CRANberries
Wed, 21 May 2008
Package vegan updated to version 1.13-0 with previous version 1.11-4 dated 2008-04-24
Author: Jari Oksanen, Roeland Kindt, Pierre Legendre, Bob O'Hara, Gavin L. Simpson,
M. Henry H. Stevens
Title: Community Ecology Package
Description: Ordination methods, diversity analysis and other
functions for community and vegetation ecologists.
Diff between vegan versions 1.11-4 dated 2008-04-24 and 1.13-0 dated 2008-05-21
vegan-1.11-4/vegan/R/ordispantree.R |only
vegan-1.11-4/vegan/R/permDisper.R |only
vegan-1.11-4/vegan/R/print.permDisper.R |only
vegan-1.13-0/vegan/DESCRIPTION | 11
vegan-1.13-0/vegan/R/TukeyHSD.betadisper.R |only
vegan-1.13-0/vegan/R/adonis.R | 21 +
vegan-1.13-0/vegan/R/betadisper.R | 8
vegan-1.13-0/vegan/R/betadiver.R |only
vegan-1.13-0/vegan/R/biplot.rda.R | 36 +-
vegan-1.13-0/vegan/R/capscale.R | 24 +
vegan-1.13-0/vegan/R/designdist.R | 14
vegan-1.13-0/vegan/R/lines.spantree.R | 6
vegan-1.13-0/vegan/R/metaMDS.R | 8
vegan-1.13-0/vegan/R/metaMDSdist.R | 2
vegan-1.13-0/vegan/R/mso.R |only
vegan-1.13-0/vegan/R/nestedtemp.R |only
vegan-1.13-0/vegan/R/ordiArgAbsorber.R |only
vegan-1.13-0/vegan/R/ordiTerminfo.R | 6
vegan-1.13-0/vegan/R/ordiarrows.R | 14
vegan-1.13-0/vegan/R/ordicluster.R | 5
vegan-1.13-0/vegan/R/ordiellipse.R | 29 -
vegan-1.13-0/vegan/R/ordihull.R | 10
vegan-1.13-0/vegan/R/ordisegments.R | 9
vegan-1.13-0/vegan/R/ordispider.R | 11
vegan-1.13-0/vegan/R/orditkplot.R | 106 ++++++
vegan-1.13-0/vegan/R/orditorp.R | 45 +-
vegan-1.13-0/vegan/R/permute.R |only
vegan-1.13-0/vegan/R/permutest.betadisper.R |only
vegan-1.13-0/vegan/R/permutest.cca.R | 6
vegan-1.13-0/vegan/R/plot.betadiver.R |only
vegan-1.13-0/vegan/R/plot.cca.R | 2
vegan-1.13-0/vegan/R/plot.mso.R |only
vegan-1.13-0/vegan/R/plot.nestedtemp.R |only
vegan-1.13-0/vegan/R/points.decorana.R | 5
vegan-1.13-0/vegan/R/print.capscale.R |only
vegan-1.13-0/vegan/R/print.metaMDS.R | 9
vegan-1.13-0/vegan/R/print.nestedtemp.R |only
vegan-1.13-0/vegan/R/print.permutest.betadisper.R |only
vegan-1.13-0/vegan/R/print.summary.cca.R | 7
vegan-1.13-0/vegan/R/rarefy.R | 17 -
vegan-1.13-0/vegan/R/rgl.isomap.R |only
vegan-1.13-0/vegan/R/scores.betadiver.R |only
vegan-1.13-0/vegan/R/screeplot.cca.R | 11
vegan-1.13-0/vegan/R/screeplot.decorana.R | 3
vegan-1.13-0/vegan/R/screeplot.prcomp.R | 11
vegan-1.13-0/vegan/R/screeplot.princomp.R | 11
vegan-1.13-0/vegan/R/specaccum.R | 9
vegan-1.13-0/vegan/R/summary.cca.R | 4
vegan-1.13-0/vegan/R/text.decorana.R | 12
vegan-1.13-0/vegan/R/zzz.R | 7
vegan-1.13-0/vegan/inst/ChangeLog | 341 +++++++++++++++++++---
vegan-1.13-0/vegan/inst/NEWS | 68 ++++
vegan-1.13-0/vegan/inst/doc/FAQ-vegan.pdf |binary
vegan-1.13-0/vegan/inst/doc/FAQ-vegan.texi | 1
vegan-1.13-0/vegan/inst/doc/Makefile | 2
vegan-1.13-0/vegan/inst/doc/decision-vegan.Rnw | 152 +++++++++
vegan-1.13-0/vegan/inst/doc/decision-vegan.pdf |binary
vegan-1.13-0/vegan/inst/doc/decision-vegan.tex | 170 +++++++++-
vegan-1.13-0/vegan/inst/doc/diversity-vegan.Rnw | 32 +-
vegan-1.13-0/vegan/inst/doc/diversity-vegan.pdf |binary
vegan-1.13-0/vegan/inst/doc/diversity-vegan.tex | 138 +++++---
vegan-1.13-0/vegan/inst/doc/intro-vegan.Rnw | 2
vegan-1.13-0/vegan/inst/doc/intro-vegan.pdf |binary
vegan-1.13-0/vegan/inst/doc/intro-vegan.tex | 67 ++--
vegan-1.13-0/vegan/inst/doc/vegan.bib | 43 ++
vegan-1.13-0/vegan/man/BCI.Rd | 10
vegan-1.13-0/vegan/man/anova.cca.Rd | 10
vegan-1.13-0/vegan/man/betadisper.Rd | 96 ++++--
vegan-1.13-0/vegan/man/betadiver.Rd |only
vegan-1.13-0/vegan/man/biplot.rda.Rd | 8
vegan-1.13-0/vegan/man/capscale.Rd | 31 +-
vegan-1.13-0/vegan/man/designdist.Rd | 20 -
vegan-1.13-0/vegan/man/diversity.Rd | 15
vegan-1.13-0/vegan/man/isomap.Rd | 15
vegan-1.13-0/vegan/man/metaMDS.Rd | 17 -
vegan-1.13-0/vegan/man/mso.Rd |only
vegan-1.13-0/vegan/man/oecosimu.Rd | 56 ++-
vegan-1.13-0/vegan/man/ordihull.Rd | 7
vegan-1.13-0/vegan/man/orditkplot.Rd | 19 +
vegan-1.13-0/vegan/man/permuted.index2.Rd | 71 ++++
vegan-1.13-0/vegan/man/permutest.betadisper.Rd |only
vegan-1.13-0/vegan/man/screeplot.cca.Rd | 7
vegan-1.13-0/vegan/man/specaccum.Rd | 5
vegan-1.13-0/vegan/man/taxondive.Rd | 2
vegan-1.13-0/vegan/man/vegan-internal.Rd | 4
vegan-1.13-0/vegan/man/vegandocs.Rd | 4
vegan-1.13-0/vegan/man/vegdist.Rd | 4
87 files changed, 1486 insertions(+), 410 deletions(-)
More information about vegan at CRAN
posted at: 13:19 | path: /cran/updated | permanent link to this entry
Package seqinr updated to version 1.1-6 with previous version 1.1-5 dated 2007-12-18
Author: Delphine Charif and Jean R. Lobry and Anamaria Necsulea and Leonor Palmeira and Simon Penel
Title: Biological Sequences Retrieval and Analysis
Description: Exploratory data analysis and data visualization
for biological sequence (DNA and protein) data. Include also
utilities for sequence data management under the ACNUC system.
Diff between seqinr versions 1.1-5 dated 2007-12-18 and 1.1-6 dated 2008-05-21
seqinr-1.1-5/seqinr/inst/doc/seqinr_1_1-5.pdf |only
seqinr-1.1-6/seqinr/DESCRIPTION | 6
seqinr-1.1-6/seqinr/R/choosebank.R | 9
seqinr-1.1-6/seqinr/R/clientid.R | 8
seqinr-1.1-6/seqinr/R/count.R | 52
seqinr-1.1-6/seqinr/R/gb2fasta.R | 2
seqinr-1.1-6/seqinr/R/modifylist.R | 7
seqinr-1.1-6/seqinr/R/oriloc.R | 15
seqinr-1.1-6/seqinr/R/parser.socket.R | 25
seqinr-1.1-6/seqinr/R/prepgetannots.R |only
seqinr-1.1-6/seqinr/R/reverse.align.R | 115
seqinr-1.1-6/seqinr/data/revaligntest.RData |only
seqinr-1.1-6/seqinr/inst/doc/seqinr_1_1-6.pdf |only
seqinr-1.1-6/seqinr/inst/doc/src/appendix/FAQ.rnw | 64
seqinr-1.1-6/seqinr/inst/doc/src/appendix/FAQ.tex | 97
seqinr-1.1-6/seqinr/inst/doc/src/appendix/fdl.tex | 6
seqinr-1.1-6/seqinr/inst/doc/src/appendix/gencodes.tex | 19
seqinr-1.1-6/seqinr/inst/doc/src/appendix/releasenotes.rnw | 83
seqinr-1.1-6/seqinr/inst/doc/src/appendix/releasenotes.tex | 112
seqinr-1.1-6/seqinr/inst/doc/src/appendix/rundontrun.rnw | 33
seqinr-1.1-6/seqinr/inst/doc/src/appendix/rundontrun.tex | 301 --
seqinr-1.1-6/seqinr/inst/doc/src/appendix/subsequences.tex | 975 ++++--
seqinr-1.1-6/seqinr/inst/doc/src/book/book.rnw | 73
seqinr-1.1-6/seqinr/inst/doc/src/config/book.bib | 41
seqinr-1.1-6/seqinr/inst/doc/src/config/commonrnw.rnw | 7
seqinr-1.1-6/seqinr/inst/doc/src/figs/cover.pdf | 8
seqinr-1.1-6/seqinr/inst/doc/src/figs/libraryBuilding.pdf |only
seqinr-1.1-6/seqinr/inst/doc/src/figs/prochlo.png |only
seqinr-1.1-6/seqinr/inst/doc/src/frontmatter/cover.tex | 14
seqinr-1.1-6/seqinr/inst/doc/src/mainmatter/acnucsocket.rnw | 21
seqinr-1.1-6/seqinr/inst/doc/src/mainmatter/acnucsocket.tex | 117
seqinr-1.1-6/seqinr/inst/doc/src/mainmatter/dealseq.rnw | 134
seqinr-1.1-6/seqinr/inst/doc/src/mainmatter/dealseq.tex | 255 +
seqinr-1.1-6/seqinr/inst/doc/src/mainmatter/extractseqs.rnw |only
seqinr-1.1-6/seqinr/inst/doc/src/mainmatter/extractseqs.tex |only
seqinr-1.1-6/seqinr/inst/doc/src/mainmatter/getseqacnuc.rnw | 708 ----
seqinr-1.1-6/seqinr/inst/doc/src/mainmatter/getseqacnuc.tex | 1625 -----------
seqinr-1.1-6/seqinr/inst/doc/src/mainmatter/getseqflat.rnw | 42
seqinr-1.1-6/seqinr/inst/doc/src/mainmatter/getseqflat.tex | 152 -
seqinr-1.1-6/seqinr/inst/doc/src/mainmatter/introduction.rnw | 16
seqinr-1.1-6/seqinr/inst/doc/src/mainmatter/introduction.tex | 57
seqinr-1.1-6/seqinr/inst/doc/src/mainmatter/multivariate.tex | 19
seqinr-1.1-6/seqinr/inst/doc/src/mainmatter/nonparastats.rnw | 109
seqinr-1.1-6/seqinr/inst/doc/src/mainmatter/nonparastats.tex | 162 -
seqinr-1.1-6/seqinr/inst/doc/src/mainmatter/querylang.rnw |only
seqinr-1.1-6/seqinr/inst/doc/src/mainmatter/querylang.tex |only
seqinr-1.1-6/seqinr/inst/doc/src/misc/seqinRtodolist.txt | 2
seqinr-1.1-6/seqinr/inst/doc/src/tables/aacost.tex | 4
seqinr-1.1-6/seqinr/inst/doc/src/tables/dpqrtable.tex | 4
seqinr-1.1-6/seqinr/inst/doc/src/tables/toyaa.tex | 4
seqinr-1.1-6/seqinr/inst/doc/src/tables/toycodon.tex | 4
seqinr-1.1-6/seqinr/inst/sequences/humanMito.fasta |only
seqinr-1.1-6/seqinr/man/acnucopen.Rd | 3
seqinr-1.1-6/seqinr/man/choosebank.Rd | 23
seqinr-1.1-6/seqinr/man/count.Rd | 71
seqinr-1.1-6/seqinr/man/draw.rearranged.oriloc.Rd | 13
seqinr-1.1-6/seqinr/man/getAnnot.Rd | 2
seqinr-1.1-6/seqinr/man/modifylist.Rd | 6
seqinr-1.1-6/seqinr/man/oriloc.Rd | 13
seqinr-1.1-6/seqinr/man/parser.socket.Rd | 6
seqinr-1.1-6/seqinr/man/prepgatannots.Rd |only
seqinr-1.1-6/seqinr/man/prochlo.Rd | 99
seqinr-1.1-6/seqinr/man/revaligntest.Rd |only
seqinr-1.1-6/seqinr/man/reverse.align.Rd | 41
64 files changed, 2501 insertions(+), 3283 deletions(-)
More information about seqinr at CRAN
posted at: 13:19 | path: /cran/updated | permanent link to this entry
Package plotrix updated to version 2.4-2 with previous version 2.4-1 dated 2008-04-08
Author: Jim Lemon ,
Ben Bolker ,
Sander Oom ,
Eduardo Klein ,
Barry Rowlingson ,
Hadley Wickham ,
Anupam Tyagi ,
Olivier Eterradossi ,
Gabor Grothendieck ,
Michael Toews
John Kane
Title: Various plotting functions
Description: Lots of plots, various labeling, axis and color scaling functions.
Diff between plotrix versions 2.4-1 dated 2008-04-08 and 2.4-2 dated 2008-05-21
DESCRIPTION | 6 +++---
INDEX | 2 ++
R/barhier.R |only
R/brkdn.plot.R | 13 +++++++++----
R/lengthKey.R |only
R/radial.plot.R | 2 +-
R/thigmophobe.R | 2 ++
R/vectorField.R |only
man/barhier.Rd |only
man/brkdn.plot.Rd | 4 ++--
man/color.scale.Rd | 5 +++++
man/color2D.matplot.Rd | 11 +++++++++--
man/lengthKey.Rd |only
man/std.error.Rd | 2 +-
man/twoord.plot.Rd | 26 ++++++++++++++++++++++++++
man/vectorField.Rd |only
16 files changed, 60 insertions(+), 13 deletions(-)
More information about plotrix at CRAN
posted at: 13:18 | path: /cran/updated | permanent link to this entry
New package dti with initial version 0.5-4
Package: dti
Version: 0.5-4
Date: 2008-05-20
Title: DTI Analysis
Author: Karsten Tabelow
Joerg Polzehl
Maintainer: Karsten Tabelow
Depends: R (>= 2.5.0), methods, adimpro, fmri
Description: Diffusion Weighted Imaging is a Magnetic Resonance Imaging
modality, that measures diffusion of water in tissues like the human brain.
The package contains R-functions to process diffusion-weighted data in the
context of the diffusion tensor model (DTI). This includes the calculation
of anisotropy measures and, most important, the implementation of our structural
adaptive smoothing algorithm as described in K. Tabelow, J. Polzehl, V. Spokoiny,
and H.U. Voss, Diffusion Tensor Imaging: Structural Adaptive Smoothing,
Neuroimage 39(4), 1763-1773 (2008).
License: GPL (>=2)
Copyright: This package is
Copyright (C) 2005-2008 Weierstrass Institute for
Applied Analysis and Stochastics.
URL: http://www.wias-berlin.de/projects/matheon_a3
Packaged: Wed May 21 15:46:14 2008; tabelow
More information about dti at CRAN
posted at: 13:18 | path: /cran/new | permanent link to this entry
Package doBy updated to version 3.0 with previous version 2.3 dated 2008-03-26
Author: Søren Højsgaard
Title: Groupwise computations of summary statistics and other utilities
Description: Facilities for groupwise computations of summary statistics and other facilities for working with grouped data (similar to what can be achieved by proc means or proc summary of the SAS system).
Diff between doBy versions 2.3 dated 2008-03-26 and 3.0 dated 2008-05-21
doBy-2.3/doBy/inst/doc/doBy.tex |only
doBy-3.0/doBy/ChangeLog | 9
doBy-3.0/doBy/DESCRIPTION | 4
doBy-3.0/doBy/NAMESPACE | 2
doBy-3.0/doBy/R/summaryBy.R | 1019 +++++++++---
doBy-3.0/doBy/inst/doc/.build.timestamp |only
doBy-3.0/doBy/inst/doc/doBy.Rnw | 47
doBy-3.0/doBy/inst/doc/doBy.pdf | 2661 +++++++++++++++-----------------
doBy-3.0/doBy/man/summaryBy.Rd | 17
9 files changed, 2082 insertions(+), 1677 deletions(-)
More information about doBy at CRAN
posted at: 13:18 | path: /cran/updated | permanent link to this entry
Package crank updated to version 1.0 with previous version 0.9 dated 2008-01-15
Author: Jim Lemon ,
Title: Completing ranks
Description: Functions for completing and recalculating rankings.
Diff between crank versions 0.9 dated 2008-01-15 and 1.0 dated 2008-05-21
DESCRIPTION | 6 +++---
INDEX | 11 ++++++++++-
R/fillArows.R |only
R/getLWargs.R |only
R/listBuilder.R |only
R/listCrawler.R |only
R/lwscreen.R |only
R/muranks.R | 1 +
R/page.test.R |only
R/permute.R |only
man/fillArow.Rd |only
man/fillArows.Rd |only
man/getLWargs.Rd |only
man/listBuilder.Rd |only
man/listCrawler.Rd |only
man/lw.FriedmanTest.Rd |only
man/lwscreen.Rd |only
man/meanranks.Rd | 2 +-
man/muranks.Rd | 20 ++++++++++++++++++++
man/page.trend.test.Rd |only
man/permute.Rd |only
man/print.lwstat.Rd |only
man/print.page.trend.test.Rd |only
23 files changed, 35 insertions(+), 5 deletions(-)
More information about crank at CRAN
posted at: 13:18 | path: /cran/updated | permanent link to this entry
Package adimpro updated to version 0.6.3 with previous version 0.6.2 dated 2008-05-20
Author: Karsten Tabelow ,
Joerg Polzehl
Title: Adaptive Smoothing of Digital Images
Description: This package implements tools for manipulationg digital images and the Propagation Separation approach
by Polzehl and Spokoiny (2006) for smoothing digital images.
Diff between adimpro versions 0.6.2 dated 2008-05-20 and 0.6.3 dated 2008-05-21
DESCRIPTION | 6 +++---
R/io.R | 33 +++++++++++++++++++++------------
R/misc.r | 4 ++++
README | 15 +++++++++++----
demo/awsimage.r | 4 ++++
demo/color.r | 4 ++++
demo/io.r | 5 ++++-
demo/manipulate.r | 5 ++++-
demo/raw.r | 4 ++++
man/adjust.image.Rd | 4 ++++
man/awsimage.Rd | 4 ++++
man/colorspace.Rd | 4 ++++
man/edges.Rd | 5 ++++-
man/imganiso2D.Rd | 4 ++++
man/plot.adimpro.Rd | 4 ++++
man/rotate.image.Rd | 4 ++++
man/show.image.Rd | 4 ++++
man/shrink.image.Rd | 4 ++++
18 files changed, 95 insertions(+), 22 deletions(-)
More information about adimpro at CRAN
posted at: 13:18 | path: /cran/updated | permanent link to this entry
Package Rwave updated to version 1.24-2 with previous version 1.24-1 dated 2008-05-02
Author: S original by Rene Carmona and
Bruno Torresani ;
R port by Brandon Whitcher
Title: Time-Frequency analysis of 1-D signals
Description: Rwave is a library of R functions which provide an
environment for the Time-Frequency analysis of 1-D signals (and
especially for the wavelet and Gabor transforms of noisy signals).
It was originally written for Splus by Rene Carmona, Bruno Torresani,
and Wen L. Hwang, first at the University of California at Irvine and
then at Princeton University. Credit should also be given to Andrea
Wang whose functions on the dyadic wavelet transform are included.
Rwave is based on the book:
"Practical Time-Frequency Analysis: Gabor and Wavelet Transforms with
an Implementation in S", by Rene Carmona, Wen L. Hwang and Bruno
Torresani, Academic Press, 1998.
Diff between Rwave versions 1.24-1 dated 2008-05-02 and 1.24-2 dated 2008-05-21
DESCRIPTION | 6 +++---
R/00util.R | 3 +--
R/Cwt_Morlet.R | 15 +++++----------
R/Cwt_Squeezing.R | 5 ++---
R/Cwt_Thierry.R | 9 +++------
R/Cwt_phase.R | 5 ++---
R/cwt_dog.R | 9 +++------
R/gRidge_Irregular.R | 2 +-
R/gRidge_Recons.R | 2 +-
R/gabor.R | 15 ++++-----------
R/mgabor.R | 5 ++---
R/radar.r | 7 +++----
R/recon2d.r | 7 +++----
R/skernel.r | 6 ++----
R/wv.R | 3 +--
src/Swave.h | 2 --
src/kernel.h | 1 -
17 files changed, 36 insertions(+), 66 deletions(-)
More information about Rwave at CRAN
posted at: 05:18 | path: /cran/updated | permanent link to this entry
