Author: Karline Soetaert
Diff between NetIndices versions 1.2 dated 2009-01-16 and 1.3 dated 2009-06-17
Title: Estimating network indices, including trophic structure of
foodwebs in R
Description: Given a network (e.g. a food web), estimates several
network indices. These include: Ascendency network indices,
Direct and indirect dependencies, Effective measures, Environ
network indices, General network indices, Pathway analysis,
Network uncertainty indices and constraint efficiencies and the
trophic level and omnivory indices of food webs.
NetIndices-1.2/NetIndices/inst/doc/Sweave.sty |only
NetIndices-1.2/NetIndices/inst/doc/netindices.tex |only
NetIndices-1.3/NetIndices/DESCRIPTION | 35 -
NetIndices-1.3/NetIndices/R/AscInd.R |only
NetIndices-1.3/NetIndices/R/Dependency.R |only
NetIndices-1.3/NetIndices/R/EffInd.R |only
NetIndices-1.3/NetIndices/R/EnvInd.R |only
NetIndices-1.3/NetIndices/R/GenInd.R |only
NetIndices-1.3/NetIndices/R/NetIndices.R | 739 ++--------------------
NetIndices-1.3/NetIndices/R/PathInd.R |only
NetIndices-1.3/NetIndices/R/TrophInd.R |only
NetIndices-1.3/NetIndices/R/UnInd.R |only
NetIndices-1.3/NetIndices/inst/doc/NetIndices.bib | 23
NetIndices-1.3/NetIndices/inst/doc/NetIndices.pdf |binary
NetIndices-1.3/NetIndices/inst/doc/NetIndices.rnw | 229 +++---
NetIndices-1.3/NetIndices/man/AscInd.Rd | 100 ++
NetIndices-1.3/NetIndices/man/Conesprings.Rd | 82 +-
NetIndices-1.3/NetIndices/man/Dependency.Rd | 40 -
NetIndices-1.3/NetIndices/man/EffInd.Rd | 66 +
NetIndices-1.3/NetIndices/man/EnvInd.Rd | 118 ++-
NetIndices-1.3/NetIndices/man/GenInd.Rd | 107 ++-
NetIndices-1.3/NetIndices/man/NetIndices.Rd | 31
NetIndices-1.3/NetIndices/man/PathInd.Rd | 92 ++
NetIndices-1.3/NetIndices/man/Takapoto.Rd | 77 +-
NetIndices-1.3/NetIndices/man/TrophInd.Rd | 89 +-
NetIndices-1.3/NetIndices/man/UncInd.Rd | 102 ++-
26 files changed, 899 insertions(+), 1031 deletions(-)
Author: Karline Soetaert
Diff between LIM versions 1.2 dated 2009-01-20 and 1.3 dated 2009-06-17
Title: Linear Inverse Model examples and solution methods.
Description: Functions that read and solve linear inverse problems
(food web problems, linear programming problems). These
problems find solutions to linear or quadratic functions: min
or max (f(x)), where f(x) = ||Ax-b||^2 or f(x) = sum(ai*xi)
subject to equality constraints Ex=f and inequality constraints
Gx>=h. Uses package limSolve.
DESCRIPTION | 35
R/Flowmatrix.R |only
R/LIM.r | 564 -------
R/Ldei.R |only
R/Linp.R |only
R/Lsei.R |only
R/Plotranges.R |only
R/Variables.R |only
R/Varranges.R |only
R/Xranges.R |only
R/Xsample.R |only
R/read.limfile.r | 1661 +++++++++++------------
inst/doc/LIM.Rnw | 1515 +++++++++++----------
inst/doc/LIM.pdf | 3097 ++++++++++++++++++++++---------------------
inst/doc/vignettes.bib | 434 ------
man/FILERigaAutumn.Rd | 75 -
man/Flowmatrix.Rd | 41
man/LIM.Rd | 37
man/LIMBlending.Rd | 91 -
man/LIMBrouageMudflat.Rd | 85 -
man/LIMCaliforniaSediment.Rd | 91 -
man/LIMEcoli.Rd | 97 -
man/LIMEverglades.Rd | 77 -
man/LIMRigaAutumn.Rd | 77 -
man/LIMRigaSpring.Rd | 90 -
man/LIMRigaSummer.Rd | 86 -
man/LIMScheldtIntertidal.Rd | 99 -
man/LIMTakapoto.Rd | 75 -
man/Ldei.Rd | 108 +
man/Linp.Rd | 114 +
man/Lsei.Rd | 174 +-
man/PrintMat.Rd | 28
man/Read.Rd | 164 +-
man/Setup.Rd | 133 +
man/Variables.Rd | 40
man/Varranges.Rd | 41
man/Xranges.Rd | 41
man/Xsample.Rd | 68
man/plotranges.Rd | 103 -
39 files changed, 4749 insertions(+), 4592 deletions(-)
Author: Jari Oksanen, Roeland Kindt, Pierre Legendre, Bob O'Hara, Gavin
L. Simpson, Peter Solymos, M. Henry H. Stevens, Helene Wagner
Title: Community Ecology Package
Description: Ordination methods, diversity analysis and other functions
for community and vegetation ecologists.
Diff between vegan versions 1.15-2 dated 2009-04-15 and 1.15-3 dated 2009-06-17
DESCRIPTION | 8 R/adonis.R | 5 R/anosim.R | 4 R/anova.ccabyaxis.R | 12 R/anova.ccabymargin.R | 8 R/anova.ccabyterm.R | 16 R/capscale.R | 42 - R/eigenvals.R |only R/factorfit.R | 2 R/kendall.global.R | 3 R/mantel.R | 56 - R/mantel.partial.R | 74 - R/meandist.R |only R/mrpp.R | 2 R/ordiGetData.R | 4 R/ordilattice.getEnvfit.R | 2 R/ordisurf.R | 10 R/orditkplot.R | 4 R/ordixyplot.R | 2 R/panel.ordi.R | 4 R/plot.anosim.R | 2 R/plot.meandist.R |only R/print.anosim.R | 2 R/print.cca.R | 11 R/print.factorfit.R | 5 R/print.mantel.R | 2 R/print.mrpp.R | 2 R/print.permutest.cca.R | 2 R/print.protest.R | 2 R/print.summary.cca.R | 8 R/print.summary.meandist.R |only R/print.vectorfit.R | 5 R/protest.R | 4 R/summary.cca.R | 13 R/summary.meandist.R |only R/taxa2dist.R | 2 R/tsallis.R | 11 R/vectorfit.R | 2 R/wcmdscale.R | 7 inst/ChangeLog | 49 + inst/NEWS | 61 + inst/doc/FAQ-vegan.pdf |binary inst/doc/FAQ-vegan.texi | 32 inst/doc/decision-vegan.pdf | 1638 +++++++++++++++++++++---------------------- inst/doc/decision-vegan.tex | 16 inst/doc/diversity-vegan.pdf |binary inst/doc/diversity-vegan.tex | 69 - inst/doc/intro-vegan.pdf |binary inst/doc/intro-vegan.tex | 61 - man/anosim.Rd | 2 man/capscale.Rd | 70 + man/cca.object.Rd | 4 man/eigenvals.Rd |only man/envfit.Rd | 4 man/mantel.Rd | 4 man/metaMDS.Rd | 4 man/mrpp.Rd | 39 - man/ordisurf.Rd | 5 man/procrustes.Rd | 2 man/tsallis.Rd | 26 60 files changed, 1298 insertions(+), 1126 deletions(-)
Author: Karline Soetaert
Diff between shape versions 1.2.1 dated 2009-02-20 and 1.2.2 dated 2009-06-17
Title: Functions for plotting graphical shapes, colors
Description: Functions for plotting graphical shapes such as ellipses,
circles, cylinders, arrows, ... Support for the book "A
practical guide to ecological modelling - using R as a
simulation platform" by Karline Soetaert and Peter M.J. Herman
(2009). Springer. Includes demo(colorshapes)
shape-1.2.1/shape/man/graycol.Rd |only
shape-1.2.2/shape/DESCRIPTION | 35
shape-1.2.2/shape/R/A4.R |only
shape-1.2.2/shape/R/Arrowhead.R |only
shape-1.2.2/shape/R/Arrows.R |only
shape-1.2.2/shape/R/colorlegend.R |only
shape-1.2.2/shape/R/cylindersegment.R |only
shape-1.2.2/shape/R/drapecol.R |only
shape-1.2.2/shape/R/emptyplot.R |only
shape-1.2.2/shape/R/femmecol.R |only
shape-1.2.2/shape/R/filledcircle.R |only
shape-1.2.2/shape/R/filledcylinder.R |only
shape-1.2.2/shape/R/filledellipse.R |only
shape-1.2.2/shape/R/filledmultigonal.R |only
shape-1.2.2/shape/R/filledrectangle.R |only
shape-1.2.2/shape/R/filledshape.R |only
shape-1.2.2/shape/R/getellipse.R |only
shape-1.2.2/shape/R/greycol.R |only
shape-1.2.2/shape/R/intpalette.R |only
shape-1.2.2/shape/R/plotcircle.R |only
shape-1.2.2/shape/R/plotellipse.R |only
shape-1.2.2/shape/R/rotatexy.R |only
shape-1.2.2/shape/R/roundrect.R |only
shape-1.2.2/shape/R/shadepalette.R |only
shape-1.2.2/shape/R/shape.R | 981 --
shape-1.2.2/shape/R/writelabel.R |only
shape-1.2.2/shape/inst/doc/shape.Rnw | 55
shape-1.2.2/shape/inst/doc/shape.pdf |11444 +++++++++++++++---------------
shape-1.2.2/shape/inst/doc/vignettes.bib | 38
shape-1.2.2/shape/man/A4.Rd | 19
shape-1.2.2/shape/man/Arrowhead.Rd | 95
shape-1.2.2/shape/man/Arrows.Rd | 129
shape-1.2.2/shape/man/colorlegend.Rd | 106
shape-1.2.2/shape/man/cylindersegment.Rd | 81
shape-1.2.2/shape/man/drapecol.Rd | 50
shape-1.2.2/shape/man/emptyplot.Rd | 43
shape-1.2.2/shape/man/femmecol.Rd | 39
shape-1.2.2/shape/man/filledcircle.Rd | 83
shape-1.2.2/shape/man/filledcylinder.Rd | 97
shape-1.2.2/shape/man/filledellipse.Rd | 117
shape-1.2.2/shape/man/filledmultigonal.Rd | 99
shape-1.2.2/shape/man/filledrectangle.Rd | 100
shape-1.2.2/shape/man/filledshape.Rd | 84
shape-1.2.2/shape/man/getellipse.Rd | 64
shape-1.2.2/shape/man/greycol.Rd | 48
shape-1.2.2/shape/man/intpalette.Rd | 51
shape-1.2.2/shape/man/plotcircle.Rd | 45
shape-1.2.2/shape/man/plotellipse.Rd | 133
shape-1.2.2/shape/man/rotatexy.Rd | 43
shape-1.2.2/shape/man/roundrect.Rd | 59
shape-1.2.2/shape/man/shadepalette.Rd | 47
shape-1.2.2/shape/man/shape.Rd | 28
shape-1.2.2/shape/man/writelabel.Rd | 31
53 files changed, 7118 insertions(+), 7126 deletions(-)
Author: Torsten Hothorn, Kurt Hornik, Carolin Strobl and Achim Zeileis
Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning. The
core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems,
including nominal, ordinal, numeric, censored as well as
multivariate response variables and arbitrary measurement
scales of the covariates. Based on conditional inference trees,
cforest() provides an implementation of Breiman's random
forests. The function mob() implements an algorithm for
recursive partitioning based on parametric models (e.g. linear
models, GLMs or survival regression) employing parameter
instability tests for split selection. Extensible functionality
for visualizing tree-structured regression models is available.
Diff between party versions 0.9-997 dated 2009-06-04 and 0.9-998 dated 2009-06-17
DESCRIPTION | 8 NEWS | 7 R/Classes.R | 4 R/ConditionalTree.R | 4 inst/doc/MOB.pdf | 14 inst/doc/party.pdf |binary inst/documentation/html/Classes_8c-source.html | 18 inst/documentation/html/Classes_8c.html | 102 inst/documentation/html/Classes_8c_0e317821da8f3bc0fb6da5006abb81f6_cgraph.map | 4 inst/documentation/html/Classes_8c_0e317821da8f3bc0fb6da5006abb81f6_cgraph.md5 | 2 inst/documentation/html/Classes_8c_0e317821da8f3bc0fb6da5006abb81f6_cgraph.png |binary inst/documentation/html/Classes_8c__incl.map | 30 inst/documentation/html/Classes_8c__incl.md5 | 2 inst/documentation/html/Classes_8c__incl.png |binary inst/documentation/html/Classes_8c_a160107e2d687d3fa2411af7e25763ef_cgraph.map | 2 inst/documentation/html/Classes_8c_a160107e2d687d3fa2411af7e25763ef_cgraph.md5 | 2 inst/documentation/html/Classes_8c_a160107e2d687d3fa2411af7e25763ef_cgraph.png |binary inst/documentation/html/Classes_8c_ba4726f56726372030e1e104b2f2b076_cgraph.map | 2 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inst/documentation/man/man3/Node.h.3 | 10 inst/documentation/man/man3/Predict.c.3 | 2 inst/documentation/man/man3/Predict.h.3 | 2 inst/documentation/man/man3/RandomForest.c.3 | 2 inst/documentation/man/man3/S3Classes.c.3 | 2 inst/documentation/man/man3/S3Classes.h.3 | 2 inst/documentation/man/man3/Splits.c.3 | 2 inst/documentation/man/man3/Splits.h.3 | 2 inst/documentation/man/man3/SurrogateSplits.c.3 | 2 inst/documentation/man/man3/SurrogateSplits.h.3 | 2 inst/documentation/man/man3/TestStatistic.c.3 | 2 inst/documentation/man/man3/TestStatistic.h.3 | 2 inst/documentation/man/man3/TreeGrow.c.3 | 2 inst/documentation/man/man3/TreeGrow.h.3 | 2 inst/documentation/man/man3/Utils.c.3 | 4 inst/documentation/man/man3/Utils.h.3 | 2 inst/documentation/man/man3/_home_hothorn_projects_svn_Rpkgs_trunk_party_src_.3 | 5 inst/documentation/man/man3/mvt.f.3 | 212 inst/documentation/man/man3/mvt.h.3 | 2 inst/documentation/man/man3/party.h.3 | 2 inst/documentation/man/man3/todo.3 | 2 src/Classes.c | 6 src/Classes.h | 2 src/IndependenceTest.c | 18 src/IndependenceTest.h | 2 src/Node.c | 9 src/Node.h | 2 src/SurrogateSplits.c | 4 src/TreeGrow.c | 6 1063 files changed, 39727 insertions(+), 36483 deletions(-)
Author: Florian Camphausen, Matthias Kohl, Peter Ruckdeschel, Thomas
Stabla
Title: Object orientated implementation of distributions
Description: Object orientated implementation of distributions
Diff between distr versions 2.1 dated 2009-04-15 and 2.1.1 dated 2009-06-17
DESCRIPTION | 8 ++-- R/internalUtils.R | 1 inst/doc/.build.timestamp |only inst/doc/Rplots.pdf | 64 ++++++++++++++++---------------- inst/doc/newDistributions-AbscDist.eps |only inst/doc/newDistributions-AbscDist.pdf |only inst/doc/newDistributions-DiscrDist.eps |only inst/doc/newDistributions-DiscrDist.pdf |only inst/doc/newDistributions-exam1.eps |only inst/doc/newDistributions-exam1.pdf |only inst/doc/newDistributions.pdf |binary inst/doc/newDistributions.tex |only man/Unif-class.Rd | 20 +++++++--- 13 files changed, 51 insertions(+), 42 deletions(-)
Author: Karline Soetaert
Diff between diagram versions 1.3.1 dated 2009-02-20 and 1.4 dated 2009-06-17
Title: Functions for visualising simple graphs (networks), plotting
flow diagrams
Description: Visualises simple graphs (networks) based on a transition
matrix, utilities to plot flow diagrams, visualising webs,...
Support for the book "A practical guide to ecological modelling
- using R as a simulation platform" by Karline Soetaert and
Peter M.J. Herman (2009). Springer. Includes demo(flowchart),
demo(plotmat), demo(plotweb)
diagram-1.3.1/diagram/R/diagram.r |only
diagram-1.4/diagram/DESCRIPTION | 38
diagram-1.4/diagram/R/bentarrow.R |only
diagram-1.4/diagram/R/coordinates.R |only
diagram-1.4/diagram/R/curvedarrow.R |only
diagram-1.4/diagram/R/openplotmat.R |only
diagram-1.4/diagram/R/plotmat.R |only
diagram-1.4/diagram/R/plotweb.R |only
diagram-1.4/diagram/R/segmentarrow.R |only
diagram-1.4/diagram/R/selfarrow.R |only
diagram-1.4/diagram/R/shadowbox.R |only
diagram-1.4/diagram/R/splitarrow.R |only
diagram-1.4/diagram/R/straightarrow.R |only
diagram-1.4/diagram/R/textdiamond.R |only
diagram-1.4/diagram/R/textellipse.R |only
diagram-1.4/diagram/R/textempty.R |only
diagram-1.4/diagram/R/texthexa.R |only
diagram-1.4/diagram/R/textmulti.R |only
diagram-1.4/diagram/R/textplain.R |only
diagram-1.4/diagram/R/textrect.R |only
diagram-1.4/diagram/R/textround.R |only
diagram-1.4/diagram/R/treearrow.R |only
diagram-1.4/diagram/demo/plotmat.r | 2
diagram-1.4/diagram/inst/doc/diagram.Rnw | 91 -
diagram-1.4/diagram/inst/doc/diagram.pdf | 2208 ++++++++++++++---------------
diagram-1.4/diagram/inst/doc/vignettes.bib | 41
diagram-1.4/diagram/man/Rigaweb.Rd | 71
diagram-1.4/diagram/man/Takapotoweb.Rd | 75
diagram-1.4/diagram/man/Teasel.Rd | 63
diagram-1.4/diagram/man/bentarrow.Rd | 97 -
diagram-1.4/diagram/man/coordinates.Rd | 83 -
diagram-1.4/diagram/man/curvedarrow.Rd | 109 -
diagram-1.4/diagram/man/diagram.Rd | 36
diagram-1.4/diagram/man/openplotmat.Rd | 28
diagram-1.4/diagram/man/plotmat.Rd | 358 +++-
diagram-1.4/diagram/man/plotweb.Rd | 194 +-
diagram-1.4/diagram/man/segmentarrow.Rd | 120 +
diagram-1.4/diagram/man/selfarrow.Rd | 89 -
diagram-1.4/diagram/man/shadowbox.Rd | 105 -
diagram-1.4/diagram/man/splitarrow.Rd | 116 +
diagram-1.4/diagram/man/straightarrow.Rd | 82 -
diagram-1.4/diagram/man/textdiamond.Rd | 78 -
diagram-1.4/diagram/man/textellipse.Rd | 81 -
diagram-1.4/diagram/man/textempty.Rd | 49
diagram-1.4/diagram/man/texthexa.Rd | 78 -
diagram-1.4/diagram/man/textmulti.Rd | 77 -
diagram-1.4/diagram/man/textplain.Rd | 50
diagram-1.4/diagram/man/textrect.Rd | 73
diagram-1.4/diagram/man/textround.Rd | 79 -
diagram-1.4/diagram/man/treearrow.Rd | 121 +
50 files changed, 2844 insertions(+), 1848 deletions(-)
Author: Jussi Klemela
Diff between delt versions 0.7.0 dated 2008-02-29 and 0.8.0 dated 2009-06-17
Title: Estimation of multivariate densities with adaptive histograms
Description: The package implements methods for estimating multivariate
densities: adaptive histograms (greedy histograms and
CART-histograms), stagewise minimization, and bootstrap
aggregation are included in the package.
delt-0.7.0/delt/R/crosvali.R |only
delt-0.7.0/delt/R/dentseq.R |only
delt-0.7.0/delt/R/modetreeD.R |only
delt-0.7.0/delt/R/omaindmat.R |only
delt-0.7.0/delt/R/profaah.R |only
delt-0.7.0/delt/R/profavah.R |only
delt-0.7.0/delt/R/prunecv.R |only
delt-0.8.0/delt/DESCRIPTION | 22 +++++++++++-----------
delt-0.8.0/delt/R/allocolo.R | 15 ++++++++-------
delt-0.8.0/delt/R/denmean.R | 11 ++++++-----
delt-0.8.0/delt/R/densplitF.R | 11 +++++------
delt-0.8.0/delt/R/densplitR.R | 31 ++++++++++++++++---------------
delt-0.8.0/delt/R/findsplit.R | 11 ++++++-----
delt-0.8.0/delt/R/plotparti.R | 7 ++++---
delt-0.8.0/delt/man/delt-package.Rd | 8 ++++----
delt-0.8.0/delt/man/plotparti.Rd | 3 ++-
16 files changed, 62 insertions(+), 57 deletions(-)
Author: Bill Venables
Title: Construction of factorial designs
Description: This small library contains a series of simple tools for
constructing and manipulating confounded and fractional
factorial designs.
Diff between conf.design versions 0.0-4 dated 2005-04-08 and 1.0 dated 2009-06-17
conf.design-0.0-4/conf.design/INDEX |only conf.design-0.0-4/conf.design/README.design |only conf.design-1.0/conf.design/DESCRIPTION | 24 ++++++++++++------------ conf.design-1.0/conf.design/LICENSE |only conf.design-1.0/conf.design/inst |only 5 files changed, 12 insertions(+), 12 deletions(-)
Author: Marc Schwartz
Diff between WriteXLS versions 1.7.1 dated 2009-05-29 and 1.8.0 dated 2009-06-17
Title: Cross-platform Perl based R function to create Excel 2003 (XLS)
files
Description: Cross-platform perl based R function to create Excel (XLS)
files from one or more data frames. Each data frame will be
written to a separate named worksheet in the Excel spreadsheet.
The worksheet name will be the name of the data frame it
contains or can be specified by the user.
DESCRIPTION | 10 +++++-----
R/WriteXLS.R | 14 ++++++++++++--
inst/Perl/WriteXLS.pl | 15 +++++++++++----
man/WriteXLS.Rd | 10 +++++++---
4 files changed, 35 insertions(+), 14 deletions(-)
Author: Washington Junger
Diff between pgam versions 0.4.8 dated 2007-12-18 and 0.4.9 dated 2009-06-17
Title: Poisson-Gamma Additive Models.
Description: This work is an extension of the state space model for
Poisson count data, Poisson-Gamma model, towards a
semiparametric specification. Just like the generalized
additive models (GAM), cubic splines are used for covariate
smoothing. The semiparametric models are fitted by an iterative
process that combines maximization of likelihood and
backfitting algorithm.
pgam-0.4.8/pgam/src/Makevars |only
pgam-0.4.9/pgam/DESCRIPTION | 23 ++++++++++++++++-------
pgam-0.4.9/pgam/R/pgam.r | 6 +++---
pgam-0.4.9/pgam/R/zzz.r | 11 ++++++-----
pgam-0.4.9/pgam/man/AIC.pgam.Rd | 2 +-
pgam-0.4.9/pgam/man/aihrio.Rd | 2 +-
pgam-0.4.9/pgam/man/backfitting.Rd | 2 +-
pgam-0.4.9/pgam/man/bksmooth.Rd | 2 +-
pgam-0.4.9/pgam/man/coef.pgam.Rd | 2 +-
pgam-0.4.9/pgam/man/deviance.pgam.Rd | 2 +-
pgam-0.4.9/pgam/man/envelope.Rd | 1 -
pgam-0.4.9/pgam/man/fitted.pgam.Rd | 2 +-
pgam-0.4.9/pgam/man/g.Rd | 2 +-
pgam-0.4.9/pgam/man/logLik.pgam.Rd | 2 +-
pgam-0.4.9/pgam/man/pgam.Rd | 2 +-
pgam-0.4.9/pgam/man/pgam.filter.Rd | 2 +-
pgam-0.4.9/pgam/man/pgam.fit.Rd | 2 +-
pgam-0.4.9/pgam/man/pgam.likelihood.Rd | 2 +-
pgam-0.4.9/pgam/man/predict.pgam.Rd | 2 +-
pgam-0.4.9/pgam/man/residuals.pgam.Rd | 2 +-
pgam-0.4.9/pgam/man/summary.pgam.Rd | 2 +-
21 files changed, 41 insertions(+), 32 deletions(-)
Author: Dai Feng and Luke Tierney
Title: Miscellaneous 3D Plots
Description: A collection of miscellaneous 3d plots, including
isosurfaces.
Diff between misc3d versions 0.6-1 dated 2008-05-28 and 0.6-3 dated 2009-06-17
DESCRIPTION | 8 ++++-- NAMESPACE | 2 - R/image3d.R | 4 +-- R/slices3d.R | 68 +++++++++++++++++++++++++++++++++++++++++++++---------- R/triangles.R | 13 +++++----- inst |only man/slices3d.Rd | 35 +++++++++++++++++++++------- man/triangles.Rd | 6 ++++ 8 files changed, 103 insertions(+), 33 deletions(-)
Author: Andrew Gelman
Diff between mi versions 0.07-4 dated 2009-06-14 and 0.08-01 dated 2009-06-17
Title: Missing Data Imputation and Model Checking
Description: Missing-data imputation and model checking
CHANGELOG | 13 +++++++++++++
DESCRIPTION | 6 +++---
R/AllInternal.R | 18 ++++++++++++++----
R/mi.R | 24 +++++++++++++++++++++---
R/mi.binary.R | 14 ++++++++++----
R/mi.continuous.R | 11 +++++++++--
R/mi.count.R | 33 +++++++++++++++++++++++----------
R/mi.info.R | 27 +++++++++++++--------------
R/mi.polr.R | 5 ++++-
R/mi.pooled.R | 9 ++++++---
man/mi.Rd | 3 +--
man/mi.binary.Rd | 6 +++---
man/mi.continuous.Rd | 2 +-
man/mi.count.Rd | 2 +-
14 files changed, 122 insertions(+), 51 deletions(-)
Author: Peter Solymos
Title: Multivariate Data Handling in Ecology and Biogeography
Description: A framework package aimed to provide standardized
computational environment for specialist work via object
classes to represent the data coded by samples, taxa and
segments (i.e. subpopulations, repeated measures). It supports
easy processing of the data along with cross tabulation and
relational data tables for samples and taxa. An object of class
`mefa' is a project specific compendium of the data and can be
easily used in further analyses. Methods are provided for
extraction, aggregation, conversion, plotting, summary and
reporting of `mefa' objects. Reports can be generated in plain
text or LaTeX format. Vignette contains worked examples.
Diff between mefa versions 3.0-1 dated 2009-05-04 and 3.1-0 dated 2009-06-17
DESCRIPTION | 10 +++++----- R/as.data.frame.dist.R |only R/as.data.frame.mefa.R | 1 + R/cdrop.R |only R/dist2vec.R |only R/extract.mefa.R | 4 ++++ R/is.dist.R |only R/mat2list.R |only R/mfill.R |only R/rdrop.R |only R/report.mefa.R | 12 +++++------- R/vec2dist.R |only inst/ChangeLog | 25 ++++++++++++++++++++++++- inst/doc/mefa.pdf |binary man/aggregate.mefa.Rd | 6 +++--- man/as.mefa.Rd | 6 +++--- man/dist2vec.Rd |only man/dolina.Rd | 10 +++++----- man/fill.na.Rd | 6 +++--- man/inflate.Rd | 6 +++--- man/label.Rd | 6 +++--- man/mat2list.Rd |only man/mefa.Rd | 6 +++--- man/mefaCheck.Rd | 6 +++--- man/mefaCrosstab.Rd | 6 +++--- man/mefaNestedless.Rd | 6 +++--- man/mefaTables.Rd | 6 +++--- man/mefadocs.Rd | 2 +- man/mefalogo.Rd | 6 +++--- man/mefaweb.Rd | 6 +++--- man/melt.mefa.Rd | 6 +++--- man/plot.mefa.Rd | 6 +++--- man/qvector.Rd | 6 +++--- man/report.mefa.Rd | 12 ++++++------ man/stcs.Rd | 6 +++--- 35 files changed, 99 insertions(+), 73 deletions(-)
Author: Andy Bunn
Title: Dendrochronology Program Library in R
Description: This package contains functions for performing some
standard tree-ring analyses.
Diff between dplR versions 1.1.8 dated 2009-03-24 and 1.1.9 dated 2009-06-17
DESCRIPTION | 6 +++--- R/read.rwl.R | 15 +++++++++++---- man/read.rwl.Rd | 6 +++++- 3 files changed, 19 insertions(+), 8 deletions(-)
Author: Nardini, C. and Liu, Y-H.
Title: Performance of N-ary classification testing
Description: Evaluate the performance of classifying
Diff between Multiclasstesting versions 1.0.0 dated 2009-04-23 and 1.2.0 dated 2009-06-17
Multiclasstesting-1.0.0/Multiclasstesting/inst/doc/NclasstestViggnette.Rnw |only Multiclasstesting-1.0.0/Multiclasstesting/inst/doc/NclasstestViggnette.pdf |only Multiclasstesting-1.0.0/Multiclasstesting/inst/doc/NclasstestViggnette.tex |only Multiclasstesting-1.2.0/Multiclasstesting/DESCRIPTION | 8 - Multiclasstesting-1.2.0/Multiclasstesting/R/Nclasstest.R | 23 ++++- Multiclasstesting-1.2.0/Multiclasstesting/inst/doc/NclasstestVignette.Rnw |only Multiclasstesting-1.2.0/Multiclasstesting/inst/doc/NclasstestVignette.pdf |only Multiclasstesting-1.2.0/Multiclasstesting/man/Multiclasstesting-package.Rd | 6 - Multiclasstesting-1.2.0/Multiclasstesting/man/Nclasstest.Rd | 41 ++++++---- 9 files changed, 49 insertions(+), 29 deletions(-)
More information about Multiclasstesting at CRAN
Permanent link
Author: Andrew O. Finley
Diff between MBA versions 0.0-5 dated 2009-03-05 and 0.0-6 dated 2009-06-17
Title: Multilevel B-spline Approximation
Description: Scattered data interpolation with Multilevel B-Splines
DESCRIPTION | 9
configure | 3242 ++++++++++++++++++++++++++++++++++--------------------------
2 files changed, 1896 insertions(+), 1355 deletions(-)
Author: Dimitris Rizopoulos
Diff between JM versions 0.2-2 dated 2008-12-15 and 0.3-0 dated 2009-06-17
Title: Joint Modelling of Longitudinal and Survival Data
Description: Shared parameter models for the joint modelling of
longitudinal and time-to-event data.
JM-0.2-2/JM/R/weibullGH.fit.R |only
JM-0.3-0/JM/DESCRIPTION | 29 ++---
JM-0.3-0/JM/R/HessLongPH.R | 2
JM-0.3-0/JM/R/HessSurvPH.R | 2
JM-0.3-0/JM/R/LogLik.chGH.R | 2
JM-0.3-0/JM/R/LogLik.chLaplace.R | 2
JM-0.3-0/JM/R/LogLik.phGH.R | 26 ++--
JM-0.3-0/JM/R/LogLik.piecewiseGH.R |only
JM-0.3-0/JM/R/LogLik.weibullAFTGH.R |only
JM-0.3-0/JM/R/LogLik.weibullGH.R | 15 +-
JM-0.3-0/JM/R/MI.fixed.times.R | 13 +-
JM-0.3-0/JM/R/MI.random.times.R | 14 +-
JM-0.3-0/JM/R/SclongCH.R | 2
JM-0.3-0/JM/R/Score.chGH.R | 2
JM-0.3-0/JM/R/Score.chLaplace.R | 2
JM-0.3-0/JM/R/Score.phGH.R | 62 ++++++----
JM-0.3-0/JM/R/Score.piecewiseGH.R |only
JM-0.3-0/JM/R/Score.weibullAFTGH.R |only
JM-0.3-0/JM/R/Score.weibullGH.R | 35 ++++--
JM-0.3-0/JM/R/ScsurvCH.R | 2
JM-0.3-0/JM/R/anova.jointModel.R | 4
JM-0.3-0/JM/R/cd.vec.R | 2
JM-0.3-0/JM/R/chGH.fit.R | 2
JM-0.3-0/JM/R/chLaplace.fit.R | 2
JM-0.3-0/JM/R/chol.transf.R | 2
JM-0.3-0/JM/R/coef.flexCPH.R | 2
JM-0.3-0/JM/R/coef.jointModel.R | 7 -
JM-0.3-0/JM/R/coef.weibull.frailty.R | 2
JM-0.3-0/JM/R/deriv.D.R | 2
JM-0.3-0/JM/R/dmvnorm.R | 2
JM-0.3-0/JM/R/dmvt.R | 2
JM-0.3-0/JM/R/fd.vec.R | 2
JM-0.3-0/JM/R/fitted.jointModel.R | 95 ++++++++++++++--
JM-0.3-0/JM/R/fixef.jointModel.R | 7 -
JM-0.3-0/JM/R/flexCPH.R | 2
JM-0.3-0/JM/R/flexCPH.fit.R | 2
JM-0.3-0/JM/R/fn.b.R | 2
JM-0.3-0/JM/R/gauher.R | 2
JM-0.3-0/JM/R/gaussKronrod.R |only
JM-0.3-0/JM/R/gr.b.R | 2
JM-0.3-0/JM/R/gr.longAFTWB.R |only
JM-0.3-0/JM/R/gr.longCH.R | 2
JM-0.3-0/JM/R/gr.longPC.R |only
JM-0.3-0/JM/R/gr.longPH.R | 27 +++-
JM-0.3-0/JM/R/gr.longWB.R | 19 ++-
JM-0.3-0/JM/R/gr.survAFTWB.R |only
JM-0.3-0/JM/R/gr.survCH.R | 2
JM-0.3-0/JM/R/gr.survPC.R |only
JM-0.3-0/JM/R/gr.survPH.R | 32 +++--
JM-0.3-0/JM/R/gr.survWB.R | 19 +--
JM-0.3-0/JM/R/initial.surv.R | 51 +++++++--
JM-0.3-0/JM/R/jacobian.R | 2
JM-0.3-0/JM/R/jacobian2.R | 2
JM-0.3-0/JM/R/jointModel.R | 120 ++++++++++++++++-----
JM-0.3-0/JM/R/logLik.flexCPH.R | 2
JM-0.3-0/JM/R/logLik.jointModel.R | 2
JM-0.3-0/JM/R/logLik.weibull.frailty.R | 2
JM-0.3-0/JM/R/logsurvCH.R | 2
JM-0.3-0/JM/R/nearPD.R | 2
JM-0.3-0/JM/R/opt.longAFTWB.R |only
JM-0.3-0/JM/R/opt.longPC.R |only
JM-0.3-0/JM/R/opt.longPH.R |only
JM-0.3-0/JM/R/opt.longWB.R | 10 +
JM-0.3-0/JM/R/opt.survAFTWB.R |only
JM-0.3-0/JM/R/opt.survCH.R | 2
JM-0.3-0/JM/R/opt.survPC.R |only
JM-0.3-0/JM/R/opt.survPH.R | 27 ++--
JM-0.3-0/JM/R/opt.survWB.R | 13 +-
JM-0.3-0/JM/R/phGH.fit.R | 143 ++++++++++++++-----------
JM-0.3-0/JM/R/piecewiseAFTGH.fit.R |only
JM-0.3-0/JM/R/piecewisePHGH.fit.R |only
JM-0.3-0/JM/R/plot.flexCPH.R | 2
JM-0.3-0/JM/R/plot.jointModel.R | 147 ++++++++++++++++++++------
JM-0.3-0/JM/R/posterior.b.R | 33 ++++-
JM-0.3-0/JM/R/predict.b.R | 2
JM-0.3-0/JM/R/predict.jointModel.R | 2
JM-0.3-0/JM/R/print.aov.jointModel.R | 2
JM-0.3-0/JM/R/print.flexCPH.R | 2
JM-0.3-0/JM/R/print.jointModel.R | 4
JM-0.3-0/JM/R/print.summary.flexCPH.R | 2
JM-0.3-0/JM/R/print.summary.jointModel.R | 20 ++-
JM-0.3-0/JM/R/print.summary.weibull.frailty.R | 2
JM-0.3-0/JM/R/print.weibull.frailty.R | 2
JM-0.3-0/JM/R/ranef.jointModel.R | 2
JM-0.3-0/JM/R/residuals.jointModel.R | 27 ++--
JM-0.3-0/JM/R/rmvt.R | 2
JM-0.3-0/JM/R/summary.flexCPH.R | 2
JM-0.3-0/JM/R/summary.jointModel.R | 13 +-
JM-0.3-0/JM/R/summary.weibull.frailty.R | 2
JM-0.3-0/JM/R/update.bCH.R | 2
JM-0.3-0/JM/R/vcov.flexCPH.R | 2
JM-0.3-0/JM/R/vcov.jointModel.R | 2
JM-0.3-0/JM/R/vcov.weibull.frailty.R | 2
JM-0.3-0/JM/R/weibull.frailty.R | 2
JM-0.3-0/JM/R/weibull.frailty.fit.R | 2
JM-0.3-0/JM/R/weibullAFTGH.fit.R |only
JM-0.3-0/JM/R/weibullPHGH.fit.R |only
JM-0.3-0/JM/data/aids.id.rda |binary
JM-0.3-0/JM/data/aids.rda |binary
JM-0.3-0/JM/data/pbc2.id.rda |binary
JM-0.3-0/JM/data/pbc2.rda |binary
JM-0.3-0/JM/data/prothro.rda |only
JM-0.3-0/JM/data/prothros.rda |only
JM-0.3-0/JM/inst/NEWS | 11 +
JM-0.3-0/JM/man/JM.Rd | 21 ++-
JM-0.3-0/JM/man/jointModel.Rd | 61 +++++-----
JM-0.3-0/JM/man/prothro.Rd |only
JM-0.3-0/JM/man/residuals.Rd | 6 -
108 files changed, 820 insertions(+), 393 deletions(-)