neotoma2

neotoma2: An R package to access data from the Neotoma Paleoecology Database - Published in JOSS (2023)

https://github.com/neotomadb/neotoma2

Science Score: 100.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 2 DOI reference(s) in README and JOSS metadata
✓
Academic publication links
Links to: joss.theoj.org, zenodo.org
✓
Committers with academic emails
2 of 7 committers (28.6%) from academic institutions
○
Institutional organization owner
✓
JOSS paper metadata
Published in Journal of Open Source Software

Keywords

earthcube neotoma nsf paleoecology r rstats

Last synced: 4 months ago · JSON representation ·

Repository

Repository for the updated neotoma R package.

Basic Info

Host: GitHub
Owner: NeotomaDB
License: other
Language: R
Default Branch: production
Homepage: http://open.neotomadb.org/neotoma2
Size: 18.8 MB

Statistics

Stars: 9
Watchers: 6
Forks: 11
Open Issues: 11
Releases: 9

Topics

earthcube neotoma nsf paleoecology r rstats

Created over 5 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Code of conduct Citation Codemeta

`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:

r 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:

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.

Owner

Name: The Neotoma Paleoecology Database Collective
Login: NeotomaDB
Kind: organization
Location: Global

Website: https://neotomadb.org
Repositories: 56
Profile: https://github.com/NeotomaDB

Data and code supporting collaboration and outreach around the Neotoma Paleoecology Database

JOSS Publication

neotoma2: An R package to access data from the Neotoma Paleoecology Database

Published

November 28, 2023

DOI

10.21105/joss.05561

Volume 8, Issue 91, Page 5561

Authors

Socorro Dominguez Vidaña

HT Data

Simon J. Goring

Department of Geography, University of Wisconsin -- Madison, Center for Climatic Research, University of Wisconsin -- Madison

Editor

Chris Vernon

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
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- family-names: "Goring"
  given-names: "Simon"
  orcid: "https://orcid.org/0000-0002-2700-4605"
title: "neotoma2: An R package to access data from the Neotoma Paleoecology Database"
version: 1.0.3
doi: 10.5281/zenodo.7892992
date-released: 2023-11-16
url: "https://github.com/NeotomaDB/neotoma2"

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GitHub Events

Total

Create event: 7
Issues event: 1
Release event: 2
Watch event: 1
Delete event: 6
Issue comment event: 3
Push event: 35
Pull request review event: 1
Pull request event: 2
Fork event: 1

Last Year

Create event: 7
Issues event: 1
Release event: 2
Watch event: 1
Delete event: 6
Issue comment event: 3
Push event: 35
Pull request review event: 1
Pull request event: 2
Fork event: 1

Committers

Last synced: 5 months ago

All Time

Total Commits: 794
Total Committers: 7
Avg Commits per committer: 113.429
Development Distribution Score (DDS): 0.457

Past Year

Commits: 49
Committers: 2
Avg Commits per committer: 24.5
Development Distribution Score (DDS): 0.02

Top Committers

Name	Email	Commits
Socorro	s**z@h**m	431
SimonGoring	g**g@w**u	249
Jerrin Jacob	8****1	65
dfcharles	d**3@d**u	41
JMRHobbs	j**k@s**g	5
Juanjo Bazán	j**n@g**m	2
Erik Zepeda	E**9@g**m	1

Committer Domains (Top 20 + Academic)

smm.org: 1 drexel.edu: 1 wisc.edu: 1 ht-data.com: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 31
Total pull requests: 17
Average time to close issues: 7 months
Average time to close pull requests: 21 days
Total issue authors: 15
Total pull request authors: 5
Average comments per issue: 1.16
Average comments per pull request: 0.59
Merged pull requests: 15
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 2
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: 26 days
Issue authors: 2
Pull request authors: 1
Average comments per issue: 2.5
Average comments per pull request: 0.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

SimonGoring (8)
kanishkan91 (5)
mhesselbarth (4)
jamoschla (1)
UgoBisson (1)
richardjtelford (1)
jessicablois (1)
AMBarbosa (1)
jenkinslauren (1)
hannahcarroll (1)
vjpsyverson (1)
Rekyt (1)
sedv8808 (1)
andydawson (1)
amy-mcg (1)

Pull Request Authors

sedv8808 (9)
SimonGoring (4)
xuanxu (2)
dfcharles (1)
ErikZepeda59 (1)

Top Labels

Issue Labels

enhancement (2) bug (2) documentation (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 351 last-month
Total docker downloads: 11

Total dependent packages: 0
Total dependent repositories: 3
Total versions: 8
Total maintainers: 1

cran.r-project.org: neotoma2

Working with the Neotoma Paleoecology Database

Homepage: https://github.com/NeotomaDB/neotoma2
Documentation: http://cran.r-project.org/web/packages/neotoma2/neotoma2.pdf
License: MIT + file LICENSE
Latest release: 1.0.7
published 6 months ago

Versions: 8
Dependent Packages: 0
Dependent Repositories: 3
Downloads: 351 Last month
Docker Downloads: 11

Rankings

Forks count: 6.8%

Dependent repos count: 16.5%

Stargazers count: 21.9%

Average: 24.4%

Docker downloads count: 25.7%

Dependent packages count: 28.7%

Downloads: 47.0%

Maintainers (1)

s.dominguez@ht-data.com

Last synced: 4 months ago

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actions/upload-artifact v3 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/draft-pdf.yml actions

actions/checkout v3 composite
actions/upload-artifact v1 composite
openjournals/openjournals-draft-action master composite

inst/doc/neotoma2-package_files/leaflet-markercluster-1.0.5/package.json npm

jake ~0.5.16 development
jshint ~2.1.3 development
karma ~0.8.5 development
leaflet ~1.0.3 development
magic-string ^0.7.0 development
mocha ~1.10.0 development
uglify-js ~2.6.0 development

neotoma2

Science Score: 100.0%

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neotoma2 R Package

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JOSS Publication

neotoma2: An R package to access data from the Neotoma Paleoecology Database

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cran.r-project.org: neotoma2

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`neotoma2` R Package