updating JOSS paper, readme and index to add statement of need and li…

…nks to rOpenSci docs site

README.Rmd

@@ -14,14 +14,15 @@ knitr::opts_chunk$set(
 
 # cde <img src="docs/logo/logo.png" align="right" height=140/>
 [![Travis-CI Build Status](https://travis-ci.org/ropensci/cde.svg?branch=master)](https://travis-ci.org/ropensci/cde) [![Coverage Status](https://coveralls.io/repos/github/ropensci/cde/badge.svg?branch=master)](https://coveralls.io/github/ropensci/cde?branch=master) [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![](https://badges.ropensci.org/284_status.svg)](https://github.com/ropensci/onboarding/issues/284) [![DOI](https://zenodo.org/badge/92712854.svg)](https://zenodo.org/badge/latestdoi/92712854)
+[![status](http://joss.theoj.org/papers/0d35f75e861fcf47556d70571e226589/status.svg)](http://joss.theoj.org/papers/0d35f75e861fcf47556d70571e226589)
 
 ## Introduction
 
 Within Europe, the [Water Framework Directive](http://ec.europa.eu/environment/water/water-framework/index_en.html) (WFD) sets EU-wide standards for how the quality of surface- and ground-waters across Europe is assessed and classified. Assessment of quality using the WFD is based on a range of elements that vary depending on the type of water being assessed and are combined to give an overall classification of waterbodies into five classes (High, Good, Moderate, Poor and Bad) for surface waters and two classes (Good or Poor) for groundwaters.
 
 In the UK the Environment Agency (EA) is the competent authority responsible for monitoring and assessment of water quality within England. The EA have made the reporting data relating to the requirements of the WFD available via the Catchment Data Explorer (CDE) website, [https://environment.data.gov.uk/catchment-planning/](https://environment.data.gov.uk/catchment-planning/). 
 
-`cde` is a package for R which facilitates searching and download of the WFD reporting data for all waterbodies from the EA CDE website.
+`cde` is a package for R which facilitates searching and download of the WFD reporting data for all waterbodies from the EA CDE website. The ability to access these data from within the R environment allows for efficient collation and interrogation of data and reproducible  analysis of trends or patterns in water quality and pressures on waterbodies across England.
 
 The types of data that can be downloaded are: WFD status classification data, Reasons for Not Achieving Good (RNAG) status, objectives set for waterbodies, measures put in place to improve water quality and details of associated protected areas.
 
@@ -38,7 +39,7 @@ remotes::install_github("ropensci/cde")
 
 ## Basic usage
 
-Details of how to use the package can be found at [https://ropensci.github.io/cde](https://ropensci.github.io/cde).
+Details of how to use the package can be found at [https://docs.ropensci.org/cde](https://docs.ropensci.org/cde).
 
 [![ropensci_footer](https://ropensci.org/public_images/github_footer.png)](https://ropensci.org)
 

README.md

@@ -12,6 +12,7 @@ state and is being actively
 developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![](https://badges.ropensci.org/284_status.svg)](https://github.com/ropensci/onboarding/issues/284)
 [![DOI](https://zenodo.org/badge/92712854.svg)](https://zenodo.org/badge/latestdoi/92712854)
+[![status](http://joss.theoj.org/papers/0d35f75e861fcf47556d70571e226589/status.svg)](http://joss.theoj.org/papers/0d35f75e861fcf47556d70571e226589)
 
 ## Introduction
 

index.Rmd

@@ -14,14 +14,14 @@ knitr::opts_chunk$set(
 
 # cde <img src="docs/logo/logo.png" align="right" height=140/>
 [![Travis-CI Build Status](https://travis-ci.org/ropensci/cde.svg?branch=master)](https://travis-ci.org/ropensci/cde) [![Coverage Status](https://coveralls.io/repos/github/ropensci/cde/badge.svg?branch=master)](https://coveralls.io/github/ropensci/cde?branch=master) [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![](https://badges.ropensci.org/284_status.svg)](https://github.com/ropensci/onboarding/issues/284) [![DOI](https://zenodo.org/badge/92712854.svg)](https://zenodo.org/badge/latestdoi/92712854)
-
+[![status](http://joss.theoj.org/papers/0d35f75e861fcf47556d70571e226589/status.svg)](http://joss.theoj.org/papers/0d35f75e861fcf47556d70571e226589)
 ## Introduction
 
 Within Europe, the [Water Framework Directive](http://ec.europa.eu/environment/water/water-framework/index_en.html) (WFD) sets EU-wide standards for how the quality of surface- and ground-waters across Europe is assessed and classified. Assessment of quality using the WFD is based on a range of elements that vary depending on the type of water being assessed and are combined to give an overall classification of waterbodies into five classes (High, Good, Moderate, Poor and Bad) for surface waters and two classes (Good or Poor) for groundwaters.
 
 In the UK the Environment Agency (EA) is the competent authority responsible for monitoring and assessment of water quality within England. The EA have made the reporting data relating to the requirements of the WFD available via the Catchment Data Explorer (CDE) website, [https://environment.data.gov.uk/catchment-planning/](https://environment.data.gov.uk/catchment-planning/). 
 
-`cde` is a package for R which facilitates searching and download of the WFD reporting data for all waterbodies from the EA CDE website.
+`cde` is a package for R which facilitates searching and download of the WFD reporting data for all waterbodies from the EA CDE website. The ability to access these data from within the R environment allows for efficient collation and interrogation of data and reproducible  analysis of trends or patterns in water quality and pressures on waterbodies across England.
 
 The types of data that can be downloaded are: WFD status classification data, Reasons for Not Achieving Good (RNAG) status, objectives set for waterbodies, measures put in place to improve water quality and details of associated protected areas.
 
@@ -38,6 +38,6 @@ remotes::install_github("ropensci/cde")
 
 ## Basic usage
 
-See the [Get started](https://ropensci.github.io/cde/articles/cde.html) vignette or [Reference](https://ropensci.github.io/cde/reference/index.html) sections above for details of the different functions.
+See the [Get started](https://docs.ropensci.org/cde/articles/cde.html) vignette or [Reference](https://docs.ropensci.org/cde/reference/index.html) sections above for details of the different functions.
 
 [![ropensci_footer](https://ropensci.org/public_images/github_footer.png)](https://ropensci.org)

index.md

@@ -12,8 +12,8 @@ state and is being actively
 developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![](https://badges.ropensci.org/284_status.svg)](https://github.com/ropensci/onboarding/issues/284)
 [![DOI](https://zenodo.org/badge/92712854.svg)](https://zenodo.org/badge/latestdoi/92712854)
-
-## Introduction
+[![status](http://joss.theoj.org/papers/0d35f75e861fcf47556d70571e226589/status.svg)](http://joss.theoj.org/papers/0d35f75e861fcf47556d70571e226589)
+\#\# Introduction
 
 Within Europe, the [Water Framework
 Directive](http://ec.europa.eu/environment/water/water-framework/index_en.html)
@@ -32,7 +32,11 @@ requirements of the WFD available via the Catchment Data Explorer (CDE)
 website, <https://environment.data.gov.uk/catchment-planning/>.
 
 `cde` is a package for R which facilitates searching and download of the
-WFD reporting data for all waterbodies from the EA CDE website.
+WFD reporting data for all waterbodies from the EA CDE website. The
+ability to access these data from within the R environment allows for
+efficient collation and interrogation of data and reproducible analysis
+of trends or patterns in water quality and pressures on waterbodies
+across England.
 
 The types of data that can be downloaded are: WFD status classification
 data, Reasons for Not Achieving Good (RNAG) status, objectives set for
@@ -55,10 +59,10 @@ remotes::install_github("ropensci/cde")
 
 ## Basic usage
 
-See the [Get started](https://ropensci.github.io/cde/articles/cde.html)
+See the [Get started](https://docs.ropensci.org/cde/articles/cde.html)
 vignette or
-[Reference](https://ropensci.github.io/cde/reference/index.html)
-sections above for details of the different
+[Reference](https://docs.ropensci.org/cde/reference/index.html) sections
+above for details of the different
 functions.
 
 [![ropensci\_footer](https://ropensci.org/public_images/github_footer.png)](https://ropensci.org)

paper/paper.md

@@ -19,7 +19,7 @@ bibliography: paper.bib
 
 Globally, issues around water quality and quantity are expected to increase in coming decades, set against a background of already widespread degradation [@WWAPUnitedNationsWorldWaterAssessmentProgramme/UN-Water2018]. Within Europe, the [Water Framework Directive](http://ec.europa.eu/environment/water/water-framework/) (WFD) set EU-wide standards for how the quality of surface waters and groundwater across Europe is assessed and classified [@Communities2000]. Assessment of quality under the WFD is based on a range of elements that vary depending on the type of water being assessed. The elements cover biological, chemical and hydromorphological/quantitative components with a hierarchical structure. These are combined to give an overall classification of waterbodies into five classes (High, Good, Moderate, Poor and Bad) for surface waters and two classes (Good or Poor) for groundwaters. The overall aim of the WFD is that all European surface waters and groundwater will reach at least Good status by 2027, although there have been a number of issues with implementation [@Voulvoulis2017].
 
-In the UK, the Environment Agency (EA) is the competent authority responsible for monitoring and assessment of water quality within England. The EA have made the reporting data relating to the requirements of the WFD available via the Catchment Data Explorer (CDE) website [https://environment.data.gov.uk/catchment-planning/](https://environment.data.gov.uk/catchment-planning/). The ``cde`` package for R [@RCoreTeam2019] provides functions that facilitate the querying, download and plotting of the data available on the CDE site, allowing efficient collation of data for the analysis of trends or patterns in water quality and pressures on waterbodies across England.
+In the UK, the Environment Agency (EA) is the competent authority responsible for monitoring and assessment of water quality within England. The EA have made all of the reporting data relating to the requirements of the WFD available via the Catchment Data Explorer (CDE) website [https://environment.data.gov.uk/catchment-planning/](https://environment.data.gov.uk/catchment-planning/). The ``cde`` package for R [@RCoreTeam2019] provides functions that facilitate the querying, download and plotting of the data available on the CDE site. The ability to access these data from within the R environment allows for efficient collation and interrogation of data and reproducible  analysis of trends or patterns in water quality and pressures on waterbodies across England.
 
 The package allows users to search for waterbodies, catchments or River Basin Districts that match given search strings. Having identified the relevant sites, the following types of data can be downloaded: