The neotoma2 R package represents a set of breaking changes with the original neotoma R package. 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.
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.
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.
All products of the Neotoma Paleoecology Database are licensed under an MIT License unless otherwise noted.
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.
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')The expectation for this repository is that all commits to the prod branch will support a clean package build.
This project is built with R > v4.0. The packages needed for proper package use are detailled in the DESCRIPTION file for this repository.
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.
This project is to be evaluated using the following metrics:
- Completion of core functionality for data access
- Completion of core functionality for data presentation
- Completion of clear vignettes for major data types or Constituent Databases represented within the Neotoma Database.