diff --git a/DESCRIPTION b/DESCRIPTION index ce3f41de..a0b2142b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -53,6 +53,6 @@ VignetteBuilder: knitr Description: Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) . License: GPL (>= 2) -URL: https://sdray.github.io/ade4/, http://pbil.univ-lyon1.fr/ADE-4/ -BugReports: https://github.com/sdray/ade4/issues +URL: https://adeverse.github.io/ade4/, http://pbil.univ-lyon1.fr/ADE-4/ +BugReports: https://github.com/adeverse/ade4/issues Encoding: UTF-8 diff --git a/README.md b/README.md index 7bac4fe9..e0398e3b 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,27 @@ # [ade4](http://pbil.univ-lyon1.fr/ADE-4/) + [![CRAN_Release_Badge](http://www.r-pkg.org/badges/version-ago/ade4)](http://cran.r-project.org/package=ade4) [![CRAN Downloads](https://cranlogs.r-pkg.org/badges/ade4)](https://cran.r-project.org/package=ade4) -[![R-CMD-check](https://github.com/sdray/ade4/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/sdray/ade4/actions/workflows/R-CMD-check.yaml) +[![R-CMD-check](https://github.com/adeverse/ade4/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/adeverse/ade4/actions/workflows/R-CMD-check.yaml) [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences +--------------------------- + +**Please note! Since January 2024, this repository has belonged to the *adeverse* organization.** +To avoid confusion, we strongly recommend updating any existing local clones to point to the new +repository URL. You can do this by using `git remote` on the command line: + +`git remote set-url origin git@github.com:adeverse/ade4.git` + +or + +`git remote set-url origin https://github.com/adeverse/ade4.git` + +--------------------------- + + Installing *ade4* ------------- @@ -21,7 +37,7 @@ To install the development version from github: Then: ```r -remotes::install_github("sdray/ade4") +remotes::install_github("adeverse/ade4") ``` The stable version can be installed from CRAN using: diff --git a/_pkgdown.yml b/_pkgdown.yml index 6a339811..f70457c9 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -54,7 +54,7 @@ navbar: icon: fa-leaf href: https://lbbe-web.univ-lyon1.fr/en - icon: fa-github - href: https://github.com/sdray/ade4 + href: https://github.com/adeverse/ade4 reference: diff --git a/pkgdown/index.md b/pkgdown/index.md index e9a04219..5ba4c533 100644 --- a/pkgdown/index.md +++ b/pkgdown/index.md @@ -1,7 +1,7 @@ # Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences (**ade4**) [![CRAN_Release_Badge](http://www.r-pkg.org/badges/version-ago/ade4)](http://cran.r-project.org/package=ade4) [![CRAN Downloads](https://cranlogs.r-pkg.org/badges/ade4)](https://cran.r-project.org/package=ade4) -[![R-CMD-check](https://github.com/sdray/ade4/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/sdray/ade4/actions/workflows/R-CMD-check.yaml) +[![R-CMD-check](https://github.com/adeverse/ade4/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/adeverse/ade4/actions/workflows/R-CMD-check.yaml) [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) ## Presentation @@ -10,9 +10,9 @@ **ade4** is a package for the [**R** software](https://www.r-project.org) since 2002. It contains functions for exploratory multivariate data analysis and graphical display, many numerical data sets and bibliographic references. Simple one-table methods are described in [Chessel et al. (2004)](http://pbil.univ-lyon1.fr/JTHome/ref/ade4-Rnews.pdf). Two-table and K-table methods are described in [Dray et al. (2007)](http://pbil.univ-lyon1.fr/ade4/article/rnews2/rnews2.pdf). The theory of the duality diagram and its implementation in ade4 are discussed in [Dray et Dufour (2007)](http://pbil.univ-lyon1.fr/ade4/article/jss/jss.pdf). -A book in the *Springer Series in Statistics* collection, [**"Multivariate Analysis of Ecological Data with ade4"**](http://sdray.github.io/ade4/articles/book.html) presents the package. The examples and the graphs in this book can be [**reproduced online here**](https://lbbe-shiny.univ-lyon1.fr/Reproducible_Research/Book/). +A book in the *Springer Series in Statistics* collection, [**"Multivariate Analysis of Ecological Data with ade4"**](http://adeverse.github.io/ade4/articles/book.html) presents the package. The examples and the graphs in this book can be [**reproduced online here**](https://lbbe-shiny.univ-lyon1.fr/Reproducible_Research/Book/). -If you use **ade4**, please consider citing [these references](http://sdray.github.io/ade4/authors.html#citation) ! +If you use **ade4**, please consider citing [these references](http://adeverse.github.io/ade4/authors.html#citation) !

@@ -30,7 +30,7 @@ If you use **ade4**, please consider citing [these references](http://sdray.gith ### Installing **ade4** -[This page](http://sdray.github.io/ade4/articles/install.html) explains how to install the **ade4** package in **R**. +[This page](http://adeverse.github.io/ade4/articles/install.html) explains how to install the **ade4** package in **R**. ### Vignettes @@ -38,26 +38,26 @@ Several vignettes are available to help you get started with **ade4** (more to c - [Graphical representation of multivariate data](https://cran.r-project.org/web/packages/adegraphics/vignettes/adegraphics.html) -- [Description of environmental variables structures](http://sdray.github.io/ade4/articles/ChapEnvVarStruct.html) +- [Description of environmental variables structures](http://adeverse.github.io/ade4/articles/ChapEnvVarStruct.html) -- [Description of species structures](http://sdray.github.io/ade4/articles/ChapSpeciesStruct.html) +- [Description of species structures](http://adeverse.github.io/ade4/articles/ChapSpeciesStruct.html) -- [Taking into account groups of sites](http://sdray.github.io/ade4/articles/ChapBetGr.html) +- [Taking into account groups of sites](http://adeverse.github.io/ade4/articles/ChapBetGr.html) -- [Description of species-environment relationships](http://sdray.github.io/ade4/articles/Chap2tables.html) +- [Description of species-environment relationships](http://adeverse.github.io/ade4/articles/Chap2tables.html) -- [Analysing Changes in Structures](http://sdray.github.io/ade4/articles/ChapKtables.html) +- [Analysing Changes in Structures](http://adeverse.github.io/ade4/articles/ChapKtables.html) -- [Analysing Changes in Co-structures](http://sdray.github.io/ade4/articles/Chap2Ktables.html) +- [Analysing Changes in Co-structures](http://adeverse.github.io/ade4/articles/Chap2Ktables.html) ### List of function references -You can also find a list of functions available to users on the [reference page](http://sdray.github.io/ade4/reference/index.html). +You can also find a list of functions available to users on the [reference page](http://adeverse.github.io/ade4/reference/index.html). ### Other resources -Check out the [ade4 book](http://sdray.github.io/ade4/articles/book.html) and its [shiny application](https://lbbe-shiny.univ-lyon1.fr/Reproducible_Research/Book/) for a complete introduction to the package and to rerun the code present in the book. -You can also check these [bibliographic references](http://sdray.github.io/ade4/articles/papers.html) to help you understand **ade4** methods. +Check out the [ade4 book](http://adeverse.github.io/ade4/articles/book.html) and its [shiny application](https://lbbe-shiny.univ-lyon1.fr/Reproducible_Research/Book/) for a complete introduction to the package and to rerun the code present in the book. +You can also check these [bibliographic references](http://adeverse.github.io/ade4/articles/papers.html) to help you understand **ade4** methods. Note for nostalgics 😉 : the **old ade4 web site** is still available here: [http://pbil.univ-lyon1.fr/ADE-4/](http://pbil.univ-lyon1.fr/ADE-4/accueil2.php). @@ -68,5 +68,5 @@ You will be able to download the R script used to generate the results as well a ### Getting help: FAQ & Mailing list -You can also check the [FAQ section](http://sdray.github.io/ade4/articles/faq.html) to check if your question has already been answered or ask for help on the **ade4** mailing list [adelist](https://listes.univ-lyon1.fr/sympa/info/adelist). +You can also check the [FAQ section](http://adeverse.github.io/ade4/articles/faq.html) to check if your question has already been answered or ask for help on the **ade4** mailing list [adelist](https://listes.univ-lyon1.fr/sympa/info/adelist). \ diff --git a/vignettes/articles/get_started.Rmd b/vignettes/articles/get_started.Rmd index 276b659a..b2ee743a 100644 --- a/vignettes/articles/get_started.Rmd +++ b/vignettes/articles/get_started.Rmd @@ -5,12 +5,12 @@ title: "Getting started with ade4" ## Vignettes We provide some vignettes to help you get started with `ade4.` -You can also find a list of functions available to users on our [reference page](http://sdray.github.io/ade4/reference/index.html). +You can also find a list of functions available to users on our [reference page](http://adeverse.github.io/ade4/reference/index.html). ## Ressources Check out the [`ade4` book](https://link.springer.com/book/10.1007/978-1-4939-8850-1) and its [shiny application](https://ade4.shinyapps.io/Book/) for a complete introduction to the package and to rerun the code present in the book. -You can also find hereafter some [papers](http://sdray.github.io/ade4/articles/papers.html) to help you understand `ade4` methods. +You can also find hereafter some [papers](http://adeverse.github.io/ade4/articles/papers.html) to help you understand `ade4` methods. ## Shinyapps @@ -19,4 +19,4 @@ You will be able to download the R script used to generate the results as well a ## Getting help -You can swing by our [FAQ section](http://sdray.github.io/ade4/articles/faq.html) to check if your question has already been answered or ask for help on the `ade4` mailing list [adelist](https://listes.univ-lyon1.fr/sympa/info/adelist). +You can swing by our [FAQ section](http://adeverse.github.io/ade4/articles/faq.html) to check if your question has already been answered or ask for help on the `ade4` mailing list [adelist](https://listes.univ-lyon1.fr/sympa/info/adelist). diff --git a/vignettes/articles/install.Rmd b/vignettes/articles/install.Rmd index 5f2fc6d6..3cca11fb 100644 --- a/vignettes/articles/install.Rmd +++ b/vignettes/articles/install.Rmd @@ -4,7 +4,7 @@ title: "Installing `ade4`" [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/ade4)](http://cran.r-project.org/package=ade4) [![CRAN Downloads](https://cranlogs.r-pkg.org/badges/ade4)](https://cran.r-project.org/package=ade4) -[![R-CMD-check](https://github.com/sdray/ade4/workflows/R-CMD-check/badge.svg)](https://github.com/sdray/ade4/actions) +[![R-CMD-check](https://github.com/adeverse/ade4/workflows/R-CMD-check/badge.svg)](https://github.com/adeverse/ade4/actions) [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) ## The current *stable* version can be installed from CRAN using: @@ -25,7 +25,7 @@ install.packages("ade4") 3. Then you can use the following command: ```r -remotes::install_github("sdray/ade4") +remotes::install_github("adeverse/ade4") ``` **Note:** If you do not wish to install the development environments Rtools (Windows) or XCode (Mac), you can get pre-compiled binary packages here: diff --git a/vignettes/faq.Rmd b/vignettes/faq.Rmd index de132bad..21686ff7 100644 --- a/vignettes/faq.Rmd +++ b/vignettes/faq.Rmd @@ -26,7 +26,7 @@ The easiest way to install ade4 is to use `install.packages("ade4")` in your R s To install the development version from github: ```r -remotes::install_github("sdray/ade4") +remotes::install_github("adeverse/ade4") ``` ### How do I know which `ade4` version I'm using?