Author: Jae H. Kim
Title: Variance Ratio tests and spectral shape tests for Weak-form
Market Efficiency
Description: A collection of variance ratio and spectral shapte tests
Diff between vrtest versions 0.93 dated 2009-05-08 and 0.94 dated 2009-06-24
DESCRIPTION | 10 +++++----- man/vrtest-package.Rd | 6 +++--- 2 files changed, 8 insertions(+), 8 deletions(-)
Author: Jeff Hallman
Diff between tis versions 1.5 dated 2009-01-03 and 1.6 dated 2009-06-24
Title: Time Indexes and Time Indexed Series
Description: Functions and S3 classes for time indexes and time indexed
series, which are compatible with FAME frequencies.
DESCRIPTION | 23 +++--
NAMESPACE | 6 -
NEWS | 6 +
R/convenientTi.R | 6 -
R/fortify.tis.R |only
R/holidays.R | 201 ++++++++++++++++++++++++++++++++++++++++--------
R/nber.R | 6 -
R/nberShade.ggplot.R |only
R/ti.R | 2
R/tisPlot.R | 2
cleanup | 2
man/cbind.tis.Rd | 2
man/fortify.tis.Rd |only
man/holidays.Rd | 26 ++++--
man/nberShade.Rd | 16 +++
man/nberShade.ggplot.Rd |only
man/scatterPlot.Rd | 2
17 files changed, 236 insertions(+), 64 deletions(-)
Author: Brian Lee Yung Rowe
Title: Provides various portfolio optimization strategies including
random matrix theory and shrinkage estimators
Description: Portfolio optimization typically requires an estimate of a
covariance matrix of asset returns. There are many approaches
for constructing such a covariance matrix, some using the
sample covariance matrix as a starting point. This package
provides implementations for two such methods: random matrix
theory and shrinkage estimation. Each method attempts to clean
or remove noise related to the sampling process from the sample
covariance matrix.
Diff between tawny versions 1.0 dated 2009-04-15 and 1.1.0 dated 2009-06-24
DESCRIPTION | 12 +- R/divergence.R | 51 ++++++++++- R/filter.R |only R/framework.R | 204 ++------------------------------------------- R/random_matrix.R | 52 ++++++----- R/shrinkage.R | 49 +++++++--- R/util.R |only data/sp500.subset.RData |binary man/cov.shrink.Rd | 13 ++ man/divergence.Rd | 11 +- man/filter.RMT.Rd | 23 +++-- man/getPortfolioReturns.Rd | 2 man/optimizePortfolio.Rd | 22 ++++ man/plotPerformance.Rd | 2 man/tawny-package.Rd | 8 - 15 files changed, 194 insertions(+), 255 deletions(-)
Author: Andrew O. Finley
Diff between spBayes versions 0.1-2 dated 2009-03-24 and 0.1-3 dated 2009-06-24
Title: Univariate and Multivariate Spatial Modeling
Description: spBayes fits univariate and multivariate models with
Markov chain Monte Carlo (MCMC).
DESCRIPTION | 8 +--
R/spGLM.R | 20 ++++++---
R/spLM.R | 20 ++++++---
R/spMvGLM.R | 22 +++++++---
R/spMvLM.R | 25 ++++++++---
inst/doc/spBayes-vignette.pdf |binary
man/spGLM.Rd | 92 ++++++++++++++++++++++++++++++++++++------
man/spLM.Rd | 5 +-
man/spMvGLM.Rd | 20 ++++-----
man/spMvLM.Rd | 33 +++++++--------
man/spPredict.Rd | 12 +++--
src/spMvGLM.cpp | 2
src/spMvLM.cpp | 8 +--
13 files changed, 187 insertions(+), 80 deletions(-)
Author: Josef Leydold and Wolfgang H\"ormann
Title: R interface to the UNU.RAN random variate generators
Description: Interface to the UNU.RAN library for Universal Non-Uniform
RANdom variate generators
Diff between Runuran versions 0.9.0 dated 2009-02-26 and 0.10.0 dated 2009-06-24
Runuran-0.10.0/Runuran/DESCRIPTION | 14 Runuran-0.10.0/Runuran/NAMESPACE | 2 Runuran-0.10.0/Runuran/NEWS | 11 Runuran-0.10.0/Runuran/R/Runuran.R | 86 Runuran-0.10.0/Runuran/inst/doc/Runuran.pdf | 3141 +++++----- Runuran-0.10.0/Runuran/inst/doc/src/advanced.Rnw | 8 Runuran-0.10.0/Runuran/inst/doc/src/pitfalls.Rnw | 53 Runuran-0.10.0/Runuran/inst/doc/src/universal.Rnw | 6 Runuran-0.10.0/Runuran/inst/doc/src/version.tex | 2 Runuran-0.10.0/Runuran/man/Runuran-package.Rd | 17 Runuran-0.10.0/Runuran/man/dau.new.Rd | 2 Runuran-0.10.0/Runuran/man/dgt.new.Rd | 3 Runuran-0.10.0/Runuran/man/unuran-class.Rd | 18 Runuran-0.10.0/Runuran/man/unuran.packed-methods.Rd |only Runuran-0.10.0/Runuran/man/uq.Rd | 41 Runuran-0.10.0/Runuran/src/Makevars.in | 4 Runuran-0.10.0/Runuran/src/Runuran.c | 402 + Runuran-0.10.0/Runuran/src/Runuran.h | 40 Runuran-0.10.0/Runuran/src/Runuran_pinv.c |only Runuran-0.10.0/Runuran/src/Runuran_source.h |only Runuran-0.10.0/Runuran/src/unuran-src/distr/cont.c | 26 Runuran-0.10.0/Runuran/src/unuran-src/methods/dgt.c | 26 Runuran-0.10.0/Runuran/src/unuran-src/methods/dgt.h | 1 Runuran-0.10.0/Runuran/src/unuran-src/methods/pinv.c | 3 Runuran-0.10.0/Runuran/src/unuran-src/methods/pinv_info.ch | 2 Runuran-0.10.0/Runuran/src/unuran-src/methods/pinv_init.ch | 47 Runuran-0.10.0/Runuran/src/unuran-src/methods/pinv_newton.ch | 26 Runuran-0.10.0/Runuran/src/unuran-src/methods/pinv_prep.ch | 4 Runuran-0.10.0/Runuran/src/unuran-src/methods/x_gen.c | 3 Runuran-0.10.0/Runuran/src/unuran-src/unuran.h | 1 Runuran-0.10.0/Runuran/src/unuran-src/utils/error.c | 2 Runuran-0.10.0/Runuran/src/unuran-src/utils/lobatto.c | 29 Runuran-0.10.0/Runuran/src/unuran-src/utils/lobatto_source.h | 2 Runuran-0.10.0/Runuran/tests/test_advanced.R | 4 Runuran-0.10.0/Runuran/tests/test_deprecated.R | 4 Runuran-0.10.0/Runuran/tests/test_distributions_cont.R | 4 Runuran-0.10.0/Runuran/tests/test_distributions_discr.R | 4 Runuran-0.10.0/Runuran/tests/test_packed.R |only Runuran-0.10.0/Runuran/tests/test_routines.R | 4 Runuran-0.10.0/Runuran/tests/test_universal.R | 4 Runuran-0.10.0/Runuran/tests/test_unuran.R | 68 Runuran-0.9.0/Runuran/src/unuran-src/distributions/obsolete_gen |only 42 files changed, 2412 insertions(+), 1702 deletions(-)
Author: Originally Michael Lapsley, from Oct 2002 Brian Ripley
Title: ODBC Database Access
Description: An ODBC database interface
Diff between RODBC versions 1.2-5 dated 2009-01-21 and 1.2-6 dated 2009-06-24
RODBC-1.2-5/RODBC/README.orig |only RODBC-1.2-5/RODBC/man/RODBC.Rd |only RODBC-1.2-5/RODBC/man/RODBCtables.Rd |only RODBC-1.2-6/RODBC/ChangeLog | 53 +++- RODBC-1.2-6/RODBC/DESCRIPTION | 15 - RODBC-1.2-6/RODBC/INSTALL |only RODBC-1.2-6/RODBC/R/RODBC.R | 42 ++- RODBC-1.2-6/RODBC/R/sql.R | 122 ++++++---- RODBC-1.2-6/RODBC/R/win.R | 47 ---- RODBC-1.2-6/RODBC/README | 130 +++-------- RODBC-1.2-6/RODBC/inst/README | 130 +++-------- RODBC-1.2-6/RODBC/inst/po |only RODBC-1.2-6/RODBC/inst/tests.R | 54 +--- RODBC-1.2-6/RODBC/man/RODBC-internal.Rd | 5 RODBC-1.2-6/RODBC/man/RODBC-package.Rd |only RODBC-1.2-6/RODBC/man/odbc.Rd | 56 ++-- RODBC-1.2-6/RODBC/man/odbcClose.Rd | 7 RODBC-1.2-6/RODBC/man/odbcConnect.Rd | 69 +++-- RODBC-1.2-6/RODBC/man/odbcDataSources.Rd | 22 + RODBC-1.2-6/RODBC/man/odbcErrors.Rd | 2 RODBC-1.2-6/RODBC/man/odbcGetInfo.Rd | 16 - RODBC-1.2-6/RODBC/man/odbcSetAutoCommit.Rd | 10 RODBC-1.2-6/RODBC/man/setSqlTypeInfo.Rd | 9 RODBC-1.2-6/RODBC/man/sqlColumns.Rd |only RODBC-1.2-6/RODBC/man/sqlCopy.Rd | 22 + RODBC-1.2-6/RODBC/man/sqlDrop.Rd |only RODBC-1.2-6/RODBC/man/sqlFetch.Rd | 36 +-- RODBC-1.2-6/RODBC/man/sqlQuery.Rd | 76 +++--- RODBC-1.2-6/RODBC/man/sqlSave.Rd | 78 +++--- RODBC-1.2-6/RODBC/man/sqlTables.Rd | 69 +++++ RODBC-1.2-6/RODBC/man/sqlTypeInfo.Rd | 32 +- RODBC-1.2-6/RODBC/po/R-RODBC.pot | 13 - RODBC-1.2-6/RODBC/po/R-en@quot.po |only RODBC-1.2-6/RODBC/po/RODBC.pot | 64 ++--- RODBC-1.2-6/RODBC/po/en@quot.po |only RODBC-1.2-6/RODBC/src/RODBC.c | 334 ++++++++++++++++++----------- RODBC-1.2-6/RODBC/tests |only 37 files changed, 844 insertions(+), 669 deletions(-)
Author: Charles J. Geyer
Diff between rcdd versions 1.1-1 dated 2008-09-01 and 1.1-2 dated 2009-06-24
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.
rcdd-1.1-1/rcdd/inst/doc/.build.timestamp |only
rcdd-1.1-2/rcdd/CHANGES | 3 +++
rcdd-1.1-2/rcdd/DESCRIPTION | 30 ++++++++++++++++--------------
rcdd-1.1-2/rcdd/inst/doc/vinny.Rnw | 13 ++++++++++++-
rcdd-1.1-2/rcdd/inst/doc/vinny.pdf |binary
rcdd-1.1-2/rcdd/inst/doc/vinny.tex | 5 ++++-
6 files changed, 35 insertions(+), 16 deletions(-)
Author: Graham Williams
Diff between rattle versions 2.4.54 dated 2009-03-24 and 2.4.79 dated 2009-06-24
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.
rattle-2.4.54/rattle/man/listRPartRules.Rd |only
rattle-2.4.79/rattle/CITATION | 4
rattle-2.4.79/rattle/DESCRIPTION | 14
rattle-2.4.79/rattle/NAMESPACE | 4
rattle-2.4.79/rattle/R/data.R | 283 +-
rattle-2.4.79/rattle/R/evaluate.R | 114
rattle-2.4.79/rattle/R/explore.R |only
rattle-2.4.79/rattle/R/hclust.R | 6
rattle-2.4.79/rattle/R/help.R | 32
rattle-2.4.79/rattle/R/log.R | 48
rattle-2.4.79/rattle/R/model.R | 60
rattle-2.4.79/rattle/R/projects.R | 68
rattle-2.4.79/rattle/R/random_forest.R | 12
rattle-2.4.79/rattle/R/rattle.R | 2520 +-------------------
rattle-2.4.79/rattle/R/report.R | 3
rattle-2.4.79/rattle/R/rpart.R | 10
rattle-2.4.79/rattle/R/textview.R | 6
rattle-2.4.79/rattle/R/transform.R | 349 +-
rattle-2.4.79/rattle/R/zzz.R | 56
rattle-2.4.79/rattle/data/audit.RData |binary
rattle-2.4.79/rattle/data/weather.RData |binary
rattle-2.4.79/rattle/data/weatherCanberra.RData |only
rattle-2.4.79/rattle/data/weatherSydney.RData |only
rattle-2.4.79/rattle/inst/arff/weather.arff | 762 +++---
rattle-2.4.79/rattle/inst/arff/weatherCanberra.arff |only
rattle-2.4.79/rattle/inst/arff/weatherSydney.arff |only
rattle-2.4.79/rattle/inst/csv/weather.csv | 723 ++---
rattle-2.4.79/rattle/inst/csv/weatherCanberra.csv |only
rattle-2.4.79/rattle/inst/csv/weatherSydney.csv |only
rattle-2.4.79/rattle/inst/etc/rattle.glade | 2299 ++++++++++--------
rattle-2.4.79/rattle/inst/etc/textviews.xml | 143 -
rattle-2.4.79/rattle/inst/etc/tooltips.xml | 4
rattle-2.4.79/rattle/man/asRules.Rd |only
rattle-2.4.79/rattle/man/asRules.rpart.Rd |only
rattle-2.4.79/rattle/man/drawTreeNodes.Rd | 2
rattle-2.4.79/rattle/man/internal.Rd | 4
rattle-2.4.79/rattle/man/plotRisk.Rd | 5
rattle-2.4.79/rattle/man/weather.Rd | 24
38 files changed, 2957 insertions(+), 4598 deletions(-)
Author: Aaron A. King, Edward L. Ionides, Carles Martinez Breto, Steve
Ellner, Bruce Kendall
Title: Statistical inference for partially observed Markov processes
Description: Inference methods for partially-observed Markov processes
Diff between pomp versions 0.24-5 dated 2009-06-07 and 0.24-7 dated 2009-06-24
pomp-0.24-5/pomp/R/mvnorm.R |only pomp-0.24-7/pomp/DESCRIPTION | 13 +++---- pomp-0.24-7/pomp/NAMESPACE | 1 pomp-0.24-7/pomp/R/nlf-guts.R | 28 --------------- pomp-0.24-7/pomp/inst/ChangeLog | 16 +++++++++ pomp-0.24-7/pomp/inst/doc/advanced_topics_in_pomp.pdf |binary pomp-0.24-7/pomp/inst/doc/intro_to_pomp.pdf |binary pomp-0.24-7/pomp/src/initstate.c | 32 +++++++++++++----- pomp-0.24-7/pomp/src/lookup_table.c | 1 9 files changed, 49 insertions(+), 42 deletions(-)
Author: Graham Williams, Michael Hahsler (arules), Zementis Inc, Hemant
Ishwaran, Udaya B. Kogalur, Rajarshi Guha
Title: Generate PMML for various models
Description: The Predictive Modelling Markup Language (PMML) is a
language for representing models, in an application independent
way. Such models can then be loaded into other applications
supporting PMML, including ADAPA from Zementis, Teradata
Warehouse Miner and IBM's DB2. The package provides a generic
pmml function to generate pmml for an object. Using a S3
generic function the approriate method for the class of the
supplied object is dispatched. The package currently supports
the export of PMML for linear regression, SVMs, rpart
classification trees, randomSurvivalForest forest models, and
kmeans clusters. This package is part of the Rattle toolkit.
Diff between pmml versions 1.2.10 dated 2009-03-09 and 1.2.15 dated 2009-06-24
DESCRIPTION | 37 ++++--- NAMESPACE | 2 R/pmml.R | 246 +++++++++++++++++++++++++++++++++++++++------------ R/pmml.arules.R | 2 R/pmml.lm.R | 29 ++++-- R/pmml.rpart.R | 36 ++++++- man/pmml.Rd | 8 + man/pmml.arules.Rd | 2 man/pmmlCanExport.Rd |only 9 files changed, 277 insertions(+), 85 deletions(-)
Author: Hadley Wickham
Diff between plyr versions 0.1.8 dated 2009-04-21 and 0.1.9 dated 2009-06-24
Title: Tools for splitting, applying and combining data
Description: plyr is a set of tools that solves a common set of
problems: you need to break a big problem down into manageable
pieces, operate on each pieces and then put all the pieces back
together. For example, you might want to fit a model to each
spatial location or time point in your study, summarise data by
panels or collapse high-dimensional arrays to simpler summary
statistics.
DESCRIPTION | 6 +++---
NEWS | 8 ++++++++
R/helper-summarise.r |only
R/quote.r | 20 ++++++++++++++++++--
R/rbind.r | 10 ++++++----
R/simplify-vector.r | 3 ++-
R/split-data-frame.r | 2 +-
man/as-quoted-3f.rd | 3 +++
man/rbind-fill-di.rd | 11 ++++++++++-
man/summarise-n4.rd |only
10 files changed, 51 insertions(+), 12 deletions(-)
Author: Thomas A. Gerds
Title: Prediction Error Curves for Survival Models
Description: Validation of predicted surival probabilities using
inverse weighting and resampling.
Diff between pec versions 1.1.0 dated 2009-04-15 and 1.1.1 dated 2009-06-24
DESCRIPTION | 6 +++--- man/R2crps.Rd | 2 ++ man/ipcw.Rd | 5 +++-- src/pec.c | 4 ++-- 4 files changed, 10 insertions(+), 7 deletions(-)
Author: Andrew Gelman
Diff between mi versions 0.08-02 dated 2009-06-19 and 0.08-03 dated 2009-06-24
Title: Missing Data Imputation and Model Checking
Description: Missing-data imputation and model checking
CHANGELOG | 12 ++++++++++++
DESCRIPTION | 8 ++++----
R/mi.R | 10 +++++-----
R/mi.binary.R | 2 +-
R/mi.continuous.R | 2 +-
R/mi.count.R | 2 +-
R/mi.pmm.R | 2 +-
7 files changed, 25 insertions(+), 13 deletions(-)
Author: Nicholas J. Lewin-Koh and Roger Bivand, contributions by Edzer
J. Pebesma, Eric Archer, Adrian Baddeley, Hans-Jörg Bibiko,
Stéphane Dray, David Forrest, Patrick Giraudoux, Duncan
Golicher, Virgilio Gómez Rubio, Patrick Hausmann, Thomas
Jagger, Sebastian P. Luque, Don MacQueen, Andrew Niccolai and
Tom Short
Title: Tools for reading and handling spatial objects
Description: Set of tools for manipulating and reading geographic data,
in particular ESRI shapefiles; C code used from shapelib. It
includes binary access to GSHHS shoreline files. The package
also provides interface wrappers for exchanging spatial objects
with packages such as PBSmapping, spatstat, maps, RArcInfo,
Stata tmap, WinBUGS, Mondrian, and others.
Diff between maptools versions 0.7-23 dated 2009-05-27 and 0.7-25 dated 2009-06-24
ChangeLog | 10 ++++++++++ DESCRIPTION | 8 ++++---- R/SpatialPolys-methods.R | 12 +++++++++--- inst/ChangeLog | 10 ++++++++++ 4 files changed, 33 insertions(+), 7 deletions(-)
Author: Deepayan Sarkar
Diff between latticeExtra versions 0.5-4 dated 2008-11-02 and 0.6-1 dated 2009-06-24
Title: Extra Graphical Utilities Based on Lattice
Description: Extra graphical utilities based on lattice
DESCRIPTION | 11 -
NAMESPACE | 15 +
R/c.trellis.R | 342 ++++++++++++++++++++++-----------------
R/doubleYScale.R |only
R/layer.R | 425 ++++++++++++++-----------------------------------
R/marginal.plot.R | 317 ++++++++++++++++++------------------
R/panel.3dmisc.R | 2
R/panel.lmlineq.R |only
R/segplot.R | 17 +
R/tileplot.R | 228 +++++++++++++-------------
data/EastAuClimate.txt |only
inst/NEWS | 22 ++
man/EastAuClimate.Rd |only
man/as.layer.Rd | 81 +++------
man/c.trellis.Rd | 75 +++++---
man/doubleYScale.Rd |only
man/marginal.plot.Rd | 25 +-
man/panel.lmlineq.Rd |only
man/panel.segplot.Rd | 12 -
19 files changed, 752 insertions(+), 820 deletions(-)
Author: Christina Stahl and David Meyer
Title: Knowledge Space Theory
Description: Knowledge Space Theory is a set-theoretical framework,
which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The kst-package
provides basic functionalities to generate, handle, and
manipulate knowledge structures and knowledge spaces.
Diff between kst versions 0.1.8 dated 2009-01-09 and 0.1-9 dated 2009-06-24
DESCRIPTION | 31 +++++++++++++++++-------------- R/reduction.kstructure.R | 2 +- inst/doc/kst.Rnw | 5 ----- inst/doc/kst.pdf |binary man/plot.Rd | 8 -------- 5 files changed, 18 insertions(+), 28 deletions(-)
Author: Tarn Duong
Diff between ks versions 1.6.3 dated 2009-04-04 and 1.6.5 dated 2009-06-24
Title: Kernel smoothing
Description: Kernel density estimators and kernel discriminant analysis
for multivariate data
ks-1.6.3/ks/R-future |only
ks-1.6.5/ks/DESCRIPTION | 8 +--
ks-1.6.5/ks/R/binning.R | 67 ++++++++++++++++++--------------
ks-1.6.5/ks/R/kda.R | 26 +++++++-----
ks-1.6.5/ks/R/kdde.R | 12 +++--
ks-1.6.5/ks/R/kde.R | 88 +++++++++++++++++++++++++------------------
ks-1.6.5/ks/R/mise.R | 4 -
ks-1.6.5/ks/R/normal.R | 35 ++++++++++-------
ks-1.6.5/ks/R/selector.R | 2
ks-1.6.5/ks/README | 13 +++++-
ks-1.6.5/ks/inst/doc/kde.pdf |binary
ks-1.6.5/ks/man/binning.Rd | 3 -
ks-1.6.5/ks/man/drvkde.Rd | 4 -
ks-1.6.5/ks/man/kda.kde.Rd | 10 +++-
ks-1.6.5/ks/man/kde.Rd | 8 ++-
ks-1.6.5/ks/src/linbin.f | 15 +++----
ks-1.6.5/ks/src/linbin2D.f | 12 ++---
ks-1.6.5/ks/src/linbin3D.f | 20 ++++-----
ks-1.6.5/ks/src/linbin4D.f | 76 ++++++++++++++++++++++---------------
19 files changed, 239 insertions(+), 164 deletions(-)
Author: Christian Roever, Nils Raabe, Karsten Luebke, Uwe Ligges, Gero
Szepannek, Marc Zentgraf
Title: Classification and visualization
Description: Miscellaneous functions for classification and
visualization developed at the Fakultaet Statistik, Technische
Universitaet Dortmund
Diff between klaR versions 0.5-8 dated 2009-01-09 and 0.5-9 dated 2009-06-24
DESCRIPTION | 33 +++++++++++++++++++-------------- R/partimat.R | 5 +++-- 2 files changed, 22 insertions(+), 16 deletions(-)
Author: Achim Zeileis, Bettina Gruen
Title: Automatic Generation of Standardized Exams for Large-Lecture
Courses
Description: Sweave-based automatic generation of exams with
multiple-choice questions and arithmetic problems.
Diff between exams versions 1.0-0 dated 2009-02-20 and 1.0-1 dated 2009-06-24
DESCRIPTION | 13 ++++++++----- NEWS | 8 ++++++++ inst/doc/exams.Rnw | 2 +- inst/doc/exams.pdf |binary inst/exercises/anova.Rnw | 2 +- man/exams.Rd | 14 +++++++------- 6 files changed, 25 insertions(+), 14 deletions(-)
Author: Virasakdi Chongsuvivatwong
Diff between epicalc versions 2.8.1.1 dated 2009-02-15 and 2.9.0.0 dated 2009-06-24
Title: Epidemiological calculator
Description: Functions making R easy for epidemiological calculation.
DESCRIPTION | 26 ++++++++++++++------------
R/epicalc.R | 1 +
2 files changed, 15 insertions(+), 12 deletions(-)
Author: Roger D. Peng
Diff between cacher versions 1.0 dated 2008-12-21 and 1.1 dated 2009-06-24
Title: Tools for caching and distributing statistical analyses
Description: This package provides tools for caching statistical
analyses in key-value databases which can subsequently be
distributed over the web.
DESCRIPTION | 17 +++++---
NAMESPACE | 6 +++
R/cacheDB.R | 6 ++-
R/utils.R | 8 +++-
R/verify.R | 22 ++++++-----
R/vizcache.R | 103 +++++++++++++++++++++++++++++++++++++++++++---------
TODO | 2 +
inst/doc/cacher.pdf |binary
man/cache.Rd | 13 ++++--
man/code.Rd | 2 -
man/graphcode.Rd |only
man/objectcode.Rd |only
man/package.Rd | 10 ++++-
13 files changed, 146 insertions(+), 43 deletions(-)
Author: Jose Claudio Faria & Clarice Garcia Borges Demetrio
Title: Biplot of Multivariate Data Based on Principal Components
Analysis
Description: Implements biplot (2d and 3d) of multivariate data based
on principal components analysis and diagnostic tools of the
quality of the reduction.
Diff between bpca versions 1.0.2 dated 2008-08-17 and 1.0.3 dated 2009-06-24
bpca-1.0.2/bpca/demo/bpca.lbd2-4.static.3d.R |only bpca-1.0.3/bpca/ChangeLog | 7 ++ bpca-1.0.3/bpca/DESCRIPTION | 31 ++++----- bpca-1.0.3/bpca/R/plot.bpca.2d.R | 31 +++++---- bpca-1.0.3/bpca/R/plot.bpca.3d.R | 82 +++++++++++------------- bpca-1.0.3/bpca/demo/00Index | 28 ++++---- bpca-1.0.3/bpca/demo/bpca.R | 68 +------------------ bpca-1.0.3/bpca/demo/bpca.dinamic.3d.R | 19 ++++- bpca-1.0.3/bpca/demo/bpca.lambda2_4.static.3d.R |only bpca-1.0.3/bpca/demo/bpca.static.2d.R | 8 +- bpca-1.0.3/bpca/demo/bpca.static.3d.R | 10 +- bpca-1.0.3/bpca/demo/comparation.R | 9 +- bpca-1.0.3/bpca/demo/dt.tools.R | 1 bpca-1.0.3/bpca/demo/gge.check.R | 9 +- bpca-1.0.3/bpca/demo/iris.R | 6 + bpca-1.0.3/bpca/demo/iris.var.rd.R | 8 +- bpca-1.0.3/bpca/demo/rock.var.rd.R | 11 ++- bpca-1.0.3/bpca/demo/var.rb.2d.R | 6 + bpca-1.0.3/bpca/demo/var.rb.3d.R | 6 + bpca-1.0.3/bpca/demo/var.rd.2d.R | 6 + bpca-1.0.3/bpca/man/bpca-package.Rd | 20 +++-- bpca-1.0.3/bpca/man/bpca.Rd | 81 +++++++++++++---------- bpca-1.0.3/bpca/man/dt.tools.Rd | 1 bpca-1.0.3/bpca/man/gabriel1971.Rd | 2 bpca-1.0.3/bpca/man/plot.Rd | 38 ++++++----- bpca-1.0.3/bpca/man/qbpca.Rd | 8 +- bpca-1.0.3/bpca/man/summary.Rd | 1 bpca-1.0.3/bpca/man/var.rbf.Rd | 1 bpca-1.0.3/bpca/man/var.rdf.Rd | 7 +- bpca-1.0.3/bpca/pdf |only 30 files changed, 262 insertions(+), 243 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 3.8 dated 2009-06-10 and 3.9 dated 2009-06-24
bigmemory-3.8/bigmemory/COPYING |only bigmemory-3.8/bigmemory/NAMESPACE |only bigmemory-3.8/bigmemory/configure |only bigmemory-3.8/bigmemory/include/boost/array.hpp |only bigmemory-3.8/bigmemory/include/boost/cstdint.hpp |only bigmemory-3.8/bigmemory/include/boost/detail |only bigmemory-3.8/bigmemory/include/boost/exception |only bigmemory-3.8/bigmemory/include/boost/interprocess |only bigmemory-3.8/bigmemory/include/boost/io_fwd.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/O1_size.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/advance.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/advance_fwd.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/alias.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/always.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/and.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/apply.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/apply_wrap.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/arg_fwd.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/arithmetic.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/at.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/at_fwd.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/O1_size_impl.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/adl_barrier.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/advance_backward.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/advance_forward.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/apply_1st.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/arg_typedef.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/arithmetic_op.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/arity.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/arity_spec.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/at_impl.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/back_impl.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/basic_bind.hpp |only 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bigmemory-3.8/bigmemory/include/boost/mpl/aux_/largest_int.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/logical_op.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/msvc_dtw.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/msvc_eti_base.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/msvc_is_class.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/msvc_never_true.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/msvc_type.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/na.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/na_assert.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/na_fwd.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/na_spec.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/nested_type_wknd.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/nttp_decl.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/aux_/numeric_cast_utils.hpp |only 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|only bigmemory-3.8/bigmemory/include/boost/mpl/min.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/min_element.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/min_max.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/modulus.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/multiplies.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/multiset |only bigmemory-3.8/bigmemory/include/boost/mpl/next_prior.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/not.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/not_equal_to.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/numeric_cast.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/order.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/pair.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/partition.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/plus.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/pop_front.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/pop_front_fwd.hpp |only 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bigmemory-3.8/bigmemory/include/boost/mpl/size_t_fwd.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/sizeof.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/stable_partition.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/transform.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/transform_view.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/unique.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/upper_bound.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/value_type.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/value_type_fwd.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/vector |only bigmemory-3.8/bigmemory/include/boost/mpl/vector.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/void.hpp |only bigmemory-3.8/bigmemory/include/boost/mpl/void_fwd.hpp |only bigmemory-3.8/bigmemory/include/boost/noncopyable.hpp |only bigmemory-3.8/bigmemory/include/boost/numeric |only bigmemory-3.8/bigmemory/include/boost/random |only bigmemory-3.8/bigmemory/include/boost/shared_ptr.hpp |only bigmemory-3.8/bigmemory/include/boost/static_assert.hpp |only bigmemory-3.8/bigmemory/include/boost/throw_exception.hpp |only bigmemory-3.8/bigmemory/include/boost/type_traits |only bigmemory-3.8/bigmemory/include/boost/uuid |only bigmemory-3.8/bigmemory/include/boost/uuid.hpp |only bigmemory-3.8/bigmemory/man/big.sub.matrix.Rd |only bigmemory-3.9/bigmemory/DESCRIPTION | 8 bigmemory-3.9/bigmemory/R/bigmatrix.R | 574 ++++- bigmemory-3.9/bigmemory/R/bigmatrixLib.R | 40 bigmemory-3.9/bigmemory/R/bigmatrixShm.R | 73 bigmemory-3.9/bigmemory/R/utils.R | 4 bigmemory-3.9/bigmemory/configure.Rout | 6 bigmemory-3.9/bigmemory/include/boost/mpl/aux_/preprocessed/no_ttp/list.hpp | 285 -- bigmemory-3.9/bigmemory/man/attach.big.matrix.Rd | 4 bigmemory-3.9/bigmemory/man/big.matrix-class.Rd | 15 bigmemory-3.9/bigmemory/man/big.matrix.Rd | 9 bigmemory-3.9/bigmemory/man/bigmemory-package.Rd | 15 bigmemory-3.9/bigmemory/man/deepcopy.Rd | 13 bigmemory-3.9/bigmemory/man/mwhich.Rd | 5 bigmemory-3.9/bigmemory/src/BigMatrix.cpp | 60 bigmemory-3.9/bigmemory/src/BigMatrix.h | 30 bigmemory-3.9/bigmemory/src/BigMatrixAccessor.hpp | 14 bigmemory-3.9/bigmemory/src/BigMemoryDefines.h | 2 bigmemory-3.9/bigmemory/src/BigMemoryMutex.cpp | 23 bigmemory-3.9/bigmemory/src/BigMemoryMutex.h | 23 bigmemory-3.9/bigmemory/src/CUserMutex.cpp | 2 bigmemory-3.9/bigmemory/src/Cbigmemory.cpp | 1003 +++++++--- bigmemory-3.9/bigmemory/src/CbigmemoryLib.cpp | 31 bigmemory-3.9/bigmemory/src/SharedCounter.cpp | 23 bigmemory-3.9/bigmemory/src/SharedCounter.h | 23 bigmemory-3.9/bigmemory/src/bigmemoryutils.cpp | 23 bigmemory-3.9/bigmemory/src/isna.hpp | 23 bigmemory-3.9/bigmemory/src/util.cpp | 2 bigmemory-3.9/bigmemory/src/util.h | 2 312 files changed, 1569 insertions(+), 766 deletions(-)
Author: Jae. H. Kim
Title: Bootstrap Prediction Intervals and Bias-Corrected Forecasting
Description: Bias-Corrected Forecasting and Bootstrap Prediction
Intervals for Autoregressive Time Series
Diff between BootPR versions 0.57 dated 2009-05-04 and 0.58 dated 2009-06-24
DESCRIPTION | 10 +++++----- man/BootAfterBootPI.Rd | 5 ++++- man/BootBC.Rd | 5 ++++- man/BootPR-package.Rd | 6 +++--- man/ShamanStine.PI.Rd | 5 ++++- man/Stine.Shaman.Rd | 6 +++++- 6 files changed, 25 insertions(+), 12 deletions(-)
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
Gangolf Jobb, Christoph Heibl, Daniel Lawson, Vincent Lefort,
Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander,
Rainer Opgen-Rhein, Korbinian Strimmer, Damien de Vienne
Title: Analyses of Phylogenetics and Evolution
Description: ape provides functions for reading, writing, plotting, and
manipulating phylogenetic trees, analyses of comparative data
in a phylogenetic framework, analyses of diversification and
macroevolution, computing distances from allelic and nucleotide
data, reading nucleotide sequences, and several tools such as
Mantel's test, computation of minimum spanning tree, the
population parameter theta based on various approaches,
nucleotide diversity, generalized skyline plots, estimation of
absolute evolutionary rates and clock-like trees using mean
path lengths, non-parametric rate smoothing and penalized
likelihood. Phylogeny estimation can be done with the NJ,
BIONJ, and ME methods.
Diff between ape versions 2.3 dated 2009-03-30 and 2.3-1 dated 2009-06-24
ape-2.3-1/ape/ChangeLog | 54 ++++++++++++++++ ape-2.3-1/ape/DESCRIPTION | 13 +--- ape-2.3-1/ape/R/CDAM.global.R | 2 ape-2.3-1/ape/R/DNA.R | 15 +++- ape-2.3-1/ape/R/ace.R | 31 ++++----- ape-2.3-1/ape/R/balance.R | 6 - ape-2.3-1/ape/R/birthdeath.R | 8 +- ape-2.3-1/ape/R/branching.times.R | 6 - ape-2.3-1/ape/R/cherry.R | 22 +++--- ape-2.3-1/ape/R/compar.ou.R | 6 - ape-2.3-1/ape/R/dist.gene.R | 6 - ape-2.3-1/ape/R/dist.topo.R | 8 +- ape-2.3-1/ape/R/drop.tip.R | 103 +++++++++++++++++++------------- ape-2.3-1/ape/R/gammaStat.R | 6 - ape-2.3-1/ape/R/is.binary.tree.R | 4 - ape-2.3-1/ape/R/is.monophyletic.R |only ape-2.3-1/ape/R/is.ultrametric.R | 4 - ape-2.3-1/ape/R/klastorin.R | 59 ------------------ ape-2.3-1/ape/R/ltt.plot.R | 8 +- ape-2.3-1/ape/R/mrca.R | 6 - ape-2.3-1/ape/R/pic.R | 6 - ape-2.3-1/ape/R/read.nexus.R | 5 - ape-2.3-1/ape/R/read.tree.R | 4 - ape-2.3-1/ape/R/root.R | 10 +-- ape-2.3-1/ape/R/rotate.R | 2 ape-2.3-1/ape/R/rtree.R | 17 ++--- ape-2.3-1/ape/R/summary.phylo.R | 19 +++-- ape-2.3-1/ape/R/vcv.phylo.R | 6 - ape-2.3-1/ape/R/which.edge.R | 6 - ape-2.3-1/ape/R/write.dna.R | 6 - ape-2.3-1/ape/R/write.tree.R | 13 ++-- ape-2.3-1/ape/R/yule.R | 23 +++++-- ape-2.3-1/ape/R/zoom.R | 13 +--- ape-2.3-1/ape/Thanks | 2 ape-2.3-1/ape/inst/doc/MoranI.pdf |binary ape-2.3-1/ape/man/DNAbin.Rd | 5 + ape-2.3-1/ape/man/Initialize.corPhyl.Rd | 2 ape-2.3-1/ape/man/ape-internal.Rd | 9 -- ape-2.3-1/ape/man/ape-package.Rd | 9 +- ape-2.3-1/ape/man/consensus.Rd | 6 - ape-2.3-1/ape/man/dist.dna.Rd | 4 - ape-2.3-1/ape/man/drop.tip.Rd | 12 ++- ape-2.3-1/ape/man/is.monophyletic.Rd |only ape-2.3-1/ape/man/makeNodeLabel.Rd | 2 ape-2.3-1/ape/man/opsin.Rd | 3 ape-2.3-1/ape/man/yule.cov.Rd | 20 +++--- ape-2.3/ape/man/klastorin.Rd |only ape-2.3/ape/src/treefunc.c |only 48 files changed, 305 insertions(+), 266 deletions(-)