update documentation to point to Atlantis-Ecosystem-Model rather than andybeet

Author: andybeet

Diff for: DESCRIPTION

@@ -6,8 +6,8 @@ Authors@R:
   c(person("Alexander", "Keth", email = "[email protected]", role = c("aut")),
     person("Andy", "Beet", email = "[email protected]", role = c("cre")))
 Description: Atlantis is an end-to-end marine ecosystem modelling framework. It was originally developed in Australia by E.A. Fulton, A.D.M. Smith and D.C. Smith (2007) and has since been adopted in many marine ecosystems around the world (<http://atlantis.cmar.csiro.au>). The output of an Atlantis simulation is stored in various file formats like .netcdf and .txt and different output structures are used for the output variables like e.g. productivity or biomass. This package is used to convert the different output types to a unified format according to the "tidy-data" approach by H. Wickham (2014) <DOI:10.18637/jss.v059.i10>. Additionally, ecological metrics like for example spatial overlap of predator and prey or consumption can be calculated and visualised with this package. Due to the unified data structure it is very easy to share model output with each other and perform model comparisons.
-URL: https://github.com/andybeet/atlantistools
-BugReports: https://github.com/andybeet/atlantistools/issues
+URL: https://github.com/Atlantis-Ecosystem-Model/atlantistools
+BugReports: https://github.com/Atlantis-Ecosystem-Model/atlantistools/issues
 Depends:
     R (>= 3.2.3)
 License: GPL-3

Diff for: README.Rmd

@@ -9,8 +9,8 @@ output:
 # atlantistools
 
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/atlantistools)](https://cran.r-project.org/package=atlantistools)
-[![R-CMD-check](https://github.com/andybeet/atlantistools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/andybeet/atlantistools/actions/workflows/R-CMD-check.yaml)
-[![gh-pages](https://github.com/andybeet/atlantistools/actions/workflows/pkgdown.yml/badge.svg)](https://github.com/andybeet/atlantistools/actions/workflows/pkgdown.yml)
+[![R-CMD-check](https://github.com/Atlantis-Ecosystem-Model/atlantistools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Atlantis-Ecosystem-Model/atlantistools/actions/workflows/R-CMD-check.yaml)
+[![gh-pages](https://github.com/Atlantis-Ecosystem-Model/atlantistools/actions/workflows/pkgdown.yml/badge.svg)](https://github.com/Atlantis-Ecosystem-Model/atlantistools/actions/workflows/pkgdown.yml)
 
 `atlantistools` is a data processing and visualisation tool for R, which helps to process output from Atlantis models within R.
 Using atlantistools makes sure that Atlantis users use the same input/output file structure which facilitates intra and inter model comparisons.
@@ -20,23 +20,24 @@ Using atlantistools makes sure that Atlantis users use the same input/output fil
 Install from CRAN: (Version 0.4.3 only)
 
 ```R
-install.packages("atlantistools")
+install.packages("Atlantis-Ecosystem-Model/atlantistools")
 ```
 
-Since version 0.4.3 all development resides on GitHub. 
+Since version 0.4.3 all development resides on GitHub. To view the changes to `atlantistools` since version 0.4.3 please read the [NEWS.md](https://Atlantis-Ecosystem-Model.github.io/atlantistools/news/index.html)
+
 To Install the development version from Github: 
 
 ```R
-remotes::install_github("")
+remotes::install_github("Atlantis-Ecosystem-Model/atlantistools")
 ```
 
 # Documentation
 
 All documentation can now be found online in the gh-pages branch of this repo
 
-Full documentation can be found [here](https://andybeet.github.io/atlantistools/index.html)
+Full documentation can be found [here](https://Atlantis-Ecosystem-Model.github.io/atlantistools/index.html)
 
-Vignettes can be found [here](https://andybeet.github.io/atlantistools/articles/)
+Vignettes can be found [here](https://Atlantis-Ecosystem-Model.github.io/atlantistools/articles/)
 
 
 

Diff for: README.md

@@ -4,8 +4,8 @@ atlantistools
 =============
 
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/atlantistools)](https://cran.r-project.org/package=atlantistools)
-[![R-CMD-check](https://github.com/andybeet/atlantistools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/andybeet/atlantistools/actions/workflows/R-CMD-check.yaml)
-[![gh-pages](https://github.com/andybeet/atlantistools/actions/workflows/pkgdown.yml/badge.svg)](https://github.com/andybeet/atlantistools/actions/workflows/pkgdown.yml)
+[![R-CMD-check](https://github.com/Atlantis-Ecosystem-Model/atlantistools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Atlantis-Ecosystem-Model/atlantistools/actions/workflows/R-CMD-check.yaml)
+[![gh-pages](https://github.com/Atlantis-Ecosystem-Model/atlantistools/actions/workflows/pkgdown.yml/badge.svg)](https://github.com/Atlantis-Ecosystem-Model/atlantistools/actions/workflows/pkgdown.yml)
 
 `atlantistools` is a data processing and visualisation tool for R, which
 helps to process output from Atlantis models within R. Using
@@ -18,14 +18,17 @@ Installation
 Install from CRAN: (Version 0.4.3 only)
 
 ``` r
-install.packages("atlantistools")
+install.packages("Atlantis-Ecosystem-Model/atlantistools")
 ```
 
-Since version 0.4.3 all development resides on GitHub. To Install the
-development version from Github:
+Since version 0.4.3 all development resides on GitHub. To view the
+changes to `atlantistools` since version 0.4.3 please read the
+[NEWS.md](https://Atlantis-Ecosystem-Model.github.io/atlantistools/news/index.html)
+
+To Install the development version from Github:
 
 ``` r
-remotes::install_github("")
+remotes::install_github("Atlantis-Ecosystem-Model/atlantistools")
 ```
 
 Documentation
@@ -35,7 +38,7 @@ All documentation can now be found online in the gh-pages branch of this
 repo
 
 Full documentation can be found
-[here](https://andybeet.github.io/atlantistools/index.html)
+[here](https://Atlantis-Ecosystem-Model.github.io/atlantistools/index.html)
 
 Vignettes can be found
-[here](https://andybeet.github.io/atlantistools/articles/)
+[here](https://Atlantis-Ecosystem-Model.github.io/atlantistools/articles/)

Diff for: vignettes/atlantistools.Rmd

@@ -18,9 +18,8 @@ knitr::opts_chunk$set(
 library(atlantistools)
 ```
 
-The original `atlantistools` was created and maintained by Alexander Keth. However development was ceased on January, 2018.
+`atlantistools` was created by [Alexander Keth](https://github.com/alketh). In October 2021 `altantistools` was transferred to the atlantis group at [CSIRO](https://github.com/Atlantis-Ecosystem-Model) for continued development
 
-This repo is forked from the original. It will be further developed here