Author: Garrett M. Dancik
Title: Maximum Likelihood Estimates of Gaussian Processes
Description: Maximum likelihood Gaussian process modeling for univariate and multi-dimensional outputs with diagnostic plots and sensitivity analysis.
Diff between mlegp versions 2.2.5 dated 2008-12-21 and 2.2.6 dated 2009-03-08
CHANGES | 3 DESCRIPTION | 6 READ_ME | 3 inst/doc/Rplots.ps |only inst/doc/gp_ex-003.eps |only inst/doc/gp_ex-003.pdf | 285 +++++++++++++++++++++--------------------- inst/doc/gp_ex.tex |only man/CV.Rd | 2 man/FANOVADecomposition.Rd | 2 man/FANOVAFunctions.Rd | 2 man/createGP.Rd | 2 man/createWindow.Rd | 2 man/gp.list.Rd | 2 man/is.gp.Rd | 2 man/mlegp-internal.Rd | 2 man/mlegp-naming-functions.Rd | 2 man/mlegp-package.Rd | 2 man/mlegp-sa-internal.Rd | 2 man/mlegp-svd-functions.Rd | 2 man/mlegp.Rd | 2 man/nice.Rd | 2 man/nugget.Rd | 2 man/paramLookup.Rd | 2 man/plot.gp.Rd | 3 man/plot.gp.list.Rd | 2 man/plotInteractionEffect.Rd | 2 man/plotMainEffects.Rd | 21 +-- man/plotObservedEffects.Rd | 2 man/predict.gp.Rd | 2 man/print.gp.Rd | 2 man/print.gp.list.Rd | 2 man/summary.gp.Rd | 2 man/summary.gp.list.Rd | 2 src/Makevars.win | 4 34 files changed, 187 insertions(+), 186 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 1.10 dated 2008-12-31 and 1.11 dated 2009-03-08
DESCRIPTION | 6 +++--- R/contour-lm.R | 9 +++++++-- R/sysdata.rda |binary inst/NEWS | 8 ++++++++ inst/doc/rsm.Rtex | 2 +- inst/doc/rsm.pdf |binary man/heli.Rd | 8 +++++--- 7 files changed, 24 insertions(+), 9 deletions(-)
Author: Ken Beath
Diff between randomLCA versions 0.6-1 dated 2008-11-09 and 0.6-2 dated 2009-03-08
Title: Random Effects Latent Class Analysis
Description: Fits random effects latent class models, as well as standard latent class models.
DESCRIPTION | 8 +--
R/bestlca.R | 8 ++-
R/fit.fixed.randomLCA.R | 15 ++++--
R/norm.gauss.hermite.R | 96 +++++++++++++++++++++++++++++++++++++++--
R/randomLCA.R | 16 +++++-
data/genderrole.rda |only
inst/NEWS | 12 +++++
inst/doc/randomLCA-example.Rnw | 59 +++++++++++++++++--------
inst/doc/randomLCA-example.pdf |binary
man/genderrole.Rd |only
man/hivtests.Rd | 2
man/randomLCA.Rd | 6 +-
src/bernoulliprob.c | 1
src/fixednlm.c |only
14 files changed, 184 insertions(+), 39 deletions(-)
Author: Yves Croissant
Diff between plm versions 1.1-0 dated 2009-02-25 and 1.1-1 dated 2009-03-08
Title: Linear models for panel data
Description: A set of estimators and tests for panel data
plm-1.1-0/plm/inst/doc/ldvm.bib |only
plm-1.1-0/plm/inst/doc/ldvm.tex |only
plm-1.1-1/plm/DESCRIPTION | 6
plm-1.1-1/plm/NAMESPACE | 2
plm-1.1-1/plm/R/fixef.R | 15
plm-1.1-1/plm/R/plm.formula.R | 27
plm-1.1-1/plm/R/plm.model.R | 6
plm-1.1-1/plm/R/pserial.R | 2
plm-1.1-1/plm/R/ptest.R | 4
plm-1.1-1/plm/R/pvcovHC.R | 4
plm-1.1-1/plm/changelog | 29
plm-1.1-1/plm/inst/doc/plm.pdf | 7101 +++++++++++++++++++++++++---------------
plm-1.1-1/plm/man/fixef.plm.Rd | 2
plm-1.1-1/plm/man/plm.Rd | 8
plm-1.1-1/plm/man/vcovHC.Rd | 1
15 files changed, 4583 insertions(+), 2624 deletions(-)
Author: C. Fraley and A.E. Raftery, Dept. of Statistics,
University of Washington.
R port by Ron Wehrens.
Title: Model-based cluster analysis (older version)
Description: Model-based cluster analysis: the 2002 version of MCLUST
Diff between mclust02 versions 2.1-17 dated 2008-05-16 and 2.1-18 dated 2009-03-08
CHANGELOG |only DESCRIPTION | 6 +++--- LICENSE | 8 +++++--- R/mclust02.R | 19 ++++--------------- man/density.Rd | 4 +--- man/estep.Rd | 10 +++++----- man/estepE.Rd | 14 +++++--------- man/me.Rd | 4 ++-- man/meE.Rd | 11 ++++++----- man/mstep.Rd | 9 +++++---- man/mstepE.Rd | 9 +++++---- man/plot.Mclust.Rd | 2 +- man/plot.mclustDA.Rd | 2 +- man/sim.Rd | 2 +- man/simE.Rd | 2 ++ man/summary.EMclust.Rd | 2 +- man/summary.EMclustN.Rd | 2 +- man/summary.Mclust.Rd | 2 +- man/summary.mclustDAtest.Rd | 2 +- man/summary.mclustDAtrain.Rd | 2 +- 20 files changed, 51 insertions(+), 61 deletions(-)
Author: Chris Fraley and Adrian Raftery
Title: Model-Based Clustering / Normal Mixture Modeling
Description: Model-based clustering and normal mixture modeling
including Bayesian regularization
Diff between mclust versions 3.1-10 dated 2008-11-30 and 3.1-10.3 dated 2009-03-08
CHANGELOG | 9 DESCRIPTION | 6 LICENSE | 8 man/mstep.Rd | 12 man/mstepE.Rd | 10 man/priorControl.Rd | 1 src/mclust.f | 1703 ++-------------------------------------------------- 7 files changed, 101 insertions(+), 1648 deletions(-)
Author: Zachariah Gompert, C. Alex Buerkle
Title: introgress
Description: introgress provides functions for analyzing introgression of genotypes between divergent, hybridizing lineages, including estimating genomic clines from multi-locus genotype data and testing for deviations from neutral expectations. Functions are also provided for maximum likelihood estimation of molecular hybrid index and graphical analysis.
Diff between introgress versions 1.0 dated 2009-02-25 and 1.1 dated 2009-03-08
DESCRIPTION | 4 R/clines.plot.R | 9 +- R/fit.c.clines.R | 29 ------ R/fit.invariant.clines.R |only R/genomic.clines.R | 185 +++++++++++++++++++++++++------------------- R/per.locus.like.R | 17 +++- data/LociDataSim1.rda |binary data/LociDataSim2.rda |binary man/AdmixDataSim1.Rd | 4 man/AdmixDom.Rd | 2 man/LociD.Rd | 2 man/LociDataSim1.Rd | 2 man/clines.plot.Rd | 7 - man/compare.clines.Rd | 6 - man/est.h.Rd | 4 man/fit.invariant.clines.Rd |only man/genomic.clines.Rd | 6 + man/introgress-package.Rd | 4 man/prepare.data.Rd | 6 - 19 files changed, 153 insertions(+), 134 deletions(-)
Author: Mark S. Handcock
Diff between ergm versions 2.2-0 dated 2009-03-01 and 2.2-1 dated 2009-03-08
Title: Fit, Simulate and Diagnose Exponential-Family Models for Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGM). "ergm" is a part of the "statnet" suite of packages for network analysis. For a list of functions type: help(package='ergm')
DESCRIPTION | 6 +++---
R/ergm.getMCMCsample.R | 31 +++++++++++++++----------------
R/ergm.mainfitloop.R | 11 +++--------
R/mcmc.diagnostics.ergm.R | 8 ++++++--
R/print.summary.ergm.R | 16 ++++------------
5 files changed, 31 insertions(+), 41 deletions(-)
Author: Luke Tierney
Diff between codetools versions 0.2-1 dated 2008-04-02 and 0.2-2 dated 2009-03-08
Title: Code Analysis Tools for R
Description: Code analysis tools for R
DESCRIPTION | 4 ++--
R/codetools.R | 7 +++++--
2 files changed, 7 insertions(+), 4 deletions(-)
Author: Heather Stoll
Diff between WhatIf versions 1.5-4 dated 2007-10-14 and 1.5-5 dated 2009-03-08
Title: WhatIf: Software for Evaluating Counterfactuals
Description: Inferences about counterfactuals are essential for prediction,
answering what if questions, and estimating causal effects.
However, when the counterfactuals posed are too far from the data at
hand, conclusions drawn from well-specified statistical analyses
become based largely on speculation hidden in convenient modeling
assumptions that few would be willing to defend. Unfortunately,
standard statistical approaches assume the veracity of the model
rather than revealing the degree of model-dependence, which makes this
problem hard to detect. WhatIf offers easy-to-apply methods to
evaluate counterfactuals that do not require sensitivity testing over
specified classes of models. If an analysis fails the tests offered
here, then we know that substantive inferences will be sensitive to at
least some modeling choices that are not based on empirical evidence,
no matter what method of inference one chooses to use. WhatIf
implements the methods for evaluating counterfactuals discussed in
Gary King and Langche Zeng, 2006, "The Dangers of Extreme
Counterfactuals," Political Analysis 14 (2); and Gary
King and Langche Zeng, 2007, "When Can History Be Our Guide? The
Pitfalls of Counterfactual Inference," International Studies
Quarterly 51 (March).
DESCRIPTION | 6
inst/doc/index.shtml | 2
inst/doc/whatif.aux | 2
inst/doc/whatif.bbl | 17
inst/doc/whatif.blg | 26
inst/doc/whatif.log | 22
inst/doc/whatif.pdf | 1435 +++++++++++++++++++++++++--------------------------
inst/doc/whatif.tex | 2
8 files changed, 766 insertions(+), 746 deletions(-)
Author: Yu-Sung Su
Diff between R2jags versions 0.01-17 dated 2009-03-05 and 0.01-18 dated 2009-03-08
Title: A Package for Running jags from R
Description: Using this package to call jags from R.
CHANGELOG | 5 +++++
DESCRIPTION | 8 ++++----
R/autojags.R | 14 +++++++-------
R/jags2.R | 7 ++++---
R/recompile.R | 6 +++---
R/update.R | 2 +-
man/jags.Rd | 3 ++-
man/jags2bugs.Rd | 2 +-
man/recompile.Rd | 5 +++--
9 files changed, 30 insertions(+), 22 deletions(-)
Author: Jon T. Schnute
Diff between PBSmodelling versions 2.01 dated 2008-10-26 and 2.06 dated 2009-03-08
Title: PBS Modelling 2.06
Description: PBS Modelling provides software to facilitate the design,
testing, and operation of computer models. It focuses particularly on
tools that make it easy to construct and edit a customized graphical
user interface (GUI). Although it depends heavily on the R interface
to the Tcl/Tk package, a user does not need to know Tcl/Tk. The
package contains examples that illustrate models built with other R
packages, including PBSmapping, deSolve, PBSddesolve, and BRugs.
It also serves as a convenient prototype for building new R packages,
along with instructions and batch files to facilitate that process.
The R directory '.../library/PBSmodelling/doc' includes a complete user
guide PBSmodelling-UG.pdf. To use this package effectively,
please consult the guide.
PBSmodelling-2.01/PBSmodelling/inst/examples/YPRWin.txt |only
PBSmodelling-2.06/PBSmodelling/DESCRIPTION | 14
PBSmodelling-2.06/PBSmodelling/NAMESPACE | 3
PBSmodelling-2.06/PBSmodelling/R/guiFuns.r | 160
PBSmodelling-2.06/PBSmodelling/R/listFuns.r |only
PBSmodelling-2.06/PBSmodelling/R/plotFuns.r |only
PBSmodelling-2.06/PBSmodelling/R/projectFuns.r | 30
PBSmodelling-2.06/PBSmodelling/R/supportFuns.r | 2023 ++--------
PBSmodelling-2.06/PBSmodelling/R/widgetDefs.r | 4
PBSmodelling-2.06/PBSmodelling/R/zzz.r | 4
PBSmodelling-2.06/PBSmodelling/inst/PBStools/RPaths.bat | 2
PBSmodelling-2.06/PBSmodelling/inst/PBStools/RmakePDF3.bat |only
PBSmodelling-2.06/PBSmodelling/inst/doc/00ReadMe.txt | 22
PBSmodelling-2.06/PBSmodelling/inst/doc/ChangeLog.txt | 48
PBSmodelling-2.06/PBSmodelling/inst/doc/PBSmodelling-UG.pdf |binary
PBSmodelling-2.06/PBSmodelling/inst/doc/PBSmodelling-Updates.pdf |only
PBSmodelling-2.06/PBSmodelling/inst/doc/PBSmodellingIntro.pdf |binary
PBSmodelling-2.06/PBSmodelling/inst/doc/index.html | 2
PBSmodelling-2.06/PBSmodelling/inst/examples/CCA.r | 6
PBSmodelling-2.06/PBSmodelling/inst/examples/SGM.r | 2
PBSmodelling-2.06/PBSmodelling/inst/examples/TestFuns.r | 6
PBSmodelling-2.06/PBSmodelling/inst/examples/TestFunsWin.txt | 4
PBSmodelling-2.06/PBSmodelling/inst/examples/YPR.r | 2
PBSmodelling-2.06/PBSmodelling/inst/examples/runExamplesWin.txt | 2
PBSmodelling-2.06/PBSmodelling/inst/examples/yprWin.txt |only
PBSmodelling-2.06/PBSmodelling/man/cleanProj.Rd | 5
PBSmodelling-2.06/PBSmodelling/man/cleanWD.Rd |only
PBSmodelling-2.06/PBSmodelling/man/convSlashes.Rd |only
PBSmodelling-2.06/PBSmodelling/man/doAction.Rd |only
PBSmodelling-2.06/PBSmodelling/man/evalCall.Rd |only
PBSmodelling-2.06/PBSmodelling/man/getPrefix.Rd |only
PBSmodelling-2.06/PBSmodelling/man/getSuffix.Rd |only
PBSmodelling-2.06/PBSmodelling/man/packList.Rd |only
PBSmodelling-2.06/PBSmodelling/man/plotBubbles.Rd | 14
PBSmodelling-2.06/PBSmodelling/man/readList.Rd | 2
PBSmodelling-2.06/PBSmodelling/man/runDemos.Rd | 4
PBSmodelling-2.06/PBSmodelling/man/showArgs.Rd | 18
PBSmodelling-2.06/PBSmodelling/man/showPacks.Rd |only
PBSmodelling-2.06/PBSmodelling/man/testAlpha.Rd |only
PBSmodelling-2.06/PBSmodelling/man/viewCode.Rd |only
PBSmodelling-2.06/PBSmodelling/man/writeList.Rd | 11
41 files changed, 652 insertions(+), 1736 deletions(-)
Author: Christian Kleiber, Achim Zeileis
Title: Applied Econometrics with R
Description: Functions, data sets, examples, demos, and vignettes for the book
Christian Kleiber and Achim Zeileis (2008),
Applied Econometrics with R, Springer-Verlag, New York.
ISBN 978-0-387-77316-2. (See the vignette for a package overview.)
Diff between AER versions 1.1-0 dated 2009-02-05 and 1.1-1 dated 2009-03-08
DESCRIPTION | 6 +++--- NEWS | 11 +++++++++++ inst/doc/AER.Rnw | 17 +++++++++++++---- inst/doc/AER.pdf |binary inst/doc/Sweave-journals.pdf | 10 +++++----- inst/doc/aer.bib | 2 +- man/Baltagi2002.Rd | 3 +-- man/CigarettesB.Rd | 3 +-- man/Fatalities.Rd | 18 +++++++++--------- man/Grunfeld.Rd | 6 +++--- man/OECDGas.Rd | 7 +++---- man/StockWatson2007.Rd | 18 +++++++++--------- man/TravelMode.Rd | 8 +++----- tests/Ch-Basics.Rout.save | 8 ++++++++ tests/Ch-Intro.Rout.save | 8 ++++++++ tests/Ch-LinearRegression.Rout.save | 34 +++++++++++++++++++++++++--------- tests/Ch-Microeconometrics.Rout.save | 8 ++++++++ tests/Ch-Programming.Rout.save | 8 ++++++++ tests/Ch-TimeSeries.Rout.save | 8 ++++++++ tests/Ch-Validation.Rout.save | 8 ++++++++ 20 files changed, 135 insertions(+), 56 deletions(-)