Author: Michael D. Sumner
Title: Spatial analysis of animal track data
Description: Functions for accessing and manipulating spatial data for
animal tracking. Filter for speed and create time spent plots
from animal track data.
Diff between trip versions 1.1-3 dated 2009-10-12 and 1.1-4 dated 2009-12-06
ChangeLog |only DESCRIPTION | 6 +-- R/trip.R | 98 ++++++++++++++++++++++++++++++------------------------------ 3 files changed, 52 insertions(+), 52 deletions(-)
Author: Fortran original by Leo Breiman and Adele Cutler, R port by
Andy Liaw and Matthew Wiener.
Title: Breiman and Cutler's random forests for classification and
regression
Description: Classification and regression based on a forest of trees
using random inputs.
Diff between randomForest versions 4.5-33 dated 2009-10-18 and 4.5-34 dated 2009-12-06
DESCRIPTION | 8 ++++---- NEWS |only R/margin.R | 2 +- R/randomForest.default.R | 2 +- R/zzz.R | 6 +++--- inst/NEWS | 6 ++++++ man/getTree.Rd | 6 +++--- man/predict.randomForest.Rd | 3 +++ man/randomForest.Rd | 3 +++ 9 files changed, 24 insertions(+), 12 deletions(-)
Author: Ian Taylor, Ian Stewart, Tommy Garrison, Andre Punt, John
Wallace, and other contributors
Title: R code for Stock Synthesis
Description: Functions for reading output, plotting, exploring and
manipulating input files for Richard Methot's Stock Synthesis
fisheries stock assessment modeling platform.
Diff between r4ss versions 1.01 dated 2009-11-16 and 1.02 dated 2009-12-06
DESCRIPTION | 8 R/SS_changepars.R | 7 R/SS_fitbiasramp.R | 30 R/SS_parlines.R | 5 R/SSv3_output.R | 58 + R/SSv3_plotpars.R | 22 R/SSv3_plots.R | 1385 ++++++++++++++++++++++++--------------------- inst/doc/r4ss_vignette.pdf |binary man/SS_parlines.Rd | 13 man/r4ss-package.Rd | 4 10 files changed, 839 insertions(+), 693 deletions(-)
Author: Eva Herrmann
Diff between plugdensity versions 0.8-1 dated 2004-11-03 and 0.8-2 dated 2009-12-06
Title: Plug-in Kernel Density Estimation
Description: Kernel density estimation with global bandwidth selection
via "plug-in".
ChangeLog |only
DESCRIPTION | 16 +++++++++-------
tests/ex.Rout.save | 9 +++++----
3 files changed, 14 insertions(+), 11 deletions(-)
Author: Wolfgang Viechtbauer
Diff between metafor versions 0.5-5 dated 2009-10-08 and 0.5-7 dated 2009-12-06
Title: Meta-Analysis Package for R
Description: The metafor package consists of a collection of functions
for conducting meta-analyses in R. Fixed- and random-effects
models (with and without moderators) can be fitted via the
general linear (mixed-effects) model. For 2x2 table data, the
Mantel-Haenszel and Peto's method are also implemented.
DESCRIPTION | 8
NAMESPACE | 2
NEWS | 27 +
R/metafor.R | 825 +++++++++++++++++++++++++----------------
man/addpoly.Rd | 4
man/addpoly.default.Rd | 4
man/addpoly.rma.Rd | 4
man/anova.rma.uni.Rd | 6
man/blup.Rd | 4
man/blup.rma.uni.Rd | 6
man/cint.Rd | 4
man/cint.rma.uni.Rd | 4
man/coef.rma.Rd | 4
man/cumul.Rd | 4
man/cumul.rma.mh.Rd | 6
man/cumul.rma.uni.Rd | 4
man/dat.bcg.Rd | 2
man/fitstats.Rd | 4
man/fitstats.rma.Rd | 4
man/fitted.rma.Rd | 4
man/forest.Rd | 4
man/forest.default.Rd | 4
man/forest.rma.Rd | 4
man/forest.rma.cumul.Rd | 4
man/funnel.Rd | 4
man/funnel.rma.Rd | 4
man/hatvalues.rma.uni.Rd | 4
man/influence.rma.uni.Rd | 24 -
man/leave1out.Rd | 4
man/leave1out.rma.mh.Rd | 6
man/leave1out.rma.uni.Rd | 4
man/logLik.rma.Rd | 4
man/metafor-package.Rd | 9
man/metafor.news.Rd |only
man/permutest.Rd |only
man/permutest.rma.uni.Rd |only
man/plot.infl.rma.uni.Rd | 14
man/plot.rma.uni.Rd | 8
man/predict.rma.uni.Rd | 6
man/print.anova.rma.uni.Rd | 4
man/print.fsn.Rd | 4
man/print.infl.rma.uni.Rd | 4
man/print.list.rma.Rd | 4
man/print.permutest.rma.uni.Rd |only
man/print.ranktest.rma.Rd | 4
man/print.regtest.rma.Rd | 4
man/print.rma.uni.Rd | 10
man/qqnorm.rma.uni.Rd | 8
man/radial.Rd | 6
man/radial.rma.Rd | 4
man/ranktest.Rd | 4
man/ranktest.rma.Rd | 4
man/regtest.Rd | 4
man/regtest.rma.Rd | 4
man/residuals.rma.Rd | 16
man/rma.mh.Rd | 2
man/rma.peto.Rd | 2
man/rma.uni.Rd | 10
man/transf.Rd | 16
man/trimfill.Rd | 4
man/trimfill.rma.uni.Rd | 4
man/vcov.rma.Rd | 4
62 files changed, 700 insertions(+), 463 deletions(-)
Author: Hrishikesh D. Vinod
Diff between meboot versions 1.0-2 dated 2009-11-20 and 1.1-1 dated 2009-12-06
Title: Maximum Entropy Bootstrap for Time Series
Description: This package performs maximum entropy density based
dependent data bootstrap. An algorithm is provided to create a
population of time series (ensemble) without assuming
stationarity. The reference paper (Vinod, H.D., 2004) explains
how the algorithm satisfies the ergodic theorem and the central
limit theorem.
meboot-1.0-2/meboot/inst/doc/airp1.pdf |only
meboot-1.0-2/meboot/inst/doc/jss.bst |only
meboot-1.0-2/meboot/inst/doc/jss.cls |only
meboot-1.0-2/meboot/inst/doc/meboot.Rnw |only
meboot-1.0-2/meboot/inst/doc/meboot.bib |only
meboot-1.0-2/meboot/inst/doc/t5ex.pdf |only
meboot-1.0-2/meboot/inst/doc/t5ex_density.pdf |only
meboot-1.1-1/meboot/DESCRIPTION | 8 ++--
meboot-1.1-1/meboot/R/checkConv.R | 47 ++++++++++++++------------
meboot-1.1-1/meboot/inst/doc/meboot.pdf |binary
meboot-1.1-1/meboot/man/checkConv.Rd | 13 +++----
11 files changed, 37 insertions(+), 31 deletions(-)
Author: Burkhardt Seifert
Diff between lpridge versions 1.0-4 dated 2007-06-25 and 1.0-5 dated 2009-12-06
Title: Local Polynomial (Ridge) Regression
Description: Local Polynomial Regression with Ridging.
DESCRIPTION | 12 +++++++-----
1 file changed, 7 insertions(+), 5 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 0.6-1 dated 2009-11-16 and 0.6-2 dated 2009-12-06
Changes-ToDo | 5 + DESCRIPTION | 8 +- R/predict.NaiveBayes.R | 143 +++++++++++++++++++++++++++------------------- inst/CITATION | 42 ++++++------- man/NaiveBayes.Rd | 2 man/b.scal.Rd | 2 man/benchB3.Rd | 2 man/calc.trans.Rd | 2 man/centerlines.Rd | 2 man/classscatter.Rd | 2 man/dkernel.Rd | 2 man/drawparti.Rd | 2 man/e.scal.Rd | 2 man/greedy.wilks.Rd | 2 man/kmodes.Rd | 2 man/loclda.Rd | 2 man/meclight.Rd | 2 man/nm.Rd | 2 man/partimat.Rd | 2 man/plineplot.Rd | 2 man/plot.NaiveBayes.Rd | 2 man/predict.NaiveBayes.Rd | 2 man/predict.loclda.Rd | 2 man/predict.meclight.Rd | 2 man/predict.sknn.Rd | 2 man/predict.svmlight.Rd | 2 man/quadplot.Rd | 2 man/quadtrafo.Rd | 2 man/sknn.Rd | 2 man/svmlight.Rd | 2 man/ucpm.Rd | 2 31 files changed, 142 insertions(+), 110 deletions(-)
Author: Dirk Eddelbuettel
Diff between digest versions 0.4.1 dated 2009-09-24 and 0.4.2 dated 2009-12-06
Title: Create cryptographic hash digests of R objects
Description: The digest package provides functions for the creation of
`hash' digests of arbitrary R objects using the md5, sha-1,
sha-256 and crc32 algorithms permitting easy comparison of R
language objects. The md5 algorithm by Ron Rivest is specified
in RFC 1321, the SHA-1 and SHA-256 algorithms are specified in
FIPS-180-1 and FIPS-180-2, and the crc32 algorithm is described
in ftp://ftp.rocksoft.com/cliens/rocksoft/papers/crc_v3.txt.
For md5, sha-1 and sha-256, this packages uses small standalone
implementations that were provided by Christophe Devine. For
crc32, code from the zlib library is used.
Please note that this package is not meant to be deployed for
cryptographic purposes for which more comprehensive (and widely
tested) libraries such as OpenSSL should be used.
DESCRIPTION | 12 +++++++-----
R/digest.R | 9 ++++++---
inst/ChangeLog | 9 +++++++++
3 files changed, 22 insertions(+), 8 deletions(-)
Author: Pin T. Ng
Diff between cobs99 versions 0.9-8 dated 2009-11-03 and 0.9-9 dated 2009-12-06
Title: Constrained B-splines -- outdated 1999 version
Description: Qualitatively Constrained (Regression) Smoothing via
Linear Programming. OUTDATED version based on He & Ng (1999),
the modified "non-simplex" algorithm of Bartels and Conn
(1980).
ChangeLog | 6 ++++++
DESCRIPTION | 8 ++++----
R/l1looDesign.R | 2 +-
tests/small-ex.Rout.save | 4 ++--
4 files changed, 13 insertions(+), 7 deletions(-)
Author: Carsten F. Dormann and Bernd Gruber, with additional code from
Mariano Devoto, Jochen Fruend, Jose Iriondo and Diego Vazquez,
also based on C-code developed by Nils Bluethgen and by Miguel
Rodriguez-Girones.
Title: Visualising bipartite networks and calculating some ecological
indices.
Description: Bipartite provides functions to viualise webs and
calculate a series of indices commonly used to describe pattern
in ecological webs. It focusses on webs consisting of only two
trophic levels, e.g. pollination webs or predator-prey-webs.
Visualisation is important to get an idea of what we are
actually looking at, while the indices summarise different
aspects of the webs topology.
Diff between bipartite versions 1.03 dated 2009-11-05 and 1.05 dated 2009-12-06
bipartite-1.03/bipartite/R/functspec.r |only bipartite-1.03/bipartite/man/functspec.Rd |only bipartite-1.05/bipartite/DESCRIPTION | 8 ++++---- bipartite-1.05/bipartite/R/specieslevel.R | 13 ++++++------- bipartite-1.05/bipartite/R/zzz.R | 6 ------ bipartite-1.05/bipartite/inst/CITATION | 10 +++++----- bipartite-1.05/bipartite/man/PAC.rd | 2 +- bipartite-1.05/bipartite/man/as.one.mode.Rd | 2 +- bipartite-1.05/bipartite/man/bipartite-package.Rd | 17 ++++++++++++----- 9 files changed, 29 insertions(+), 29 deletions(-)
Author: Original by F.L. Ramsey and D.W. Schafer, modifications by
Daniel W Schafer, Jeannie Sifneos and Berwin A Turlach
Title: Data sets from Ramsey and Schafer's "Statistical Sleuth (2nd
ed)"
Description: Data sets from Ramsey, F.L. and Schafer, D.W. (2002), "The
Statistical Sleuth: A Course in Methods of Data Analysis (2nd
ed)" Duxbury.
Diff between Sleuth2 versions 1.0-0 dated 2009-11-13 and 1.0-1 dated 2009-12-06
DESCRIPTION | 10 +++++----- R |only inst |only man/Sleuth2-package.Rd |only man/Sleuth2Manual.Rd |only 5 files changed, 5 insertions(+), 5 deletions(-)
Author: Matthias Burger
Diff between RUnit versions 0.4.22 dated 2009-04-24 and 0.4.25 dated 2009-12-06
Title: R Unit test framework
Description: R functions implementing a standard Unit Testing
framework, with additional code inspection and report
generation tools
RUnit-0.4.22/RUnit/tests/runitHTMLProtocol.r |only
RUnit-0.4.22/RUnit/tests/runitInspect.r |only
RUnit-0.4.22/RUnit/tests/runitPlotConnection.r |only
RUnit-0.4.22/RUnit/tests/runitRUnit.r |only
RUnit-0.4.22/RUnit/tests/runitS4.r |only
RUnit-0.4.22/RUnit/tests/runitSetUp.r |only
RUnit-0.4.22/RUnit/tests/runitTearDown.r |only
RUnit-0.4.22/RUnit/tests/runitTextProtocol.r |only
RUnit-0.4.25/RUnit/ChangeLog | 1632 +++-----------
RUnit-0.4.25/RUnit/DESCRIPTION | 10
RUnit-0.4.25/RUnit/NEWS | 27
RUnit-0.4.25/RUnit/R/00Init.r | 38
RUnit-0.4.25/RUnit/R/checkFuncs.r | 42
RUnit-0.4.25/RUnit/R/html.r | 4
RUnit-0.4.25/RUnit/R/htmlProtocol.r | 15
RUnit-0.4.25/RUnit/R/options.r |only
RUnit-0.4.25/RUnit/R/runit.r | 101
RUnit-0.4.25/RUnit/R/testLogger.r | 130 -
RUnit-0.4.25/RUnit/R/textProtocol.r | 84
RUnit-0.4.25/RUnit/inst/doc/RUnit.Rnw | 14
RUnit-0.4.25/RUnit/inst/doc/RUnit.dvi |binary
RUnit-0.4.25/RUnit/inst/doc/RUnit.pdf |binary
RUnit-0.4.25/RUnit/inst/doc/RUnit.ps | 182 -
RUnit-0.4.25/RUnit/inst/doc/RUnit.tex | 16
RUnit-0.4.25/RUnit/inst/examples/runitVirtualClassTest.r | 4
RUnit-0.4.25/RUnit/inst/examples/runitVirtualClassTest2.r | 2
RUnit-0.4.25/RUnit/inst/examples/runitc2f.r | 4
RUnit-0.4.25/RUnit/inst/share/R/checkCode.r | 14
RUnit-0.4.25/RUnit/inst/share/R/compareRUnitTestData.r | 10
RUnit-0.4.25/RUnit/inst/unitTests |only
RUnit-0.4.25/RUnit/man/RUnit-intro.Rd | 28
RUnit-0.4.25/RUnit/man/RUnit-options.Rd |only
RUnit-0.4.25/RUnit/man/checkFuncs.Rd | 64
RUnit-0.4.25/RUnit/man/inspect.Rd | 8
RUnit-0.4.25/RUnit/man/printHTML.trackinfo.Rd | 15
RUnit-0.4.25/RUnit/man/runit.Rd | 61
RUnit-0.4.25/RUnit/man/testCaseSetUp.Rd |only
RUnit-0.4.25/RUnit/man/textProtocol.Rd | 14
RUnit-0.4.25/RUnit/man/tracker.Rd | 8
RUnit-0.4.25/RUnit/tests/README |only
RUnit-0.4.25/RUnit/tests/runUnitTests.r |only
41 files changed, 876 insertions(+), 1651 deletions(-)
Author: TISEAN authors: Rainer Hegger, Holger Kantz, Thomas Schreiber.
R interface code by Antonio, Fabio Di Narzo, R documentation
and examples by Gianluca Gazzola
Title: R interface to Tisean algorithms
Description: Algorithms for time series analysis from nonlinear
dynamical systems theory originally made available by Rainer
Hegger, Holger Kantz and Thomas Schreiber at the site
http://www.mpipks-dresden.mpg.de/~tisean/ . A related R
package (tseriesChaos by Antonio, Fabio Di Narzo) contains
rewritten versions of a few of the TISEAN algorithms. The
intention of the present package is to use the TISEAN routines
from within R with no need of manual importing/exporting. It
is in a beta version state, though most of the functions should
be usable. Correspondence should be sent to either Marji
Lines, lines@dss.uniud.it, or to the current maintainer of the
package. This package only contains R interface code. It
requires that you have the Tisean-3.0.1 algorithms available on
your computer.
Diff between RTisean versions 3.0.10 dated 2009-02-09 and 3.0.11 dated 2009-12-06
ChangeLog | 8 +++++++- DESCRIPTION | 40 +++++++++++++++++++++++++++++----------- R/lfo-run.r | 34 +++++++++++++++++----------------- man/av_d2.Rd | 1 - man/poincare.Rd | 1 - 5 files changed, 53 insertions(+), 31 deletions(-)
Author: Daniela Witten and Rob Tibshirani and Sam Gross
Title: Penalized Multivariate Analysis
Description: Performs Penalized Multivariate Analysis: a penalized
matrix decomposition, sparse principal components analysis, and
sparse canonical correlation analysis, described in the
following papers: (1) Witten, Tibshirani and Hastie (2009) A
penalized matrix decomposition, with applications to sparse
principal components and canonical correlation analysis.
Biostatistics 10(3):515-534. (2) Witten and Tibshirani (2009)
Extensions of sparse canonical correlation analysis, with
applications to genomic data. Statistical Applications in
Genetics and Molecular Biology 8(1): Article 28.
Diff between PMA versions 1.0.4 dated 2009-10-22 and 1.0.5 dated 2009-12-06
DESCRIPTION | 8 ++--- R/CCA.R | 8 ++--- R/PMD.R | 55 +++++++++++++++++++++++++------------- man/CCA.Rd | 82 ++++++++++++++++++++++++++++++---------------------------- man/SPC.Rd | 7 +++- man/SPC.cv.Rd | 4 +- 6 files changed, 94 insertions(+), 70 deletions(-)
Author: Marko Robnik-Sikonja
Diff between CORElearn versions 0.9.22 dated 2009-09-20 and 0.9.24 dated 2009-12-06
Title: CORElearn - classification, regression, feature evaluation and
ordinal evaluation
Description: CORElearn is machine learning suite ported to R from
standalone C++ package. It contains several model learning
techniques in classification and regression, for example
classification and regression trees with optional constructive
induction and models in the leafs, random forests, kNN, naive
Bayes, and locally weighted regression. It is especially strong
in feature evaluation algorithms where it contains several
variants of Relief algorithm and many impurity based attribute
evaluation functions, e.g., Gini, information gain, MDL, DKM,
... Its additional strength is ordEval algorithm and its
visualization used for ordinal features and class. The top
level documentation is reachable through ?CORElearn.
COPYING | 29 ++++-----
ChangeLog | 3
DESCRIPTION | 12 +--
NAMESPACE | 2
R/Rinterface.R | 12 +--
R/init.R | 4 -
R/ordEval.R | 139 ++++++++++++++++++++++++++++++++++++----------
R/util.R | 42 ++++++++-----
gpl-3.0-standalone.html |only
man/CORElearn-internal.Rd | 2
man/CORElearn-package.Rd | 4 -
man/CoreModel.Rd | 6 -
man/attrEval.Rd | 4 -
man/infoCore.Rd | 2
man/optionCore.Rd | 13 ++--
man/ordEval.Rd | 4 -
man/paramCoreIO.Rd | 2
man/plot.ordEval.Rd | 17 +++--
man/predict.CoreModel.Rd | 4 -
man/preparePlot.Rd | 15 +++-
src/Rconvert.cpp | 7 +-
src/frontend.cpp | 21 +++---
src/utils.h | 6 -
23 files changed, 232 insertions(+), 118 deletions(-)
Author: Marc J. Mazerolle
Diff between AICcmodavg versions 1.04 dated 2009-11-12 and 1.05 dated 2009-12-06
Title: Model selection and multimodel inference based on (Q)AIC(c)
Description: This package includes functions to create model selection
tables based on Akaike's information criterion (AIC) and the
second-order AIC (AICc), as well as their quasi-likelihood
counterparts (QAIC, QAICc). Tables are printed with delta AIC
and Akaike weights. The package also includes functions to
conduct model averaging (multimodel inference) for a given
parameter of interest or predicted values. Other handy
functions enable the computation of relative variable
importance, evidence ratios, and confidence sets for the best
model. The present version works with linear models ('lm'
class), generalized linear models ('glm' class), linear mixed
models ('lme' class), multinomial and ordinal logistic
regressions ('multinom' and 'polr' classes).
DESCRIPTION | 8 +-
R/AICc.glm.R | 2
R/AICc.mult.R | 2
R/aictab.R | 29 ++++++++--
R/aictab.glm.R | 37 ++++++++----
R/aictab.lme.R | 22 ++++++-
R/aictab.mult.R | 46 ++++++++++-----
R/aictab.polr.R | 18 ++++--
R/confset.R | 2
R/importance.R | 4 -
R/modavg.R | 38 +++++++------
R/modavg.glm.R | 14 +++-
R/modavg.lme.R | 133 +++++++++++++++++++++++++++++++++++++---------
R/modavg.mult.R | 22 +++++--
R/modavg.polr.R | 89 +++++++++++++++++-------------
man/AICc.Rd | 18 +++---
man/AICcmodavg-package.Rd | 4 -
man/aictab.Rd | 52 ++++++++++-------
man/c_hat.Rd | 14 +++-
man/confset.Rd | 38 ++++++-------
man/evidence.Rd | 33 +++++------
man/importance.Rd | 10 +--
man/modavg.Rd | 58 ++++++++++----------
man/modavgpred.Rd | 38 ++++++-------
24 files changed, 464 insertions(+), 267 deletions(-)