Author: Klaus Schliep
Title: Phylogenetic analysis in R
Description: Phylogenetic analysis in R (Estimation of phylogenetic
trees and networks using Maximum Likelihood, Maximum Parsimony,
Distance methods & Hadamard conjugation)
Diff between phangorn versions 0.99-2 dated 2009-07-21 and 0.99-3 dated 2009-10-30
ChangeLog | 19 + DESCRIPTION | 10 NAMESPACE | 5 R/phylo.R | 860 ++++++++++++++++++++++++++++++++++++++------- inst/doc/Rplots.pdf | 276 ++++++-------- inst/doc/Trees.pdf | 902 +++++++++++++++++++++++------------------------- man/Laurasiatherian.Rd | 2 man/NJ.Rd | 4 man/SH.test.Rd | 2 man/allTrees.Rd | 17 man/bootstrap.pml.Rd | 4 man/designTree.Rd | 2 man/dfactorial.Rd | 2 man/dist.hamming.Rd | 2 man/distanceHadamard.Rd | 2 man/hadamard.Rd | 2 man/nni.Rd |only man/parsimony.Rd | 2 man/phyDat.Rd | 6 man/pml.Rd | 6 man/pmlCluster.Rd | 3 man/pmlMix.Rd | 2 man/pmlPart.Rd | 2 man/read.aa.Rd | 2 man/simSeq.Rd | 2 man/splitsNetwork.Rd | 2 man/treedist.Rd | 4 man/upgma.Rd | 2 src/phangorn.c | 270 +++++++++++++- 29 files changed, 1611 insertions(+), 803 deletions(-)
Author: Torsten Hothorn, Kurt Hornik, Mark A. van de Wiel and Achim
Zeileis
Title: Conditional Inference Procedures in a Permutation Test Framework
Description: Conditional inference procedures for the general
independence problem including two-sample, K-sample
(non-parametric ANOVA), correlation, censored, ordered and
multivariate problems.
Diff between coin versions 1.0-7 dated 2009-09-29 and 1.0-8 dated 2009-10-30
DESCRIPTION | 8 NEWS | 10 R/ExactDistributions.R | 9 inst/doc/LegoCondInf.pdf |binary inst/doc/MAXtest.pdf |binary inst/doc/coin.pdf |binary inst/doc/coin_implementation.pdf |binary inst/documentation/html/Classes_8c-source.html | 2 inst/documentation/html/Classes_8c.html | 2 inst/documentation/html/Classes_8h-source.html | 2 inst/documentation/html/Classes_8h.html | 2 inst/documentation/html/Helpers_8c-source.html | 2 inst/documentation/html/Helpers_8c.html | 2 inst/documentation/html/Helpers_8h-source.html | 2 inst/documentation/html/Helpers_8h.html | 2 inst/documentation/html/LinearStatistic_8c-source.html | 2 inst/documentation/html/LinearStatistic_8c.html | 2 inst/documentation/html/LinearStatistic_8h-source.html | 2 inst/documentation/html/LinearStatistic_8h.html | 2 inst/documentation/html/StreitbergRoehmel_8c-source.html | 2 inst/documentation/html/StreitbergRoehmel_8c.html | 2 inst/documentation/html/annotated.html | 2 inst/documentation/html/classes.html | 2 inst/documentation/html/coin__common_8h-source.html | 2 inst/documentation/html/coin__common_8h.html | 2 inst/documentation/html/dir_551893842a8579748e8cac726fc2aaac.html | 2 inst/documentation/html/dirs.html | 2 inst/documentation/html/files.html | 2 inst/documentation/html/functions.html | 2 inst/documentation/html/functions_vars.html | 2 inst/documentation/html/globals.html | 12 inst/documentation/html/globals_func.html | 12 inst/documentation/html/globals_vars.html | 2 inst/documentation/html/graph_legend.html | 2 inst/documentation/html/main.html | 2 inst/documentation/html/structcelW-members.html | 2 inst/documentation/html/structcelW.html | 4 inst/documentation/html/vandeWiel_8c-source.html | 174 +++++----- inst/documentation/html/vandeWiel_8c.html | 98 +++-- inst/documentation/html/vandeWiel_8c_18f96560e9861316db1121e8fe69ef07_cgraph.map |only inst/documentation/html/vandeWiel_8c_18f96560e9861316db1121e8fe69ef07_cgraph.md5 |only inst/documentation/html/vandeWiel_8c_18f96560e9861316db1121e8fe69ef07_cgraph.png |only inst/documentation/html/vandeWiel_8c_6bee1e9d657a3174d5a2ecafac2b1d6e_cgraph.map |only inst/documentation/html/vandeWiel_8c_6bee1e9d657a3174d5a2ecafac2b1d6e_cgraph.md5 |only inst/documentation/html/vandeWiel_8c_6bee1e9d657a3174d5a2ecafac2b1d6e_cgraph.png |only inst/documentation/html/vandeWiel_8c_b36f32483d67f870c4dca34aac14f5b9_cgraph.map |only inst/documentation/html/vandeWiel_8c_b36f32483d67f870c4dca34aac14f5b9_cgraph.md5 |only inst/documentation/html/vandeWiel_8c_b36f32483d67f870c4dca34aac14f5b9_cgraph.png |only inst/documentation/latex/dir_551893842a8579748e8cac726fc2aaac_dep.pdf | 16 inst/documentation/latex/doxygen.sty | 4 inst/documentation/latex/refman.tex | 2 inst/documentation/latex/structcelW.tex | 2 inst/documentation/latex/vandeWiel_8c.tex | 50 +- inst/documentation/latex/vandeWiel_8c_18f96560e9861316db1121e8fe69ef07_cgraph.eps |only inst/documentation/latex/vandeWiel_8c_18f96560e9861316db1121e8fe69ef07_cgraph.md5 |only inst/documentation/latex/vandeWiel_8c_18f96560e9861316db1121e8fe69ef07_cgraph.pdf |only inst/documentation/latex/vandeWiel_8c_6bee1e9d657a3174d5a2ecafac2b1d6e_cgraph.eps |only inst/documentation/latex/vandeWiel_8c_6bee1e9d657a3174d5a2ecafac2b1d6e_cgraph.md5 |only inst/documentation/latex/vandeWiel_8c_6bee1e9d657a3174d5a2ecafac2b1d6e_cgraph.pdf |only inst/documentation/latex/vandeWiel_8c_b36f32483d67f870c4dca34aac14f5b9_cgraph.eps |only inst/documentation/latex/vandeWiel_8c_b36f32483d67f870c4dca34aac14f5b9_cgraph.md5 |only inst/documentation/latex/vandeWiel_8c_b36f32483d67f870c4dca34aac14f5b9_cgraph.pdf |only inst/documentation/man/man3/Classes.c.3 | 2 inst/documentation/man/man3/Classes.h.3 | 2 inst/documentation/man/man3/Helpers.c.3 | 2 inst/documentation/man/man3/Helpers.h.3 | 2 inst/documentation/man/man3/LinearStatistic.c.3 | 2 inst/documentation/man/man3/LinearStatistic.h.3 | 2 inst/documentation/man/man3/StreitbergRoehmel.c.3 | 2 inst/documentation/man/man3/_home_hothorn_projects_svn_Rpkgs_trunk_coin_src_.3 | 2 inst/documentation/man/man3/celW.3 | 4 inst/documentation/man/man3/coin_common.h.3 | 2 inst/documentation/man/man3/vandeWiel.c.3 | 26 - src/vandeWiel.c | 30 - tests/Examples/coin-Ex.Rout.save | 11 tests/bugfixes.Rout.save | 2 tests/codetools-checks.Rout.save | 4 tests/comparisons.Rout.save | 4 tests/regtest_2sample.Rout.save | 12 tests/regtest_Ksample.Rout.save | 10 tests/regtest_MTP.Rout.save | 2 tests/regtest_contingency.Rout.save | 4 tests/regtest_correlation.Rout.save | 12 83 files changed, 321 insertions(+), 273 deletions(-)
Author: Philippe Grosjean
Title: SciViews GUI API - Unit testing
Description: A complete unit test system and functions to implement its
GUI part
Diff between svUnit versions 0.6-2 dated 2009-06-28 and 0.6-4 dated 2009-10-30
DESCRIPTION | 12 NEWS | 45 R/svUnit-internal.R | 15 TODO | 17 inst/CITATION | 10 inst/doc/svUnit.Rnw | 9 inst/doc/svUnit.lyx | 23 inst/doc/svUnit.pdf | 2419 +++++++++++++++++++-------------------- inst/komodo/sciviewskunit-ko.xpi |binary man/guiTestReport.Rd | 4 10 files changed, 1311 insertions(+), 1243 deletions(-)
Author: Russell V. Lenth
Title: Response-surface analysis
Description: Provides functions to generate response-surface designs,
fit first- and second-order response-surface models, make
contour plots, obtain the path of steepest ascent, and do
canonical analysis.
Diff between rsm versions 1.20 dated 2009-10-20 and 1.21 dated 2009-10-30
DESCRIPTION | 6 R/contour-lm.R | 4 inst/NEWS | 10 inst/doc/rsm.Rnw | 594 +++++++++++++++++++++++++++---------------------------- inst/doc/rsm.bbl |only inst/doc/rsm.blg |only inst/doc/rsm.pdf |binary 7 files changed, 310 insertions(+), 304 deletions(-)
Author: Guido Schwarzer
Diff between meta versions 1.1-2 dated 2009-10-11 and 1.1-3 dated 2009-10-30
Title: Meta-Analysis with R
Description: Fixed and random effects meta-analysis. Functions for
tests of bias, forest and funnel plot.
meta-1.1-2/meta/ChangeLogs |only
meta-1.1-3/meta/ChangeLog |only
meta-1.1-3/meta/DESCRIPTION | 8 -
meta-1.1-3/meta/INDEX | 3
meta-1.1-3/meta/NAMESPACE | 4
meta-1.1-3/meta/R/funnel.default.R | 4
meta-1.1-3/meta/R/trimfill.R | 223 -----------------------------------
meta-1.1-3/meta/R/trimfill.default.R |only
meta-1.1-3/meta/R/trimfill.meta.R |only
meta-1.1-3/meta/man/trimfill.Rd | 52 --------
meta-1.1-3/meta/man/trimfill.meta.Rd |only
11 files changed, 17 insertions(+), 277 deletions(-)
Author: Micah Altman, Jeff Gill, Michael P. McDonald
Title: Tools for testing and improving accuracy of statistical results.
Description: This is a suite of tools designed to test and improve the
accuracy of statistical computation, including: Summarization
of the sensitivity of linear and non-linear models (lm, glm,
mle, nls) to measurement and numerical error; Sensitivity
analysis of dozens of models as run through Zelig; A
generalized cholesky method for correcting non-invertable
Hessians; Tests for the global optimality of non-linear
regression and maximum likelihood results; Tools for obtaining
true random numbers using entropy collected from the system
and/or entropy servers on the internet; A method for converting
floating point numbers to normalized fractions; Benchmark data
for checking the accuracy of basic distribution functions.
Diff between accuracy versions 1.32 dated 2009-05-04 and 1.33 dated 2009-10-30
accuracy-1.32/accuracy/inst/doc/Sweave.sty |only accuracy-1.33/accuracy/CHANGELOG | 10 accuracy-1.33/accuracy/DESCRIPTION | 10 accuracy-1.33/accuracy/NAMESPACE | 1 accuracy-1.33/accuracy/R/coefFunctions.R | 2 accuracy-1.33/accuracy/R/trueRandom.R | 89 accuracy-1.33/accuracy/inst/CITATION | 2 accuracy-1.33/accuracy/inst/doc/Rplots.pdf | 1594 +++++------ accuracy-1.33/accuracy/inst/doc/accuracy_vignette-plot1a.eps | 493 +-- accuracy-1.33/accuracy/inst/doc/accuracy_vignette-plot1a.pdf | 542 +-- accuracy-1.33/accuracy/inst/doc/accuracy_vignette-plot2a.eps | 629 ++-- accuracy-1.33/accuracy/inst/doc/accuracy_vignette-plot2a.pdf | 1014 +++--- accuracy-1.33/accuracy/inst/doc/accuracy_vignette.Rnw | 5 accuracy-1.33/accuracy/inst/doc/accuracy_vignette.aux | 2 accuracy-1.33/accuracy/inst/doc/accuracy_vignette.bbl | 103 accuracy-1.33/accuracy/inst/doc/accuracy_vignette.blg | 20 accuracy-1.33/accuracy/inst/doc/accuracy_vignette.log | 385 +- accuracy-1.33/accuracy/inst/doc/accuracy_vignette.pdf |binary accuracy-1.33/accuracy/inst/doc/accuracy_vignette.tex | 48 accuracy-1.33/accuracy/man/dehaan.Rd | 4 accuracy-1.33/accuracy/man/disttest.Rd | 2 accuracy-1.33/accuracy/man/html.Rd | 2 accuracy-1.33/accuracy/man/psim.Rd | 4 accuracy-1.33/accuracy/man/pzelig.Rd | 4 accuracy-1.33/accuracy/man/starr.Rd | 6 accuracy-1.33/accuracy/man/trueRandom.Rd | 13 26 files changed, 2527 insertions(+), 2457 deletions(-)
Author: Kurt Hornik, with contributions from Christian Buchta, Torsten
Hothorn, Alexandros Karatzoglou, David Meyer, and Achim Zeileis
Title: R/Weka interface
Description: An R interface to Weka (Version 3.6.1). Weka is a
collection of machine learning algorithms for data mining tasks
written in Java, containing tools for data pre-processing,
classification, regression, clustering, association rules, and
visualization. Both the R interface and Weka itself are
contained in the RWeka package. For more information on Weka
see http://www.cs.waikato.ac.nz/~ml/weka/.
Diff between RWeka versions 0.3-22 dated 2009-10-18 and 0.3-23 dated 2009-10-30
DESCRIPTION | 8 ++++---- R/graph.R | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Author: Roger Bivand
Title: Interface between GRASS 6 geographical information system and R
Description: Interpreted interface between GRASS 6 geographical
information system and R, based on starting R from within the
GRASS environment, or running free-standing R in a temporary
GRASS location; the package provides facilities for using all
GRASS commands from the R command line.
Diff between spgrass6 versions 0.6-9 dated 2009-09-05 and 0.6-11 dated 2009-10-30
ChangeLog | 17 +++++++++++++ DESCRIPTION | 8 +++--- R/vect_link.R | 70 ++++----------------------------------------------------- R/xml1.R | 17 ++++++++----- inst/ChangeLog | 17 +++++++++++++ 5 files changed, 54 insertions(+), 75 deletions(-)
Author: Timothy H. Keitt
Diff between rgdal versions 0.6-19 dated 2009-10-05 and 0.6-20 dated 2009-10-30
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 | 9 +++++++--
DESCRIPTION | 8 ++++----
R/gdal.R | 2 +-
R/sgdf_gdal.R | 1 +
R/sp_gdal.R | 4 ++++
R/subs.R | 1 +
inst/ChangeLog | 9 +++++++--
src/gdal-bindings.cpp | 18 +++++++++++-------
8 files changed, 36 insertions(+), 16 deletions(-)
Author: Ernesto Barrios
Title: Useful Functions for Box, Hunter and Hunter II
Description: Functions and data sets reproducing some examples in Box,
Hunter and Hunter II
Diff between BHH2 versions 1.0.2 dated 2009-01-30 and 1.0.3 dated 2009-10-30
DESCRIPTION | 25 ++++++++++++++----------- R/ffDesMatrix.R | 4 ++-- R/ffFullMatrix.R | 4 ++-- inst/doc/BHH2.Rnw | 2 +- inst/doc/BHH2.pdf |binary inst/doc/auto |only man/ffDesMatrix.Rd | 4 +++- 7 files changed, 22 insertions(+), 17 deletions(-)
Author: Micah Altman
Diff between BARD versions 1.03 dated 2009-01-07 and 1.05 dated 2009-10-30
Title: Better Automated ReDistricting
Description: This is a package for automated redistricting and
heuristic exploration of redistricter revealed preference
CHANGELOG | 6
DESCRIPTION | 17
R/bardCluster.R | 528
R/bardComparison.R | 840
R/bardInteractive.R | 418
R/bardOptim.R | 2
R/bardPlan.R | 1544
R/bardProfile.R | 804
R/miniball.R | 144
R/zzz.R | 4
TODO | 3
inst/CITATION | 6
inst/doc/Rplots.pdf |792042 +++++++++++++++++++++----------------------
inst/doc/bardJSS-plot1a.eps |111605 +++---
inst/doc/bardJSS-plot1a.pdf |119722 +++---
inst/doc/bardJSS-plot2a.eps |275962 +++++++--------
inst/doc/bardJSS-plot2a.pdf |535453 ++++++++++++++---------------
inst/doc/bardJSS-plot3a.eps | 944
inst/doc/bardJSS-plot3a.pdf | 1173
inst/doc/bardJSS.Rnw | 2185
inst/doc/bardJSS.aux | 96
inst/doc/bardJSS.bbl | 32
inst/doc/bardJSS.bib | 21
inst/doc/bardJSS.blg | 62
inst/doc/bardJSS.log | 702
inst/doc/bardJSS.pdf |803365 ++++++++++++++++++++++----------------------
inst/doc/bardJSS.tex | 421
man/BARD.package.Rd | 6
src/Makevars | 2
src/Makevars.unix | 2
30 files changed, 1328765 insertions(+), 1319346 deletions(-)