyn-0.7/tsDyn/man/nlar.Rd | 5 tsDyn-0.7/tsDyn/man/resVar.Rd |only tsDyn-0.7/tsDyn/man/selectSETAR.Rd | 61 + tsDyn-0.7/tsDyn/man/setar.Rd | 33 - tsDyn-0.7/tsDyn/man/setar.sim.Rd |only tsDyn-0.7/tsDyn/man/setarTest.Rd |only tsDyn-0.7/tsDyn/man/sigmoid.Rd | 1 tsDyn-0.7/tsDyn/man/zeroyld.Rd |only tsDyn-0.7/tsDyn/tests |only 61 files changed, 1199 insertions(+), 484 deletions(-)
Author: Roger Koenker
Diff between quantreg versions 4.30 dated 2009-05-12 and 4.36 dated 2009-07-18
Title: Quantile Regression
Description: Quantile regression and related methods.
DESCRIPTION | 10 +-
R/crq.R | 4 -
R/quantreg.R | 5 +
R/rqss.R | 158 ++++++++++++++++++++++++++++++++---------------
R/tools.R |only
demo/00Index | 2
demo/rqsslasso.R |only
inst/ChangeLog | 36 ++++++++++
inst/doc/Rplots.pdf | 96 ++++++++++++++--------------
inst/doc/rq.pdf |binary
man/FAQ.Rd |only
man/dither.Rd |only
man/latex.summary.rqs.Rd | 2
man/latex.table.Rd | 9 --
man/rqss.Rd | 17 ++++-
man/rqss.object.Rd | 3
16 files changed, 223 insertions(+), 119 deletions(-)
Author: William H. Asquith
Title: L-moments, Trimmed L-moments, L-comoments, and Many
Distributions
Description: The package implements the statistical theory of L-moments
including L-moment estimation, probability-weighted moment
estimation, parameter estimation for numerous familiar and
not-so-familiar distributions, and L-moment estimation for the
same distributions from the parameters. L-moments are derived
from the expectations of order statistics and are linear with
respect to the probability- weighted moments. L-moments are
directly analogous to the well-known product moments; however,
L-moments have many advantages including unbiasedness,
robustness, and consistency with respect to the product
moments. This package is oriented around the FORTRAN algorithms
of J.R.M. Hosking, and the nomenclature for many of the
functions parallels that of the Hosking library. However,
numerous extensions are made to aid in expand of the breadth
and ease of L-moment application. Much theoretical extension of
L-moment theory has occurred in recent years. E.A.H. Elamir and
A.H. Seheult have developed the trimmed L-moments, which are
implemented in this package. Further, recent developments by
Robert Serfling and Peng Xiao have extended L-moments into
multivariate space; the so-called sample L-comoments are
implemented here. The supported distributions with moment type
shown as L (L-moments) or TL (trimmed L-moments) and additional
support for right-tail censoring ([RC]) include: Cauchy(TL),
Exponential(L), Gamma(L), Generalized Extreme Value(L),
Generalized Lambda(L & TL), Generalized Logistic (L),
Generalized Normal(L), Generalized Pareto(L[RC] & TL),
Gumbel(L), Normal(L), Kappa(L), Pearson Type III(L), Reverse
Gumbel(L[RC]), Wakeby(L), and Weibull(L).
Diff between lmomco versions 0.96.3 dated 2009-02-23 and 0.97.1 dated 2009-07-18
lmomco-0.96.3/lmomco/junk.R |only lmomco-0.97.1/lmomco/ChangeLog | 9 +++ lmomco-0.97.1/lmomco/DESCRIPTION | 61 +++++++++++++++------------ lmomco-0.97.1/lmomco/INDEX | 16 +++++++ lmomco-0.97.1/lmomco/R/are.par.valid.R | 3 + lmomco-0.97.1/lmomco/R/are.parln3.valid.R |only lmomco-0.97.1/lmomco/R/cdfln3.R |only lmomco-0.97.1/lmomco/R/is.ln3.R |only lmomco-0.97.1/lmomco/R/lmom.test.ln3.R |only lmomco-0.97.1/lmomco/R/lmomln3.R |only lmomco-0.97.1/lmomco/R/lmomray.R | 2 lmomco-0.97.1/lmomco/R/lmomrevgum.R | 2 lmomco-0.97.1/lmomco/R/par2cdf.R | 3 + lmomco-0.97.1/lmomco/R/par2lmom.R | 3 + lmomco-0.97.1/lmomco/R/par2pdf.R | 3 + lmomco-0.97.1/lmomco/R/par2qua.R | 3 + lmomco-0.97.1/lmomco/R/parln3.R |only lmomco-0.97.1/lmomco/R/parray.R | 8 +-- lmomco-0.97.1/lmomco/R/pdfln3.R |only lmomco-0.97.1/lmomco/R/qualn3.R |only lmomco-0.97.1/lmomco/R/vec2par.R | 7 ++- lmomco-0.97.1/lmomco/man/are.par.valid.Rd | 2 lmomco-0.97.1/lmomco/man/are.parln3.valid.Rd |only lmomco-0.97.1/lmomco/man/are.parray.valid.Rd | 4 - lmomco-0.97.1/lmomco/man/cdfln3.Rd |only lmomco-0.97.1/lmomco/man/is.ln3.Rd |only lmomco-0.97.1/lmomco/man/lmom.test.ln3.Rd |only lmomco-0.97.1/lmomco/man/lmomln3.Rd |only lmomco-0.97.1/lmomco/man/par2lmom.Rd | 2 lmomco-0.97.1/lmomco/man/parln3.Rd |only lmomco-0.97.1/lmomco/man/pdfln3.Rd |only lmomco-0.97.1/lmomco/man/qualn3.Rd |only lmomco-0.97.1/lmomco/man/vec2par.Rd | 4 + 33 files changed, 94 insertions(+), 38 deletions(-)
Author: Heloise Lavigne and Aurelien Proye and Jean-Pierre Gattuso.
Portions of code and/or corrections were contributed by
Jean-Marie Epitalon, Andreas Hofmann, Bernard Gentili, Jim Orr
and Karline Soetaert
Title: Calculates parameters of the seawater carbonate system
Description: Calculates parameters of the seawater carbonate system
Diff between seacarb versions 2.1.3 dated 2009-06-28 and 2.1.4 dated 2009-07-18
ChangeLog | 6 ++++++ DESCRIPTION | 8 ++++---- man/bjerrum.Rd | 15 ++++++++------- man/buffer.Rd | 22 +++++++++++++++------- man/carb.Rd | 20 ++++++++++---------- man/pCa.Rd | 9 ++++++--- man/pHconv.Rd | 6 ++++-- man/pHinsi.Rd | 3 ++- man/pTA.Rd | 9 ++++++--- man/pgas.Rd | 6 ++++-- man/pmix.Rd | 6 ++++-- man/ppH.Rd | 9 ++++++--- man/psi.Rd | 6 ++++-- 13 files changed, 79 insertions(+), 46 deletions(-)
Author: Benjamin P. Bryant
Title: Scenario Discovery Tools to Support Robust Decision Making
Description: Implements algorithms to help with scenario discovery -
currently only modified version of the the Patient Rule
Induction Method.
Diff between sdtoolkit versions 2.22 dated 2009-03-06 and 2.3 dated 2009-07-18
DESCRIPTION | 27 ++++++++++++++++----------- R/sd.start.r | 13 ++++++------- R/sdprim.r | 8 ++++++++ R/sdwarranty.r |only R/trajplot.r | 8 +++++--- man/1sdtoolkit-package.Rd | 4 ++-- man/sdprim.Rd | 3 +-- man/undocumented.rd | 4 +++- 8 files changed, 41 insertions(+), 26 deletions(-)
Author: Yves Tillé
Diff between sampling versions 2.1 dated 2008-12-15 and 2.2 dated 2009-07-18
Title: Survey Sampling
Description: Functions for drawing and calibrating samples.
DESCRIPTION | 29 +++--
inst/doc/Rplots.pdf | 231 +++++++++++++++++++++++++----------------------
inst/doc/UPexamples.pdf |binary
inst/doc/calibration.pdf |binary
man/UPbrewer.Rd | 14 +-
man/UPopips.Rd | 11 --
man/calibev.Rd | 28 +++--
man/checkcalibration.Rd | 5 -
man/regest_strata.Rd | 4
man/rhg.Rd | 4
man/rhg_strata.Rd | 2
11 files changed, 175 insertions(+), 153 deletions(-)
Author: Arne Henningsen
Diff between sampleSelection versions 0.6-4 dated 2009-01-26 and 0.6-6 dated 2009-07-18
More information about sampleSelection at CRAN
Title: Sample Selection Models
Description: Estimation of Sample Selection Models
DESCRIPTION | 14
R/coef.probit.R | 2
R/coef.selection.R | 2
R/heckit2fit.R | 15
R/heckit5fit.R | 27
R/print.summary.probit.R | 9
R/probit.R | 4
R/selection.R | 17
R/summary.probit.R | 7
R/summary.selection.R | 14
R/vcov.probit.R | 2
R/vcov.selection.R | 2
inst/doc/selection.pdf | 1826 +++++++++++++++++++++++-----------------------
man/probit.Rd | 12
man/selection.Rd | 5
tests/heckit.Rout.save | 39
tests/probit.Rout.save | 18
tests/selection.Rout.save | 26
18 files changed, 1068 insertions(+), 973 deletions(-)
Permanent link
Author: Timothy H. Keitt
Diff between rgdal versions 0.6-9 dated 2009-06-26 and 0.6-10 dated 2009-07-18
Title: Bindings for the Geospatial Data Abstraction Library
Description: Provides bindings to Frank Warmerdam's Geospatial Data
Abstraction Library (GDAL) (>= 1.3.1) and access to
projection/transformation operations from the PROJ.4 library.
The GDAL and PROJ.4 libraries are external to the package, and,
when installing the package from source, must be correctly
installed first. Both GDAL raster and OGR vector map data can
be imported into R, and GDAL raster data and OGR vector data
exported. Use is made of classes defined in the sp package.
ChangeLog | 13 +++++++++++--
DESCRIPTION | 8 ++++----
R/ogr.R | 29 +++++++++++++++++++++++++----
R/ogr_sp.R | 32 +++++++++++++++++++++++++-------
inst/ChangeLog | 13 +++++++++++--
man/readOGR.Rd | 2 ++
src/ogrsource.cpp | 14 ++++++++++----
7 files changed, 88 insertions(+), 23 deletions(-)
Author: Rajarshi Guha
Diff between rcdk versions 2.9.2 dated 2009-02-25 and 2.9.3 dated 2009-07-18
Title: rcdk - Interface to the CDK Libraries
Description: This package allows the user to access functionality in
the CDK, a Java framework for cheminformatics. This allows the
user to load molecules, evaluate fingerprints, calculate
molecular descriptors and so on. In addition the CDK API allows
the user to view structures in 2D.
DESCRIPTION | 23 +-
R/io.R | 4
R/rcdk.R | 15 +
inst/cont/rcdk.jar |binary
inst/doc/rcdk.pdf | 507 ++++++++++++++++++++++++++---------------------------
man/loadmol.Rd | 5
man/ops.Rd | 10 -
man/parsesmiles.Rd | 8
8 files changed, 302 insertions(+), 270 deletions(-)
Author: Charles J. Geyer
Diff between rcdd versions 1.1-2 dated 2009-06-24 and 1.1-3 dated 2009-07-18
Title: rcdd (Computational Geometry)
Description: R interface to (some of) cddlib, see
http://www.ifor.math.ethz.ch/~fukuda/cdd_home/cdd.html converts
back and forth between two representations of a convex
polytope: as solution of a set of linear equalities and
inequalities and as convex hull of set of points and rays, also
does linear programming and redundant generator elimination
(for example, convex hull in n dimensions), all with exact
infinite-precision rational arithmetic.
CHANGES | 2 ++
DESCRIPTION | 8 ++++----
inst/doc/vinny.pdf |binary
inst/doc/vinny.tex | 4 ++--
4 files changed, 8 insertions(+), 6 deletions(-)
Author: Graham Williams
Diff between rattle versions 2.4.79 dated 2009-06-24 and 2.4.83 dated 2009-07-18
Title: A graphical user interface for data mining in R using GTK
Description: Rattle (the R Analytic Tool To Learn Easily) provides a
Gnome (RGtk2) based interface to R functionality for data
mining. The aim is to provide a simple and intuitive interface
that allows a user to quickly load data from a CSV file (or via
ODBC), transform and explore the data, build and evaluate
models, and export models as PMML (predictive modelling markup
language) or as scores. All of this with knowing little about
R. All R commands are logged and commented through the log tab
and so available to the user as a script file or as an aide to
the user to interact directly with R itself. Rattle also
exports a number of utility functions and the graphical user
interface, invoked as rattle(), does not need to be run to
deploy these.
DESCRIPTION | 8
R/data.R | 7
R/evaluate.R | 6
R/explore.R | 14
R/export.R | 15
R/log.R | 8
R/projects.R | 12
R/rattle.R | 27
R/transform.R | 39 +
R/zzz.R | 12
data/weather.RData |binary
data/weatherCanberra.RData |binary
data/weatherSydney.RData |binary
inst/arff/weather.arff | 10
inst/arff/weatherCanberra.arff | 40 +
inst/arff/weatherSydney.arff | 36 +
inst/csv/weatherCanberra.csv | 1182 +++++++++++++++++++++--------------------
inst/csv/weatherSydney.csv | 1002 +++++++++++++++++-----------------
inst/etc/Rlogo.png |only
inst/etc/rattle.glade | 30 -
inst/etc/textviews.xml | 8
21 files changed, 1332 insertions(+), 1124 deletions(-)
Author: Brian S. Yandell
Diff between qtlbim versions 1.9.3 dated 2009-03-22 and 1.9.4 dated 2009-07-18
Title: QTL Bayesian Interval Mapping
Description: Functions for model selection for genetic architecture.
DESCRIPTION | 8
R/genoprob.R | 3
R/io.R | 18
R/mcmc.R | 12
R/scan.R | 269
R/slice.R | 2
inst/doc/bpPDF/slide-15-6.pdf | 198
inst/doc/bpPDF/slide1hpd.pdf | 36
inst/doc/bpPDF/slide2LOD-1.pdf | 26
inst/doc/prototype.qtl.hyper.slides.pdf | 2307 +-
inst/doc/qtlbim.pdf |binary
inst/doc/qtlbimPDF/FIG-QBBF.pdf | 84
inst/doc/qtlbimPDF/FIG-QBCODA.pdf | 38
inst/doc/qtlbimPDF/FIG-QBDIAG.pdf | 134
inst/doc/qtlbimPDF/FIG-QBEPI.pdf | 6206 ++---
inst/doc/qtlbimPDF/FIG-QBHPD.pdf | 36
inst/doc/qtlbimPDF/FIG-QBLOCI34.pdf | 7480 +++---
inst/doc/qtlbimPDF/FIG-Scanone-HyperLPD.pdf | 32
inst/doc/qtlbimPDF/FIG-Scanone-HyperSubset.pdf | 32
inst/doc/qtlbimPDF/FIG-Scantwo-HyperData.pdf | 32
inst/doc/qtlbimPDF/besthc.pdf | 30
inst/doc/qtlbimPDF/bestmds.pdf | 30
inst/doc/qtlbimPDF/closenqtl.pdf | 26
inst/doc/qtlbimPDF/closepat.pdf | 26
inst/doc/qtlbimPDF/mult.pdf |28828 ++++++++++++-------------
inst/doc/qtlbimPDF/multmerge.pdf |15188 ++++++-------
inst/doc/qtlbimPDF/one.pdf | 32
man/plot.scantwo.Rd | 4
man/qb-internal.Rd | 3
man/scanone.Rd | 2
man/sliceone.Rd | 2
man/summary.scanone.Rd | 7
32 files changed, 30656 insertions(+), 30475 deletions(-)
Author: Andrea Spano'
Title: Variables and Attributes Control Charts
Description: qAnalyst performs: control charts for variables and
attributes according to Douglas C. Montgomery Introduction to
Statistical Quality Control book, Capability analysis for
normal and non - normal distributions and Distributions
Identification
Diff between qAnalyst versions 0.5.4 dated 2008-06-13 and 0.5.5 dated 2009-07-18
DESCRIPTION | 18 ++++-- R/plot.capability.R | 144 ++++++++++++++++++++++++++++------------------------ R/plot.spc.R | 81 ++++++++++++++++------------- README | 6 ++ man/testFun.Rd | 3 - 5 files changed, 145 insertions(+), 107 deletions(-)
Author: William Revelle
Diff between psych versions 1.0-75 dated 2009-07-01 and 1.0-76 dated 2009-07-18
Title: Procedures for Psychological, Psychometric, and Personality
Research
Description: A number of routines for personality, psychometrics and
experimental psychology. Functions are primarily for scale
construction using factor analysis, cluster analysis and
reliability analysis, although others provide basic descriptive
statistics. Functions for simulating particular item and test
structures are included. Several functions serve as a useful
front end for structural equation modeling. For more
information, see the personality-project.org/r webpage.
CHANGES | 8
DESCRIPTION | 8
R/Promax.R | 2
R/factor.stats.R | 6
R/print.psych.fa.R | 20
R/print.psych.omega.R | 25
R/r.test.R | 2
R/schmid.R | 1
inst/doc/overview.pdf | 3129 +++++++++++++++++++++----------------------
inst/doc/psych_for_sem.pdf | 3239 +++++++++++++++++++++------------------------
man/00.psych-package.Rd | 4
man/VSS.scree.Rd | 3
man/bifactor.Rd | 3
man/fa.Rd | 2
man/omega.Rd | 3
man/poly.mat.Rd | 2
man/polychor.matrix.Rd | 10
man/principal.Rd | 24
man/schmid.Rd | 3
19 files changed, 3243 insertions(+), 3251 deletions(-)
Author: Jelle Goeman
Diff between penalized versions 0.9-24 dated 2009-05-28 and 0.9-25 dated 2009-07-18
Title: L1 (lasso) and L2 (ridge) penalized estimation in GLMs and in
the Cox model
Description: A package for fitting possibly high dimensional penalized
regression models. The penalty structure can be any combination
of an L1 penalty (lasso), an L2 penalty (ridge) and a
positivity constraint on the regression coefficients. The
supported regression models are linear, logistic and poisson
regression and the Cox Proportional Hazards model.
Cross-validation routines allow optimization of the tuning
parameters.
DESCRIPTION | 8
R/cox.R | 1
changelog.txt | 3
inst/doc/Rplots.pdf |13556 +++++++++++++++++++++++++------------------------
inst/doc/penalized.Rnw | 2
inst/doc/penalized.pdf |binary
6 files changed, 7071 insertions(+), 6499 deletions(-)
Author: Peter Filzmoser Heinrich Fritz Klaudius Kalcher
Title: Robust PCA by Projection Pursuit
Description: Robust PCA by Projection Pursuit
Diff between pcaPP versions 1.6 dated 2009-01-23 and 1.7 dated 2009-07-18
DESCRIPTION | 14 +++++++------- src/conv.cpp | 3 ++- 2 files changed, 9 insertions(+), 8 deletions(-)
Author: Sven Adler
Title: WA, WA-PLS, MW and POM for paleolimnology
Description: This package contains functions for paleolimnology -
wa-regression (see also package analogue by G. Simpson!),
wa-pls and the mowing-window approch. The function palplot
allows a first plot of the data including a trend analysis. The
pom function is just a first test version.
Diff between paltran versions 1.1 dated 2009-06-26 and 1.2-0 dated 2009-07-18
paltran-1.1/paltran/R/pom.R |only paltran-1.1/paltran/man/pom.Rd |only paltran-1.2-0/paltran/DESCRIPTION | 6 - paltran-1.2-0/paltran/R/mft.R |only paltran-1.2-0/paltran/R/mw.R | 6 - paltran-1.2-0/paltran/R/wa.R | 22 ++-- paltran-1.2-0/paltran/R/wapls.R | 142 ++++++++++++++------------- paltran-1.2-0/paltran/man/mft.Rd |only paltran-1.2-0/paltran/man/mw.Rd | 11 +- paltran-1.2-0/paltran/man/paltran-package.Rd | 2 paltran-1.2-0/paltran/man/wapls.Rd | 5 11 files changed, 107 insertions(+), 87 deletions(-)
Author: Torsten Hothorn, Frank Bretz and Peter Westfall with
contributions by Richard M. Heiberger and Andre
Schuetzenmeister
Title: Simultaneous Inference in General Parametric Models
Description: Simultaneous tests and confidence intervals for general
linear hypotheses in parametric models, including linear,
generalized linear, linear mixed effects, and survival models.
Diff between multcomp versions 1.1-0 dated 2009-06-08 and 1.1-1 dated 2009-07-18
DESCRIPTION | 6 NEWS | 5 R/cld.R | 12 inst/CHANGES | 5 inst/doc/chfls1.bbl |only inst/doc/chfls1.blg |only inst/doc/chfls1.pdf |binary inst/doc/generalsiminf.bbl |only inst/doc/generalsiminf.blg |only inst/doc/generalsiminf.pdf | 1016 ++++++++++++++++++++--------------------- inst/doc/multcomp-examples.pdf |binary tests/bugfix.R | 9 tests/bugfix.Rout.save | 16 13 files changed, 555 insertions(+), 514 deletions(-)
Author: Christopher Jackson
Diff between msm versions 0.9.1 dated 2009-06-14 and 0.9.2 dated 2009-07-18
Title: Multi-state Markov and hidden Markov models in continuous time
Description: Functions for fitting general continuous-time Markov and
hidden Markov multi-state models to longitudinal data. Both
Markov transition rates and the hidden Markov output process
can be modelled in terms of covariates. A variety of
observation schemes are supported, including processes observed
at arbitrary times, completely-observed processes, and censored
states.
ChangeLog | 11 +++++++++++
DESCRIPTION | 8 ++++----
R/msm.R | 2 ++
inst/NEWS | 11 +++++++++++
inst/doc/msm-manual.pdf |binary
src/pijt.c | 17 +++++++++++++----
tests/simple.R | 12 ++++++------
7 files changed, 47 insertions(+), 14 deletions(-)
Author: Dai Feng and Luke Tierney
Title: Miscellaneous 3D Plots
Description: A collection of miscellaneous 3d plots, including
isosurfaces.
Diff between misc3d versions 0.6-3 dated 2009-06-17 and 0.7-0 dated 2009-07-18
DESCRIPTION | 6 +++--- R/slices3d.R | 15 ++++++++++----- man/slices3d.Rd | 15 +++++++++++++-- 3 files changed, 26 insertions(+), 10 deletions(-)
Author: Luke Keele
Diff between mediation versions 1.0 dated 2009-06-14 and 2.0 dated 2009-07-18
Title: R Package for Causal Mediation Analysis
Description: mediation is a publicly available R package that allows
both parametric and nonparametric causal mediation analysis.
It implements the methods and suggestions in Imai, Keele, and
Yamamoto (2008) and Imai, Keele, Tingley (2009). In addition
to the estimation of causal mediation effects, the software
also allows researchers to conduct sensitivity analysis for
certain parametric models.
mediation-1.0/mediation/data/job.RData |only
mediation-1.0/mediation/data/job.Rd |only
mediation-1.0/mediation/man/job.Rd |only
mediation-2.0/mediation/ChangeLog |only
mediation-2.0/mediation/DESCRIPTION | 8
mediation-2.0/mediation/R/mediate.R | 271 +++++-----
mediation-2.0/mediation/R/medsens.R | 653 +++++++++++++++++--------
mediation-2.0/mediation/R/medsensr2.R |only
mediation-2.0/mediation/man/mediate.Rd | 72 +-
mediation-2.0/mediation/man/medsens.Rd | 109 +---
mediation-2.0/mediation/man/plot.medsens.Rd | 44 +
mediation-2.0/mediation/man/summary.mediate.Rd | 14
mediation-2.0/mediation/man/summary.medsens.Rd | 35 -
13 files changed, 737 insertions(+), 469 deletions(-)
Author: Ott Toomet
Diff between maxLik versions 0.5-10 dated 2009-01-26 and 0.5-12 dated 2009-07-18
Title: Maximum Likelihood Estimation
Description: Tools for Maximum Likelihood Estimation
DESCRIPTION | 14
INDEX | 1
NAMESPACE |only
R/maxBHHH.R | 30 +
R/maximType.R | 3
R/print.maxLik.R |only
R/returnMessage.R | 2
R/summary.maxLik.R | 14
man/compareDerivatives.Rd | 1
man/maxLik.Rd | 12
tests/examples.R | 42 +-
tests/examples.Rout.save | 915 +++++++++++++++++++++++++++++++++++++++++++++-
12 files changed, 990 insertions(+), 44 deletions(-)
Author: J. R. M. Hosking
Title: Regional frequency analysis using L-moments
Description: Functions for regional frequency analysis using the
methods of J. R. M. Hosking and J. R. Wallis (1997), "Regional
frequency analysis: an approach based on L-moments".
Diff between lmomRFA versions 2.0 dated 2009-05-04 and 2.1 dated 2009-07-18
DESCRIPTION | 8 ++++---- NAMESPACE | 1 + NEWS | 8 ++++++++ R/lmomRFA.r | 2 +- man/Cascades.Rd | 2 ++ 5 files changed, 16 insertions(+), 5 deletions(-)
Author: J. R. M. Hosking
Title: L-moments
Description: Functions related to L-moments: computation of L-moments
of distributions and data samples; parameter estimation;
L-moment ratio diagram; plot vs. quantiles of an extreme-value
distribution.
Diff between lmom versions 1.3 dated 2009-05-04 and 1.4 dated 2009-07-18
DESCRIPTION | 8 ++++---- NAMESPACE | 3 +++ NEWS | 8 ++++++++ R/lmom.r | 22 ++++++++++++++++++++++ man/lmom-package.Rd | 4 ++++ man/lmrdpoints.Rd |only 6 files changed, 41 insertions(+), 4 deletions(-)
Author: Pavel N. Krivitsky
Diff between latentnet versions 2.1-1 dated 2008-02-29 and 2.2 dated 2009-07-18
Title: Latent position and cluster models for statistical networks
Description: A package to fit and simulate latent position and cluster
models for statistical networks.
latentnet-2.1-1/latentnet/R/ergmm.sample.utils.R |only
latentnet-2.1-1/latentnet/R/labelswitch.R |only
latentnet-2.1-1/latentnet/man/ergmm.par.object.Rd |only
latentnet-2.1-1/latentnet/src/post_utils.c |only
latentnet-2.1-1/latentnet/src/post_utils.h |only
latentnet-2.2/latentnet/ChangeLog |only
latentnet-2.2/latentnet/DESCRIPTION | 25 -
latentnet-2.2/latentnet/LICENSE | 2
latentnet-2.2/latentnet/R/InitErgmm.fixed.R | 34 -
latentnet-2.2/latentnet/R/InitErgmm.latent.R | 23
latentnet-2.2/latentnet/R/InitErgmm.random.R |only
latentnet-2.2/latentnet/R/bayesmbc.MCMC.C.R | 40 -
latentnet-2.2/latentnet/R/bayesmbc.R | 41 +
latentnet-2.2/latentnet/R/ergmm.MCMC.C.R | 188 +++++--
latentnet-2.2/latentnet/R/ergmm.R | 100 +---
latentnet-2.2/latentnet/R/ergmm.defaults.R | 11
latentnet-2.2/latentnet/R/ergmm.families.R | 26 -
latentnet-2.2/latentnet/R/ergmm.geodesicmatrix.R | 6
latentnet-2.2/latentnet/R/ergmm.get.model.R | 50 +-
latentnet-2.2/latentnet/R/ergmm.initvals.R | 155 ++++--
latentnet-2.2/latentnet/R/ergmm.par.R | 24 -
latentnet-2.2/latentnet/R/ergmm.permutation.R | 5
latentnet-2.2/latentnet/R/ergmm.probs.R | 397 +++++++++++-----
latentnet-2.2/latentnet/R/ergmm.statseval.R | 249 ++++++----
latentnet-2.2/latentnet/R/ergmm.tuner.R | 109 +++-
latentnet-2.2/latentnet/R/gof.ergmm.R | 29 -
latentnet-2.2/latentnet/R/label.switching.R |only
latentnet-2.2/latentnet/R/mcmc.diagnostics.ergmm.R | 23
latentnet-2.2/latentnet/R/merge.ergmm.R |only
latentnet-2.2/latentnet/R/plot.ergmm.R | 424 +++++++++++-------
latentnet-2.2/latentnet/R/predict.ergmm.R | 88 +++
latentnet-2.2/latentnet/R/print.ergmm.R |only
latentnet-2.2/latentnet/R/print.ergmm.model.R | 21
latentnet-2.2/latentnet/R/procrustes.R |only
latentnet-2.2/latentnet/R/robust.inverse.R | 12
latentnet-2.2/latentnet/R/simulate.ergmm.R | 62 +-
latentnet-2.2/latentnet/R/summary.ergmm.R | 223 ++++++---
latentnet-2.2/latentnet/R/utilities.R | 45 +
latentnet-2.2/latentnet/R/zzz.R | 6
latentnet-2.2/latentnet/data/tribes.RData |binary
latentnet-2.2/latentnet/inst/CITATION | 45 +
latentnet-2.2/latentnet/man/as.mcmc.list.ergmm.Rd | 2
latentnet-2.2/latentnet/man/davis.Rd | 16
latentnet-2.2/latentnet/man/ergmm.Rd | 37 -
latentnet-2.2/latentnet/man/ergmm.control.Rd | 27 -
latentnet-2.2/latentnet/man/ergmm.object.Rd | 59 +-
latentnet-2.2/latentnet/man/ergmm.par.list.object.Rd | 44 +
latentnet-2.2/latentnet/man/ergmm.prior.Rd | 4
latentnet-2.2/latentnet/man/latentnet-internal.Rd | 31 +
latentnet-2.2/latentnet/man/latentnet.Rd | 36 -
latentnet-2.2/latentnet/man/mcmc.diagnostics.ergmm.Rd | 2
latentnet-2.2/latentnet/man/merge.ergmm.Rd |only
latentnet-2.2/latentnet/man/plot.ergmm.Rd | 86 ++-
latentnet-2.2/latentnet/man/predict.ergmm.Rd | 2
latentnet-2.2/latentnet/man/simulate.ergmm.Rd | 8
latentnet-2.2/latentnet/man/summary.ergmm.Rd | 11
latentnet-2.2/latentnet/man/terms.ergmm.Rd | 83 +++
latentnet-2.2/latentnet/man/tribes.Rd | 16
latentnet-2.2/latentnet/src/ergmm_probs.c | 85 +++
latentnet-2.2/latentnet/src/ergmm_probs.h | 5
latentnet-2.2/latentnet/src/ergmm_sampler.c | 136 +++++
latentnet-2.2/latentnet/src/ergmm_sampler.h | 38 +
latentnet-2.2/latentnet/src/ergmm_structs.h | 18
latentnet-2.2/latentnet/src/ergmm_updaters.c | 149 +++++-
latentnet-2.2/latentnet/src/ergmm_updaters.h | 7
latentnet-2.2/latentnet/src/ergmm_utils.c | 27 +
latentnet-2.2/latentnet/src/ergmm_utils.h | 2
latentnet-2.2/latentnet/src/kl_switch.c |only
latentnet-2.2/latentnet/src/kl_switch.h |only
latentnet-2.2/latentnet/src/matrix_utils.c | 45 +
latentnet-2.2/latentnet/src/matrix_utils.h | 2
latentnet-2.2/latentnet/src/mbc_sampler.c | 20
latentnet-2.2/latentnet/src/post_predict.c |only
latentnet-2.2/latentnet/src/post_predict.h |only
latentnet-2.2/latentnet/src/procrustes.c |only
latentnet-2.2/latentnet/src/procrustes.h |only
latentnet-2.2/latentnet/tests/nolatent.R | 20
latentnet-2.2/latentnet/tests/nomixing.R | 2
latentnet-2.2/latentnet/tests/onlymcmc.R | 2
latentnet-2.2/latentnet/tests/plots.R | 23
80 files changed, 2439 insertions(+), 1069 deletions(-)
Author: Klaus Schliep & Klaus Hechenbichler
Title: Weighted k-Nearest Neighbors
Description: Weighted k-Nearest Neighbors Classification and Regression
Diff between kknn versions 1.0-6 dated 2008-07-20 and 1.0-7 dated 2009-07-18
DESCRIPTION | 22 ++++++++++++---------- man/kknn.Rd | 2 +- man/train.kknn.Rd | 2 +- src/dm.c | 2 +- 4 files changed, 15 insertions(+), 13 deletions(-)
Author: Original S functions by Stuart Coles, R port and R
documentation files by Alec Stephenson.
Title: An Introduction to Statistical Modeling of Extreme Values
Description: Functions to support the computations carried out in `An
Introduction to Statistical Modeling of Extreme Values' by
Stuart Coles. The functions may be divided into the following
groups; maxima/minima, order statistics, peaks over thresholds
and point processes.
Diff between ismev versions 1.33 dated 2009-05-13 and 1.34 dated 2009-07-18
DESCRIPTION | 8 ++++---- R/gev.R | 36 ++++++++++++++++++++++++++++++++---- R/gpd.R | 32 ++++++++++++++++++++++++++++---- man/ismev-internal.Rd | 3 +++ 4 files changed, 67 insertions(+), 12 deletions(-)
Author: Richard Bourgon
Diff between intervals versions 0.12.2 dated 2009-06-28 and 0.13.0 dated 2009-07-18
Title: Tools for working with points and intervals
Description: Tools for working with and comparing sets of points and
intervals.
DESCRIPTION | 10
NAMESPACE | 5
NEWS | 11
R/as.matrix.R |only
R/interval_included-methods.R |only
inst/doc/intervals_overview.pdf | 549 ++++++++++++++----------------
man/Intervals_virtual-class.Rd | 5
man/Intervals_virtual_or_numeric-class.Rd | 8
man/as.matrix.Intervals.Rd |only
man/interval_included-methods.Rd |only
man/intervals-package.Rd | 3
11 files changed, 301 insertions(+), 290 deletions(-)
Author: Sebastien Dejean, Ignacio Gonzalez and Kim-Anh Le Cao
Title: Integrate Omics data project
Description: The package supplies two efficients methodologies:
regularized CCA and sparse PLS to unravel relationships between
two heterogeneous data sets of size (nxp) and (nxq) where the p
and q variables are measured on the same samples or individuals
n. These data may come from high throughput technologies, such
as omics data (e.g. transcriptomics, metabolomics or proteomics
data) that require an integrative or joint analysis. However,
integrOmics can also be applied to any other large data sets
where p+q>>n. rCCA is a regularized version of CCA to deal with
the large number of variables. sPLS allows variable selection
in a one step procedure and two frameworks are proposed:
regression and canonical analysis. Numerous graphical outputs
are provided to help interpreting the results.
Diff between integrOmics versions 2.1 dated 2009-06-26 and 2.3 dated 2009-07-18
integrOmics-2.1/integrOmics/R/rccNet.R |only integrOmics-2.1/integrOmics/man/rccNet.Rd |only integrOmics-2.3/integrOmics/DESCRIPTION | 26 +-- integrOmics-2.3/integrOmics/NAMESPACE | 72 +++++----- integrOmics-2.3/integrOmics/R/network.rcc.R |only integrOmics-2.3/integrOmics/R/network.spls.R |only integrOmics-2.3/integrOmics/R/predict.R | 182 +++++++++++++-------------- integrOmics-2.3/integrOmics/man/network.Rd |only integrOmics-2.3/integrOmics/man/predict.Rd | 1 9 files changed, 142 insertions(+), 139 deletions(-)
Author: Rense Nieuwenhuis, Ben Pelzer, Manfred te Grotenhuis
Title: Tools for detecting influential data in mixed effects models
Description: influence.ME provides a collection of tools for
calculating measures of influential data for mixed effects
models. It analyses models that were estimated using lme4. The
basic rationale behind identifying influential data is that
when iteratively single units are omitted from the data, models
based on these data should not produce substantially different
estimates. To standardize the assessment of how influential a
(single group of) observation(s) is, several measures of
influence are common practice. First, DFBETAS is a standardized
measure of the absolute difference between the estimate with a
particular case included and the estimate without that
particular case. Second, Cook's distance provides an overall
measurement of the change in all parameter estimates, or a
selection thereof.
Diff between influence.ME versions 0.6.1 dated 2009-04-27 and 0.7 dated 2009-07-18
DESCRIPTION | 15 ++++++++------- R/dp.ME.cook.R | 17 ++++++----------- R/estex.R | 6 +++--- R/exclude.influence.R | 12 +++++++++++- man/ME.cook.Rd | 4 ++-- man/ME.dfbetas.Rd | 4 ++-- man/ME.pchange.Rd | 22 +++++++++++----------- man/dp.ME.cook.Rd | 6 +++--- man/dp.ME.pchange.Rd | 2 +- man/estex.Rd | 10 +++++++--- man/exclude.influence.Rd | 8 ++++++-- man/grouping.levels.Rd | 3 --- man/influence.ME-package.Rd | 16 ++++++++-------- 13 files changed, 68 insertions(+), 57 deletions(-)
Author: Edzer J. Pebesma
Diff between gstat versions 0.9-61 dated 2009-07-02 and 0.9-62 dated 2009-07-18
Title: geostatistical modelling, prediction and simulation
Description: variogram modelling; simple, ordinary and universal point
or block (co)kriging, sequential Gaussian or indicator
(co)simulation; variogram and variogram map plotting utility
functions.
DESCRIPTION | 8
R/krigeTg.R | 6
inst/doc/gstat.pdf |29387 +++++++++++++++++++++++++++--------------------------
man/krigeTg.Rd | 11
man/pcb.Rd | 2
5 files changed, 15134 insertions(+), 14280 deletions(-)
Author: Brian Lee Yung Rowe
Title: Futile function utilities
Description: A collection of utility functions to expedite software
development
Diff between futile versions 1.0.2 dated 2009-05-28 and 1.1.1 dated 2009-07-18
futile-1.0.2/futile/R/logLevel.R |only futile-1.0.2/futile/man/logLevel.Rd |only futile-1.1.1/futile/DESCRIPTION | 9 +++++---- futile-1.1.1/futile/NAMESPACE |only futile-1.1.1/futile/R/aptions.R |only futile-1.1.1/futile/R/general.R | 14 ++++++++++++++ futile-1.1.1/futile/R/logger.R |only futile-1.1.1/futile/man/futile-package.Rd | 11 ++++++----- futile-1.1.1/futile/man/logger.Rd |only futile-1.1.1/futile/man/mid.Rd | 25 +++++++++++++++++++------ futile-1.1.1/futile/man/options.manager.Rd |only 11 files changed, 44 insertions(+), 15 deletions(-)
Author: Virasakdi Chongsuvivatwong
Diff between epicalc versions 2.9.0.2 dated 2009-06-25 and 2.9.1.2 dated 2009-07-18
Title: Epidemiological calculator
Description: Functions making R easy for epidemiological calculation.
DESCRIPTION | 8 +++---
R/epicalc.R | 65 ++++++++++++++++++++++++++++++++++--------------------
data/Xerop.rdata |only
man/Xerop.rd |only
man/lagVar.rd | 18 +++++++++-----
man/markVisits.rd | 4 ++-
6 files changed, 61 insertions(+), 34 deletions(-)
Author: Kosuke Imai
Diff between eco versions 3.1-2 dated 2009-02-01 and 3.1-4 dated 2009-07-18
Title: R Package for Ecological Inference in 2x2 Tables
Description: eco is a publicly available R package that implements the
Bayesian and likelihood methods proposed in Imai, Lu, and
Strauss (2008) for ecological inference in $2 \times 2$ tables
as well as the method of bounds introduced by Duncan and Davis
(1953). The package fits both parametric and nonparametric
models using either the Expectation-Maximization algorithms
(for likelihood models) or the Markov chain Monte Carlo
algorithms (for Bayesian models). For all models, the
individual-level data can be directly incorporated into the
estimation whenever such data are available. Along with
in-sample and out-of-sample predictions, the package also
provides a functionality which allows one to quantify the
effect of data aggregation on parameter estimation and
hypothesis testing under the parametric likelihood models.
DESCRIPTION | 42 ++++++++++++++++++++++--------------------
NAMESPACE | 3 ++-
R/Qfun.R |only
man/Qfun.Rd |only
man/eco.Rd | 9 ++++++---
man/ecoML.Rd | 9 ++++++---
man/ecoNP.Rd | 9 ++++++---
man/summary.eco.Rd | 6 ++++--
man/summary.ecoML.Rd | 7 +++++--
man/summary.ecoNP.Rd | 6 ++++--
10 files changed, 55 insertions(+), 36 deletions(-)
Author: Christian Ritz
Diff between drc versions 1.7-0 dated 2009-06-08 and 1.7-2 dated 2009-07-18
Title: Analysis of dose-response curves
Description: Analysis of one or multiple curves with focus on
concentration-response, dose-response and time-response curves
used, for example in biology, environmental sciences, medicine,
pharmacology, toxicology.
DESCRIPTION | 8 ++++----
NAMESPACE | 3 ++-
NEWS | 4 ++++
R/lin.test.R |only
R/mr.test.R |only
R/neill.test.R |only
data/etmotc.rda |only
man/CRS.4a.Rd | 1 +
man/etmotc.Rd |only
man/lin.test.Rd |only
man/mr.test.Rd |only
man/neill.test.Rd |only
man/plot.drc.Rd | 2 +-
13 files changed, 12 insertions(+), 6 deletions(-)
Author: Antonio Gasparrini and Ben Armstrong
Title: Distributed Lag Non-linear Models
Description: The package dlnm contains functions to specify basis and
cross-basis matrices in order to run distributed lag models and
their non-linear extension, then to predict and graph the
results for a fitted model.
Diff between dlnm versions 0.1.0 dated 2009-07-01 and 0.2.1 dated 2009-07-18
DESCRIPTION | 8 ++++---- R/crossbasis.R | 2 +- R/crossplot.R | 8 ++++++-- R/crosspred.R | 2 +- R/mkbasis.R | 24 ++++++++++++++++-------- R/mklagbasis.R | 2 +- inst/CITATION | 2 +- inst/dlnmChangeLog |only inst/doc |only man/crossbasis.Rd | 34 +++++++++++++++++++--------------- man/crossplot.Rd | 8 ++++++-- man/crosspred.Rd | 23 +++++++++++++---------- man/dlnm-internal.Rd | 4 +++- man/dlnm-package.Rd | 8 ++++++-- 14 files changed, 77 insertions(+), 48 deletions(-)
Author: Ingmar Visser
Diff between depmix versions 0.9.4 dated 2008-08-07 and 0.9.6 dated 2009-07-18
Title: Dependent Mixture Models
Description: Fit (multigroup) mixtures of latent Markov models on mixed
categorical and continuous (timeseries) data
CHANGES | 15 +
DESCRIPTION | 15 -
R/depmix-internal.R | 454 ++++++++++++++++++++++++++++++++++
R/depmix.R | 36 +-
R/generate.R | 56 ++++
R/lca.R | 60 ++++
R/markovdata.R | 109 ++++++++
R/mgdmm.R | 217 ++++++++++++++++
R/mixdmm.R | 182 +++++++++++++
README | 76 ++---
man/depmix-internal.Rd | 144 +++++-----
man/discrimination.Rd | 66 ++---
man/dmm.Rd | 506 +++++++++++++++++++-------------------
man/fitdmm.Rd | 644 ++++++++++++++++++++++++-------------------------
man/generate.Rd | 146 +++++------
man/mgdmm.Rd | 210 +++++++--------
man/mixdmm.Rd | 224 ++++++++---------
man/speed.Rd | 60 ++--
18 files changed, 2152 insertions(+), 1068 deletions(-)
Author: Jun Yan
Diff between copula versions 0.8-7 dated 2009-06-10 and 0.8-8 dated 2009-07-18
Title: Multivariate dependence with copulas
Description: Classes (S4) of commonly used copulas including elliptical
(normal and t), Archimedean (Clayton, Gumbel, Frank, and
Ali-Mikhail-Haq), extreme value (Gumbel, Husler-Reiss,
Galambos, and t-EV), and other families (Plackett and
Farlie-Gumbel-Morgenstern). Methods for density, distribution,
random number generation, bivariate dependence measures,
perspective and contour plots. Functions for fitting copula
models with variance estimate. Independence tests among random
variables and random vectors. Serial independence tests for
univariate and multivariate continuous time series.
Goodness-of-fit tests for copulas based on multipliers and on
the parametric bootstrap.
DESCRIPTION | 16 ++++++-------
NAMESPACE | 5 ++++
R/Classes.R | 21 +++++++++++++++++
R/Copula.R | 21 +++++++++++++++++
R/E.R | 2 -
R/amhCopula.R | 2 -
R/archmCopula.R | 21 +++++++++++++++++
R/asymCopula.R | 34 +++++++++++++++++++++++++---
R/claytonCopula.R | 3 --
R/debye.R | 2 -
R/derCdfPdf.R | 3 --
R/ellipCopula.R | 21 +++++++++++++++++
R/evTests.R | 2 +
R/fgmCopula.R | 2 -
R/fitCopula.R | 12 +++++-----
R/fitMvdc.R | 21 +++++++++++++++++
R/frankCopula.R | 4 +--
R/galambosCopula.R | 2 -
R/galambosExpr-math.R | 2 -
R/gofTests.R | 43 ++++++++++++++++++++++--------------
R/graphics.R | 2 -
R/gumbelCopula.R | 2 -
R/huslerReissCopula.R | 9 +++----
R/indepCopula.R | 2 -
R/indepTests.R | 53 ++++++++++++++++++++++++++++++++++++---------
R/logseries.R | 2 -
R/mvdc.R | 3 --
R/normalCopula.R | 2 -
R/plackettCopula.R | 2 -
R/skewNormalCopula.R | 2 -
R/stable.R | 2 -
R/sysdata.rda |binary
R/tCopula.R | 3 --
R/tevCopula.R | 15 +++++++++++-
data |only
man/indepTest.Rd | 17 ++++++++------
man/loss.Rd |only
man/multIndepTest.Rd | 10 +++++---
man/multSerialIndepTest.Rd | 10 +++++---
man/rdj.Rd |only
man/serialIndepTest.Rd | 9 +++++--
man/uranium.Rd |only
src/empcop.stat.c | 2 -
src/empcop.stat.h | 2 -
src/empcopm.test.c | 9 ++++---
src/empcops.test.c | 8 +++---
src/empcopsm.test.c | 9 ++++---
src/empcopu.test.c | 7 ++---
src/evtest.c | 10 ++------
src/fgm.c | 2 -
src/set.utils.c | 2 -
src/set.utils.h | 2 -
52 files changed, 318 insertions(+), 119 deletions(-)
Author: Max Kuhn, contributions from Steve Weston, Jed Wing and James
Forester
Title: A collection of contrast methods
Description: Contrast methods, in the style of the Design package, for
fit objects produced by the lm, glm, gls, and geese functions.
Diff between contrast versions 0.9 dated 2009-01-26 and 0.10 dated 2009-07-18
DESCRIPTION | 15 +++++++++------ R/gets.R | 3 ++- inst/CHANGES |only inst/doc/contrast.pdf |binary 4 files changed, 11 insertions(+), 7 deletions(-)
Author: Venkatraman E. Seshan
Title: Clinical Trial Design and Data Analysis Functions
Description: Utilities to make your clinical collaborations easier if
not fun.
Diff between clinfun versions 0.8.4 dated 2008-12-04 and 0.8.5 dated 2009-07-18
CHANGES | 6 ++++++ DESCRIPTION | 13 ++++++++----- R/jonkheere.R | 13 ++++++++----- man/permtests.Rd | 5 ++++- 4 files changed, 26 insertions(+), 11 deletions(-)
Author: Daniel Samarov
Diff between calib versions 2.0.0 dated 2009-01-28 and 2.0.1 dated 2009-07-18
Title: Statistical tool for calibration of plate based bioassays
Description: Provides basic S4 data structures and routines for
calibration of bioassays
DESCRIPTION | 33 ++--
R/calibfit-accessors.R | 2
R/calibfit-diagnosticFunctions.R | 277 ++++++++-------------------------------
R/calibfit-functions.R | 10 -
inst/doc/HowTo-calib.pdf |binary
inst/doc/Rplots.pdf | 252 +++++++++++++++++------------------
6 files changed, 212 insertions(+), 362 deletions(-)
Author: Christian Zang
Title: Bootstrapped Response and Correlation Functions
Description: Calculation of Bootstrapped Response and Correlation
Functions for Use in Dendroclimatology
Diff between bootRes versions 0.1 dated 2009-06-24 and 0.2 dated 2009-07-18
Changelog |only DESCRIPTION | 8 ++++---- R/bcf.R | 13 +++++++++---- R/brf.R | 14 +++++++++----- R/dcplot.R | 39 ++++++++++++++++++++++++++++++++------- R/dendroclim.R | 8 ++++---- R/pmat.R | 33 +++++++++++++++++++++------------ man/dcplot.Rd | 3 +++ man/dendroclim.Rd | 12 +++++++++--- 9 files changed, 91 insertions(+), 39 deletions(-)
Author: Lester L. Yuan
Title: Compute biological inferences
Description: Imports benthic count data, reformats this data, and
computes environmental inferences from this data.
Diff between bio.infer versions 1.2-3 dated 2009-03-06 and 1.2-4 dated 2009-07-18
DESCRIPTION | 29 ++++++++++++++++------------- R/trait.stat.R | 4 ++-- chm |only 3 files changed, 18 insertions(+), 15 deletions(-)
Author: Michael J. Kane and John W. Emerson
Title: Manage massive matrices in R using C++, with support for shared
memory and memory-mapped files.
Description: Use C++ to create, store, access, and manipulate massive
matrices. Matrices may optionally be allocated to shared
memory and/or may use memory-mapped files.
Diff between bigmemory versions 3.9 dated 2009-06-24 and 3.10 dated 2009-07-18
COPYING |only DESCRIPTION | 8 NAMESPACE |only R/bigmatrixLib.R | 133 ---- R/bigmemoryAnalytics.R |only configure |only configure.Rout | 2 include/boost/array.hpp |only include/boost/cstdint.hpp |only include/boost/detail |only include/boost/exception |only include/boost/interprocess |only include/boost/io_fwd.hpp |only include/boost/mpl/O1_size.hpp |only include/boost/mpl/advance.hpp |only include/boost/mpl/advance_fwd.hpp |only include/boost/mpl/alias.hpp |only include/boost/mpl/always.hpp |only include/boost/mpl/and.hpp |only include/boost/mpl/apply.hpp |only include/boost/mpl/apply_wrap.hpp |only include/boost/mpl/arg_fwd.hpp |only include/boost/mpl/arithmetic.hpp |only include/boost/mpl/at.hpp |only include/boost/mpl/at_fwd.hpp |only include/boost/mpl/aux_/O1_size_impl.hpp |only include/boost/mpl/aux_/adl_barrier.hpp |only include/boost/mpl/aux_/advance_backward.hpp |only include/boost/mpl/aux_/advance_forward.hpp |only include/boost/mpl/aux_/apply_1st.hpp |only include/boost/mpl/aux_/arg_typedef.hpp |only include/boost/mpl/aux_/arithmetic_op.hpp |only include/boost/mpl/aux_/arity.hpp |only include/boost/mpl/aux_/arity_spec.hpp |only include/boost/mpl/aux_/at_impl.hpp |only include/boost/mpl/aux_/back_impl.hpp |only include/boost/mpl/aux_/basic_bind.hpp |only include/boost/mpl/aux_/begin_end_impl.hpp |only include/boost/mpl/aux_/clear_impl.hpp |only include/boost/mpl/aux_/common_name_wknd.hpp |only include/boost/mpl/aux_/comparison_op.hpp |only include/boost/mpl/aux_/config |only include/boost/mpl/aux_/contains_impl.hpp |only include/boost/mpl/aux_/count_args.hpp |only include/boost/mpl/aux_/count_impl.hpp |only include/boost/mpl/aux_/empty_impl.hpp |only include/boost/mpl/aux_/erase_impl.hpp |only include/boost/mpl/aux_/erase_key_impl.hpp |only include/boost/mpl/aux_/filter_iter.hpp |only include/boost/mpl/aux_/find_if_pred.hpp |only include/boost/mpl/aux_/fold_impl.hpp |only include/boost/mpl/aux_/fold_impl_body.hpp |only include/boost/mpl/aux_/fold_op.hpp |only include/boost/mpl/aux_/fold_pred.hpp |only include/boost/mpl/aux_/front_impl.hpp |only include/boost/mpl/aux_/full_lambda.hpp |only include/boost/mpl/aux_/has_apply.hpp |only include/boost/mpl/aux_/has_begin.hpp |only include/boost/mpl/aux_/has_key_impl.hpp |only include/boost/mpl/aux_/has_rebind.hpp |only include/boost/mpl/aux_/has_size.hpp |only include/boost/mpl/aux_/has_tag.hpp |only include/boost/mpl/aux_/has_type.hpp |only include/boost/mpl/aux_/include_preprocessed.hpp |only include/boost/mpl/aux_/insert_impl.hpp |only include/boost/mpl/aux_/insert_range_impl.hpp |only include/boost/mpl/aux_/inserter_algorithm.hpp |only include/boost/mpl/aux_/integral_wrapper.hpp |only include/boost/mpl/aux_/is_msvc_eti_arg.hpp |only include/boost/mpl/aux_/iter_apply.hpp |only include/boost/mpl/aux_/iter_fold_if_impl.hpp |only include/boost/mpl/aux_/iter_fold_impl.hpp |only include/boost/mpl/aux_/iter_push_front.hpp |only include/boost/mpl/aux_/joint_iter.hpp |only include/boost/mpl/aux_/lambda_arity_param.hpp |only include/boost/mpl/aux_/lambda_no_ctps.hpp |only include/boost/mpl/aux_/lambda_spec.hpp |only include/boost/mpl/aux_/lambda_support.hpp |only include/boost/mpl/aux_/largest_int.hpp |only include/boost/mpl/aux_/logical_op.hpp |only include/boost/mpl/aux_/msvc_dtw.hpp |only include/boost/mpl/aux_/msvc_eti_base.hpp |only include/boost/mpl/aux_/msvc_is_class.hpp |only include/boost/mpl/aux_/msvc_never_true.hpp |only include/boost/mpl/aux_/msvc_type.hpp |only include/boost/mpl/aux_/na.hpp |only include/boost/mpl/aux_/na_assert.hpp |only include/boost/mpl/aux_/na_fwd.hpp |only include/boost/mpl/aux_/na_spec.hpp |only include/boost/mpl/aux_/nested_type_wknd.hpp |only include/boost/mpl/aux_/nttp_decl.hpp |only include/boost/mpl/aux_/numeric_cast_utils.hpp |only include/boost/mpl/aux_/numeric_op.hpp |only include/boost/mpl/aux_/order_impl.hpp |only include/boost/mpl/aux_/overload_names.hpp |only include/boost/mpl/aux_/partition_op.hpp |only include/boost/mpl/aux_/pop_back_impl.hpp |only include/boost/mpl/aux_/pop_front_impl.hpp |only include/boost/mpl/aux_/preprocessed/bcc |only include/boost/mpl/aux_/preprocessed/bcc551 |only include/boost/mpl/aux_/preprocessed/dmc |only include/boost/mpl/aux_/preprocessed/gcc |only include/boost/mpl/aux_/preprocessed/mwcw |only include/boost/mpl/aux_/preprocessed/no_ttp/advance_backward.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/advance_forward.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/and.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/apply.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/apply_wrap.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/basic_bind.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/bind_fwd.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/bitor.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/deque.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/divides.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/equal_to.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/fold_impl.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/full_lambda.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/greater.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/greater_equal.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/inherit.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/iter_fold_impl.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/lambda_no_ctps.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/less.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/list.hpp | 285 +++++++++- include/boost/mpl/aux_/preprocessed/no_ttp/list_c.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/map.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/modulus.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/not_equal_to.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/plus.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/quote.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/reverse_fold_impl.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/set.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/set_c.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/shift_right.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/template_arity.hpp |only include/boost/mpl/aux_/preprocessed/no_ttp/vector.hpp |only include/boost/mpl/aux_/preprocessor |only include/boost/mpl/aux_/ptr_to_ref.hpp |only include/boost/mpl/aux_/push_back_impl.hpp |only include/boost/mpl/aux_/push_front_impl.hpp |only include/boost/mpl/aux_/range_c |only include/boost/mpl/aux_/reverse_fold_impl.hpp |only include/boost/mpl/aux_/reverse_fold_impl_body.hpp |only include/boost/mpl/aux_/reverse_iter_fold_impl.hpp |only include/boost/mpl/aux_/sequence_wrapper.hpp |only include/boost/mpl/aux_/shift_op.hpp |only include/boost/mpl/aux_/single_element_iter.hpp |only include/boost/mpl/aux_/size_impl.hpp |only include/boost/mpl/aux_/sort_impl.hpp |only include/boost/mpl/aux_/static_cast.hpp |only include/boost/mpl/aux_/template_arity.hpp |only include/boost/mpl/aux_/template_arity_fwd.hpp |only include/boost/mpl/aux_/test |only include/boost/mpl/aux_/test.hpp |only include/boost/mpl/aux_/traits_lambda_spec.hpp |only include/boost/mpl/aux_/transform_iter.hpp |only include/boost/mpl/aux_/type_wrapper.hpp |only include/boost/mpl/aux_/unwrap.hpp |only include/boost/mpl/aux_/value_wknd.hpp |only include/boost/mpl/aux_/yes_no.hpp |only include/boost/mpl/back.hpp |only include/boost/mpl/back_fwd.hpp |only include/boost/mpl/begin.hpp |only include/boost/mpl/begin_end.hpp |only include/boost/mpl/begin_end_fwd.hpp |only include/boost/mpl/bind_fwd.hpp |only include/boost/mpl/bitand.hpp |only include/boost/mpl/bitor.hpp |only include/boost/mpl/bitwise.hpp |only include/boost/mpl/bool_fwd.hpp |only include/boost/mpl/clear.hpp |only include/boost/mpl/clear_fwd.hpp |only include/boost/mpl/comparison.hpp |only include/boost/mpl/contains.hpp |only include/boost/mpl/contains_fwd.hpp |only include/boost/mpl/copy.hpp |only include/boost/mpl/copy_if.hpp |only include/boost/mpl/count.hpp |only include/boost/mpl/count_fwd.hpp |only include/boost/mpl/count_if.hpp |only include/boost/mpl/deque.hpp |only include/boost/mpl/distance.hpp |only include/boost/mpl/distance_fwd.hpp |only include/boost/mpl/divides.hpp |only include/boost/mpl/empty.hpp |only include/boost/mpl/empty_base.hpp |only include/boost/mpl/empty_fwd.hpp |only include/boost/mpl/end.hpp |only include/boost/mpl/equal.hpp |only include/boost/mpl/equal_to.hpp |only include/boost/mpl/erase.hpp |only include/boost/mpl/erase_key.hpp |only include/boost/mpl/find.hpp |only include/boost/mpl/find_if.hpp |only include/boost/mpl/fold.hpp |only include/boost/mpl/for_each.hpp |only include/boost/mpl/front.hpp |only include/boost/mpl/front_fwd.hpp |only include/boost/mpl/front_inserter.hpp |only include/boost/mpl/greater.hpp |only include/boost/mpl/greater_equal.hpp |only include/boost/mpl/has_key.hpp |only include/boost/mpl/has_key_fwd.hpp |only include/boost/mpl/if.hpp |only include/boost/mpl/index_if.hpp |only include/boost/mpl/index_of.hpp |only include/boost/mpl/inherit.hpp |only include/boost/mpl/insert.hpp |only include/boost/mpl/insert_fwd.hpp |only include/boost/mpl/insert_range.hpp |only include/boost/mpl/inserter.hpp |only include/boost/mpl/integral_c.hpp |only include/boost/mpl/integral_c_fwd.hpp |only include/boost/mpl/is_placeholder.hpp |only include/boost/mpl/is_sequence.hpp |only include/boost/mpl/iter_fold.hpp |only include/boost/mpl/iter_fold_if.hpp |only include/boost/mpl/iterator_category.hpp |only include/boost/mpl/iterator_range.hpp |only include/boost/mpl/iterator_tags.hpp |only include/boost/mpl/key_type.hpp |only include/boost/mpl/key_type_fwd.hpp |only include/boost/mpl/lambda.hpp |only include/boost/mpl/lambda_fwd.hpp |only include/boost/mpl/less.hpp |only include/boost/mpl/limits |only include/boost/mpl/list |only include/boost/mpl/list.hpp |only include/boost/mpl/list_c.hpp |only include/boost/mpl/logical.hpp |only include/boost/mpl/long.hpp |only include/boost/mpl/long_fwd.hpp |only include/boost/mpl/map |only include/boost/mpl/map.hpp |only include/boost/mpl/max.hpp |only include/boost/mpl/min.hpp |only include/boost/mpl/min_element.hpp |only include/boost/mpl/min_max.hpp |only include/boost/mpl/modulus.hpp |only include/boost/mpl/multiplies.hpp |only include/boost/mpl/multiset |only include/boost/mpl/next_prior.hpp |only include/boost/mpl/not.hpp |only include/boost/mpl/not_equal_to.hpp |only include/boost/mpl/numeric_cast.hpp |only include/boost/mpl/order.hpp |only include/boost/mpl/pair.hpp |only include/boost/mpl/partition.hpp |only include/boost/mpl/plus.hpp |only include/boost/mpl/pop_front.hpp |only include/boost/mpl/pop_front_fwd.hpp |only include/boost/mpl/print.hpp |only include/boost/mpl/push_back.hpp |only include/boost/mpl/push_back_fwd.hpp |only include/boost/mpl/push_front_fwd.hpp |only include/boost/mpl/quote.hpp |only include/boost/mpl/range_c.hpp |only include/boost/mpl/remove.hpp |only include/boost/mpl/replace.hpp |only include/boost/mpl/replace_if.hpp |only include/boost/mpl/reverse.hpp |only include/boost/mpl/reverse_fold.hpp |only include/boost/mpl/reverse_iter_fold.hpp |only include/boost/mpl/set |only include/boost/mpl/set.hpp |only include/boost/mpl/set_c.hpp |only include/boost/mpl/shift_right.hpp |only include/boost/mpl/size_t_fwd.hpp |only include/boost/mpl/sizeof.hpp |only include/boost/mpl/stable_partition.hpp |only include/boost/mpl/transform.hpp |only include/boost/mpl/transform_view.hpp |only include/boost/mpl/unique.hpp |only include/boost/mpl/upper_bound.hpp |only include/boost/mpl/value_type.hpp |only include/boost/mpl/value_type_fwd.hpp |only include/boost/mpl/vector |only include/boost/mpl/vector.hpp |only include/boost/mpl/void.hpp |only include/boost/mpl/void_fwd.hpp |only include/boost/noncopyable.hpp |only include/boost/numeric |only include/boost/random |only include/boost/shared_ptr.hpp |only include/boost/static_assert.hpp |only include/boost/throw_exception.hpp |only include/boost/type_traits |only include/boost/uuid |only include/boost/uuid.hpp |only man/biglm.big.matrix.Rd | 24 man/bigmemory-package.Rd | 4 290 files changed, 302 insertions(+), 154 deletions(-)
Author: Paul Hiemstra
Diff between automap versions 1.0-0 dated 2009-03-19 and 1.0-2 dated 2009-07-18
Title: Automatic interpolation package
Description: This package performs an automatic interpolation by
automatically estimating the variogram and then calling gstat.
DESCRIPTION | 8 ++--
R/autoKrige.cv.r | 2 -
R/autoKrige.r | 20 +++++++++--
R/autofitVariogram.r | 2 -
R/plot.posPredictionInterval.r | 3 -
R/summary.autoKrige.r | 2 +
R/summary.autofitVariogram.r | 2 +
README | 6 ++-
SvnLog | 72 +++++++++++++++++++++++++++++++++++++++++
inst/CITATION | 2 -
man/autoKrige.rd | 22 ++++++++++--
man/autofitVariogram.rd | 5 +-
tests/autoKrige.cv.Rout.save | 46 ++++++++++++++++++--------
tests/automap.Rout.save | 8 +++-
14 files changed, 164 insertions(+), 36 deletions(-)
Author: Beatriz Pateiro-Lopez, Alberto Rodriguez-Casal.
Title: Generalization of the convex hull of a sample of points in the
plane
Description: This package computes the alpha-shape and alpha-convex
hull of a given sample of points in the plane. The concepts of
alpha-shape and alpha-convex hull generalize the definition of
the convex hull of a finite set of points. The programming is
based on the duality between the Voronoi diagram and Delaunay
triangulation. The package also includes a function that
returns the Delaunay mesh of a given sample of points and its
dual Voronoi diagram in one single object.
Diff between alphahull versions 0.1 dated 2009-03-28 and 0.1-1 dated 2009-07-18
alphahull-0.1-1/alphahull/DESCRIPTION | 10 alphahull-0.1-1/alphahull/R/ahull.R | 373 ++++++++++----------- alphahull-0.1-1/alphahull/R/anglesArc.R | 15 alphahull-0.1-1/alphahull/R/arc.R | 10 alphahull-0.1-1/alphahull/R/ashape.R | 154 +++----- alphahull-0.1-1/alphahull/R/complement.R | 353 +++++++++---------- alphahull-0.1-1/alphahull/R/delvor.R | 107 +++--- alphahull-0.1-1/alphahull/R/dummycoor.R | 42 +- alphahull-0.1-1/alphahull/R/inahull.R | 117 +++--- alphahull-0.1-1/alphahull/R/inter.R | 82 ++-- alphahull-0.1-1/alphahull/R/koch.R |only alphahull-0.1-1/alphahull/R/lengthahull.R | 16 alphahull-0.1-1/alphahull/R/plot.ahull.R | 134 +++---- alphahull-0.1-1/alphahull/R/plot.ashape.R | 112 +++--- alphahull-0.1-1/alphahull/R/plot.delvor.R | 98 ++--- alphahull-0.1-1/alphahull/R/rkoch.R |only alphahull-0.1-1/alphahull/R/rotation.R | 19 - alphahull-0.1-1/alphahull/R/tricircum.R | 42 -- alphahull-0.1-1/alphahull/inst |only alphahull-0.1-1/alphahull/man/ahull.Rd | 16 alphahull-0.1-1/alphahull/man/alphahull-package.Rd | 6 alphahull-0.1-1/alphahull/man/anglesArc.Rd | 4 alphahull-0.1-1/alphahull/man/arc.Rd | 8 alphahull-0.1-1/alphahull/man/ashape.Rd | 31 - alphahull-0.1-1/alphahull/man/complement.Rd | 6 alphahull-0.1-1/alphahull/man/delvor.Rd | 6 alphahull-0.1-1/alphahull/man/inahull.Rd | 10 alphahull-0.1-1/alphahull/man/koch.Rd |only alphahull-0.1-1/alphahull/man/lengthahull.Rd | 6 alphahull-0.1-1/alphahull/man/plot.ahull.Rd | 21 - alphahull-0.1-1/alphahull/man/plot.ashape.Rd | 38 +- alphahull-0.1-1/alphahull/man/plot.delvor.Rd | 4 alphahull-0.1-1/alphahull/man/rkoch.Rd |only alphahull-0.1-1/alphahull/man/rotation.Rd | 2 alphahull-0.1-1/alphahull/man/tricircum.Rd | 6 alphahull-0.1/alphahull/Read-and-delete-me |only 36 files changed, 909 insertions(+), 939 deletions(-)
Author: Juan R González, Lluís Armengol, Elisabet Guinó, Xavier Solé,
and Víctor Moreno
Title: SNPs-based whole genome association studies
Description: This package carries out most common analysis when
performing whole genome association studies. These analyses
include descriptive statistics and exploratory analysis of
missing values, calculation of Hardy-Weinberg equilibrium,
analysis of association based on generalized linear models
(either for quantitative or binary traits), and analysis of
multiple SNPs (haplotype and epistasis analysis). Permutation
test and related tests (sum statistic and truncated product)
are also implemented.
Diff between SNPassoc versions 1.5-8 dated 2009-03-09 and 1.6-0 dated 2009-07-18
DESCRIPTION | 36 +++++++++---- R/GenomicControl.R | 40 ++++++--------- R/intervals.haplo.glm.R | 124 +++++++++++++++++++++++++----------------------- R/plot.WGassociation.R | 79 +++++++++++++++++------------- R/z[.WGassociation.R | 6 +- inst/docs/changelog.txt | 10 +++ man/GenomicControl.Rd | 2 src/SNPassoc.f | 25 +++++---- 8 files changed, 182 insertions(+), 140 deletions(-)
Author: Markus Loecher, Sense Networks
Title: Overlays on Google map tiles in R
Description: This package serves two purposes: (i) Provide a
comfortable R interface to query the Google server for static
maps, and (ii) Use the map as a background image to overlay
plots within R. This requires proper coordinate scaling. NOTE:
To do anything but downloading static map tiles, RgoogleMaps
needs EITHER rgdal OR ReadImages installed ! Such an OR
dependency is difficult to express in the Depends field, so I
moved both packages to suggested. rgdal is your package if you
prefer png file format and ReadImages if you prefer jpg format.
In the latter case, you will also need the libjpeg library
installed.
Diff between RgoogleMaps versions 1.1.3 dated 2009-06-18 and 1.1.4 dated 2009-07-18
DESCRIPTION | 21 ++++++++++++++------- inst/doc/RgoogleMaps-intro.pdf |binary man/RgoogleMaps-package.Rd | 8 ++++---- 3 files changed, 18 insertions(+), 11 deletions(-)
Author: Hector Corrada Bravo, with contributions from Stefan Theussl
Title: R interface to CPLEX
Description: R interface to CPLEX solvers for linear, quadratic, and
(linear and quadratic) mixed integer programs. A working
installation of CPLEX is required for usage of the Rcplex
package. See the file "INSTALL" for details on how to install
the Rcplex package in Linux/Unix-like systems and Windows
systems. Support for sparse matrices is provided by an S3-style
class "simple_triplet_matrix" from package slam and by objects
from the Matrix package class hierarchy.
Diff between Rcplex versions 0.2-1 dated 2008-10-16 and 0.2-2 dated 2009-07-18
Rcplex-0.2-1/Rcplex/R/sparse.R |only Rcplex-0.2-1/Rcplex/man/simple_triplet_matrix.Rd |only Rcplex-0.2-2/Rcplex/DESCRIPTION | 21 ++++++++++++++++----- Rcplex-0.2-2/Rcplex/NAMESPACE | 11 +---------- Rcplex-0.2-2/Rcplex/R/Rcplex.R | 2 +- Rcplex-0.2-2/Rcplex/inst/INSTALL | 12 ++++++++++-- Rcplex-0.2-2/Rcplex/inst/NEWS | 2 ++ Rcplex-0.2-2/Rcplex/src/Rcplex_utils.c | 4 ++-- 8 files changed, 32 insertions(+), 20 deletions(-)
Author: Jake Bowers
Diff between RItools versions 0.1-7 dated 2009-06-25 and 0.1-8 dated 2009-07-18
Title: Randomization inference tools
Description: Tools for randomization inference.
ChangeLog | 19 ++++++++++++++++
DESCRIPTION | 8 +++---
R/harmonic.R | 2 -
R/plot.xbal.R | 2 +
R/xBalance.R | 2 -
R/xBalance.make.stratwts.R | 10 ++++++--
R/xBalanceEngine.R | 2 -
R/xtable.xbal.R | 3 --
ToDo | 6 -----
man/xtable.xbal.Rd | 44 ++++++++++---------------------------
tests/xBalanceTests.Rout.save | 49 +++++++++++++++++++++---------------------
11 files changed, 74 insertions(+), 73 deletions(-)
Author: Michael Lawrence
Diff between RGtk2 versions 2.12.13 dated 2009-06-14 and 2.12.15 dated 2009-07-18
Title: R bindings for Gtk 2.8.0 and above
Description: Facilities in the R language for programming graphical
interfaces using Gtk, the Gimp Tool Kit.
RGtk2-2.12.13/RGtk2/man/GtkPageSetupUnixDialog.Rd |only
RGtk2-2.12.13/RGtk2/man/GtkPrintJob.Rd |only
RGtk2-2.12.13/RGtk2/man/GtkPrintUnixDialog.Rd |only
RGtk2-2.12.13/RGtk2/man/GtkPrinter.Rd |only
RGtk2-2.12.15/RGtk2/DESCRIPTION | 6 ++---
RGtk2-2.12.15/RGtk2/R/gdkManuals.R | 2 -
RGtk2-2.12.15/RGtk2/demo/appWindow.R | 12 +++++++----
RGtk2-2.12.15/RGtk2/demo/iconView.R | 2 -
RGtk2-2.12.15/RGtk2/src/Rgtk.c | 2 +
RGtk2-2.12.15/RGtk2/src/conversion.c | 3 +-
RGtk2-2.12.15/RGtk2/src/gdkManuals.c | 2 -
RGtk2-2.12.15/RGtk2/src/gobject.c | 23 ++++++++++++++--------
RGtk2-2.12.15/RGtk2/src/gtkManuals.c | 19 +++++++++++-------
13 files changed, 45 insertions(+), 26 deletions(-)
Author: David Harte
Title: Time Dependent Point Process Modelling
Description: This package fits and analyses time dependent marked point
process models with an emphasis on earthquake modelling. For a
more detailed introduction to the package, see the topic
"PtProcess". A list of recent changes can be found in the topic
"Changes".
Diff between PtProcess versions 3.1-3 dated 2009-01-26 and 3.1-4 dated 2009-07-18
DESCRIPTION | 19 +++++++++++++------ man/Changes.Rd | 2 ++ man/Phuket.Rd | 4 +++- 3 files changed, 18 insertions(+), 7 deletions(-)
Author: Andrew D. Martin
Diff between MCMCpack versions 1.0-1 dated 2009-07-01 and 1.0-2 dated 2009-07-18
Title: Markov chain Monte Carlo (MCMC) Package
Description: This package contains functions to perform Bayesian
inference using posterior simulation for a number of
statistical models. Most simulation is done in compiled C++
written in the Scythe Statistical Library Version 1.0.2. All
models return coda mcmc objects that can then be summarized
using the coda package. MCMCpack also contains some useful
utility functions, including some additional density functions
and pseudo-random number generators for statistical
distributions, a general purpose Metropolis sampling algorithm,
and tools for visualization.
MCMCpack-1.0-1/MCMCpack/R/MCMCpoissonChangepoint.R |only
MCMCpack-1.0-1/MCMCpack/man/MCMCpoissonChangepoint.Rd |only
MCMCpack-1.0-1/MCMCpack/src/MCMCpoissonChangepoint.cc |only
MCMCpack-1.0-2/MCMCpack/DESCRIPTION | 8
MCMCpack-1.0-2/MCMCpack/HISTORY | 10
MCMCpack-1.0-2/MCMCpack/NAMESPACE | 3
MCMCpack-1.0-2/MCMCpack/R/MCMCbinaryChange.R |only
MCMCpack-1.0-2/MCMCpack/R/MCMCpoissonChange.R |only
MCMCpack-1.0-2/MCMCpack/R/btsutil.R | 308 +++++++++++-------
MCMCpack-1.0-2/MCMCpack/man/MCMCbinaryChange.Rd |only
MCMCpack-1.0-2/MCMCpack/man/MCMCpoissonChange.Rd |only
MCMCpack-1.0-2/MCMCpack/man/plotChangepoint.Rd | 14
MCMCpack-1.0-2/MCMCpack/man/plotState.Rd | 11
MCMCpack-1.0-2/MCMCpack/src/MCMCbinaryChange.cc |only
MCMCpack-1.0-2/MCMCpack/src/MCMCpoissonChange.cc |only
15 files changed, 232 insertions(+), 122 deletions(-)
Author: Corneliu Henegar
Diff between FunNet versions 1.00-6 dated 2009-01-18 and 1.00-7 dated 2009-07-18
Title: Integrative Functional Analysis of Transcriptional Networks
Description: FunNet is an integrative tool for analyzing gene
co-expression networks built from microarray expression data.
The analytic model implemented in this library involves two
abstraction layers: transcriptional and functional (biological
roles). A functional profiling technique using Gene Ontology &
KEGG annotations is applied to extract a list of relevant
biological themes from microarray expression profiling data.
Afterwards multiple-instance representations are built to
relate significant themes to their transcriptional instances
(i.e. the two layers of the model). An adapted non-linear
dynamical system model is used to quantify the proximity of
relevant genomic themes based on the similarity of the
expression profiles of their gene instances. Eventually an
unsupervised multiple-instance clustering procedure, relying on
the two abstraction layers, is used to identify the structure
of the co-expression network composed from modules of
functionally related transcripts. Functional and
transcriptional maps of the co-expression network are provided
separately together with detailed information on the network
centrality of related transcripts and genomic themes.
FunNet-1.00-6/FunNet/man/HS.GO.DIR.BP.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/HS.GO.DIR.CC.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/HS.GO.DIR.MF.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/HS.KEGG.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/HS.locus.name.Rd |only
FunNet-1.00-6/FunNet/man/HS.unigene.Rd |only
FunNet-1.00-6/FunNet/man/MM.GO.DIR.BP.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/MM.GO.DIR.CC.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/MM.GO.DIR.MF.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/MM.KEGG.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/MM.locus.name.Rd |only
FunNet-1.00-6/FunNet/man/MM.unigene.Rd |only
FunNet-1.00-6/FunNet/man/RN.GO.DIR.BP.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/RN.GO.DIR.CC.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/RN.GO.DIR.MF.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/RN.KEGG.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/RN.locus.name.Rd |only
FunNet-1.00-6/FunNet/man/RN.unigene.Rd |only
FunNet-1.00-6/FunNet/man/SC.GO.DIR.BP.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/SC.GO.DIR.CC.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/SC.GO.DIR.MF.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/SC.KEGG.file.annot.Rd |only
FunNet-1.00-6/FunNet/man/SC.locus.name.Rd |only
FunNet-1.00-6/FunNet/man/SC.orf.Rd |only
FunNet-1.00-7/FunNet/DESCRIPTION | 51 +--
FunNet-1.00-7/FunNet/R/Annotations.R | 324 ++++++--------------
FunNet-1.00-7/FunNet/R/FunNet.R | 231 ++++++++++----
FunNet-1.00-7/FunNet/R/sysdata.rda |binary
FunNet-1.00-7/FunNet/man/Annotations.Rd | 10
FunNet-1.00-7/FunNet/man/FunNet.Rd | 14
FunNet-1.00-7/FunNet/man/annot.base.Rd |only
FunNet-1.00-7/FunNet/man/species.Rd |only
32 files changed, 322 insertions(+), 308 deletions(-)
Author: Ulrike Groemping
Title: Fractional Factorial designs with 2-level factors
Description: This package creates regular and non-regular Fractional
Factorial designs. Furthermore, analysis tools for Fractional
Factorial designs with 2-level factors are offered (main
effects and interaction plots for all factors simultaneously,
cube plot for looking at the simultaneous effects of three
factors, full or half normal plot, alias structure in a more
readable format than with the built-in function alias). The
package is currently subject to intensive development. While
much of the intended functionality is already available, some
changes and improvements are still to be expected. Suggestions
are welcome.
Diff between FrF2 versions 0.94 dated 2009-06-28 and 0.95 dated 2009-07-18
DESCRIPTION | 8 R/FrF2.R | 14 R/IAPlot.R | 47 ++ R/MEPlot.R | 2 R/estimable2fis.R | 4 R/pb.R | 32 - R/sysdata.rda |binary inst/NEWS | 19 + man/CatalogueAccessors.Rd | 8 man/FrF2-package.Rd | 11 man/FrF2.Rd | 5 man/IAPlot.Rd | 46 +- man/pb.Rd | 3 tests/FrF2test.Rout.save | 800 +++++++++++++++++++++++++++++++++++++--------- 14 files changed, 788 insertions(+), 211 deletions(-)
Author: David Luethi, Philipp Erb
Title: Fast Kalman Filter
Description: This is a flexible implementation of the Kalman filter. It
is entirely written in C and relies fully on linear algebra
subroutines contained in BLAS and LAPACK. Due to the speed of
the filter, the fitting of high-dimensional linear state space
models to large datasets becomes possible. This package also
contains a plot function for the visualization of the state
vector and graphical diagnostics of the residuals.
Diff between FKF versions 0.0.1 dated 2009-02-12 and 0.0.2 dated 2009-07-18
ChangeLog | 5 +++++ DESCRIPTION | 22 ++++++++++++++++------ Fixme | 2 +- NAMESPACE | 2 +- R/fkf.r | 9 +++++++-- man/fkf.Rd | 4 ++-- src/fkflib.c | 23 +++++++++++++++++------ 7 files changed, 49 insertions(+), 18 deletions(-)
Author: Ulrike Groemping
Title: Full factorials, orthogonal arrays and base utilities for DoE
packages
Description: This package creates full factorial experimental designs
and designs based on orthogonal arrays for (industrial)
experiments. Additionally, it provides some utility functions
used also by other DoE packages.
Diff between DoE.base versions 0.3 dated 2009-06-28 and 0.4-1 dated 2009-07-18
DESCRIPTION | 10 ++++----- NAMESPACE | 7 ++++-- R/DesignAccessors.r | 11 +++++++++- R/contr.FrF2.R |only R/export.design.R | 48 ++++++++++++++++++++++++++++++-------------- R/fac.design.R | 11 +++++++++- R/fix.R |only R/fix.default.R |only R/fix.design.R |only R/oa.design.R | 29 +++++++++++++++++++++----- R/sysdata.rda |binary inst/NEWS | 20 ++++++++++++++++++ man/arrays.Rd | 6 +++-- man/class-design.Rd | 55 +++++++++++++++++++++++++++++++++++++-------------- man/contr.FrF2.Rd |only man/export.design.Rd | 34 ++++++++++++++++++++----------- man/fac.design.Rd | 13 ++++++++++++ man/fix.design.Rd |only man/oa.design.Rd | 40 ++++++++++++++++++++++++++++--------- man/utitlities.Rd | 1 20 files changed, 217 insertions(+), 68 deletions(-)
Author: Simon Urbanek
Diff between Cairo versions 1.4-4 dated 2008-10-19 and 1.4-5 dated 2009-07-18
Title: R graphics device using cairo graphics library for creating
high-quality bitmap (PNG, JPEG, TIFF), vector (PDF, SVG,
PostScript) and display (X11 and Win32) output.
Description: This package provides a Cairo graphics device that can be
use to create high-quality vector (PDF, PostScript and SVG) and
bitmap output (PNG,JPEG,TIFF), and high-quality rendering in
displays (X11 and Win32). Since it uses the same back-end for
all output, copying across formats is WYSIWYG. Files are
created without the dependence on X11 or other external
programs. This device supports alpha channel (semi-transparent
drawing) and resulting images can contain transparent and
semi-transparent regions. It is ideal for use in server
environemnts (file output) and as a replacement for other
devices that don't have Cairo's capabilities such as alpha
support or anti-aliasing. Backends are modular such that any
subset of backends is supported.
DESCRIPTION | 27 ++++++++++++++++++++++-----
NEWS | 5 +++++
configure.win | 2 +-
src/cairobem.c | 2 +-
src/cairogd.h | 2 +-
5 files changed, 30 insertions(+), 8 deletions(-)
Author: Alessio Boattini and Federico C. F. Calboli; Vincente Canto
Cassola together with Martin Maechler authored the function
mtx.exp.
Title: Biodemography functions
Description: The Biodem package provides a number of functions for
Biodemographycal analysis.
Diff between Biodem versions 0.1 dated 2005-04-25 and 0.2 dated 2009-07-18
DESCRIPTION | 17 +++++++++++------ R/mal.phi.R | 1 + R/mtx.exp.R | 3 +++ R/rri.R | 3 --- R/sur.freq.R | 14 +++++++------- man/sur.freq.Rd | 4 ++-- 6 files changed, 24 insertions(+), 18 deletions(-)
Author: Thomas Kneib, Felix Heinzl, Andreas Brezger, Daniel Sabanes
Bove
Title: R Utilities Accompanying the Software Package BayesX
Description: This package provides functionality for exploring and
visualising estimation results obtained with the software
package BayesX for structured additive regression. It also
provides functions that allow to read, write and manipulate map
objects that are required in spatial analyses performed with
BayesX, a free software for estimating structured additive
regression models (http://www.stat.uni-muenchen.de/~bayesx).
Diff between BayesX versions 0.2 dated 2009-03-11 and 0.2-3 dated 2009-07-18
BayesX-0.2-3/BayesX/DESCRIPTION | 15 - BayesX-0.2-3/BayesX/R/bnd2gra.R | 132 ++++++++--- BayesX-0.2-3/BayesX/R/createxymap.R | 4 BayesX-0.2-3/BayesX/R/drawmap.R | 17 - BayesX-0.2-3/BayesX/R/extractSamples.R | 17 - BayesX-0.2-3/BayesX/R/get.centroids.R | 26 +- BayesX-0.2-3/BayesX/R/read.bnd.R | 152 +++++++++---- BayesX-0.2-3/BayesX/R/read.gra.R | 5 BayesX-0.2-3/BayesX/R/round.bnd.R | 14 - BayesX-0.2-3/BayesX/R/shp2bnd.R | 304 ++++++++++++++++---------- BayesX-0.2-3/BayesX/R/spAndBndConversion.R | 60 ++--- BayesX-0.2-3/BayesX/R/write.bnd.R | 73 ++++-- BayesX-0.2-3/BayesX/inst/ChangeLog |only BayesX-0.2-3/BayesX/man/BayesX-package.Rd | 2 BayesX-0.2-3/BayesX/man/drawmap.Rd | 9 BayesX-0.2-3/BayesX/man/extractSamples.Rd | 3 BayesX-0.2-3/BayesX/man/plotautocor.Rd | 3 BayesX-0.2-3/BayesX/man/plotnonp.Rd | 16 - BayesX-0.2-3/BayesX/man/plotsurf.Rd | 6 BayesX-0.2-3/BayesX/man/read.bnd.Rd | 4 BayesX-0.2-3/BayesX/man/shp2bnd.Rd | 7 BayesX-0.2-3/BayesX/man/spAndBndConversion.Rd | 16 + BayesX-0.2/BayesX/ChangeLog |only 23 files changed, 571 insertions(+), 314 deletions(-)
Author: Karel Van den Meersche
Diff between BCE versions 1.3 dated 2009-06-03 and 1.4 dated 2009-07-18
Title: Bayesian composition estimator: estimating sample (taxonomic)
composition from biomarker data
Description: Function to estimates taxonomic compositions from
biomarker data, using a Bayesian approach.
DESCRIPTION | 10 ++--
man/BCE.Rd | 126 ++++++++++++++++++++++++++++++++++-------------------
man/bceInput.Rd | 17 +++++--
man/bceOutput.rd | 15 ++++--
man/export.bce.Rd | 18 +++++--
man/pairs.bce.Rd | 30 +++++++++---
man/plot.bce.Rd | 12 +++--
man/rescaleRows.Rd | 19 +++++--
man/summary.bce.Rd | 64 ++++++++++++++++++--------
man/tlsce.Rd | 62 ++++++++++++++++++--------
10 files changed, 255 insertions(+), 118 deletions(-)
Author: Robin K. S. Hankin
Title: Bayesian Analysis of Computer Code Output (BACCO)
Description: The BACCO bundle of packages is replaced by the BACCO
package, which provides a vignette that illustrates the
constituent packages (emulator, approximator, calibrator) in
use.
Diff between BACCO versions 1.1-4 dated 2009-05-05 and 2.0 dated 2009-07-18
BACCO-1.1-4/BACCO/approximator |only BACCO-1.1-4/BACCO/calibrator |only BACCO-1.1-4/BACCO/emulator |only BACCO-2.0/BACCO/DESCRIPTION | 28 +++++++++++++++------------- BACCO-2.0/BACCO/inst |only BACCO-2.0/BACCO/man |only 6 files changed, 15 insertions(+), 13 deletions(-)
Author: James Honaker
Diff between Amelia versions 1.2-9 dated 2009-07-02 and 1.2-12 dated 2009-07-18
Title: Amelia II: A Program for Missing Data
Description: Amelia II "multiply imputes" missing data in a single
cross-section (such as a survey), from a time series (like
variables collected for each year in a country), or from a
time-series-cross-sectional data set (such as collected by
years for each of several countries). Amelia II implements our
bootstrapping-based algorithm that gives essentially the same
answers as the standard IP or EMis approaches, is usually
considerably faster than existing approaches and can handle
many more variables. Unlike Amelia I and other statistically
rigorous imputation software, it virtually never crashes (but
please let us know if you find to the contrary!). The program
also generalizes existing approaches by allowing for trends in
time series across observations within a cross-sectional unit,
as well as priors that allow experts to incorporate beliefs
they have about the values of missing cells in their data.
Amelia II also includes useful diagnostics of the fit of
multiple imputation models. The program works from the R
command line or via a graphical user interface that does not
require users to know R.
ChangeLog |only
DESCRIPTION | 8
NEWS |only
R/amcheck.r | 80 -
R/ameliagui.r | 14
R/emb.r | 4
README | 25
inst/doc/amelia.Rnw | 2
inst/doc/amelia.pdf | 2376 +++++++++++++++++++++++++--------------------------
inst/doc/copyRd.Rout | 2
inst/doc/index.shtml | 14
11 files changed, 1246 insertions(+), 1279 deletions(-)