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ChangeLog
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ChangeLog
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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>