R Observatory: Metrics for neotoma2 version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

neotoma2

1.1.0Package record

Working with the Neotoma Paleoecology Database

1packages depend

5.9Kdownloads / year

52.6%test coverage

13/13flavors OK

Overview

About

Maintained by Socorro Dominguez VidanaCRAN page ↗GitHub ↗Issues ↗

Access and manipulation of data using the Neotoma Paleoecology Database. https://api.neotomadb.org/api-docs/. Examples in functions that require API access are not executed during CRAN checks. Vignettes do not execute as to avoid API calls during CRAN checks.

Changes in 1.1.0

Added count() to tally sites, collection units, or datasets in a record object.
samples() gains a chronname argument to report ages against a chosen chronology.
filter() now handles multiple conditions together with spatial (loc) filters.
More robust parsing of malformed API records (empty slots no longer create phantom IDs).
Faster parseURL() and automatic retry when the API is temporarily unavailable.
all_data = TRUE stops as soon as a page comes back short, rather than spending an extra request to confirm the end of the results. Queries whose results fit in one page now cost one request instead of two.
A request that times out is retried at most once. Retrying a slow query stacks work onto an API that is already struggling, which made spatial (loc) queries worse rather than better; other transient failures still retry as before.
Raised the default request timeout to 180 seconds, above the observed latency of the spatial endpoints, so healthy-but-slow queries are no longer aborted mid-flight. NEOTOMA_TIMEOUT and NEOTOMA_RETRIES still override both.

Show all changes in 1.1.0Hide the rest of the changes in 1.1.0

A spatial geometry is now converted once per query rather than once per page, and the API's parameter list is fetched once per session rather than on every get_*() call.
Paginated queries report their progress in interactive sessions.
Improved chronologies() function to show a data frame instead of the raw format of chronologies data.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("neotoma2", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("NeotomaDB/neotoma2")

Development version from NeotomaDB/neotoma2. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-neotoma2

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-neotoma2

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-neotoma2

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 3.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-19
NOTE12 OK, 1 NOTE2026-07-11
OK13 OK2026-04-30
NOTE13 OK, 1 NOTE2026-04-12
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.0

READMEYes · 825 wordsVignettesYes · 1 · staticNEWSYes · 100% structured · mentions 1.1.0Citation fileYes · software entry only

Help pages: 86 (2 internal)
Examples that run: 23%7 run in a plain check · 23 never run
Exported functions with examples: 45%
Documented parameters: 99%
Return-value docs: 98%
Help pages citing references: 0%

Vignettes (1)

The neotoma2 R Package HTML

How these are measured

Downloads

5.9K

CRAN downloads in the past year

Rank #4,478 · ~16/day · ~494/mo

Releases R versions

Daily download trend is not available in this view yet.

87330 days

1.9K90 days

5.9K1 year

Compare downloads with other packages →

Also on170 r2u10 autocran

How downloads are counted

Repository

neotomadb/neotoma2 ↗Organization: NeotomaDB

12Stars

13Forks

8Open issues

0Open PRs

15Releases

1,079Commits

9Commit identities

neotomapaleoecologyrstatsrearthcubensf

1,079 commits · Last activity 2026-09-15 · +9.1% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 67%
Median days to close, 50 most recently updated closed issues: 97
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-04-30 · 92026-10-08 · 12

How these are measured

PracticesBeta

11 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/neotomadb/neotoma2 on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (1)

Code of conduct

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-09-15 · The repository has a site deploy workflow

Coverage (1)

Coverage reporting

Show all practicesHide 2 practices

CRAN release process (1)

cran-comments.md

Research and citation (3)

CITATION.cffcodemeta.jsonJOSS paper

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

23 external dependencies (excludes base and recommended)

Installing neotoma2 adds 80 packages (47 with compiled code, 67 MB of source tarballs). Heaviest: stringi 11 MB, sf 9.3 MB, bslib 5.6 MB.

Depends (0)

none

Imports (17)

rlang sf leaflet magrittr digest geojsonsf purrr httr jsonlitemethodsdplyr assertthat stringr progress uuidutilstidyr

LinkingTo (0)

none

Suggests (8)

Bchron covr ggplot2 httptest knitr pkgdown rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

refuginator

How these are counted

Code & Tests

People & History

People (3)

Socorro Dominguez Vidana

Author, Maintainer · added in 1.1.0

Simon Goring

Author

Nick Hoffman

Author · added in 1.1.0

Maintainer since 1.0.3 (2024), previously Simon Goring (1.0.0 to 1.0.2)

Releases (14)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1.0Latest
record
2026-04-23 · current release · diff ↗ ·
added 1 export
count
1.0.12
record
2026-04-23 · diff ↗
1.0.11
record
2025-12-14 · diff ↗
1.0.10
record
2025-12-06 · diff ↗
1.0.9
record
2025-11-26 · diff ↗
1.0.8
record
2025-11-18 · diff ↗ ·
removed 5 exports
add_chronology, build_specimen, selectMatch, set_publications, showMatch

added 8 exports
clean, get_documentation, get_speleothems, getids.sites, set_publication, set_speleothem, speleothemdetails, speleothems
1.0.7
record
2025-07-15 · diff ↗ ·
removed 9 exports
build_chron, build_collunits, build_dataset, build_sample, build_sites, get_specimens, parseURL, specimens, toJSON
unarchivedReturned to CRAN
2025-06-25
1.0.6
record
2025-06-25 · diff ↗ ·
added 2 exports
get_taxa, get_taxon
archivedRemoved from CRAN
2025-06-02
policy violation On Internet access
R
R 4.5.0 released · 2025-04-11
1.0.5
record
2024-08-21 · diff ↗
unarchivedReturned to CRAN
2024-07-28
1.0.4
record
2024-07-28 · diff ↗
archivedRemoved from CRAN
2024-06-14
policy violation On Internet access

Show 7 earlier eventsHide 7 earlier events

R
R 4.4.0 released · 2024-04-24
1.0.3
record
2024-02-28 · diff ↗ ·
removed 5 exports
clean, cleanNULL, fix_null, testNull, use_na

added 1 export
get_stats
1.0.2
record
2023-06-29 · diff ↗
1.0.1
record
2023-05-23 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.0
record
2023-04-20
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-04-20
Total releases: 14 / 3 yrs
License: MIT + file LICENSE OSI
Download size: 438 KB

Appears in task views

Paleontology

Cite

Cite this package

Run in R for the authors' entry:

citation("neotoma2")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.5281/zenodo.8114874.

The repository also keeps a CITATION.cff.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for neotoma2 version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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