release of ade4 1.5-2

R/procuste.R, man/procuste.Rd: value 'nfact' is renamed 'nf'

man/coinertia.Rd: Small typo fix

R/betweencoinertia.R: Fixed a bug introduced in print.betcoi function

src/tests.c: Correct a small bug in loops for the acm case

R/randtest-internal.R, src/testrlq.c, src/tests.c: Clean the C code and correct a small bug (R strings were transformed in integers in C) that provokes problems on Mac OS X (thanks to Vincent Miele for his help)

R/rlq.R: Correct the number of repetitions in randtest.rlq (was nrepet+1 instead of nrepet)

R/betweencoinertia.R, R/coinertia.R, man/coinertia.Rd: Edited print functions for coinertia and betweencoinertia analyses

R/scatter.fca.R: Bug correction in the call to s.distri: needed to be pass the xax and yax params

R/sco.gauss.R: Correct a bug: dnorm has 'sd' as arguments and not 'var' (Thanks to Alice Julien-Laferriere)

release of ade4 1.5-1

R/randtest.cca.R, R/randtest.pcaiv.R, R/randtest.pcaivortho.R: Calls to Fortran routine 'dqrls' are replaced by public 'lm.wfit'

R/bca.rlq.R, R/between.R, R/betweencoinertia.R, R/coinertia.R, R/corkdist.R, R/discrimin.R, R/dpcoa.R, R/dudi.R, R/dudi.acm.R, R/kplot.sepan.R, R/mcoa.R, R/multispati.R, R/niche.R, R/randtest.coinertia.R, R/randtest.discrimin.R, R/rlq.R, R/rtest.between.R, R/rtest.discrimin.R, R/scatter.acm.R, R/scatter.fca.R, R/score.acm.R, R/score.coa.R, R/score.mix.R, R/score.pca.R, R/testdim.R, R/wca.rlq.R, R/withincoinertia.R, R/witwit.R, R/witwitsepan.R: Use eval.parent(..) instead of eval(.., sys.frame(0)) to allow the call of ade4 functions inside other functions

R/coinertia.R: Update the summary.coinertia function that now returns invisible results

R/dudi.R: To avoid confusion, the term 'Explained' is replaced by 'Projected' in the summary.dudi function

R/pcaiv.R, R/pcaivortho.R, man/pcaiv.Rd, man/pcaivortho.Rd: New functions 'summary.pcaiv' and 'summary.pcaivortho'

R/dudi.R, man/dudi.Rd: New function 'summary.dudi'

R/variance.phylog.R, man/variance.phylog.Rd: Returned is now an 'anova' object (was 'table')

R/bca.rlq.R, R/between.R, R/betweencoinertia.R, R/coinertia.R, R/discrimin.R, R/dpcoa.R, R/dudi.R, R/foucart.R, R/ktab.R, R/mcoa.R, R/mfa.R, R/multispati.R, R/niche.R, R/nipals.R, R/pcaiv.R, R/pcaivortho.R, R/pta.R, R/rlq.R, R/sepan.R, R/statis.R, R/variance.phylog.R, R/wca.rlq.R, R/within.R, R/withincoinertia.R, R/witwit.R: Outputs produced by print.

functions are now matrices (were table)

R/coinertia.R: Fix the problem of complex eigenvalues sometimes returned by eigen in the case n < (p, q)

R/orthogram.R, man/ade4-deprecated.Rd, man/orthogram.Rd: Orthogram function is now deprecated.

src/testdim.c: Correct a small bug (void function cannot return values)

man/neig.Rd: Modify an example due to a change in the deldir package

release of ade4 1.5-0

R/between.R, R/betweencoinertia.R, R/within.R, R/withincoinertia.R, man/between.Rd, man/betweencoinertia.Rd, man/plot.between.Rd, man/plot.within.Rd, man/within.Rd, man/withincoinertia.Rd: Functions within, withincoinertia, betwee, betweencoinertia are now deprecated to avoid a conflict names with the base::: within. New generic bca, wca with methods bca.dudi, bca.coinertia, wca.dudi and wca.coinertia should be used instead.

man/scatter.Rd: Correct a typo

man/scatter.Rd: Add the doc for the 'main' argument

R/dudi.R, man/scatter.Rd: New generic functions 'biplot' and 'screeplot' to plot the outputs of an analysis (class dudi)

data/macroloire.rda, data/rhizobium.rda, data/woangers.rda: Compress some ASCII data files

R/quasieuclid.R: Attributes of the original dist object are preserved

R/cailliez.R, R/lingoes.R, man/cailliez.Rd, man/lingoes.Rd: Add an argument to correct (or not) null distances

R/is.euclid.R: Add a warning for null distances

man/corvus.Rd: Correct a typo concerning the units of two variables (cm -> mm). Thanks to Peter Saly

ChangeLog: release of ade4 1.4-16

release of ade4 1.4-16

data/meaudret.rda: Updated meaudret environmental dataframe names

man/triangle.class.Rd: Remove auto-generated content in the documentation

R/s.class.R: argument 'pch' is now recycled so that one symbol could be assigned to each point. Thanks to Vincent Le Garrec for his question.

man/dist.binary.Rd: Correct some bibliographic references. Thanks to Pierre Legendre.

R/dist.ktab.R: Correct a small bug in the ldist.ktab function

man/ktab.match2ktabs.Rd: removed deprecated email address in ktab.match2ktabs documentation file

R/scalewt.R: Fixed a bug in the scaling of multivariate data using scalewt: when units of the variable were too heterogeneous, variables with the smallest variances were not scaled. This did not affect dudi.pca, but other functions such as discrimin.

man/rlq.Rd: Correct a typo in the description

man/rlq.Rd: Correct a typo in the description

man/fourthcorner.Rd: Add information on the outputs of the print and summary functions

man/banque.Rd, man/dudi.fca.Rd, man/fruits.Rd, man/meau.Rd, man/meaudret.Rd, man/monde84.Rd, man/ours.Rd, man/rhizobium.Rd, man/woangers.Rd, man/worksurv.Rd: Correct the use of the command '\item' in '\enumerate' environment

R/plot.4thcorner.R, man/fourthcorner.Rd, src/fourthcorner.c: The argument 'type' in plot.4thcorner can now takes the value D2 to plot correlation instead of homogeneity statistics in the case of qualitative / quantitative association

man/dist.ktab.Rd, man/woangers.Rd: Put some examples in '\dontrun' to speed up the checking of example

ChangeLog: release of ade4 1.4-14

release of ade4 1.4-14

DESCRIPTION, man/area.plot.Rd, man/neig.Rd, man/oribatid.Rd: Use the package 'deldir' instead of 'tripack' which has serious license issues. Correct the use of the class polylist which is not exported in the new version of maptools (0.7-27)

R/costatis.R: changes to the costatis function to remove cat outputs in non-interactive mode (i.e., when scannf = FALSE)

R/s.match.class.R, man/s.match.class.Rd: Add new function 's.match.class' to represent two systems of coordinates and a partitioning

R/betweencoinertia.R, R/withincoinertia.R, man/betweencoinertia.Rd, man/withincoinertia.Rd: Add new functions 'betweencoinertia' and 'withincoinertia' for between- and within-coinertia analysis

R/costatis.R, R/statico.R, man/costatis.Rd, man/statico.Rd, man/wgcoia.Rd: New functions to perform STATICO and CO-STATIS

R/kdisteuclid.R: Use 'match.arg' to evaluate the value of the 'method' argument

release of ade4 1.4-13

data/meaudret.rda: addition of the species names in the dataset

man/meau.Rd, man/meaudret.Rd: information about the link between the two datasets meau and meaudret has been added

R/phylog.R, R/plot.phylog.R: Correct bug in the use of basic regular expressions (argument 'extended' is deprecated R 2.11.0)

R/originality.R, man/originality.Rd: new methods have been added in the originality function

data/woangers.rda, man/woangers.Rd, man/rhizobium.Rd, data/rhizobium.rda, data/macroloire.rda, man/macroloire.Rd: three new data sets added

R/dist.ktab.R, man/dist.ktab.Rd: new functions of distance for multiple types of variables

R/apqe.R, man/apqe.Rd: new functions for diversity partitioning

R/mdpcoa.R, man/mdpcoa.Rd: new functions for multiple dpcoa

ChangeLog: release of ade4 1.4-12

release of ade4 1.4-12

data/toxicity.rda, man/toxicity.Rd: Correct species names and table dimensions (thanks to Jean Lobry)

R/dudi.R: bug on row.names in as.dudi (thanks to Jean Lobry)

R/newick2phylog.R: Correct bug in the use of basic regular expressions

man/multispati.Rd, man/multispati.randtest.Rd, man/multispati.rtest.Rd: update links to spdep functions in the documentation

R/newick2phylog.R, man/s.value.Rd, man/variance.phylog.Rd: Minor bugs have been fixes. Replace extended = FALSE by fixed = TRUE

man/scatter.dudi.Rd: added some precision about biplots in scatter.dudi.Rd

R/pta.R: corrected a small bug in row names of supIX and supIY df

R/dist.binary.R, man/dist.binary.Rd: Numeric matrix can be used for the 'df' argument (request of E. Paradis)

R/area.plot.R: argument nclasslegend is now active. bug identified by C. Calenge

ChangeLog: release of ade4 1.4-11

release of ade4 1.4-11

man/buech.Rd, man/corvus.Rd, man/dist.binary.Rd, man/dist.prop.Rd, man/dist.quant.Rd, man/kplot.mcoa.Rd, man/kplot.pta.Rd, man/ktab.Rd, man/maples.Rd, man/mcoa.Rd, man/mfa.Rd, man/njplot.Rd, man/orthogram.Rd, man/phylog.Rd, man/randtest.coinertia.Rd, man/scatter.fca.Rd, man/scatterutil.Rd, man/supcol.Rd, man/withinpca.Rd: Make Rd files pass R-2.9.0 (devel) parser 2 checks

man/randEH.Rd: replace PD in EH

man/optimEH.Rd: replace PD in EH

ChangeLog: release of ade4 1.4-10

release of ade4 1.4-10

R/combine.4thcorner.R, R/fourthcorner.R, R/fourthcorner2.R, R/plot.4thcorner.R, R/print.4thcorner.R, R/summary.4thcorner.R, man/fourthcorner.Rd, src/fourthcorner.c: new functions implementing the fourthcorner method and extensions presented in Dray and Legendre (2008)

src/adesub.c, src/adesub.h, src/testdim.c: new functions to permute matrices used in testdim and fourthcorner are now in adesub

man/RVdist.randtest.Rd, man/randtest-internal.Rd, man/scatterutil.Rd: remove empty sections

man/dudi.fca.Rd: add a second argument to the \item macro

man/witwit.coa.Rd: remove invalid whitespaces

R/gearymoran.R: small typo repared

R/gearymoran.R: Added a match.arg to gearymoran (in multivariate case, was messed up.

R/niche.R: Add a global test of the average marginality for all species

R/dudi.acm.R, R/dudi.coa.R, R/dudi.dec.R, R/dudi.fca.R, R/dudi.hillsmith.R, R/dudi.mix.R, R/dudi.nsc.R, R/dudi.pca.R: Added a as.data.frame(df) to dudi methods.

data/abouheif.eg.rda: new data files

data/acacia.rda, data/aminoacyl.rda, data/apis108.rda, data/ardeche.rda, data/arrival.rda, data/atlas.rda, data/atya.rda, data/avijons.rda, data/avimedi.rda, data/aviurba.rda, data/bacteria.rda, data/banque.rda, data/baran95.rda, data/bf88.rda, data/bordeaux.rda, data/bsetal97.rda, data/buech.rda, data/butterfly.rda, data/capitales.rda, data/carni19.rda, data/carni70.rda, data/carniherbi49.rda, data/casitas.rda, data/chatcat.rda, data/chats.rda, data/chazeb.rda, data/chevaine.rda, data/clementines.rda, data/cnc2003.rda, data/coleo.rda, data/corvus.rda, data/deug.rda, data/doubs.rda, data/dunedata.rda, data/ecg.rda, data/ecomor.rda, data/elec88.rda, data/escopage.rda, data/euro123.rda, data/fission.rda, data/friday87.rda, data/fruits.rda, data/ggtortoises.rda, data/granulo.rda, data/hdpg.rda, data/housetasks.rda, data/humDNAm.rda, data/ichtyo.rda, data/irishdata.rda, data/julliot.rda, data/jv73.rda, data/kcponds.rda, data/lascaux.rda, data/lizards.rda, data/macaca.rda, data/macon.rda, data/mafragh.rda, data/maples.rda, data/mariages.rda, data/meau.rda, data/meaudret.rda, data/microsatt.rda, data/mjrochet.rda, data/mollusc.rda, data/monde84.rda, data/morphosport.rda, data/newick.eg.rda, data/njplot.rda, data/olympic.rda, data/oribatid.rda, data/ours.rda, data/palm.rda, data/pap.rda, data/perthi02.rda, data/presid2002.rda, data/procella.rda, data/rankrock.rda, data/rhone.rda, data/rpjdl.rda, data/santacatalina.rda, data/sarcelles.rda, data/seconde.rda, data/skulls.rda, data/steppe.rda, data/syndicats.rda, data/t3012.rda, data/tarentaise.rda, data/taxo.eg.rda, data/tintoodiel.rda, data/tithonia.rda, data/tortues.rda, data/toxicity.rda, data/trichometeo.rda, data/ungulates.rda, data/vegtf.rda, data/veuvage.rda, data/westafrica.rda, data/worksurv.rda, data/yanomama.rda, data/zealand.rda: new data files

data/abouheif.eg.rda, data/acacia.rda, data/aminoacyl.rda, data/apis108.rda, data/ardeche.rda, data/arrival.rda, data/atlas.rda, data/atya.rda, data/avijons.rda, data/avimedi.rda, data/aviurba.rda, data/bacteria.rda, data/banque.rda, data/baran95.rda, data/bf88.rda, data/bordeaux.rda, data/bsetal97.rda, data/buech.rda, data/butterfly.rda, data/capitales.rda, data/carni19.rda, data/carni70.rda, data/carniherbi49.rda, data/casitas.rda, data/chatcat.rda, data/chats.rda, data/chazeb.rda, data/chevaine.rda, data/clementines.rda, data/cnc2003.rda, data/coleo.rda, data/corvus.rda, data/deug.rda, data/doubs.rda, data/dunedata.rda, data/ecg.rda, data/ecomor.rda, data/elec88.rda, data/escopage.rda, data/euro123.rda, data/fission.rda, data/friday87.rda, data/fruits.rda, data/ggtortoises.rda, data/granulo.rda, data/hdpg.rda, data/housetasks.rda, data/humDNAm.rda, data/ichtyo.rda, data/irishdata.rda, data/julliot.rda, data/jv73.rda, data/kcponds.rda, data/lascaux.rda, data/lizards.rda, data/macaca.rda, data/macon.rda, data/mafragh.rda, data/maples.rda, data/mariages.rda, data/meau.rda, data/meaudret.rda, data/microsatt.rda, data/mjrochet.rda, data/mollusc.rda, data/monde84.rda, data/morphosport.rda, data/newick.eg.rda, data/njplot.rda, data/olympic.rda, data/oribatid.rda, data/ours.rda, data/palm.rda, data/pap.rda, data/perthi02.rda, data/presid2002.rda, data/procella.rda, data/rankrock.rda, data/rhone.rda, data/rpjdl.rda, data/santacatalina.rda, data/sarcelles.rda, data/seconde.rda, data/skulls.rda, data/steppe.rda, data/syndicats.rda, data/t3012.rda, data/tarentaise.rda, data/taxo.eg.rda, data/tintoodiel.rda, data/tithonia.rda, data/tortues.rda, data/toxicity.rda, data/trichometeo.rda, data/ungulates.rda, data/vegtf.rda, data/veuvage.rda, data/westafrica.rda, data/worksurv.rda, data/yanomama.rda, data/zealand.rda: remove corrupted data files

ChangeLog, DESCRIPTION, INDEX, R, TITLE, data, inst, man, src: move from trunk to pkg after initial import using cvs2svn

man: remove man folder

R: remove R folder

ChangeLog, DESCRIPTION, INDEX, R, TITLE, data, inst, man, src: move from trunk to pkg after initial import using cvs2svn

ChangeLog, DESCRIPTION: release of ade4 1.4-9

R/niche.R: Correct a syntax error

R/mantel.randtest.R, R/procuste.randtest.R: Correct a bug. The number of repetitions was not correct ((nrepet + 1) instead of nrepet)

R/niche.R, R/randtest.between.R, R/randtest.coinertia.R, R/randtest.discrimin.R: Correct a bug. The number of repetitions was not correct ((nrepet + 1) instead of nrepet)

R/krandtest.R, R/randtest.amova.R, man/krandtest.Rd: the class krandtest now accepts a vector of alternative hypotheses instead of a common alternative hypothesis for the k tests (email of Kim Milferstedt on RHelp)

ChangeLog, DESCRIPTION: release of ade4 1.4-8

R/dudi.acm.R: bug correction (mail of JR Lobry on adelist): (any(row.w) < 0) vs. (any(row.w < 0))

R/dudi.R: bug correction (mail of JR Lobry on adelist): any(col.w) < 0 vs. any(col.w < 0)

data/ggtortoises.rda: pixmap S3 objects transformed into S4 class

ChangeLog, DESCRIPTION: release of ade4 1.4-7

data/capitales.rda: pixmap S3 objects transformed into S4 class

ChangeLog, DESCRIPTION: release of ade4 1.4-6

R/phylog.R: Correct a bug in phylog.extract (mail of S. Ollier)

src/adesub.c, src/adesub.h, src/testrlq.c: matcentragehi in now in adesub

R/nipals.R, man/nipals.Rd: New function for NIPALS algorithm, i.e. PCA with (or without) NA

man/randtest.Rd: add some words about the computation of pvalues for two-sided test

man/ade4.package.Rd: empty log message

man/pcaiv.Rd: empty log message

man/table.phylog.Rd: Example table.phylog set to dontrun

man/multispati.Rd, man/vegtf.Rd: Update the source reference: Dray et al. (2008)

man/dudi.pca.Rd: Modifications : explanations about values (cent and norm) ; it{} into emph{}.

man/dudi.pca.Rd: Modification of explanations ($cent and $norm)

R/sco.distri.R: correct a bug (identified by S. Pavoine): default label argument was badly considered when one column contains only O's

R/scatter.R, R/scatterutil.R, man/scatter.Rd, man/scatterutil.Rd: New utility function scatterutil.sco and scatterutil.convrot90 for 1D graphical representation

R/sco.gauss.R, man/sco.gauss.Rd: New function sco.gauss for 1D graphical representation

R/sco.match.R, man/sco.match.Rd: New function sco.match for 1D graphical representation

R/sco.class.R, man/sco.class.Rd: New function sco.class for 1D graphical representation

R/sco.label.R, man/sco.label.Rd: New function sco.label for 1D graphical representation

R/sco.qual.R: Functions of this file are now in sco.label.R and sco.gauss.R

inst/CITATION: Add two new references to the CITATION file

R/randtest.cca.R, R/randtest.pcaiv.R, R/randtest.pcaivortho.R, man/randtest.pcaiv.Rd: News functions for permutation tests in constrained analysis

src/testdim.c: Correct a bug in memory allocation of the function svdd

man/sco.label.Rd: added function: Draws evenly spaced labels, each label linked to the corresponding value of a numeric score

man/sco.gauss.Rd: added function: Draws Gauss curves with the same mean and variance as the scores of indivivuals belonging to categories of several factors

man/veuvage.Rd: Correstion of illegal accented character in exemple code

R/sco.qual.R: adds two functions: sco.gauss and sco.label (draw Gauss curves on a score by categories of several factors)

R/newick2phylog.R: Correct a bug. In newick2phylog.addtools, eigen does not return an orthogonal basis when there are null eigenvalues (Wscores). Vectors are now orthogonalized using qr

DESCRIPTION: Change License to GPL (>=2)

ChangeLog: empty log message

ChangeLog, DESCRIPTION: release of ade4 1.4-5

man/dunedata.Rd, man/steppe.Rd: Replace non_function by Doctype

src/testdim.c, src/tests.c: Correction of a bug in the declaration of variables

ChangeLog: release of ade4 1.4-4

release of ade4 1.4-4

R/coinertia.R, R/dudi.R, R/dudi.pco.R: Modification of the call of the imported function chooseaxes for the use of the ade4TkGUI package

R/within.pca.R, R/withinpca.R, man/ktab.Rd, man/ktab.match2ktabs.Rd, man/pta.Rd, man/statis.Rd, man/within.pca.Rd, man/withinpca.Rd: The function within.pca is renamed withinpca

R/ktab.R, man/ktab.Rd: Change the names of the arguments of the function '[.ktab'

man/amova.Rd, man/between.Rd, man/coinertia.Rd, man/corkdist.Rd, man/discrimin.Rd, man/dpcoa.Rd, man/dudi.Rd, man/dudi.acm.Rd, man/dudi.pco.Rd, man/foucart.Rd, man/is.euclid.Rd, man/kplot.foucart.Rd, man/kplot.mcoa.Rd, man/kplot.mfa.Rd, man/kplot.pta.Rd, man/kplot.sepan.Rd, man/kplot.statis.Rd, man/krandtest.Rd, man/ktab.Rd, man/mcoa.Rd, man/mfa.Rd, man/multispati.Rd, man/neig.Rd, man/niche.Rd, man/orthobasis.Rd, man/pcaiv.Rd, man/phylog.Rd, man/plot.phylog.Rd, man/procuste.Rd, man/pta.Rd, man/randtest.Rd, man/randtest.amova.Rd, man/randtest.between.Rd, man/randtest.coinertia.Rd, man/randtest.discrimin.Rd, man/reconst.Rd, man/rlq.Rd, man/rtest.Rd, man/rtest.between.Rd, man/rtest.discrimin.Rd, man/scatter.acm.Rd, man/scatter.coa.Rd, man/scatter.dudi.Rd, man/scatter.fca.Rd, man/score.acm.Rd, man/score.coa.Rd, man/score.mix.Rd, man/score.pca.Rd, man/sepan.Rd, man/statis.Rd, man/supcol.Rd, man/suprow.Rd, man/testdim.Rd, man/within.Rd, man/witwit.coa.Rd: Correct usage entries for S3 methods

DESCRIPTION: suggests ade4TkGUI

R/randtest.between.R: modif eval pour ne pas chercher dans l'environnement global directement

src/Makevars: replace CRLF (DOS) by LF (Unix)

R/coinertia.R, R/dudi.R, R/dudi.pco.R: modif pour variable globale ade4TkGUIFlag

man/PI2newick.Rd, man/RV.rtest.Rd, man/RVdist.randtest.Rd, man/aminoacyl.Rd, man/ardeche.Rd, man/area.plot.Rd, man/as.taxo.Rd, man/atlas.Rd, man/atya.Rd, man/avijons.Rd, man/aviurba.Rd, man/baran95.Rd, man/between.Rd, man/bicenter.wt.Rd, man/buech.Rd, man/cailliez.Rd, man/carni70.Rd, man/casitas.Rd, man/cca.Rd, man/chatcat.Rd, man/chats.Rd, man/clementines.Rd, man/coinertia.Rd, man/corkdist.Rd, man/discrimin.Rd, man/discrimin.coa.Rd, man/dist.binary.Rd, man/dist.dudi.Rd, man/dist.genet.Rd, man/dist.neig.Rd, man/dist.prop.Rd, man/dist.quant.Rd, man/divcmax.Rd, man/dotchart.phylog.Rd, man/dotcircle.Rd, man/doubs.Rd, man/dpcoa.Rd, man/dudi.Rd, man/dudi.acm.Rd, man/dudi.coa.Rd, man/dudi.dec.Rd, man/dudi.fca.Rd, man/dudi.mix.Rd, man/dudi.nsc.Rd, man/dudi.pca.Rd, man/dudi.pco.Rd, man/escopage.Rd, man/euro123.Rd, man/fruits.Rd, man/fuzzygenet.Rd, man/gearymoran.Rd, man/genet.Rd, man/granulo.Rd, man/gridrowcol.Rd, man/ichtyo.Rd, man/inertia.dudi.Rd, man/is.euclid.Rd, man/julliot.Rd, man/jv73.Rd, man/kdist.Rd, man/kdist2ktab.Rd, man/kdisteuclid.Rd, man/kplot.foucart.Rd, man/kplot.mcoa.Rd, man/kplot.mfa.Rd, man/kplot.pta.Rd, man/kplot.sepan.Rd, man/kplot.statis.Rd, man/ktab.Rd, man/ktab.data.frame.Rd, man/ktab.list.df.Rd, man/ktab.list.dudi.Rd, man/ktab.match2ktabs.Rd, man/ktab.within.Rd, man/lascaux.Rd, man/lingoes.Rd, man/macon.Rd, man/mafragh.Rd, man/mantel.rtest.Rd, man/mariages.Rd, man/mcoa.Rd, man/meau.Rd, man/meaudret.Rd, man/mfa.Rd, man/microsatt.Rd, man/mjrochet.Rd, man/mld.Rd, man/mollusc.Rd, man/monde84.Rd, man/morphosport.Rd, man/mstree.Rd, man/multispati.Rd, man/multispati.randtest.Rd, man/multispati.rtest.Rd, man/neig.Rd, man/newick.eg.Rd, man/newick2phylog.Rd, man/niche.Rd, man/njplot.Rd, man/orthobasis.Rd, man/orthogram.Rd, man/ours.Rd, man/palm.Rd, man/pcaiv.Rd, man/pcaivortho.Rd, man/pcoscaled.Rd, man/phylog.Rd, man/plot.phylog.Rd, man/procuste.Rd, man/procuste.rtest.Rd, man/pta.Rd, man/quasieuclid.Rd, man/reconst.Rd, man/rhone.Rd, man/rpjdl.Rd, man/rtest.Rd, man/rtest.between.Rd, man/rtest.discrimin.Rd, man/s.arrow.Rd, man/s.chull.Rd, man/s.class.Rd, man/s.corcircle.Rd, man/s.distri.Rd, man/s.hist.Rd, man/s.image.Rd, man/s.kde2d.Rd, man/s.label.Rd, man/s.logo.Rd, man/s.match.Rd, man/s.multinom.Rd, man/s.traject.Rd, man/s.value.Rd, man/sarcelles.Rd, man/scalewt.Rd, man/scatter.Rd, man/scatter.acm.Rd, man/scatter.coa.Rd, man/scatter.dudi.Rd, man/scatter.fca.Rd, man/sco.boxplot.Rd, man/sco.distri.Rd, man/sco.quant.Rd, man/score.Rd, man/score.acm.Rd, man/score.coa.Rd, man/score.mix.Rd, man/score.pca.Rd, man/sepan.Rd, man/statis.Rd, man/steppe.Rd, man/supcol.Rd, man/suprow.Rd, man/symbols.phylog.Rd, man/t3012.Rd, man/table.cont.Rd, man/table.dist.Rd, man/table.paint.Rd, man/table.phylog.Rd, man/table.value.Rd, man/tarentaise.Rd, man/triangle.class.Rd, man/triangle.plot.Rd, man/trichometeo.Rd, man/ungulates.Rd, man/uniquewt.df.Rd, man/variance.phylog.Rd, man/veuvage.Rd, man/westafrica.Rd, man/within.Rd, man/within.pca.Rd, man/witwit.coa.Rd, man/worksurv.Rd: Added the encoding of Rd files and remove the email of Daniel Chessel (he is retired)

R/scatter.acm.R: Clean R files: replace T by TRUE.

R/newick2phylog.R: Clean R files: remove multiple function definitions (floc1(s) becomes floc1,floc2,floc3. Thanks to UsagePackageCheck of codetools

R/multispati.R, R/multispati.randtest.R, R/multispati.rtest.R, R/neig.R, R/orthobasis.R, R/s.image.R, R/s.kde2d.R, R/s.logo.R: Clean R files: correct imported function definition. Thanks to UsagePackageCheck of codetools

R/orthogram.R: Correct a bug: test for the choice between orthobas, neig or phylog

R/scatter.acm.R: Correct a bug: replace score. by score.acm

R/kplot.foucart.R, R/kplot.mfa.R, R/mcoa.R, R/rlq.R, R/score.coa.R, R/sepan.R, R/variance.phylog.R: Clean R files: remove local variables assigned but not used. Thanks to checkUsagePackage of codetools

R/PI2newick.R, R/RV.rtest.R, R/RVdist.randtest.R, R/amova.R, R/area.plot.R, R/as.taxo.R, R/between.R, R/coinertia.R, R/corkdist.R, R/disc.R, R/discrimin.R, R/discrimin.coa.R, R/dist.dudi.R, R/dist.genet.R, R/dotcircle.R, R/dudi.coa.R, R/dudi.dec.R, R/dudi.nsc.R, R/foucart.R, R/fuzzygenet.R, R/genet.R, R/gridrowcol.R, R/kplot.foucart.R, R/kplot.mfa.R, R/kplot.statis.R, R/ktab.R, R/ktab.list.dudi.R, R/ktab.match2ktabs.R, R/ktab.within.R, R/lingoes.R, R/mcoa.R, R/mld.R, R/multispati.R, R/newick2phylog.R, R/niche.R, R/optimEH.R, R/orthobasis.R, R/orthogram.R, R/pcaiv.R, R/phylog.R, R/plot.phylog.R, R/procuste.R, R/rlq.R, R/rtest.between.R, R/s.corcircle.R, R/s.hist.R, R/s.image.R, R/scatter.R, R/sco.distri.R, R/score.acm.R, R/score.coa.R, R/score.mix.R, R/sepan.R, R/statis.R, R/symbols.phylog.R, R/table.cont.R, R/table.phylog.R, R/uniquewt.df.R, R/variance.phylog.R, R/within.R, R/within.pca.R: Clean R files: remove local variables assigned but not used. Thanks to checkUsagePackage of codetools

man/bordeaux.Rd, man/cca.Rd, man/dudi.hillsmith.Rd, man/elec88.Rd, man/seconde.Rd: Clean Rd files: remove unmatched right brace

R/testdim.R, man/testdim.Rd, src/Makevars, src/testdim.c: New function testdim to estimate the number of axes in multivariate analysis

R/gearymoran.R, R/krandtest.R, R/niche.R, R/orthogram.R, R/randtest.amova.R, man/gearymoran.Rd, man/krandtest.Rd, man/niche.Rd, man/orthogram.Rd: reimplementation of the class krandtest and new function as.krandtest

man/vegtf.Rd: correction of a bug in the example section

R/score.coa.R, man/score.coa.Rd: new function reciprocal.coa (see http: //listes.univ-lyon1.fr/wws/arc/adelist/2007-07/msg00007.html)

R/sco.distri.R, man/sco.distri.Rd: sco.distri returns a data.frame with means and variances (see http: //listes.univ-lyon1.fr/wws/arc/adelist/2007-06/msg00018.html)

R/scatter.R, R/sepan.R, R/witwitsepan.R: Add yaxt argument to scatterutil.eigen (see http: //listes.univ-lyon1.fr/wws/arc/adelist/2007-07/msg00022.html)

R/multispati.R: Correct legend in plot.multispati

data/vegtf.rda, man/vegtf.Rd: New vegetation data set to illustrate multispati analysis

R/niche.R, man/niche.Rd: New functions niche.param and rtest.niche

R/area.plot.R: the function area2poly is modified to export the bbox attribute for each polygon

R/s.corcircle.R: correct bug of the grid argument. see http: //listes.univ-lyon1.fr/wws/arc/adelist/2007-07/msg00001.html

R/randtest-internal.R, R/rlq.R: correct bugs in memory allocation (C interface). These bugs have been identified using valgrind by B. Ripley (12/06/2007)

man/dunedata.Rd: correct the number of rows and columns in the help file

ChangeLog, DESCRIPTION: release of ade4 1.4-3

man/suprow.Rd: correct the example section

ChangeLog: New ChangeLog

data/atlas.rda, data/avijons.rda, data/aviurba.rda, data/baran95.rda, data/bf88.rda, data/chevaine.rda, data/cnc2003.rda, data/elec88.rda, data/monde84.rda, data/rankrock.rda, data/rpjdl.rda, data/sarcelles.rda, data/steppe.rda, data/t3012.rda, data/tarentaise.rda, data/veuvage.rda, data/westafrica.rda: remove non ASCII characters in data

ChangeLog, R/dudi.pco.R: reviewed by:

R/dudi.pco.R: sub and csub arguments are now actually passed to s.label

ChangeLog, R/add.scatter.R, man/add.scatter.Rd, man/scatter.Rd: R/scatter.R: removed add.scatter.eig

man/scatter.Rd: removed add.scatter.eig

R/add.scatter.R: new functions add.scatter and add.scatter.eig

man/add.scatter.Rd: doc for add.scatter and add.scatter.eig

R/scatter.add.R, man/scatter.add.Rd: empty log message

ChangeLog, R/add.graph.R: reviewed by:

R/add.graph.R:

R/dpcoa.R:

R/dudi.pco.R:

R/kplot.sepan.R:

R/mfa.R:

R/pta.R:

R/scatter.R:

R/scatter.add.R:

R/scatter.coa.R:

R/scatter.dudi.R:

R/statis.R:

man/scatter.Rd:

man/scatter.add.Rd:

ChangeLog, R/dpcoa.R, R/dudi.pco.R, R/kplot.sepan.R, R/mfa.R, R/pta.R, R/scatter.R, R/scatter.add.R, R/scatter.coa.R, R/scatter.dudi.R, R/statis.R, man/add.graph.Rd, man/scatter.Rd, man/scatter.add.Rd: reviewed by:

R/dpcoa.R:

R/dudi.pco.R:

R/kplot.sepan.R:

R/mfa.R:

R/pta.R:

R/scatter.R:

R/scatter.add.R:

R/scatter.coa.R:

R/scatter.dudi.R:

R/statis.R:

man/add.graph.Rd:

man/scatter.Rd:

man/scatter.add.Rd:

ChangeLog, R/add.graph.R, R/dpcoa.R, R/dudi.pco.R, R/kplot.sepan.R, R/mfa.R, R/pta.R, R/scatter.R, R/scatter.coa.R, R/scatter.dudi.R, R/statis.R, man/add.graph.Rd, man/dudi.pca.Rd, man/scatter.Rd, man/scatter.dudi.Rd: reviewed by:

R/add.graph.R: ajout de la fonction (contient add.graph et la nouvelle version de add.scatter.eig)

man/add.graph.Rd: ajout de la doc (add.graph et add.scatter.eig)

R/dpcoa.R: appel de add.scatter.eig: nf supprime

R/dudi.pco.R: appel de add.scatter.eig: nf supprime

R/kplot.sepan.R: appel de add.scatter.eig: nf supprime

R/mfa.R: appel de add.scatter.eig: nf supprime

R/pta.R: appel de add.scatter.eig: nf supprime

R/scatter.R: add.scatter.eig supprime (migre vers add.graph.R)

R/scatter.coa.R: appel de add.scatter.eig: nf supprime

R/scatter.dudi.R: appel de add.scatter.eig: nf supprime

R/statis.R: appel de add.scatter.eig: nf supprime

man/dudi.pca.Rd: modifications faites par Anne

man/scatter.Rd: enleve add.scatter.eig de la doc (migre vers add.graph.Rd)

man/scatter.dudi.Rd: appel de add.scatter.eig: nf supprime

ChangeLog, data/rpjdl.rda: reviewed by:

data/rpjdl.rda: removed accents

ChangeLog, R/s.arrow.R, man/s.arrow.Rd: R/s.arrow.R: added the "boxes" argument

man/s.arrow.Rd: added the "boxes" argument