NPSdataverse

NPSdataverse: a suite of R packages for data processing, authoring Ecological Metadata Language metadata, checking data-metadata congruence, and accessing data - Published in JOSS (2025)

https://github.com/nationalparkservice/npsdataverse

Keywords

Repository

Loads a suite of R packages for creating and manipulating data packages including interacting with DataStore.

README.Rmd

---
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)
  [![status](https://joss.theoj.org/papers/4f0f426403cd0e5f089ad527fb66ce51/status.svg)](https://joss.theoj.org/papers/4f0f426403cd0e5f089ad527fb66ce51)
  

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# NPSdataverse

```{r echo=FALSE, fig.align="center"}
#| fig.alt: >
#|  Image diagraming NPSdataverse and its consituent packages using hexicons
#|  A hexicon of NPSdataverse points to the hexicons for the 4 NPS-maintained
#|  packages that load with the NPSdataverse: QCkit, EMLeditor, DPchecker, and
#|  NPSutils. The key external packages EML and EMLassemblyline that also load
#|  are included in a text box.
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).

## Installation

You can install the development version of NPSdataverse from [GitHub](https://github.com/) with:

``` r
# install.packages("pak")
pak::pkg_install("nationalparkservice/NPSdataverse")
```

NPSdataverse will install the following R packages:

| Package | Location|
|---------|---------|
|**QCkit**| https://nationalparkservice.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|

***
(R packages in **bold** are developed by NPS)

## Usage

```{r setup, eval = FALSE}
pak::pkg_install("nationalparkservice/NPSdataverse")
library(NPSdataverse)
```


## Troubleshooting installation

If `pak::pkg_install()` throws an error, try `remotes::install_github("nationalparkservice/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
prompted to install or update these dependencies. The initial installation can
take some time and require multiple iterative package updates/installs. 
Depending on how they were initially installed, some dependent packages may fail
update or to install. In this case you can try running 

``` r
.libPaths()
```
to find where your packages are located on your local machine. Navigate to that
location and delete the offending package. Then try to re-install.


## Updating NPSdataverse packages

Many of the NPSdataverse packages are in a phase of rapid development. When you
load the NPSdataverse (using `library(NPSdataverse)`), if you are online, NPSdataverse will check
for new versions of the packages stored on GitHub (all the packages except
r/EML). NPSdataverse will tell you if all your packages are up to date. 
Conversely if any of the NPSdataverse packages need to be updated, NPSdataverse
will indicate which packages need updating and how to perform the updates. If 
you do not get any notices about whether your packages are up to date or not, 
then the NPSdataverse package itself needs to be updated. See Installation for 
instructions on how to update the NPSdataverse package.

## Creating data packages

If you are creating a data package and need to generate EML metadata make sure all of your .csv data files are in a single folder. 

After loading NPSdataverse, from within Rstudio select the "File" menu. Select "New File" from the drop down menu and choose "R Markdown". In the dialog box that pops up, select "From Template" and then click on the template labelled "Editable_EML_Creation_Workflow" and click "OK". 

```{r echo=FALSE, out.width='45%', fig.align="center"}
#| fig.alt: >
#|    A screenshot with highlights indicating how to access the EML script
#|    This figure shows step 1.
knitr::include_graphics("man/figures/open_rmd.png")

```

 
```{r echo=FALSE, out.width='45%', fig.show='hold', fig.align='center'}
#| fig.alt: >
#|    A screenshot with highlights indicating how to access the EML script
#|    This figure shows step 2.
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.

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