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.
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.
Class definitions and new methods should be added to the files
02_genericDefinitions.R respectively, to ensure they are properly loaded during the package build process.
neotoma2 package is built for R. Build tools include elements from the
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:
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.
There is considerable information in the vignettes for the package, which can be accessed directly.
This project is built with R > v4.0. The packages needed for proper package use are detailled in the
DESCRIPTION file for this repository.
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: