2023-01-30 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION: ---------- release of ade4 1.7-22 ----------
2023-01-29 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* src/testsCpp.cpp: remove useless declarations of spl1 lists array remove useless declarations of spl1 lists array
2023-01-27 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* ChangeLog: ---------- release of ade4 1.7-21 ----------
2023-01-27 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION: ---------- release of ade4 1.7-21 ----------
2023-01-27 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* : Reduce pnm size to lighten the package
2023-01-25 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .github/workflows/build-bin-macOS-arm64.yaml: Delete the workflow
to build binaries under mac-arm64 configuration not yet available with github actions:
https://github.com/actions/runner-images/issues/2187
2023-01-25 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .github/workflows/build-bin-macOS-arm64.yaml: Update
build-bin-macOS-arm64.yaml
2023-01-24 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .github/workflows/build-bin-macOS-arm64.yaml: Update
build-bin-macOS-arm64.yaml: try another label for arm64
2023-01-23 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .github/workflows/build-bin-macOS-arm64.yaml,
.github/workflows/build-bin-macOS.yaml,
.github/workflows/build-bin-windows.yaml: Update workflows to build
binaries for maOS and windows: correct misprints
2023-01-23 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .github/workflows/build-bin-macOS-arm64.yaml: Update
build-bin-macOS-arm64.yaml
2023-01-23 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .github/workflows/build-bin-macOS-arm64.yaml: Update
build-bin-macOS-arm64
2023-01-23 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .github/workflows/build-bin-macOS-arm64.yaml,
.github/workflows/build-bin-macOS.yaml: Separate the workflow script
to handle two architectures for mac (intel and arm)
2023-01-23 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .github/workflows/build-bin-macOS.yaml: Update build-bin-macOS:
try to also build the package with an 'arm' configuration for macOS
2023-01-23 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .github/workflows/build-bin-windows.yaml: Add
build-bin-windows.yaml
2023-01-23 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .github/workflows/build-bin-macOS.yaml: Correct a misprint in
build-bin-macOS.yaml
2023-01-23 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .github/workflows/build-bin-macOS.yaml: Add the workflow
build-bin-macOS.yaml
2023-01-20 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .github/workflows/R-CMD-check-rcpp.yaml: Delete
R-CMD-check-rcpp.yaml after merging the ade4-rcpp branch
2023-01-17 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* : commit e484cff4deb9bd91f7e09e39ce11f0170454616f Author: Aurélie
Siberchicot <aurelie.siberchicot@univ-lyon1.fr> Date: Mon Jan 16
15:37:38 2023 +0100
2023-01-16 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .github/workflows/R-CMD-check-rcpp.yaml: Update
R-CMD-check-rcpp.yaml: add libraries for macOS
2023-01-16 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .github/workflows/R-CMD-check.yaml: Update R-CMD-check.yaml: add
libraries for macOS
2023-01-13 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* R/randtest.between.R: Update randtest.between.R put back the definition of X.lw
2023-01-13 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .github/workflows/R-CMD-check.yaml: Update R-CMD-check.yaml: add
xquartz for macOS
2023-01-13 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .github/workflows/R-CMD-check-rcpp.yaml: Correct indentation in
R-CMD-check-rcpp
2023-01-13 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .github/workflows/R-CMD-check-rcpp.yaml: Add a copy of
R-CMD-check-rcpp.yaml in the ade4-Rcpp branch
2023-01-13 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .Rbuildignore: A minor commit to in the ade4-Rcpp branch to
trigger R-CMD-check-rcpp
2023-01-13 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .github/workflows/R-CMD-check.yaml: Correct a misprint in
R-CMD-check.yaml
2023-01-13 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .github/workflows/R-CMD-check.yaml: Update R-CMD-check.yaml:
install udunits for macOS
2023-01-11 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .github/workflows/R-CMD-check.yaml: Update R-CMD-check.yaml: a lot
of tags are deprecated
2023-01-11 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .github/workflows/R-CMD-check-rcpp.yaml,
.github/workflows/R-CMD-check.yaml: Add a workflow to check the
ade4-Rcpp branch
2023-01-11 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* README.md: Update README
2023-01-11 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* R/dist.ktab.R: Correct a bug in the function 'ldist.ktab' for
fuzzy data
2023-01-04 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* R/mantel.randtest.R, R/randtest.between.R: Cleaning R code Cleaning R code for unused variables after moving from C to C++
calls
2023-01-03 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* : commit 3b3c2d79a1587998868e8599849dfec84afa3ece Author: Aurélie
Siberchicot <aurelie.siberchicot@univ-lyon1.fr> Date: Tue Jan 3
15:59:01 2023 +0100
2023-01-02 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* R/dist.ktab.R: Just indent
2022-11-02 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/presid2002.Rd: Update URL in presid2002
2022-11-01 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* ChangeLog: ---------- release of ade4 1.7-20 ----------
2022-11-01 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION: ---------- release of ade4 1.7-20 ----------
2022-11-01 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* R/area.plot.R, R/kdisteuclid.R, R/s.label.R, R/s.logo.R,
R/s.value.R, R/supdist.R: Correct if() conditions comparing class()
to string, now use inherits() as required by R CMD check
2022-11-01 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/atlas.Rd, man/atya.Rd, man/avijons.Rd, man/bca.Rd,
man/bca.coinertia.Rd, man/buech.Rd, man/butterfly.Rd,
man/bwca.dpcoa.Rd, man/capitales.Rd, man/elec88.Rd,
man/ggtortoises.Rd, man/irishdata.Rd, man/julliot.Rd, man/jv73.Rd,
man/kcponds.Rd, man/mafragh.Rd, man/pcw.Rd, man/sarcelles.Rd,
man/supdist.Rd, man/suprow.pta.Rd, man/t3012.Rd, man/tintoodiel.Rd,
man/vegtf.Rd, man/wca.Rd, man/wca.coinertia.Rd, man/zealand.Rd: Add
a newline at the end of several Rd files
2022-10-28 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* src/fourthcorner.c: Correct a bug to deal with non-integers values
in table L Homogenity/correlation ratio measures require to have at least 23
individuals per class to be computed (computing a variance requires
at leats 2 indiciduals). When dealing with non-integres values in L
(e.g. cover, proportion), we must count the number of non-null cells
(correpondence) but not the total abundance (which can be less than
1 and thus induces a bug in the if condition)
2022-10-20 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* src/divsub.c, src/phylog.c, src/testamova.c: Change encoding from
ISO-8859 to UTF-8 Modify the encoding to properly manage accented characters in
comments. It induced a WARNING on Rdevel (mail by K Hornick)
2022-10-20 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* man/chickenk.Rd, man/multispati.Rd, man/randboot.Rd: Remove LateX
special characters Remove symbols that returns a NOTE in Rdevel
2022-06-29 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* man/randtest.Rd: added links to other methods & functions for
permutation tests
2022-05-05 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* R/procuste.R, R/procuste.randtest.R: Update of procuste analysis
permutation test Functions ade4:::randtest.procuste and procuste.randtest now call
the R function procuste.rtest instead of calling the C function
testprocuste
2022-05-05 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* : Update mafragh.rda version = 2 for compat with R 2.5
2022-05-05 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* : Update mafragh.rda set class of mafragh$spenames$scientific and mafragh$spenames$code
to character
2022-04-19 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* ChangeLog: ---------- release of ade4 1.7-19 ----------
2022-04-19 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION: ---------- release of ade4 1.7-19 ----------
2022-04-19 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/pcw.Rd: Update a help file: a 'url' tag becomes a 'doi' tag
2022-03-07 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* README.md: Add a badge for the licence required to apply for BlueHats Semester of Code
2022-01-04 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* src/testdim.c: Specify string lengths to BLAS/LAPACK routines to
allow compilation using new compilers The solution is to pass the unit string lengths explicitly using
FCONE defined in Rconfig.h if USE_FC_LEN_T is defined. See
http://developer.r-project.org/blosxom.cgi/R-devel/2019/08/29#n2019-08-29. Update required by B. Ripley by email (18/09/2021) for compatibility for next R versions
2021-12-30 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* R/loocv.R: Update loocv.R modifications for the case p = 1 (only one variable): need to avoid
type coercition from dataframe to vector. And also, no need to check
axis direction.
2021-12-14 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* man/supdist.Rd: Update supdist.Rd Supplementary distances plotted in red in supdist example
2021-10-08 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* man/houmousr.Rd: Added the houmousr data set House Mouse morphometric data set, used in: Thioulouse, J., Renaud,
S., Dufour, AB. et al. Overcoming the Spurious Groups Problem in
Between-Group PCA. Evol Biol (2021).
https://doi.org/10.1007/s11692-021-09550-0
2021-09-29 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/pcw.Rd: Update URL
2021-09-16 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* ChangeLog: ---------- release of ade4 1.7-18 ----------
2021-09-16 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION: ---------- release of ade4 1.7-18 ----------
2021-09-16 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/loocv.bca.Rd: Update the help file of 'loocv.bca': the 'url'
tag becomes 'doi' for the references
2021-09-15 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* man/loocv.bca.Rd: Update loocv.bca.Rd
2021-09-14 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/pcw.Rd: Update URL
2021-07-07 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* NAMESPACE, R/loocv.R, man/loocv.bca.Rd, man/loocv.discrimin.Rd:
updates to print and plot functions for loocv objects updates to print and plot functions for bca and discrimin loocv
objects
2021-07-06 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* NAMESPACE, R/loocv.R, man/loocv.bca.Rd, man/loocv.discrimin.Rd,
src/init.c: added print and plot functions for loocv Added print and (dummy) plot functions for loocv objects (bca +
discrimin). Added two classes for the corresponding objects:
bcaloocv and discloocv. Added the attributes and matched calls to
these objects in the loocv functions. Plot functions are really
implemented only in adegraphics.
2021-06-17 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* ChangeLog: ---------- release of ade4 1.7-17 ----------
2021-06-17 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION: ---------- release of ade4 1.7-17 ----------
2021-06-17 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .Rbuildignore, .gitignore: Update the files .Rbuildignore and
.gitignore
2021-06-17 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/loocv.R, man/loocv.bca.Rd, man/loocv.discrimin.Rd: Remove sPRESS
which is not included in Thioulouse et al submitted paper
2021-05-25 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* : commit 3d4d3529323ddefb6ff3fe4df067c2a11e5bd8fc Author: Aurélie
Siberchicot <aurelie.siberchicot@univ-lyon1.fr> Date: Tue May 25
10:22:11 2021 +0200
2021-05-21 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* R/loocv.R, man/loocv.bca.Rd, man/loocv.discrimin.Rd: added
DeltaOij in loocv ouputs added DeltaOij in loocv ouputs
2021-05-18 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/bwca.dpcoa.Rd: Update the link to the soilmicrob dataset: it
is now a symbolic https link
2021-04-27 Jean <jean@thioulouse.fr>
* man/loocv.bca.Rd, man/loocv.discrimin.Rd: update loocv docs update to loocv.between and loocv.discrimin Rd doc files
2021-04-26 Jean <jean@thioulouse.fr>
* DESCRIPTION, NAMESPACE, R/loocv.R: remove progress + parallel
packages from Imports move progress + parallel packages from Imports to Suggests. Changes
to DESCRIPTION, NAMESPACE and loocv.R
2021-04-20 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/mbpcaiv.Rd, man/mbpls.Rd, man/multiblock.Rd,
man/randboot.multiblock.Rd, man/supdist.Rd,
man/testdim.multiblock.Rd: Update help files: \href becomes \doi for
doi references
2021-04-16 Jean <jean@thioulouse.fr>
* man/loocv.bca.Rd, man/loocv.discrimin.Rd: typos in loocv docs
2021-04-16 Jean <jean@thioulouse.fr>
* man/loocv.discrimin.Rd: Update loocv.discrimin.Rd
2021-04-16 Jean <jean@thioulouse.fr>
* man/loocv.discrimin.Rd: Update loocv.discrimin.Rd
2021-04-16 Jean <jean@thioulouse.fr>
* man/loocv.discrimin.Rd: Update loocv.discrimin.Rd
2021-04-16 Jean <jean@thioulouse.fr>
* man/loocv.discrimin.Rd: Update loocv.discrimin.Rd
2021-04-16 Jean <jean@thioulouse.fr>
* man/loocv.discrimin.Rd: Update loocv.discrimin.Rd
2021-04-16 Jean <jean@thioulouse.fr>
* man/loocv.discrimin.Rd: Update loocv.discrimin.Rd
2021-04-16 Jean <jean@thioulouse.fr>
* man/loocv.discrimin.Rd: Update loocv.discrimin.Rd
2021-04-16 Jean <jean@thioulouse.fr>
* man/loocv.bca.Rd, man/loocv.discrimin.Rd, man/loocv.dudi.Rd: typos
in loocv functions doc
2021-04-16 Jean <jean@thioulouse.fr>
* R/loocv.R: added overlap index in loocv.discrimin
2021-04-15 Jean <jean@thioulouse.fr>
* : commit 133407fe79f38836b762100049ab6418bf315013 Author: Jean
<jean@thioulouse.fr> Date: Thu Apr 15 15:28:22 2021 +0200
2021-03-24 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* R/mcoa.R: Update mcoa.R Problem in function summary.mcoa, sumry[, 6] object$cov2[i, ] should
be a 1 column df (or a vector)
2021-02-18 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .Rbuildignore, .travis.yml, README.md, appveyor.yml: Delete files
and code about travis and appveyor
2021-02-18 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .Rbuildignore, .github/.gitignore,
.github/workflows/R-CMD-check.yaml, README.md: Add a github workflow
to check the package
2021-01-07 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* R/fourthcorner.R, R/fourthcorner2.R, man/fourthcorner.Rd: Correct
a bug: add a stop message in functions fourthcorner and
fourthcorner2 when the R or Q matrix don't contain numeric values or
factors.
2020-11-02 Jean Thioulouse <jean@thioulouse.eu>
* man/loocv.dudi.Rd: added details
2020-10-30 Jean <jean@thioulouse.fr>
* man/loocv.bca.Rd, man/loocv.dudi.Rd: added links in loocv docs added links in loocv.bca.Rd and loocv.dudi.Rd
2020-10-29 Jean <jean@thioulouse.fr>
* man/loocv.dudi.Rd: Update loocv.dudi.Rd updated loocv.dudi.Rd (doc was based on a previous version of the
function)
2020-10-28 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* ChangeLog: ---------- release of ade4 1.7-16 ----------
2020-10-28 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION: ---------- release of ade4 1.7-16 ----------
2020-10-28 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/loocv.bca.Rd: Correct typo
2020-10-27 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/loocv.bca.Rd, man/loocv.discrimin.Rd, man/loocv.dudi.Rd,
man/pcw.Rd, man/varipart.Rd: Correct typos
2020-10-20 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION, man/arrival.Rd, man/casitas.Rd, man/kcponds.Rd,
man/mbpcaiv.Rd, man/mbpls.Rd, man/multiblock.Rd, man/pcw.Rd,
man/presid2002.Rd, man/randboot.multiblock.Rd,
man/testdim.multiblock.Rd: Update some URL in rd files
2020-10-19 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* man/loocv.discrimin.Rd: Update loocv.discrimin.Rd use generic loocv instead of loocv.discrimin in first exemple
(skulls)
2020-10-19 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* DESCRIPTION, NAMESPACE, R/loocv.R, man/loocv.bca.Rd,
man/loocv.discrimin.Rd, man/loocv.dudi.Rd: Add a new generic method
"loocv" These new functions allows to perform leave one-out cross-validation
for several simple dudi, between and discrimin classes
2020-09-28 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* R/suprow.R: Update a warning in 'suprow.dudi'
2020-06-24 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* inst/CITATION: Update the CITATION file
2020-06-18 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION: Remove date
2020-06-18 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/apis108.Rd: Update URL
2020-04-23 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* : commit 9991a008cd8276469ed5987dfebc7bab48241ac1 Author:
Stéphane Dray <stephane.dray@univ-lyon1.fr> Date: Thu Apr 23
17:21:53 2020 +0200
2020-02-13 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* ChangeLog: ---------- release of ade4 1.7-15 ----------
2020-02-13 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* DESCRIPTION: ---------- release of ade4 1.7-15 ----------
2020-02-10 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* DESCRIPTION, man/cailliez.Rd, man/kdisteuclid.Rd, man/oribatid.Rd:
Remove some broken URL
2020-02-03 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* DESCRIPTION: ---------- release of ade4 1.7-14 ----------
2020-02-03 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* DESCRIPTION: Packages sp and pixmap are now in 'Imports'as they
defined S4 classes used in some data sets. Mail by B. Ripley
2019-10-14 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* NAMESPACE, R/suprowpta.R, man/suprowpta.Rd: New function
'suprowpta'
2019-09-24 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/randtest.Rd: Trunk a line in a help file
2019-09-20 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* R/krandtest.R, man/krandtest.Rd, man/randtest.Rd: Udpate and
uniformize the help pages of 'krandtest' and 'randtest'
2019-09-19 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* NAMESPACE, R/krandtest.R, man/krandtest.Rd: Add [ and [[ methods
for krandtest
2019-08-07 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/dist.binary.R, R/dist.ktab.R, man/kdist.Rd: Correct a typo:
"Sockal" is now "Sokal" (Comment by P. Legendre)
2019-05-17 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/apis108.Rd, man/casitas.Rd, man/chevaine.Rd, man/hdpg.Rd:
Simplify the examples of the datasets 'apis108', 'casitas',
'chevaine' and 'hdpg' (no longer use deprecated genetic functions)
2019-05-17 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/s.kde2d.Rd: Update the example used with 's.kde2d'
2019-04-11 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* NAMESPACE, R/ade4-deprecated.R, R/dist.genet.R, R/fuzzygenet.R,
R/genet.R, man/ade4-deprecated.Rd, man/dist.genet.Rd,
man/fuzzygenet.Rd, man/genet.Rd: The functions 'dist.genet',
'fuzzygenet', 'char2genet', 'count2genet' and 'freq2genet' are
removed
2019-04-10 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* NAMESPACE, R/EH.R, R/ade4-deprecated.R, R/optimEH.R,
R/orisaved.R, R/randEH.R, man/EH.Rd, man/ade4-deprecated.Rd,
man/optimEH.Rd, man/orisaved.Rd, man/randEH.Rd: The functions 'EH',
'randEH', 'optimEH' and 'orisaved' are removed
2019-04-10 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* R/multispati.R, man/multispati.Rd: The 'print.multispati',
'plot.multispati' and 'summary.multispati' methods are now
deprecated
2018-10-18 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* R/dist.ktab.R: Correct a bug in 'dist.ktab', 'ldist.ktab' and
'kdist.cor'
2018-09-03 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/bacteria.Rd: Add url in the help page of 'bacteria' data
2018-08-30 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION: ---------- release of ade4 1.7-13 ----------
2018-08-30 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* inst/CITATION, man/bacteria.Rd: Correct invalid URL
2018-08-30 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* ChangeLog: ---------- release of ade4 1.7-12 ----------
2018-08-30 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION: ---------- release of ade4 1.7-12 ----------
2018-08-29 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* DESCRIPTION, inst/CITATION, man/ade4.package.Rd, man/mbpcaiv.Rd,
man/mbpls.Rd, man/multiblock.Rd, man/randboot.multiblock.Rd,
man/testdim.multiblock.Rd: Update citation and add reference to the
new JSS paper
2018-08-20 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/varipart.R: Clean the code
2018-08-06 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/varipart.R: Start a new and faster implementation to deal with
unweighted models
2018-08-03 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/varipart.R, man/varipart.Rd: The function 'varipart' now accepts
a matrix, vector or data.frame as response table
2018-08-03 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* NAMESPACE, R/varipart.R, man/varipart.Rd: Improve varipart to
compute adjusted fractions when no covaribales are considered and
add a new method 'print.varipart'
2018-08-03 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* man/dist.ktab.Rd: Correct a link to a function in the doc
2018-07-06 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/rlq.R: Correct a typo in the summary.rlq function (mail by
Manfred Jensen, 29/06/2018)
2018-06-22 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/maples.Rd: Correct a bibliographic reference
2018-06-20 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/dpcoa.R: correct a small bug in summary.dpcoa
2018-05-23 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* R/inertia.dudi.R: Update output names in inertia.dudi
2018-05-15 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/inertia.dudi.Rd: Update the help file of 'inertia.dudi'
2018-05-15 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/inertia.dudi.Rd: Update the help file of 'inertia.dudi'
2018-05-15 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* R/inertia.dudi.R: Update 'inertia.dudi' and 'summary.inertia'
2018-05-14 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/orthobasis.R: Correct the output for orthobasis that contains
only one column (and transformed to vector by default, i.e. when
drop = TRUE)
2018-04-25 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* R/foucart.R: issue raised by Didier Plat https://github.com/sdray/ade4/issues/13
2018-04-05 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* ChangeLog: ---------- release of ade4 1.7-11 ----------
2018-04-05 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION: ---------- release of ade4 1.7-11 ----------
2018-04-04 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* R/randtest.pcaiv.R: Error in dimnames() vs names() in formula fmla L. 14 : dimnames(df)[[2]] was replaced by names(df)[[2]], which is
not good. Replaced by names(df).
2018-03-29 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* R/coinertia.R: Misprint in print.coinertia
2018-03-16 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/dudi.mix.R: Correct the extracting in tab (now by drop = FALSE)
to deal with cases with only two levels (bug identified by Ceres
Barros on GitHub, issue 10)
2018-03-14 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* NAMESPACE, R/suprow.R, man/suprow.Rd: Add new method "suprow.fca"
(proposition by Martial Ferreol on Github)
2018-03-14 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/dudi.coa.R: Correct a bug to deal with large numbers in integer
matrix (bug found by Angela Fuentes Pardo, email 10/02/2018)
2018-01-16 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* .travis.yml: Remove last commit (was an error)
2018-01-16 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* .travis.yml: Add 'RANN' to allow building vignette
2018-01-03 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .travis.yml: Update .travis.yml Remove the '--run-dontrun' argument in the 'r_check_args' tag
2018-01-03 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .travis.yml: Update .travis.yml Remove the 'travis_wait' use
2018-01-03 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .travis.yml: Update .travis.yml Add a tag to extend the time the command has to finish.
2018-01-03 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .travis.yml: Update .travis.yml Add 'r_check_args' and 'r_packages' tags
2017-12-15 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* ChangeLog: ---------- release of ade4 1.7-10 ----------
2017-12-15 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION: ---------- release of ade4 1.7-10 ----------
2017-12-15 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION: Correct misprint in the title in the DESCRIPTION file
2017-12-15 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION: ---------- release of ade4 1.7-9 ----------
2017-12-06 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/mantel.randtest.R, R/mantel.rtest.R: Returned objects now belong
to subclass "mantelrtest" (to implement a 'msr.mantelrtest' in
adespatial).
2017-12-06 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/randtest.R, man/randtest.Rd: Add a new argument to function
as.randtest to specify subclasses for the returned object (by
default NULL)
2017-12-05 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* R/coinertia.R, R/dudi.R, R/dudi.pco.R, R/mbpcaiv.R, R/mbpls.R,
R/mcoa.R, R/statis.R, R/utilities.R: Add a message containing the
function called for the 'dudi' creation, after user selects nf
(Feature request by Zhian N. Kamvar, on Github, 2017-11-07)
2017-12-04 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* R/dudi.R: Add a message containing the complete call when users
interactively choose the number of axes in an analysis
2017-11-03 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* .travis.yml: Remove addons packages as 'rgdal' is no longer
required
2017-11-03 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* DESCRIPTION, man/area.plot.Rd, man/atya.Rd, man/avijons.Rd,
man/kcponds.Rd, man/mafragh.Rd, man/multispati.Rd,
man/multispati.randtest.Rd, man/multispati.rtest.Rd, man/neig.Rd,
man/tintoodiel.Rd: Remove dependencies to maptools and spData
(examples with columbus data set are removed)
2017-11-03 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* : commit 0d0c2004ce328889b7644f0f86bfc74bc6e552b5 Author:
Stéphane Dray <stephane.dray@univ-lyon1.fr> Date: Fri Nov 3
11:27:42 2017 +0100
2017-11-02 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* R/dist.genet.R, R/fuzzygenet.R, R/genet.R, man/dist.genet.Rd,
man/fuzzygenet.Rd, man/genet.Rd: The functions 'char2genet',
'count2genet', 'freq2genet', 'dist.genet' and 'fuzzygenet' are
deprecated and are now in the 'adegenet' package
2017-11-02 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* R/EH.R, R/ade4-deprecated.R, R/multispati.R, R/optimEH.R,
R/orisaved.R, R/randEH.R: Correct a misprint
2017-11-02 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/optimEH.Rd, man/orisaved.Rd, man/randEH.Rd: Correct typo in
the help files of the 'optimEH', 'orisaved' and 'randEH' deprecated
functions
2017-11-02 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* R/multispati.R, man/multispati.Rd: The 'multispati' function is
now deprecated
2017-11-01 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* DESCRIPTION, NAMESPACE, R/mbpcaiv.R, R/mbpls.R, R/s.kde2d.R,
man/score.coa.Rd: Add dagnelie.test package MASS in Imports and
update calls to MASS functions/Data
2017-11-01 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/dagnelie.test.R, man/dagnelie.test.Rd: Adds Dagnelie's test for
multivariate normality
2017-10-31 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION: Specify the required version for the spData package
2017-10-31 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/nipals.R: Correct a bug in the computation of biased sd from
unbiased estimator. Thanks to Kevin Wright that identified the
problem.
2017-10-30 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION, man/area.plot.Rd, man/neig.Rd: Correct import the
'columbus' data from the spData package that was moved from the
spdep package
2017-10-30 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* : Merge pull request #7 from zkamvar/patch-1 Reset par in kde2d
2017-10-30 Zhian N. Kamvar <zkamvar@gmail.com>
* R/s.kde2d.R: reset par in kde2d
2017-10-25 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/atya.Rd, man/avijons.Rd, man/buech.Rd, man/butterfly.Rd,
man/capitales.Rd, man/elec88.Rd, man/ggtortoises.Rd,
man/irishdata.Rd, man/julliot.Rd, man/jv73.Rd, man/kcponds.Rd,
man/mafragh.Rd, man/sarcelles.Rd, man/t3012.Rd, man/tintoodiel.Rd,
man/vegtf.Rd, man/zealand.Rd: Update help files for data
2017-10-19 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* R/EH.R, R/optimEH.R, R/orisaved.R, R/randEH.R, man/EH.Rd,
man/optimEH.Rd, man/orisaved.Rd, man/randEH.Rd: The 'EH', 'optimEH',
'orisaved' and 'randEH' functions are now deprecated
2017-10-19 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/ade4-deprecated.Rd: Update the 'ade4-deprecated' file: a
precision is added and the formatting is updated
2017-10-18 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/carni70.Rd, man/julliot.Rd, man/mjrochet.Rd, man/palm.Rd,
man/ungulates.Rd, man/variance.phylog.Rd: Update examples that call
the 'orthogram' function
2017-10-18 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/gridrowcol.Rd, man/mld.Rd, man/orthobasis.Rd: Update
cross-references for 'othogram'
2017-10-18 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/orthogram.Rd: Remove the help page of 'orthogram' because it
is deprecated
2017-10-18 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* R/ade4-deprecated.R, R/orthogram.R: The R code of the 'orthogram'
function is pasted in the 'ade4-deprecated.R' file and the
'orthogram.R' file is removed
2017-10-18 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* NAMESPACE: The 'orthogram' function is no longer exported because
it is deprecated
2017-10-18 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/bca.coinertia.Rd, man/wca.coinertia.Rd, man/withinpca.Rd:
Update cross-references for 'between' and 'within' functions
2017-10-18 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* R/ade4-deprecated.R, R/bca.R, R/bca.coinertia.R, R/wca.R,
R/wca.coinertia.R: Move the 'between', 'betweencoinertia', 'within'
and 'withincoinertia' R functions in the 'ade4-deprecated' file
2017-10-18 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* R/ade4-deprecated.R: Add an 'ade4-deprecated' file to store the R
code for deprecated functions
2017-10-18 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/ade4-deprecated.Rd: Update the 'ade4-deprecated' help file:
the 'between', 'betweencoinertia', 'within' and 'withincoinertia'
functions are added as deprecated
2017-10-18 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* R/bca.R, R/bca.coinertia.R, R/between.R, R/betweencoinertia.R,
R/wca.R, R/wca.coinertia.R, R/within.R, R/withincoinertia.R: Rename
R files for the 'bca', 'bca.coinertia', 'wca' and 'wca.coinertia'
functions
2017-10-18 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/bca.Rd, man/bca.coinertia.Rd, man/between.Rd,
man/betweencoinertia.Rd, man/wca.Rd, man/wca.coinertia.Rd,
man/within.Rd, man/withincoinertia.Rd: Rename help files for the
'bca', 'bca.coinertia', 'wca' and 'bca.coinertia' functions
2017-10-18 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/between.Rd, man/betweencoinertia.Rd, man/within.Rd,
man/withincoinertia.Rd: Update the help file because the 'between',
'betweencoinertia', 'within' and 'withincoinertia' are deprecated
2017-10-09 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* R/between.R, R/betweencoinertia.R, R/orthogram.R, R/within.R,
R/withincoinertia.R: Update the call to the '.Deprecated' function
2017-10-09 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/multiblock.R: Remove an unrequired space
2017-09-18 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* : commit 7b6de30d8740e9df053e0caa76d5c22cbd939dba Author: Aurélie
Siberchicot <aurelie.siberchicot@univ-lyon1.fr> Date: Mon Sep 18
15:03:04 2017 +0200
2017-08-21 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* : commit 5fc0e8ce3d26264fb2a7cf6b16672bcd236dd5d9 Author:
Stéphane Dray <stephane.dray@univ-lyon1.fr> Date: Mon Aug 21
14:02:01 2017 +0200
2017-08-09 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* ChangeLog: ---------- release of ade4 1.7-8 ----------
2017-08-09 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION: Correct misprints in the DESCRIPTION file
2017-08-09 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* ChangeLog: ---------- release of ade4 1.7-8 ----------
2017-08-09 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION: ---------- release of ade4 1.7-8 ----------
2017-08-09 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/divcmax.Rd: Update the example in 'divcmax' with correction
sent by Sandrine Pavoine
2017-08-09 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* DESCRIPTION: Extend the 'Description' field as requested by Uwe
Ligges
2017-07-20 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* ChangeLog: ---------- release of ade4 1.7-7 ----------
2017-07-20 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION: ---------- release of ade4 1.7-7 ----------
2017-07-19 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* NAMESPACE, R/varipart.R, man/varipart.Rd: Implement a very simple
version of variation partitioning (useful for msr method in
adespatial)
2017-07-11 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/randtest.pcaiv.R, R/randtest.pcaivortho.R: Solve a bug to deal
properly with 'strange' variables names (environmental variables in
mafragh)
2017-07-04 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/supdist.R: Add 'drop' argrument to deal with cases where only
one supplementary individual is considered.
2017-06-29 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/multiblock.R: The '...' argument is now passed to the
as.krandboot function
2017-06-29 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* man/statico.krandtest.Rd: species data must be in the second ktab
2017-06-29 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* R/statico.R: species data should not be restandardized in each
table
2017-06-23 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/atlas.Rd, man/elec88.Rd, man/irishdata.Rd: Update the help
files of 'atlas', 'elec88' and 'irishdata'
2017-06-23 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/mafragh.Rd: Update the mafragh data set: spenames is now a
data frame with short names and a new Spatial.contour object is
added.
2017-06-23 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* README.md: Update README.md
2017-06-23 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* README.md: Update README.md
2017-06-20 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* README.md: Update README.md
2017-06-20 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* README.md: Update README.md
2017-06-19 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/supdist.Rd: Clean the 'supdist' help file
2017-06-18 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* NAMESPACE: added function supdist to project additional items in a
PCO analysis
2017-06-18 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* man/supdist.Rd: Projection of additional items in a PCO analysis
2017-06-18 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* R/supdist.R: Projection of additional items in a PCO analysis
2017-06-15 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/mafragh.Rd: Correct the mafragh bibliography
2017-06-02 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/mafragh.Rd: Update the 'mafragh' data set
2017-05-12 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/krandtest.R, R/randtest.R: Update as.randtest/as.krandtest
functions to deal with cases with 0 repetitions (useful for
msr.4thcorner method implemented in adespatial)
2017-04-21 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* NAMESPACE, R/ade4toR.R, man/ade4toR.Rd: The 'ade4toR' and
'Rtoade4' unused functions are removed.
2017-04-21 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* NAMESPACE, R/cca.R, R/randtest.cca.R: The 'cca' function is
removed.
2017-04-21 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* NAMESPACE, R/cca.R, R/pcaiv.R, R/randtest.cca.R,
R/randtest.pcaiv.R, man/arrival.Rd, man/cca.Rd, man/pcaiv.Rd,
man/randtest.pcaiv.Rd, man/rpjdl.Rd: The 'cca' function is no longer
used.
2017-04-11 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/s.logo.Rd: Update the example of the 's.logo' function
2017-04-07 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/between.R: Correct a small bug to deal with weights in wca plots
2017-03-23 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* ChangeLog: ---------- release of ade4 1.7-6 ----------
2017-03-23 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION: ---------- release of ade4 1.7-6 ----------
2017-03-23 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* NAMESPACE: Fix an error with C routines in a Linux configuration
2017-03-22 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* NAMESPACE, src/init.c: Fix an error with C routines in a Windows
configuration (32bit)
2017-03-22 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/divcmax.Rd: Example in divcmax becomes 'dontrun', pending
correction
2017-03-20 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* NAMESPACE, src/init.c: Register native routines (new
recommendations in R-3.4.0)
2017-02-24 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/dist.ktab.R: Remove some useless checks
2017-02-16 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/casitas.Rd: Update an invalid URL
2017-02-14 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/dist.ktab.R: Revert commit
0894456972fea6668635069832ef6a7739c1f150 (bug was not fixed by the
previous corrections).
2017-02-14 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* NAMESPACE, R/RV.rtest.R, R/RVdist.randtest.R, R/betwitdpcoa.R,
R/combine.4thcorner.R, R/corkdist.R, R/costatis.R,
R/fourthcorner.R, R/fourthcorner.rlq.R, R/fourthcorner2.R,
R/gearymoran.R, R/krandtest.R, R/mantel.randtest.R,
R/mantel.rtest.R, R/multispati.randtest.R, R/multispati.rtest.R,
R/niche.R, R/orthogram.R, R/plot.4thcorner.R, R/procuste.R,
R/procuste.randtest.R, R/procuste.rtest.R, R/randtest.R,
R/randtest.amova.R, R/randtest.between.R, R/randtest.cca.R,
R/randtest.coinertia.R, R/randtest.discrimin.R, R/randtest.dpcoa.R,
R/randtest.pcaiv.R, R/randtest.pcaivortho.R, R/randtest.rlq.R,
R/rtest.R, R/rtest.between.R, R/rtest.discrimin.R, R/statico.R,
R/testdim.R, man/RV.rtest.Rd, man/RVdist.randtest.Rd,
man/combine.4thcorner.Rd, man/corkdist.Rd,
man/costatis.randtest.Rd, man/fourthcorner.Rd, man/krandtest.Rd,
man/mantel.randtest.Rd, man/mantel.rtest.Rd,
man/multispati.randtest.Rd, man/multispati.rtest.Rd,
man/orthogram.Rd, man/procuste.randtest.Rd, man/procuste.rtest.Rd,
man/randtest.Rd, man/rtest.Rd, man/statico.krandtest.Rd: Modify the
structures of classes (randtest and rtest) to store outputs of
randomization procedures
2017-02-10 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/dist.ktab.R: Correct a bug in the management of fuzzy data.
Message of Jean-Yves BARNAGAUD on adelist (08/02/2017).
2017-02-10 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/dist.ktab.R: Reindent lines
2017-02-01 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/divc.Rd, man/divcmax.Rd, man/lizards.Rd, man/newick.eg.Rd,
man/randboot.Rd, man/randxval.Rd: Correct some typo
2017-01-31 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/bwca.dpcoa.Rd, man/fourthcorner.Rd, man/mafragh.Rd,
man/phylog.Rd: Update bibliographic references (in press)
2017-01-23 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/bwca.dpcoa.Rd, man/julliot.Rd, man/mafragh.Rd,
man/multispati.Rd, man/nipals.Rd, man/olympic.Rd, man/pcw.Rd,
man/sarcelles.Rd: Solve errors in examples not runned
2017-01-18 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/area.plot.Rd, man/atya.Rd, man/avijons.Rd, man/julliot.Rd:
Correct the import of functions of the suggested packages used in
some examples.
2017-01-18 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/acacia.Rd, man/area.plot.Rd, man/avijons.Rd, man/between.Rd,
man/butterfly.Rd, man/capitales.Rd, man/cca.Rd, man/corvus.Rd,
man/doubs.Rd, man/dudi.fca.Rd, man/euro123.Rd, man/gearymoran.Rd,
man/ggtortoises.Rd, man/gridrowcol.Rd, man/julliot.Rd,
man/kcponds.Rd, man/lascaux.Rd, man/mafragh.Rd, man/meau.Rd,
man/multispati.Rd, man/nipals.Rd, man/olympic.Rd,
man/orthobasis.Rd, man/pcaivortho.Rd, man/pcw.Rd,
man/plot.between.Rd, man/plot.within.Rd, man/presid2002.Rd,
man/procuste.Rd, man/randEH.Rd, man/santacatalina.Rd,
man/scatter.coa.Rd, man/t3012.Rd, man/trichometeo.Rd,
man/westafrica.Rd, man/witwit.coa.Rd, man/zealand.Rd: Complete some
T/F in TRUE/FALSE
2017-01-18 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION, man/area.plot.Rd, man/atlas.Rd, man/atya.Rd,
man/avijons.Rd, man/buech.Rd, man/butterfly.Rd, man/capitales.Rd,
man/elec88.Rd, man/ggtortoises.Rd, man/irishdata.Rd,
man/julliot.Rd, man/jv73.Rd, man/kcponds.Rd, man/mafragh.Rd,
man/maples.Rd, man/mdpcoa.Rd, man/multispati.Rd,
man/multispati.randtest.Rd, man/multispati.rtest.Rd, man/neig.Rd,
man/nipals.Rd, man/olympic.Rd, man/oribatid.Rd, man/phylog.Rd,
man/rhizobium.Rd, man/s.image.Rd, man/s.kde2d.Rd, man/s.logo.Rd,
man/t3012.Rd, man/tintoodiel.Rd, man/vegtf.Rd, man/westafrica.Rd:
'quiet' parameter becomes 'quietly' in the 'requireNamespace'
function. Add 'adephylo' in the suggested packages. Correct the
import of functions of the suggested packages used in examples.
2017-01-13 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/between.R: use weights to properly darw ellipses when
non-uniform row weights are used.
2017-01-13 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/within.R: Correct a small bug in plot of wca. Use weights to
plot ellipses (this allow that ellipses are centred on 0 when coa is
used). Thanks to Sylvain Dolédec.
2017-01-12 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/chats.Rd: Correct typos in a help file
2016-12-20 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/rpjdl.Rd: Correct the species number in the help file of rpjdl
2016-12-13 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* ChangeLog: ---------- release of ade4 1.7-5 ----------
2016-12-13 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION: ---------- release of ade4 1.7-5 ----------
2016-12-13 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* README.md: Add badge
2016-11-28 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/PI2newick.Rd, man/ade4.package.Rd, man/adegraphicsLoaded.Rd,
man/aminoacyl.Rd, man/apqe.Rd, man/ardeche.Rd, man/as.taxo.Rd,
man/atlas.Rd, man/atya.Rd, man/avijons.Rd, man/aviurba.Rd,
man/banque.Rd, man/baran95.Rd, man/bca.rlq.Rd, man/between.Rd,
man/betweencoinertia.Rd, man/buech.Rd, man/bwca.dpcoa.Rd,
man/cailliez.Rd, man/carni70.Rd, man/carniherbi49.Rd,
man/casitas.Rd, man/cca.Rd, man/chatcat.Rd, man/chats.Rd,
man/clementines.Rd, man/coinertia.Rd, man/combine.4thcorner.Rd,
man/corkdist.Rd, man/costatis.Rd, man/costatis.randtest.Rd,
man/discrimin.Rd, man/discrimin.coa.Rd, man/dist.binary.Rd,
man/dist.dudi.Rd, man/dist.genet.Rd, man/dist.ktab.Rd,
man/dist.neig.Rd, man/dist.prop.Rd, man/dist.quant.Rd,
man/divcmax.Rd, man/dotchart.phylog.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.hillsmith.Rd, man/dudi.mix.Rd,
man/dudi.nsc.Rd, man/dudi.pca.Rd, man/dudi.pco.Rd, man/escopage.Rd,
man/euro123.Rd, man/foucart.Rd, man/fourthcorner.Rd, man/fruits.Rd,
man/gearymoran.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/krandtest.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/macroloire.Rd,
man/mantel.rtest.Rd, man/mariages.Rd, man/mbpcaiv.Rd, man/mbpls.Rd,
man/mcoa.Rd, man/mdpcoa.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/multiblock.Rd, man/multispati.randtest.Rd,
man/multispati.rtest.Rd, man/newick.eg.Rd, man/newick2phylog.Rd,
man/niche.Rd, man/nipals.Rd, man/njplot.Rd, man/originality.Rd,
man/orthobasis.Rd, man/orthogram.Rd, man/ours.Rd, man/palm.Rd,
man/pcaiv.Rd, man/pcaivortho.Rd, man/phylog.Rd,
man/plot.between.Rd, man/plot.phylog.Rd, man/plot.within.Rd,
man/procuste.Rd, man/procuste.rtest.Rd, man/pta.Rd,
man/quasieuclid.Rd, man/randboot.multiblock.Rd,
man/randtest.coinertia.Rd, man/randtest.pcaiv.Rd, man/reconst.Rd,
man/rhone.Rd, man/rlq.Rd, man/rpjdl.Rd, man/s.match.class.Rd,
man/sarcelles.Rd, man/scalewt.Rd, man/scatter.Rd,
man/scatter.fca.Rd, man/scatterutil.Rd, man/sco.class.Rd,
man/sco.gauss.Rd, man/sco.label.Rd, man/sco.match.Rd,
man/statico.Rd, man/statico.krandtest.Rd, man/steppe.Rd,
man/supcol.Rd, man/suprow.Rd, man/symbols.phylog.Rd,
man/syndicats.Rd, man/t3012.Rd, man/table.phylog.Rd,
man/tarentaise.Rd, man/testdim.Rd, man/testdim.multiblock.Rd,
man/trichometeo.Rd, man/ungulates.Rd, man/variance.phylog.Rd,
man/veuvage.Rd, man/wca.rlq.Rd, man/westafrica.Rd, man/within.Rd,
man/withincoinertia.Rd, man/withinpca.Rd, man/witwit.coa.Rd,
man/woangers.Rd, man/worksurv.Rd, src/adesub.c: Correct encoding of
Rd files
2016-11-25 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* man/gearymoran.Rd, man/mafragh.Rd, man/multispati.Rd,
man/multispati.randtest.Rd, man/multispati.rtest.Rd: Update and
clean 'mafragh' data
2016-11-21 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* : Merge pull request #4 from zkamvar/zkamvar-patch-1 Fix bug in randtest.amova
2016-11-20 Zhian N. Kamvar <kamvarz@science.oregonstate.edu>
* R/randtest.amova.R: fix bug in randtest.amova This bug came up in
https://groups.google.com/forum/#!topic/poppr/D1gpqgQM2F0 There is no issue when comparing three hierarchical levels, but when
there are four or more, the alternate hypothesis for every fourth
level is incorrect due to the recycling of c("less", "greater",
"greater").
2016-10-18 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/nipals.R: Correct a small bug identified by Denis Clot in the
rescaling of sd
2016-09-27 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/orthobasis.R: Correct a minor bug in the print method of
orthobasis objects
2016-09-12 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* README.md: Update homepage
2016-07-22 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* man/dist.ktab.Rd: Update the doc to indicate that ordered
variables are not yet considered.
2016-06-10 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* : commit 7a4a263d8ac2822ee89f1cf167e4e118c03b4023 Author:
Stéphane Dray <stephane.dray@univ-lyon1.fr> Date: Fri Jun 10
15:50:04 2016 +0200
2016-05-20 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .Rbuildignore, man/pcw.Rd: Update Rbuildignore
2016-05-13 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/scatterutil.R: Correct a bug when covariance is null (ellipses
were reversed)
2016-05-13 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/dudi.pco.R: Correct a bug in the scaling of normed components
with non-uniform weights
2016-05-02 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* NAMESPACE, R/inertia.dudi.R, man/inertia.dudi.Rd: The function
'inertia.dudi' now becomes a method. It returns object of class
'inertia' with 'print' and 'summary' methods
2016-03-21 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* man/elec88.Rd: Update the doc and add informations on nb, Spatial
and Spatialcontour
2016-03-04 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* NAMESPACE, R/suprow.R, man/suprow.Rd: New methods suprow.acm,
suprow.mix and predict.dudi
2016-03-04 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/dudi.hillsmith.R: Function dudi.hillsmith now returns vectors
center and norm (useful for the suprow.mix function)
2016-03-01 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* : DESCRIPTION: ---------- release of ade4 1.7-4 ----------
2016-02-24 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* : Merge pull request #3 from Rekyt/patch-1 Correct Reference with DOI
2016-02-22 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* .gitignore: Add a configure file to ignore some files in the Git
repository
2016-02-21 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* : commit 93fe29b91eb21adeb4f08e07b432b3b61d54e07a Author:
Stéphane Dray <stephane.dray@univ-lyon1.fr> Date: Sun Feb 21
14:33:14 2016 +0100
2016-01-22 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* R/mfa.R: print.mfa print mfa object class
2015-12-16 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* : commit e983689cedf4c297aae70ee4dcce8cecca1a6b54 Author:
Stéphane Dray <stephane.dray@univ-lyon1.fr> Date: Wed Dec 16
10:45:46 2015 +0100
2015-11-26 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* README.md: Add references to the binary packages
2015-11-24 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/dpcoa.R: Update the plot function to represent species (and
sites or their diversity according to RaoDecomp argument)
2015-11-24 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/dpcoa.R: Correct a small bug in the handling of species names
2015-11-24 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* : commit 4691e39258ac4c2f743d97f94cbc2b6d94d53ec1 Author:
Stéphane Dray <stephane.dray@univ-lyon1.fr> Date: Tue Nov 24
13:58:43 2015 +0100
2015-11-24 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/randtest.dpcoa.R, man/randtest.dpcoa.Rd: Add new function
randtest.dpcoa
2015-11-10 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* DESCRIPTION: Add BugReports field
2015-11-10 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* ChangeLog: ---------- release of ade4 1.7-3 ----------
2015-11-10 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* : commit 13ff73165e429972dbfaa2d44f8eaef4ca826324 Author:
Stéphane Dray <stephane.dray@univ-lyon1.fr> Date: Tue Nov 10
10:04:42 2015 +0100
2015-11-10 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* DESCRIPTION: ---------- release of ade4 1.7-3 ----------
2015-10-19 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* R/ktab.R: Change ktab.util.names to allow for ktabs with varying
numbers of rows (columns)
2015-10-14 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION: Suggest the 'CircStats' package which is used in Rd
cross-references
2015-09-21 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/randtest-internal.R, R/randtest.discrimin.R,
src/fourthcorner.c, src/tests.c: Remove some unused variables in C
code
2015-09-18 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* README.md: Add badges and informations for Mac and Windows users
2015-09-18 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* .travis.yml: Change setting for travis(error was produced due to
unchanged dates and version numbers)
2015-09-18 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* .Rbuildignore, appveyor.yml: Add windows check (via appveyor)
2015-09-18 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/mbpcaiv.R, R/mbpls.R, R/multiblock.R: Udate multiblock methods
to deal with non-centred data
2015-09-18 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* .Rbuildignore: Add README.md to .Rbuildignore
2015-09-15 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/scalewt.R, man/scalewt.Rd: Correct a bug to allow scaling
without centring
2015-09-09 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* : Reorder the levels of season (spring as first)
2015-09-09 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/randtest.rlq.R: Correct a bug to deal with a single trait and/or
environmental variable (email by C. ter Braak 28/08/2015)
2015-09-09 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* .Rbuildignore, .travis.yml, README.md: Add travis support and
README
2015-08-27 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* R/dudi.R: Use make.unique instead of make.names to produce
row.names for outputs. The second is devoted to names (e.g., by
avoiding integer which are authorized as row.names)
2015-08-26 Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>
* R/pta.R: Modify the levels names of supTI
2015-07-15 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* : Reorder the levels of the 'design' factor (use temporal instead
of alphabetic order)
2015-07-02 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION, NAMESPACE: The default packages other than 'base' are
now imported (new item for r-devel)
2015-06-12 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* R/dudi.fca.R, R/utilities.R: Modify the '$call' in 'dudi.fpca'
2015-06-08 Stéphane Dray <stephane.dray@univ-lyon1.fr>
* NAMESPACE, R/cca.R, man/cca.Rd: New summary method for 'cca'
objects
2015-06-01 Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
* DESCRIPTION, man/add.scatter.Rd: Update an exemple which uses the
new function 'plotEig' of 'adegraphics'
2015-04-14 07:38 aursiber
* DESCRIPTION: ---------- release of ade4 1.7-2 ----------
2015-04-08 13:27 aursiber
* DESCRIPTION: ---------- release of ade4 1.7-1 ----------
2015-04-08 09:25 sdray
* DESCRIPTION, NAMESPACE, R/orthobasis.R, man/orthobasis.Rd: Add
new functions to handle orthobasis objects. The orthobasis.listw
function is removed and will be available in the forthcoming
adespatial
2015-04-03 16:28 aursiber
* man/kplot.sepan.Rd: The 'kplot.sepan.coa' function becomes
'kplotsepan.coa' in 'adegraphics' also
2015-04-03 14:30 aursiber
* NAMESPACE, R/kplot.sepan.R, man/kplot.sepan.Rd: The
'kplot.sepan.coa' function becomes 'kplotsepan.coa'
2015-04-03 14:04 aursiber
* DESCRIPTION, man/abouheif.eg.Rd, man/avijons.Rd, man/baran95.Rd,
man/bsetal97.Rd, man/capitales.Rd, man/chevaine.Rd,
man/cnc2003.Rd, man/doubs.Rd, man/ecomor.Rd, man/euro123.Rd,
man/ggtortoises.Rd, man/hdpg.Rd, man/jv73.Rd, man/lascaux.Rd,
man/lizards.Rd, man/mafragh.Rd, man/maples.Rd, man/microsatt.Rd,
man/mjrochet.Rd, man/newick.eg.Rd, man/oribatid.Rd, man/pap.Rd,
man/presid2002.Rd, man/procella.Rd, man/rpjdl.Rd,
man/tarentaise.Rd, man/trichometeo.Rd: Remove invalid url in man
files
2015-03-29 11:59 sdray
* R/combine.4thcorner.R, R/plot.4thcorner.R: Update the outputs of
the combine.4thcorner functions to avoid bugs when the 'D' stat
can not be computed (factor with only one level)
2015-03-23 15:40 aursiber
* DESCRIPTION: ---------- release of ade4 1.7-0 ----------
2015-03-23 10:52 sdray
* DESCRIPTION: Aurelie is the new official maintainer
2015-03-23 08:45 sdray
* R/coinertia.R, R/rlq.R: Improve the outputs of the RLQ/coinertia
analysis
2015-03-20 09:13 aursiber
* DESCRIPTION, R/mbpcaiv.R, R/mbpls.R, R/multispati.R,
R/orthobasis.R, R/s.image.R, R/s.kde2d.R, R/s.logo.R,
man/area.plot.Rd, man/atlas.Rd, man/atya.Rd, man/avijons.Rd,
man/buech.Rd, man/butterfly.Rd, man/capitales.Rd, man/ecg.Rd,
man/elec88.Rd, man/ggtortoises.Rd, man/irishdata.Rd,
man/julliot.Rd, man/jv73.Rd, man/kcponds.Rd, man/mafragh.Rd,
man/maples.Rd, man/mdpcoa.Rd, man/multispati.Rd,
man/multispati.randtest.Rd, man/multispati.rtest.Rd, man/neig.Rd,
man/nipals.Rd, man/olympic.Rd, man/oribatid.Rd, man/pcw.Rd,
man/phylog.Rd, man/rhizobium.Rd, man/s.image.Rd, man/s.kde2d.Rd,
man/s.logo.Rd, man/sarcelles.Rd, man/score.coa.Rd, man/t3012.Rd,
man/tintoodiel.Rd, man/vegtf.Rd, man/westafrica.Rd: Update the
use of packages listed in 'Suggests' according with R-3.1.3
2015-03-18 14:07 sdray
* R/between.R: Correct a bug in 1D plot of plot.between (message of
Matthieu Salpeteur 18/03/2015 on adelist)
2015-02-19 19:03 sdray
* R/dist.dudi.R: Correct a bug to deal with null distances (message
of Robin Cura on adelist 16/02/2015
2015-02-18 15:03 sdray
* R/krandboot.R, R/krandxval.R, R/mbpcaiv.R, R/mbpls.R,
R/multiblock.R, R/randxval.R, man/mbpcaiv.Rd, man/mbpls.Rd,
man/multiblock.Rd, man/randboot.multiblock.Rd,
man/testdim.multiblock.Rd: Update some functions related to
multiblock methods. Use 'ginv' to deal with matrices are not of
full rank.
2015-01-15 11:50 sdray
* NAMESPACE, R/betwitdpcoa.R, man/bwca.dpcoa.Rd: Add new functions
to perform between- within dpcoa (Dray et al. 2015, MER)
2015-01-09 12:35 sdray
* src/adesub.c: remove the unused variable 'seed'
2015-01-08 16:47 aursiber
* man/add.scatter.Rd, man/area.plot.Rd, man/atlas.Rd,
man/capitales.Rd, man/chats.Rd, man/corvus.Rd, man/divcmax.Rd,
man/gridrowcol.Rd, man/irishdata.Rd, man/mstree.Rd,
man/orthobasis.Rd, man/pcw.Rd, man/randxval.Rd, man/rtest.Rd,
man/s.class.Rd, man/s.corcircle.Rd, man/s.distri.Rd,
man/s.image.Rd, man/s.label.Rd, man/s.logo.Rd, man/s.match.Rd,
man/s.traject.Rd, man/s.value.Rd, man/santacatalina.Rd,
man/scatterutil.Rd, man/score.Rd, man/table.value.Rd,
man/toxicity.Rd, man/triangle.class.Rd, man/westafrica.Rd,
man/worksurv.Rd: Modify examples due to modifications in
adegraphics
2015-01-08 16:36 sdray
* src/adesub.c, src/adesub.h: Remove calls to C random number
generators (now use R RNG)
2015-01-08 13:59 thioulouse
* NAMESPACE, R/costatis.R, R/ktab.R, R/pta.R, R/statico.R,
man/costatis.Rd, man/costatis.randtest.Rd, man/statico.Rd,
man/statico.krandtest.Rd: Added statico.krandtest and
costatis.randtest funtions for permutation tests
2014-12-08 14:33 sdray
* R/fourthcorner.R, R/fourthcorner.rlq.R, R/print.4thcorner.R:
Correct a bug to display properly the outputs in the case of 1
trait x 1 env variable
2014-11-28 09:38 aursiber
* man/scatter.coa.Rd: Correct the documentation of the used method
in 'scatter.coa'
2014-11-14 08:42 sdray
* R/mdpcoa.R: correct the call to dist.dna of the ape package
2014-11-14 08:41 sdray
* NAMESPACE, R/dpcoa.R, R/mdpcoa.R, man/dpcoa.Rd, man/humDNAm.Rd:
Update the dpcoa function: names of outputs are modified and the
df argument shoul be a site-by-species nor a species-by-sites
matrix. This allows to be more coherent with other methods
2014-11-05 15:32 sdray
* man/atlas.Rd, man/butterfly.Rd, man/chats.Rd, man/dpcoa.Rd,
man/gearymoran.Rd, man/gridrowcol.Rd, man/orthobasis.Rd: Modify
examples due to modifications in adegraphics
2014-10-30 15:04 sdray
* data/capitales.rda, man/capitales.Rd: Transform the Spatial
component from SpatialPolygonsDataFrame to SpatialPolygons
2014-09-11 14:50 sdray
* NAMESPACE, R/procuste.R, man/macaca.Rd, man/procuste.Rd: Change
names of arguments and outputs of 'procuste' function and add a
method 'randtest' for procuste class
2014-09-02 12:04 sdray
* data/pcw.rda, man/pcw.Rd: Add new dataset (distribution of trees
in forest plots along the panama canal)
2014-07-23 14:09 sdray
* R/fourthcorner.rlq.R: Correct a small bug (used names instead of
colnames on a matrix)
2014-06-18 15:26 aursiber
* DESCRIPTION, NAMESPACE, man/acacia.Rd, man/add.scatter.Rd,
man/aravo.Rd, man/ardeche.Rd, man/area.plot.Rd, man/atlas.Rd,
man/atya.Rd, man/avijons.Rd, man/avimedi.Rd, man/bacteria.Rd,
man/banque.Rd, man/baran95.Rd, man/between.Rd,
man/betweencoinertia.Rd, man/bf88.Rd, man/buech.Rd,
man/butterfly.Rd, man/capitales.Rd, man/carni70.Rd, man/cca.Rd,
man/chats.Rd, man/chazeb.Rd, man/chevaine.Rd, man/clementines.Rd,
man/coinertia.Rd, man/coleo.Rd, man/corkdist.Rd, man/corvus.Rd,
man/deug.Rd, man/discrimin.Rd, man/dist.prop.Rd,
man/dist.quant.Rd, man/doubs.Rd, man/dpcoa.Rd, man/dudi.acm.Rd,
man/dudi.coa.Rd, man/dudi.fca.Rd, man/dudi.hillsmith.Rd,
man/dudi.mix.Rd, man/dudi.nsc.Rd, man/dudi.pca.Rd, man/ecomor.Rd,
man/elec88.Rd, man/euro123.Rd, man/foucart.Rd, man/friday87.Rd,
man/fruits.Rd, man/gearymoran.Rd, man/ggtortoises.Rd,
man/granulo.Rd, man/gridrowcol.Rd, man/hdpg.Rd,
man/housetasks.Rd, man/humDNAm.Rd, man/irishdata.Rd,
man/julliot.Rd, man/jv73.Rd, man/kcponds.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.list.df.Rd,
man/ktab.list.dudi.Rd, man/lascaux.Rd, man/macaca.Rd,
man/macroloire.Rd, man/mafragh.Rd, man/mariages.Rd, man/meau.Rd,
man/meaudret.Rd, man/microsatt.Rd, man/mollusc.Rd, man/mstree.Rd,
man/multiblock.Rd, man/multispati.Rd, man/neig.Rd, man/niche.Rd,
man/nipals.Rd, man/olympic.Rd, man/oribatid.Rd,
man/orthobasis.Rd, man/ours.Rd, man/pcaivortho.Rd,
man/plot.between.Rd, man/plot.within.Rd, man/presid2002.Rd,
man/procuste.Rd, man/pta.Rd, man/rankrock.Rd, man/rpjdl.Rd,
man/s.chull.Rd, man/s.image.Rd, man/s.kde2d.Rd,
man/s.match.class.Rd, man/santacatalina.Rd, man/sarcelles.Rd,
man/scatter.acm.Rd, man/scatter.coa.Rd, man/scatter.dudi.Rd,
man/scatter.fca.Rd, man/sco.distri.Rd, man/score.acm.Rd,
man/score.pca.Rd, man/seconde.Rd, man/skulls.Rd, man/statis.Rd,
man/supcol.Rd, man/suprow.Rd, man/t3012.Rd, man/table.paint.Rd,
man/tintoodiel.Rd, man/tortues.Rd, man/toxicity.Rd,
man/triangle.plot.Rd, man/trichometeo.Rd, man/vegtf.Rd,
man/wca.rlq.Rd, man/westafrica.Rd, man/within.Rd,
man/withincoinertia.Rd, man/withinpca.Rd, man/witwit.coa.Rd,
man/worksurv.Rd, man/zealand.Rd: Update the examples to become
effective when 'adegraphics' is loaded
2014-05-20 13:30 sdray
* R/add.scatter.R, man/EH.Rd, man/PI2newick.Rd, man/add.scatter.Rd,
man/aminoacyl.Rd, man/amova.Rd, man/as.taxo.Rd, man/bacteria.Rd,
man/between.Rd, man/betweencoinertia.Rd, man/cailliez.Rd,
man/cca.Rd, man/coinertia.Rd, man/corkdist.Rd, man/disc.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/divc.Rd, man/divcmax.Rd,
man/dotchart.phylog.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.hillsmith.Rd, man/dudi.mix.Rd,
man/dudi.nsc.Rd, man/dudi.pca.Rd, man/dudi.pco.Rd,
man/foucart.Rd, man/gearymoran.Rd, man/gridrowcol.Rd,
man/inertia.dudi.Rd, man/is.euclid.Rd, man/kdist.Rd,
man/kdist2ktab.Rd, man/kdisteuclid.Rd, man/krandtest.Rd,
man/ktab.Rd, man/ktab.data.frame.Rd, man/ktab.list.df.Rd,
man/ktab.list.dudi.Rd, man/ktab.within.Rd, man/lingoes.Rd,
man/mantel.randtest.Rd, man/mantel.rtest.Rd, man/mcoa.Rd,
man/mfa.Rd, man/mld.Rd, man/multispati.Rd,
man/multispati.randtest.Rd, man/multispati.rtest.Rd,
man/newick.eg.Rd, man/newick2phylog.Rd, man/niche.Rd,
man/nipals.Rd, man/njplot.Rd, man/optimEH.Rd, man/originality.Rd,
man/orisaved.Rd, man/orthobasis.Rd, man/orthogram.Rd,
man/palm.Rd, man/pcaiv.Rd, man/pcaivortho.Rd, man/phylog.Rd,
man/plot.between.Rd, man/plot.phylog.Rd, man/plot.within.Rd,
man/procuste.Rd, man/procuste.randtest.Rd, man/procuste.rtest.Rd,
man/pta.Rd, man/quasieuclid.Rd, man/randEH.Rd,
man/randtest.amova.Rd, man/randtest.between.Rd,
man/randtest.coinertia.Rd, man/randtest.discrimin.Rd,
man/randtest.pcaiv.Rd, man/reconst.Rd, man/rlq.Rd, man/s.logo.Rd,
man/s.match.class.Rd, man/scatterutil.Rd, man/sco.class.Rd,
man/sco.gauss.Rd, man/sco.label.Rd, man/sco.match.Rd,
man/supcol.Rd, man/suprow.Rd, man/symbols.phylog.Rd,
man/table.phylog.Rd, man/testdim.Rd, man/variance.phylog.Rd,
man/westafrica.Rd, man/within.Rd, man/withincoinertia.Rd,
man/withinpca.Rd, man/witwit.coa.Rd: Update email addresses
2014-05-16 15:38 sdray
* NAMESPACE, R/between.R, R/within.R, man/plot.between.Rd,
man/plot.within.Rd: New summary method for within and between
classes
2014-05-16 15:19 sdray
* R/randtest.between.R: Clean the code
2014-04-18 15:50 aursiber
* R/scatterutil.R, man/area.plot.Rd, man/carni70.Rd,
man/divcmax.Rd, man/dudi.acm.Rd, man/ecomor.Rd, man/julliot.Rd,
man/microsatt.Rd, man/newick2phylog.Rd, man/orthogram.Rd,
man/presid2002.Rd, man/score.Rd: Correct the examples which are
not run
2014-04-17 15:44 sdray
* NAMESPACE, R/krandboot.R, R/krandxval.R, R/mbpcaiv.R, R/mbpls.R,
R/multiblock.R, R/randboot.R, R/randxval.R, man/mbpcaiv.Rd,
man/mbpls.Rd, man/multiblock.Rd, man/randboot.Rd,
man/randboot.multiblock.Rd, man/randxval.Rd,
man/testdim.multiblock.Rd: Add new functions for multiblock
analysis (coll. with S. Bougeard): multiblock pcaiv and
multiblock pls. Add new functions and classes to manage results
of two-fold cross-validation and bootstrap
2014-04-17 15:39 sdray
* data/chickenk.rda, man/chickenk.Rd: New data set chickenk
2014-04-17 15:24 sdray
* R/testdim.R, man/testdim.Rd: Change argument name for testdim
method
2014-04-17 15:22 sdray
* NAMESPACE, man/bacteria.Rd, man/dudi.acm.Rd,
man/dudi.hillsmith.Rd, man/dudi.mix.Rd, man/santacatalina.Rd,
man/scatter.coa.Rd: Unexport methods for generic functions
scatter and score
2014-04-17 15:19 sdray
* NAMESPACE, man/adegraphicsLoaded.Rd: Export the function
adegraphicsLoaded
2014-04-17 08:19 sdray
* R/utilities.R: New function 'adegraphicsLoaded' to test if
adegraphics is loaded
2014-04-15 08:41 sdray
* NAMESPACE, R/dudi.R, R/ktab.R, man/dudi.Rd, man/ktab.Rd: Improve
'[.ktab' and add '[.dudi': extraction methods allow to select
rows and/or columns of dudi and ktab objects
2014-04-15 07:44 sdray
* ., NAMESPACE, R/ktab.R, R/ktab.data.frame.R, R/ktab.list.df.R,
R/ktab.list.dudi.R, R/ktab.match2ktabs.R, R/ktab.within.R,
man/ktab.Rd: Clean the building of TL, TC, T4 (they contain names
and not numbers) and remove two bugs (building of TC and in
[.ktab)
2014-04-11 07:45 sdray
* R/fourthcorner.rlq.R: Correct a typo
2014-03-13 17:36 sdray
* R/randtest.rlq.R, src/fourthcorner.c, src/tests.c: Correct some
minor bugs and typos
2014-01-14 15:27 thioulouse
* R/foucart.R, R/kplot.foucart.R, R/kplot.mcoa.R, R/kplot.mfa.R,
R/kplot.pta.R, R/kplot.sepan.R, R/kplot.statis.R, R/ktab.R,
R/ktab.data.frame.R, R/ktab.list.df.R, R/ktab.list.dudi.R,
R/ktab.match2ktabs.R, R/ktab.within.R, R/mcoa.R, R/mdpcoa.R,
R/mfa.R, R/pta.R, R/sepan.R, R/statis.R: Global update of TL TC
and T4 ktab elements
2014-01-07 15:16 thioulouse
* R/ktab.R, R/pta.R: row names correction of supIX and supIY in a
kcoinertia pta
2013-12-03 13:22 sdray
* data/mafragh.rda: Modify the order of the sites in the
'SpatialPoints' object to be coherent with the 'nb' object
2013-11-19 15:58 sdray
* DESCRIPTION: ---------- release of ade4 1.6-2 ----------
2013-11-19 15:56 sdray
* NAMESPACE: Re-export some internal/utility functions that are
used by other packages
2013-11-19 15:55 sdray
* TITLE: Remove the TITLE file which is no more used
2013-11-15 22:41 sdray
* DESCRIPTION: ---------- release of ade4 1.6-1 ----------
2013-11-15 22:43 sdray
* man/add.scatter.Rd, man/capitales.Rd, man/dist.ktab.Rd,
man/dotchart.phylog.Rd, man/fourthcorner.Rd, man/nipals.Rd,
man/s.match.class.Rd, man/scatter.Rd: Reduce line widths
2013-11-14 12:47 sdray
* DESCRIPTION: ---------- release of ade4 1.6-0 ----------
2013-10-30 12:23 sdray
* NAMESPACE, man/acacia.Rd, man/add.scatter.Rd, man/ade4toR.Rd,
man/as.taxo.Rd, man/avimedi.Rd, man/baran95.Rd,
man/combine.4thcorner.Rd, man/costatis.Rd, man/fourthcorner.Rd,
man/granulo.Rd, man/kplot.pta.Rd, man/kplot.sepan.Rd,
man/kplot.statis.Rd, man/ktab.match2ktabs.Rd, man/ktab.within.Rd,
man/meau.Rd, man/meaudret.Rd, man/pcaivortho.Rd, man/phylog.Rd,
man/plot.phylog.Rd, man/randtest.amova.Rd, man/reconst.Rd,
man/rhone.Rd, man/rlq.Rd, man/rtest.between.Rd,
man/scatterutil.Rd, man/statico.Rd, man/statis.Rd, man/supcol.Rd,
man/suprow.Rd, man/taxo.eg.Rd, man/ungulates.Rd: The NAMESPACE
file (which exported all functions) has be completely rewritten.
Utilities and deprecated functions are not exported. S3 methods
are declared. Several help pages have been modified to manage
these changes.
2013-10-30 12:20 sdray
* R/rtest.between.R: Now the rtest.between can handle objects
created with between and bca functions
2013-10-30 12:19 sdray
* R/supcol.R, R/suprow.R: suprow.default and supcol.default become
suprow.dudi and supcol.dudi
2013-10-28 13:55 sdray
* R/statis.R: Improve the speed of statis function. Thanks to
Benoit Thieurmel (email sent 11/01/2013)
2013-10-28 12:53 sdray
* R/mcoa.R: Correct a bug in the scaling of Tl1. Thanks to P. Bady,
adelist 3/10/2013
2013-10-03 11:26 sdray
* R/ktab.within.R: Correct a bug in ktab.within: column names were
not handle correctly in some cases (Thanks to Pierre Bady,
message on adelist 3/10/2013). Moreover, the order of bloc is
given by levels and nor unique
2013-09-19 15:58 sdray
* data/atlas.rda, data/atya.rda, data/avijons.rda, data/buech.rda,
data/butterfly.rda, data/capitales.rda, data/elec88.rda,
data/ggtortoises.rda, data/irishdata.rda, data/julliot.rda,
data/jv73.rda, data/kcponds.rda, data/mafragh.rda,
data/sarcelles.rda, data/t3012.rda, data/tintoodiel.rda,
data/vegtf.rda, data/zealand.rda, man/cailliez.Rd,
man/capitales.Rd, man/lingoes.Rd, man/s.logo.Rd: Correct a small
bug in data files and update the help files to pass R CMD check
2013-09-19 11:39 sdray
* data/atlas.rda, data/atya.rda, data/avijons.rda, data/buech.rda,
data/butterfly.rda, data/capitales.rda, data/elec88.rda,
data/ggtortoises.rda, data/irishdata.rda, data/julliot.rda,
data/jv73.rda, data/kcponds.rda, data/mafragh.rda,
data/sarcelles.rda, data/t3012.rda, data/tintoodiel.rda,
data/vegtf.rda, data/zealand.rda: Add Spatial/nb objects in data
files to prepare the future deprecation of area/neig/contour
objects. Moreover, spatial information in data sets 't3012',
'elec88' and 'capitales' has been updated (coordinate system,
city names, etc).
2013-09-17 15:08 sdray
* R/scalewt.R: Correct a small bug in scalewt
2013-07-23 22:24 sdray
* R/plot.4thcorner.R, man/fourthcorner.Rd: Add colors in
fourthcorner plots
2013-05-28 08:10 sdray
* R/scalewt.R: correct a small bug in scalewt when scale = FALSE
2013-05-07 21:45 sdray
* R/combine.4thcorner.R, R/fourthcorner.R, R/fourthcorner.rlq.R,
R/fourthcorner2.R, R/p.adjust.4thcorner.R, R/plot.4thcorner.R,
R/print.4thcorner.R, R/summary.4thcorner.R, R/table.value.R,
man/combine.4thcorner.Rd, man/fourthcorner.Rd, man/rlq.Rd,
src/fourthcorner.c: Complete reimplementation of the outputs of
fourthcorner functions. Now they return krandtest/randtest
objects and adjustments for multiple tests can be used.
Experimental fourthcorner.rlq
2013-05-07 19:51 sdray
* data/aravo.rda, man/aravo.Rd: New dataset: aravo
2013-05-03 16:01 sdray
* R/scatterutil.R: New argument 'bg' for scatterutil.base function
2013-04-30 21:07 sdray
* R/randtest-internal.R, R/randtest.coinertia.R, R/randtest.rlq.R,
R/rlq.R, man/rlq.Rd, src/adesub.c, src/adesub.h, src/testrlq.c,
src/tests.c: Use the new 'dudi.type' function. New 'modeltype'
argument for randtest.rlq. New function 'combine.randtest.rlq'.
2013-04-29 15:55 sdray
* R/krandtest.R, man/krandtest.Rd: Update the doc of krandtest
2013-04-29 15:29 sdray
* R/dudi.acm.R: Use the new fac2disj utility function
2013-04-29 15:28 sdray
* R/dudi.acm.R, R/dudi.hillsmith.R, R/dudi.mix.R, R/fourthcorner.R,
R/fourthcorner2.R, R/rlq.R, R/s.class.R, R/s.match.class.R,
R/triangle.class.R, man/ade4-internal.Rd: Use the new fac2disj
utility function
2013-04-29 13:14 sdray
* R/krandtest.R: krandtest can now handle adjustments for multiple
testing
2013-04-26 15:31 sdray
* R/coinertia.R: Correct a small bug in the choice of the number of
kept axes
2013-04-26 15:26 sdray
* R/dudi.acm.R, R/utilities.R, man/ade4-internal.Rd,
man/randtest-internal.Rd: New utilities functions
2013-04-26 15:03 sdray
* R/scalewt.R, man/scalewt.Rd: New functions to compute weighted
mean/var/cov for the levels of a factor
2013-04-26 11:38 sdray
* R/dpcoa.R: dpcoa now returns
2013-04-05 12:31 sdray
* DESCRIPTION: ---------- release of ade4 1.5-2 ----------
2013-01-09 14:42 sdray
* R/procuste.R, man/procuste.Rd: value 'nfact' is renamed 'nf'
2012-10-18 10:27 thioulouse
* man/coinertia.Rd: Small typo fix
2012-10-18 10:26 thioulouse
* R/betweencoinertia.R: Fixed a bug introduced in print.betcoi
function
2012-10-17 16:29 sdray
* src/tests.c: Correct a small bug in loops for the acm case
2012-10-17 15:49 sdray
* 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)
2012-10-17 15:47 sdray
* R/rlq.R: Correct the number of repetitions in randtest.rlq (was
nrepet+1 instead of nrepet)
2012-10-16 13:32 thioulouse
* R/betweencoinertia.R, R/coinertia.R, man/coinertia.Rd: Edited
print functions for coinertia and betweencoinertia analyses
2012-10-16 13:30 thioulouse
* R/scatter.fca.R: Bug correction in the call to s.distri: needed
to be pass the xax and yax params
2012-09-21 16:02 sdray
* R/sco.gauss.R: Correct a bug: dnorm has 'sd' as arguments and not
'var' (Thanks to Alice Julien-Laferriere)
2012-09-14 11:21 sdray
* DESCRIPTION: ---------- release of ade4 1.5-1 ----------
2012-09-14 11:19 sdray
* R/randtest.cca.R, R/randtest.pcaiv.R, R/randtest.pcaivortho.R:
Calls to Fortran routine 'dqrls' are replaced by public 'lm.wfit'
2012-07-27 14:49 sdray
* 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
2012-07-25 13:30 sdray
* R/coinertia.R: Update the summary.coinertia function that now
returns invisible results
2012-07-25 13:28 sdray
* R/dudi.R: To avoid confusion, the term 'Explained' is replaced by
'Projected' in the summary.dudi function
2012-07-25 12:47 sdray
* R/pcaiv.R, R/pcaivortho.R, man/pcaiv.Rd, man/pcaivortho.Rd: New
functions 'summary.pcaiv' and 'summary.pcaivortho'
2012-07-25 12:46 sdray
* R/dudi.R, man/dudi.Rd: New function 'summary.dudi'
2012-07-25 10:53 sdray
* R/variance.phylog.R, man/variance.phylog.Rd: Returned is now an
'anova' object (was 'table')
2012-07-25 09:23 sdray
* 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)
2012-07-10 12:03 thioulouse
* R/coinertia.R: Fix the problem of complex eigenvalues sometimes
returned by eigen in the case n < (p, q)
2012-06-01 07:23 jombart
* R/orthogram.R, man/ade4-deprecated.Rd, man/orthogram.Rd:
Orthogram function is now deprecated.
2012-04-23 12:29 sdray
* src/testdim.c: Correct a small bug (void function cannot return
values)
2012-04-23 07:59 sdray
* man/neig.Rd: Modify an example due to a change in the deldir
package
2012-04-19 11:11 sdray
* DESCRIPTION: ---------- release of ade4 1.5-0 ----------
2012-04-17 15:23 sdray
* R/bca.rlq.R, R/wca.rlq.R, data/piosphere.rda, man/bca.rlq.Rd,
man/piosphere.Rd, man/wca.rlq.Rd: Add functions/data for partial
RLQ analysis proposed by Wesuls et al (2012)
2012-04-16 13:06 sdray
* R/ade4toR.R, R/amova.R, R/area.plot.R, R/between.R,
R/betweencoinertia.R, R/cailliez.R, R/coinertia.R, R/corkdist.R,
R/costatis.R, R/discrimin.R, R/dist.quant.R, R/dotcircle.R,
R/dpcoa.R, R/dudi.acm.R, R/dudi.hillsmith.R, R/dudi.pco.R,
R/foucart.R, R/gearymoran.R, R/is.euclid.R, R/kdisteuclid.R,
R/kplot.foucart.R, R/kplot.mcoa.R, R/kplot.mfa.R, R/kplot.pta.R,
R/kplot.sepan.R, R/kplot.statis.R, R/lingoes.R, R/mcoa.R,
R/mdpcoa.R, R/mfa.R, R/multispati.R, R/neig.R, R/newick2phylog.R,
R/niche.R, R/nipals.R, R/orthobasis.R, R/orthogram.R, R/pcaiv.R,
R/pcaivortho.R, R/plot.phylog.R, R/procuste.R, R/pta.R,
R/quasieuclid.R, R/rlq.R, R/s.arrow.R, R/s.corcircle.R,
R/s.hist.R, R/s.kde2d.R, R/s.match.R, R/s.multinom.R,
R/s.traject.R, R/s.value.R, R/scatter.acm.R, R/scatter.coa.R,
R/scatter.dudi.R, R/scatter.fca.R, R/scatterutil.R,
R/sco.quant.R, R/score.acm.R, R/score.mix.R, R/sepan.R,
R/statis.R, R/symbols.phylog.R, R/table.cont.R, R/table.dist.R,
R/table.paint.R, R/table.phylog.R, R/table.value.R,
R/triangle.plot.R, R/within.R, R/withincoinertia.R, R/witwit.R,
R/witwitsepan.R: Use full argument names to avoid partial
matching
2012-04-07 21:29 sdray
* DESCRIPTION: ---------- release of ade4 1.4-18 ----------
2012-04-07 21:16 sdray
* R/testdim.R, src/testdim.c: Modify testdim functions to avoid
calls to 'exit' in C code
2012-04-07 21:13 sdray
* NAMESPACE, R/ade4.R: Remove .FirstLib and use NAMESPACE
(UseDynLib) to load DLL
2012-04-02 16:23 sdray
* data/bacteria.rda, data/capitales.rda, data/elec88.rda,
data/hdpg.rda, data/irishdata.rda, data/lascaux.rda,
data/mafragh.rda, data/perthi02.rda, data/tarentaise.rda,
data/vegtf.rda: resave some data files to improve file
compression
2012-03-16 05:55 sdray
* DESCRIPTION: Update email addresses
2012-01-20 12:45 jombart
* DESCRIPTION, NAMESPACE: Added a namespace (the default one
generated by R 2.14.1) to ensure compatibility with older R
release. Now stating the dependency on R >= 2.10 in DESCRIPTION.
2011-11-07 15:21 sdray
* R/mantel.rtest.R: Improve the performance (speed) of the
permutation procedure (suggestion by Josh Wiley jwiley.psych at
gmail.com)
2011-05-11 11:31 sdray
* INDEX: Delete INDEX file so that it would be generated and
updated automatically
2011-04-22 11:13 sdray
* R/randtest.between.R, man/randtest.between.Rd: Update the
function to deal with objects created by the new bca function
2011-04-11 14:23 sdray
* DESCRIPTION: ---------- release of ade4 1.4-17 ----------
2011-04-07 12:00 sdray
* R/pcaiv.R: Correct a bug: intercept is not included in 'cor'
to avoid a warning produced by scalewt
2011-04-07 11:32 sdray
* R/mfa.R, man/mfa.Rd, man/statis.Rd: Correct the documentation
(suggestion by D. Laloe) and improve the code of mfa (use of
match.arg to consider the argument 'option'
2011-04-07 11:10 sdray
* R/withinpca.R, man/withinpca.Rd: Improve the documentation
(suggestion by L. Dubroca on adelist 01/03/2011) and the code
(suggestion by D. Laloe)
2011-04-07 07:45 sdray
* 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.
2011-04-06 16:06 sdray
* man/scatter.Rd: Correct a typo
2011-04-06 16:06 sdray
* man/scatter.Rd: Add the doc for the 'main' argument
2011-04-06 14:33 sdray
* R/dudi.R, man/scatter.Rd: New generic functions 'biplot' and
'screeplot' to plot the outputs of an analysis (class dudi)
2011-02-24 14:11 sdray
* data/macroloire.rda, data/rhizobium.rda, data/woangers.rda:
Compress some ASCII data files
2011-02-24 14:00 sdray
* R/quasieuclid.R: Attributes of the original dist object are
preserved
2011-02-24 13:55 sdray
* R/cailliez.R, R/lingoes.R, man/cailliez.Rd, man/lingoes.Rd: Add
an argument to correct (or not) null distances
2011-02-24 13:47 sdray
* R/is.euclid.R: Add a warning for null distances
2010-09-27 14:42 sdray
* man/corvus.Rd: Correct a typo concerning the units of two
variables (cm -> mm). Thanks to Peter Saly
2010-08-18 15:25 sdray
* ChangeLog: ---------- release of ade4 1.4-16 ----------
2010-08-18 15:10 sdray
* DESCRIPTION: ---------- release of ade4 1.4-16 ----------
2010-05-08 05:41 thioulouse
* data/meaudret.rda: Updated meaudret environmental dataframe names
2010-05-06 16:16 sdray
* man/triangle.class.Rd: Remove auto-generated content in the
documentation
2010-04-29 14:49 sdray
* 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.
2010-04-12 08:10 sdray
* man/dist.binary.Rd: Correct some bibliographic references. Thanks
to Pierre Legendre.
2010-03-19 13:19 sdray
* R/dist.ktab.R: Correct a small bug in the ldist.ktab function
2010-03-10 09:13 thioulouse
* man/ktab.match2ktabs.Rd: removed deprecated email address in
ktab.match2ktabs documentation file
2010-03-05 15:06 jombart
* 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.
2010-02-10 12:12 sdray
* man/rlq.Rd: Correct a typo in the description
2010-02-10 12:00 sdray
* man/rlq.Rd: Correct a typo in the description
2009-12-18 08:46 sdray
* man/fourthcorner.Rd: Add information on the outputs of the print
and summary functions
2009-12-09 14:49 sdray
* 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
2009-12-04 13:33 sdray
* 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
2009-12-04 13:28 sdray
* man/dist.ktab.Rd, man/woangers.Rd: Put some examples in
'\dontrun' to speed up the checking of example
2009-12-03 13:27 sdray
* ChangeLog: ---------- release of ade4 1.4-14 ----------
2009-12-03 13:22 sdray
* DESCRIPTION: ---------- release of ade4 1.4-14 ----------
2009-12-01 10:01 sdray
* 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)
2009-11-12 12:08 thioulouse
* R/costatis.R: changes to the costatis function to remove cat
outputs in non-interactive mode (i.e., when scannf = FALSE)
2009-11-12 08:40 sdray
* 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
2009-11-12 08:38 sdray
* R/betweencoinertia.R, R/withincoinertia.R, man/betweencoinertia.Rd,
man/withincoinertia.Rd: Add new functions
'betweencoinertia' and 'withincoinertia' for between- and
within-coinertia analysis
2009-11-09 12:06 thioulouse
* R/costatis.R, R/statico.R, man/costatis.Rd, man/statico.Rd,
man/wgcoia.Rd: New functions to perform STATICO and CO-STATIS
2009-10-30 08:49 sdray
* R/kdisteuclid.R: Use 'match.arg' to evaluate the value of the
'method' argument
2009-10-29 08:56 sdray
* DESCRIPTION: ---------- release of ade4 1.4-13 ----------
2009-10-28 15:29 abdufour
* data/meaudret.rda: addition of the species names in the dataset
2009-10-28 15:08 abdufour
* man/meau.Rd, man/meaudret.Rd: information about the link between
the two datasets meau and meaudret has been added
2009-10-28 14:13 sdray
* R/phylog.R, R/plot.phylog.R: Correct bug in the use of basic
regular expressions (argument 'extended' is deprecated R 2.11.0)
2009-10-27 14:50 spavoine
* R/originality.R, man/originality.Rd: new methods have been added
in the originality function
2009-10-27 14:08 spavoine
* data/woangers.rda, man/woangers.Rd, man/rhizobium.Rd, data/rhizobium.rda,
data/macroloire.rda, man/macroloire.Rd: three new data sets added
2009-10-27 14:05 spavoine
* R/dist.ktab.R, man/dist.ktab.Rd: new functions of distance for
multiple types of variables
2009-10-27 14:01 spavoine
* R/apqe.R, man/apqe.Rd: new functions for diversity partitioning
2009-10-27 13:59 spavoine
* R/mdpcoa.R, man/mdpcoa.Rd: new functions for multiple dpcoa
2009-10-23 12:21 sdray
* ChangeLog: ---------- release of ade4 1.4-12 ----------
2009-10-23 12:19 sdray
* DESCRIPTION: ---------- release of ade4 1.4-12 ----------
2009-10-21 14:18 sdray
* data/toxicity.rda, man/toxicity.Rd: Correct species names and
table dimensions (thanks to Jean Lobry)
2009-10-21 13:34 thioulouse
* R/dudi.R: bug on row.names in as.dudi (thanks to Jean Lobry)
2009-10-20 14:18 sdray
* R/newick2phylog.R: Correct bug in the use of basic regular
expressions
2009-10-20 14:15 sdray
* man/multispati.Rd, man/multispati.randtest.Rd,
man/multispati.rtest.Rd: update links to spdep functions in the
documentation
2009-10-02 09:07 simonpenel
* R/newick2phylog.R, man/s.value.Rd, man/variance.phylog.Rd: Minor
bugs have been fixes. Replace extended = FALSE by fixed = TRUE
2009-09-22 08:10 thioulouse
* man/scatter.dudi.Rd: added some precision about biplots in
scatter.dudi.Rd
2009-07-24 14:53 thioulouse
* R/pta.R: corrected a small bug in row names of supIX and supIY df
2009-05-11 09:19 sdray
* R/dist.binary.R, man/dist.binary.Rd: Numeric matrix can be used
for the 'df' argument (request of E. Paradis)
2009-04-20 15:53 sdray
* R/area.plot.R: argument nclasslegend is now active. bug
identified by C. Calenge
2009-04-01 11:11 sdray
* ChangeLog: ---------- release of ade4 1.4-11 ----------
2009-04-01 11:07 sdray
* DESCRIPTION: ---------- release of ade4 1.4-11 ----------
2009-03-26 14:14 sdray
* 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
2009-02-03 12:39 abdufour
* man/randEH.Rd: replace PD in EH
2009-02-03 12:32 abdufour
* man/optimEH.Rd: replace PD in EH
2008-12-12 14:04 sdray
* ChangeLog: ---------- release of ade4 1.4-10 ----------
2008-12-12 14:03 sdray
* DESCRIPTION: ---------- release of ade4 1.4-10 ----------
2008-12-11 14:45 sdray
* 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)
2008-12-11 13:23 sdray
* src/adesub.c, src/adesub.h, src/testdim.c: new functions to
permute matrices used in testdim and fourthcorner are now in
adesub
2008-12-11 13:14 sdray
* man/RVdist.randtest.Rd, man/randtest-internal.Rd,
man/scatterutil.Rd: remove empty sections
2008-12-11 13:05 sdray
* man/dudi.fca.Rd: add a second argument to the \item macro
2008-12-11 13:04 sdray
* man/witwit.coa.Rd: remove invalid whitespaces
2008-12-01 15:34 jombart
* R/gearymoran.R: small typo repared
2008-12-01 15:19 jombart
* R/gearymoran.R: Added a match.arg to gearymoran (in multivariate
case, was messed up.
2008-06-30 10:55 sdray
* R/niche.R: Add a global test of the average marginality for all
species
2008-06-13 10:33 jombart
* 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.
2008-06-11 11:04 sdray
* data/abouheif.eg.rda: new data files
2008-06-11 10:59 sdray
* 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
2008-06-11 10:58 sdray
* 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
2008-06-10 14:12 sdray
* ChangeLog, DESCRIPTION, INDEX, R, TITLE, data, inst, man, src:
move from trunk to pkg after initial import using cvs2svn
2008-06-10 14:01 sdray
* man: remove man folder
2008-06-10 14:01 sdray
* R: remove R folder
2008-06-10 14:12 sdray
* ChangeLog, DESCRIPTION, INDEX, R, TITLE, data, inst, man, src:
move from trunk to pkg after initial import using cvs2svn
2008-05-23 14:12 dray
* ChangeLog, DESCRIPTION: ---------- release of ade4 1.4-9
----------
2008-05-23 12:12 dray
* R/niche.R: Correct a syntax error
2008-05-23 12:00 dray
* R/mantel.randtest.R, R/procuste.randtest.R: Correct a bug. The
number of repetitions was not correct ((nrepet + 1) instead of
nrepet)
2008-05-23 11:53 dray
* 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)
2008-05-23 11:46 dray
* 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)
2008-05-16 13:54 dray
* ChangeLog, DESCRIPTION: ---------- release of ade4 1.4-8
----------
2008-05-07 11:29 jthioulo
* R/dudi.acm.R: bug correction (mail of JR Lobry on adelist):
(any(row.w) < 0) vs. (any(row.w < 0))
2008-05-07 11:27 jthioulo
* R/dudi.R: bug correction (mail of JR Lobry on adelist):
any(col.w) < 0 vs. any(col.w < 0)
2008-04-18 14:37 penel
* data/ggtortoises.rda: pixmap S3 objects transformed into S4 class
2008-04-18 13:33 dray
* ChangeLog, DESCRIPTION: ---------- release of ade4 1.4-7
----------
2008-04-18 13:31 dray
* data/capitales.rda: pixmap S3 objects transformed into S4 class
2008-04-17 11:05 dray
* ChangeLog, DESCRIPTION: ---------- release of ade4 1.4-6
----------
2008-04-16 17:02 dray
* R/phylog.R: Correct a bug in phylog.extract (mail of S. Ollier)
2008-04-16 16:36 dray
* src/adesub.c, src/adesub.h, src/testrlq.c: matcentragehi in now
in adesub
2008-04-16 16:33 dray
* R/nipals.R, man/nipals.Rd: New function for NIPALS algorithm,
i.e. PCA with (or without) NA
2008-04-16 16:31 dray
* man/randtest.Rd: add some words about the computation of pvalues
for two-sided test
2008-04-16 13:18 dufour
* man/ade4.package.Rd: *** empty log message ***
2008-04-16 10:12 dufour
* man/pcaiv.Rd: *** empty log message ***
2008-04-14 12:41 penel
* man/table.phylog.Rd: Example table.phylog set to dontrun
2008-04-02 11:16 dray
* man/multispati.Rd, man/vegtf.Rd: Update the source reference:
Dray et al. (2008)
2008-03-27 14:28 dufour
* man/dudi.pca.Rd: Modifications : explanations about values (cent
and norm) ; it{} into emph{}.
2008-03-27 13:47 dufour
* man/dudi.pca.Rd: Modification of explanations ($cent and $norm)
2008-03-26 10:29 dray
* R/sco.distri.R: correct a bug (identified by S. Pavoine): default
label argument was badly considered when one column contains only
O's
2008-03-20 15:10 dray
* R/scatter.R, R/scatterutil.R, man/scatter.Rd, man/scatterutil.Rd:
New utility function scatterutil.sco and scatterutil.convrot90
for 1D graphical representation
2008-03-20 15:06 dray
* R/sco.gauss.R, man/sco.gauss.Rd: New function sco.gauss for 1D
graphical representation
2008-03-20 15:05 dray
* R/sco.match.R, man/sco.match.Rd: New function sco.match for 1D
graphical representation
2008-03-20 15:05 dray
* R/sco.class.R, man/sco.class.Rd: New function sco.class for 1D
graphical representation
2008-03-20 15:05 dray
* R/sco.label.R, man/sco.label.Rd: New function sco.label for 1D
graphical representation
2008-03-19 16:00 dray
* R/sco.qual.R: Functions of this file are now in sco.label.R and
sco.gauss.R
2008-03-18 14:18 dray
* inst/CITATION: Add two new references to the CITATION file
2008-03-17 15:47 dray
* R/randtest.cca.R, R/randtest.pcaiv.R, R/randtest.pcaivortho.R,
man/randtest.pcaiv.Rd: News functions for permutation tests in
constrained analysis
2008-02-05 13:26 dray
* src/testdim.c: Correct a bug in memory allocation of the function
svdd
2008-01-29 15:07 jthioulo
* man/sco.label.Rd: added function: Draws evenly spaced labels,
each label linked to the corresponding value of a numeric score
2008-01-29 15:07 jthioulo
* 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
2008-01-29 15:04 jthioulo
* man/veuvage.Rd: Correstion of illegal accented character in
exemple code
2008-01-29 15:04 jthioulo
* R/sco.qual.R: adds two functions: sco.gauss and sco.label (draw
Gauss curves on a score by categories of several factors)
2007-11-09 17:19 dray
* 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
2007-10-16 14:41 penel
* DESCRIPTION: Change License to GPL (>=2)
2007-10-16 14:35 penel
* ChangeLog: *** empty log message ***
2007-10-12 11:37 penel
* ChangeLog, DESCRIPTION: ---------- release of ade4 1.4-5
----------
2007-10-11 15:50 penel
* man/dunedata.Rd, man/steppe.Rd: Replace non_function by Doctype
2007-10-09 10:54 penel
* src/testdim.c, src/tests.c: Correction of a bug in the
declaration of variables
2007-09-25 11:16 dray
* ChangeLog: ---------- release of ade4 1.4-4 ----------
2007-09-25 11:10 dray
* DESCRIPTION: ---------- release of ade4 1.4-4 ----------
2007-09-20 15:48 dray
* 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
2007-09-17 16:23 dray
* 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
2007-09-17 15:12 dray
* R/ktab.R, man/ktab.Rd: Change the names of the arguments of the
function '[.ktab'
2007-09-17 13:05 dray
* 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
2007-09-14 11:58 jthioulo
* DESCRIPTION: suggests ade4TkGUI
2007-09-14 09:15 jthioulo
* R/randtest.between.R: modif eval pour ne pas chercher dans
l'environnement global directement
2007-09-13 11:57 dray
* src/Makevars: replace CRLF (DOS) by LF (Unix)
2007-09-13 11:18 jthioulo
* R/coinertia.R, R/dudi.R, R/dudi.pco.R: modif pour variable
globale ade4TkGUIFlag
2007-09-06 17:08 dray
* 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)
2007-09-06 15:11 dray
* R/scatter.acm.R: Clean R files: replace T by TRUE.
2007-09-06 15:03 dray
* R/newick2phylog.R: Clean R files: remove multiple function
definitions (floc1(s) becomes floc1,floc2,floc3. Thanks to
UsagePackageCheck of codetools
2007-09-06 14:55 dray
* 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
2007-09-06 13:53 dray
* R/orthogram.R: Correct a bug: test for the choice between
orthobas, neig or phylog
2007-09-06 12:21 dray
* R/scatter.acm.R: Correct a bug: replace score. by score.acm
2007-09-06 12:19 dray
* 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
2007-09-06 11:58 dray
* 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
2007-09-06 08:08 dray
* man/bordeaux.Rd, man/cca.Rd, man/dudi.hillsmith.Rd,
man/elec88.Rd, man/seconde.Rd: Clean Rd files: remove unmatched
right brace
2007-09-04 16:12 dray
* R/testdim.R, man/testdim.Rd, src/Makevars, src/testdim.c: New
function testdim to estimate the number of axes in multivariate
analysis
2007-09-04 15:07 dray
* 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
2007-09-04 14:50 dray
* man/vegtf.Rd: correction of a bug in the example section
2007-09-03 16:53 dray
* 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)
2007-09-03 16:26 dray
* 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)
2007-09-03 15:24 dray
* 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)
2007-09-03 15:04 dray
* R/multispati.R: Correct legend in plot.multispati
2007-09-03 14:58 dray
* data/vegtf.rda, man/vegtf.Rd: New vegetation data set to
illustrate multispati analysis
2007-09-03 14:51 dray
* R/niche.R, man/niche.Rd: New functions niche.param and
rtest.niche
2007-08-29 16:20 dray
* R/area.plot.R: the function area2poly is modified to export the
bbox attribute for each polygon
2007-08-29 16:00 dray
* R/s.corcircle.R: correct bug of the grid argument. see
http://listes.univ-lyon1.fr/wws/arc/adelist/2007-07/msg00001.html
2007-08-29 15:47 dray
* 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)
2007-06-15 07:49 dray
* man/dunedata.Rd: correct the number of rows and columns in the
help file
2007-04-16 12:56 dray
* ChangeLog, DESCRIPTION: ---------- release of ade4 1.4-3
----------
2007-04-12 13:39 dray
* man/suprow.Rd: correct the example section
2007-04-12 13:08 dray
* ChangeLog: New ChangeLog
2007-04-12 12:58 dray
* 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
2007-03-26 16:47 jombart
* ChangeLog, R/dudi.pco.R: reviewed by: <delete if not using a
buddy>
* R/dudi.pco.R: sub and csub arguments are now actually passed to
s.label
2007-03-12 14:34 jombart
* 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
2007-03-12 14:27 jombart
* R/scatter.add.R, man/scatter.add.Rd: *** empty log message ***
2007-03-12 14:06 jombart
* ChangeLog, R/add.graph.R: reviewed by: <delete if not using a
buddy>
* 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:
2007-03-12 14:04 jombart
* 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: <delete if not using a buddy>
* 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:
2007-03-10 10:38 jombart
* 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: <delete if not
using a buddy>
* 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
2007-03-07 18:46 jombart
* ChangeLog, data/rpjdl.rda: reviewed by: <delete if not using a
buddy>
* data/rpjdl.rda: removed accents
2007-02-19 09:53 jthioulo
* 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
2007-02-16 09:13 dray
* ChangeLog, man/orthogram.Rd: * man/orthogram.Rd: update the
reference to Ollier et al.