diff --git a/.Rbuildignore b/.Rbuildignore index edec5c0..56546a9 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -18,3 +18,4 @@ ^codemeta\.json$ ^vignettes/emodnet.wfs\.Rmd\.orig$ ^\.lintr$ +^inst/submission\.md$ diff --git a/README.Rmd b/README.Rmd index b847244..4ade8c0 100644 --- a/README.Rmd +++ b/README.Rmd @@ -21,6 +21,7 @@ options(timeout = 2000) [![R-CMD-check](https://github.com/EMODnet/emodnet.wfs/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/EMODnet/emodnet.wfs/actions/workflows/R-CMD-check.yaml) [![Codecov test coverage](https://codecov.io/gh/EMODnet/emodnet.wfs/branch/main/graph/badge.svg)](https://app.codecov.io/gh/EMODnet/emodnet.wfs/tree/main) [![Codecov test coverage](https://codecov.io/gh/EMODnet/emodnet.wfs/graph/badge.svg)](https://app.codecov.io/gh/EMODnet/emodnet.wfs) +[![DOI](https://zenodo.org/badge/DOI/10.14284/679.svg)](https://doi.org/10.14284/679) The goal of emodnet.wfs is to allow interrogation of and access to [EMODnet's, European Marine Observation and Data Network, geographic vector data](https://emodnet.ec.europa.eu/en/emodnet-web-service-documentation#inline-nav-3) in R though the [EMODnet Web Feature Services](https://emodnet.ec.europa.eu/en/data). diff --git a/README.md b/README.md index 6fa889d..b8714ef 100644 --- a/README.md +++ b/README.md @@ -13,6 +13,7 @@ developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.re coverage](https://codecov.io/gh/EMODnet/emodnet.wfs/branch/main/graph/badge.svg)](https://app.codecov.io/gh/EMODnet/emodnet.wfs/tree/main) [![Codecov test coverage](https://codecov.io/gh/EMODnet/emodnet.wfs/graph/badge.svg)](https://app.codecov.io/gh/EMODnet/emodnet.wfs) +[![DOI](https://zenodo.org/badge/DOI/10.14284/679.svg)](https://doi.org/10.14284/679) The goal of emodnet.wfs is to allow interrogation of and access to @@ -463,9 +464,10 @@ citation(package = "emodnet.wfs") #> To cite package 'emodnet.wfs' in publications use: #> #> Krystalli A, Fernández-Bejarano S, Salmon M (????). _emodnet.wfs: -#> Access EMODnet Web Feature Service data through R_. R package version -#> 2.0.1.9001. Integrated data products created under the European -#> Marine Observation Data Network (EMODnet) Biology project +#> Access EMODnet Web Feature Service data through R_. doi:10.14284/679 +#> , R package version 2.0.2.9000. +#> Integrated data products created under the European Marine +#> Observation Data Network (EMODnet) Biology project #> (EASME/EMFF/2017/1.3.1.2/02/SI2.789013), funded by the by the #> European Union under Regulation (EU) No 508/2014 of the European #> Parliament and of the Council of 15 May 2014 on the European Maritime @@ -476,8 +478,9 @@ citation(package = "emodnet.wfs") #> @Manual{, #> title = {{emodnet.wfs}: Access EMODnet Web Feature Service data through R}, #> author = {Anna Krystalli and Salvador Fernández-Bejarano and Maëlle Salmon}, -#> note = {R package version 2.0.1.9001. Integrated data products created under the European Marine Observation Data Network (EMODnet) Biology project (EASME/EMFF/2017/1.3.1.2/02/SI2.789013), funded by the by the European Union under Regulation (EU) No 508/2014 of the European Parliament and of the Council of 15 May 2014 on the European Maritime and Fisheries Fund}, +#> note = {R package version 2.0.2.9000. Integrated data products created under the European Marine Observation Data Network (EMODnet) Biology project (EASME/EMFF/2017/1.3.1.2/02/SI2.789013), funded by the by the European Union under Regulation (EU) No 508/2014 of the European Parliament and of the Council of 15 May 2014 on the European Maritime and Fisheries Fund}, #> url = {https://github.com/EMODnet/emodnet.wfs}, +#> doi = {10.14284/679}, #> } ``` diff --git a/inst/CITATION b/inst/CITATION index 1cea231..edcea6b 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -10,4 +10,5 @@ bibentry(bibtype = "Manual", ), year = year, note = note, - url = "https://github.com/EMODnet/emodnet.wfs") + url = "https://github.com/EMODnet/emodnet.wfs", + doi = "10.14284/679") diff --git a/inst/submission.md b/inst/submission.md new file mode 100644 index 0000000..83ac229 --- /dev/null +++ b/inst/submission.md @@ -0,0 +1,181 @@ + + +Submitting Author Name: Maëlle Salmon +Submitting Author Github Handle: @maelle +Other Package Authors Github handles: (comma separated, delete if none) @salvafern, @annakrystalli +Repository: https://github.com/EMODnet/emodnet.wfs/ +Version submitted: 2.0.2 +Submission type: Standard +Editor: TBD +Reviewers: TBD + +Archive: TBD +Version accepted: TBD +Language: en + +--- + + + +- Paste the full DESCRIPTION file inside a code block below: + +``` +Package: emodnet.wfs +Title: Access EMODnet Web Feature Service data through R +Version: 2.0.2 +Authors@R: c( + person("Anna", "Krystalli", , "annakrystalli@googlemail.com", role = "aut", + comment = c(ORCID = "0000-0002-2378-4915")), + person("Salvador", "Fernández-Bejarano", , "salvador.fernandez@vliz.be", role = c("aut", "cre"), + comment = c(ORCID = "0000-0003-0535-7677")), + person("Thomas J", "Webb", , "t.j.webb@sheffield.ac.uk", role = "ctb"), + person("European Marine Observation Data Network (EMODnet) Biology project", "European Commission's Directorate - General for Maritime Affairs and Fisheries (DG MARE)", , "bio@emodnet.eu", role = "cph"), + person("VLIZ (VLAAMS INSTITUUT VOOR DE ZEE)", , , "info@vliz.be", role = "fnd"), + person("Maëlle", "Salmon", , "msmaellesalmon@gmail.com", role = "aut", + comment = c(ORCID = "0000-0002-2815-0399")) + ) +Description: Access and interrogate EMODnet (European Marine Observation and Data Network) + Web Feature Service data through R. +License: MIT + file LICENSE +URL: https://emodnet.github.io/emodnet.wfs/, + https://github.com/EMODnet/emodnet.wfs +BugReports: https://github.com/EMODnet/emodnet.wfs/issues +Depends: + R (>= 3.6.0) +Imports: + checkmate, + cli, + dplyr, + lifecycle, + magrittr, + memoise, + ows4R (>= 0.4), + purrr, + rlang, + sf, + tibble, + utils, + whoami +Suggests: + covr, + httptest, + knitr, + mapview, + readr, + rmarkdown, + skimr, + testthat (>= 3.1.2), + testthis, + withr +Config/Needs/readme: rerddap +VignetteBuilder: + knitr +Config/testthat/edition: 3 +Encoding: UTF-8 +LazyData: true +Roxygen: list(markdown = TRUE) +RoxygenNote: 7.3.2 +SystemRequirements: C++11, GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>= + 4.8.0) +Remotes: + eblondel/ows4R + +``` + + +## Scope + +- Please indicate which category or categories from our [package fit policies](https://ropensci.github.io/dev_guide/policies.html#package-categories) this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.): + + - [x] data retrieval + - [ ] data extraction + - [ ] data munging + - [ ] data deposition + - [ ] data validation and testing + - [ ] workflow automation + - [ ] version control + - [ ] citation management and bibliometrics + - [ ] scientific software wrappers + - [ ] field and lab reproducibility tools + - [ ] database software bindings + - [x] geospatial data + - [ ] text analysis + +- Explain how and why the package falls under these categories (briefly, 1-2 sentences): + +The package allow interrogation of and access to EMODnet’s, European Marine Observation and Data Network, geographic vector data. + +- Who is the target audience and what are scientific applications of this package? + +The target audience of the package are EMODnet users that might need programmatic access to EMODnet's geographic vector data. +The package allows to include EMODnet vector data into scientific pipelines without needing to manually explore and download data from the [EMODnet Geographic Viewer](https://emodnet.ec.europa.eu/geoviewer/). +The data covers seven disciplinary themes (bathymetry, geology, physics, chemistry, biology, seabed habitats and human activities). + +- Are there other R packages that accomplish the same thing? If so, how does yours differ or meet [our criteria for best-in-category](https://ropensci.github.io/dev_guide/policies.html#overlap)? + +No, to our knowledge emodnet.wfs is the only package that provides access to EMODnet data in R though the EMODnet Web Feature +Services. +The emodnet.wfs package was developed in collaboration with other EMODnet members. + +There are in total three ways to access EMODnet data that complement each other and which we documented in [emodnet.wfs README](https://github.com/EMODnet/emodnet.wfs?tab=readme-ov-file#other-web-services): + +- Some EMODnet data are also published in an [ERDDAP +server](https://erddap.emodnet.eu). One can access these data in R using +the rOpenSci [rerddap R package](https://docs.ropensci.org/rerddap/). + +- This package emodnet.wfs uses [Web Feature +Services](https://www.ogc.org/standard/wfs/), hence it is limited to +getting vector data. EMODnet also hosts raster data that can be accessed +via [Web Coverage Services (WCS)](https://www.ogc.org/standard/wcs/). +The R package [EMODnetWCS](https://github.com/EMODnet/EMODnetWCS) makes +these data available in R. We intend to also submit the latter to software review at one point (and we intend to rename it). + +- (If applicable) Does your package comply with our [guidance around _Ethics, Data Privacy and Human Subjects Research_](https://devguide.ropensci.org/policies.html#ethics-data-privacy-and-human-subjects-research)? + +N/A + +- If you made a pre-submission inquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted. + +- Explain reasons for any [`pkgcheck` items](https://docs.ropensci.org/pkgcheck/) which your package is unable to pass. + +## Technical checks + +Confirm each of the following by checking the box. + +- [x] I have read the [rOpenSci packaging guide](https://devguide.ropensci.org/building.html). +- [x] I have read the [author guide](https://devdevguide.netlify.app/authors-guide.html) and I expect to maintain this package for at least 2 years or to find a replacement. + +This package: + +- [x] does not violate the Terms of Service of any service it interacts with. +- [x] has a CRAN and OSI accepted license. +- [x] contains a [README with instructions for installing the development version](https://ropensci.github.io/dev_guide/building.html#readme). +- [x] includes [documentation with examples for all functions, created with roxygen2](https://ropensci.github.io/dev_guide/building.html#documentation). +- [x] contains a vignette with examples of its essential functions and uses. +- [x] has a [test suite](https://ropensci.github.io/dev_guide/building.html#testing). +- [x] has [continuous integration](https://ropensci.github.io/dev_guide/ci.html), including reporting of test coverage. + +## Publication options + +- [x] Do you intend for this package to go on CRAN? +- [ ] Do you intend for this package to go on Bioconductor? + +- [ ] Do you wish to submit an Applications Article about your package to [Methods in Ecology and Evolution](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/)? If so: + +
+MEE Options + +- [ ] The package is novel and will be of interest to the broad readership of the journal. +- [ ] The manuscript describing the package is no longer than 3000 words. +- [ ] You intend to archive the code for the package in a long-term repository which meets the requirements of the journal (see [MEE's Policy on Publishing Code](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/journal-resources/policy-on-publishing-code.html)) +- (*Scope: Do consider MEE's [Aims and Scope](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/aims-and-scope/read-full-aims-and-scope.html) for your manuscript. We make no guarantee that your manuscript will be within MEE scope.*) +- (*Although not required, we strongly recommend having a full manuscript prepared when you submit here.*) +- (*Please do not submit your package separately to Methods in Ecology and Evolution*) + +
+ +## Code of conduct + +- [x] I agree to abide by [rOpenSci's Code of Conduct](https://ropensci.org/code-of-conduct/) during the review process and in maintaining my package should it be accepted.