neotoma2 R PackageTheneotoma2 R package represents a set of breakingchanges with the originalneotoma R package. Theneotoma package was deprecated following end-of-life forthe Neotoma Windows Server in 2020 and the migration of the Neotomabackend infrastructure to a PostgreSQL database and JavaScript API.
Theneotoma2 package is built on the newNeotoma API and isintended as a starting point for a fully interactive experience with theNeotoma Paleoecology Database,to support both data access and data input through R.
This project is an open project, and contributions are welcome fromany individual. All contributors to this project are bound by acodeof conduct. Please review and follow this code of conduct as part ofyour contribution.
Issues and bug reports are always welcome. Code clean-up, and featureadditions can be done either through pull requests toprojectforks orprojectbranches.
Please direct development questions to Simon Goring by email:goring@wisc.edu.
All products of the Neotoma Paleoecology Database are licensed underanMIT License unless otherwise noted.
All R functions for the package should be written in theR folder. Any documentation should be added to.R files usingroxygen2notation. Because we are usingroxygen2 for documentationin this package, all edits to documentation should take place in theassociated functions.R file. The files in theman folder should not be manually changed.
Class definitions and new methods should be added to the files01_classDefinitions.R and02_genericDefinitions.R respectively, to ensure they areproperly loaded during the package build process.
Theneotoma2 package is built for R. Build tools includeelements from theusethis,devtools andtestthat R packages, and build and compilation occurswithin (and outside) the RStudio IDE environment.
Package use requires the use of thedevtools::install_github() function, to pull this workingrepository into a user’s environment:
devtools::install_github('NeotomaDB/neotoma2',build_vignettes =TRUE)The expectation for this repository is that all commits to theprod branch will support a clean package build. This issupported throughGitHub Actionsin the.github folder of the repository.
There is considerable information in the vignettes for the package,which can beaccesseddirectly.
In order to see the total available sites that can be queried by thispackage, use the function:
neotoma2::get_stats(start=0, end=1)This project is built with R > v4.0. The packages needed forproper package use are detailed in theDESCRIPTION file forthis repository.
Theneotoma2 R package pulls data from theNeotoma Paleoecology Database.Neotoma maintains apermissivedata use policy. Within the data use policy there is a statement onco-authorship which reads:
Normal ethics apply to co-authorship of scientific publications.Paleoecological datasets are labor-intensive and complex: they takeyears to generate and always have additional attributes and metadata notcaptured in Neotoma. Neotoma data quality also relies on expert curationby data stewards, each associated with one or more ConstituentDatabases.Users of data stored in Neotoma’s ConstituentDatabases should consider inviting the original data contributor, orConstituent Database steward(s), to be a co-author(s) of any resultantpublications if that contributor’s data are a major portion of thedataset analyzed, or if a data contributor or steward makes asignificant contribution to the analysis of the data or to theinterpretation of results. For large-scale studies using manyNeotoma records, contacting all contributors or stewards or making themco-authors will not be practical, possible, or reasonable. Under nocircumstance should authorship be attributed to data contributors orstewards, individually or collectively, without their explicitconsent.
This project is to be evaluated using the following metrics: