From 81b8cc5b87b1c5bb918d94ef70e7ab2e887bdcac Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Wed, 22 Apr 2026 12:18:18 -0600 Subject: [PATCH 1/2] Update URLs documentation, etc for DGEC migration --- CONTRIBUTING.md | 18 +++++++++--------- DESCRIPTION | 17 +++++++---------- NEWS.md | 3 +++ R/updateR.R | 12 ++++++------ README.Rmd | 20 ++++++++++---------- README.md | 24 ++++++++++++++---------- vignettes/NPSdataverse.Rmd | 8 +++++--- 7 files changed, 54 insertions(+), 48 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 084babb..8c6b5a1 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -30,13 +30,13 @@ All types of contributions are encouraged and valued. See the [Table of Contents ## I Have a Question -> If you want to ask a question, we assume that you have read the available [Documentation](https://nationalparkservice.github.io/NPSdataverse/). +> If you want to ask a question, we assume that you have read the available [Documentation](https://doi-nps.github.io/NPSdataverse/). -Before you ask a question, it is best to search for existing [Issues](https://github.com/nationalparkservice/NPSdataverse/issues) that might help you. In case you have found a suitable issue and still need clarification, you can write your question in this issue. It is also advisable to search the internet for answers first. +Before you ask a question, it is best to search for existing [Issues](https://github.com/doi-nps/NPSdataverse/issues) that might help you. In case you have found a suitable issue and still need clarification, you can write your question in this issue. It is also advisable to search the internet for answers first. If you then still feel the need to ask a question and need clarification, we recommend the following: -- Open an [Issue](https://github.com/nationalparkservice/NPSdataverse/issues/new/choose). +- Open an [Issue](https://github.com/doi-nps/NPSdataverse/issues/new/choose). - Provide as much context as you can about what you're running into. - Provide project and platform versions , depending on what seems relevant. @@ -57,8 +57,8 @@ We will then take care of the issue as soon as possible. A good bug report shouldn't leave others needing to chase you up for more information. Therefore, we ask you to investigate carefully, collect information and describe the issue in detail in your report. Please complete the following steps in advance to help us fix any potential bug as fast as possible. - Make sure that you are using the latest version. -- Determine if your bug is really a bug and not an error on your side e.g. using incompatible environment components/versions (Make sure that you have read the [documentation](https://nationalparkservice.github.io/NPSdataverse/). If you are looking for support, you might want to check [this section](#i-have-a-question)). -- To see if other users have experienced (and potentially already solved) the same issue you are having, check if there is not already a bug report existing for your bug or error in the [bug tracker](https://github.com/nationalparkservice/NPSdataverse/issues/new/choose). +- Determine if your bug is really a bug and not an error on your side e.g. using incompatible environment components/versions (Make sure that you have read the [documentation](https://doi-nps.github.io/NPSdataverse/). If you are looking for support, you might want to check [this section](#i-have-a-question)). +- To see if other users have experienced (and potentially already solved) the same issue you are having, check if there is not already a bug report existing for your bug or error in the [bug tracker](https://github.com/doi-nps/NPSdataverse/issues/new/choose). - Also make sure to search the internet to see if users outside of the GitHub community have discussed the issue. - Collect information about the bug: - Stack trace (Traceback) @@ -75,7 +75,7 @@ A good bug report shouldn't leave others needing to chase you up for more inform We use GitHub issues to track bugs and errors. If you run into an issue with the project: -- Open an [Issue](https://github.com/nationalparkservice/NPSdataverse/issues/new/choose). (Since we can't be sure at this point whether it is a bug or not, we ask you not to talk about a bug yet and not to label the issue.) +- Open an [Issue](https://github.com/doi-nps/NPSdataverse/issues/new/choose). (Since we can't be sure at this point whether it is a bug or not, we ask you not to talk about a bug yet and not to label the issue.) - Explain the behavior you would expect and the actual behavior. - Please provide as much context as possible and describe the *reproduction steps* that someone else can follow to recreate the issue on their own. This usually includes your code. For good bug reports you should isolate the problem and create a reduced test case. See [https://gist.github.com/hadley/270442](https://gist.github.com/hadley/270442) for a great run down on how to create reproducible examples. - Provide the information you collected in the previous section. @@ -94,15 +94,15 @@ This section guides you through submitting an enhancement **including completely #### Before Submitting an Enhancement - Make sure that you are using the latest version. -- Read the [documentation](https://nationalparkservice.github.io/NPSdataverse/) carefully and find out if the functionality is already covered, maybe by an individual configuration. -- Perform a [search](https://github.com/nationalparkservice/NPSdataverse/issues) to see if the enhancement has already been suggested. If it has, add a comment to the existing issue instead of opening a new one. +- Read the [documentation](https://doi-nps.github.io/NPSdataverse/) carefully and find out if the functionality is already covered, maybe by an individual configuration. +- Perform a [search](https://github.com/doi-nps/NPSdataverse/issues) to see if the enhancement has already been suggested. If it has, add a comment to the existing issue instead of opening a new one. - Find out whether your idea fits with the scope and aims of the project. It's up to you to make a strong case to convince the project's developers of the merits of this feature. Keep in mind that we want features that will be useful to the majority of our users and not just a small subset. If you're just targeting a minority of users, consider writing an add-on/plugin library or package. - Please consult with the developers if you would like to create an add-on package. Maybe we can help! #### How Do I Submit a Good Enhancement Suggestion? -Enhancement suggestions are tracked as [GitHub issues](https://github.com/nationalparkservice/NPSdataverse/issues). +Enhancement suggestions are tracked as [GitHub issues](https://github.com/doi-nps/NPSdataverse/issues). - Use a **clear and descriptive title** for the issue to identify the suggestion. - Provide a **step-by-step description of the suggested enhancement** in as many details as possible. diff --git a/DESCRIPTION b/DESCRIPTION index d5ce85e..c2d673c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -7,10 +7,7 @@ Authors@R: c( comment = c(ORCID = "0000-0001-7591-5035")), person(given="Judd", family="Patterson", email="Judd_Patterson@nps.gov", role= "aut", - comment = c(ORCID = "0000-0002-0951-7917")), - person(given="Joe", family="DeVivo", email="Joe_DeVivo@nps.gov", - role= "aut", - comment = c(ORCID = "0000-0002-0414-7865")) + comment = c(ORCID = "0000-0002-0951-7917")) ) Description: Loads a suite of R packages for creating and manipulating data packages including interacting with DataStore. License: MIT + file LICENSE @@ -32,16 +29,16 @@ Imports: stringr, tibble Remotes: - nationalparkservice/DPchecker, - nationalparkservice/EMLeditor, - nationalparkservice/NPSutils, - nationalparkservice/QCkit, + doi-nps/DPchecker, + doi-nps/EMLeditor, + doi-nps/NPSutils, + doi-nps/QCkit, EDIorg/EMLassemblyline Suggests: knitr, rmarkdown, testthat (>= 3.0.0) VignetteBuilder: knitr -URL: https://github.com/nationalparkservice/NPSdataverse -BugReports: https://github.com/nationalparkservice/NPSdataverse/issues +URL: https://github.com/doi-nps/NPSdataverse +BugReports: https://github.com/doi-nps/NPSdataverse/issues Config/testthat/edition: 3 diff --git a/NEWS.md b/NEWS.md index e8be06f..d6c6454 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,7 @@ # NPSdataverse 1.1.0 +2026-04-22 +* Update URLs and add code.json for migration to DGEC + 2025-04-21 * Update JOSS badge to "in review" diff --git a/R/updateR.R b/R/updateR.R index 95e3017..3aea379 100644 --- a/R/updateR.R +++ b/R/updateR.R @@ -16,12 +16,12 @@ "NPSdataverse" ), repo = c( - "nationalparkservice", - "nationalparkservice", - "nationalparkservice", - "nationalparkservice", + "doi-nps", + "doi-nps", + "doi-nps", + "doi-nps", "EDIorg", - "nationalparkservice"), + "doi-nps"), branch = c( "master", "main", @@ -54,7 +54,7 @@ "{.strong To update {cli::qty(length(old_pkgs$package))}th{?is/ese} {cli::qty(length(old_pkgs$package))}package{?s}, please run:\n}" ) cli::cat_line("detach_NPSdataverse()") - cli::cat_line("devtools::install_github(\"", old_pkgs$repo, "/", old_pkgs$package, "\")") + cli::cat_line("remotes::install_github(\"", old_pkgs$repo, "/", old_pkgs$package, "\")") cli::cat_line("\nClose R and Rstudio. Open a new R session and reload the NPSdataverse.") cli::cat_line() } else { diff --git a/README.Rmd b/README.Rmd index d931126..5b46560 100644 --- a/README.Rmd +++ b/README.Rmd @@ -5,7 +5,7 @@ output: github_document - [![R-CMD-check](https://github.com/nationalparkservice/NPSdataverse/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nationalparkservice/NPSdataverse/actions/workflows/R-CMD-check.yaml) + [![R-CMD-check](https://github.com/doi-nps/NPSdataverse/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nationalparkservice/NPSdataverse/actions/workflows/R-CMD-check.yaml) [![status](https://joss.theoj.org/papers/4f0f426403cd0e5f089ad527fb66ce51/status.svg)](https://joss.theoj.org/papers/4f0f426403cd0e5f089ad527fb66ce51) @@ -30,7 +30,7 @@ knitr::opts_chunk$set( knitr::include_graphics("man/figures/NPSdataverse_overview.jpg") # ![alt text]("man/figures/NPSdataverse_overview.jpg") ``` -NPSdataverse loads a suite of R packages for creating, manipulating, and accessing data packages including interacting with DataStore. This is an early version of the NPSdataverse. Please request enhancements and bug fixes through [Issues](https://github.com/nationalparkservice/NPSdataverse/issues). +NPSdataverse loads a suite of R packages for creating, manipulating, and accessing data packages including interacting with DataStore. This is an early version of the NPSdataverse. Please request enhancements and bug fixes through [Issues](https://github.com/doi-nps/NPSdataverse/issues). ## Installation @@ -38,19 +38,19 @@ You can install the development version of NPSdataverse from [GitHub](https://gi ``` r # install.packages("pak") -pak::pkg_install("nationalparkservice/NPSdataverse") +pak::pkg_install("doi-nps/NPSdataverse") ``` NPSdataverse will install the following R packages: | Package | Location| |---------|---------| -|**QCkit**| https://nationalparkservice.github.io/QCkit| +|**QCkit**| https://doi-nps.github.io/QCkit| |EMLassemblyline (EAL)| https://ediorg.github.io/EMLassemblyline| |EML| https://cran.r-project.org/package=EML| -|**EMLeditor**| https://nationalparkservice.github.io/EMLeditor| -|**DPchecker**| https://nationalparkservice.github.io/DPchecker| -|**NPSutils**| https://nationalparkservice.github.io/NPSutils| +|**EMLeditor**| https://doi-nps.github.io/EMLeditor| +|**DPchecker**| https://doi-nps.github.io/DPchecker| +|**NPSutils**| https://doi-nps.github.io/NPSutils| *** (R packages in **bold** are developed by NPS) @@ -58,14 +58,14 @@ NPSdataverse will install the following R packages: ## Usage ```{r setup, eval = FALSE} -pak::pkg_install("nationalparkservice/NPSdataverse") +pak::pkg_install("doi-nps/NPSdataverse") library(NPSdataverse) ``` ## Troubleshooting installation -If `pak::pkg_install()` throws an error, try `remotes::install_github("nationalparkservice/NPSdataverse")` instead. +If `pak::pkg_install()` throws an error, try `remotes::install_github("doi-nps/NPSdataverse")` instead. Each package within the NPSdataverse has a number of dependencies, most of which are hosted on CRAN. During the initial install of NPSdataverse, you may be @@ -116,5 +116,5 @@ knitr::include_graphics("man/figures/EMLtemplate.png") -This will open a new file on that you can edit to generate EML metadata for your data package. See the [web pages associated with EMLeditor](https://nationalparkservice.github.io/EMLeditor/) for additional information, instructions, and examples. +This will open a new file on that you can edit to generate EML metadata for your data package. See the [web pages associated with EMLeditor](https://doi-nps.github.io/EMLeditor/) for additional information, instructions, and examples. diff --git a/README.md b/README.md index 5567465..f12001a 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ -[![R-CMD-check](https://github.com/nationalparkservice/NPSdataverse/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nationalparkservice/NPSdataverse/actions/workflows/R-CMD-check.yaml) +[![R-CMD-check](https://github.com/doi-nps/NPSdataverse/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/doi-nps/NPSdataverse/actions/workflows/R-CMD-check.yaml) [![status](https://joss.theoj.org/papers/4f0f426403cd0e5f089ad527fb66ce51/status.svg)](https://joss.theoj.org/papers/4f0f426403cd0e5f089ad527fb66ce51) @@ -14,7 +14,7 @@ NPSdataverse loads a suite of R packages for creating, manipulating, and accessing data packages including interacting with DataStore. This is an early version of the NPSdataverse. Please request enhancements and bug fixes through -[Issues](https://github.com/nationalparkservice/NPSdataverse/issues). +[Issues](https://github.com/doi-nps/NPSdataverse/issues). ## Installation @@ -23,19 +23,21 @@ You can install the development version of NPSdataverse from ``` r # install.packages("pak") -pak::pkg_install("nationalparkservice/NPSdataverse") +pak::pkg_install("doi-nps/NPSdataverse") +# alternatively: +remotes::install_github("doi-nps/NPSdataverse") ``` NPSdataverse will install the following R packages: | Package | Location | |-----------------------|---------------------------------------------------| -| **QCkit** | | +| **QCkit** | | | EMLassemblyline (EAL) | | | EML | | -| **EMLeditor** | | -| **DPchecker** | | -| **NPSutils** | | +| **EMLeditor** | | +| **DPchecker** | | +| **NPSutils** | | ------------------------------------------------------------------------ @@ -44,14 +46,16 @@ NPSdataverse will install the following R packages: ## Usage ``` r -pak::pkg_install("nationalparkservice/NPSdataverse") +pak::pkg_install("doi-nps/NPSdataverse") +# or: +# remotes::install_github("doi-nps/NPSdataverse") library(NPSdataverse) ``` ## Troubleshooting installation If `pak::pkg_install()` throws an error, try -`remotes::install_github("nationalparkservice/NPSdataverse")` instead. +`remotes::install_github("doi-nps/NPSdataverse")` instead. Each package within the NPSdataverse has a number of dependencies, most of which are hosted on CRAN. During the initial install of NPSdataverse, @@ -98,5 +102,5 @@ the template labelled “Editable_EML_Creation_Workflow” and click “OK”. This will open a new file on that you can edit to generate EML metadata for your data package. See the [web pages associated with -EMLeditor](https://nationalparkservice.github.io/EMLeditor/) for +EMLeditor](https://doi-nps.github.io/EMLeditor/) for additional information, instructions, and examples. diff --git a/vignettes/NPSdataverse.Rmd b/vignettes/NPSdataverse.Rmd index f02fd7d..312ff1d 100644 --- a/vignettes/NPSdataverse.Rmd +++ b/vignettes/NPSdataverse.Rmd @@ -17,15 +17,17 @@ knitr::opts_chunk$set( ## Summary -The [NPSdataverse](https://nationalparkservice.github.io/NPSdataverse/) is a suite of R packages developed to create, document, publish, and access data and metadata in open and machine-readable formats.NPSdataverse is modeled off of the tidyverse concept of several packages built with a common goal [@Wickham2019].The NPSdataverse supports Ecological Metadata Language (EML) metadata and .csv data files. Some of the constituent R packages ([EML](https://docs.ropensci.org/EML/) and [EMLassemblyline](https://ediorg.github.io/EMLassemblyline/)) are general-use and aimed at authoring EML documents. Other R packages ([QCkit](https://nationalparkservice.github.io/QCkit/), [EMLeditor](https://nationalparkservice.github.io/EMLeditor/), [DPchecker](https://nationalparkservice.github.io/DPchecker/) and [NPSutils](https://nationalparkservice.github.io/NPSutils/)) are designed and maintained by the National Park Service (NPS).Although many functions within the NPSdataverse packages are NPS-specific (particularly some API calls), whenever possible the functions are written so that they can also be used by the general public. Scientists conducting permitted research in NPS units can utilize the NPSdataverse to efficiently and consistently meet the data delivery requirements of their permits. Additionally, the packages will be useful for data management plans in a wide variety of grant proposals and for anyone that needs to create open data and machine-readable metadata. The ability to swiftly and easily author, edit, and check Ecological Metadata Language (EML) metadata in a reproducible fashion will be useful for data publication at any number of repositories or data journals. Finally, a scripted interface for downloading NPS data and leveraging metadata while loading it into R or other platforms for subsequent analyses and visualizations will be useful to researchers in the government, academia, and industry as well as the public. +The [NPSdataverse](https://doi-nps.github.io/NPSdataverse/) is a suite of R packages developed to create, document, publish, and access data and metadata in open and machine-readable formats.NPSdataverse is modeled off of the tidyverse concept of several packages built with a common goal [@Wickham2019].The NPSdataverse supports Ecological Metadata Language (EML) metadata and .csv data files. Some of the constituent R packages ([EML](https://docs.ropensci.org/EML/) and [EMLassemblyline](https://ediorg.github.io/EMLassemblyline/)) are general-use and aimed at authoring EML documents. Other R packages ([QCkit](https://doi-nps.github.io/QCkit/), [EMLeditor](https://doi-nps.github.io/EMLeditor/), [DPchecker](https://doi-nps.github.io/DPchecker/) and [NPSutils](https://doi-nps.github.io/NPSutils/)) are designed and maintained by the National Park Service (NPS).Although many functions within the NPSdataverse packages are NPS-specific (particularly some API calls), whenever possible the functions are written so that they can also be used by the general public. Scientists conducting permitted research in NPS units can utilize the NPSdataverse to efficiently and consistently meet the data delivery requirements of their permits. Additionally, the packages will be useful for data management plans in a wide variety of grant proposals and for anyone that needs to create open data and machine-readable metadata. The ability to swiftly and easily author, edit, and check Ecological Metadata Language (EML) metadata in a reproducible fashion will be useful for data publication at any number of repositories or data journals. Finally, a scripted interface for downloading NPS data and leveraging metadata while loading it into R or other platforms for subsequent analyses and visualizations will be useful to researchers in the government, academia, and industry as well as the public. ## Usage -The [NPSdataverse](https://nationalparkservice.github.io/NPSdataverse/) package is a meta-package that loads packages within the NPSdataverse into R [@Baker_NPSdataverse2025]. The NPSdataverse provides a convenient way to download, install, and load many of the R packages needed to create and access data packages, which consist of rich Ecological Metadata Language metadata and .csv data files: +The [NPSdataverse](https://doi-nps.github.io/NPSdataverse/) package is a meta-package that loads packages within the NPSdataverse into R [@Baker_NPSdataverse2025]. The NPSdataverse provides a convenient way to download, install, and load many of the R packages needed to create and access data packages, which consist of rich Ecological Metadata Language metadata and .csv data files: ```{r setup, eval = FALSE} -pak::pkg_install("nationalparkservice/NPSdataverse") +pak::pkg_install("doi-nps/NPSdataverse") +#alternatively: +remotes::install_github("doi-nps/NPSdataverse") library(NPSdataverse) ``` From a3f85922b8b659ac16459c0fff6d9cba1637203b Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Wed, 22 Apr 2026 12:18:49 -0600 Subject: [PATCH 2/2] Update documentation, URLs, etc prior to DGEC migration --- DESCRIPTION | 2 +- code.json | 55 +++++++++++++++++++++++ docs/404.html | 6 +-- docs/LICENSE-text.html | 6 +-- docs/LICENSE.html | 6 +-- docs/articles/NPSdataverse.html | 49 ++++++++++---------- docs/articles/index.html | 6 +-- docs/authors.html | 22 ++++----- docs/index.html | 39 ++++++++-------- docs/news/index.html | 9 ++-- docs/paper.html | 20 ++++----- docs/pkgdown.yml | 6 +-- docs/reference/NPSdataverse_packages.html | 15 ++++--- docs/reference/detach_NPSdataverse.html | 8 ++-- docs/reference/dot-update_git_repos.html | 8 ++-- docs/reference/index.html | 6 +-- docs/reference/is_online.html | 8 ++-- docs/sitemap.xml | 1 + 18 files changed, 164 insertions(+), 108 deletions(-) create mode 100644 code.json diff --git a/DESCRIPTION b/DESCRIPTION index c2d673c..2ddadc4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -13,7 +13,7 @@ Description: Loads a suite of R packages for creating and manipulating data pack License: MIT + file LICENSE Encoding: UTF-8 Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.2 +RoxygenNote: 7.3.3 Imports: cli, DPchecker (>= 1.0.0), diff --git a/code.json b/code.json new file mode 100644 index 0000000..45bbede --- /dev/null +++ b/code.json @@ -0,0 +1,55 @@ +[ + { + "name": "NPSdataverse", + "organization": "NATIONAL PARK SERVICE", + "description": "Loads a suite of R packages for creating and manipulating data packages including interacting with DataStore.", + "version": "1.1.0", + "status": "ongoing development", + "permissions": { + "usageType": "openSource", + "licenses": [ + { + "name": "Public Domain, CC0-1.0", + "URL": "https://github.com/DOI-NPS/NPSdataverse" + } + ] + }, + "homepageURL": "https://github.com/DOI-NPS/NPSdataverse", + "downloadURL": "https://github.com/DOI-NPS/NPSdataverse", + "disclaimerURL": "hhtps://github.com/DOI-NPS/NPSdataverse/blob/main/LICENSE", + "repositoryURL": "https://github.com/DOI-NPS/NPSdataverse", + "vcs": "git", + "laborHours": 1, + "tags": [ + "NRSS", + "IMD", + "metadata", + "r", + "accessible", + "open-data", + "datastore", + "data-package", + "r-package", + "ecological-metadata-language", + "eml", + "data-packages", + "national-parks", + "findable", + "interoperable", + "eml-metadata", + "machine-readable" + "national-park-service", + "reuseable" + ], + "languages": [ + "R" + ], + "contact": { + "name": "Robert Baker", + "email": "robert_baker@nps.gov" + }, + "date": { + "metadataLastUpdated": "2026-04-22" + } + } +] diff --git a/docs/404.html b/docs/404.html index 05738c9..2a0e025 100644 --- a/docs/404.html +++ b/docs/404.html @@ -50,7 +50,7 @@
  • - + @@ -86,12 +86,12 @@

    Page not found (404)

    -

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    +

    Developed by Robert Baker, Judd Patterson.

    -

    Site built with pkgdown 2.1.2.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 4c2df82..546a896 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -32,7 +32,7 @@ Changelog
  • - + @@ -64,11 +64,11 @@

    License

    -

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    +

    Developed by Robert Baker, Judd Patterson.

    -

    Site built with pkgdown 2.1.2.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/LICENSE.html b/docs/LICENSE.html index b2dfbfe..cc8c704 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -32,7 +32,7 @@ Changelog
  • - + @@ -68,11 +68,11 @@

    MIT License

    -

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    +

    Developed by Robert Baker, Judd Patterson.

    -

    Site built with pkgdown 2.1.2.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/articles/NPSdataverse.html b/docs/articles/NPSdataverse.html index 7620a20..818ec02 100644 --- a/docs/articles/NPSdataverse.html +++ b/docs/articles/NPSdataverse.html @@ -50,7 +50,7 @@
  • - + @@ -71,7 +71,7 @@

    NPSdataverse

    - Source: vignettes/NPSdataverse.Rmd + Source: vignettes/NPSdataverse.Rmd @@ -81,19 +81,16 @@

    NPSdataverse

    Summary

    -

    The NPSdataverse -is a suite of R packages developed to create, document, publish, and -access data and metadata in open and machine-readable -formats.NPSdataverse is modeled off of the tidyverse concept of several -packages built with a common goal (Wickham et al. -2019).The NPSdataverse supports Ecological Metadata Language -(EML) metadata and .csv data files. Some of the constituent R packages -(EML and EMLassemblyline) +

    The NPSdataverse is a +suite of R packages developed to create, document, publish, and access +data and metadata in open and machine-readable formats.NPSdataverse is +modeled off of the tidyverse concept of several packages built with a +common goal (Wickham et al. 2019).The +NPSdataverse supports Ecological Metadata Language (EML) metadata and +.csv data files. Some of the constituent R packages (EML and EMLassemblyline) are general-use and aimed at authoring EML documents. Other R packages -(QCkit, EMLeditor, -DPchecker -and NPSutils) are -designed and maintained by the National Park Service (NPS).Although many +(QCkit, EMLeditor, DPchecker and NPSutils) are designed +and maintained by the National Park Service (NPS).Although many functions within the NPSdataverse packages are NPS-specific (particularly some API calls), whenever possible the functions are written so that they can also be used by the general public. Scientists @@ -113,16 +110,18 @@

    Summary

    Usage

    -

    The NPSdataverse -package is a meta-package that loads packages within the NPSdataverse -into R (Baker, Patterson, and DeVivo -2025). The NPSdataverse provides a convenient way to download, -install, and load many of the R packages needed to create and access -data packages, which consist of rich Ecological Metadata Language -metadata and .csv data files:

    +

    The NPSdataverse package +is a meta-package that loads packages within the NPSdataverse into R +(Baker, Patterson, and DeVivo 2025). The +NPSdataverse provides a convenient way to download, install, and load +many of the R packages needed to create and access data packages, which +consist of rich Ecological Metadata Language metadata and .csv data +files:

    -pak::pkg_install("nationalparkservice/NPSdataverse")
-library(NPSdataverse)
    +pak::pkg_install("doi-nps/NPSdataverse") +#alternatively: +remotes::install_github("doi-nps/NPSdataverse") +library(NPSdataverse)

    NPSdataverse will automatically check that the latest version of each R package is being loaded: either from the main development branch on GitHub.com or the @@ -281,12 +280,12 @@

    References

    -

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    +

    Developed by Robert Baker, Judd Patterson.

    -

    Site built with pkgdown 2.1.2.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/articles/index.html b/docs/articles/index.html index 5c847d4..73dc29f 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -32,7 +32,7 @@ Changelog

  • - + @@ -61,11 +61,11 @@

    All vignettes

    -

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    +

    Developed by Robert Baker, Judd Patterson.

    -

    Site built with pkgdown 2.1.2.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/authors.html b/docs/authors.html index 74ffcf6..833c182 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -32,7 +32,7 @@ Changelog
  • - + @@ -59,29 +59,25 @@

    Authors and Citation

    Judd Patterson. Author.

    • -
  • -

    Joe DeVivo. Author. -

    -

Citation

- Source: DESCRIPTION + Source: DESCRIPTION
-

Baker R, Patterson J, DeVivo J (2025). +

Baker R, Patterson J (2026). NPSdataverse: Tools and Packages for Data and Metadata Manipulation. -R package version 1.1.0, https://github.com/nationalparkservice/NPSdataverse. +R package version 1.1.0, https://github.com/doi-nps/NPSdataverse. 

@Manual{,
   title = {NPSdataverse: Tools and Packages for Data and Metadata Manipulation},
-  author = {Robert Baker and Judd Patterson and Joe DeVivo},
-  year = {2025},
+  author = {Robert Baker and Judd Patterson},
+  year = {2026},
   note = {R package version 1.1.0},
-  url = {https://github.com/nationalparkservice/NPSdataverse},
+  url = {https://github.com/doi-nps/NPSdataverse},
 }
@@ -91,11 +87,11 @@

Citation

-

Developed by Robert Baker, Judd Patterson, Joe DeVivo.

+

Developed by Robert Baker, Judd Patterson.

-

Site built with pkgdown 2.1.2.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/index.html b/docs/index.html index 7ef9550..e37f216 100644 --- a/docs/index.html +++ b/docs/index.html @@ -51,7 +51,7 @@
  • - + @@ -47,11 +47,12 @@

    Changelog

    - Source: NEWS.md + Source: NEWS.md

    NPSdataverse 1.1.0

    +

    2026-04-22 * Update URLs and add code.json for migration to DGEC

    2025-04-21 * Update JOSS badge to “in review”

    2025-03-12 * Updated to MIT license, which is OSI approved and NPS approved and a standard R license.

    2025-03-10 * Updated license to OSI-approved “Zero-Clause BSD” in support of JOSS submission.

    @@ -91,11 +92,11 @@

    NPS
    -

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    +

    Developed by Robert Baker, Judd Patterson.

    -

    Site built with pkgdown 2.1.2.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/paper.html b/docs/paper.html index 8fc4520..b34ebf8 100644 --- a/docs/paper.html +++ b/docs/paper.html @@ -32,7 +32,7 @@ Changelog
  • - + @@ -63,8 +63,8 @@

    Statement of Need

    NPSdataverse R package

    The NPSdataverse package is a meta-package that loads packages within the NPSdataverse into R [@Baker_NPSdataverse2025]. NPSdataverse provides a convenient way to download, install, and load many of the R packages needed to create and access data packages, which consist of rich Ecological Metadata Language metadata and .csv data files:

    -
    pak::pkg_install("nationalparkservice/NPSdataverse")
-library(NPSdataverse)
    +
    pak::pkg_install("nationalparkservice/NPSdataverse")
+library(NPSdataverse)

    NPSdataverse will automatically check that the latest version of each R package is being loaded: either from the main development branch on GitHub.com or the latest version on CRAN. If updates are indicated, the user will be alerted and given instructions on how to update the relevant packages. To prevent API limits at GitHub (and to facilitate scripted workflows such as those at High Performance Computing facilities), NPSdataverse only checks for updates from an interactive R session and will skip checks when the system is not on-line or GitHub.com is not responding.

    @@ -77,12 +77,12 @@

    EML R package

    EMLassembyline R package

    -

    The EMLassemblyline package builds upon EML and adds substantial functionality [@Smith2022]. For instance, EMLassemblyline allows the user to supply .csv files, which are used to generate template .txt files. Users can adjust the template files as needed and use the EMLassemblyline::make_eml() function to generate an R-object that can be exported via EML as an EML-fomatted .xml file. EMLassemblyline includes the ability to generate entire taxonomic backbones from lists of scientific names via API calls to ITIS, GBIF, or Worms. EMLassemblyline will validate the R object against the EML schema and provide helpful hints on what might have gone wrong during the EMLassemblyline::make_eml() process. EMLassemblyline provides an efficient bridge between .csv data and EML metadata for users who are familiar with R but may not be experts on the EML schema or the detailed nested lists needed to create EML within R via the EML package. Products from the EMLassemblyline pipeline are suitable for publication at multiple repositories including the Environmental Data Initiative.

    +

    The EMLassemblyline package builds upon EML and adds substantial functionality [@Smith2022]. For instance, EMLassemblyline allows the user to supply .csv files, which are used to generate template .txt files. Users can adjust the template files as needed and use the EMLassemblyline::make_eml() function to generate an R-object that can be exported via EML as an EML-fomatted .xml file. EMLassemblyline includes the ability to generate entire taxonomic backbones from lists of scientific names via API calls to ITIS, GBIF, or Worms. EMLassemblyline will validate the R object against the EML schema and provide helpful hints on what might have gone wrong during the EMLassemblyline::make_eml() process. EMLassemblyline provides an efficient bridge between .csv data and EML metadata for users who are familiar with R but may not be experts on the EML schema or the detailed nested lists needed to create EML within R via the EML package. Products from the EMLassemblyline pipeline are suitable for publication at multiple repositories including the Environmental Data Initiative.

    EMLeditor R package

    The EMLeditor package allows users to quickly and easily view components of metadata in R and make on-the-fly edits to metadata [@Baker_EMLeditor2025]. Edits made to EML objects using EMLeditor do not require re-running the EMLassemblyline functions to make EML. This is a significant improvement because running EMLassemblyline functions can be time consuming, especially if there are many taxa that need to be resolved. EMLeditor includes the ability to pick specific licenses (CC0, CC-BY, etc.), add ORCIDs, include organizations as authors, and much more. EMLeditor also adds specific content necessary to be compliant with NPS’s DataStore. With the proper permissions, EMLeditor can be used to generate draft references and reserve DOIs on DataStore as well as upload data and metadata files to DataStore. Finally, EMLeditor contains a .rmd template file that, after loading the package, is accessible in Rstudio under Files > New File > R markdown. The template provides an editable script that walks the user through using EMLassemblyline, EMLeditor, and DPchecker to create and validate EML metadata in R.

    -

    EMLeditor “set” class functions (which includes all functions that begin with “set_” such as “EMLeditor::set_abstract()”) will add several NPS-specific items to the metadata using their default settings. For instance, these functions will set NPS as the publisher, Fort Collins as the publication location, and will add a “for or by NPS = TRUE” statement to the metadata. To invoke these functions without adding the NPS-specific metadata elements, set the parameter NPS = FALSE when calling each “set_” class function. Non-NPS publisher information can be added using the EMLeditor::set_publisher() function with the parameters for_or_by_NPS and NPS set to FALSE:

    +

    EMLeditor “set” class functions (which includes all functions that begin with “set_” such as “EMLeditor::set_abstract()”) will add several NPS-specific items to the metadata using their default settings. For instance, these functions will set NPS as the publisher, Fort Collins as the publication location, and will add a “for or by NPS = TRUE” statement to the metadata. To invoke these functions without adding the NPS-specific metadata elements, set the parameter NPS = FALSE when calling each “set_” class function. Non-NPS publisher information can be added using the EMLeditor::set_publisher() function with the parameters for_or_by_NPS and NPS set to FALSE:

    #set the abstract without NPS-specific information:
 
 new_metadata1 <- set_abstract(eml_object = old_metadata,
@@ -112,7 +112,7 @@ 
    EMLeditor R package
 
    DPchecker R Package
    
-
    The DPchecker (“Data Package checker”) package provides feedback on data-metadata congruence [@Baker_DPchecker2025]. Here, a “data package” consists of the EML metadata file with a filename that ends in *_metadata.xml and one or more data files in .csv format, all of which are in a single directory (and the directory contains no extraneous .csv or .xml files). DPchecker is useful for both data package authors and reviewers. DPchecker goes beyond validating EML objects in R against the EML schema. Using the DPchecker::run_congruence_checks function, DPchecker will conduct a series of 46 tests. These are divided into several categories to check whether:
    
+
    The DPchecker (“Data Package checker”) package provides feedback on data-metadata congruence [@Baker_DPchecker2025]. Here, a “data package” consists of the EML metadata file with a filename that ends in *_metadata.xml and one or more data files in .csv format, all of which are in a single directory (and the directory contains no extraneous .csv or .xml files). DPchecker is useful for both data package authors and reviewers. DPchecker goes beyond validating EML objects in R against the EML schema. Using the DPchecker::run_congruence_checks function, DPchecker will conduct a series of 46 tests. These are divided into several categories to check whether:
    
 
    1. Metadata are well formatted (file names are not duplicated, files specify the field delimiter, data files have URLs, the proper delimiter and header row numbers are present, etc.).
      2. 
 
    2. Metadata elements necessary for DataStore automated extraction are present (creators have valid surnames, publication date is present and in the correct ISO-8601 format, keywords are present, abstract and methods are present and well formatted, etc).
      3. 
 
    3. Recommended EML elements are present including ORCiDs and a notes section.
      4. 
@@ -127,12 +127,12 @@ 
      NPSutils R Package# download a data package from datastore:
 # the data package will be downloaded to ./data/2300498
 
-NPSutils::get_data_package(2300498)
+NPSutils::get_data_package(2300498)
 
 # load the data package into R, and use the metadata to call column types
 # returns a list of tibbles; each tibble corresponds to a single data file
 
-mojn <- NPSutils::load_data_package(2300498, assign_attributes = TRUE)
    +mojn <- NPSutils::load_data_package(2300498, assign_attributes = TRUE)

    Acknowledgements

    @@ -155,11 +155,11 @@

    References -

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    +

    Developed by Robert Baker, Judd Patterson.

    -

    Site built with pkgdown 2.1.2.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index b32c80c..244754b 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,6 +1,6 @@ -pandoc: '3.4' -pkgdown: 2.1.2 +pandoc: 3.6.3 +pkgdown: 2.2.0 pkgdown_sha: ~ articles: NPSdataverse: NPSdataverse.html -last_built: 2025-07-14T22:58Z +last_built: 2026-04-22T18:17Z diff --git a/docs/reference/NPSdataverse_packages.html b/docs/reference/NPSdataverse_packages.html index 884e1df..92c303b 100644 --- a/docs/reference/NPSdataverse_packages.html +++ b/docs/reference/NPSdataverse_packages.html @@ -32,7 +32,7 @@ Changelog

  • - + @@ -47,7 +47,7 @@

    List all packages imported by NPSdataverse

    - Source: R/attach.R + Source: R/attach.R
    @@ -63,9 +63,10 @@

    List all packages imported by NPSdataverse

    Examples

    NPSdataverse_packages()
-#>  [1] "cli"             "crayon"          "DPchecker"       "EML"            
-#>  [5] "EMLassemblyline" "EMLeditor"       "NPSutils"        "QCkit"          
-#>  [9] "rstudioapi"      "utils"           "remotes"         "lifecycle"      
+#>  [1] "cli"             "DPchecker"       "EML"             "EMLassemblyline"
+#>  [5] "EMLeditor"       "NPSutils"        "QCkit"           "utils"          
+#>  [9] "lifecycle"       "gh"              "readr"           "stringr"        
+#> [13] "tibble"
    @@ -76,11 +77,11 @@

    Examples

    -

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    +

    Developed by Robert Baker, Judd Patterson.

    -

    Site built with pkgdown 2.1.2.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/detach_NPSdataverse.html b/docs/reference/detach_NPSdataverse.html index f3e3993..abe30ae 100644 --- a/docs/reference/detach_NPSdataverse.html +++ b/docs/reference/detach_NPSdataverse.html @@ -32,7 +32,7 @@ Changelog
  • - + @@ -47,7 +47,7 @@

    Detach all loaded packages

    - Source: R/attach.R + Source: R/attach.R
    @@ -79,11 +79,11 @@

    Examples

    -

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    +

    Developed by Robert Baker, Judd Patterson.

    -

    Site built with pkgdown 2.1.2.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/dot-update_git_repos.html b/docs/reference/dot-update_git_repos.html index 822710e..c18a7d4 100644 --- a/docs/reference/dot-update_git_repos.html +++ b/docs/reference/dot-update_git_repos.html @@ -32,7 +32,7 @@ Changelog
  • - + @@ -47,7 +47,7 @@

    Update info for git repos in NPSdataverse

    - Source: R/updateR.R + Source: R/updateR.R
    @@ -72,11 +72,11 @@

    Value

    -

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    +

    Developed by Robert Baker, Judd Patterson.

    -

    Site built with pkgdown 2.1.2.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/reference/index.html b/docs/reference/index.html index c6fa78a..3595cf8 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -32,7 +32,7 @@ Changelog
  • - + @@ -47,7 +47,7 @@

    Check internet connectivity

    - Source: R/attach.R + Source: R/attach.R
    @@ -86,11 +86,11 @@

    Examples

    -

    Developed by Robert Baker, Judd Patterson, Joe DeVivo.

    +

    Developed by Robert Baker, Judd Patterson.

    -

    Site built with pkgdown 2.1.2.

    +

    Site built with pkgdown 2.2.0.

    diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 8586df4..894eaa4 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -10,6 +10,7 @@ /news/index.html /paper.html /reference/detach_NPSdataverse.html +/reference/dot-latest_github_version.html /reference/dot-update_git_repos.html /reference/index.html /reference/is_online.html