StratPal

0.7.1

Stratigraphic Paleobiology Modeling Pipelines

0packages depend

2.9Kdownloads / year

99.7%test coverage

13/13checks pass

Overview

About

Maintained by Niklas HohmannFirst published 2024-08-239 releasesCRAN page ↗GitHub ↗

The fossil record is a joint expression of ecological, taphonomic, evolutionary, and stratigraphic processes (Holland and Patzkowsky, 2012, ISBN:978-0226649382). This package allowing to simulate biological processes in the time domain (e.g., trait evolution, fossil abundance, phylogenetic trees), and examine how their expression in the rock record (stratigraphic domain) is influenced based on age-depth models, ecological niche models, and taphonomic effects. Functions simulating common processes used in modeling trait evolution, biostratigraphy or event type data such as first/last occurrences are provided and can be used standalone or as part of a pipeline. The package comes with example data sets and tutorials in several vignettes, which can be used as a template to set up one's own simulation.

Install

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

install.packages("StratPal", 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("MindTheGap-ERC/StratPal")

Development version from MindTheGap-ERC/StratPal. 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-stratpal

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-StratPal

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-StratPal

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

Health

CRAN checks

13OK

Slowest check: 1.8 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.37

99.7%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-30
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-25
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-21
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-20
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 14 earlier snapshots

ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-17
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-09
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-21
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-16
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-15
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-07
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-06
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-03
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-02
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-29
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-28
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 481 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 96%
Documented parameters: 100%
Return-value docs: 100%
References docs: 13%

Downloads

2.9K

CRAN downloads in the past year

Rank #20,350 · ~8/day · ~244/mo

Releases R versions

Daily download trend is not available in this view yet.

16430 days

59490 days

2.9K1 year

Compare downloads with other packages →

Also on124 r2u48 autocran

Repository

GitHub ↗ mindthegap-erc/stratpal

2Stars

0Forks

0Open issues

0Open PRs

9Releases

258Commits

2Contributors

palaeobiologypalaeontologypaleobiologypaleontologystratigraphic-paleobiologystratigraphy

License Apache-2.0 · 258 commits · Last activity 2026-04-28

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/mindthegap-erc/stratpal on 2026-07-19.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Research and citation (1)

CITATION.cff

Lint, format, editor (1)

RStudio project

Show all practices

Coverage (1)

.covrignore

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

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2

Imports (2)

admtools paleoTS

LinkingTo (0)

none

Suggests (6)

ape FossilSim knitr rmarkdown spelling testthat (>= 3.0.0)

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 1,958 (42%)Vignettes 1,360 (29%)Rd 1,301 (28%)

Code characteristics

Object systems

S310

Cyclomatic complexity: 2.0 median / 10 max
Test cases: 79 / 0.37 per code line

Test coverage

Line coverage

100%

Expression

99.7%

Tests / Examples

99.7% / 70% ex

Functions

40 29 exported

Complexity

2.7 avg / 10 max

Call network

40 nodes / 14 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

40 functions

Function	Cyclo	Coverage
ignore_unused_imports	1	0%
all_preserved exp	1	100%
apply_niche exp	1	100%
apply_taphonomy exp	1	100%
as_char_mat exp	1	100%
bounded_niche exp	2	100%

People & History

People (1)

Maintainer (1)

Niklas Hohmann

Author, Maintainer

Authors (1)

Niklas Hohmann

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.7.1Latest
2025-12-06 · current release · diff ↗
0.7.0
2025-11-24 · diff ↗
0.6.0
2025-08-27 · diff ↗
0.5.0
2025-05-21 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.4.0
2025-03-27 · diff ↗
0.3.1
2025-02-20 · diff ↗
0.3.0
2024-11-21 · diff ↗
0.2.0
2024-10-04 · diff ↗
0.1.1
2024-08-23
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-08-23
Total releases: 9 / 2 yrs
License: Apache License (>= 2)
Minimum R: ≥ 4.2
Bundled data: 126 KB / 1 file
Download size: 1.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Paleontology

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