Title: Functions to access vegetation databases (Turboveg and VegetWeb)
and prepare data for analysis
Diff between vegdata versions 0.3 dated 2011-05-19 and 0.3.1 dated 2011-06-30
Description: Handling of vegetation data sets from personal Turboveg or
online VegetWeb Databases. Taxonomic harmonization of datasets
with the help of the German taxonomical standard list
"GermanSL".
Author: Florian Jansen
Maintainer: Florian Jansen
vegdata-0.3.1/vegdata/DESCRIPTION | 8 +-
vegdata-0.3.1/vegdata/R/syntab.r | 4 -
vegdata-0.3.1/vegdata/R/tax.r | 46 +++++++-------
vegdata-0.3.1/vegdata/R/taxval.r | 20 +++---
vegdata-0.3.1/vegdata/R/tv.coverperc.r | 2
vegdata-0.3.1/vegdata/R/tv.home.r | 2
vegdata-0.3.1/vegdata/R/tv.obs.r | 2
vegdata-0.3.1/vegdata/R/tv.refl.r | 2
vegdata-0.3.1/vegdata/R/tv.veg.r | 34 +++++++---
vegdata-0.3.1/vegdata/R/zzz.r | 4 -
vegdata-0.3.1/vegdata/inst/ChangeLog | 4 +
vegdata-0.3.1/vegdata/inst/doc/vegdata.pdf |binary
vegdata-0.3.1/vegdata/inst/tvdata/Data/elbaue/tvabund.dbf |binary
vegdata-0.3.1/vegdata/inst/tvdata/Popup |only
vegdata-0.3.1/vegdata/inst/tvdata/Species/GermanSL1.2 |only
vegdata-0.3.1/vegdata/man/tax.Rd | 7 +-
vegdata-0.3.1/vegdata/man/tv.Veg.Rd | 4 -
vegdata-0.3.1/vegdata/man/vegdata-internal.Rd | 1
vegdata-0.3/vegdata/R/tv.taxval.r |only
vegdata-0.3/vegdata/inst/tvdata/Species/GermanSL1.1 |only
20 files changed, 81 insertions(+), 59 deletions(-)
Title: Make it easier to work with strings.
Diff between stringr versions 0.4 dated 2010-08-24 and 0.5 dated 2011-06-30
Description: stringr is a set of simple wrappers that make R's string
functions more consistent, simpler and easier to use. It does
this by ensuring that: function and argument names (and
positions) are consistent, all functions deal with NA's and
zero length character appropriately, and the output data
structures from each function matches the input data structures
of other functions.
Author: Hadley Wickham
Maintainer: Hadley Wickham
stringr-0.4/stringr/inst/doc |only
stringr-0.5/stringr/DESCRIPTION | 22 ++++++++++++----------
stringr-0.5/stringr/NAMESPACE | 3 +++
stringr-0.5/stringr/NEWS | 21 +++++++++++++++++++++
stringr-0.5/stringr/R/count.r |only
stringr-0.5/stringr/R/dup.r | 13 ++++++++++---
stringr-0.5/stringr/R/length.r | 2 +-
stringr-0.5/stringr/R/locate.r | 10 ++++------
stringr-0.5/stringr/R/pad-trim.r | 6 +++++-
stringr-0.5/stringr/R/sub.r | 2 +-
stringr-0.5/stringr/R/vectorise.r | 2 +-
stringr-0.5/stringr/R/word.r |only
stringr-0.5/stringr/R/wrap.r |only
stringr-0.5/stringr/inst/tests/test-check.r | 15 ++++++---------
stringr-0.5/stringr/inst/tests/test-count.r |only
stringr-0.5/stringr/inst/tests/test-detect.r | 3 ---
stringr-0.5/stringr/inst/tests/test-dup.r | 3 ---
stringr-0.5/stringr/inst/tests/test-extract.r | 3 ---
stringr-0.5/stringr/inst/tests/test-join.r | 3 ---
stringr-0.5/stringr/inst/tests/test-length.r | 18 ++++++++++++------
stringr-0.5/stringr/inst/tests/test-locate.r | 3 ---
stringr-0.5/stringr/inst/tests/test-match.r | 3 ---
stringr-0.5/stringr/inst/tests/test-pad.r | 3 ---
stringr-0.5/stringr/inst/tests/test-split.r | 3 ---
stringr-0.5/stringr/inst/tests/test-sub.r | 3 ---
stringr-0.5/stringr/inst/tests/test-trim.r | 3 ---
stringr-0.5/stringr/man/check_pattern.Rd | 5 +++--
stringr-0.5/stringr/man/check_string.Rd | 3 ++-
stringr-0.5/stringr/man/fixed.Rd | 7 ++++---
stringr-0.5/stringr/man/ignore.case.Rd | 4 ++--
stringr-0.5/stringr/man/invert_match.Rd | 4 ++--
stringr-0.5/stringr/man/str_c.Rd | 18 ++++++++++--------
stringr-0.5/stringr/man/str_count.Rd |only
stringr-0.5/stringr/man/str_dup.Rd | 3 ++-
stringr-0.5/stringr/man/str_extract.Rd | 4 ++--
stringr-0.5/stringr/man/str_extract_all.Rd | 4 ++--
stringr-0.5/stringr/man/str_locate.Rd | 7 ++++---
stringr-0.5/stringr/man/str_locate_all.Rd | 10 +++++++---
stringr-0.5/stringr/man/str_match.Rd | 4 ++--
stringr-0.5/stringr/man/str_match_all.Rd | 4 ++--
stringr-0.5/stringr/man/str_pad.Rd | 6 +++---
stringr-0.5/stringr/man/str_replace.Rd | 8 +++++---
stringr-0.5/stringr/man/str_replace_all.Rd | 5 +++--
stringr-0.5/stringr/man/str_split.Rd | 6 +++---
stringr-0.5/stringr/man/str_split_fixed.Rd | 4 ++--
stringr-0.5/stringr/man/str_sub.Rd | 16 +++++++++-------
stringr-0.5/stringr/man/str_sub_replace.Rd | 7 ++++---
stringr-0.5/stringr/man/str_trim.Rd | 2 +-
stringr-0.5/stringr/man/str_wrap.Rd |only
stringr-0.5/stringr/man/word.Rd |only
stringr-0.5/stringr/tests/test-all.R | 3 +--
51 files changed, 151 insertions(+), 127 deletions(-)
Title: R packge for simulating biological sequence evolution
Diff between phylosim versions 0.15 dated 2011-06-28 and 0.16 dated 2011-06-30
Description: PhyloSim is an extensible object-oriented framework for
the Monte Carlo simulation of sequence evolution written in 100
percent R. It is built on the top of the R.oo and ape packages
and uses Gillespie's direct method to simulate substitutions,
insertions and deletions.
Author: Botond Sipos
Maintainer: Botond Sipos
DESCRIPTION | 6 +++---
inst/doc/PhyloSim.Rnw | 28 +++++++++++++++++-----------
inst/doc/PhyloSim.pdf |binary
3 files changed, 20 insertions(+), 14 deletions(-)
Title: Phylogenetic analysis in R
Diff between phangorn versions 1.4-0 dated 2011-03-27 and 1.4-1 dated 2011-06-30
Description: Phylogenetic analysis in R (Estimation of phylogenetic
trees and networks using Maximum Likelihood, Maximum Parsimony,
Distance methods & Hadamard conjugation)
Author: Klaus Schliep, Emmanuel Paradis
Maintainer: Klaus Schliep
ChangeLog | 46 +
DESCRIPTION | 14
NAMESPACE | 12
R/phylo.R | 1859 ++++++++++++++++++++++++++++-------------
R/sysdata.rda |binary
data/Laurasiatherian.RData |binary
data/chloroplast.RData |binary
data/yeast.RData |binary
inst/doc/Ancestral.Rnw | 7
inst/doc/Ancestral.pdf |binary
inst/doc/Trees.Rnw | 72 +
inst/doc/Trees.pdf |binary
inst/doc/phangorn-specials.pdf |binary
inst/doc/phangorn.bib | 30
inst/extdata/MtZoa.dat |only
inst/extdata/cpREV.dat |only
inst/extdata/mtArt.dat |only
inst/extdata/mtREV24.dat |only
inst/extdata/mtmam.dat |only
man/bab.Rd |only
man/consensusNet.Rd | 10
man/designTree.Rd | 29
man/dist.hamming.Rd | 9
man/getClans.Rd | 7
man/modelTest.Rd | 13
man/parsimony.Rd | 5
man/phangorn-package.Rd | 4
man/phyDat.Rd | 2
man/pml.Rd | 37
man/pmlCluster.Rd | 5
man/splitsNetwork.Rd | 2
man/upgma.Rd | 6
src/phangorn.c | 379 +++-----
33 files changed, 1664 insertions(+), 884 deletions(-)
Title: Simulation of high-dimensional data and parallelized repeated
penalized regression
Diff between pensim versions 1.0.2 dated 2011-02-03 and 1.0.3 dated 2011-06-30
Description: Simulation of continuous, correlated high-dimensional data
with time to event or binary response, and parallelized
functions for Lasso, Ridge, and Elastic Net penalized
regression with repeated starts and two-dimensional tuning of
the Elastic Net.
Author: L. Waldron, M. Pintilie, M.-S. Tsao, F. A. Shepherd, C.
Huttenhower*, I. Jurisica* (*equal contribution)
Maintainer: Levi Waldron
Changelog |only
DESCRIPTION | 18 +++---
R/create.data.R | 136 +++++++++++++++++++++++++------------------------
data/beer.exprs.rda |binary
data/beer.survival.rda |binary
data/datalist |only
man/create.data.Rd | 10 ++-
man/opt1D.Rd | 2
man/opt2D.Rd | 2
man/pensim-package.Rd | 6 +-
man/scan.l1l2.Rd | 2
11 files changed, 96 insertions(+), 80 deletions(-)
Title: ML estimation for multivariate normal data with missing values.
Diff between mvnmle versions 0.1-8 dated 2008-03-27 and 0.1-10 dated 2011-06-30
Description: Finds the maximum likelihood estimate of the mean vector
and variance-covariance matrix for multivariate normal data
with missing values.
Author: Kevin Gross, with help from Douglas Bates
Maintainer: Kevin Gross
DESCRIPTION | 26 ++++++++++++++------------
R/getclf.R | 4 ++--
R/mlest.R | 2 +-
data/apple.rda |binary
data/missvals.rda |binary
man/apple.Rd | 1 +
man/getstartvals.Rd | 4 ++--
man/missvals.Rd | 1 +
man/mlest.Rd | 5 ++---
9 files changed, 23 insertions(+), 20 deletions(-)
Title: statistical methods for analysing multivariate abundance data
Diff between mvabund versions 0.1-11.1 dated 2011-04-24 and 2.2-4 dated 2011-06-30
Description: A set of tools for displaying, modeling and analysing
multivariate abundance data in community ecology. See
mvabund-package.Rd for details of overall package organization.
The package is implemented with the Gnu Scientific Library
(http://www.gnu.org/software/gsl/) and Rcpp
(http://dirk.eddelbuettel.com/code/rcpp.html) R / C++ classes.
Author: Yi Wang, Ulrike Naumann, Stephen Wright and David Warton
Maintainer: Yi Wang
mvabund-0.1-11.1/mvabund/R/nbinall.R |only
mvabund-0.1-11.1/mvabund/R/nbinall2.R |only
mvabund-0.1-11.1/mvabund/man/default.boxplot.mvabund.Rd |only
mvabund-0.1-11.1/mvabund/man/default.meanvar.plot.Rd |only
mvabund-0.1-11.1/mvabund/man/default.plot.manylm.Rd |only
mvabund-0.1-11.1/mvabund/man/default.plot.mvabund.Rd |only
mvabund-0.1-11.1/mvabund/man/default.plotMvaFactor.Rd |only
mvabund-2.2-4/mvabund/DESCRIPTION | 22
mvabund-2.2-4/mvabund/NAMESPACE | 15
mvabund-2.2-4/mvabund/R/RidgeParamEst.R | 64 -
mvabund-2.2-4/mvabund/R/anova.manyglm.R |only
mvabund-2.2-4/mvabund/R/anova.manylm.R | 72 -
mvabund-2.2-4/mvabund/R/best.r.sq.R | 4
mvabund-2.2-4/mvabund/R/boxplot.mvabund.R | 2
mvabund-2.2-4/mvabund/R/default.boxplot.mvabund.R | 142 +--
mvabund-2.2-4/mvabund/R/default.boxplot.mvformula.R | 40
mvabund-2.2-4/mvabund/R/default.meanvar.plot.R | 75 -
mvabund-2.2-4/mvabund/R/default.plot.manyglm.R |only
mvabund-2.2-4/mvabund/R/default.plot.manylm.R | 619 ++++++--------
mvabund-2.2-4/mvabund/R/default.plot.mvabund.R | 416 +++------
mvabund-2.2-4/mvabund/R/default.plot.mvformula.R | 114 +-
mvabund-2.2-4/mvabund/R/default.plotMvaFactor.R | 681 +++++++---------
mvabund-2.2-4/mvabund/R/default.print.anova.manyglm.R |only
mvabund-2.2-4/mvabund/R/default.print.summary.manyglm.R |only
mvabund-2.2-4/mvabund/R/formulaUnimva.R | 4
mvabund-2.2-4/mvabund/R/manyglm.R |only
mvabund-2.2-4/mvabund/R/manylm.R | 23
mvabund-2.2-4/mvabund/R/plot.manyglm.R |only
mvabund-2.2-4/mvabund/R/plot.manylm.R | 50 -
mvabund-2.2-4/mvabund/R/plot.mvabund.R | 8
mvabund-2.2-4/mvabund/R/plotMvaFactor.R | 5
mvabund-2.2-4/mvabund/R/predict.manyglm.R |only
mvabund-2.2-4/mvabund/R/predict.manylm.R | 40
mvabund-2.2-4/mvabund/R/print.anova.manyglm.R |only
mvabund-2.2-4/mvabund/R/print.anova.manylm.R | 24
mvabund-2.2-4/mvabund/R/print.manyglm.R |only
mvabund-2.2-4/mvabund/R/print.summary.manyglm.R |only
mvabund-2.2-4/mvabund/R/print.summary.manylm.R | 36
mvabund-2.2-4/mvabund/R/summary.manyglm.R |only
mvabund-2.2-4/mvabund/R/summary.manylm.R | 6
mvabund-2.2-4/mvabund/R/transAxis.SW.R | 6
mvabund-2.2-4/mvabund/R/variable.names.manyglm.R |only
mvabund-2.2-4/mvabund/R/weights.manyglm.R |only
mvabund-2.2-4/mvabund/configure | 69 +
mvabund-2.2-4/mvabund/configure.ac | 8
mvabund-2.2-4/mvabund/configure.win | 1
mvabund-2.2-4/mvabund/data/Tasmania.RData |only
mvabund-2.2-4/mvabund/man/Tasmania.Rd |only
mvabund-2.2-4/mvabund/man/anova.manyglm.Rd |only
mvabund-2.2-4/mvabund/man/anova.manylm.Rd | 29
mvabund-2.2-4/mvabund/man/boxplot.mvabund.Rd | 77 -
mvabund-2.2-4/mvabund/man/manyglm.Rd |only
mvabund-2.2-4/mvabund/man/manylm.Rd | 14
mvabund-2.2-4/mvabund/man/meanvar.plot.Rd | 27
mvabund-2.2-4/mvabund/man/mvabund-package.Rd | 63 -
mvabund-2.2-4/mvabund/man/plot.manylm.Rd | 70 +
mvabund-2.2-4/mvabund/man/plot.mvabund.Rd | 112 +-
mvabund-2.2-4/mvabund/man/plotMvaFactor.Rd | 61 -
mvabund-2.2-4/mvabund/man/predict.manyglm.Rd |only
mvabund-2.2-4/mvabund/man/predict.manylm.Rd |only
mvabund-2.2-4/mvabund/man/shiftpoints.Rd |only
mvabund-2.2-4/mvabund/man/summary.manyglm.Rd |only
mvabund-2.2-4/mvabund/man/summary.manylm.Rd | 54 -
mvabund-2.2-4/mvabund/src/Makevars.in | 4
mvabund-2.2-4/mvabund/src/Makevars.win | 11
mvabund-2.2-4/mvabund/src/RtoAnovaCpp.cpp | 18
mvabund-2.2-4/mvabund/src/RtoGlm.cpp |only
mvabund-2.2-4/mvabund/src/RtoGlmAnova.cpp |only
mvabund-2.2-4/mvabund/src/RtoGlmSmry.cpp |only
mvabund-2.2-4/mvabund/src/RtoSmryCpp.cpp | 3
mvabund-2.2-4/mvabund/src/anova.cpp | 42
mvabund-2.2-4/mvabund/src/calctest.cpp | 293 ++++++
mvabund-2.2-4/mvabund/src/glm.cpp |only
mvabund-2.2-4/mvabund/src/glmtest.cpp |only
mvabund-2.2-4/mvabund/src/io.cpp |only
mvabund-2.2-4/mvabund/src/resampTest.h | 346 +++++++-
mvabund-2.2-4/mvabund/src/rmv.h |only
mvabund-2.2-4/mvabund/src/rnd.cpp |only
mvabund-2.2-4/mvabund/src/simutility.cpp |only
mvabund-2.2-4/mvabund/src/summary.cpp | 39
80 files changed, 2051 insertions(+), 1758 deletions(-)
Title: Create Plots from MCMC Output
Diff between mcmcplots versions 0.1 dated 2010-07-06 and 0.2 dated 2011-06-30
Description: MCMC plots
Author: S. McKay Curtis
Maintainer: S. McKay Curtis
DESCRIPTION | 6 +--
NAMESPACE | 3 +
NEWS |only
R/autplot1.R | 18 ++++++---
R/caterplot.R | 96 ++++++++++++++++++++++++++++++++++++++----------
R/caterpoints.R | 13 ++++--
R/corplot.R | 36 ++++++++++++++++--
R/denoverplot.R | 11 ++++-
R/denplot.R | 12 ++++--
R/graypr.R | 5 +-
R/mcmcplot.R | 91 +++++++++++++++++++++++----------------------
R/mcmcplot1.R | 15 ++++++-
R/mcmcplotsPalette.R | 8 ++--
R/traplot.R | 5 +-
R/traplot1.R | 2 -
man/autplot1.Rd | 7 ++-
man/caterplot.Rd | 22 +++++++----
man/caterpoints.Rd | 17 +++-----
man/corplot.Rd | 5 ++
man/denoverplot.Rd | 5 +-
man/denplot.Rd | 5 +-
man/mcmcplotsPalette.Rd | 5 +-
man/traplot.Rd | 5 ++
23 files changed, 266 insertions(+), 126 deletions(-)
Title: Less Code, More Results
Diff between lessR versions 1.9.7 dated 2011-06-15 and 1.9.8 dated 2011-06-30
Description: Each function accomplishes the work of several or more
standard R functions. For example, two function calls, rad()
and full(), together read the csv data and generate descriptive
statistics for all variables in the data frame, plus histograms
and bar charts for all respective numerical and non-numerical
variables. The function smd.t.test introduces the ODDSMD plot,
which displays the Overlapping Density Distributions of two
independent groups as well as a visual display of the mean
difference and standardized mean difference. Other functions
provide for descriptive statistics, the t-test from descriptive
statistics, a comprehensive regression analysis, color
plotting, color bar chart, color histogram, color box plot,
density curves, a calibrated power curve plotted with colors,
and the reading and display of csv formatted data. The function
help.me provides a help system that suggests specific analyses
and functions.
Author: David W. Gerbing, School of Business Administration, Portland
State University
Maintainer: David W. Gerbing
DESCRIPTION | 10 ++---
R/describe.factor.R | 2 -
R/describe.formula.R | 28 ++++++++--------
R/rad.R | 13 +++++++
R/reg.R | 82 +++++++++++++++++++++++++++++++++----------------
R/smd.t.test.default.R | 2 -
man/color.density.Rd | 2 -
man/out.Rd | 2 -
man/rad.Rd | 2 -
man/reg.Rd | 52 +++++++++++++++++--------------
10 files changed, 121 insertions(+), 74 deletions(-)
Title: Lattice Graphics
Diff between lattice versions 0.19-26 dated 2011-04-24 and 0.19-30 dated 2011-06-30
Description: Lattice is a powerful and elegant high-level data
visualization system, with an emphasis on multivariate data,
that is sufficient for typical graphics needs, and is also
flexible enough to handle most nonstandard requirements. See
?Lattice for an introduction.
Author: Deepayan Sarkar
Maintainer: Deepayan Sarkar
DESCRIPTION | 10 -
NAMESPACE | 6
NEWS | 2
R/cloud.R | 18 +-
R/interaction.R | 33 +++-
R/legend.R | 114 +++++++++++---
R/miscellaneous.R | 50 +++---
R/panel.smooth.R |only
R/panel.superpose.R |only
R/panels.R | 367 ----------------------------------------------
R/print.trellis.R | 33 +++-
R/settings.R | 11 -
R/strip.R | 25 ++-
SvnLog | 164 ++++++++++++++++++++
data/barley.rda |binary
data/environmental.rda |binary
data/ethanol.rda |binary
data/melanoma.rda |binary
data/singer.rda |binary
demo/lattice.R | 14 +
man/interaction.Rd | 21 ++
man/llines.Rd | 24 +--
man/panel.functions.Rd | 227 +++++++++++++++++-----------
man/panel.loess.Rd |only
man/panel.spline.Rd |only
man/panel.xyplot.Rd | 17 +-
man/prepanel.functions.Rd | 47 ++++-
po/R-lattice.pot | 2
28 files changed, 609 insertions(+), 576 deletions(-)
Title: Monte Carlo Exact Tests for Log-linear models
Diff between exactLoglinTest versions 1.3.6 dated 2006-10-09 and 1.3.7 dated 2011-06-30
More information about exactLoglinTest at CRAN
Description: Monte Carlo and MCMC goodness of fit tests for log-linear
models
Author: Brian Caffo
Maintainer: Brian Caffo
exactLoglinTest-1.3.6/exactLoglinTest/inst/doc/exactLoglinTest.tex |only
exactLoglinTest-1.3.7/exactLoglinTest/DESCRIPTION | 24
exactLoglinTest-1.3.7/exactLoglinTest/R/gof.R | 2
exactLoglinTest-1.3.7/exactLoglinTest/R/simtable.bab.R | 8
exactLoglinTest-1.3.7/exactLoglinTest/R/simtable.cab.R | 11
exactLoglinTest-1.3.7/exactLoglinTest/R/update.bab.R | 9
exactLoglinTest-1.3.7/exactLoglinTest/R/update.cab.R | 10
exactLoglinTest-1.3.7/exactLoglinTest/inst/doc/database.mcexact.bib | 10
exactLoglinTest-1.3.7/exactLoglinTest/inst/doc/exactLoglinTest.Rnw | 268 +++++-----
exactLoglinTest-1.3.7/exactLoglinTest/inst/doc/exactLoglinTest.pdf |binary
exactLoglinTest-1.3.7/exactLoglinTest/man/gof.Rd | 2
exactLoglinTest-1.3.7/exactLoglinTest/src/multinorm.c | 32 +
exactLoglinTest-1.3.7/exactLoglinTest/src/multinormfull.c | 9
13 files changed, 235 insertions(+), 150 deletions(-)
Permanent link
Title: Evolutionary Multiobjective Optimization Algorithms
Diff between emoa versions 0.4-4 dated 2011-06-17 and 0.4-5 dated 2011-06-30
Description: Collection of building blocks for the design and analysis
of evolutionary multiobjective optimization algorithms.
Author: Olaf Mersmann
Maintainer: Olaf Mersmann
ChangeLog | 22 +++++++++++++++
DESCRIPTION | 6 ++--
inst/unittests/runit-ei.r | 19 +++++++++----
src/eps_ind.c | 66 +++++++++++++++++++++++-----------------------
4 files changed, 71 insertions(+), 42 deletions(-)
Title: Tools to make developing R code easier
Diff between devtools versions 0.2 dated 2011-06-29 and 0.3 dated 2011-06-30
Description: Collection of package development tools
Author: Hadley Wickham
Maintainer: Hadley Wickham
devtools-0.2/devtools/R/update-src.r |only
devtools-0.2/devtools/man/is.git.Rd |only
devtools-0.2/devtools/man/is.svn.Rd |only
devtools-0.2/devtools/man/update_src.Rd |only
devtools-0.3/devtools/DESCRIPTION | 19 +++++-----
devtools-0.3/devtools/NAMESPACE | 2 -
devtools-0.3/devtools/NEWS | 17 +++++++++
devtools-0.3/devtools/R/bash.r |only
devtools-0.3/devtools/R/build.r |only
devtools-0.3/devtools/R/check.r | 16 +++-----
devtools-0.3/devtools/R/devel-mode.r | 2 -
devtools-0.3/devtools/R/has-devel.r | 2 -
devtools-0.3/devtools/R/install.r | 12 ++----
devtools-0.3/devtools/R/load-code.r | 3 +
devtools-0.3/devtools/R/release.r | 13 ++----
devtools-0.3/devtools/R/system.r | 5 +-
devtools-0.3/devtools/README.md | 60 +++++++++++++++++---------------
devtools-0.3/devtools/man/bash.Rd |only
devtools-0.3/devtools/man/build.Rd |only
19 files changed, 82 insertions(+), 69 deletions(-)
Title: Tools for caching Sweave computations
Diff between cacheSweave versions 0.4-5 dated 2010-11-30 and 0.5 dated 2011-06-30
Description: Tools for caching Sweave computations and storing them in
key-value databases
Author: Roger D. Peng
Maintainer: Roger D. Peng
cacheSweave-0.4-5/cacheSweave/inst/doc/cacheSweave.tex |only
cacheSweave-0.5/cacheSweave/DESCRIPTION | 10
cacheSweave-0.5/cacheSweave/R/SweaveCache.R | 305 -----------------
cacheSweave-0.5/cacheSweave/inst/doc/cacheSweave.pdf |binary
cacheSweave-0.5/cacheSweave/tests/reg-tests.Rout.save | 17
5 files changed, 23 insertions(+), 309 deletions(-)
Title: Bayesian quantile regression
Diff between bayesQR versions 1.2 dated 2011-05-26 and 1.3 dated 2011-06-30
Description: Bayesian quantile regression using the asymmetric Laplace
distribution, both continuous as well as binary dependent
variables are supported. The package consists of
implementations of the methods of Yu & Moyeed (2001), Benoit &
Van den Poel (2011) and Alhamzawi, Yu & Benoit (2011).
Author: Dries F. Benoit, Rahim Al-Hamzawi, Keming Yu, Dirk Van den Poel
Maintainer: Dries F. Benoit
DESCRIPTION | 12 ++++++------
NAMESPACE | 2 +-
R/QRc.AL.R |only
man/QRb.Rd | 6 +++---
man/QRc.AL.Rd |only
man/QRc.Rd | 8 ++++----
src/QRc_AL_mcmc.f95 |only
src/QRc_mcmc.f95 | 35 ++++++++++++++++++++++++++---------
8 files changed, 40 insertions(+), 23 deletions(-)
Title: A collection of statistical tools for biologists
Diff between asbio versions 0.3-35 dated 2011-05-19 and 0.3-36 dated 2011-06-30
Description: Contains functions from: "Foundational Statistics for
Biologists; A Textbook Using R" (Under contract; CRC Press;
Release: Spring 2012)
Author: Ken Aho; many thanks to V. Winston and D. Roberts
Maintainer: Ken Aho
asbio-0.3-35/asbio/R/Mode.R |only
asbio-0.3-36/asbio/DESCRIPTION | 6 +++---
asbio-0.3-36/asbio/R/Mode.r |only
asbio-0.3-36/asbio/R/anm.ls.r | 2 +-
asbio-0.3-36/asbio/R/illusions.r | 2 +-
asbio-0.3-36/asbio/R/loglik.plot.r | 2 +-
asbio-0.3-36/asbio/R/one.sample.z.R | 4 +++-
asbio-0.3-36/asbio/data/refinery.rda |only
asbio-0.3-36/asbio/man/anm.ls.rd | 2 +-
asbio-0.3-36/asbio/man/loglik.plot.rd | 6 +++---
asbio-0.3-36/asbio/man/refinery.rd |only
11 files changed, 13 insertions(+), 11 deletions(-)
Title: Agricultural datasets
Diff between agridat versions 1.01 dated 2011-05-02 and 1.2 dated 2011-06-30
Description: Datasets from books and papers related to agriculture.
Simple analyses included.
Author: Kevin Wright
Maintainer: Kevin Wright
agridat-1.01/agridat/data/stroup.splitplot.rda |only
agridat-1.01/agridat/raw/00permissions.txt |only
agridat-1.01/agridat/raw/allcroft.lodging.r |only
agridat-1.01/agridat/raw/aust.soy.r |only
agridat-1.01/agridat/raw/australia_soybean.csv |only
agridat-1.01/agridat/raw/besag.met.r |only
agridat-1.01/agridat/raw/gomez.fractionalfactorial.r |only
agridat-1.01/agridat/raw/gomez.groupsplit.r |only
agridat-1.01/agridat/raw/gomez.groupsplit.xls |only
agridat-1.01/agridat/raw/gomez.groupsplit.xlsx |only
agridat-1.01/agridat/raw/gomez.splitsplit.r |only
agridat-1.01/agridat/raw/gomez.stripsplitplot.r |only
agridat-1.01/agridat/raw/hughes.grapes.r |only
agridat-1.01/agridat/raw/kempton.rowcol.csv |only
agridat-1.01/agridat/raw/kempton.rowcol.r |only
agridat-1.01/agridat/raw/smith.uniformity3.r |only
agridat-1.01/agridat/raw/student.barley.r |only
agridat-1.01/agridat/raw/student.barley.xls |only
agridat-1.01/agridat/raw/talbot.potato.r |only
agridat-1.01/agridat/raw/talbot.potato_x.csv |only
agridat-1.01/agridat/raw/talbot.potato_y.csv |only
agridat-1.01/agridat/raw/theobald.covariate.csv |only
agridat-1.01/agridat/raw/theobald.covariate.r |only
agridat-1.01/agridat/raw/vargas.wheat1.xls |only
agridat-1.01/agridat/raw/vargas1998.r |only
agridat-1.01/agridat/raw/vargas1998b_x.csv |only
agridat-1.01/agridat/raw/vargas1998b_y.csv |only
agridat-1.01/agridat/raw/verbyla.cow.csv |only
agridat-1.01/agridat/raw/verbyla.cow.r |only
agridat-1.01/agridat/raw/verbyla.lupin.r |only
agridat-1.01/agridat/raw/verbyla_lupin.txt |only
agridat-1.2/agridat/DESCRIPTION | 15 +-
agridat-1.2/agridat/NEWS | 18 ++-
agridat-1.2/agridat/R/desplot.r | 16 +-
agridat-1.2/agridat/data/aastveit.barley.rda |only
agridat-1.2/agridat/data/gathmann.bt.txt.gz |only
agridat-1.2/agridat/data/kempton.competition.txt.gz |only
agridat-1.2/agridat/data/stroup.nin.txt.gz |binary
agridat-1.2/agridat/data/stroup.splitplot.txt.gz |only
agridat-1.2/agridat/data/wedderburn.barley.txt.gz |only
agridat-1.2/agridat/man/aastveit.barley.Rd |only
agridat-1.2/agridat/man/agridat.Rd | 108 +++++++++----------
agridat-1.2/agridat/man/crowder.germination.Rd | 11 -
agridat-1.2/agridat/man/desplot.Rd | 4
agridat-1.2/agridat/man/gathmann.bt.Rd |only
agridat-1.2/agridat/man/hughes.grapes.Rd | 4
agridat-1.2/agridat/man/kempton.competition.Rd |only
agridat-1.2/agridat/man/stroup.nin.Rd | 42 ++-----
agridat-1.2/agridat/man/talbot.potato.Rd | 8 -
agridat-1.2/agridat/man/vargas.wheat1.Rd | 9 -
agridat-1.2/agridat/man/verbyla.lupin.Rd | 24 +++-
agridat-1.2/agridat/man/wedderburn.barley.Rd |only
52 files changed, 137 insertions(+), 122 deletions(-)
Title: Rcpp integration for Armadillo templated linear algebra library
Diff between RcppArmadillo versions 0.2.23 dated 2011-06-24 and 0.2.25 dated 2011-06-30
Description: R and Armadillo integration using Rcpp Armadillo is a
templated C++ linear algebra library (by Conrad Sanderson) that
aims towards a good balance between speed and ease of use.
Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions.
Various matrix decompositions are provided through optional
integration with LAPACK and ATLAS libraries.
A delayed evaluation approach is employed (during compile time) to
combine several operations into one, and to reduce (or
eliminate) the need for temporaries. This is accomplished
through recursive templates and template meta-programming.
This library is useful if C++ has been decided as the language of
choice (due to speed and/or integration capabilities), rather
than another language.
The RcppArmadillo package includes the header files from the templated
Armadillo library (currently version 2.0.0). Thus users do not
need to install Armadillo itself in order to use RcppArmadillo.
This Armadillo integration provides a nice illustration of the
capabilities of the Rcpp package for seamless R and C++
integration.
Armadillo is licensed under the GNU LGPL version 3 or later, while
RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is
licenses under the GNU GPL version 2 or later, as is the rest
of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Romain Francois, Dirk Eddelbuettel and Doug Bates
ChangeLog | 12 +++++
DESCRIPTION | 10 ++--
inst/NEWS | 36 +++++++++++++++-
inst/include/armadillo_bits/arma_version.hpp | 10 ++--
inst/include/armadillo_bits/auxlib_meat.hpp | 4 -
inst/include/armadillo_bits/diagmat_proxy.hpp | 4 -
inst/include/armadillo_bits/fn_misc.hpp | 58 ++++++++++++++------------
inst/include/armadillo_bits/fn_princomp.hpp | 31 +++++++++++++
inst/include/armadillo_bits/subview_meat.hpp | 2
9 files changed, 126 insertions(+), 41 deletions(-)
Title: R Code for MARK Analysis
Diff between RMark versions 2.0.4 dated 2011-06-02 and 2.0.5 dated 2011-06-30
Description: This package provides an interface to the software package
MARK developed by Gary White. MARK is freely available at
(http://www.phidot.org/software/mark/download/) but is not open
source.
Author: Jeff Laake
Maintainer: Jeff Laake
DESCRIPTION | 29 ++++++++-
R/add.design.data.R | 5 +
R/compute.design.data.R | 2
R/make.design.data.R | 109 ++++++++++++++++++-----------------
R/make.mark.model.R | 19 ++++++
R/model.average.list.r | 2
R/model.average.marklist.R | 2
R/process.data.R | 31 ++++++----
R/release.gof.R | 13 ++--
R/run.mark.model.R | 5 +
R/setup.model.R | 21 +++---
R/setup.parameters.R | 130 +++++++++++++++++++++++++++++++++++++++++-
R/zzz.R | 42 ++++++++-----
data/IELogitNormalMR.rda |only
data/LogitNormalMR.rda |only
data/PoissonMR.rda |only
data/Poisson_twoMR.rda |only
man/IELogitNormalMR.Rd |only
man/LogitNormalMR.Rd |only
man/PoissonMR.Rd |only
man/Poisson_twoMR.Rd |only
man/Whatsnew.Rd | 21 ++++++
man/model.average.list.Rd | 4 -
man/model.average.marklist.Rd | 8 +-
man/process.data.Rd | 3
man/release.gof.Rd | 4 -
26 files changed, 342 insertions(+), 108 deletions(-)