coffee

0.4.3

Chronological Ordering for Fossils and Environmental Events

0packages depend

3.9Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Maarten BlaauwFirst published 2021-08-216 releasesCRAN page ↗GitHub ↗

While individual calibrated radiocarbon dates can span several centuries, combining multiple dates together with any chronological constraints can make a chronology much more robust and precise. This package uses Bayesian methods to enforce the chronological ordering of radiocarbon and other dates, for example for trees with multiple radiocarbon dates spaced at exactly known intervals (e.g., 10 annual rings). For methods see Christen 2003 doi:10.11141/ia.13.2. Another example is sites where the relative chronological position of the dates is taken into account - the ages of dates further down a site must be older than those of dates further up (Buck, Kenworthy, Litton and Smith 1991 doi:10.1017/S0003598X00080534; Nicholls and Jones 2001 doi:10.1111/1467-9876.00250). The paper accompanying this R package is Blaauw et al. 2024 doi:10.1017/RDC.2024.56.

Install

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

install.packages("coffee", 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("Maarten14C/coffee")

Development version from Maarten14C/coffee. 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-coffee

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-coffee

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-coffee

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 3.4 min · r-oldrel-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 138 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 80%
Documented parameters: 100%
Return-value docs: 86%
References docs: 13%

Downloads

3.9K

CRAN downloads in the past year

Rank #13,195 · ~11/day · ~323/mo

Releases R versions

Daily download trend is not available in this view yet.

20130 days

77290 days

3.9K1 year

Compare downloads with other packages →

Also on104 r2u

Repository

GitHub ↗ maarten14c/coffee

7Stars

0Forks

0Open issues

0Open PRs

0Releases

58Commits

2Contributors

58 commits · Last activity 2025-12-11 · 0% stars, 30d

Stars over time

2024-09-30 · 72026-07-07 · 7

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/maarten14c/coffee on 2026-08-02.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (3)

data.table rintcal rice

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown utf8

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Maarten Blaauw

Author, Maintainer

Authors (3)

Maarten Blaauw

Author, Maintainer

Marco A. Aquino Lopez

Author, Contributor · added in 0.2.0

J. Andres Christen

Author, Contributor, Copyright holder

Contributors (2)

Marco A. Aquino Lopez

Author, Contributor · added in 0.2.0

J. Andres Christen

Author, Contributor, Copyright holder

J. Andres Christen

Author, Contributor, Copyright holder

Package Timeline

6 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.4.3Latest
2024-12-06 · current release · diff ↗
0.4.1
2024-09-26 · diff ↗
0.4.0
2024-09-04 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.3.0
2024-01-29 · diff ↗
0.2.0
2023-07-14 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.1.1
2021-08-21
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-08-21
Total releases: 6 / 5 yrs
License: GPL (>= 2) OSI
Download size: 854 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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