Author: Nicole Kraemer, Juliane Schaefer
Title: Regularized estimation of partial correlation matrices
Description: The package estimates the matrix of partial correlations
based on different regularized regression methods: lasso,
adaptive lasso, PLS, and Ridge Regression.
Diff between parcor versions 0.1 dated 2009-04-29 and 0.2 dated 2009-11-12
DESCRIPTION | 10 +++---- R/adalasso.R | 61 +++++++++++++++++++++++------------------------- R/mylars.R | 40 +++++++++++++++---------------- R/performance.pcor.R | 2 - man/Beta2parcor.Rd | 4 --- man/adalasso.Rd | 10 +++---- man/adalasso.net.Rd | 8 ++---- man/mylars.Rd | 24 +++++++++--------- man/parcor-package.Rd | 4 --- man/performance.pcor.Rd | 2 - man/pls.net.Rd | 12 +++------ man/ridge.cv.Rd | 10 +++---- man/ridge.net.Rd | 10 ++----- 13 files changed, 89 insertions(+), 108 deletions(-)
Author: Kenneth Knoblauch and Laurence T. Maloney, based in part on C
code written by Laurence T. Maloney and J. N. Yang
Title: Maximum Likelihood Difference Scaling
Description: Difference scaling is a method for scaling perceived
supra-threshold differences. The package contains functions
that allow the user to design and run a difference scaling
experiment, to fit the resulting data by maximum likelihood and
test the internal validity of the estimated scale.
Diff between MLDS versions 0.2-3 dated 2009-09-29 and 0.2-5 dated 2009-11-12
DESCRIPTION | 8 ++++---- inst/CITATION |only inst/NEWS | 6 ++++++ man/runQuadExperiment.Rd | 6 +++--- 4 files changed, 13 insertions(+), 7 deletions(-)
Author: Jarrod Hadfield
Title: MCMC Generalised Linear Mixed Models
Description: MCMC Generalised Linear Mixed Models
Diff between MCMCglmm versions 1.12 dated 2009-10-03 and 1.13 dated 2009-11-12
DESCRIPTION | 8 +- R/MCMCglmm.R | 143 +++++++++++++++++++++--------------------------- R/buildZ.R | 27 +++++++-- R/find.components.R | 8 ++ R/inverseA.R | 3 - R/posterior.mode.R | 9 +-- R/rbv.R | 1 inst/doc/Figures/TEST.R | 41 ++++++------- inst/doc/Tutorial.pdf |binary man/MCMCglmm.Rd | 11 +-- man/posterior.mode.Rd | 2 11 files changed, 126 insertions(+), 127 deletions(-)
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by (in alphabetical order): Ben Bolker, Lodewijk
Bonebakker, Robert Gentleman, Wolfgang Huber Andy Liaw, Thomas
Lumley, Martin Maechler, Arni Magnusson, Steffen Moeller, Marc
Schwartz, Bill Venables
Title: Various R programming tools for plotting data
Description: Various R programming tools for plotting data
Diff between gplots versions 2.7.3 dated 2009-10-23 and 2.7.4 dated 2009-11-12
DESCRIPTION | 6 +++--- NEWS | 7 +++++++ R/plotmeans.R | 11 ++++++----- inst/NEWS | 7 +++++++ tests/plotmeans_nobars.R |only 5 files changed, 23 insertions(+), 8 deletions(-)
Author: J. O. Ramsay
Diff between fda versions 2.1.3 dated 2009-10-18 and 2.2.0 dated 2009-11-12
Title: Functional Data Analysis
Description: These functions were developed to support functional data
analysis as described in Ramsay, J. O. and Silverman, B. W.
(2005) Functional Data Analysis. New York: Springer. They were
ported from earlier versions in Matlab and S-PLUS. An
introduction appears in Ramsay, J. O., Hooker, Giles, and
Graves, Spencer (2009) Functional Data Analysis with R and
Matlab (Springer). The package includes data sets and script
files working many examples including all but one of the 76
figures in this latter book.
fda-2.1.3/fda/R/register.newfd.R |only
fda-2.1.3/fda/R/use.proper.basis.R |only
fda-2.1.3/fda/inst/Matlab/additions |only
fda-2.1.3/fda/inst/Matlab/fdaM/@bibasis/@bibasis.zip |only
fda-2.1.3/fda/inst/Matlab/fdaM/@bibasis/bibasis.asv |only
fda-2.1.3/fda/inst/Matlab/fdaM/@bifdPar/@bifdPar.zip |only
fda-2.1.3/fda/inst/Matlab/fdaM/@bifdPar/@fdPar.zip |only
fda-2.1.3/fda/inst/scripts/fda-script-progress.xls |only
fda-2.1.3/fda/inst/scripts/pda.fd.test.R |only
fda-2.1.3/fda/man/register.newfd.rd |only
fda-2.2.0/fda/DESCRIPTION | 10
fda-2.2.0/fda/R/Fperm.fd.R | 12
fda-2.2.0/fda/R/Fstat.fd.R | 5
fda-2.2.0/fda/R/basisfd.R | 52 +++
fda-2.2.0/fda/R/bifdPar.R |only
fda-2.2.0/fda/R/eval.posfd.R | 2
fda-2.2.0/fda/R/fRegress.CV.R | 117 +++----
fda-2.2.0/fda/R/fRegress.R |only
fda-2.2.0/fda/R/fRegress.stderr.R | 12
fda-2.2.0/fda/R/fRegressArgCheck.R |only
fda-2.2.0/fda/R/fd.R | 272 ++++++++++++++---
fda-2.2.0/fda/R/linmod.R | 32 --
fda-2.2.0/fda/R/register.fd.R | 89 ++---
fda-2.2.0/fda/R/smooth.basis.R | 2
fda-2.2.0/fda/R/smooth.pos.R | 70 ++--
fda-2.2.0/fda/R/subscript.R | 4
fda-2.2.0/fda/R/varmx.R | 23 +
fda-2.2.0/fda/R/varmx.pca.fd.R | 46 +-
fda-2.2.0/fda/inst/Matlab/fdaM/@basis/basis.m | 26 +
fda-2.2.0/fda/inst/Matlab/fdaM/@basis/getbasismatrix.m | 15
fda-2.2.0/fda/inst/Matlab/fdaM/@basis/getbasistype.m | 6
fda-2.2.0/fda/inst/Matlab/fdaM/@basis/getbasisvalues.m | 2
fda-2.2.0/fda/inst/Matlab/fdaM/@basis/times.m | 2
fda-2.2.0/fda/inst/Matlab/fdaM/@bifdPar/bifdPar.m | 52 +--
fda-2.2.0/fda/inst/Matlab/fdaM/@fd/mpower.m |only
fda-2.2.0/fda/inst/Matlab/fdaM/@fd/power.m |only
fda-2.2.0/fda/inst/Matlab/fdaM/Fperm_fd.m | 202 ++++++------
fda-2.2.0/fda/inst/Matlab/fdaM/Fstat_fd.m | 75 +---
fda-2.2.0/fda/inst/Matlab/fdaM/fRegress_CV.m | 141 ++++----
fda-2.2.0/fda/inst/Matlab/fdaM/smooth_basis.m | 166 ++--------
fda-2.2.0/fda/inst/Matlab/fdaM/tperm_fd.m | 206 ++++++------
fda-2.2.0/fda/inst/Matlab/fdaM/varmx.m | 53 +--
fda-2.2.0/fda/inst/Matlab/fdaM/varmx_pca.m | 8
fda-2.2.0/fda/inst/scripts/fdarm-ch01.R | 174 ++++++++--
fda-2.2.0/fda/inst/scripts/fdarm-ch01.m |only
fda-2.2.0/fda/inst/scripts/fdarm-ch02.R | 81 ++++-
fda-2.2.0/fda/inst/scripts/fdarm-ch03.R | 93 ++++-
fda-2.2.0/fda/inst/scripts/fdarm-ch03.m |only
fda-2.2.0/fda/inst/scripts/fdarm-ch04.R | 244 ++++++++++-----
fda-2.2.0/fda/inst/scripts/fdarm-ch04.m |only
fda-2.2.0/fda/inst/scripts/fdarm-ch05.R | 188 ++++++++++-
fda-2.2.0/fda/inst/scripts/fdarm-ch05.m |only
fda-2.2.0/fda/inst/scripts/fdarm-ch06.R | 158 +++++++--
fda-2.2.0/fda/inst/scripts/fdarm-ch06.m |only
fda-2.2.0/fda/inst/scripts/fdarm-ch07.R | 109 ++++--
fda-2.2.0/fda/inst/scripts/fdarm-ch07.m |only
fda-2.2.0/fda/inst/scripts/fdarm-ch08.R | 95 ++++-
fda-2.2.0/fda/inst/scripts/fdarm-ch08.m |only
fda-2.2.0/fda/inst/scripts/fdarm-ch09.R | 61 +++
fda-2.2.0/fda/inst/scripts/fdarm-ch09.m |only
fda-2.2.0/fda/inst/scripts/fdarm-ch10.R | 259 +++++++++++-----
fda-2.2.0/fda/inst/scripts/fdarm-ch10.m |only
fda-2.2.0/fda/inst/scripts/fdarm-ch11.m |only
fda-2.2.0/fda/man/bifdPar.Rd |only
fda-2.2.0/fda/man/eval.posfd.Rd | 161 +++++-----
fda-2.2.0/fda/man/fRegress.CV.Rd | 193 +++---------
fda-2.2.0/fda/man/fRegress.Rd | 7
fda-2.2.0/fda/man/fRegress.stderr.Rd | 149 ++++-----
fda-2.2.0/fda/man/fda-internal.Rd | 2
fda-2.2.0/fda/man/linmod.Rd | 90 +++--
fda-2.2.0/fda/man/smooth.basis.Rd | 9
fda-2.2.0/fda/man/varmx.Rd | 85 ++---
72 files changed, 2362 insertions(+), 1498 deletions(-)
Author: Enrico Glaab
Title: Generate 3D visualizations for data exploration on the web
Description: vrmlgen creates 3D scatter and bar plots, visualizations
of 3D meshes, parametric functions and height maps in
web-formats like the Virtual Reality Markup Language (VRML,
filetype .wrl) and the LiveGraphics3D format.
Diff between vrmlgen versions 1.1 dated 2009-10-12 and 1.2 dated 2009-11-12
DESCRIPTION | 18 +-- R/lbar.R | 90 ++++++++++++++--- R/lcloud.R | 247 +++++++++++++++++++++++++++++++++++++------------ R/lmesh.R |only R/vbar.R | 128 +++++++++++++++++++------ R/vcloud.R | 6 - R/vmesh.R |only man/lbar.Rd | 33 +++++- man/lcloud.Rd | 39 ++++++- man/lmesh.Rd |only man/vbar.Rd | 36 +++++-- man/vcloud.Rd | 32 ++++-- man/vmesh.Rd |only man/vrmlgen-package.Rd | 12 +- 14 files changed, 489 insertions(+), 152 deletions(-)
Author: D.J.J. Walvoort, D.J. Brus, and J.J. de Gruijter
Title: Spatial Coverage Sampling and Random Sampling from Compact
Geographical Strata
Description: Spatial coverage sampling and random sampling from compact
geographical strata created by k-means.
Diff between spcosa versions 0.1-5 dated 2009-09-09 and 0.2-0 dated 2009-11-12
DESCRIPTION | 16 NEWS | 8 R/method_stratify-SpatialPixels.R | 75 R/onLoad.R | 8 inst/doc/spcosa.pdf | 4371 ++++++++++++++++++-------------------- man/spcosa-package.Rd | 29 man/stratify-methods.Rd | 6 tests/unitTesting.html | 14 8 files changed, 2225 insertions(+), 2302 deletions(-)
Author: Tuomas Rajala
Title: Graphs for spatial point patterns
Description: Graphs, graph visualization and graph component
calculations, ment to be used as a tool in spatial point
pattern analysis. See package 'spatstat' for more info about
spatial point patterns.
Diff between spatgraphs versions 2.27 dated 2009-09-18 and 2.30 dated 2009-11-12
DESCRIPTION | 10 +++++----- R/edgelengths.R | 4 ++-- R/plot.R | 26 ++++++++++++++++++++------ R/spatgraph.R | 2 +- R/summary.R |only change.log | 11 +++++++++++ man/spatgraphs-other.Rd | 5 +++-- man/spatgraphs-package.Rd | 3 ++- man/spatgraphs-plot.sg.Rd | 1 + man/spatgraphs-sg.Rd | 3 +++ src/Graph.cpp | 6 +++--- src/dists.cpp | 2 +- 12 files changed, 52 insertions(+), 21 deletions(-)
Author: Peter Danenberg
Diff between roxygen versions 0.1 dated 2008-08-31 and 0.1-2 dated 2009-11-12
Title: Literate Programming in R
Description: A Doxygen-like in-source documentation system for Rd,
collation, namespace and callgraphs.
roxygen-0.1-2/roxygen/DESCRIPTION | 21
roxygen-0.1-2/roxygen/NAMESPACE | 5
roxygen-0.1-2/roxygen/R/Rd.R | 950
roxygen-0.1-2/roxygen/R/Rd2.R |only
roxygen-0.1-2/roxygen/R/Rdapi.R |only
roxygen-0.1-2/roxygen/R/Rdmerge.R |only
roxygen-0.1-2/roxygen/R/Rdtank.R |only
roxygen-0.1-2/roxygen/R/callgraph.R | 540
roxygen-0.1-2/roxygen/R/collate.R | 332
roxygen-0.1-2/roxygen/R/functional.R | 1
roxygen-0.1-2/roxygen/R/memoize.R |only
roxygen-0.1-2/roxygen/R/namespace.R | 328
roxygen-0.1-2/roxygen/R/parse.R | 43
roxygen-0.1-2/roxygen/R/parseS4.R |only
roxygen-0.1-2/roxygen/R/roclet.R | 8
roxygen-0.1-2/roxygen/R/roxygen.R | 2
roxygen-0.1-2/roxygen/R/roxygenize.R | 21
roxygen-0.1-2/roxygen/R/string.R | 336
roxygen-0.1-2/roxygen/README | 4
roxygen-0.1-2/roxygen/inst/doc/Compose-callgraph.pdf |binary
roxygen-0.1-2/roxygen/inst/doc/GSoC-idea.tex |only
roxygen-0.1-2/roxygen/inst/doc/helloRoxygen/DESCRIPTION | 22
roxygen-0.1-2/roxygen/inst/doc/helloRoxygen/man/helloRoxygen-package.Rd | 10
roxygen-0.1-2/roxygen/inst/doc/parse.file-callgraph.pdf |binary
roxygen-0.1-2/roxygen/inst/doc/pseudoprime/DESCRIPTION | 26
roxygen-0.1-2/roxygen/inst/doc/pseudoprime/NAMESPACE | 2
roxygen-0.1-2/roxygen/inst/doc/pseudoprime/man/fermat.test.Rd | 32
roxygen-0.1-2/roxygen/inst/doc/pseudoprime/man/is.pseudoprime.Rd | 38
roxygen-0.1-2/roxygen/inst/doc/pseudoprime/man/pseudoprime-package.Rd | 50
roxygen-0.1-2/roxygen/inst/doc/roxygen-manual.pdf |13275 +++++-----
roxygen-0.1-2/roxygen/inst/doc/roxygen.Rnw | 350
roxygen-0.1-2/roxygen/inst/doc/roxygen.aux | 40
roxygen-0.1-2/roxygen/inst/doc/roxygen.bbl | 26
roxygen-0.1-2/roxygen/inst/doc/roxygen.blg | 48
roxygen-0.1-2/roxygen/inst/doc/roxygen.log | 1277
roxygen-0.1-2/roxygen/inst/doc/roxygen.pdf |binary
roxygen-0.1-2/roxygen/inst/doc/roxygen.tex | 357
roxygen-0.1-2/roxygen/inst/doc/roxygen.toc | 12
roxygen-0.1-2/roxygen/inst/doc/roxygenize-callgraph.pdf |binary
roxygen-0.1-2/roxygen/man/assign.parent.Rd | 2
roxygen-0.1-2/roxygen/man/cat.description.Rd | 2
roxygen-0.1-2/roxygen/man/expression.from.partitum.Rd |only
roxygen-0.1-2/roxygen/man/make.Rd.roclet.Rd | 20
roxygen-0.1-2/roxygen/man/make.Rd2.roclet.Rd |only
roxygen-0.1-2/roxygen/man/make.callgraph.roclet.Rd | 2
roxygen-0.1-2/roxygen/man/make.collate.roclet.Rd | 2
roxygen-0.1-2/roxygen/man/make.namespace.roclet.Rd | 2
roxygen-0.1-2/roxygen/man/parse.ref.srcref.Rd | 8
roxygen-0.1-2/roxygen/man/roxygen-package.Rd | 2
roxygen-0.1-2/roxygen/man/roxygenize.Rd | 5
roxygen-0.1/roxygen/inst/doc/.build.timestamp |only
roxygen-0.1/roxygen/inst/doc/helloRoxygen/Read-and-delete-me |only
roxygen-0.1/roxygen/inst/doc/pseudoprime/inst/doc/fermat.test-callgraph.pdf |only
roxygen-0.1/roxygen/sandbox |only
54 files changed, 9584 insertions(+), 8617 deletions(-)
Author: Nicole Kraemer
Diff between ppls versions 1.03 dated 2009-01-24 and 1.04 dated 2009-11-12
Title: Penalized Partial Least Squares
Description: This package contains linear and nonlinear regression
methods based on Partial Least Squares and Penalization
Techniques.
DESCRIPTION | 28 ++++++++++++++++------------
man/Penalty.matrix.Rd | 2 +-
man/penalized.pls.cv.Rd | 3 +--
3 files changed, 18 insertions(+), 15 deletions(-)
Author: Arthur Allignol
Title: Nelson-Aalen estimator of the cumulative hazard in multistate
models
Description: This package computes the Nelson-Aalen estimator of the
cumulative transition hazard for multistate models.
Diff between mvna versions 1.1-10 dated 2009-10-14 and 1.2 dated 2009-11-12
mvna-1.1-10/mvna/src/risk_set_mvna.cc |only mvna-1.2/mvna/ChangeLog | 43 ++++++++++++-- mvna-1.2/mvna/DESCRIPTION | 8 +- mvna-1.2/mvna/NAMESPACE | 4 + mvna-1.2/mvna/R/lines.mvna.R |only mvna-1.2/mvna/R/mvna.R | 41 +++++++++----- mvna-1.2/mvna/R/plot.mvna.R | 98 ++++++++++++++++++++-------------- mvna-1.2/mvna/R/predict.mvna.R | 54 ++++++++++-------- mvna-1.2/mvna/R/print.mvna.R | 39 ++++++------- mvna-1.2/mvna/R/print.summary.mvna.R |only mvna-1.2/mvna/R/summary.mvna.R |only mvna-1.2/mvna/R/xyplot.mvna.R | 85 +++++++++++------------------ mvna-1.2/mvna/man/abortion.Rd | 7 +- mvna-1.2/mvna/man/lines.mvna.Rd |only mvna-1.2/mvna/man/msmplot.Rd | 17 +++-- mvna-1.2/mvna/man/mvna.Rd | 39 ++++++------- mvna-1.2/mvna/man/plot.mvna.Rd | 53 +++++++++++------- mvna-1.2/mvna/man/predict.mvna.Rd | 42 +++++++++----- mvna-1.2/mvna/man/print.mvna.Rd | 15 ++--- mvna-1.2/mvna/man/sir.adm.Rd | 3 - mvna-1.2/mvna/man/sir.cont.Rd | 5 + mvna-1.2/mvna/man/summary.mvna.Rd |only mvna-1.2/mvna/man/xyplot.mvna.Rd | 46 ++++++++------- mvna-1.2/mvna/src/risk_set_mvna.c |only mvna-1.2/mvna/tests |only 25 files changed, 341 insertions(+), 258 deletions(-)
Author: Martin Elff
Title: Tools for Management of Survey Data, Graphics, Programming,
Statistics, and Simulation
Description: One of the aims of this package is to make life easier for
useRs who deal with survey data sets. It provides an
infrastructure for the management of survey data including
value labels, definable missing values, recoding of variables,
production of code books, and import of (subsets of) SPSS and
Stata files. Further, it provides functionality to produce
tables and data frames of arbitrary descriptive statistics and
(almost) publication-ready tables of regression model
estimates. Also some convenience tools for graphics,
programming, and simulation are provided.
Diff between memisc versions 0.95-22 dated 2009-10-15 and 0.95-23 dated 2009-11-12
DESCRIPTION | 8 +-- INDEX |only NEWS |only R/zzz.R | 86 +--------------------------------------- inst/doc/anes48.pdf |binary src/dta-for-R.c | 6 +- src/numeric_if_possible.c | 6 +- src/pspp-portableStream-for-R.c | 2 src/readfixed.c | 4 - 9 files changed, 16 insertions(+), 96 deletions(-)
Author: Arthur Allignol
Title: Empirical Transition Matrix
Description: Matrix of transition probabilities for any
time-inhomogeneous multistate model with finite state space
Diff between etm versions 0.4-6 dated 2009-09-03 and 0.4-7 dated 2009-11-12
ChangeLog | 81 ++++++++++++++++++++++++++++++------------------------ DESCRIPTION | 8 ++--- NAMESPACE | 1 R/lines.etm.R |only R/plot.etm.R | 80 ++++++++++++++++++++++++++++++++++------------------- R/xyplot.etm.R | 20 +++++++++---- man/lines.etm.Rd |only man/plot.etm.Rd | 17 ++++++++++- man/xyplot.etm.Rd | 10 ++---- 9 files changed, 134 insertions(+), 83 deletions(-)
Author: Yihui Xie
Title: Demonstrate Animations in Statistics
Description: This package consists of various functions for animations
in statistics, covering many areas such as probability theory,
mathematical statistics, multivariate statistics, nonparametric
statistics, sampling survey, linear models, time series,
computational statistics, data mining and machine learning.
These functions might be of help in teaching statistics and
data analysis.
Diff between animation versions 1.0-8 dated 2009-11-06 and 1.0-9 dated 2009-11-12
DESCRIPTION | 8 ++--- R/ani.options.R | 28 ++++++++++------- R/ani.start.R | 10 +++--- R/ani.stop.R | 16 +++++----- R/brownian.motion.R | 4 -- R/saveLatex.R |only R/saveMovie.R | 74 ++++++++++++++++++++++++++++++++++++++++++----- R/saveSWF.r | 4 +- R/write.rss.R | 12 +++---- R/zzz.R | 6 --- inst/NEWS | 66 +++++++++++++++++++++++++++++++++++------ man/BM.circle.Rd | 10 ++---- man/HuSpeech.Rd | 5 ++- man/Rosling.bubbles.Rd | 6 +-- man/ani.options.Rd | 19 ++++++------ man/ani.start.Rd | 2 - man/ani.stop.Rd | 2 - man/animation-package.Rd | 2 - man/bisection.method.Rd | 9 ++--- man/buffon.needle.Rd | 13 ++++---- man/clt.ani.Rd | 8 ++--- man/conf.int.Rd | 11 +++--- man/cv.ani.Rd | 13 ++++---- man/cv.nfeaturesLDA.Rd | 13 +++----- man/ecol.death.sim.Rd | 8 +++-- man/flip.coin.Rd | 10 +++--- man/g.brownian.motion.Rd | 6 +-- man/grad.desc.Rd | 8 ++--- man/highlight.def.Rd | 8 ++--- man/kfcv.Rd | 3 - man/kmeans.ani.Rd | 14 +++++--- man/knn.ani.Rd | 6 +-- man/least.squares.Rd | 15 +++++---- man/lln.ani.Rd | 6 +-- man/moving.block.Rd | 1 man/mwar.ani.Rd | 8 ++--- man/newton.method.Rd | 15 +++++---- man/pageview.Rd | 8 ++--- man/quincunx.Rd | 10 +++--- man/sample.cluster.Rd | 4 +- man/sample.simple.Rd | 5 +-- man/sample.strat.Rd | 2 - man/sample.system.Rd | 5 +-- man/saveLatex.Rd |only man/saveMovie.Rd | 10 +++--- man/saveSWF.Rd | 8 ++--- man/sim.qqnorm.Rd | 4 +- man/tidy.source.Rd | 7 +++- man/vi.grid.illusion.Rd | 8 +++-- man/vi.lilac.chaser.Rd | 6 +-- man/write.rss.Rd | 37 +++++++++++------------ tests |only 52 files changed, 341 insertions(+), 222 deletions(-)
Author: Erin Hodgess
Diff between RcmdrPlugin.qual versions 0.3.0 dated 2009-11-01 and 0.4.0 dated 2009-11-12
More information about RcmdrPlugin.qual at CRAN
Title: Rcmdr plugin for quality control course
Description: This package provides an Rcmdr "plug-in" based on the
Quality control class Stat 4300
DESCRIPTION | 8 +++---
R/RcmdrPlugin.qual.R | 51 +++++++++++++++++++++++++++++++++++++++
inst/etc/menus.txt | 1
man/RcmdrPlugin.qual-internal.Rd | 1
4 files changed, 57 insertions(+), 4 deletions(-)
Permanent link
Author: Reinhold Hatzinger, Patrick Mair, Norman Verhelst
Title: Rasch Sampler
Description: Sampling binary matrices with fixed margins
Diff between RaschSampler versions 0.8-2 dated 2009-08-19 and 0.8-3 dated 2009-11-12
DESCRIPTION | 8 ++++---- R/rserror.R | 4 ++-- data/xmplbig.rda |binary man/RaschSampler.package.Rd | 14 ++++++++++---- man/rsampler.Rd | 8 ++++---- man/xmpl.Rd | 4 ++-- src/RaschSampler.f90 | 18 ++++-------------- 7 files changed, 26 insertions(+), 30 deletions(-)
Author: Yu-Sung Su
Diff between R2jags versions 0.01-26 dated 2009-10-13 and 0.01-27 dated 2009-11-12
Title: A Package for Running jags from R
Description: Using this package to call jags from R.
CHANGELOG | 11 +++++++++++
DESCRIPTION | 8 ++++----
R/jags.R | 39 +++++++++++++++++++++++++++++++++------
R/jags.sims.R | 4 ++--
R/jags2.R | 26 +++++++++++++++++++++-----
man/jags.Rd | 5 +++--
6 files changed, 74 insertions(+), 19 deletions(-)
Author: Jarrod Hadfield
Title: ML and MCMC Methods for Pedigree Reconstruction and Analysis
Description: The primary aim of MasterBayes is to use MCMC techniques
to integrate over uncertainty in pedigree configurations
estimated from molecular markers and phenotypic data. Emphasis
is put on the marginal distribution of parameters that relate
the phenotypic data to the pedigree. All simulation is done in
compiled C++ for efficency.
Diff between MasterBayes versions 2.44 dated 2009-07-21 and 2.45 dated 2009-11-12
MasterBayes-2.44/MasterBayes/inst/doc/Tutorial.tex |only MasterBayes-2.45/MasterBayes/DESCRIPTION | 8 MasterBayes-2.45/MasterBayes/NAMESPACE | 4 MasterBayes-2.45/MasterBayes/R/ErrorCheck.R | 14 MasterBayes-2.45/MasterBayes/R/MCMCped.R | 31 MasterBayes-2.45/MasterBayes/R/MLE.popsize.R | 5 MasterBayes-2.45/MasterBayes/R/consensusG.R |only MasterBayes-2.45/MasterBayes/R/fillX.G.R | 9 MasterBayes-2.45/MasterBayes/R/getPost.R | 4 MasterBayes-2.45/MasterBayes/R/getXlist.R | 17 MasterBayes-2.45/MasterBayes/R/getsPandtP.R | 54 MasterBayes-2.45/MasterBayes/R/insertPed.R |only MasterBayes-2.45/MasterBayes/R/varPed.R | 105 MasterBayes-2.45/MasterBayes/inst/doc/Figures/Tutorial.Rnw | 8 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-006.eps | 27 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-006.pdf | 6 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-007.eps | 27 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-007.pdf | 6 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-008.eps | 43 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-008.pdf | 6 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-009.eps | 27 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-009.pdf | 6 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-023.eps | 5853 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-023.pdf | 7052 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-028.eps | 6197 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-028.pdf | 7059 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-031.eps | 5936 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-031.pdf | 6569 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-036.eps |25154 - MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-036.pdf |20067 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-040.eps | 6364 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-040.pdf | 6562 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-045.eps | 5716 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-045.pdf | 6554 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-048.eps | 5991 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-048.pdf | 6548 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-051.eps |10800 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-051.pdf |11088 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-059.eps |16359 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-059.pdf |21063 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-062.eps |16161 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-062.pdf |20697 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-065.eps | 6161 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-065.pdf | 7091 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-070.eps | 6399 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-070.pdf | 7050 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-072.eps | 6200 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-072.pdf | 7070 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-075.eps | 6634 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-075.pdf | 7086 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-078.eps | 6206 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-078.pdf | 7022 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-080.eps | 5806 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-080.pdf | 6548 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-083.eps | 6168 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-083.pdf | 7064 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-086.eps | 5988 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-086.pdf | 7040 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-089.eps | 6559 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-089.pdf | 7070 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-092.eps |10066 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-092.pdf |11079 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-095.eps | 6267 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-095.pdf | 7040 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-098.eps | 5998 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-098.pdf | 7045 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-101.eps | 9608 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-101.pdf |11044 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-104.eps |11294 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-104.pdf |13971 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-107.eps |19796 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-107.pdf |14072 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-EPP2Test.eps | 6168 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-EPP2Test.pdf | 7064 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-EPPmerge.eps | 5988 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-EPPmerge.pdf | 7040 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-Herm.approx.eps | 9608 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-Herm.approx.pdf |11044 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-Herm.eps | 5998 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-Herm.pdf | 7045 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-MGped.eps | 6267 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-MGped.pdf | 7040 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.DSconfig.eps |10800 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.DSconfig.pdf |11088 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.INT.cntr.eps |16161 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.INT.cntr.pdf |20697 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.INT.eps |16359 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.INT.pdf |21063 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.ass.mat.approx.eps |10066 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.ass.mat.approx.pdf |11079 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.ass.mat.eps | 6559 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.ass.mat.pdf | 7070 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.config.eps | 5991 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.config.pdf | 6548 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.miss.eps | 6399 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.miss.pdf | 7050 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.miss2.eps | 6206 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.miss2.pdf | 7022 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.miss2US.eps | 5806 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.miss2US.pdf | 6548 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.missTest.eps | 6634 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.missTest.pdf | 7086 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.missUS.eps | 6200 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.missUS.pdf | 7070 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.pedEE2.eps | 5716 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model.pedEE2.pdf | 6554 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model2beta.eps | 5853 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model2beta.pdf | 7052 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model3beta.eps | 6197 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model3beta.pdf | 7059 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model4US.eps | 5936 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model4US.pdf | 6569 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model5.eps |25154 - MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model5.pdf |20067 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model6US.eps | 6364 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-model6US.pdf | 6562 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-mon1.eps |11294 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-mon1.pdf |13971 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-mon2.eps |19796 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-mon2.pdf |14072 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-ys.eps | 6161 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial-ys.pdf | 7091 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial.Rnw | 205 MasterBayes-2.45/MasterBayes/inst/doc/Tutorial.pdf |246082 ++++------ MasterBayes-2.45/MasterBayes/man/GdataPed.Rd | 2 MasterBayes-2.45/MasterBayes/man/MLE.beta.Rd | 2 MasterBayes-2.45/MasterBayes/man/MLE.ped.Rd | 2 MasterBayes-2.45/MasterBayes/man/MLE.popsize.Rd | 8 MasterBayes-2.45/MasterBayes/man/autocorrP.Rd | 4 MasterBayes-2.45/MasterBayes/man/beta.loglik.Rd | 2 MasterBayes-2.45/MasterBayes/man/consenusG.Rd |only MasterBayes-2.45/MasterBayes/man/extractA.Rd | 2 MasterBayes-2.45/MasterBayes/man/fillX.G.Rd | 3 MasterBayes-2.45/MasterBayes/man/genotype.list.Rd | 4 MasterBayes-2.45/MasterBayes/man/genotypeD.Rd | 2 MasterBayes-2.45/MasterBayes/man/getXlist.Rd | 2 MasterBayes-2.45/MasterBayes/man/insertPed.Rd |only MasterBayes-2.45/MasterBayes/man/legalG.Rd | 2 MasterBayes-2.45/MasterBayes/man/mismatches.Rd | 2 MasterBayes-2.45/MasterBayes/man/modeG.Rd | 2 MasterBayes-2.45/MasterBayes/man/modeP.Rd | 2 MasterBayes-2.45/MasterBayes/man/orderPed.Rd | 2 MasterBayes-2.45/MasterBayes/man/popsize.loglik.Rd | 4 MasterBayes-2.45/MasterBayes/man/post.pairs.Rd | 2 MasterBayes-2.45/MasterBayes/man/priorPed.Rd | 3 MasterBayes-2.45/MasterBayes/man/reordXlist.Rd | 2 MasterBayes-2.45/MasterBayes/man/simpedigree.Rd | 2 MasterBayes-2.45/MasterBayes/man/startPed.Rd | 3 MasterBayes-2.45/MasterBayes/man/summary.genotypeD.Rd | 2 MasterBayes-2.45/MasterBayes/man/tunePed.Rd | 2 MasterBayes-2.45/MasterBayes/man/varPed.Rd | 4 MasterBayes-2.45/MasterBayes/src/MCMCped.cc | 15 MasterBayes-2.45/MasterBayes/src/SampDomG.cc | 2 MasterBayes-2.45/MasterBayes/src/SampG.cc | 2 MasterBayes-2.45/MasterBayes/src/calcX_Gcervus.cc | 17 MasterBayes-2.45/MasterBayes/src/calcX_GcervusD.cc | 1 MasterBayes-2.45/MasterBayes/src/fillXG.cc | 5 157 files changed, 587069 insertions(+), 588198 deletions(-)
Author: Marc J. Mazerolle
Diff between AICcmodavg versions 1.03 dated 2009-10-22 and 1.04 dated 2009-11-12
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/aictab.R | 2 -
R/confset.R | 2 -
R/evidence.R | 2 -
R/importance.R | 2 -
R/modavg.R | 18 +++++----
R/modavg.glm.R | 90 ++++++++++++++++++++++++++++++++++++++++------
R/modavg.lme.R | 37 ++++++++++++++++--
R/modavg.mult.R | 76 ++++++++++++++++++++++++++++++--------
R/modavg.polr.R | 33 +++++++++++++---
R/modavgpred.R | 68 +++++++++++++++++++++++++++++++++-
man/AICcmodavg-package.Rd | 20 +++++-----
man/aictab.Rd | 18 ++++++---
man/confset.Rd | 8 +++-
man/evidence.Rd | 5 +-
man/importance.Rd | 4 ++
man/modavg.Rd | 28 +++++++++++---
man/modavgpred.Rd | 22 +++++++++--
18 files changed, 360 insertions(+), 83 deletions(-)