Author: Allan Strand
Diff between rmetasim versions 1.1.05 dated 2008-05-03 and 1.1.09 dated 2009-10-08
Title: An individual-based population genetic simulation environment
Description: An interface between R and the metasim simulation engine.
Facilitates the use of the metasim engine to build and run
individual based population genetics simulations. The
simulation environment is documented in: Allan Strand. Metasim
1.0: an individual-based environment for simulating population
genetics of complex population dynamics. Mol. Ecol. Notes,
2:373-376, 2002. (Please contact Allan Strand with comments,
bug reports, etc). This version represents a significant
alteration of function names that hopefully increases
consistency and reduces the chances of collisions with other
packages naming conventions. For a spatially-explicit, but
slower, package with a similar interface, see kernelPop
CHANGELOG | 15 ++++++++++++++-
DESCRIPTION | 36 ++++++++++++++++++------------------
NAMESPACE | 1 -
R/amova.R | 32 ++++++++++++++++++++++++++++++--
R/ape_interface.R | 9 +++++----
R/coal2rmet.R |only
R/diversity.R | 2 +-
R/landscape.allelefreq.R |only
R/landscape.sample.R | 21 +++++++++++++++++----
R/simcoal.R | 2 +-
man/landscape.amova.Rd | 2 +-
man/landscape.amova.locus.Rd | 2 +-
man/landscape.amova.pairwise.Rd | 2 +-
man/landscape.demography.Rd | 5 ++---
man/landscape.sample.Rd | 8 ++++++--
15 files changed, 97 insertions(+), 40 deletions(-)
Author: Lester L. Yuan
Title: Compute biological inferences
Description: Imports benthic count data, reformats this data, and
computes environmental inferences from this data.
Diff between bio.infer versions 1.2-4 dated 2009-07-18 and 1.2-5 dated 2009-10-08
DESCRIPTION | 8 ++++---- R/parse.taxon.name.R | 28 +++++++++++++++++++--------- 2 files changed, 23 insertions(+), 13 deletions(-)
Author: Friedrich Leisch and Andreas Weingessel and Kurt Hornik
Title: Generation of Artificial Binary Data
Description: Generation of correlated artificial binary data.
Diff between bindata versions 0.9-15 dated 2009-09-18 and 0.9-16 dated 2009-10-08
DESCRIPTION | 12 ++++++------ R/simul.commonprob.R | 18 +++++++----------- 2 files changed, 13 insertions(+), 17 deletions(-)
Author: Ulrike Groemping
Title: R Commander Plugin for (industrial) Design of Experiments
Description: WARNING: This package is currently in beta status! The
package provides a platform-independent GUI for design of
experiments. It is implemented as a plugin to the R-Commander,
which is a more general graphical user interface for statistics
in R based on tcl/tk. DoE functionality can be accessed through
the menu Design that is added to the R-Commander menus.
Diff between RcmdrPlugin.DoE versions 0.5-4 dated 2009-10-08 and 0.5-5 dated 2009-10-08
DESCRIPTION | 6 +++--- inst/NEWS | 4 ++++ inst/etc/menus.txt | 2 +- man/Menu.Analyze.Rd | 14 ++++++-------- man/Menu.FrF2level.Rd | 2 +- man/Menu.ccd.Rd | 6 +++--- man/Menu.fac.Rd | 2 +- man/Menu.facTab1.Rd | 5 +++-- man/Menu.linearModelDesign.Rd | 2 +- 9 files changed, 23 insertions(+), 20 deletions(-)
More information about RcmdrPlugin.DoE at CRAN
Permanent link
Author: Han Lin Shang and Rob J Hyndman
Title: Rainbow plots, bagplots and boxplots for functional data
Description: Functions and datasets for functional data display and
outlier detection.
Diff between rainbow versions 1.4 dated 2009-09-04 and 1.5 dated 2009-10-08
rainbow-1.4/rainbow/data/Francemortality.rda |only rainbow-1.4/rainbow/data/Francesmoothmortality.rda |only rainbow-1.4/rainbow/man/Francemortality.Rd |only rainbow-1.5/rainbow/CHANGELOG | 20 ++++++++++++------ rainbow-1.5/rainbow/DESCRIPTION | 8 +++---- rainbow-1.5/rainbow/data/Australiafertility.rda |binary rainbow-1.5/rainbow/data/Australiasmoothfertility.rda |binary rainbow-1.5/rainbow/data/Simulationdata.rda |binary rainbow-1.5/rainbow/man/Australiafertility.Rd | 2 - rainbow-1.5/rainbow/man/ElNino.Rd | 7 ++++++ rainbow-1.5/rainbow/man/Simulationdata.Rd | 2 - rainbow-1.5/rainbow/man/fboxplot.Rd | 2 - rainbow-1.5/rainbow/man/fds.Rd | 13 +++-------- rainbow-1.5/rainbow/man/foutliers.Rd | 2 - rainbow-1.5/rainbow/man/lines.fds.Rd | 8 ++----- rainbow-1.5/rainbow/man/plot.fdepth.Rd | 4 --- rainbow-1.5/rainbow/man/plot.fds.Rd | 10 ++++----- rainbow-1.5/rainbow/man/points.fds.Rd | 9 ++------ rainbow-1.5/rainbow/man/rainbow-package.Rd | 2 - 19 files changed, 46 insertions(+), 43 deletions(-)
Author: Wolfgang Viechtbauer
Diff between metafor versions 0.5-4 dated 2009-09-18 and 0.5-5 dated 2009-10-08
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.
metafor-0.5-4/metafor/man/plot.rma.uni.infl.Rd |only
metafor-0.5-4/metafor/man/print.rma.list.Rd |only
metafor-0.5-4/metafor/man/print.rma.uni.infl.Rd |only
metafor-0.5-5/metafor/DESCRIPTION | 8
metafor-0.5-5/metafor/NAMESPACE | 13
metafor-0.5-5/metafor/NEWS | 17
metafor-0.5-5/metafor/R/metafor.R | 1131 +++++++++++++++++-------
metafor-0.5-5/metafor/man/anova.rma.uni.Rd | 7
metafor-0.5-5/metafor/man/blup.rma.uni.Rd | 30
metafor-0.5-5/metafor/man/cint.rma.uni.Rd | 5
metafor-0.5-5/metafor/man/cumul.Rd |only
metafor-0.5-5/metafor/man/cumul.rma.mh.Rd |only
metafor-0.5-5/metafor/man/cumul.rma.uni.Rd |only
metafor-0.5-5/metafor/man/escalc.Rd | 14
metafor-0.5-5/metafor/man/fitstats.rma.Rd | 9
metafor-0.5-5/metafor/man/forest.Rd | 9
metafor-0.5-5/metafor/man/forest.default.Rd | 3
metafor-0.5-5/metafor/man/forest.rma.Rd | 25
metafor-0.5-5/metafor/man/forest.rma.cumul.Rd |only
metafor-0.5-5/metafor/man/fsn.Rd | 12
metafor-0.5-5/metafor/man/influence.rma.uni.Rd | 8
metafor-0.5-5/metafor/man/leave1out.Rd |only
metafor-0.5-5/metafor/man/leave1out.rma.mh.Rd |only
metafor-0.5-5/metafor/man/leave1out.rma.uni.Rd |only
metafor-0.5-5/metafor/man/plot.infl.rma.uni.Rd |only
metafor-0.5-5/metafor/man/predict.rma.uni.Rd | 4
metafor-0.5-5/metafor/man/print.infl.rma.uni.Rd |only
metafor-0.5-5/metafor/man/print.list.rma.Rd |only
metafor-0.5-5/metafor/man/qqnorm.rma.uni.Rd | 5
metafor-0.5-5/metafor/man/radial.rma.Rd | 2
metafor-0.5-5/metafor/man/ranktest.rma.Rd | 5
metafor-0.5-5/metafor/man/regtest.rma.Rd | 12
metafor-0.5-5/metafor/man/residuals.rma.Rd | 4
metafor-0.5-5/metafor/man/rma.mh.Rd | 8
metafor-0.5-5/metafor/man/rma.peto.Rd | 4
metafor-0.5-5/metafor/man/rma.uni.Rd | 25
36 files changed, 967 insertions(+), 393 deletions(-)
Author: Rob J Hyndman and Han Lin Shang
Title: Functional time series analysis
Description: Functions for functional time series
Diff between ftsa versions 1.0 dated 2009-09-12 and 1.1 dated 2009-10-08
CHANGELOG |only DESCRIPTION | 8 ++++---- man/dynupdate.Rd | 2 +- man/forecast.ftsm.Rd | 2 +- man/ftsa-package.Rd | 8 ++++---- man/ftsm.Rd | 2 +- man/plot.fm.Rd | 2 +- man/plot.ftsf.Rd | 2 +- 8 files changed, 13 insertions(+), 13 deletions(-)
Author: Jun Yan
Diff between copula versions 0.8-10 dated 2009-07-30 and 0.8-12 dated 2009-10-08
Title: Multivariate dependence with copulas
Description: Classes (S4) of commonly used copulas including elliptical
(normal and t), Archimedean (Clayton, Gumbel, Frank, and
Ali-Mikhail-Haq), extreme value (Gumbel, Husler-Reiss,
Galambos, and t-EV), and other families (Plackett and
Farlie-Gumbel-Morgenstern). Methods for density, distribution,
random number generation, bivariate dependence measures,
perspective and contour plots. Functions for fitting copula
models with variance estimate. Independence tests among random
variables and random vectors. Serial independence tests for
univariate and multivariate continuous time series.
Goodness-of-fit tests for copulas based on multipliers and on
the parametric bootstrap.
ChangeLog | 11 ++++++++
DESCRIPTION | 10 +++----
NAMESPACE | 1
R/Copula.R | 38 ++++++++++++++---------------
R/evTests.R | 64 +++++++++++++++++++++++++++++++------------------
R/schlatherCopula.R | 4 +--
man/copula-internal.Rd | 1
man/evTest.Rd |only
man/gofCopula.Rd | 2 -
9 files changed, 80 insertions(+), 51 deletions(-)
Author: Ulrike Groemping
Title: R Commander Plugin for (industrial) Design of Experiments
Description: WARNING: This package is currently in beta status! The
package provides a platform-independent GUI for design of
experiments. It is implemented as a plugin to the R-Commander,
which is a more general graphical user interface for statistics
in R based on tcl/tk. DoE functionality can be accessed through
the menu Design that is added to the R-Commander menus.
Diff between RcmdrPlugin.DoE versions 0.5-3 dated 2009-09-28 and 0.5-4 dated 2009-10-08
DESCRIPTION | 12 ++++++------ R/Menu.EffectPlots.R | 18 +++++++----------- R/Menu.FrF2level.R | 6 ++++-- R/Menu.IAPlot.R | 23 +++++++++-------------- inst/NEWS | 11 +++++++++++ inst/etc/menus.txt | 1 + 6 files changed, 38 insertions(+), 33 deletions(-)
More information about RcmdrPlugin.DoE at CRAN
Permanent link
Author: M. Suzette Blanchard
Diff between PKtools versions 1.4-0 dated 2008-04-16 and 1.5-0 dated 2009-10-08
Title: unified computational interfaces for pop PK
Description: computations for WinBUGS, NONMEM V, NLME
PKtools-1.4-0/PKtools/inst/PKtools.Setup.pdf |only
PKtools-1.4-0/PKtools/inst/README |only
PKtools-1.4-0/PKtools/inst/nonmemAdd/control.model3 |only
PKtools-1.4-0/PKtools/inst/nonmemAdd/control.model5 |only
PKtools-1.4-0/PKtools/inst/nonmemAdd/control.model6 |only
PKtools-1.4-0/PKtools/man/PKtoolsInternal.Rd |only
PKtools-1.5-0/PKtools/DESCRIPTION | 18
PKtools-1.5-0/PKtools/NAMESPACE |only
PKtools-1.5-0/PKtools/R/PKtools.R | 4234 ++++++++--------
PKtools-1.5-0/PKtools/README |only
PKtools-1.5-0/PKtools/inst/doc/PKtools.Setup.pdf |only
PKtools-1.5-0/PKtools/inst/doc/PKtools.pdf | 4873 +++++++++----------
PKtools-1.5-0/PKtools/inst/doc/PKtoolsVignette.pdf |binary
PKtools-1.5-0/PKtools/inst/nonmemAdd/control.theosq0 |only
PKtools-1.5-0/PKtools/man/AICcomp.Rd | 18
PKtools-1.5-0/PKtools/man/HTMLtools.Rd | 24
PKtools-1.5-0/PKtools/man/PKtools.AIC.Rd | 7
PKtools-1.5-0/PKtools/man/RunNLME.Rd | 5
PKtools-1.5-0/PKtools/man/RunNM.Rd | 4
PKtools-1.5-0/PKtools/man/RunWB.Rd | 11
PKtools-1.5-0/PKtools/man/bugs.Rd | 15
PKtools-1.5-0/PKtools/man/coVar.id.Rd | 5
PKtools-1.5-0/PKtools/man/desc.Rd | 10
PKtools-1.5-0/PKtools/man/diagplot.Rd | 16
PKtools-1.5-0/PKtools/man/diagtrplot.Rd | 14
PKtools-1.5-0/PKtools/man/indEst.Rd | 10
PKtools-1.5-0/PKtools/man/lonecpmt.Rd |only
PKtools-1.5-0/PKtools/man/obvsprplot.Rd | 26
PKtools-1.5-0/PKtools/man/paramEst.Rd | 16
PKtools-1.5-0/PKtools/man/pk.Rd | 6
PKtools-1.5-0/PKtools/man/residplot.Rd | 22
PKtools-1.5-0/PKtools/man/sonecpmt.Rd |only
PKtools-1.5-0/PKtools/man/tex.Rd | 22
PKtools-1.5-0/PKtools/man/trplot.Rd | 27
34 files changed, 4623 insertions(+), 4760 deletions(-)
Author: Douglas Bates
Diff between Matrix versions 0.999375-30 dated 2009-07-30 and 0.999375-31 dated 2009-10-08
Title: Sparse and Dense Matrix Classes and Methods
Description: Classes and methods for dense and sparse matrices and
operations on them using Lapack and SuiteSparse.
ChangeLog | 120 +++
DESCRIPTION | 8
NAMESPACE | 1
R/AllGeneric.R | 29
R/Auxiliaries.R | 47 +
R/CHMfactor.R | 53 +
R/Matrix.R | 71 +-
R/Ops.R | 1184 +++++++++++++++++++++-----------------
R/Tsparse.R | 3
R/dMatrix.R | 2
R/ddenseMatrix.R | 8
R/denseMatrix.R | 12
R/dgCMatrix.R | 5
R/diagMatrix.R | 19
R/dsyMatrix.R | 12
R/dtrMatrix.R | 20
R/kronecker.R | 57 -
R/not.R | 35 +
R/pMatrix.R | 3
R/products.R | 4
R/spModels.R | 54 +
R/sparseMatrix.R | 18
R/sparseVector.R | 69 +-
R/zzz.R | 4
TODO | 1
inst/Doxyfile | 1353 +++++++++++++++++++++++++-------------------
inst/doc/Comparisons.pdf |binary
inst/doc/Design-issues.pdf |binary
inst/doc/Intro2Matrix.pdf | 739 ++++++++++++------------
inst/doc/Introduction.pdf |binary
inst/doc/sparseModels.pdf |binary
inst/include/Matrix.h | 2
inst/include/Matrix_stubs.c | 34 +
inst/include/cholmod.h | 3
inst/test-tools.R | 4
man/CHMfactor-class.Rd | 14
man/Matrix-class.Rd | 2
man/Xtrct-methods.Rd | 4
man/atomicVector-class.Rd | 4
man/cBind.Rd | 4
man/chol2inv-methods.Rd |only
man/dMatrix-class.Rd | 28
man/ddenseMatrix-class.Rd | 11
man/dgCMatrix-class.Rd | 2
man/dgeMatrix-class.Rd | 2
man/diagonalMatrix-class.Rd | 4
man/dpoMatrix-class.Rd | 26
man/dsparseMatrix-class.Rd | 4
man/dsyMatrix-class.Rd | 1
man/kronecker-methods.Rd | 2
man/nMatrix-class.Rd | 26
man/pMatrix-class.Rd | 1
man/spMatrix.Rd | 5
man/sparse.model.matrix.Rd | 2
man/sparseQR-class.Rd | 8
man/sparseVector-class.Rd | 23
src/Mutils.c | 32 -
src/Mutils.h | 7
src/chm_common.c | 122 +++
src/chm_common.h | 3
src/dgCMatrix.c | 7
src/dgeMatrix.c | 2
src/dsCMatrix.c | 17
src/dtrMatrix.c | 17
src/dtrMatrix.h | 1
src/init.c | 4
tests/Simple.R | 5
tests/factorizing.R | 20
tests/group-methods.R | 36 +
tests/indexing.R | 10
tests/indexing.Rout.save | 71 --
tests/matprod.R | 12
tests/spModel.matrix.R | 17
tests/validObj.R | 3
74 files changed, 2779 insertions(+), 1754 deletions(-)
Author: Ulrike Groemping
Title: Fractional Factorial designs with 2-level factors
Description: This package creates regular and non-regular Fractional
Factorial designs. Furthermore, analysis tools for Fractional
Factorial designs with 2-level factors are offered (main
effects and interaction plots for all factors simultaneously,
cube plot for looking at the simultaneous effects of three
factors, full or half normal plot, alias structure in a more
readable format than with the built-in function alias). The
package is currently subject to intensive development. While
much of the intended functionality is already available, some
changes and improvements are still to be expected. Suggestions
are welcome.
Diff between FrF2 versions 0.97-10 dated 2009-09-18 and 1.0 dated 2009-10-08
DESCRIPTION | 8 ++++---- NAMESPACE | 7 ++++++- R/DanielPlot.R | 23 ++++++++++++++++++++++- R/FrF2.R | 12 +++++++----- R/IAPlot.R | 19 +++++++++++++++++-- R/MEPlot.R | 18 ++++++++++++++++-- R/contr.FrF2.R | 4 ++-- R/print.catlg.R | 14 ++++++++++++-- R/sysdata.rda |binary inst/NEWS | 15 +++++++++++---- man/CatalogueAccessors.Rd | 20 +++++++++++++++++--- man/DanielPlot.Rd | 25 +++++++++++++++++++++---- man/FrF2-package.Rd | 8 ++++++++ man/FrF2.Rd | 28 +++++++++++++++------------- man/IAPlot.Rd | 33 ++++++++++++++++++++++++++++----- 15 files changed, 186 insertions(+), 48 deletions(-)