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(-)
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(-)
Author: Jim Lemon
Diff between plotrix versions 2.4-1 dated 2008-04-08 and 2.4-2 dated 2008-05-21
Title: Various plotting functions
Description: Lots of plots, various labeling, axis and color scaling functions.
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(-)
Author: Søren Højsgaard
Diff between doBy versions 2.3 dated 2008-03-26 and 3.0 dated 2008-05-21
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).
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(-)
Author: Jim Lemon
Diff between crank versions 0.9 dated 2008-01-15 and 1.0 dated 2008-05-21
Title: Completing ranks
Description: Functions for completing and recalculating rankings.
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(-)
Author: Karsten Tabelow
Diff between adimpro versions 0.6.2 dated 2008-05-20 and 0.6.3 dated 2008-05-21
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.
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(-)
Author: S original by Rene Carmona
Diff between Rwave versions 1.24-1 dated 2008-05-02 and 1.24-2 dated 2008-05-21
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.
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(-)