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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)

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:

  • CRAN release 1.0.8 with speleothem data support and improved documentation. Target December, 2025
  • Maintenance Github 1.0.7 release DONE June 15, 2025
  • Maintenance Github 1.0.6 release DONE June 23, 2025
  • Maintenance Github 1.0.5 release, DONE December 27, 2024
  • 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.

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Version

Install

install.packages('neotoma2')

Monthly Downloads

531

Version

1.0.8

License

MIT + file LICENSE

Issues

10

Pull Requests

0

Stars

9

Forks

12

Maintainer

Dominguez Vidana Socorro

Last Published

November 18th, 2025

Functions in neotoma2 (1.0.8)

datasets

Extract datasets from a sites object.
coordinates,sites-method

Return the latitude and longitude of sites
doi

Obtain the DOI for publications or datasets.
chronologies,collunit-method

Extract chronologies from a sites or collunits object.
chronologies

Obtain the chronology from a record or multiple records.
filter

Apply a filter for Neotoma sites objects.
doi,sites-method

Obtain dataset DOIs from records.
dataset-class

S4 class for datasets information
get_documentation

get_documentation
get_publications

Get publication information for Neotoma records
get_speleothems

get_speleothems
get_downloads

get_downloads
get_stats

get_stats
get_taxa

get_taxa
get_table

Get table record from Neotoma
coordinates

Obtain coordinates from a sites object.
%>%

Pipe operator See magrittr::%>% for details.
get_taxon

get_taxon
getids

Get object IDs
get_datasets

get_datasets
get_contacts

Get contact information for Neotoma contributors
get_manual

get_manual
pingNeotoma

pingNeotoma
names,collunit-method

Get a neotoma2 object's slot names
publications_classes

An S4 class for Neotoma publications.
set_dataset

set Site Information for Fossil Sites
set_default,chronologies-method

Change the default age model for a record.
get_sites

get_sites
set_collunit

set Site Information for Fossil Sites
set_contact

Set contact information for a new record.
missingOrNULL-class

c Method - Combine objects, including NULL
set_sample

set Sample Information
set_server

Set Neotoma API Source or Server
length,chronologies-method

length
plot

Plot site coordinates using a basic plot.
set_publication

Create a new publication (or publication set)
set_default

Set the default chronology within a collectionunit.
samples,sites-method

samples
samples

Obtain samples from a record or multiple records.
set_site

set Site Information for Fossil Sites
plotLeaflet

plotLeaflet
plotLeaflet,sites-method

plotLeaflet
get_params

get_params
[,collunits,numeric-method

sub
speleothems,sites-method

speleothems
speleothemdetails

Obtain speleothems and samples from a record or multiple records.
set_speleothem

Set Speleothem
[[,chronologies,numeric-method

sub-sub
repositories_classes

S4 class for repository information
show,collunits-method

Display a sites object or nested slots.
samples_classes

S4 class for samples information
set_chronology

set chronology information for a new record.
[[<-,collunits-method

sub-subset
[<-,collunit,character-method

subset
specimens_classes

S4 class for specimens information
summary,sites-method

Summary of objects within a sites object.
toWide

toWide
taxa,sites-method

Extract taxonomic data from a set of sites.
speleothemdetails,sites-method

speleothemdetails
speleothems

Obtain speleothems from a record or multiple records.
taxa

taxa
taxa_classes

S4 class for taxa information
speleothems_classes

S4 class for speleothem information
sites_classes

An S4 class for sites information
as.data.frame,chronology-method

as.data.frame
author_classes

An S4 class for the authors of a Neotoma publication.
chroncontrols,sites-method

Recover information about the chron controls for a collectionunit.
c,chronologies-method

c - Combine neotoma2 objects
chroncontrols

chroncontrols
check_contacts

Check contact information for a record against Neotoma contributors
$,chronology-method

cash
add_chronology

Add a new chronology into an existing collectionunit.
$<-,chronology-method

cash-set
chroncontrols,site-method

Recover information about the chron controls for a collectionunit.
collunits,sites-method

Extract collunits from a sites object.
collunits

Extract collection units from a sites object
clean

clean Neotoma objects to remove duplicates and empty objects.
cite_data

Generate a data citation from a Neotoma2 object.
datasets,collunits-method

Extract datasets from a sites or collunits object.
collunits_classes

S4 class for collection units information.
contacts_classes

An S4 class for multi-contact information from the Neotoma Paleoecology Database.
chronologies_classes

S4 class for chronologies information
cite_data,sites-method

Obtain data citations from multiple records.