neotoma2 R Package
The neotoma2 R package represents a set of breaking changes with the original neotoma R package. The neotoma package was deprecated following end-of-life for the Neotoma Windows Server in 2020 and the migration of the Neotoma backend infrastructure to a PostgreSQL database and JavaScript API.
The neotoma2 package is built on the new Neotoma API and is intended as a starting point for a fully interactive experience with the Neotoma Paleoecology Database, to support both data access and data input through R.
Contributors
This project is an open project, and contributions are welcome from any individual. All contributors to this project are bound by a code of conduct. Please review and follow this code of conduct as part of your contribution.
Tips for Contributing
Issues and bug reports are always welcome. Code clean-up, and feature additions can be done either through pull requests to project forks or project branches.
Please direct development questions to Simon Goring by email: goring@wisc.edu.
All products of the Neotoma Paleoecology Database are licensed under an MIT License unless otherwise noted.
How to use this repository
All R functions for the package should be written in the R folder. Any documentation should be added to .R files using roxygen2 notation. Because we are using roxygen2 for documentation in this package, all edits to documentation should take place in the associated functions .R file. The files in the man folder should not be manually changed.
Class definitions and new methods should be added to the files 01_classDefinitions.R and 02_genericDefinitions.R respectively, to ensure they are properly loaded during the package build process.
Development Workflow Overview
The neotoma2 package is built for R. Build tools include elements from the usethis, devtools and testthat R packages, and build and compilation occurs within (and outside) the RStudio IDE environment.
Package use requires the use of the devtools::install_github() function, to pull this working repository into a user's environment:
devtools::install_github('NeotomaDB/neotoma2', build_vignettes = TRUE)To see the rendered vignette, you can also visit the following site: https://open.neotomadb.org/neotoma2/inst/doc/neotoma2-package.html
The expectation for this repository is that all commits to the prod branch will support a clean package build. This is supported through GitHub Actions in the .github folder of the repository.
Analysis Workflow Overview
There is considerable information in the vignettes for the package, which can be accessed directly.
Report of Sites Statistics
In order to see the total available sites that can be queried by this package, use the function:
neotoma2::get_stats(start=0, end=1)System Requirements
This project is built with R > v4.0. The packages needed for proper package use are detailed in the DESCRIPTION file for this repository.
Data Requirements
The neotoma2 R package pulls data from the Neotoma Paleoecology Database. Neotoma maintains a permissive data use policy. Within the data use policy there is a statement on co-authorship which reads:
Normal ethics apply to co-authorship of scientific publications. Paleoecological datasets are labor-intensive and complex: they take years to generate and always have additional attributes and metadata not captured in Neotoma. Neotoma data quality also relies on expert curation by data stewards, each associated with one or more Constituent Databases. Users of data stored in Neotoma’s Constituent Databases should consider inviting the original data contributor, or Constituent Database steward(s), to be a co-author(s) of any resultant publications if that contributor’s data are a major portion of the dataset analyzed, or if a data contributor or steward makes a significant contribution to the analysis of the data or to the interpretation of results. For large-scale studies using many Neotoma records, contacting all contributors or stewards or making them co-authors will not be practical, possible, or reasonable. Under no circumstance should authorship be attributed to data contributors or stewards, individually or collectively, without their explicit consent.
Metrics
This project is to be evaluated using the following metrics:
- Maintenance Github 1.0.4 release, DONE July 23, 2024
- Updated production Branch with CRAN changes, May 24, 2024.
- Maintenance Github 1.0.3 release, DONE February 28, 2024
- Published JOSS paper, DONE 28 November, 2023
- Submitted paper to JOSS DONE 03 May, 2023
- Completion CRAN 1.0.0 release DONE April 23, 2023
- Completion of core functionality for data access DONE Feb 10, 2022
- Completion of core functionality for data presentation DONE
- Completion of clear vignettes for major data types or Constituent Databases represented within the Neotoma Database.